From 5d0cf655236dc90175617d8d58cdc90fbc3ca8c9 Mon Sep 17 00:00:00 2001
From: BjornFJohansson <bjornjobb@gmail.com>
Date: Fri, 7 Nov 2025 07:29:46 +0000
Subject: [PATCH 01/22] created stubs UploadedFileSource and RepositoryIdSource

---
 src/pydna/opencloning_models.py | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/src/pydna/opencloning_models.py b/src/pydna/opencloning_models.py
index d9f39897..b08ba42e 100644
--- a/src/pydna/opencloning_models.py
+++ b/src/pydna/opencloning_models.py
@@ -346,6 +346,32 @@ def from_subfragment_representation(
         return AssemblySource(input=input_list, circular=is_circular)
 
 
+class UploadedFileSource(Source):
+
+    def _kwargs(self, seq_id: int) -> dict:
+        return {
+            **super()._kwargs(seq_id),
+            "left_edge": self._cutsite_to_model(self.left_edge),
+            "right_edge": self._cutsite_to_model(self.right_edge),
+        }
+
+    def to_pydantic_model(self, seq_id: int):
+        return self._target_model()(**self._kwargs(seq_id))
+
+
+class RepositoryIdSource(Source):
+
+    def _kwargs(self, seq_id: int) -> dict:
+        return {
+            **super()._kwargs(seq_id),
+            "left_edge": self._cutsite_to_model(self.left_edge),
+            "right_edge": self._cutsite_to_model(self.right_edge),
+        }
+
+    def to_pydantic_model(self, seq_id: int):
+        return self._target_model()(**self._kwargs(seq_id))
+
+
 class RestrictionAndLigationSource(AssemblySource):
     restriction_enzymes: list[AbstractCut]
 

From 4ea594198a925a523f378740d25c8c7fed7e1f41 Mon Sep 17 00:00:00 2001
From: BjornFJohansson <bjornjobb@gmail.com>
Date: Fri, 7 Nov 2025 08:09:27 +0000
Subject: [PATCH 02/22] next step

---
 src/pydna/opencloning_models.py | 28 ++++++++++++++++++++++++----
 1 file changed, 24 insertions(+), 4 deletions(-)

diff --git a/src/pydna/opencloning_models.py b/src/pydna/opencloning_models.py
index b08ba42e..2512bce6 100644
--- a/src/pydna/opencloning_models.py
+++ b/src/pydna/opencloning_models.py
@@ -348,11 +348,23 @@ def from_subfragment_representation(
 
 class UploadedFileSource(Source):
 
+      # "id": 1,
+      # "type": "UploadedFileSource",
+      # "output_name": null,
+      # "database_id": null,
+      # "input": [],
+      # "sequence_file_format": "fasta",
+      # "file_name": "seq2.fasta",
+      # "index_in_file": 0,
+      # "circularize": false,
+      # "coordinates": null,
+      # "output": 1
+
     def _kwargs(self, seq_id: int) -> dict:
         return {
             **super()._kwargs(seq_id),
-            "left_edge": self._cutsite_to_model(self.left_edge),
-            "right_edge": self._cutsite_to_model(self.right_edge),
+            "file_name": ?,
+            "index_in_file": ?
         }
 
     def to_pydantic_model(self, seq_id: int):
@@ -361,11 +373,19 @@ def to_pydantic_model(self, seq_id: int):
 
 class RepositoryIdSource(Source):
 
+    # "id": 2,
+    # "type": "RepositoryIdSource",
+    # "output_name": null,
+    # "database_id": null,
+    # "input": [],
+    # "repository_id": "NM_001018957.2",
+    # "repository_name": "genbank"
+
     def _kwargs(self, seq_id: int) -> dict:
         return {
             **super()._kwargs(seq_id),
-            "left_edge": self._cutsite_to_model(self.left_edge),
-            "right_edge": self._cutsite_to_model(self.right_edge),
+            "repository_id": ?,
+            "repository_name": ?
         }
 
     def to_pydantic_model(self, seq_id: int):

From 27307e39c696322a3509591f63cdd9700b34430a Mon Sep 17 00:00:00 2001
From: BjornFJohansson <bjornjobb@gmail.com>
Date: Fri, 7 Nov 2025 08:10:23 +0000
Subject: [PATCH 03/22] next step2

---
 src/pydna/opencloning_models.py | 34 +++++++++++++--------------------
 1 file changed, 13 insertions(+), 21 deletions(-)

diff --git a/src/pydna/opencloning_models.py b/src/pydna/opencloning_models.py
index 2512bce6..9cfcbce5 100644
--- a/src/pydna/opencloning_models.py
+++ b/src/pydna/opencloning_models.py
@@ -348,24 +348,20 @@ def from_subfragment_representation(
 
 class UploadedFileSource(Source):
 
-      # "id": 1,
-      # "type": "UploadedFileSource",
-      # "output_name": null,
-      # "database_id": null,
-      # "input": [],
-      # "sequence_file_format": "fasta",
-      # "file_name": "seq2.fasta",
-      # "index_in_file": 0,
-      # "circularize": false,
-      # "coordinates": null,
-      # "output": 1
+    # "id": 1,
+    # "type": "UploadedFileSource",
+    # "output_name": null,
+    # "database_id": null,
+    # "input": [],
+    # "sequence_file_format": "fasta",
+    # "file_name": "seq2.fasta",
+    # "index_in_file": 0,
+    # "circularize": false,
+    # "coordinates": null,
+    # "output": 1
 
     def _kwargs(self, seq_id: int) -> dict:
-        return {
-            **super()._kwargs(seq_id),
-            "file_name": ?,
-            "index_in_file": ?
-        }
+        return {**super()._kwargs(seq_id), "file_name": "?", "index_in_file": "?"}
 
     def to_pydantic_model(self, seq_id: int):
         return self._target_model()(**self._kwargs(seq_id))
@@ -382,11 +378,7 @@ class RepositoryIdSource(Source):
     # "repository_name": "genbank"
 
     def _kwargs(self, seq_id: int) -> dict:
-        return {
-            **super()._kwargs(seq_id),
-            "repository_id": ?,
-            "repository_name": ?
-        }
+        return {**super()._kwargs(seq_id), "repository_id": "?", "repository_name": "?"}
 
     def to_pydantic_model(self, seq_id: int):
         return self._target_model()(**self._kwargs(seq_id))

From 71649645dc0fc596b48aa4a78bc9d780830a9e27 Mon Sep 17 00:00:00 2001
From: BjornFJohansson <bjornjobb@gmail.com>
Date: Fri, 7 Nov 2025 16:52:40 +0000
Subject: [PATCH 04/22] added rudimentary source/history for local files read
 in reader/parser and sequences downloaded from genbank.

---
 src/pydna/afile.fasta           |  2 ++
 src/pydna/genbank.py            | 31 +++++++++++++++++--------------
 src/pydna/opencloning_models.py | 30 ++++++++++++++++++++++--------
 src/pydna/parsers.py            | 10 ++++++++--
 4 files changed, 49 insertions(+), 24 deletions(-)
 create mode 100644 src/pydna/afile.fasta

diff --git a/src/pydna/afile.fasta b/src/pydna/afile.fasta
new file mode 100644
index 00000000..80075a6d
--- /dev/null
+++ b/src/pydna/afile.fasta
@@ -0,0 +1,2 @@
+>fn
+gatc
diff --git a/src/pydna/genbank.py b/src/pydna/genbank.py
index c8b8a00b..6cd96043 100644
--- a/src/pydna/genbank.py
+++ b/src/pydna/genbank.py
@@ -12,21 +12,16 @@
 `pydna.ini` file. See the documentation of :func:`pydna.open_config_folder`"""
 
 # from pydna.utils import memorize as _memorize
+from pydna.opencloning_models import RepositoryIdSource
 from pydna.genbankrecord import GenbankRecord as _GenbankRecord
 from pydna.readers import read as _read
 
 from Bio import Entrez as _Entrez
+from Bio.SeqFeature import SimpleLocation
 from typing import Literal as _Literal, Optional as _Optional
 import re as _re
 import os as _os
 
-# import logging as _logging
-
-# _module_logger = _logging.getLogger("pydna." + __name__)
-
-
-# TODO http://httpbin.org/ use for testing?
-
 
 class Genbank:
     """Class to facilitate download from genbank. It is easier and
@@ -179,12 +174,23 @@ def nucleotide(
 
         # _module_logger.info("text[:160]  %s", text[:160])
 
-        return _GenbankRecord(
-            _read(text), item=item, start=seq_start, stop=seq_stop, strand=strand
+        result = _read(text)
+
+        result.source = RepositoryIdSource(
+            repository_id=item,
+            repository_name="genbank",
+            location=SimpleLocation(seq_start, seq_stop, strand),
         )
+        return result
+
+        # return _GenbankRecord(
+        #     _read(text), item=item, start=seq_start, stop=seq_stop, strand=strand
+        # )
 
 
-def genbank(accession: str = "CS570233.1", *args, **kwargs) -> _GenbankRecord:
+def genbank(
+    accession: str = "CS570233.1", *args, email=None, **kwargs
+) -> _GenbankRecord:
     """
     Download a genbank nuclotide record.
 
@@ -229,9 +235,6 @@ def genbank(accession: str = "CS570233.1", *args, **kwargs) -> _GenbankRecord:
         //
 
     """
-    email = _os.getenv("pydna_email")
-    # _module_logger.info("#### genbank function called ####")
-    # _module_logger.info("email      %s", email)
-    # _module_logger.info("accession  %s", email)
+    email = email or _os.getenv("pydna_email")
     gb = Genbank(email)
     return gb.nucleotide(accession, *args, **kwargs)
diff --git a/src/pydna/opencloning_models.py b/src/pydna/opencloning_models.py
index 9cfcbce5..731441e8 100644
--- a/src/pydna/opencloning_models.py
+++ b/src/pydna/opencloning_models.py
@@ -51,6 +51,8 @@
     CreLoxRecombinationSource as _CreLoxRecombinationSource,
     PCRSource as _PCRSource,
     CRISPRSource as _CRISPRSource,
+    RepositoryIdSource as _RepositoryIdSource,  # here!
+    UploadedFileSource as _UploadedFileSource,
 )
 from Bio.SeqFeature import Location, LocationParserError
 from Bio.Restriction.Restriction import AbstractCut
@@ -348,6 +350,11 @@ def from_subfragment_representation(
 
 class UploadedFileSource(Source):
 
+    TARGET_MODEL: ClassVar[Type[_UploadedFileSource]] = _UploadedFileSource
+
+    file_name: str
+    index_in_file: int
+
     # "id": 1,
     # "type": "UploadedFileSource",
     # "output_name": null,
@@ -361,14 +368,20 @@ class UploadedFileSource(Source):
     # "output": 1
 
     def _kwargs(self, seq_id: int) -> dict:
-        return {**super()._kwargs(seq_id), "file_name": "?", "index_in_file": "?"}
-
-    def to_pydantic_model(self, seq_id: int):
-        return self._target_model()(**self._kwargs(seq_id))
+        return {
+            **super()._kwargs(seq_id),
+            "file_name": self.filename,
+            "index_in_file": self.index_in_file,
+        }
 
 
 class RepositoryIdSource(Source):
 
+    TARGET_MODEL: ClassVar[Type[_RepositoryIdSource]] = _RepositoryIdSource
+    repository_id: str
+    repository_name: str
+    location: Location
+
     # "id": 2,
     # "type": "RepositoryIdSource",
     # "output_name": null,
@@ -378,10 +391,11 @@ class RepositoryIdSource(Source):
     # "repository_name": "genbank"
 
     def _kwargs(self, seq_id: int) -> dict:
-        return {**super()._kwargs(seq_id), "repository_id": "?", "repository_name": "?"}
-
-    def to_pydantic_model(self, seq_id: int):
-        return self._target_model()(**self._kwargs(seq_id))
+        return {
+            **super()._kwargs(seq_id),
+            "repository_id": self.repository_id,
+            "repository_name": self.repository_name,
+        }
 
 
 class RestrictionAndLigationSource(AssemblySource):
diff --git a/src/pydna/parsers.py b/src/pydna/parsers.py
index 46f43c8e..2914c113 100644
--- a/src/pydna/parsers.py
+++ b/src/pydna/parsers.py
@@ -13,7 +13,8 @@
 import textwrap as _textwrap
 
 from Bio import SeqIO as _SeqIO
-from pydna.genbankfile import GenbankFile as _GenbankFile
+
+# from pydna.genbankfile import GenbankFile as _GenbankFile
 from pydna.dseqrecord import Dseqrecord as _Dseqrecord
 from pydna.primer import Primer as _Primer
 
@@ -197,7 +198,12 @@ def parse(data, ds=True):
             # parsed.features = nfs
             for s in newsequences:
                 if ds and path:
-                    sequences.append(_GenbankFile.from_SeqRecord(s, path=path))
+                    from pydna.opencloning_models import UploadedFileSource
+
+                    result = _Dseqrecord.from_SeqRecord(s)
+                    result.source = UploadedFileSource(file_name=path, index_in_file=0)
+                    sequences.append(result)
+                    # sequences.append(_GenbankFile.from_SeqRecord(s, path=path))
                 elif ds:
                     sequences.append(_Dseqrecord.from_SeqRecord(s))
                 else:

From b6c5fb4eee02e16ad09ec7a164cb43f02a151840 Mon Sep 17 00:00:00 2001
From: BjornFJohansson <bjornjobb@gmail.com>
Date: Fri, 7 Nov 2025 17:15:14 +0000
Subject: [PATCH 05/22] fixed fields in model

---
 src/pydna/opencloning_models.py | 4 +++-
 src/pydna/parsers.py            | 4 +++-
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/src/pydna/opencloning_models.py b/src/pydna/opencloning_models.py
index 731441e8..327c813c 100644
--- a/src/pydna/opencloning_models.py
+++ b/src/pydna/opencloning_models.py
@@ -354,6 +354,7 @@ class UploadedFileSource(Source):
 
     file_name: str
     index_in_file: int
+    sequence_file_format: str
 
     # "id": 1,
     # "type": "UploadedFileSource",
@@ -370,8 +371,9 @@ class UploadedFileSource(Source):
     def _kwargs(self, seq_id: int) -> dict:
         return {
             **super()._kwargs(seq_id),
-            "file_name": self.filename,
+            "file_name": self.file_name,
             "index_in_file": self.index_in_file,
+            "sequence_file_format": self.sequence_file_format,
         }
 
 
diff --git a/src/pydna/parsers.py b/src/pydna/parsers.py
index 2914c113..9d0e7dc7 100644
--- a/src/pydna/parsers.py
+++ b/src/pydna/parsers.py
@@ -201,7 +201,9 @@ def parse(data, ds=True):
                     from pydna.opencloning_models import UploadedFileSource
 
                     result = _Dseqrecord.from_SeqRecord(s)
-                    result.source = UploadedFileSource(file_name=path, index_in_file=0)
+                    result.source = UploadedFileSource(
+                        file_name=path, sequence_file_format="genbank", index_in_file=0
+                    )
                     sequences.append(result)
                     # sequences.append(_GenbankFile.from_SeqRecord(s, path=path))
                 elif ds:

From 1e817b4c4e001f277666ecbef6632d2a9d394aad Mon Sep 17 00:00:00 2001
From: Manuel Lera-Ramirez <manulera14@gmail.com>
Date: Mon, 17 Nov 2025 19:02:28 +0000
Subject: [PATCH 06/22] enable higher opencloning-linkml versions

---
 poetry.lock    | 439 ++++++++++++++++++-------------------------------
 pyproject.toml |   2 +-
 2 files changed, 163 insertions(+), 278 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index d6dec7ae..9e845f25 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 2.1.3 and should not be changed by hand.
+# This file is automatically @generated by Poetry 2.0.1 and should not be changed by hand.
 
 [[package]]
 name = "accessible-pygments"
@@ -7,6 +7,7 @@ description = "A collection of accessible pygments styles"
 optional = false
 python-versions = ">=3.9"
 groups = ["docs"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "accessible_pygments-0.0.5-py3-none-any.whl", hash = "sha256:88ae3211e68a1d0b011504b2ffc1691feafce124b845bd072ab6f9f66f34d4b7"},
     {file = "accessible_pygments-0.0.5.tar.gz", hash = "sha256:40918d3e6a2b619ad424cb91e556bd3bd8865443d9f22f1dcdf79e33c8046872"},
@@ -26,6 +27,7 @@ description = "A light, configurable Sphinx theme"
 optional = false
 python-versions = ">=3.10"
 groups = ["docs"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "alabaster-1.0.0-py3-none-any.whl", hash = "sha256:fc6786402dc3fcb2de3cabd5fe455a2db534b371124f1f21de8731783dec828b"},
     {file = "alabaster-1.0.0.tar.gz", hash = "sha256:c00dca57bca26fa62a6d7d0a9fcce65f3e026e9bfe33e9c538fd3fbb2144fd9e"},
@@ -38,6 +40,7 @@ description = "Reusable constraint types to use with typing.Annotated"
 optional = false
 python-versions = ">=3.8"
 groups = ["main"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "annotated_types-0.7.0-py3-none-any.whl", hash = "sha256:1f02e8b43a8fbbc3f3e0d4f0f4bfc8131bcb4eebe8849b8e5c773f3a1c582a53"},
     {file = "annotated_types-0.7.0.tar.gz", hash = "sha256:aff07c09a53a08bc8cfccb9c85b05f1aa9a2a6f23728d790723543408344ce89"},
@@ -50,6 +53,7 @@ description = "A small Python module for determining appropriate platform-specif
 optional = false
 python-versions = "*"
 groups = ["main"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "appdirs-1.4.4-py2.py3-none-any.whl", hash = "sha256:a841dacd6b99318a741b166adb07e19ee71a274450e68237b4650ca1055ab128"},
     {file = "appdirs-1.4.4.tar.gz", hash = "sha256:7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41"},
@@ -62,7 +66,7 @@ description = "Disable App Nap on macOS >= 10.9"
 optional = false
 python-versions = ">=3.6"
 groups = ["docs", "test"]
-markers = "platform_system == \"Darwin\""
+markers = "(python_version <= \"3.11\" or python_version >= \"3.12\") and platform_system == \"Darwin\""
 files = [
     {file = "appnope-0.1.4-py2.py3-none-any.whl", hash = "sha256:502575ee11cd7a28c0205f379b525beefebab9d161b7c964670864014ed7213c"},
     {file = "appnope-0.1.4.tar.gz", hash = "sha256:1de3860566df9caf38f01f86f65e0e13e379af54f9e4bee1e66b48f2efffd1ee"},
@@ -75,6 +79,7 @@ description = "Annotate AST trees with source code positions"
 optional = false
 python-versions = ">=3.8"
 groups = ["docs", "test"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "asttokens-3.0.0-py3-none-any.whl", hash = "sha256:e3078351a059199dd5138cb1c706e6430c05eff2ff136af5eb4790f9d28932e2"},
     {file = "asttokens-3.0.0.tar.gz", hash = "sha256:0dcd8baa8d62b0c1d118b399b2ddba3c4aff271d0d7a9e0d4c1681c79035bbc7"},
@@ -91,6 +96,7 @@ description = "Classes Without Boilerplate"
 optional = false
 python-versions = ">=3.9"
 groups = ["dev", "docs", "test"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "attrs-25.4.0-py3-none-any.whl", hash = "sha256:adcf7e2a1fb3b36ac48d97835bb6d8ade15b8dcce26aba8bf1d14847b57a3373"},
     {file = "attrs-25.4.0.tar.gz", hash = "sha256:16d5969b87f0859ef33a48b35d55ac1be6e42ae49d5e853b597db70c35c57e11"},
@@ -103,6 +109,7 @@ description = "A tool that automatically formats Python code to conform to the P
 optional = false
 python-versions = ">=3.9"
 groups = ["dev"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "autopep8-2.3.2-py2.py3-none-any.whl", hash = "sha256:ce8ad498672c845a0c3de2629c15b635ec2b05ef8177a6e7c91c74f3e9b51128"},
     {file = "autopep8-2.3.2.tar.gz", hash = "sha256:89440a4f969197b69a995e4ce0661b031f455a9f776d2c5ba3dbd83466931758"},
@@ -119,13 +126,14 @@ description = "Internationalization utilities"
 optional = false
 python-versions = ">=3.8"
 groups = ["docs"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "babel-2.17.0-py3-none-any.whl", hash = "sha256:4d0b53093fdfb4b21c92b5213dba5a1b23885afa8383709427046b21c366e5f2"},
     {file = "babel-2.17.0.tar.gz", hash = "sha256:0c54cffb19f690cdcc52a3b50bcbf71e07a808d1c80d549f2459b9d2cf0afb9d"},
 ]
 
 [package.extras]
-dev = ["backports.zoneinfo ; python_version < \"3.9\"", "freezegun (>=1.0,<2.0)", "jinja2 (>=3.0)", "pytest (>=6.0)", "pytest-cov", "pytz", "setuptools", "tzdata ; sys_platform == \"win32\""]
+dev = ["backports.zoneinfo", "freezegun (>=1.0,<2.0)", "jinja2 (>=3.0)", "pytest (>=6.0)", "pytest-cov", "pytz", "setuptools", "tzdata"]
 
 [[package]]
 name = "beautifulsoup4"
@@ -134,6 +142,7 @@ description = "Screen-scraping library"
 optional = false
 python-versions = ">=3.7.0"
 groups = ["docs"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "beautifulsoup4-4.14.2-py3-none-any.whl", hash = "sha256:5ef6fa3a8cbece8488d66985560f97ed091e22bbc4e9c2338508a9d5de6d4515"},
     {file = "beautifulsoup4-4.14.2.tar.gz", hash = "sha256:2a98ab9f944a11acee9cc848508ec28d9228abfd522ef0fad6a02a72e0ded69e"},
@@ -157,6 +166,7 @@ description = "Freely available tools for computational molecular biology."
 optional = false
 python-versions = ">=3.9"
 groups = ["main"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "biopython-1.85-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:a6308053a61f3bdbb11504ece4cf24e264c6f1d6fad278f7e59e6b84b0d9a7b4"},
     {file = "biopython-1.85-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:434dd23e972b0c89e128f2ebbd16b38075d609184f4f1fd16368035f923019c2"},
@@ -202,6 +212,7 @@ description = "The uncompromising code formatter."
 optional = false
 python-versions = ">=3.9"
 groups = ["dev"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
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@@ -250,7 +261,7 @@ description = "Python implementation of codon adaptation index"
 optional = true
 python-versions = ">=3.8"
 groups = ["main"]
-markers = "extra == \"express\""
+markers = "(python_version <= \"3.11\" or python_version >= \"3.12\") and extra == \"express\""
 files = [
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@@ -272,7 +283,7 @@ files = [
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-markers = {main = "extra == \"download\""}
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 [[package]]
 name = "cffi"
@@ -281,7 +292,7 @@ description = "Foreign Function Interface for Python calling C code."
 optional = false
 python-versions = ">=3.9"
 groups = ["docs", "test"]
-markers = "implementation_name == \"pypy\""
+markers = "(python_version <= \"3.11\" or python_version >= \"3.12\") and implementation_name == \"pypy\""
 files = [
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@@ -379,6 +390,7 @@ description = "Validate configuration and produce human readable error messages.
 optional = false
 python-versions = ">=3.8"
 groups = ["dev"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
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 [[package]]
 name = "click"
@@ -519,7 +531,7 @@ files = [
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 [package.dependencies]
 colorama = {version = "*", markers = "platform_system == \"Windows\""}
@@ -535,7 +547,7 @@ files = [
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+markers = {main = "extra == \"express\" and platform_system == \"Windows\" and (python_version <= \"3.11\" or python_version >= \"3.12\")", dev = "(python_version <= \"3.11\" or python_version >= \"3.12\") and platform_system == \"Windows\"", docs = "(platform_system == \"Windows\" or sys_platform == \"win32\") and (python_version <= \"3.11\" or python_version >= \"3.12\")", test = "(python_version <= \"3.11\" or python_version >= \"3.12\") and sys_platform == \"win32\""}
 
 [[package]]
 name = "comm"
@@ -544,6 +556,7 @@ description = "Jupyter Python Comm implementation, for usage in ipykernel, xeus-
 optional = false
 python-versions = ">=3.8"
 groups = ["docs", "test"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
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@@ -559,7 +572,7 @@ description = "Python library for calculating contours of 2D quadrilateral grids
 optional = true
 python-versions = ">=3.10"
 groups = ["main"]
-markers = "python_version == \"3.10\" and extra == \"gel\""
+markers = "(python_version <= \"3.11\" or python_version >= \"3.12\") and extra == \"gel\""
 files = [
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@@ -630,99 +643,6 @@ mypy = ["bokeh", "contourpy[bokeh,docs]", "docutils-stubs", "mypy (==1.15.0)", "
 test = ["Pillow", "contourpy[test-no-images]", "matplotlib"]
 test-no-images = ["pytest", "pytest-cov", "pytest-rerunfailures", "pytest-xdist", "wurlitzer"]
 
-[[package]]
-name = "contourpy"
-version = "1.3.3"
-description = "Python library for calculating contours of 2D quadrilateral grids"
-optional = true
-python-versions = ">=3.11"
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-    {file = "contourpy-1.3.3-cp314-cp314t-musllinux_1_2_aarch64.whl", hash = "sha256:2a2a8b627d5cc6b7c41a4beff6c5ad5eb848c88255fda4a8745f7e901b32d8e4"},
-    {file = "contourpy-1.3.3-cp314-cp314t-musllinux_1_2_x86_64.whl", hash = "sha256:fd6ec6be509c787f1caf6b247f0b1ca598bef13f4ddeaa126b7658215529ba0f"},
-    {file = "contourpy-1.3.3-cp314-cp314t-win32.whl", hash = "sha256:e74a9a0f5e3fff48fb5a7f2fd2b9b70a3fe014a67522f79b7cca4c0c7e43c9ae"},
-    {file = "contourpy-1.3.3-cp314-cp314t-win_amd64.whl", hash = "sha256:13b68d6a62db8eafaebb8039218921399baf6e47bf85006fd8529f2a08ef33fc"},
-    {file = "contourpy-1.3.3-cp314-cp314t-win_arm64.whl", hash = "sha256:b7448cb5a725bb1e35ce88771b86fba35ef418952474492cf7c764059933ff8b"},
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-    {file = "contourpy-1.3.3-pp311-pypy311_pp73-macosx_11_0_arm64.whl", hash = "sha256:0c1fc238306b35f246d61a1d416a627348b5cf0648648a031e14bb8705fcdfe8"},
-    {file = "contourpy-1.3.3-pp311-pypy311_pp73-manylinux_2_26_aarch64.manylinux_2_28_aarch64.whl", hash = "sha256:70f9aad7de812d6541d29d2bbf8feb22ff7e1c299523db288004e3157ff4674e"},
-    {file = "contourpy-1.3.3-pp311-pypy311_pp73-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl", hash = "sha256:5ed3657edf08512fc3fe81b510e35c2012fbd3081d2e26160f27ca28affec989"},
-    {file = "contourpy-1.3.3-pp311-pypy311_pp73-win_amd64.whl", hash = "sha256:3d1a3799d62d45c18bafd41c5fa05120b96a28079f2393af559b843d1a966a77"},
-    {file = "contourpy-1.3.3.tar.gz", hash = "sha256:083e12155b210502d0bca491432bb04d56dc3432f95a979b429f2848c3dbe880"},
-]
-
-[package.dependencies]
-numpy = ">=1.25"
-
-[package.extras]
-bokeh = ["bokeh", "selenium"]
-docs = ["furo", "sphinx (>=7.2)", "sphinx-copybutton"]
-mypy = ["bokeh", "contourpy[bokeh,docs]", "docutils-stubs", "mypy (==1.17.0)", "types-Pillow"]
-test = ["Pillow", "contourpy[test-no-images]", "matplotlib"]
-test-no-images = ["pytest", "pytest-cov", "pytest-rerunfailures", "pytest-xdist", "wurlitzer"]
-
 [[package]]
 name = "coverage"
 version = "7.11.0"
@@ -730,6 +650,7 @@ description = "Code coverage measurement for Python"
 optional = false
 python-versions = ">=3.10"
 groups = ["test"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "coverage-7.11.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:eb53f1e8adeeb2e78962bade0c08bfdc461853c7969706ed901821e009b35e31"},
     {file = "coverage-7.11.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:d9a03ec6cb9f40a5c360f138b88266fd8f58408d71e89f536b4f91d85721d075"},
@@ -829,7 +750,7 @@ files = [
 tomli = {version = "*", optional = true, markers = "python_full_version <= \"3.11.0a6\" and extra == \"toml\""}
 
 [package.extras]
-toml = ["tomli ; python_full_version <= \"3.11.0a6\""]
+toml = ["tomli"]
 
 [[package]]
 name = "cycler"
@@ -838,7 +759,7 @@ description = "Composable style cycles"
 optional = true
 python-versions = ">=3.8"
 groups = ["main"]
-markers = "extra == \"gel\""
+markers = "(python_version <= \"3.11\" or python_version >= \"3.12\") and extra == \"gel\""
 files = [
     {file = "cycler-0.12.1-py3-none-any.whl", hash = "sha256:85cef7cff222d8644161529808465972e51340599459b8ac3ccbac5a854e0d30"},
     {file = "cycler-0.12.1.tar.gz", hash = "sha256:88bb128f02ba341da8ef447245a9e138fae777f6a23943da4540077d3601eb1c"},
@@ -855,6 +776,7 @@ description = "An implementation of the Debug Adapter Protocol for Python"
 optional = false
 python-versions = ">=3.8"
 groups = ["docs", "test"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "debugpy-1.8.17-cp310-cp310-macosx_15_0_x86_64.whl", hash = "sha256:c41d2ce8bbaddcc0009cc73f65318eedfa3dbc88a8298081deb05389f1ab5542"},
     {file = "debugpy-1.8.17-cp310-cp310-manylinux_2_34_x86_64.whl", hash = "sha256:1440fd514e1b815edd5861ca394786f90eb24960eb26d6f7200994333b1d79e3"},
@@ -895,6 +817,7 @@ description = "Decorators for Humans"
 optional = false
 python-versions = ">=3.8"
 groups = ["docs", "test"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "decorator-5.2.1-py3-none-any.whl", hash = "sha256:d316bb415a2d9e2d2b3abcc4084c6502fc09240e292cd76a76afc106a1c8e04a"},
     {file = "decorator-5.2.1.tar.gz", hash = "sha256:65f266143752f734b0a7cc83c46f4618af75b8c5911b00ccb61d0ac9b6da0360"},
@@ -907,6 +830,7 @@ description = "Distribution utilities"
 optional = false
 python-versions = "*"
 groups = ["dev"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "distlib-0.4.0-py2.py3-none-any.whl", hash = "sha256:9659f7d87e46584a30b5780e43ac7a2143098441670ff0a49d5f9034c54a6c16"},
     {file = "distlib-0.4.0.tar.gz", hash = "sha256:feec40075be03a04501a973d81f633735b4b69f98b05450592310c0f401a4e0d"},
@@ -919,6 +843,7 @@ description = "Docutils -- Python Documentation Utilities"
 optional = false
 python-versions = ">=3.9"
 groups = ["docs"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "docutils-0.21.2-py3-none-any.whl", hash = "sha256:dafca5b9e384f0e419294eb4d2ff9fa826435bf15f15b7bd45723e8ad76811b2"},
     {file = "docutils-0.21.2.tar.gz", hash = "sha256:3a6b18732edf182daa3cd12775bbb338cf5691468f91eeeb109deff6ebfa986f"},
@@ -931,7 +856,7 @@ description = "Backport of PEP 654 (exception groups)"
 optional = false
 python-versions = ">=3.7"
 groups = ["docs", "test"]
-markers = "python_version == \"3.10\""
+markers = "python_version < \"3.11\""
 files = [
     {file = "exceptiongroup-1.3.0-py3-none-any.whl", hash = "sha256:4d111e6e0c13d0644cad6ddaa7ed0261a0b36971f6d23e7ec9b4b9097da78a10"},
     {file = "exceptiongroup-1.3.0.tar.gz", hash = "sha256:b241f5885f560bc56a59ee63ca4c6a8bfa46ae4ad651af316d4e81817bb9fd88"},
@@ -950,13 +875,14 @@ description = "Get the currently executing AST node of a frame, and other inform
 optional = false
 python-versions = ">=3.8"
 groups = ["docs", "test"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "executing-2.2.1-py2.py3-none-any.whl", hash = "sha256:760643d3452b4d777d295bb167ccc74c64a81df23fb5e08eff250c425a4b2017"},
     {file = "executing-2.2.1.tar.gz", hash = "sha256:3632cc370565f6648cc328b32435bd120a1e4ebb20c77e3fdde9a13cd1e533c4"},
 ]
 
 [package.extras]
-tests = ["asttokens (>=2.1.0)", "coverage", "coverage-enable-subprocess", "ipython", "littleutils", "pytest", "rich ; python_version >= \"3.11\""]
+tests = ["asttokens (>=2.1.0)", "coverage", "coverage-enable-subprocess", "ipython", "littleutils", "pytest", "rich"]
 
 [[package]]
 name = "fastjsonschema"
@@ -965,6 +891,7 @@ description = "Fastest Python implementation of JSON schema"
 optional = false
 python-versions = "*"
 groups = ["dev", "docs", "test"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "fastjsonschema-2.21.2-py3-none-any.whl", hash = "sha256:1c797122d0a86c5cace2e54bf4e819c36223b552017172f32c5c024a6b77e463"},
     {file = "fastjsonschema-2.21.2.tar.gz", hash = "sha256:b1eb43748041c880796cd077f1a07c3d94e93ae84bba5ed36800a33554ae05de"},
@@ -980,6 +907,7 @@ description = "A platform independent file lock."
 optional = false
 python-versions = ">=3.10"
 groups = ["dev"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "filelock-3.20.0-py3-none-any.whl", hash = "sha256:339b4732ffda5cd79b13f4e2711a31b0365ce445d95d243bb996273d072546a2"},
     {file = "filelock-3.20.0.tar.gz", hash = "sha256:711e943b4ec6be42e1d4e6690b48dc175c822967466bb31c0c293f34334c13f4"},
@@ -992,6 +920,7 @@ description = "the modular source code checker: pep8 pyflakes and co"
 optional = false
 python-versions = ">=3.9"
 groups = ["dev"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "flake8-7.3.0-py2.py3-none-any.whl", hash = "sha256:b9696257b9ce8beb888cdbe31cf885c90d31928fe202be0889a7cdafad32f01e"},
     {file = "flake8-7.3.0.tar.gz", hash = "sha256:fe044858146b9fc69b551a4b490d69cf960fcb78ad1edcb84e7fbb1b4a8e3872"},
@@ -1009,6 +938,7 @@ description = "A plugin for flake8 finding likely bugs and design problems in yo
 optional = false
 python-versions = ">=3.8.1"
 groups = ["dev"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "flake8_bugbear-24.12.12-py3-none-any.whl", hash = "sha256:1b6967436f65ca22a42e5373aaa6f2d87966ade9aa38d4baf2a1be550767545e"},
     {file = "flake8_bugbear-24.12.12.tar.gz", hash = "sha256:46273cef0a6b6ff48ca2d69e472f41420a42a46e24b2a8972e4f0d6733d12a64"},
@@ -1028,7 +958,7 @@ description = "Tools to manipulate font files"
 optional = true
 python-versions = ">=3.9"
 groups = ["main"]
-markers = "extra == \"gel\""
+markers = "(python_version <= \"3.11\" or python_version >= \"3.12\") and extra == \"gel\""
 files = [
     {file = "fonttools-4.60.1-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:9a52f254ce051e196b8fe2af4634c2d2f02c981756c6464dc192f1b6050b4e28"},
     {file = "fonttools-4.60.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:c7420a2696a44650120cdd269a5d2e56a477e2bfa9d95e86229059beb1c19e15"},
@@ -1091,17 +1021,17 @@ files = [
 ]
 
 [package.extras]
-all = ["brotli (>=1.0.1) ; platform_python_implementation == \"CPython\"", "brotlicffi (>=0.8.0) ; platform_python_implementation != \"CPython\"", "lxml (>=4.0)", "lz4 (>=1.7.4.2)", "matplotlib", "munkres ; platform_python_implementation == \"PyPy\"", "pycairo", "scipy ; platform_python_implementation != \"PyPy\"", "skia-pathops (>=0.5.0)", "sympy", "uharfbuzz (>=0.23.0)", "unicodedata2 (>=15.1.0) ; python_version <= \"3.12\"", "xattr ; sys_platform == \"darwin\"", "zopfli (>=0.1.4)"]
+all = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "lxml (>=4.0)", "lz4 (>=1.7.4.2)", "matplotlib", "munkres", "pycairo", "scipy", "skia-pathops (>=0.5.0)", "sympy", "uharfbuzz (>=0.23.0)", "unicodedata2 (>=15.1.0)", "xattr", "zopfli (>=0.1.4)"]
 graphite = ["lz4 (>=1.7.4.2)"]
-interpolatable = ["munkres ; platform_python_implementation == \"PyPy\"", "pycairo", "scipy ; platform_python_implementation != \"PyPy\""]
+interpolatable = ["munkres", "pycairo", "scipy"]
 lxml = ["lxml (>=4.0)"]
 pathops = ["skia-pathops (>=0.5.0)"]
 plot = ["matplotlib"]
 repacker = ["uharfbuzz (>=0.23.0)"]
 symfont = ["sympy"]
-type1 = ["xattr ; sys_platform == \"darwin\""]
-unicode = ["unicodedata2 (>=15.1.0) ; python_version <= \"3.12\""]
-woff = ["brotli (>=1.0.1) ; platform_python_implementation == \"CPython\"", "brotlicffi (>=0.8.0) ; platform_python_implementation != \"CPython\"", "zopfli (>=0.1.4)"]
+type1 = ["xattr"]
+unicode = ["unicodedata2 (>=15.1.0)"]
+woff = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "zopfli (>=0.1.4)"]
 
 [[package]]
 name = "gprof2dot"
@@ -1110,6 +1040,7 @@ description = "Generate a dot graph from the output of several profilers."
 optional = false
 python-versions = ">=3.8"
 groups = ["test"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "gprof2dot-2025.4.14-py3-none-any.whl", hash = "sha256:0742e4c0b4409a5e8777e739388a11e1ed3750be86895655312ea7c20bd0090e"},
     {file = "gprof2dot-2025.4.14.tar.gz", hash = "sha256:35743e2d2ca027bf48fa7cba37021aaf4a27beeae1ae8e05a50b55f1f921a6ce"},
@@ -1122,7 +1053,7 @@ description = "Lightweight in-process concurrent programming"
 optional = false
 python-versions = ">=3.9"
 groups = ["docs"]
-markers = "platform_machine == \"aarch64\" or platform_machine == \"ppc64le\" or platform_machine == \"x86_64\" or platform_machine == \"amd64\" or platform_machine == \"AMD64\" or platform_machine == \"win32\" or platform_machine == \"WIN32\""
+markers = "(python_version <= \"3.11\" or python_version >= \"3.12\") and (platform_machine == \"aarch64\" or platform_machine == \"ppc64le\" or platform_machine == \"x86_64\" or platform_machine == \"amd64\" or platform_machine == \"AMD64\" or platform_machine == \"win32\" or platform_machine == \"WIN32\")"
 files = [
     {file = "greenlet-3.2.4-cp310-cp310-macosx_11_0_universal2.whl", hash = "sha256:8c68325b0d0acf8d91dde4e6f930967dd52a5302cd4062932a6b2e7c2969f47c"},
     {file = "greenlet-3.2.4-cp310-cp310-manylinux2014_aarch64.manylinux_2_17_aarch64.whl", hash = "sha256:94385f101946790ae13da500603491f04a76b6e4c059dab271b3ce2e283b2590"},
@@ -1191,6 +1122,7 @@ description = "File identification library for Python"
 optional = false
 python-versions = ">=3.9"
 groups = ["dev"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "identify-2.6.15-py2.py3-none-any.whl", hash = "sha256:1181ef7608e00704db228516541eb83a88a9f94433a8c80bb9b5bd54b1d81757"},
     {file = "identify-2.6.15.tar.gz", hash = "sha256:e4f4864b96c6557ef2a1e1c951771838f4edc9df3a72ec7118b338801b11c7bf"},
@@ -1210,7 +1142,7 @@ files = [
     {file = "idna-3.11-py3-none-any.whl", hash = "sha256:771a87f49d9defaf64091e6e6fe9c18d4833f140bd19464795bc32d966ca37ea"},
     {file = "idna-3.11.tar.gz", hash = "sha256:795dafcc9c04ed0c1fb032c2aa73654d8e8c5023a7df64a53f39190ada629902"},
 ]
-markers = {main = "extra == \"download\""}
+markers = {main = "(python_version <= \"3.11\" or python_version >= \"3.12\") and extra == \"download\"", docs = "python_version <= \"3.11\" or python_version >= \"3.12\"", test = "python_version <= \"3.11\" or python_version >= \"3.12\""}
 
 [package.extras]
 all = ["flake8 (>=7.1.1)", "mypy (>=1.11.2)", "pytest (>=8.3.2)", "ruff (>=0.6.2)"]
@@ -1222,6 +1154,7 @@ description = "Getting image size from png/jpeg/jpeg2000/gif file"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 groups = ["docs"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "imagesize-1.4.1-py2.py3-none-any.whl", hash = "sha256:0d8d18d08f840c19d0ee7ca1fd82490fdc3729b7ac93f49870406ddde8ef8d8b"},
     {file = "imagesize-1.4.1.tar.gz", hash = "sha256:69150444affb9cb0d5cc5a92b3676f0b2fb7cd9ae39e947a5e11a36b4497cd4a"},
@@ -1234,6 +1167,7 @@ description = "Read metadata from Python packages"
 optional = false
 python-versions = ">=3.9"
 groups = ["docs"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "importlib_metadata-8.7.0-py3-none-any.whl", hash = "sha256:e5dd1551894c77868a30651cef00984d50e1002d06942a7101d34870c5f02afd"},
     {file = "importlib_metadata-8.7.0.tar.gz", hash = "sha256:d13b81ad223b890aa16c5471f2ac3056cf76c5f10f82d6f9292f0b415f389000"},
@@ -1243,12 +1177,12 @@ files = [
 zipp = ">=3.20"
 
 [package.extras]
-check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1) ; sys_platform != \"cygwin\""]
+check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"]
 cover = ["pytest-cov"]
 doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
 enabler = ["pytest-enabler (>=2.2)"]
 perf = ["ipython"]
-test = ["flufl.flake8", "importlib_resources (>=1.3) ; python_version < \"3.9\"", "jaraco.test (>=5.4)", "packaging", "pyfakefs", "pytest (>=6,!=8.1.*)", "pytest-perf (>=0.9.2)"]
+test = ["flufl.flake8", "importlib_resources (>=1.3)", "jaraco.test (>=5.4)", "packaging", "pyfakefs", "pytest (>=6,!=8.1.*)", "pytest-perf (>=0.9.2)"]
 type = ["pytest-mypy"]
 
 [[package]]
@@ -1258,6 +1192,7 @@ description = "brain-dead simple config-ini parsing"
 optional = false
 python-versions = ">=3.10"
 groups = ["test"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "iniconfig-2.3.0-py3-none-any.whl", hash = "sha256:f631c04d2c48c52b84d0d0549c99ff3859c98df65b3101406327ecc7d53fbf12"},
     {file = "iniconfig-2.3.0.tar.gz", hash = "sha256:c76315c77db068650d49c5b56314774a7804df16fee4402c1f19d6d15d8c4730"},
@@ -1270,6 +1205,7 @@ description = "IPython Kernel for Jupyter"
 optional = false
 python-versions = ">=3.10"
 groups = ["docs", "test"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "ipykernel-7.1.0-py3-none-any.whl", hash = "sha256:763b5ec6c5b7776f6a8d7ce09b267693b4e5ce75cb50ae696aaefb3c85e1ea4c"},
     {file = "ipykernel-7.1.0.tar.gz", hash = "sha256:58a3fc88533d5930c3546dc7eac66c6d288acde4f801e2001e65edc5dc9cf0db"},
@@ -1304,7 +1240,7 @@ description = "IPython: Productive Interactive Computing"
 optional = false
 python-versions = ">=3.10"
 groups = ["docs", "test"]
-markers = "python_version == \"3.10\""
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "ipython-8.37.0-py3-none-any.whl", hash = "sha256:ed87326596b878932dbcb171e3e698845434d8c61b8d8cd474bf663041a9dcf2"},
     {file = "ipython-8.37.0.tar.gz", hash = "sha256:ca815841e1a41a1e6b73a0b08f3038af9b2252564d01fc405356d34033012216"},
@@ -1326,7 +1262,7 @@ typing_extensions = {version = ">=4.6", markers = "python_version < \"3.12\""}
 [package.extras]
 all = ["ipython[black,doc,kernel,matplotlib,nbconvert,nbformat,notebook,parallel,qtconsole]", "ipython[test,test-extra]"]
 black = ["black"]
-doc = ["docrepr", "exceptiongroup", "intersphinx_registry", "ipykernel", "ipython[test]", "matplotlib", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "sphinxcontrib-jquery", "tomli ; python_version < \"3.11\"", "typing_extensions"]
+doc = ["docrepr", "exceptiongroup", "intersphinx_registry", "ipykernel", "ipython[test]", "matplotlib", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "sphinxcontrib-jquery", "tomli", "typing_extensions"]
 kernel = ["ipykernel"]
 matplotlib = ["matplotlib"]
 nbconvert = ["nbconvert"]
@@ -1337,56 +1273,6 @@ qtconsole = ["qtconsole"]
 test = ["packaging", "pickleshare", "pytest", "pytest-asyncio (<0.22)", "testpath"]
 test-extra = ["curio", "ipython[test]", "jupyter_ai", "matplotlib (!=3.2.0)", "nbformat", "numpy (>=1.23)", "pandas", "trio"]
 
-[[package]]
-name = "ipython"
-version = "9.6.0"
-description = "IPython: Productive Interactive Computing"
-optional = false
-python-versions = ">=3.11"
-groups = ["docs", "test"]
-markers = "python_version >= \"3.11\""
-files = [
-    {file = "ipython-9.6.0-py3-none-any.whl", hash = "sha256:5f77efafc886d2f023442479b8149e7d86547ad0a979e9da9f045d252f648196"},
-    {file = "ipython-9.6.0.tar.gz", hash = "sha256:5603d6d5d356378be5043e69441a072b50a5b33b4503428c77b04cb8ce7bc731"},
-]
-
-[package.dependencies]
-colorama = {version = "*", markers = "sys_platform == \"win32\""}
-decorator = "*"
-ipython-pygments-lexers = "*"
-jedi = ">=0.16"
-matplotlib-inline = "*"
-pexpect = {version = ">4.3", markers = "sys_platform != \"win32\" and sys_platform != \"emscripten\""}
-prompt_toolkit = ">=3.0.41,<3.1.0"
-pygments = ">=2.4.0"
-stack_data = "*"
-traitlets = ">=5.13.0"
-typing_extensions = {version = ">=4.6", markers = "python_version < \"3.12\""}
-
-[package.extras]
-all = ["ipython[doc,matplotlib,test,test-extra]"]
-black = ["black"]
-doc = ["docrepr", "exceptiongroup", "intersphinx_registry", "ipykernel", "ipython[matplotlib,test]", "setuptools (>=61.2)", "sphinx (>=1.3)", "sphinx-rtd-theme", "sphinx_toml (==0.0.4)", "typing_extensions"]
-matplotlib = ["matplotlib (>3.7)"]
-test = ["packaging", "pytest", "pytest-asyncio", "testpath"]
-test-extra = ["curio", "ipykernel", "ipython[matplotlib]", "ipython[test]", "jupyter_ai", "nbclient", "nbformat", "numpy (>=1.25)", "pandas (>2.0)", "trio"]
-
-[[package]]
-name = "ipython-pygments-lexers"
-version = "1.1.1"
-description = "Defines a variety of Pygments lexers for highlighting IPython code."
-optional = false
-python-versions = ">=3.8"
-groups = ["docs", "test"]
-markers = "python_version >= \"3.11\""
-files = [
-    {file = "ipython_pygments_lexers-1.1.1-py3-none-any.whl", hash = "sha256:a9462224a505ade19a605f71f8fa63c2048833ce50abc86768a0d81d876dc81c"},
-    {file = "ipython_pygments_lexers-1.1.1.tar.gz", hash = "sha256:09c0138009e56b6854f9535736f4171d855c8c08a563a0dcd8022f78355c7e81"},
-]
-
-[package.dependencies]
-pygments = "*"
-
 [[package]]
 name = "jedi"
 version = "0.19.2"
@@ -1394,6 +1280,7 @@ description = "An autocompletion tool for Python that can be used for text edito
 optional = false
 python-versions = ">=3.6"
 groups = ["docs", "test"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "jedi-0.19.2-py2.py3-none-any.whl", hash = "sha256:a8ef22bde8490f57fe5c7681a3c83cb58874daf72b4784de3cce5b6ef6edb5b9"},
     {file = "jedi-0.19.2.tar.gz", hash = "sha256:4770dc3de41bde3966b02eb84fbcf557fb33cce26ad23da12c742fb50ecb11f0"},
@@ -1414,6 +1301,7 @@ description = "A very fast and expressive template engine."
 optional = false
 python-versions = ">=3.7"
 groups = ["docs"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "jinja2-3.1.6-py3-none-any.whl", hash = "sha256:85ece4451f492d0c13c5dd7c13a64681a86afae63a5f347908daf103ce6d2f67"},
     {file = "jinja2-3.1.6.tar.gz", hash = "sha256:0137fb05990d35f1275a587e9aee6d56da821fc83491a0fb838183be43f66d6d"},
@@ -1432,6 +1320,7 @@ description = "An implementation of JSON Schema validation for Python"
 optional = false
 python-versions = ">=3.9"
 groups = ["dev", "docs", "test"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "jsonschema-4.25.1-py3-none-any.whl", hash = "sha256:3fba0169e345c7175110351d456342c364814cfcf3b964ba4587f22915230a63"},
     {file = "jsonschema-4.25.1.tar.gz", hash = "sha256:e4a9655ce0da0c0b67a085847e00a3a51449e1157f4f75e9fb5aa545e122eb85"},
@@ -1454,6 +1343,7 @@ description = "The JSON Schema meta-schemas and vocabularies, exposed as a Regis
 optional = false
 python-versions = ">=3.9"
 groups = ["dev", "docs", "test"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "jsonschema_specifications-2025.9.1-py3-none-any.whl", hash = "sha256:98802fee3a11ee76ecaca44429fda8a41bff98b00a0f2838151b113f210cc6fe"},
     {file = "jsonschema_specifications-2025.9.1.tar.gz", hash = "sha256:b540987f239e745613c7a9176f3edb72b832a4ac465cf02712288397832b5e8d"},
@@ -1469,6 +1359,7 @@ description = "A defined interface for working with a cache of jupyter notebooks
 optional = false
 python-versions = ">=3.9"
 groups = ["docs"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "jupyter_cache-1.0.1-py3-none-any.whl", hash = "sha256:9c3cafd825ba7da8b5830485343091143dff903e4d8c69db9349b728b140abf6"},
     {file = "jupyter_cache-1.0.1.tar.gz", hash = "sha256:16e808eb19e3fb67a223db906e131ea6e01f03aa27f49a7214ce6a5fec186fb9"},
@@ -1497,6 +1388,7 @@ description = "Jupyter protocol implementation and client libraries"
 optional = false
 python-versions = ">=3.8"
 groups = ["docs", "test"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "jupyter_client-8.6.3-py3-none-any.whl", hash = "sha256:e8a19cc986cc45905ac3362915f410f3af85424b4c0905e94fa5f2cb08e8f23f"},
     {file = "jupyter_client-8.6.3.tar.gz", hash = "sha256:35b3a0947c4a6e9d589eb97d7d4cd5e90f910ee73101611f01283732bd6d9419"},
@@ -1511,7 +1403,7 @@ traitlets = ">=5.3"
 
 [package.extras]
 docs = ["ipykernel", "myst-parser", "pydata-sphinx-theme", "sphinx (>=4)", "sphinx-autodoc-typehints", "sphinxcontrib-github-alt", "sphinxcontrib-spelling"]
-test = ["coverage", "ipykernel (>=6.14)", "mypy", "paramiko ; sys_platform == \"win32\"", "pre-commit", "pytest (<8.2.0)", "pytest-cov", "pytest-jupyter[client] (>=0.4.1)", "pytest-timeout"]
+test = ["coverage", "ipykernel (>=6.14)", "mypy", "paramiko", "pre-commit", "pytest (<8.2.0)", "pytest-cov", "pytest-jupyter[client] (>=0.4.1)", "pytest-timeout"]
 
 [[package]]
 name = "jupyter-core"
@@ -1520,6 +1412,7 @@ description = "Jupyter core package. A base package on which Jupyter projects re
 optional = false
 python-versions = ">=3.10"
 groups = ["dev", "docs", "test"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "jupyter_core-5.9.1-py3-none-any.whl", hash = "sha256:ebf87fdc6073d142e114c72c9e29a9d7ca03fad818c5d300ce2adc1fb0743407"},
     {file = "jupyter_core-5.9.1.tar.gz", hash = "sha256:4d09aaff303b9566c3ce657f580bd089ff5c91f5f89cf7d8846c3cdf465b5508"},
@@ -1540,7 +1433,7 @@ description = "A fast implementation of the Cassowary constraint solver"
 optional = true
 python-versions = ">=3.10"
 groups = ["main"]
-markers = "extra == \"gel\""
+markers = "(python_version <= \"3.11\" or python_version >= \"3.12\") and extra == \"gel\""
 files = [
     {file = "kiwisolver-1.4.9-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:b4b4d74bda2b8ebf4da5bd42af11d02d04428b2c32846e4c2c93219df8a7987b"},
     {file = "kiwisolver-1.4.9-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:fb3b8132019ea572f4611d770991000d7f58127560c4889729248eb5852a102f"},
@@ -1652,6 +1545,7 @@ description = "Python port of markdown-it. Markdown parsing, done right!"
 optional = false
 python-versions = ">=3.8"
 groups = ["docs"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "markdown-it-py-3.0.0.tar.gz", hash = "sha256:e3f60a94fa066dc52ec76661e37c851cb232d92f9886b15cb560aaada2df8feb"},
     {file = "markdown_it_py-3.0.0-py3-none-any.whl", hash = "sha256:355216845c60bd96232cd8d8c40e8f9765cc86f46880e43a8fd22dc1a1a8cab1"},
@@ -1677,6 +1571,7 @@ description = "Safely add untrusted strings to HTML/XML markup."
 optional = false
 python-versions = ">=3.9"
 groups = ["docs"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "markupsafe-3.0.3-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:2f981d352f04553a7171b8e44369f2af4055f888dfb147d55e42d29e29e74559"},
     {file = "markupsafe-3.0.3-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:e1c1493fb6e50ab01d20a22826e57520f1284df32f2d8601fdd90b6304601419"},
@@ -1776,7 +1671,7 @@ description = "Python plotting package"
 optional = true
 python-versions = ">=3.10"
 groups = ["main"]
-markers = "extra == \"gel\""
+markers = "(python_version <= \"3.11\" or python_version >= \"3.12\") and extra == \"gel\""
 files = [
     {file = "matplotlib-3.10.7-cp310-cp310-macosx_10_12_x86_64.whl", hash = "sha256:7ac81eee3b7c266dd92cee1cd658407b16c57eed08c7421fa354ed68234de380"},
     {file = "matplotlib-3.10.7-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:667ecd5d8d37813a845053d8f5bf110b534c3c9f30e69ebd25d4701385935a6d"},
@@ -1856,6 +1751,7 @@ description = "Inline Matplotlib backend for Jupyter"
 optional = false
 python-versions = ">=3.9"
 groups = ["docs", "test"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "matplotlib_inline-0.2.1-py3-none-any.whl", hash = "sha256:d56ce5156ba6085e00a9d54fead6ed29a9c47e215cd1bba2e976ef39f5710a76"},
     {file = "matplotlib_inline-0.2.1.tar.gz", hash = "sha256:e1ee949c340d771fc39e241ea75683deb94762c8fa5f2927ec57c83c4dffa9fe"},
@@ -1874,6 +1770,7 @@ description = "McCabe checker, plugin for flake8"
 optional = false
 python-versions = ">=3.6"
 groups = ["dev"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "mccabe-0.7.0-py2.py3-none-any.whl", hash = "sha256:6c2d30ab6be0e4a46919781807b4f0d834ebdd6c6e3dca0bda5a15f863427b6e"},
     {file = "mccabe-0.7.0.tar.gz", hash = "sha256:348e0240c33b60bbdf4e523192ef919f28cb2c3d7d5c7794f74009290f236325"},
@@ -1886,6 +1783,7 @@ description = "Collection of plugins for markdown-it-py"
 optional = false
 python-versions = ">=3.10"
 groups = ["docs"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "mdit_py_plugins-0.5.0-py3-none-any.whl", hash = "sha256:07a08422fc1936a5d26d146759e9155ea466e842f5ab2f7d2266dd084c8dab1f"},
     {file = "mdit_py_plugins-0.5.0.tar.gz", hash = "sha256:f4918cb50119f50446560513a8e311d574ff6aaed72606ddae6d35716fe809c6"},
@@ -1906,6 +1804,7 @@ description = "Markdown URL utilities"
 optional = false
 python-versions = ">=3.7"
 groups = ["docs"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "mdurl-0.1.2-py3-none-any.whl", hash = "sha256:84008a41e51615a49fc9966191ff91509e3c40b939176e643fd50a5c2196b8f8"},
     {file = "mdurl-0.1.2.tar.gz", hash = "sha256:bb413d29f5eea38f31dd4754dd7377d4465116fb207585f97bf925588687c1ba"},
@@ -1918,6 +1817,7 @@ description = "Type system extensions for programs checked with the mypy type ch
 optional = false
 python-versions = ">=3.8"
 groups = ["dev"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "mypy_extensions-1.1.0-py3-none-any.whl", hash = "sha256:1be4cccdb0f2482337c4743e60421de3a356cd97508abadd57d47403e94f5505"},
     {file = "mypy_extensions-1.1.0.tar.gz", hash = "sha256:52e68efc3284861e772bbcd66823fde5ae21fd2fdb51c62a211403730b916558"},
@@ -1930,6 +1830,7 @@ description = "A Jupyter Notebook Sphinx reader built on top of the MyST markdow
 optional = false
 python-versions = ">=3.9"
 groups = ["docs"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "myst_nb-1.3.0-py3-none-any.whl", hash = "sha256:1f36af3c19964960ec4e51ac30949b6ed6df220356ffa8d60dd410885e132d7d"},
     {file = "myst_nb-1.3.0.tar.gz", hash = "sha256:df3cd4680f51a5af673fd46b38b562be3559aef1475e906ed0f2e66e4587ce4b"},
@@ -1959,6 +1860,7 @@ description = "An extended [CommonMark](https://spec.commonmark.org/) compliant
 optional = false
 python-versions = ">=3.10"
 groups = ["docs"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "myst_parser-4.0.1-py3-none-any.whl", hash = "sha256:9134e88959ec3b5780aedf8a99680ea242869d012e8821db3126d427edc9c95d"},
     {file = "myst_parser-4.0.1.tar.gz", hash = "sha256:5cfea715e4f3574138aecbf7d54132296bfd72bb614d31168f48c477a830a7c4"},
@@ -1986,6 +1888,7 @@ description = "A client library for executing notebooks. Formerly nbconvert's Ex
 optional = false
 python-versions = ">=3.9.0"
 groups = ["docs"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "nbclient-0.10.2-py3-none-any.whl", hash = "sha256:4ffee11e788b4a27fabeb7955547e4318a5298f34342a4bfd01f2e1faaeadc3d"},
     {file = "nbclient-0.10.2.tar.gz", hash = "sha256:90b7fc6b810630db87a6d0c2250b1f0ab4cf4d3c27a299b0cde78a4ed3fd9193"},
@@ -2009,6 +1912,7 @@ description = "The Jupyter Notebook format"
 optional = false
 python-versions = ">=3.8"
 groups = ["dev", "docs", "test"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "nbformat-5.10.4-py3-none-any.whl", hash = "sha256:3b48d6c8fbca4b299bf3982ea7db1af21580e4fec269ad087b9e81588891200b"},
     {file = "nbformat-5.10.4.tar.gz", hash = "sha256:322168b14f937a5d11362988ecac2a4952d3d8e3a2cbeb2319584631226d5b3a"},
@@ -2031,6 +1935,7 @@ description = "Strips outputs from Jupyter and IPython notebooks"
 optional = false
 python-versions = ">=3.8"
 groups = ["dev"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "nbstripout-0.7.1-py2.py3-none-any.whl", hash = "sha256:dfb0688b42b02ff13925e583313fc009c87342ad13b79ae0329357749aa6ed0c"},
     {file = "nbstripout-0.7.1.tar.gz", hash = "sha256:2aad3454dc13e356f2fc94917856bc44f2bed3add77e8ba9f3a78003074bcd84"},
@@ -2046,6 +1951,7 @@ description = "A py.test plugin to validate Jupyter notebooks"
 optional = false
 python-versions = ">=3.7, <4"
 groups = ["test"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "nbval-0.11.0-py2.py3-none-any.whl", hash = "sha256:307aecc866c9a1e8a13bb5bbb008a702bacfda2394dff6fe504a3108a58042a0"},
     {file = "nbval-0.11.0.tar.gz", hash = "sha256:77c95797607b0a968babd2597ee3494102d25c3ad37435debbdac0e46e379094"},
@@ -2065,6 +1971,7 @@ description = "Patch asyncio to allow nested event loops"
 optional = false
 python-versions = ">=3.5"
 groups = ["docs", "test"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "nest_asyncio-1.6.0-py3-none-any.whl", hash = "sha256:87af6efd6b5e897c81050477ef65c62e2b2f35d51703cae01aff2905b1852e1c"},
     {file = "nest_asyncio-1.6.0.tar.gz", hash = "sha256:6f172d5449aca15afd6c646851f4e31e02c598d553a667e38cafa997cfec55fe"},
@@ -2077,7 +1984,7 @@ description = "Python package for creating and manipulating graphs and networks"
 optional = false
 python-versions = ">=3.10"
 groups = ["main"]
-markers = "python_version == \"3.10\""
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "networkx-3.4.2-py3-none-any.whl", hash = "sha256:df5d4365b724cf81b8c6a7312509d0c22386097011ad1abe274afd5e9d3bbc5f"},
     {file = "networkx-3.4.2.tar.gz", hash = "sha256:307c3669428c5362aab27c8a1260aa8f47c4e91d3891f48be0141738d8d053e1"},
@@ -2091,28 +1998,6 @@ example = ["cairocffi (>=1.7)", "contextily (>=1.6)", "igraph (>=0.11)", "momepy
 extra = ["lxml (>=4.6)", "pydot (>=3.0.1)", "pygraphviz (>=1.14)", "sympy (>=1.10)"]
 test = ["pytest (>=7.2)", "pytest-cov (>=4.0)"]
 
-[[package]]
-name = "networkx"
-version = "3.5"
-description = "Python package for creating and manipulating graphs and networks"
-optional = false
-python-versions = ">=3.11"
-groups = ["main"]
-markers = "python_version >= \"3.11\""
-files = [
-    {file = "networkx-3.5-py3-none-any.whl", hash = "sha256:0030d386a9a06dee3565298b4a734b68589749a544acbb6c412dc9e2489ec6ec"},
-    {file = "networkx-3.5.tar.gz", hash = "sha256:d4c6f9cf81f52d69230866796b82afbccdec3db7ae4fbd1b65ea750feed50037"},
-]
-
-[package.extras]
-default = ["matplotlib (>=3.8)", "numpy (>=1.25)", "pandas (>=2.0)", "scipy (>=1.11.2)"]
-developer = ["mypy (>=1.15)", "pre-commit (>=4.1)"]
-doc = ["intersphinx-registry", "myst-nb (>=1.1)", "numpydoc (>=1.8.0)", "pillow (>=10)", "pydata-sphinx-theme (>=0.16)", "sphinx (>=8.0)", "sphinx-gallery (>=0.18)", "texext (>=0.6.7)"]
-example = ["cairocffi (>=1.7)", "contextily (>=1.6)", "igraph (>=0.11)", "momepy (>=0.7.2)", "osmnx (>=2.0.0)", "scikit-learn (>=1.5)", "seaborn (>=0.13)"]
-extra = ["lxml (>=4.6)", "pydot (>=3.0.1)", "pygraphviz (>=1.14)", "sympy (>=1.10)"]
-test = ["pytest (>=7.2)", "pytest-cov (>=4.0)", "pytest-xdist (>=3.0)"]
-test-extras = ["pytest-mpl", "pytest-randomly"]
-
 [[package]]
 name = "nodeenv"
 version = "1.9.1"
@@ -2120,6 +2005,7 @@ description = "Node.js virtual environment builder"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
 groups = ["dev"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "nodeenv-1.9.1-py2.py3-none-any.whl", hash = "sha256:ba11c9782d29c27c70ffbdda2d7415098754709be8a7056d79a737cd901155c9"},
     {file = "nodeenv-1.9.1.tar.gz", hash = "sha256:6ec12890a2dab7946721edbfbcd91f3319c6ccc9aec47be7c7e6b7011ee6645f"},
@@ -2132,7 +2018,7 @@ description = "Fundamental package for array computing in Python"
 optional = false
 python-versions = ">=3.10"
 groups = ["main", "docs"]
-markers = "python_version == \"3.10\""
+markers = "python_version <= \"3.11\""
 files = [
     {file = "numpy-2.2.6-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:b412caa66f72040e6d268491a59f2c43bf03eb6c96dd8f0307829feb7fa2b6fb"},
     {file = "numpy-2.2.6-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:8e41fd67c52b86603a91c1a505ebaef50b3314de0213461c7a6e99c9a3beff90"},
@@ -2198,7 +2084,7 @@ description = "Fundamental package for array computing in Python"
 optional = false
 python-versions = ">=3.11"
 groups = ["main", "docs"]
-markers = "python_version >= \"3.11\""
+markers = "python_version >= \"3.12\""
 files = [
     {file = "numpy-2.3.4-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:e78aecd2800b32e8347ce49316d3eaf04aed849cd5b38e0af39f829a4e59f5eb"},
     {file = "numpy-2.3.4-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:7fd09cc5d65bda1e79432859c40978010622112e9194e581e3415a3eccc7f43f"},
@@ -2283,6 +2169,7 @@ description = "Sphinx extension to support docstrings in Numpy format"
 optional = false
 python-versions = ">=3.9"
 groups = ["docs"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "numpydoc-1.9.0-py3-none-any.whl", hash = "sha256:8a2983b2d62bfd0a8c470c7caa25e7e0c3d163875cdec12a8a1034020a9d1135"},
     {file = "numpydoc-1.9.0.tar.gz", hash = "sha256:5fec64908fe041acc4b3afc2a32c49aab1540cf581876f5563d68bb129e27c5b"},
@@ -2299,6 +2186,7 @@ description = "A LinkML data model for OpenCloning"
 optional = false
 python-versions = "<4.0,>=3.10"
 groups = ["main"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "opencloning_linkml-0.4.5-py3-none-any.whl", hash = "sha256:74cc57cef349a544c48fd05eb4942c9f8de5f96b011afbd4f15ab3a3e7226df3"},
     {file = "opencloning_linkml-0.4.5.tar.gz", hash = "sha256:58bf4eeafafae2e6e1eb7af413674c070d1915fc7c36590ace412bb9660e2d4d"},
@@ -2321,7 +2209,7 @@ files = [
     {file = "packaging-25.0-py3-none-any.whl", hash = "sha256:29572ef2b1f17581046b3a2227d5c611fb25ec70ca1ba8554b24b0e69331a484"},
     {file = "packaging-25.0.tar.gz", hash = "sha256:d443872c98d677bf60f6a1f2f8c1cb748e8fe762d2bf9d3148b5599295b0fc4f"},
 ]
-markers = {main = "extra == \"gel\""}
+markers = {main = "(python_version <= \"3.11\" or python_version >= \"3.12\") and extra == \"gel\"", dev = "python_version <= \"3.11\" or python_version >= \"3.12\"", docs = "python_version <= \"3.11\" or python_version >= \"3.12\"", test = "python_version <= \"3.11\" or python_version >= \"3.12\""}
 
 [[package]]
 name = "pandas"
@@ -2330,6 +2218,7 @@ description = "Powerful data structures for data analysis, time series, and stat
 optional = false
 python-versions = ">=3.9"
 groups = ["docs"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "pandas-2.3.3-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:376c6446ae31770764215a6c937f72d917f214b43560603cd60da6408f183b6c"},
     {file = "pandas-2.3.3-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:e19d192383eab2f4ceb30b412b22ea30690c9e618f78870357ae1d682912015a"},
@@ -2430,6 +2319,7 @@ description = "A Python Parser"
 optional = false
 python-versions = ">=3.6"
 groups = ["docs", "test"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "parso-0.8.5-py2.py3-none-any.whl", hash = "sha256:646204b5ee239c396d040b90f9e272e9a8017c630092bf59980beb62fd033887"},
     {file = "parso-0.8.5.tar.gz", hash = "sha256:034d7354a9a018bdce352f48b2a8a450f05e9d6ee85db84764e9b6bd96dafe5a"},
@@ -2446,6 +2336,7 @@ description = "Utility library for gitignore style pattern matching of file path
 optional = false
 python-versions = ">=3.8"
 groups = ["dev"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "pathspec-0.12.1-py3-none-any.whl", hash = "sha256:a0d503e138a4c123b27490a4f7beda6a01c6f288df0e4a8b79c7eb0dc7b4cc08"},
     {file = "pathspec-0.12.1.tar.gz", hash = "sha256:a482d51503a1ab33b1c67a6c3813a26953dbdc71c31dacaef9a838c4e29f5712"},
@@ -2458,7 +2349,7 @@ description = "Pexpect allows easy control of interactive console applications."
 optional = false
 python-versions = "*"
 groups = ["docs", "test"]
-markers = "sys_platform != \"win32\" and sys_platform != \"emscripten\""
+markers = "(python_version <= \"3.11\" or python_version >= \"3.12\") and (sys_platform != \"win32\" and sys_platform != \"emscripten\")"
 files = [
     {file = "pexpect-4.9.0-py2.py3-none-any.whl", hash = "sha256:7236d1e080e4936be2dc3e326cec0af72acf9212a7e1d060210e70a47e253523"},
     {file = "pexpect-4.9.0.tar.gz", hash = "sha256:ee7d41123f3c9911050ea2c2dac107568dc43b2d3b0c7557a33212c398ead30f"},
@@ -2474,7 +2365,7 @@ description = "Python Imaging Library (fork)"
 optional = true
 python-versions = ">=3.10"
 groups = ["main"]
-markers = "extra == \"gel\""
+markers = "(python_version <= \"3.11\" or python_version >= \"3.12\") and extra == \"gel\""
 files = [
     {file = "pillow-12.0.0-cp310-cp310-macosx_10_10_x86_64.whl", hash = "sha256:3adfb466bbc544b926d50fe8f4a4e6abd8c6bffd28a26177594e6e9b2b76572b"},
     {file = "pillow-12.0.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:1ac11e8ea4f611c3c0147424eae514028b5e9077dd99ab91e1bd7bc33ff145e1"},
@@ -2584,6 +2475,7 @@ description = "A small Python package for determining appropriate platform-speci
 optional = false
 python-versions = ">=3.10"
 groups = ["dev", "docs", "test"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "platformdirs-4.5.0-py3-none-any.whl", hash = "sha256:e578a81bb873cbb89a41fcc904c7ef523cc18284b7e3b3ccf06aca1403b7ebd3"},
     {file = "platformdirs-4.5.0.tar.gz", hash = "sha256:70ddccdd7c99fc5942e9fc25636a8b34d04c24b335100223152c2803e4063312"},
@@ -2601,6 +2493,7 @@ description = "plugin and hook calling mechanisms for python"
 optional = false
 python-versions = ">=3.9"
 groups = ["test"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "pluggy-1.6.0-py3-none-any.whl", hash = "sha256:e920276dd6813095e9377c0bc5566d94c932c33b27a3e3945d8389c374dd4746"},
     {file = "pluggy-1.6.0.tar.gz", hash = "sha256:7dcc130b76258d33b90f61b658791dede3486c3e6bfb003ee5c9bfb396dd22f3"},
@@ -2617,6 +2510,7 @@ description = "A framework for managing and maintaining multi-language pre-commi
 optional = false
 python-versions = ">=3.9"
 groups = ["dev"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "pre_commit-4.3.0-py2.py3-none-any.whl", hash = "sha256:2b0747ad7e6e967169136edffee14c16e148a778a54e4f967921aa1ebf2308d8"},
     {file = "pre_commit-4.3.0.tar.gz", hash = "sha256:499fe450cc9d42e9d58e606262795ecb64dd05438943c62b66f6a8673da30b16"},
@@ -2636,6 +2530,7 @@ description = "A simple Python library for easily displaying tabular data in a v
 optional = false
 python-versions = ">=3.9"
 groups = ["main"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "prettytable-3.16.0-py3-none-any.whl", hash = "sha256:b5eccfabb82222f5aa46b798ff02a8452cf530a352c31bddfa29be41242863aa"},
     {file = "prettytable-3.16.0.tar.gz", hash = "sha256:3c64b31719d961bf69c9a7e03d0c1e477320906a98da63952bc6698d6164ff57"},
@@ -2654,6 +2549,7 @@ description = "Library for building powerful interactive command lines in Python
 optional = false
 python-versions = ">=3.8"
 groups = ["docs", "test"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "prompt_toolkit-3.0.52-py3-none-any.whl", hash = "sha256:9aac639a3bbd33284347de5ad8d68ecc044b91a762dc39b7c21095fcd6a19955"},
     {file = "prompt_toolkit-3.0.52.tar.gz", hash = "sha256:28cde192929c8e7321de85de1ddbe736f1375148b02f2e17edd840042b1be855"},
@@ -2669,6 +2565,7 @@ description = "Cross-platform lib for process and system monitoring."
 optional = false
 python-versions = ">=3.6"
 groups = ["docs", "test"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "psutil-7.1.2-cp313-cp313t-macosx_10_13_x86_64.whl", hash = "sha256:0cc5c6889b9871f231ed5455a9a02149e388fffcb30b607fb7a8896a6d95f22e"},
     {file = "psutil-7.1.2-cp313-cp313t-macosx_11_0_arm64.whl", hash = "sha256:8e9e77a977208d84aa363a4a12e0f72189d58bbf4e46b49aae29a2c6e93ef206"},
@@ -2692,8 +2589,8 @@ files = [
 ]
 
 [package.extras]
-dev = ["abi3audit", "black", "check-manifest", "coverage", "packaging", "pylint", "pyperf", "pypinfo", "pyreadline ; os_name == \"nt\"", "pytest", "pytest-cov", "pytest-instafail", "pytest-subtests", "pytest-xdist", "pywin32 ; os_name == \"nt\" and platform_python_implementation != \"PyPy\"", "requests", "rstcheck", "ruff", "setuptools", "sphinx", "sphinx_rtd_theme", "toml-sort", "twine", "validate-pyproject[all]", "virtualenv", "vulture", "wheel", "wheel ; os_name == \"nt\" and platform_python_implementation != \"PyPy\"", "wmi ; os_name == \"nt\" and platform_python_implementation != \"PyPy\""]
-test = ["pytest", "pytest-instafail", "pytest-subtests", "pytest-xdist", "pywin32 ; os_name == \"nt\" and platform_python_implementation != \"PyPy\"", "setuptools", "wheel ; os_name == \"nt\" and platform_python_implementation != \"PyPy\"", "wmi ; os_name == \"nt\" and platform_python_implementation != \"PyPy\""]
+dev = ["abi3audit", "black", "check-manifest", "coverage", "packaging", "pylint", "pyperf", "pypinfo", "pyreadline", "pytest", "pytest-cov", "pytest-instafail", "pytest-subtests", "pytest-xdist", "pywin32", "requests", "rstcheck", "ruff", "setuptools", "sphinx", "sphinx_rtd_theme", "toml-sort", "twine", "validate-pyproject[all]", "virtualenv", "vulture", "wheel", "wheel", "wmi"]
+test = ["pytest", "pytest-instafail", "pytest-subtests", "pytest-xdist", "pywin32", "setuptools", "wheel", "wmi"]
 
 [[package]]
 name = "ptyprocess"
@@ -2702,7 +2599,7 @@ description = "Run a subprocess in a pseudo terminal"
 optional = false
 python-versions = "*"
 groups = ["docs", "test"]
-markers = "sys_platform != \"win32\" and sys_platform != \"emscripten\""
+markers = "(python_version <= \"3.11\" or python_version >= \"3.12\") and (sys_platform != \"win32\" and sys_platform != \"emscripten\")"
 files = [
     {file = "ptyprocess-0.7.0-py2.py3-none-any.whl", hash = "sha256:4b41f3967fce3af57cc7e94b888626c18bf37a083e3651ca8feeb66d492fef35"},
     {file = "ptyprocess-0.7.0.tar.gz", hash = "sha256:5c5d0a3b48ceee0b48485e0c26037c0acd7d29765ca3fbb5cb3831d347423220"},
@@ -2715,6 +2612,7 @@ description = "Safely evaluate AST nodes without side effects"
 optional = false
 python-versions = "*"
 groups = ["docs", "test"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "pure_eval-0.2.3-py3-none-any.whl", hash = "sha256:1db8e35b67b3d218d818ae653e27f06c3aa420901fa7b081ca98cbedc874e0d0"},
     {file = "pure_eval-0.2.3.tar.gz", hash = "sha256:5f4e983f40564c576c7c8635ae88db5956bb2229d7e9237d03b3c0b0190eaf42"},
@@ -2730,6 +2628,7 @@ description = "Python style guide checker"
 optional = false
 python-versions = ">=3.9"
 groups = ["dev"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "pycodestyle-2.14.0-py2.py3-none-any.whl", hash = "sha256:dd6bf7cb4ee77f8e016f9c8e74a35ddd9f67e1d5fd4184d86c3b98e07099f42d"},
     {file = "pycodestyle-2.14.0.tar.gz", hash = "sha256:c4b5b517d278089ff9d0abdec919cd97262a3367449ea1c8b49b91529167b783"},
@@ -2742,7 +2641,7 @@ description = "C parser in Python"
 optional = false
 python-versions = ">=3.8"
 groups = ["docs", "test"]
-markers = "implementation_name == \"pypy\""
+markers = "(python_version <= \"3.11\" or python_version >= \"3.12\") and implementation_name == \"pypy\""
 files = [
     {file = "pycparser-2.23-py3-none-any.whl", hash = "sha256:e5c6e8d3fbad53479cab09ac03729e0a9faf2bee3db8208a550daf5af81a5934"},
     {file = "pycparser-2.23.tar.gz", hash = "sha256:78816d4f24add8f10a06d6f05b4d424ad9e96cfebf68a4ddc99c65c0720d00c2"},
@@ -2755,6 +2654,7 @@ description = "Data validation using Python type hints"
 optional = false
 python-versions = ">=3.9"
 groups = ["main"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "pydantic-2.12.3-py3-none-any.whl", hash = "sha256:6986454a854bc3bc6e5443e1369e06a3a456af9d339eda45510f517d9ea5c6bf"},
     {file = "pydantic-2.12.3.tar.gz", hash = "sha256:1da1c82b0fc140bb0103bc1441ffe062154c8d38491189751ee00fd8ca65ce74"},
@@ -2768,7 +2668,7 @@ typing-inspection = ">=0.4.2"
 
 [package.extras]
 email = ["email-validator (>=2.0.0)"]
-timezone = ["tzdata ; python_version >= \"3.9\" and platform_system == \"Windows\""]
+timezone = ["tzdata"]
 
 [[package]]
 name = "pydantic-core"
@@ -2777,6 +2677,7 @@ description = "Core functionality for Pydantic validation and serialization"
 optional = false
 python-versions = ">=3.9"
 groups = ["main"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "pydantic_core-2.41.4-cp310-cp310-macosx_10_12_x86_64.whl", hash = "sha256:2442d9a4d38f3411f22eb9dd0912b7cbf4b7d5b6c92c4173b75d3e1ccd84e36e"},
     {file = "pydantic_core-2.41.4-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:30a9876226dda131a741afeab2702e2d127209bde3c65a2b8133f428bc5d006b"},
@@ -2907,6 +2808,7 @@ description = "Bootstrap-based Sphinx theme from the PyData community"
 optional = false
 python-versions = ">=3.9"
 groups = ["docs"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "pydata_sphinx_theme-0.15.4-py3-none-any.whl", hash = "sha256:2136ad0e9500d0949f96167e63f3e298620040aea8f9c74621959eda5d4cf8e6"},
     {file = "pydata_sphinx_theme-0.15.4.tar.gz", hash = "sha256:7762ec0ac59df3acecf49fd2f889e1b4565dbce8b88b2e29ee06fdd90645a06d"},
@@ -2936,6 +2838,7 @@ description = "String algorithms"
 optional = false
 python-versions = ">=3.9"
 groups = ["main"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "pydivsufsort-0.0.18-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:40474ee2f071fb16b33082596b35638c2c17eb37d9c0efced8b31394d6e0cacd"},
     {file = "pydivsufsort-0.0.18-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:37c660abe0f126111e8e251391a8efc88dcbb726342e18ac230c0ba79f81c1c2"},
@@ -2981,6 +2884,7 @@ description = "Pure-python FIGlet implementation"
 optional = false
 python-versions = "*"
 groups = ["main"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "pyfiglet-0.8.post1-py2.py3-none-any.whl", hash = "sha256:d555bcea17fbeaf70eaefa48bb119352487e629c9b56f30f383e2c62dd67a01c"},
     {file = "pyfiglet-0.8.post1.tar.gz", hash = "sha256:c6c2321755d09267b438ec7b936825a4910fec696292139e664ca8670e103639"},
@@ -2993,6 +2897,7 @@ description = "passive checker of Python programs"
 optional = false
 python-versions = ">=3.9"
 groups = ["dev"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "pyflakes-3.4.0-py2.py3-none-any.whl", hash = "sha256:f742a7dbd0d9cb9ea41e9a24a918996e8170c799fa528688d40dd582c8265f4f"},
     {file = "pyflakes-3.4.0.tar.gz", hash = "sha256:b24f96fafb7d2ab0ec5075b7350b3d2d2218eab42003821c06344973d3ea2f58"},
@@ -3005,6 +2910,7 @@ description = "Pygments is a syntax highlighting package written in Python."
 optional = false
 python-versions = ">=3.8"
 groups = ["docs", "test"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "pygments-2.19.2-py3-none-any.whl", hash = "sha256:86540386c03d588bb81d44bc3928634ff26449851e99741617ecb9037ee5ec0b"},
     {file = "pygments-2.19.2.tar.gz", hash = "sha256:636cb2477cec7f8952536970bc533bc43743542f70392ae026374600add5b887"},
@@ -3020,7 +2926,7 @@ description = "pyparsing - Classes and methods to define and execute parsing gra
 optional = true
 python-versions = ">=3.9"
 groups = ["main"]
-markers = "extra == \"gel\" or extra == \"download\""
+markers = "(extra == \"gel\" or extra == \"download\") and (python_version <= \"3.11\" or python_version >= \"3.12\")"
 files = [
     {file = "pyparsing-3.2.5-py3-none-any.whl", hash = "sha256:e38a4f02064cf41fe6593d328d0512495ad1f3d8a91c4f73fc401b3079a59a5e"},
     {file = "pyparsing-3.2.5.tar.gz", hash = "sha256:2df8d5b7b2802ef88e8d016a2eb9c7aeaa923529cd251ed0fe4608275d4105b6"},
@@ -3036,7 +2942,7 @@ description = "A cross-platform clipboard module for Python. (Only handles plain
 optional = true
 python-versions = "*"
 groups = ["main"]
-markers = "extra == \"clipboard\""
+markers = "(python_version <= \"3.11\" or python_version >= \"3.12\") and extra == \"clipboard\""
 files = [
     {file = "pyperclip-1.11.0-py3-none-any.whl", hash = "sha256:299403e9ff44581cb9ba2ffeed69c7aa96a008622ad0c46cb575ca75b5b84273"},
     {file = "pyperclip-1.11.0.tar.gz", hash = "sha256:244035963e4428530d9e3a6101a1ef97209c6825edab1567beac148ccc1db1b6"},
@@ -3049,6 +2955,7 @@ description = "pytest: simple powerful testing with Python"
 optional = false
 python-versions = ">=3.9"
 groups = ["test"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "pytest-8.4.2-py3-none-any.whl", hash = "sha256:872f880de3fc3a5bdc88a11b39c9710c3497a547cfa9320bc3c5e62fbf272e79"},
     {file = "pytest-8.4.2.tar.gz", hash = "sha256:86c0d0b93306b961d58d62a4db4879f27fe25513d4b969df351abdddb3c30e01"},
@@ -3073,6 +2980,7 @@ description = "Pytest plugin for measuring coverage."
 optional = false
 python-versions = ">=3.9"
 groups = ["test"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "pytest_cov-7.0.0-py3-none-any.whl", hash = "sha256:3b8e9558b16cc1479da72058bdecf8073661c7f57f7d3c5f22a1c23507f2d861"},
     {file = "pytest_cov-7.0.0.tar.gz", hash = "sha256:33c97eda2e049a0c5298e91f519302a1334c26ac65c1a483d6206fd458361af1"},
@@ -3093,6 +3001,7 @@ description = "Pytest plugin with advanced doctest features."
 optional = false
 python-versions = ">=3.9"
 groups = ["test"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "pytest_doctestplus-1.5.0-py3-none-any.whl", hash = "sha256:e13e014bab450285b3735de27a1429d4f95bca2efc7a2becd9a863247e91ae4e"},
     {file = "pytest_doctestplus-1.5.0.tar.gz", hash = "sha256:1bfb9ecf0a5a61452abd4c2a5218450d0ddd125a2c241da9e4f7f8ccf6b779fe"},
@@ -3112,6 +3021,7 @@ description = "Profiling plugin for py.test"
 optional = false
 python-versions = ">=3.6"
 groups = ["test"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "pytest-profiling-1.8.1.tar.gz", hash = "sha256:3f171fa69d5c82fa9aab76d66abd5f59da69135c37d6ae5bf7557f1b154cb08d"},
     {file = "pytest_profiling-1.8.1-py3-none-any.whl", hash = "sha256:3dd8713a96298b42d83de8f5951df3ada3e61b3e5d2a06956684175529e17aea"},
@@ -3133,7 +3043,7 @@ files = [
     {file = "python-dateutil-2.9.0.post0.tar.gz", hash = "sha256:37dd54208da7e1cd875388217d5e00ebd4179249f90fb72437e91a35459a0ad3"},
     {file = "python_dateutil-2.9.0.post0-py2.py3-none-any.whl", hash = "sha256:a8b2bc7bffae282281c8140a97d3aa9c14da0b136dfe83f850eea9a5f7470427"},
 ]
-markers = {main = "extra == \"gel\""}
+markers = {main = "(python_version <= \"3.11\" or python_version >= \"3.12\") and extra == \"gel\"", docs = "python_version <= \"3.11\" or python_version >= \"3.12\"", test = "python_version <= \"3.11\" or python_version >= \"3.12\""}
 
 [package.dependencies]
 six = ">=1.5"
@@ -3145,6 +3055,7 @@ description = "A Fast, spec compliant Python 3.13+ tokenizer that runs on older
 optional = false
 python-versions = ">=3.8"
 groups = ["dev"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "pytokens-0.2.0-py3-none-any.whl", hash = "sha256:74d4b318c67f4295c13782ddd9abcb7e297ec5630ad060eb90abf7ebbefe59f8"},
     {file = "pytokens-0.2.0.tar.gz", hash = "sha256:532d6421364e5869ea57a9523bf385f02586d4662acbcc0342afd69511b4dd43"},
@@ -3160,6 +3071,7 @@ description = "World timezone definitions, modern and historical"
 optional = false
 python-versions = "*"
 groups = ["docs"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "pytz-2025.2-py2.py3-none-any.whl", hash = "sha256:5ddf76296dd8c44c26eb8f4b6f35488f3ccbf6fbbd7adee0b7262d43f0ec2f00"},
     {file = "pytz-2025.2.tar.gz", hash = "sha256:360b9e3dbb49a209c21ad61809c7fb453643e048b38924c765813546746e81c3"},
@@ -3172,6 +3084,7 @@ description = "YAML parser and emitter for Python"
 optional = false
 python-versions = ">=3.8"
 groups = ["dev", "docs"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "PyYAML-6.0.3-cp38-cp38-macosx_10_13_x86_64.whl", hash = "sha256:c2514fceb77bc5e7a2f7adfaa1feb2fb311607c9cb518dbc378688ec73d8292f"},
     {file = "PyYAML-6.0.3-cp38-cp38-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl", hash = "sha256:9c57bb8c96f6d1808c030b1687b9b5fb476abaa47f0db9c0101f5e9f394e97f4"},
@@ -3255,6 +3168,7 @@ description = "Python bindings for 0MQ"
 optional = false
 python-versions = ">=3.8"
 groups = ["docs", "test"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "pyzmq-27.1.0-cp310-cp310-macosx_10_15_universal2.whl", hash = "sha256:508e23ec9bc44c0005c4946ea013d9317ae00ac67778bd47519fdf5a0e930ff4"},
     {file = "pyzmq-27.1.0-cp310-cp310-manylinux2014_i686.manylinux_2_17_i686.whl", hash = "sha256:507b6f430bdcf0ee48c0d30e734ea89ce5567fd7b8a0f0044a369c176aa44556"},
@@ -3360,6 +3274,7 @@ description = "JSON Referencing + Python"
 optional = false
 python-versions = ">=3.10"
 groups = ["dev", "docs", "test"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "referencing-0.37.0-py3-none-any.whl", hash = "sha256:381329a9f99628c9069361716891d34ad94af76e461dcb0335825aecc7692231"},
     {file = "referencing-0.37.0.tar.gz", hash = "sha256:44aefc3142c5b842538163acb373e24cce6632bd54bdb01b21ad5863489f50d8"},
@@ -3377,6 +3292,7 @@ description = "Alternative regular expression module, to replace re."
 optional = false
 python-versions = ">=3.8"
 groups = ["main"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "regex-2024.11.6-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:ff590880083d60acc0433f9c3f713c51f7ac6ebb9adf889c79a261ecf541aa91"},
     {file = "regex-2024.11.6-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:658f90550f38270639e83ce492f27d2c8d2cd63805c65a13a14d36ca126753f0"},
@@ -3485,7 +3401,7 @@ files = [
     {file = "requests-2.32.5-py3-none-any.whl", hash = "sha256:2462f94637a34fd532264295e186976db0f5d453d1cdd31473c85a6a161affb6"},
     {file = "requests-2.32.5.tar.gz", hash = "sha256:dbba0bac56e100853db0ea71b82b4dfd5fe2bf6d3754a8893c3af500cec7d7cf"},
 ]
-markers = {main = "extra == \"download\""}
+markers = {main = "(python_version <= \"3.11\" or python_version >= \"3.12\") and extra == \"download\"", docs = "python_version <= \"3.11\" or python_version >= \"3.12\"", test = "python_version <= \"3.11\" or python_version >= \"3.12\""}
 
 [package.dependencies]
 certifi = ">=2017.4.17"
@@ -3504,6 +3420,7 @@ description = "Mock out responses from the requests package"
 optional = false
 python-versions = ">=3.5"
 groups = ["test"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "requests-mock-1.12.1.tar.gz", hash = "sha256:e9e12e333b525156e82a3c852f22016b9158220d2f47454de9cae8a77d371401"},
     {file = "requests_mock-1.12.1-py2.py3-none-any.whl", hash = "sha256:b1e37054004cdd5e56c84454cc7df12b25f90f382159087f4b6915aaeef39563"},
@@ -3515,23 +3432,6 @@ requests = ">=2.22,<3"
 [package.extras]
 fixture = ["fixtures"]
 
-[[package]]
-name = "roman-numerals-py"
-version = "3.1.0"
-description = "Manipulate well-formed Roman numerals"
-optional = false
-python-versions = ">=3.9"
-groups = ["docs"]
-markers = "python_version >= \"3.11\""
-files = [
-    {file = "roman_numerals_py-3.1.0-py3-none-any.whl", hash = "sha256:9da2ad2fb670bcf24e81070ceb3be72f6c11c440d73bd579fbeca1e9f330954c"},
-    {file = "roman_numerals_py-3.1.0.tar.gz", hash = "sha256:be4bf804f083a4ce001b5eb7e3c0862479d10f94c936f6c4e5f250aa5ff5bd2d"},
-]
-
-[package.extras]
-lint = ["mypy (==1.15.0)", "pyright (==1.1.394)", "ruff (==0.9.7)"]
-test = ["pytest (>=8)"]
-
 [[package]]
 name = "rpds-py"
 version = "0.28.0"
@@ -3539,6 +3439,7 @@ description = "Python bindings to Rust's persistent data structures (rpds)"
 optional = false
 python-versions = ">=3.10"
 groups = ["dev", "docs", "test"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "rpds_py-0.28.0-cp310-cp310-macosx_10_12_x86_64.whl", hash = "sha256:7b6013db815417eeb56b2d9d7324e64fcd4fa289caeee6e7a78b2e11fc9b438a"},
     {file = "rpds_py-0.28.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:1a4c6b05c685c0c03f80dabaeb73e74218c49deea965ca63f76a752807397207"},
@@ -3664,7 +3565,7 @@ description = "Fundamental algorithms for scientific computing in Python"
 optional = true
 python-versions = ">=3.10"
 groups = ["main"]
-markers = "python_version == \"3.10\" and (extra == \"express\" or extra == \"gel\")"
+markers = "(extra == \"express\" or extra == \"gel\") and (python_version <= \"3.11\" or python_version >= \"3.12\")"
 files = [
     {file = "scipy-1.15.3-cp310-cp310-macosx_10_13_x86_64.whl", hash = "sha256:a345928c86d535060c9c2b25e71e87c39ab2f22fc96e9636bd74d1dbf9de448c"},
     {file = "scipy-1.15.3-cp310-cp310-macosx_12_0_arm64.whl", hash = "sha256:ad3432cb0f9ed87477a8d97f03b763fd1d57709f1bbde3c9369b1dff5503b253"},
@@ -3720,7 +3621,7 @@ numpy = ">=1.23.5,<2.5"
 [package.extras]
 dev = ["cython-lint (>=0.12.2)", "doit (>=0.36.0)", "mypy (==1.10.0)", "pycodestyle", "pydevtool", "rich-click", "ruff (>=0.0.292)", "types-psutil", "typing_extensions"]
 doc = ["intersphinx_registry", "jupyterlite-pyodide-kernel", "jupyterlite-sphinx (>=0.19.1)", "jupytext", "matplotlib (>=3.5)", "myst-nb", "numpydoc", "pooch", "pydata-sphinx-theme (>=0.15.2)", "sphinx (>=5.0.0,<8.0.0)", "sphinx-copybutton", "sphinx-design (>=0.4.0)"]
-test = ["Cython", "array-api-strict (>=2.0,<2.1.1)", "asv", "gmpy2", "hypothesis (>=6.30)", "meson", "mpmath", "ninja ; sys_platform != \"emscripten\"", "pooch", "pytest", "pytest-cov", "pytest-timeout", "pytest-xdist", "scikit-umfpack", "threadpoolctl"]
+test = ["Cython", "array-api-strict (>=2.0,<2.1.1)", "asv", "gmpy2", "hypothesis (>=6.30)", "meson", "mpmath", "ninja", "pooch", "pytest", "pytest-cov", "pytest-timeout", "pytest-xdist", "scikit-umfpack", "threadpoolctl"]
 
 [[package]]
 name = "scipy"
@@ -3729,7 +3630,7 @@ description = "Fundamental algorithms for scientific computing in Python"
 optional = true
 python-versions = ">=3.11"
 groups = ["main"]
-markers = "python_version >= \"3.11\" and (extra == \"express\" or extra == \"gel\")"
+markers = "extra == \"express\" and python_version >= \"3.12\" or extra == \"gel\" and python_version >= \"3.12\""
 files = [
     {file = "scipy-1.16.3-cp311-cp311-macosx_10_14_x86_64.whl", hash = "sha256:40be6cf99e68b6c4321e9f8782e7d5ff8265af28ef2cd56e9c9b2638fa08ad97"},
     {file = "scipy-1.16.3-cp311-cp311-macosx_12_0_arm64.whl", hash = "sha256:8be1ca9170fcb6223cc7c27f4305d680ded114a1567c0bd2bfcbf947d1b17511"},
@@ -3800,7 +3701,7 @@ numpy = ">=1.25.2,<2.6"
 [package.extras]
 dev = ["cython-lint (>=0.12.2)", "doit (>=0.36.0)", "mypy (==1.10.0)", "pycodestyle", "pydevtool", "rich-click", "ruff (>=0.0.292)", "types-psutil", "typing_extensions"]
 doc = ["intersphinx_registry", "jupyterlite-pyodide-kernel", "jupyterlite-sphinx (>=0.19.1)", "jupytext", "linkify-it-py", "matplotlib (>=3.5)", "myst-nb (>=1.2.0)", "numpydoc", "pooch", "pydata-sphinx-theme (>=0.15.2)", "sphinx (>=5.0.0,<8.2.0)", "sphinx-copybutton", "sphinx-design (>=0.4.0)"]
-test = ["Cython", "array-api-strict (>=2.3.1)", "asv", "gmpy2", "hypothesis (>=6.30)", "meson", "mpmath", "ninja ; sys_platform != \"emscripten\"", "pooch", "pytest (>=8.0.0)", "pytest-cov", "pytest-timeout", "pytest-xdist", "scikit-umfpack", "threadpoolctl"]
+test = ["Cython", "array-api-strict (>=2.3.1)", "asv", "gmpy2", "hypothesis (>=6.30)", "meson", "mpmath", "ninja", "pooch", "pytest (>=8.0.0)", "pytest-cov", "pytest-timeout", "pytest-xdist", "scikit-umfpack", "threadpoolctl"]
 
 [[package]]
 name = "seguid"
@@ -3809,13 +3710,14 @@ description = "Sequence Globally Unique Identifier (SEGUID) Checksums for Linear
 optional = false
 python-versions = "<4.0,>=3.6"
 groups = ["main"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "seguid-0.2.1-py3-none-any.whl", hash = "sha256:10767009dcee3ee1e1227e68b047e5bde82224de1fec11162c3afc4238ca6e08"},
     {file = "seguid-0.2.1.tar.gz", hash = "sha256:cc5482aea6264d5370076a82559b7ccd0810d4e38489437a9e9118affa9762e5"},
 ]
 
 [package.extras]
-pydivsufsort = ["pydivsufsort (<=0.0.14) ; python_version < \"3.9\"", "pydivsufsort (>=0.0.18) ; python_version >= \"3.9\""]
+pydivsufsort = ["pydivsufsort (<=0.0.14)", "pydivsufsort (>=0.0.18)"]
 
 [[package]]
 name = "six"
@@ -3828,7 +3730,7 @@ files = [
     {file = "six-1.17.0-py2.py3-none-any.whl", hash = "sha256:4721f391ed90541fddacab5acf947aa0d3dc7d27b2e1e8eda2be8970586c3274"},
     {file = "six-1.17.0.tar.gz", hash = "sha256:ff70335d468e7eb6ec65b95b99d3a2836546063f63acc5171de367e834932a81"},
 ]
-markers = {main = "extra == \"gel\""}
+markers = {main = "(python_version <= \"3.11\" or python_version >= \"3.12\") and extra == \"gel\"", docs = "python_version <= \"3.11\" or python_version >= \"3.12\"", test = "python_version <= \"3.11\" or python_version >= \"3.12\""}
 
 [[package]]
 name = "snowballstemmer"
@@ -3837,6 +3739,7 @@ description = "This package provides 32 stemmers for 30 languages generated from
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*"
 groups = ["docs"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "snowballstemmer-3.0.1-py3-none-any.whl", hash = "sha256:6cd7b3897da8d6c9ffb968a6781fa6532dce9c3618a4b127d920dab764a19064"},
     {file = "snowballstemmer-3.0.1.tar.gz", hash = "sha256:6d5eeeec8e9f84d4d56b847692bacf79bc2c8e90c7f80ca4444ff8b6f2e52895"},
@@ -3849,6 +3752,7 @@ description = "A modern CSS selector implementation for Beautiful Soup."
 optional = false
 python-versions = ">=3.9"
 groups = ["docs"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "soupsieve-2.8-py3-none-any.whl", hash = "sha256:0cc76456a30e20f5d7f2e14a98a4ae2ee4e5abdc7c5ea0aafe795f344bc7984c"},
     {file = "soupsieve-2.8.tar.gz", hash = "sha256:e2dd4a40a628cb5f28f6d4b0db8800b8f581b65bb380b97de22ba5ca8d72572f"},
@@ -3861,7 +3765,7 @@ description = "Python documentation generator"
 optional = false
 python-versions = ">=3.10"
 groups = ["docs"]
-markers = "python_version == \"3.10\""
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "sphinx-8.1.3-py3-none-any.whl", hash = "sha256:09719015511837b76bf6e03e42eb7595ac8c2e41eeb9c29c5b755c6b677992a2"},
     {file = "sphinx-8.1.3.tar.gz", hash = "sha256:43c1911eecb0d3e161ad78611bc905d1ad0e523e4ddc202a58a821773dc4c927"},
@@ -3891,43 +3795,6 @@ docs = ["sphinxcontrib-websupport"]
 lint = ["flake8 (>=6.0)", "mypy (==1.11.1)", "pyright (==1.1.384)", "pytest (>=6.0)", "ruff (==0.6.9)", "sphinx-lint (>=0.9)", "tomli (>=2)", "types-Pillow (==10.2.0.20240822)", "types-Pygments (==2.18.0.20240506)", "types-colorama (==0.4.15.20240311)", "types-defusedxml (==0.7.0.20240218)", "types-docutils (==0.21.0.20241005)", "types-requests (==2.32.0.20240914)", "types-urllib3 (==1.26.25.14)"]
 test = ["cython (>=3.0)", "defusedxml (>=0.7.1)", "pytest (>=8.0)", "setuptools (>=70.0)", "typing_extensions (>=4.9)"]
 
-[[package]]
-name = "sphinx"
-version = "8.2.3"
-description = "Python documentation generator"
-optional = false
-python-versions = ">=3.11"
-groups = ["docs"]
-markers = "python_version >= \"3.11\""
-files = [
-    {file = "sphinx-8.2.3-py3-none-any.whl", hash = "sha256:4405915165f13521d875a8c29c8970800a0141c14cc5416a38feca4ea5d9b9c3"},
-    {file = "sphinx-8.2.3.tar.gz", hash = "sha256:398ad29dee7f63a75888314e9424d40f52ce5a6a87ae88e7071e80af296ec348"},
-]
-
-[package.dependencies]
-alabaster = ">=0.7.14"
-babel = ">=2.13"
-colorama = {version = ">=0.4.6", markers = "sys_platform == \"win32\""}
-docutils = ">=0.20,<0.22"
-imagesize = ">=1.3"
-Jinja2 = ">=3.1"
-packaging = ">=23.0"
-Pygments = ">=2.17"
-requests = ">=2.30.0"
-roman-numerals-py = ">=1.0.0"
-snowballstemmer = ">=2.2"
-sphinxcontrib-applehelp = ">=1.0.7"
-sphinxcontrib-devhelp = ">=1.0.6"
-sphinxcontrib-htmlhelp = ">=2.0.6"
-sphinxcontrib-jsmath = ">=1.0.1"
-sphinxcontrib-qthelp = ">=1.0.6"
-sphinxcontrib-serializinghtml = ">=1.1.9"
-
-[package.extras]
-docs = ["sphinxcontrib-websupport"]
-lint = ["betterproto (==2.0.0b6)", "mypy (==1.15.0)", "pypi-attestations (==0.0.21)", "pyright (==1.1.395)", "pytest (>=8.0)", "ruff (==0.9.9)", "sphinx-lint (>=0.9)", "types-Pillow (==10.2.0.20240822)", "types-Pygments (==2.19.0.20250219)", "types-colorama (==0.4.15.20240311)", "types-defusedxml (==0.7.0.20240218)", "types-docutils (==0.21.0.20241128)", "types-requests (==2.32.0.20241016)", "types-urllib3 (==1.26.25.14)"]
-test = ["cython (>=3.0)", "defusedxml (>=0.7.1)", "pytest (>=8.0)", "pytest-xdist[psutil] (>=3.4)", "setuptools (>=70.0)", "typing_extensions (>=4.9)"]
-
 [[package]]
 name = "sphinx-book-theme"
 version = "1.1.4"
@@ -3935,6 +3802,7 @@ description = "A clean book theme for scientific explanations and documentation
 optional = false
 python-versions = ">=3.9"
 groups = ["docs"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "sphinx_book_theme-1.1.4-py3-none-any.whl", hash = "sha256:843b3f5c8684640f4a2d01abd298beb66452d1b2394cd9ef5be5ebd5640ea0e1"},
     {file = "sphinx_book_theme-1.1.4.tar.gz", hash = "sha256:73efe28af871d0a89bd05856d300e61edce0d5b2fbb7984e84454be0fedfe9ed"},
@@ -3956,6 +3824,7 @@ description = "sphinxcontrib-applehelp is a Sphinx extension which outputs Apple
 optional = false
 python-versions = ">=3.9"
 groups = ["docs"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "sphinxcontrib_applehelp-2.0.0-py3-none-any.whl", hash = "sha256:4cd3f0ec4ac5dd9c17ec65e9ab272c9b867ea77425228e68ecf08d6b28ddbdb5"},
     {file = "sphinxcontrib_applehelp-2.0.0.tar.gz", hash = "sha256:2f29ef331735ce958efa4734873f084941970894c6090408b079c61b2e1c06d1"},
@@ -3973,6 +3842,7 @@ description = "sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp
 optional = false
 python-versions = ">=3.9"
 groups = ["docs"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "sphinxcontrib_devhelp-2.0.0-py3-none-any.whl", hash = "sha256:aefb8b83854e4b0998877524d1029fd3e6879210422ee3780459e28a1f03a8a2"},
     {file = "sphinxcontrib_devhelp-2.0.0.tar.gz", hash = "sha256:411f5d96d445d1d73bb5d52133377b4248ec79db5c793ce7dbe59e074b4dd1ad"},
@@ -3990,6 +3860,7 @@ description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML h
 optional = false
 python-versions = ">=3.9"
 groups = ["docs"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "sphinxcontrib_htmlhelp-2.1.0-py3-none-any.whl", hash = "sha256:166759820b47002d22914d64a075ce08f4c46818e17cfc9470a9786b759b19f8"},
     {file = "sphinxcontrib_htmlhelp-2.1.0.tar.gz", hash = "sha256:c9e2916ace8aad64cc13a0d233ee22317f2b9025b9cf3295249fa985cc7082e9"},
@@ -4007,6 +3878,7 @@ description = "A sphinx extension which renders display math in HTML via JavaScr
 optional = false
 python-versions = ">=3.5"
 groups = ["docs"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "sphinxcontrib-jsmath-1.0.1.tar.gz", hash = "sha256:a9925e4a4587247ed2191a22df5f6970656cb8ca2bd6284309578f2153e0c4b8"},
     {file = "sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl", hash = "sha256:2ec2eaebfb78f3f2078e73666b1415417a116cc848b72e5172e596c871103178"},
@@ -4022,6 +3894,7 @@ description = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp d
 optional = false
 python-versions = ">=3.9"
 groups = ["docs"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "sphinxcontrib_qthelp-2.0.0-py3-none-any.whl", hash = "sha256:b18a828cdba941ccd6ee8445dbe72ffa3ef8cbe7505d8cd1fa0d42d3f2d5f3eb"},
     {file = "sphinxcontrib_qthelp-2.0.0.tar.gz", hash = "sha256:4fe7d0ac8fc171045be623aba3e2a8f613f8682731f9153bb2e40ece16b9bbab"},
@@ -4039,6 +3912,7 @@ description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs
 optional = false
 python-versions = ">=3.9"
 groups = ["docs"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "sphinxcontrib_serializinghtml-2.0.0-py3-none-any.whl", hash = "sha256:6e2cb0eef194e10c27ec0023bfeb25badbbb5868244cf5bc5bdc04e4464bf331"},
     {file = "sphinxcontrib_serializinghtml-2.0.0.tar.gz", hash = "sha256:e9d912827f872c029017a53f0ef2180b327c3f7fd23c87229f7a8e8b70031d4d"},
@@ -4056,6 +3930,7 @@ description = "Database Abstraction Library"
 optional = false
 python-versions = ">=3.7"
 groups = ["docs"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "SQLAlchemy-2.0.44-cp37-cp37m-macosx_10_9_x86_64.whl", hash = "sha256:471733aabb2e4848d609141a9e9d56a427c0a038f4abf65dd19d7a21fd563632"},
     {file = "SQLAlchemy-2.0.44-cp37-cp37m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:48bf7d383a35e668b984c805470518b635d48b95a3c57cb03f37eaa3551b5f9f"},
@@ -4152,6 +4027,7 @@ description = "Extract data from python stack frames and tracebacks for informat
 optional = false
 python-versions = "*"
 groups = ["docs", "test"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "stack_data-0.6.3-py3-none-any.whl", hash = "sha256:d5558e0c25a4cb0853cddad3d77da9891a08cb85dd9f9f91b9f8cd66e511e695"},
     {file = "stack_data-0.6.3.tar.gz", hash = "sha256:836a778de4fec4dcd1dcd89ed8abff8a221f58308462e1c4aa2a3cf30148f0b9"},
@@ -4172,6 +4048,7 @@ description = "Pretty-print tabular data"
 optional = false
 python-versions = ">=3.7"
 groups = ["docs"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "tabulate-0.9.0-py3-none-any.whl", hash = "sha256:024ca478df22e9340661486f85298cff5f6dcdba14f3813e8830015b9ed1948f"},
     {file = "tabulate-0.9.0.tar.gz", hash = "sha256:0095b12bf5966de529c0feb1fa08671671b3368eec77d7ef7ab114be2c068b3c"},
@@ -4187,7 +4064,6 @@ description = "A lil' TOML parser"
 optional = false
 python-versions = ">=3.8"
 groups = ["dev", "docs", "test"]
-markers = "python_version == \"3.10\""
 files = [
     {file = "tomli-2.3.0-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:88bd15eb972f3664f5ed4b57c1634a97153b4bac4479dcb6a495f41921eb7f45"},
     {file = "tomli-2.3.0-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:883b1c0d6398a6a9d29b508c331fa56adbcdff647f6ace4dfca0f50e90dfd0ba"},
@@ -4232,6 +4108,7 @@ files = [
     {file = "tomli-2.3.0-py3-none-any.whl", hash = "sha256:e95b1af3c5b07d9e643909b5abbec77cd9f1217e6d0bca72b0234736b9fb1f1b"},
     {file = "tomli-2.3.0.tar.gz", hash = "sha256:64be704a875d2a59753d80ee8a533c3fe183e3f06807ff7dc2232938ccb01549"},
 ]
+markers = {dev = "python_version < \"3.11\"", docs = "python_version < \"3.11\"", test = "python_full_version <= \"3.11.0a6\""}
 
 [[package]]
 name = "tornado"
@@ -4240,6 +4117,7 @@ description = "Tornado is a Python web framework and asynchronous networking lib
 optional = false
 python-versions = ">=3.9"
 groups = ["docs", "test"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "tornado-6.5.2-cp39-abi3-macosx_10_9_universal2.whl", hash = "sha256:2436822940d37cde62771cff8774f4f00b3c8024fe482e16ca8387b8a2724db6"},
     {file = "tornado-6.5.2-cp39-abi3-macosx_10_9_x86_64.whl", hash = "sha256:583a52c7aa94ee046854ba81d9ebb6c81ec0fd30386d96f7640c96dad45a03ef"},
@@ -4262,6 +4140,7 @@ description = "Traitlets Python configuration system"
 optional = false
 python-versions = ">=3.8"
 groups = ["dev", "docs", "test"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "traitlets-5.14.3-py3-none-any.whl", hash = "sha256:b74e89e397b1ed28cc831db7aea759ba6640cb3de13090ca145426688ff1ac4f"},
     {file = "traitlets-5.14.3.tar.gz", hash = "sha256:9ed0579d3502c94b4b3732ac120375cda96f923114522847de4b3bb98b96b6b7"},
@@ -4282,7 +4161,7 @@ files = [
     {file = "typing_extensions-4.15.0-py3-none-any.whl", hash = "sha256:f0fa19c6845758ab08074a0cfa8b7aecb71c999ca73d62883bc25cc018c4e548"},
     {file = "typing_extensions-4.15.0.tar.gz", hash = "sha256:0cea48d173cc12fa28ecabc3b837ea3cf6f38c6d1136f85cbaaf598984861466"},
 ]
-markers = {dev = "python_version <= \"3.12\"", test = "python_version <= \"3.12\""}
+markers = {main = "python_version <= \"3.11\" or python_version >= \"3.12\"", dev = "python_version >= \"3.12\" and python_version < \"3.13\" or python_version <= \"3.11\"", docs = "python_version <= \"3.11\" or python_version >= \"3.12\"", test = "python_version >= \"3.12\" and python_version < \"3.13\" or python_version <= \"3.11\""}
 
 [[package]]
 name = "typing-inspection"
@@ -4291,6 +4170,7 @@ description = "Runtime typing introspection tools"
 optional = false
 python-versions = ">=3.9"
 groups = ["main"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "typing_inspection-0.4.2-py3-none-any.whl", hash = "sha256:4ed1cacbdc298c220f1bd249ed5287caa16f34d44ef4e9c3d0cbad5b521545e7"},
     {file = "typing_inspection-0.4.2.tar.gz", hash = "sha256:ba561c48a67c5958007083d386c3295464928b01faa735ab8547c5692e87f464"},
@@ -4306,6 +4186,7 @@ description = "Provider of IANA time zone data"
 optional = false
 python-versions = ">=2"
 groups = ["docs"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "tzdata-2025.2-py2.py3-none-any.whl", hash = "sha256:1a403fada01ff9221ca8044d701868fa132215d84beb92242d9acd2147f667a8"},
     {file = "tzdata-2025.2.tar.gz", hash = "sha256:b60a638fcc0daffadf82fe0f57e53d06bdec2f36c4df66280ae79bce6bd6f2b9"},
@@ -4322,10 +4203,10 @@ files = [
     {file = "urllib3-2.5.0-py3-none-any.whl", hash = "sha256:e6b01673c0fa6a13e374b50871808eb3bf7046c4b125b216f6bf1cc604cff0dc"},
     {file = "urllib3-2.5.0.tar.gz", hash = "sha256:3fc47733c7e419d4bc3f6b3dc2b4f890bb743906a30d56ba4a5bfa4bbff92760"},
 ]
-markers = {main = "extra == \"download\""}
+markers = {main = "(python_version <= \"3.11\" or python_version >= \"3.12\") and extra == \"download\"", docs = "python_version <= \"3.11\" or python_version >= \"3.12\"", test = "python_version <= \"3.11\" or python_version >= \"3.12\""}
 
 [package.extras]
-brotli = ["brotli (>=1.0.9) ; platform_python_implementation == \"CPython\"", "brotlicffi (>=0.8.0) ; platform_python_implementation != \"CPython\""]
+brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)"]
 h2 = ["h2 (>=4,<5)"]
 socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"]
 zstd = ["zstandard (>=0.18.0)"]
@@ -4337,6 +4218,7 @@ description = "Virtual Python Environment builder"
 optional = false
 python-versions = ">=3.8"
 groups = ["dev"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "virtualenv-20.35.4-py3-none-any.whl", hash = "sha256:c21c9cede36c9753eeade68ba7d523529f228a403463376cf821eaae2b650f1b"},
     {file = "virtualenv-20.35.4.tar.gz", hash = "sha256:643d3914d73d3eeb0c552cbb12d7e82adf0e504dbf86a3182f8771a153a1971c"},
@@ -4350,7 +4232,7 @@ typing-extensions = {version = ">=4.13.2", markers = "python_version < \"3.11\""
 
 [package.extras]
 docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.2,!=7.3)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"]
-test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest (>=7.4)", "pytest-env (>=0.8.2)", "pytest-freezer (>=0.4.8) ; platform_python_implementation == \"PyPy\" or platform_python_implementation == \"GraalVM\" or platform_python_implementation == \"CPython\" and sys_platform == \"win32\" and python_version >= \"3.13\"", "pytest-mock (>=3.11.1)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "setuptools (>=68)", "time-machine (>=2.10) ; platform_python_implementation == \"CPython\""]
+test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest (>=7.4)", "pytest-env (>=0.8.2)", "pytest-freezer (>=0.4.8)", "pytest-mock (>=3.11.1)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "setuptools (>=68)", "time-machine (>=2.10)"]
 
 [[package]]
 name = "wcwidth"
@@ -4359,6 +4241,7 @@ description = "Measures the displayed width of unicode strings in a terminal"
 optional = false
 python-versions = ">=3.6"
 groups = ["main", "docs", "test"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "wcwidth-0.2.14-py2.py3-none-any.whl", hash = "sha256:a7bb560c8aee30f9957e5f9895805edd20602f2d7f720186dfd906e82b4982e1"},
     {file = "wcwidth-0.2.14.tar.gz", hash = "sha256:4d478375d31bc5395a3c55c40ccdf3354688364cd61c4f6adacaa9215d0b3605"},
@@ -4371,6 +4254,7 @@ description = "A built-package format for Python"
 optional = false
 python-versions = ">=3.8"
 groups = ["main"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "wheel-0.45.1-py3-none-any.whl", hash = "sha256:708e7481cc80179af0e556bbf0cc00b8444c7321e2700b8d8580231d13017248"},
     {file = "wheel-0.45.1.tar.gz", hash = "sha256:661e1abd9198507b1409a20c02106d9670b2576e916d58f520316666abca6729"},
@@ -4386,13 +4270,14 @@ description = "Backport of pathlib-compatible object wrapper for zip files"
 optional = false
 python-versions = ">=3.9"
 groups = ["docs"]
+markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "zipp-3.23.0-py3-none-any.whl", hash = "sha256:071652d6115ed432f5ce1d34c336c0adfd6a884660d1e9712a256d3d3bd4b14e"},
     {file = "zipp-3.23.0.tar.gz", hash = "sha256:a07157588a12518c9d4034df3fbbee09c814741a33ff63c05fa29d26a2404166"},
 ]
 
 [package.extras]
-check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1) ; sys_platform != \"cygwin\""]
+check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"]
 cover = ["pytest-cov"]
 doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
 enabler = ["pytest-enabler (>=2.2)"]
@@ -4408,4 +4293,4 @@ gel = ["matplotlib", "pillow", "scipy", "scipy"]
 [metadata]
 lock-version = "2.1"
 python-versions = ">=3.10,<4.0"
-content-hash = "bb14c4f58a1f05322e69f2ddbebac66d0878487c878fd2b2b8d0cee0d39a973c"
+content-hash = "3087cb5712ba46f202fd95cedc56096d25ff324b3c46ddf8a58de4fcd0b21392"
diff --git a/pyproject.toml b/pyproject.toml
index e921a4f3..dfa3fed6 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -60,7 +60,7 @@ scipy = [
 ]
 seguid = ">=0.0.5"
 regex = "^2024.11.6"
-opencloning-linkml = "0.4.5"
+opencloning-linkml = "^0.4.5"
 [tool.poetry.extras]
 clipboard = ["pyperclip"]
 download = ["pyparsing", "requests"]

From 5a6c7d3d4978f80240274d156b1b349c0a7c6e01 Mon Sep 17 00:00:00 2001
From: Manuel Lera-Ramirez <manulera14@gmail.com>
Date: Mon, 17 Nov 2025 23:15:14 +0000
Subject: [PATCH 07/22] support and test edge case from #488

---
 src/pydna/assembly2.py         |  3 ++-
 tests/test_module_assembly2.py | 11 +++++++++++
 2 files changed, 13 insertions(+), 1 deletion(-)

diff --git a/src/pydna/assembly2.py b/src/pydna/assembly2.py
index c896280f..d3b93933 100644
--- a/src/pydna/assembly2.py
+++ b/src/pydna/assembly2.py
@@ -2805,7 +2805,8 @@ def crispr_integration(
         # The second element of product.source.input is conventionally the insert/repair fragment
         # The other two (first and third) are the two bits of the genome
         repair_start = _location_boundaries(product.source.input[0].right_location)[0]
-        repair_end = _location_boundaries(product.source.input[2].left_location)[1]
+        # Here we do +1 because the position of the cut marks the boundary (e.g. 0:10, 10:20 if a cut is at pos 10)
+        repair_end = _location_boundaries(product.source.input[2].left_location)[1] + 1
         repair_location = create_location(repair_start, repair_end, len(genome))
         some_cuts_inside_repair = []
         all_cuts_inside_repair = []
diff --git a/tests/test_module_assembly2.py b/tests/test_module_assembly2.py
index dcdd4605..b8693074 100644
--- a/tests/test_module_assembly2.py
+++ b/tests/test_module_assembly2.py
@@ -2638,6 +2638,17 @@ def test_crispr_integration():
     assert len(products) == 1
 
 
+def test_crispr_integration_edge_case():
+    homology1 = "ATGCAAACAGTAATGATGGATGACATTCAAAGCACTGATT"
+    guide = Primer("CATTCAAAGCACTGATTaat")
+    genome = Dseqrecord(f"aaaaaa{homology1}aattggaa{homology1}tttttttt")
+
+    insert = Dseqrecord(f"{homology1}acaa{homology1}")
+
+    products = assembly.crispr_integration(genome, [insert], [guide], 40)
+    assert len(products) == 2
+
+
 def test_pcr_assembly():
 
     template = Dseqrecord("TTTTACGTACGTAAAAAAGCGCGCGCTTTTT")

From 5028df8ace272eeb84afbe25f6c41f9b8b3bea83 Mon Sep 17 00:00:00 2001
From: Manuel Lera-Ramirez <manulera14@gmail.com>
Date: Tue, 25 Nov 2025 15:25:02 +0000
Subject: [PATCH 08/22] starting to work on better serialization

---
 dummy.py                        |  7 +++++++
 src/pydna/opencloning_models.py | 14 +++++++++++++-
 2 files changed, 20 insertions(+), 1 deletion(-)
 create mode 100644 dummy.py

diff --git a/dummy.py b/dummy.py
new file mode 100644
index 00000000..a8e57f5d
--- /dev/null
+++ b/dummy.py
@@ -0,0 +1,7 @@
+# -*- coding: utf-8 -*-
+from pydna.dseqrecord import Dseqrecord
+from Bio.Restriction import EcoRI
+
+c, d = Dseqrecord("aaaaaaGAATTCtttttttt").cut(EcoRI)
+
+print(c.source.model_dump_json())
diff --git a/src/pydna/opencloning_models.py b/src/pydna/opencloning_models.py
index 327c813c..76bd9c7f 100644
--- a/src/pydna/opencloning_models.py
+++ b/src/pydna/opencloning_models.py
@@ -24,7 +24,7 @@
 from contextlib import contextmanager
 from threading import local
 
-from pydantic import BaseModel, ConfigDict, Field, field_validator
+from pydantic import BaseModel, ConfigDict, Field, field_serializer, field_validator
 
 from opencloning_linkml.datamodel import (
     CloningStrategy as _BaseCloningStrategy,
@@ -272,6 +272,12 @@ def _kwargs(self, seq_id: int) -> dict:
             "input": self.input_models(),
         }
 
+    @field_serializer("input")
+    def serialize_input(
+        self, input: list[Union[SourceInput, AssemblyFragment]]
+    ) -> list[_SourceInput | _AssemblyFragment]:
+        return [fragment.to_pydantic_model() for fragment in input]
+
     def to_pydantic_model(self, seq_id: int):
         kwargs = self._kwargs(seq_id)
         return self.TARGET_MODEL(**kwargs)
@@ -485,6 +491,12 @@ class SequenceCutSource(Source):
         _RestrictionEnzymeDigestionSource
     )
 
+    @field_serializer("left_edge", "right_edge")
+    def serialize_cut_site(
+        self, cut_site: CutSiteType | None
+    ) -> _RestrictionSequenceCut | _SequenceCut | None:
+        return self._cutsite_to_model(cut_site)
+
     @staticmethod
     def _cutsite_to_model(cut_site: CutSiteType | None):
         if cut_site is None:

From c22d42ddc747f9bf9722770f35d4a403620f83af Mon Sep 17 00:00:00 2001
From: Manuel Lera-Ramirez <manulera14@gmail.com>
Date: Tue, 25 Nov 2025 16:09:17 +0000
Subject: [PATCH 09/22] simplify serialization to avoid having to use kwargs,
 instead define serializer for non-native fields

---
 dummy.py                        |   7 --
 src/pydna/assembly2.py          |   2 +-
 src/pydna/opencloning_models.py | 111 ++++++--------------------------
 3 files changed, 22 insertions(+), 98 deletions(-)
 delete mode 100644 dummy.py

diff --git a/dummy.py b/dummy.py
deleted file mode 100644
index a8e57f5d..00000000
--- a/dummy.py
+++ /dev/null
@@ -1,7 +0,0 @@
-# -*- coding: utf-8 -*-
-from pydna.dseqrecord import Dseqrecord
-from Bio.Restriction import EcoRI
-
-c, d = Dseqrecord("aaaaaaGAATTCtttttttt").cut(EcoRI)
-
-print(c.source.model_dump_json())
diff --git a/src/pydna/assembly2.py b/src/pydna/assembly2.py
index d3b93933..12929aac 100644
--- a/src/pydna/assembly2.py
+++ b/src/pydna/assembly2.py
@@ -2036,7 +2036,7 @@ def _recast_sources(
     """
     for prod in products:
         prod.source = source_cls(
-            **prod.source.model_dump(),
+            **prod.source.to_unserialized_dict(),
             **extra_fields,
         )
     return products
diff --git a/src/pydna/opencloning_models.py b/src/pydna/opencloning_models.py
index 76bd9c7f..65bcf892 100644
--- a/src/pydna/opencloning_models.py
+++ b/src/pydna/opencloning_models.py
@@ -263,15 +263,6 @@ class Source(ConfiguredBaseModel):
     input: list[Union[SourceInput, AssemblyFragment]] = Field(default_factory=list)
     TARGET_MODEL: ClassVar[Type[_Source]] = _Source
 
-    def input_models(self):
-        return [fragment.to_pydantic_model() for fragment in self.input]
-
-    def _kwargs(self, seq_id: int) -> dict:
-        return {
-            "id": seq_id,
-            "input": self.input_models(),
-        }
-
     @field_serializer("input")
     def serialize_input(
         self, input: list[Union[SourceInput, AssemblyFragment]]
@@ -279,8 +270,15 @@ def serialize_input(
         return [fragment.to_pydantic_model() for fragment in input]
 
     def to_pydantic_model(self, seq_id: int):
-        kwargs = self._kwargs(seq_id)
-        return self.TARGET_MODEL(**kwargs)
+        model_dict = self.model_dump()
+        model_dict["id"] = seq_id
+        return self.TARGET_MODEL(**model_dict)
+
+    def to_unserialized_dict(self):
+        """
+        Converts into a dictionary without serializing the fields, this is used to be able to recast.
+        """
+        return {field: getattr(self, field) for field in self.__pydantic_fields__}
 
     def add_to_history_graph(self, history_graph: nx.DiGraph, seq: "Dseqrecord"):
         """
@@ -323,15 +321,6 @@ class AssemblySource(Source):
 
     TARGET_MODEL: ClassVar[Type[_AssemblySource]] = _AssemblySource
 
-    def _kwargs(self, seq_id: int) -> dict:
-        return {
-            **super()._kwargs(seq_id),
-            "circular": self.circular,
-        }
-
-    def to_pydantic_model(self, seq_id: int):
-        return self.TARGET_MODEL(**self._kwargs(seq_id))
-
     @classmethod
     def from_subfragment_representation(
         cls,
@@ -362,26 +351,6 @@ class UploadedFileSource(Source):
     index_in_file: int
     sequence_file_format: str
 
-    # "id": 1,
-    # "type": "UploadedFileSource",
-    # "output_name": null,
-    # "database_id": null,
-    # "input": [],
-    # "sequence_file_format": "fasta",
-    # "file_name": "seq2.fasta",
-    # "index_in_file": 0,
-    # "circularize": false,
-    # "coordinates": null,
-    # "output": 1
-
-    def _kwargs(self, seq_id: int) -> dict:
-        return {
-            **super()._kwargs(seq_id),
-            "file_name": self.file_name,
-            "index_in_file": self.index_in_file,
-            "sequence_file_format": self.sequence_file_format,
-        }
-
 
 class RepositoryIdSource(Source):
 
@@ -390,21 +359,6 @@ class RepositoryIdSource(Source):
     repository_name: str
     location: Location
 
-    # "id": 2,
-    # "type": "RepositoryIdSource",
-    # "output_name": null,
-    # "database_id": null,
-    # "input": [],
-    # "repository_id": "NM_001018957.2",
-    # "repository_name": "genbank"
-
-    def _kwargs(self, seq_id: int) -> dict:
-        return {
-            **super()._kwargs(seq_id),
-            "repository_id": self.repository_id,
-            "repository_name": self.repository_name,
-        }
-
 
 class RestrictionAndLigationSource(AssemblySource):
     restriction_enzymes: list[AbstractCut]
@@ -413,11 +367,11 @@ class RestrictionAndLigationSource(AssemblySource):
         _RestrictionAndLigationSource
     )
 
-    def _kwargs(self, seq_id: int) -> dict:
-        return {
-            **super()._kwargs(seq_id),
-            "restriction_enzymes": [str(enzyme) for enzyme in self.restriction_enzymes],
-        }
+    @field_serializer("restriction_enzymes")
+    def serialize_restriction_enzymes(
+        self, restriction_enzymes: list[AbstractCut]
+    ) -> list[str]:
+        return [str(enzyme) for enzyme in restriction_enzymes]
 
 
 class GibsonAssemblySource(AssemblySource):
@@ -447,13 +401,6 @@ class GatewaySource(AssemblySource):
     reaction_type: GatewayReactionType
     greedy: bool = Field(default=False)
 
-    def _kwargs(self, seq_id: int) -> dict:
-        return {
-            **super()._kwargs(seq_id),
-            "reaction_type": self.reaction_type,
-            "greedy": self.greedy,
-        }
-
 
 class HomologousRecombinationSource(AssemblySource):
     TARGET_MODEL: ClassVar[Type[_HomologousRecombinationSource]] = (
@@ -475,21 +422,18 @@ class PCRSource(AssemblySource):
     TARGET_MODEL: ClassVar[Type[_PCRSource]] = _PCRSource
     add_primer_features: bool = Field(default=False)
 
-    def _kwargs(self, seq_id: int) -> dict:
-        return {
-            **super()._kwargs(seq_id),
-            "add_primer_features": self.add_primer_features,
-        }
-
 
 class SequenceCutSource(Source):
     left_edge: CutSiteType | None
     right_edge: CutSiteType | None
 
-    BASE_MODEL: ClassVar[Type[_SequenceCutSource]] = _SequenceCutSource
-    ENZYME_MODEL: ClassVar[Type[_RestrictionEnzymeDigestionSource]] = (
-        _RestrictionEnzymeDigestionSource
-    )
+    @property
+    def TARGET_MODEL(self):
+        return (
+            _RestrictionEnzymeDigestionSource
+            if self._has_enzyme()
+            else _SequenceCutSource
+        )
 
     @field_serializer("left_edge", "right_edge")
     def serialize_cut_site(
@@ -527,19 +471,6 @@ def has_enzyme(edge):
 
         return has_enzyme(self.left_edge) or has_enzyme(self.right_edge)
 
-    def _target_model(self):
-        return self.ENZYME_MODEL if self._has_enzyme() else self.BASE_MODEL
-
-    def _kwargs(self, seq_id: int) -> dict:
-        return {
-            **super()._kwargs(seq_id),
-            "left_edge": self._cutsite_to_model(self.left_edge),
-            "right_edge": self._cutsite_to_model(self.right_edge),
-        }
-
-    def to_pydantic_model(self, seq_id: int):
-        return self._target_model()(**self._kwargs(seq_id))
-
 
 class CloningStrategy(_BaseCloningStrategy):
 

From 7d89f6584fd465d562f8c2fa143b164576cc749a Mon Sep 17 00:00:00 2001
From: Manuel Lera-Ramirez <manulera14@gmail.com>
Date: Tue, 25 Nov 2025 16:37:09 +0000
Subject: [PATCH 10/22] fix tests (happens because TARGET_MODEL was not
 behaving properly in SequenceCutSource before)

---
 tests/test_module_opencloning_models.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/tests/test_module_opencloning_models.py b/tests/test_module_opencloning_models.py
index 513b16dc..8e61b35b 100644
--- a/tests/test_module_opencloning_models.py
+++ b/tests/test_module_opencloning_models.py
@@ -284,13 +284,13 @@ def test_history_string(self):
             ╙── product (Dseqrecord(-18))
                 └─╼ LigationSource
                     ├─╼ c (Dseqrecord(-7))
-                    │   └─╼ Source
-                    │       └─╼ a (Dseqrecord(-18)) ╾ Source, Source
+                    │   └─╼ RestrictionEnzymeDigestionSource
+                    │       └─╼ a (Dseqrecord(-18)) ╾ RestrictionEnzymeDigestionSource, RestrictionEnzymeDigestionSource
                     ├─╼ d (Dseqrecord(-12))
-                    │   └─╼ Source
+                    │   └─╼ RestrictionEnzymeDigestionSource
                     │       └─╼  ...
                     └─╼ e (Dseqrecord(-7))
-                        └─╼ Source
+                        └─╼ RestrictionEnzymeDigestionSource
                             └─╼  ...
             """
             ).strip(),
@@ -313,7 +313,7 @@ def test_history_string(self):
             textwrap.dedent(
                 """
             ╙── custom_cut_product (Dseqrecord(-7))
-                └─╼ Source
+                └─╼ SequenceCutSource
                     └─╼ name (Dseqrecord(-18))
             """
             ).strip(),

From 4404482da0a5a440bd629b093f23c90be0815889 Mon Sep 17 00:00:00 2001
From: Manuel Lera-Ramirez <manulera14@gmail.com>
Date: Tue, 25 Nov 2025 16:39:49 +0000
Subject: [PATCH 11/22] update notebook output

---
 docs/notebooks/history.ipynb | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/docs/notebooks/history.ipynb b/docs/notebooks/history.ipynb
index 7cf5b115..94c3300d 100644
--- a/docs/notebooks/history.ipynb
+++ b/docs/notebooks/history.ipynb
@@ -186,13 +186,13 @@
       "╙── product (Dseqrecord(-18))\n",
       "    └─╼ LigationSource\n",
       "        ├─╼ c (Dseqrecord(-7))\n",
-      "        │   └─╼ Source\n",
-      "        │       └─╼ a (Dseqrecord(-18)) ╾ Source, Source\n",
+      "        │   └─╼ RestrictionEnzymeDigestionSource\n",
+      "        │       └─╼ a (Dseqrecord(-18)) ╾ RestrictionEnzymeDigestionSource, RestrictionEnzymeDigestionSource\n",
       "        ├─╼ d (Dseqrecord(-12))\n",
-      "        │   └─╼ Source\n",
+      "        │   └─╼ RestrictionEnzymeDigestionSource\n",
       "        │       └─╼  ...\n",
       "        └─╼ e (Dseqrecord(-7))\n",
-      "            └─╼ Source\n",
+      "            └─╼ RestrictionEnzymeDigestionSource\n",
       "                └─╼  ...\n"
      ]
     }
@@ -354,8 +354,8 @@
       "    └─╼ CreLoxRecombinationSource\n",
       "        └─╼ integration_product (Dseqrecord(-84))\n",
       "            └─╼ CreLoxRecombinationSource\n",
-      "                ├─╼ a (Dseqrecord(-45))\n",
-      "                └─╼ b (Dseqrecord(o39))\n"
+      "                ├─╼ genome (Dseqrecord(-45))\n",
+      "                └─╼ plasmid (Dseqrecord(o39))\n"
      ]
     }
    ],

From e5d5270046662cf6b9c033a7cdf4725d285bba23 Mon Sep 17 00:00:00 2001
From: Manuel Lera-Ramirez <manulera14@gmail.com>
Date: Tue, 25 Nov 2025 16:53:55 +0000
Subject: [PATCH 12/22] add some repositories

---
 src/pydna/opencloning_models.py | 42 ++++++++++++++++++++++++++++++++-
 1 file changed, 41 insertions(+), 1 deletion(-)

diff --git a/src/pydna/opencloning_models.py b/src/pydna/opencloning_models.py
index 65bcf892..c2b2ff1f 100644
--- a/src/pydna/opencloning_models.py
+++ b/src/pydna/opencloning_models.py
@@ -51,8 +51,14 @@
     CreLoxRecombinationSource as _CreLoxRecombinationSource,
     PCRSource as _PCRSource,
     CRISPRSource as _CRISPRSource,
-    RepositoryIdSource as _RepositoryIdSource,  # here!
+    RepositoryIdSource as _RepositoryIdSource,
     UploadedFileSource as _UploadedFileSource,
+    AddgeneIdSource as _AddgeneIdSource,
+    AddgeneSequenceType,
+    WekWikGeneIdSource as _WekWikGeneIdSource,
+    SEVASource as _SEVASource,
+    IGEMSource as _IGEMSource,
+    OpenDNACollectionsSource as _OpenDNACollectionsSource,
 )
 from Bio.SeqFeature import Location, LocationParserError
 from Bio.Restriction.Restriction import AbstractCut
@@ -355,11 +361,45 @@ class UploadedFileSource(Source):
 class RepositoryIdSource(Source):
 
     TARGET_MODEL: ClassVar[Type[_RepositoryIdSource]] = _RepositoryIdSource
+
     repository_id: str
     repository_name: str
     location: Location
 
 
+class RepositoryIdSourceWithSequenceFileUrl(RepositoryIdSource):
+    """Auxiliary class to avoid code duplication in the sources that have a sequence file url."""
+
+    sequence_file_url: Optional[str] = None
+
+
+class AddgeneIdSource(RepositoryIdSourceWithSequenceFileUrl):
+    TARGET_MODEL: ClassVar[Type[_AddgeneIdSource]] = _AddgeneIdSource
+
+    addgene_sequence_type: Optional[AddgeneSequenceType] = None
+    repository_name: str = "addgene"
+
+
+class WekWikGeneIdSource(RepositoryIdSourceWithSequenceFileUrl):
+    TARGET_MODEL: ClassVar[Type[_WekWikGeneIdSource]] = _WekWikGeneIdSource
+    repository_name: str = "wekwikgene"
+
+
+class SEVASource(RepositoryIdSourceWithSequenceFileUrl):
+    TARGET_MODEL: ClassVar[Type[_SEVASource]] = _SEVASource
+    repository_name: str = "seva"
+
+
+class IGEMSource(RepositoryIdSourceWithSequenceFileUrl):
+    TARGET_MODEL: ClassVar[Type[_IGEMSource]] = _IGEMSource
+    repository_name: str = "igem"
+
+
+class OpenDNACollectionsSource(RepositoryIdSourceWithSequenceFileUrl):
+    TARGET_MODEL: ClassVar[Type[_OpenDNACollectionsSource]] = _OpenDNACollectionsSource
+    repository_name: str = "open_dna_collections"
+
+
 class RestrictionAndLigationSource(AssemblySource):
     restriction_enzymes: list[AbstractCut]
 

From b47b060b7027be9ea69ac8f9fb11e1691ce28981 Mon Sep 17 00:00:00 2001
From: Manuel Lera-Ramirez <manulera14@gmail.com>
Date: Tue, 25 Nov 2025 18:07:31 +0000
Subject: [PATCH 13/22] add the rest of the models

---
 src/pydna/opencloning_models.py | 87 +++++++++++++++++++++++++++++++--
 1 file changed, 83 insertions(+), 4 deletions(-)

diff --git a/src/pydna/opencloning_models.py b/src/pydna/opencloning_models.py
index c2b2ff1f..166870cd 100644
--- a/src/pydna/opencloning_models.py
+++ b/src/pydna/opencloning_models.py
@@ -28,6 +28,7 @@
 
 from opencloning_linkml.datamodel import (
     CloningStrategy as _BaseCloningStrategy,
+    DatabaseSource as _DatabaseSource,
     Primer as _PrimerModel,
     Source as _Source,
     TextFileSequence as _TextFileSequence,
@@ -47,6 +48,7 @@
     LigationSource as _LigationSource,
     GatewaySource as _GatewaySource,
     GatewayReactionType,
+    AnnotationTool,
     HomologousRecombinationSource as _HomologousRecombinationSource,
     CreLoxRecombinationSource as _CreLoxRecombinationSource,
     PCRSource as _PCRSource,
@@ -55,10 +57,20 @@
     UploadedFileSource as _UploadedFileSource,
     AddgeneIdSource as _AddgeneIdSource,
     AddgeneSequenceType,
+    BenchlingUrlSource as _BenchlingUrlSource,
+    SnapGenePlasmidSource as _SnapGenePlasmidSource,
+    EuroscarfSource as _EuroscarfSource,
     WekWikGeneIdSource as _WekWikGeneIdSource,
     SEVASource as _SEVASource,
     IGEMSource as _IGEMSource,
     OpenDNACollectionsSource as _OpenDNACollectionsSource,
+    GenomeCoordinatesSource as _GenomeCoordinatesSource,
+    OligoHybridizationSource as _OligoHybridizationSource,
+    PolymeraseExtensionSource as _PolymeraseExtensionSource,
+    AnnotationSource as _AnnotationSource,
+    AnnotationReport as _AnnotationReport,
+    PlannotateAnnotationReport as _PlannotateAnnotationReport,
+    ReverseComplementSource as _ReverseComplementSource,
 )
 from Bio.SeqFeature import Location, LocationParserError
 from Bio.Restriction.Restriction import AbstractCut
@@ -86,8 +98,9 @@ def id_mode(use_python_internal_id: bool = True):
     mapping them to the OpenCloning data model. If ``use_python_internal_id`` is True,
     the built-in python ``id()`` function is used to assign ids to objects. That function
     produces a unique integer for each object in python, so it's guaranteed to be unique.
-    If ``use_python_internal_id`` is False, the object's ``.id`` attribute (must be a string integer)
-    is used to assign ids to objects. This is useful when the objects already have meaningful ids,
+    If ``use_python_internal_id`` is False, the object's ``.id`` attribute
+    (must be a string integer) is used to assign ids to objects. This is useful
+    when the objects already have meaningful ids,
     and you want to keep references to them in ``SourceInput`` objects (which sequences and
     primers are used in a particular source).
 
@@ -282,7 +295,8 @@ def to_pydantic_model(self, seq_id: int):
 
     def to_unserialized_dict(self):
         """
-        Converts into a dictionary without serializing the fields, this is used to be able to recast.
+        Converts into a dictionary without serializing the fields.
+        This is used to be able to recast.
         """
         return {field: getattr(self, field) for field in self.__pydantic_fields__}
 
@@ -349,6 +363,12 @@ def from_subfragment_representation(
         return AssemblySource(input=input_list, circular=is_circular)
 
 
+class DatabaseSource(Source):
+    TARGET_MODEL: ClassVar[Type[_DatabaseSource]] = _DatabaseSource
+
+    database_id: int
+
+
 class UploadedFileSource(Source):
 
     TARGET_MODEL: ClassVar[Type[_UploadedFileSource]] = _UploadedFileSource
@@ -368,7 +388,10 @@ class RepositoryIdSource(Source):
 
 
 class RepositoryIdSourceWithSequenceFileUrl(RepositoryIdSource):
-    """Auxiliary class to avoid code duplication in the sources that have a sequence file url."""
+    """
+    Auxiliary class to avoid code duplication in the sources that have
+    a sequence file url.
+    """
 
     sequence_file_url: Optional[str] = None
 
@@ -380,6 +403,24 @@ class AddgeneIdSource(RepositoryIdSourceWithSequenceFileUrl):
     repository_name: str = "addgene"
 
 
+class BenchlingUrlSource(RepositoryIdSource):
+    TARGET_MODEL: ClassVar[Type[_BenchlingUrlSource]] = _BenchlingUrlSource
+
+    repository_name: str = "benchling"
+
+
+class SnapGenePlasmidSource(RepositoryIdSource):
+    TARGET_MODEL: ClassVar[Type[_SnapGenePlasmidSource]] = _SnapGenePlasmidSource
+
+    repository_name: str = "snapgene"
+
+
+class EuroscarfSource(RepositoryIdSource):
+    TARGET_MODEL: ClassVar[Type[_EuroscarfSource]] = _EuroscarfSource
+
+    repository_name: str = "euroscarf"
+
+
 class WekWikGeneIdSource(RepositoryIdSourceWithSequenceFileUrl):
     TARGET_MODEL: ClassVar[Type[_WekWikGeneIdSource]] = _WekWikGeneIdSource
     repository_name: str = "wekwikgene"
@@ -400,6 +441,18 @@ class OpenDNACollectionsSource(RepositoryIdSourceWithSequenceFileUrl):
     repository_name: str = "open_dna_collections"
 
 
+class GenomeCoordinatesSource(Source):
+    TARGET_MODEL: ClassVar[Type[_GenomeCoordinatesSource]] = _GenomeCoordinatesSource
+
+    assembly_accession: Optional[str] = None
+    sequence_accession: str
+    locus_tag: Optional[str] = None
+    gene_id: Optional[int] = None
+    start: int
+    end: int
+    strand: int
+
+
 class RestrictionAndLigationSource(AssemblySource):
     restriction_enzymes: list[AbstractCut]
 
@@ -512,6 +565,32 @@ def has_enzyme(edge):
         return has_enzyme(self.left_edge) or has_enzyme(self.right_edge)
 
 
+class OligoHybridizationSource(Source):
+    TARGET_MODEL: ClassVar[Type[_OligoHybridizationSource]] = _OligoHybridizationSource
+
+    overhang_crick_3prime: Optional[int] = None
+
+
+class PolymeraseExtensionSource(Source):
+    TARGET_MODEL: ClassVar[Type[_PolymeraseExtensionSource]] = (
+        _PolymeraseExtensionSource
+    )
+
+
+class AnnotationSource(Source):
+    TARGET_MODEL: ClassVar[Type[_AnnotationSource]] = _AnnotationSource
+
+    annotation_tool: AnnotationTool
+    annotation_tool_version: Optional[str] = None
+    annotation_report: Optional[
+        list[_AnnotationReport | _PlannotateAnnotationReport]
+    ] = None
+
+
+class ReverseComplementSource(Source):
+    TARGET_MODEL: ClassVar[Type[_ReverseComplementSource]] = _ReverseComplementSource
+
+
 class CloningStrategy(_BaseCloningStrategy):
 
     # For now, we don't add anything, but the classes will not have the new

From 242bc4daeb203e15cf31c2506b709776c2d3b43d Mon Sep 17 00:00:00 2001
From: Manuel Lera-Ramirez <manulera14@gmail.com>
Date: Tue, 25 Nov 2025 18:07:57 +0000
Subject: [PATCH 14/22] add and test oligonucleotide hybridization

---
 src/pydna/oligonucleotide_hybridization.py | 124 +++++++++++++++++++++
 tests/test_module_opencloning_models.py    |  23 ++++
 2 files changed, 147 insertions(+)
 create mode 100644 src/pydna/oligonucleotide_hybridization.py

diff --git a/src/pydna/oligonucleotide_hybridization.py b/src/pydna/oligonucleotide_hybridization.py
new file mode 100644
index 00000000..d7a8db8f
--- /dev/null
+++ b/src/pydna/oligonucleotide_hybridization.py
@@ -0,0 +1,124 @@
+# -*- coding: utf-8 -*-
+"""
+This module contains the functions for oligonucleotide hybridization.
+"""
+
+from pydna.common_sub_strings import common_sub_strings
+from Bio.Seq import reverse_complement
+from pydna.primer import Primer
+from pydna.dseqrecord import Dseqrecord
+from pydna.dseq import Dseq
+from pydna.opencloning_models import OligoHybridizationSource, SourceInput
+
+
+def oligonucleotide_hybridization_overhangs(
+    fwd_oligo_seq: str, rvs_oligo_seq: str, minimal_annealing: int
+) -> list[int]:
+    """
+    Returns possible overhangs between two oligos given a minimal annealing length, and
+    returns an error if mismatches are found.
+
+    see https://github.com/manulera/OpenCloning_backend/issues/302 for notation
+
+    >>> from pydna.oligonucleotide_hybridization import oligonucleotide_hybridization_overhangs
+    >>> oligonucleotide_hybridization_overhangs("ATGGC", "GCCAT", 3)
+    [0]
+    >>> oligonucleotide_hybridization_overhangs("aATGGC", "GCCAT", 5)
+    [-1]
+    >>> oligonucleotide_hybridization_overhangs("ATGGC", "GCCATa", 5)
+    [1]
+    >>> oligonucleotide_hybridization_overhangs("ATGGC", "GCCATaaGCCAT", 5)
+    [0, 7]
+
+    If the minimal annealing length is longer than the length of the shortest oligo, it returns an empty list.
+
+    >>> oligonucleotide_hybridization_overhangs("ATGGC", "GCCATaaGCCAT", 100)
+    []
+
+    If it's possible to anneal for ``minimal_annealing`` length, but with mismatches, it raises an error.
+
+    >>> oligonucleotide_hybridization_overhangs("cATGGC", "GCCATa", 5)
+    Traceback (most recent call last):
+        ...
+    ValueError: The oligonucleotides can anneal with mismatches
+    """
+    matches = common_sub_strings(
+        fwd_oligo_seq.lower(),
+        reverse_complement(rvs_oligo_seq.lower()),
+        minimal_annealing,
+    )
+
+    for pos_fwd, pos_rvs, length in matches:
+
+        if (pos_fwd != 0 and pos_rvs != 0) or (
+            pos_fwd + length < len(fwd_oligo_seq)
+            and pos_rvs + length < len(rvs_oligo_seq)
+        ):
+            raise ValueError("The oligonucleotides can anneal with mismatches")
+
+    # Return possible overhangs
+    return [pos_rvs - pos_fwd for pos_fwd, pos_rvs, length in matches]
+
+
+def oligonucleotide_hybridization(
+    fwd_primer: Primer, rvs_primer: Primer, minimal_annealing: int
+) -> list[Dseqrecord]:
+    """
+    Returns a list of Dseqrecord objects representing the hybridization of two primers.
+
+    >>> from pydna.primer import Primer
+    >>> from pydna.oligonucleotide_hybridization import oligonucleotide_hybridization
+    >>> fwd_primer = Primer("ATGGC")
+    >>> rvs_primer = Primer("GCCA")
+    >>> oligonucleotide_hybridization(fwd_primer, rvs_primer, 3)[0].seq
+    Dseq(-5)
+    ATGGC
+     ACCG
+
+    Multiple values can be returned:
+
+    >>> rvs_primer2 = Primer("GCCATaaGCCAT")
+    >>> oligonucleotide_hybridization(fwd_primer, rvs_primer2, 3)[0].seq
+    Dseq(-12)
+    ATGGC
+    TACCGaaTACCG
+    >>> oligonucleotide_hybridization(fwd_primer, rvs_primer2, 3)[1].seq
+    Dseq(-12)
+           ATGGC
+    TACCGaaTACCG
+
+    If no possible overhangs are found, it returns an empty list.
+
+    >>> oligonucleotide_hybridization(fwd_primer, rvs_primer, 100)
+    []
+
+    If there are mismatches given the minimal annealing length, it raises an error.
+
+    >>> fwd_primer3 = Primer("cATGGC")
+    >>> rvs_primer3 = Primer("GCCATa")
+    >>> oligonucleotide_hybridization(fwd_primer3, rvs_primer3, 5)
+    Traceback (most recent call last):
+        ...
+    ValueError: The oligonucleotides can anneal with mismatches
+    """
+    possible_overhangs = oligonucleotide_hybridization_overhangs(
+        str(fwd_primer.seq), str(rvs_primer.seq), minimal_annealing
+    )
+    sources = [
+        OligoHybridizationSource(
+            overhang_crick_3prime=pos,
+            input=[SourceInput(sequence=fwd_primer), SourceInput(sequence=rvs_primer)],
+        )
+        for pos in possible_overhangs
+    ]
+    return [
+        Dseqrecord(
+            Dseq(
+                str(fwd_primer.seq),
+                str(rvs_primer.seq),
+                ovhg=source.overhang_crick_3prime,
+            ),
+            source=source,
+        )
+        for source in sources
+    ]
diff --git a/tests/test_module_opencloning_models.py b/tests/test_module_opencloning_models.py
index 8e61b35b..93dec8be 100644
--- a/tests/test_module_opencloning_models.py
+++ b/tests/test_module_opencloning_models.py
@@ -16,6 +16,7 @@
     get_id,
 )
 from pydna.primer import Primer
+from pydna.oligonucleotide_hybridization import oligonucleotide_hybridization
 from opencloning_linkml.datamodel import (
     AssemblySource as _AssemblySource,
     AssemblyFragment as _AssemblyFragment,
@@ -136,6 +137,17 @@ def get_next_id(self):
 product_gateway_BP, *_ = gateway_assembly([seq1, seq2], "BP")
 product_gateway_BP.name = "product_gateway_BP"
 
+## Oligo hybridization
+
+fwd_primer = Primer("ATGGC", name="fwd_primer")
+rvs_primer = Primer("GCCAT", name="rvs_primer")
+product_oligo_hybridization, *rest = oligonucleotide_hybridization(
+    fwd_primer, rvs_primer, 3
+)
+
+product_oligo_hybridization.name = "product_oligo_hybridization"
+
+
 # ========================================================================================
 
 
@@ -329,6 +341,17 @@ def test_history_string(self):
             """
             ).strip(),
         )
+        self.assertEqual(
+            product_oligo_hybridization.history(),
+            textwrap.dedent(
+                """
+            ╙── product_oligo_hybridization (Dseqrecord(-5))
+                └─╼ OligoHybridizationSource
+                    ├─╼ fwd_primer (id 5-mer:5'-ATGGC-3')
+                    └─╼ rvs_primer (id 5-mer:5'-GCCAT-3')
+            """
+            ).strip(),
+        )
 
 
 class AssemblySourceTest(TestCase):

From 2dfd70372f1a3d188b92cb2a880c3717adbc24bb Mon Sep 17 00:00:00 2001
From: Manuel Lera-Ramirez <manulera14@gmail.com>
Date: Tue, 25 Nov 2025 18:19:20 +0000
Subject: [PATCH 15/22] update to latest model version

---
 poetry.lock | 221 ++++++++++++++--------------------------------------
 1 file changed, 57 insertions(+), 164 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 9e845f25..3b051b79 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 2.0.1 and should not be changed by hand.
+# This file is automatically @generated by Poetry 2.1.3 and should not be changed by hand.
 
 [[package]]
 name = "accessible-pygments"
@@ -7,7 +7,6 @@ description = "A collection of accessible pygments styles"
 optional = false
 python-versions = ">=3.9"
 groups = ["docs"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "accessible_pygments-0.0.5-py3-none-any.whl", hash = "sha256:88ae3211e68a1d0b011504b2ffc1691feafce124b845bd072ab6f9f66f34d4b7"},
     {file = "accessible_pygments-0.0.5.tar.gz", hash = "sha256:40918d3e6a2b619ad424cb91e556bd3bd8865443d9f22f1dcdf79e33c8046872"},
@@ -27,7 +26,6 @@ description = "A light, configurable Sphinx theme"
 optional = false
 python-versions = ">=3.10"
 groups = ["docs"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "alabaster-1.0.0-py3-none-any.whl", hash = "sha256:fc6786402dc3fcb2de3cabd5fe455a2db534b371124f1f21de8731783dec828b"},
     {file = "alabaster-1.0.0.tar.gz", hash = "sha256:c00dca57bca26fa62a6d7d0a9fcce65f3e026e9bfe33e9c538fd3fbb2144fd9e"},
@@ -40,7 +38,6 @@ description = "Reusable constraint types to use with typing.Annotated"
 optional = false
 python-versions = ">=3.8"
 groups = ["main"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "annotated_types-0.7.0-py3-none-any.whl", hash = "sha256:1f02e8b43a8fbbc3f3e0d4f0f4bfc8131bcb4eebe8849b8e5c773f3a1c582a53"},
     {file = "annotated_types-0.7.0.tar.gz", hash = "sha256:aff07c09a53a08bc8cfccb9c85b05f1aa9a2a6f23728d790723543408344ce89"},
@@ -53,7 +50,6 @@ description = "A small Python module for determining appropriate platform-specif
 optional = false
 python-versions = "*"
 groups = ["main"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "appdirs-1.4.4-py2.py3-none-any.whl", hash = "sha256:a841dacd6b99318a741b166adb07e19ee71a274450e68237b4650ca1055ab128"},
     {file = "appdirs-1.4.4.tar.gz", hash = "sha256:7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41"},
@@ -66,7 +62,7 @@ description = "Disable App Nap on macOS >= 10.9"
 optional = false
 python-versions = ">=3.6"
 groups = ["docs", "test"]
-markers = "(python_version <= \"3.11\" or python_version >= \"3.12\") and platform_system == \"Darwin\""
+markers = "platform_system == \"Darwin\""
 files = [
     {file = "appnope-0.1.4-py2.py3-none-any.whl", hash = "sha256:502575ee11cd7a28c0205f379b525beefebab9d161b7c964670864014ed7213c"},
     {file = "appnope-0.1.4.tar.gz", hash = "sha256:1de3860566df9caf38f01f86f65e0e13e379af54f9e4bee1e66b48f2efffd1ee"},
@@ -79,7 +75,6 @@ description = "Annotate AST trees with source code positions"
 optional = false
 python-versions = ">=3.8"
 groups = ["docs", "test"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "asttokens-3.0.0-py3-none-any.whl", hash = "sha256:e3078351a059199dd5138cb1c706e6430c05eff2ff136af5eb4790f9d28932e2"},
     {file = "asttokens-3.0.0.tar.gz", hash = "sha256:0dcd8baa8d62b0c1d118b399b2ddba3c4aff271d0d7a9e0d4c1681c79035bbc7"},
@@ -96,7 +91,6 @@ description = "Classes Without Boilerplate"
 optional = false
 python-versions = ">=3.9"
 groups = ["dev", "docs", "test"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "attrs-25.4.0-py3-none-any.whl", hash = "sha256:adcf7e2a1fb3b36ac48d97835bb6d8ade15b8dcce26aba8bf1d14847b57a3373"},
     {file = "attrs-25.4.0.tar.gz", hash = "sha256:16d5969b87f0859ef33a48b35d55ac1be6e42ae49d5e853b597db70c35c57e11"},
@@ -109,7 +103,6 @@ description = "A tool that automatically formats Python code to conform to the P
 optional = false
 python-versions = ">=3.9"
 groups = ["dev"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "autopep8-2.3.2-py2.py3-none-any.whl", hash = "sha256:ce8ad498672c845a0c3de2629c15b635ec2b05ef8177a6e7c91c74f3e9b51128"},
     {file = "autopep8-2.3.2.tar.gz", hash = "sha256:89440a4f969197b69a995e4ce0661b031f455a9f776d2c5ba3dbd83466931758"},
@@ -126,14 +119,13 @@ description = "Internationalization utilities"
 optional = false
 python-versions = ">=3.8"
 groups = ["docs"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "babel-2.17.0-py3-none-any.whl", hash = "sha256:4d0b53093fdfb4b21c92b5213dba5a1b23885afa8383709427046b21c366e5f2"},
     {file = "babel-2.17.0.tar.gz", hash = "sha256:0c54cffb19f690cdcc52a3b50bcbf71e07a808d1c80d549f2459b9d2cf0afb9d"},
 ]
 
 [package.extras]
-dev = ["backports.zoneinfo", "freezegun (>=1.0,<2.0)", "jinja2 (>=3.0)", "pytest (>=6.0)", "pytest-cov", "pytz", "setuptools", "tzdata"]
+dev = ["backports.zoneinfo ; python_version < \"3.9\"", "freezegun (>=1.0,<2.0)", "jinja2 (>=3.0)", "pytest (>=6.0)", "pytest-cov", "pytz", "setuptools", "tzdata ; sys_platform == \"win32\""]
 
 [[package]]
 name = "beautifulsoup4"
@@ -142,7 +134,6 @@ description = "Screen-scraping library"
 optional = false
 python-versions = ">=3.7.0"
 groups = ["docs"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "beautifulsoup4-4.14.2-py3-none-any.whl", hash = "sha256:5ef6fa3a8cbece8488d66985560f97ed091e22bbc4e9c2338508a9d5de6d4515"},
     {file = "beautifulsoup4-4.14.2.tar.gz", hash = "sha256:2a98ab9f944a11acee9cc848508ec28d9228abfd522ef0fad6a02a72e0ded69e"},
@@ -166,7 +157,6 @@ description = "Freely available tools for computational molecular biology."
 optional = false
 python-versions = ">=3.9"
 groups = ["main"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "biopython-1.85-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:a6308053a61f3bdbb11504ece4cf24e264c6f1d6fad278f7e59e6b84b0d9a7b4"},
     {file = "biopython-1.85-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:434dd23e972b0c89e128f2ebbd16b38075d609184f4f1fd16368035f923019c2"},
@@ -212,7 +202,6 @@ description = "The uncompromising code formatter."
 optional = false
 python-versions = ">=3.9"
 groups = ["dev"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "black-25.9.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:ce41ed2614b706fd55fd0b4a6909d06b5bab344ffbfadc6ef34ae50adba3d4f7"},
     {file = "black-25.9.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:2ab0ce111ef026790e9b13bd216fa7bc48edd934ffc4cbf78808b235793cbc92"},
@@ -261,7 +250,7 @@ description = "Python implementation of codon adaptation index"
 optional = true
 python-versions = ">=3.8"
 groups = ["main"]
-markers = "(python_version <= \"3.11\" or python_version >= \"3.12\") and extra == \"express\""
+markers = "extra == \"express\""
 files = [
     {file = "cai2-1.0.5-py3-none-any.whl", hash = "sha256:1a9b30b7006defa868e9aabbc1b0ab2e53bc466c3f5b15c41228ba7853babf5f"},
     {file = "cai2-1.0.5.tar.gz", hash = "sha256:44cd23f4939f29b48b72f7c9d882f0c4b41f500a528f82a585c1425011398bbd"},
@@ -283,7 +272,7 @@ files = [
     {file = "certifi-2025.10.5-py3-none-any.whl", hash = "sha256:0f212c2744a9bb6de0c56639a6f68afe01ecd92d91f14ae897c4fe7bbeeef0de"},
     {file = "certifi-2025.10.5.tar.gz", hash = "sha256:47c09d31ccf2acf0be3f701ea53595ee7e0b8fa08801c6624be771df09ae7b43"},
 ]
-markers = {main = "(python_version <= \"3.11\" or python_version >= \"3.12\") and extra == \"download\"", docs = "python_version <= \"3.11\" or python_version >= \"3.12\"", test = "python_version <= \"3.11\" or python_version >= \"3.12\""}
+markers = {main = "extra == \"download\""}
 
 [[package]]
 name = "cffi"
@@ -292,7 +281,7 @@ description = "Foreign Function Interface for Python calling C code."
 optional = false
 python-versions = ">=3.9"
 groups = ["docs", "test"]
-markers = "(python_version <= \"3.11\" or python_version >= \"3.12\") and implementation_name == \"pypy\""
+markers = "implementation_name == \"pypy\""
 files = [
     {file = "cffi-2.0.0-cp310-cp310-macosx_10_13_x86_64.whl", hash = "sha256:0cf2d91ecc3fcc0625c2c530fe004f82c110405f101548512cce44322fa8ac44"},
     {file = "cffi-2.0.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:f73b96c41e3b2adedc34a7356e64c8eb96e03a3782b535e043a986276ce12a49"},
@@ -390,7 +379,6 @@ description = "Validate configuration and produce human readable error messages.
 optional = false
 python-versions = ">=3.8"
 groups = ["dev"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "cfgv-3.4.0-py2.py3-none-any.whl", hash = "sha256:b7265b1f29fd3316bfcd2b330d63d024f2bfd8bcb8b0272f8e19a504856c48f9"},
     {file = "cfgv-3.4.0.tar.gz", hash = "sha256:e52591d4c5f5dead8e0f673fb16db7949d2cfb3f7da4582893288f0ded8fe560"},
@@ -518,7 +506,7 @@ files = [
     {file = "charset_normalizer-3.4.4-py3-none-any.whl", hash = "sha256:7a32c560861a02ff789ad905a2fe94e3f840803362c84fecf1851cb4cf3dc37f"},
     {file = "charset_normalizer-3.4.4.tar.gz", hash = "sha256:94537985111c35f28720e43603b8e7b43a6ecfb2ce1d3058bbe955b73404e21a"},
 ]
-markers = {main = "(python_version <= \"3.11\" or python_version >= \"3.12\") and extra == \"download\"", docs = "python_version <= \"3.11\" or python_version >= \"3.12\"", test = "python_version <= \"3.11\" or python_version >= \"3.12\""}
+markers = {main = "extra == \"download\""}
 
 [[package]]
 name = "click"
@@ -531,7 +519,7 @@ files = [
     {file = "click-8.3.0-py3-none-any.whl", hash = "sha256:9b9f285302c6e3064f4330c05f05b81945b2a39544279343e6e7c5f27a9baddc"},
     {file = "click-8.3.0.tar.gz", hash = "sha256:e7b8232224eba16f4ebe410c25ced9f7875cb5f3263ffc93cc3e8da705e229c4"},
 ]
-markers = {main = "(python_version <= \"3.11\" or python_version >= \"3.12\") and extra == \"express\"", dev = "python_version <= \"3.11\" or python_version >= \"3.12\"", docs = "python_version <= \"3.11\" or python_version >= \"3.12\""}
+markers = {main = "extra == \"express\""}
 
 [package.dependencies]
 colorama = {version = "*", markers = "platform_system == \"Windows\""}
@@ -547,7 +535,7 @@ files = [
     {file = "colorama-0.4.6-py2.py3-none-any.whl", hash = "sha256:4f1d9991f5acc0ca119f9d443620b77f9d6b33703e51011c16baf57afb285fc6"},
     {file = "colorama-0.4.6.tar.gz", hash = "sha256:08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44"},
 ]
-markers = {main = "extra == \"express\" and platform_system == \"Windows\" and (python_version <= \"3.11\" or python_version >= \"3.12\")", dev = "(python_version <= \"3.11\" or python_version >= \"3.12\") and platform_system == \"Windows\"", docs = "(platform_system == \"Windows\" or sys_platform == \"win32\") and (python_version <= \"3.11\" or python_version >= \"3.12\")", test = "(python_version <= \"3.11\" or python_version >= \"3.12\") and sys_platform == \"win32\""}
+markers = {main = "platform_system == \"Windows\" and extra == \"express\"", dev = "platform_system == \"Windows\"", docs = "platform_system == \"Windows\" or sys_platform == \"win32\"", test = "sys_platform == \"win32\""}
 
 [[package]]
 name = "comm"
@@ -556,7 +544,6 @@ description = "Jupyter Python Comm implementation, for usage in ipykernel, xeus-
 optional = false
 python-versions = ">=3.8"
 groups = ["docs", "test"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "comm-0.2.3-py3-none-any.whl", hash = "sha256:c615d91d75f7f04f095b30d1c1711babd43bdc6419c1be9886a85f2f4e489417"},
     {file = "comm-0.2.3.tar.gz", hash = "sha256:2dc8048c10962d55d7ad693be1e7045d891b7ce8d999c97963a5e3e99c055971"},
@@ -572,7 +559,7 @@ description = "Python library for calculating contours of 2D quadrilateral grids
 optional = true
 python-versions = ">=3.10"
 groups = ["main"]
-markers = "(python_version <= \"3.11\" or python_version >= \"3.12\") and extra == \"gel\""
+markers = "extra == \"gel\""
 files = [
     {file = "contourpy-1.3.2-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:ba38e3f9f330af820c4b27ceb4b9c7feee5fe0493ea53a8720f4792667465934"},
     {file = "contourpy-1.3.2-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:dc41ba0714aa2968d1f8674ec97504a8f7e334f48eeacebcaa6256213acb0989"},
@@ -650,7 +637,6 @@ description = "Code coverage measurement for Python"
 optional = false
 python-versions = ">=3.10"
 groups = ["test"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "coverage-7.11.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:eb53f1e8adeeb2e78962bade0c08bfdc461853c7969706ed901821e009b35e31"},
     {file = "coverage-7.11.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:d9a03ec6cb9f40a5c360f138b88266fd8f58408d71e89f536b4f91d85721d075"},
@@ -750,7 +736,7 @@ files = [
 tomli = {version = "*", optional = true, markers = "python_full_version <= \"3.11.0a6\" and extra == \"toml\""}
 
 [package.extras]
-toml = ["tomli"]
+toml = ["tomli ; python_full_version <= \"3.11.0a6\""]
 
 [[package]]
 name = "cycler"
@@ -759,7 +745,7 @@ description = "Composable style cycles"
 optional = true
 python-versions = ">=3.8"
 groups = ["main"]
-markers = "(python_version <= \"3.11\" or python_version >= \"3.12\") and extra == \"gel\""
+markers = "extra == \"gel\""
 files = [
     {file = "cycler-0.12.1-py3-none-any.whl", hash = "sha256:85cef7cff222d8644161529808465972e51340599459b8ac3ccbac5a854e0d30"},
     {file = "cycler-0.12.1.tar.gz", hash = "sha256:88bb128f02ba341da8ef447245a9e138fae777f6a23943da4540077d3601eb1c"},
@@ -776,7 +762,6 @@ description = "An implementation of the Debug Adapter Protocol for Python"
 optional = false
 python-versions = ">=3.8"
 groups = ["docs", "test"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "debugpy-1.8.17-cp310-cp310-macosx_15_0_x86_64.whl", hash = "sha256:c41d2ce8bbaddcc0009cc73f65318eedfa3dbc88a8298081deb05389f1ab5542"},
     {file = "debugpy-1.8.17-cp310-cp310-manylinux_2_34_x86_64.whl", hash = "sha256:1440fd514e1b815edd5861ca394786f90eb24960eb26d6f7200994333b1d79e3"},
@@ -817,7 +802,6 @@ description = "Decorators for Humans"
 optional = false
 python-versions = ">=3.8"
 groups = ["docs", "test"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "decorator-5.2.1-py3-none-any.whl", hash = "sha256:d316bb415a2d9e2d2b3abcc4084c6502fc09240e292cd76a76afc106a1c8e04a"},
     {file = "decorator-5.2.1.tar.gz", hash = "sha256:65f266143752f734b0a7cc83c46f4618af75b8c5911b00ccb61d0ac9b6da0360"},
@@ -830,7 +814,6 @@ description = "Distribution utilities"
 optional = false
 python-versions = "*"
 groups = ["dev"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "distlib-0.4.0-py2.py3-none-any.whl", hash = "sha256:9659f7d87e46584a30b5780e43ac7a2143098441670ff0a49d5f9034c54a6c16"},
     {file = "distlib-0.4.0.tar.gz", hash = "sha256:feec40075be03a04501a973d81f633735b4b69f98b05450592310c0f401a4e0d"},
@@ -843,7 +826,6 @@ description = "Docutils -- Python Documentation Utilities"
 optional = false
 python-versions = ">=3.9"
 groups = ["docs"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "docutils-0.21.2-py3-none-any.whl", hash = "sha256:dafca5b9e384f0e419294eb4d2ff9fa826435bf15f15b7bd45723e8ad76811b2"},
     {file = "docutils-0.21.2.tar.gz", hash = "sha256:3a6b18732edf182daa3cd12775bbb338cf5691468f91eeeb109deff6ebfa986f"},
@@ -856,7 +838,7 @@ description = "Backport of PEP 654 (exception groups)"
 optional = false
 python-versions = ">=3.7"
 groups = ["docs", "test"]
-markers = "python_version < \"3.11\""
+markers = "python_version == \"3.10\""
 files = [
     {file = "exceptiongroup-1.3.0-py3-none-any.whl", hash = "sha256:4d111e6e0c13d0644cad6ddaa7ed0261a0b36971f6d23e7ec9b4b9097da78a10"},
     {file = "exceptiongroup-1.3.0.tar.gz", hash = "sha256:b241f5885f560bc56a59ee63ca4c6a8bfa46ae4ad651af316d4e81817bb9fd88"},
@@ -875,14 +857,13 @@ description = "Get the currently executing AST node of a frame, and other inform
 optional = false
 python-versions = ">=3.8"
 groups = ["docs", "test"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "executing-2.2.1-py2.py3-none-any.whl", hash = "sha256:760643d3452b4d777d295bb167ccc74c64a81df23fb5e08eff250c425a4b2017"},
     {file = "executing-2.2.1.tar.gz", hash = "sha256:3632cc370565f6648cc328b32435bd120a1e4ebb20c77e3fdde9a13cd1e533c4"},
 ]
 
 [package.extras]
-tests = ["asttokens (>=2.1.0)", "coverage", "coverage-enable-subprocess", "ipython", "littleutils", "pytest", "rich"]
+tests = ["asttokens (>=2.1.0)", "coverage", "coverage-enable-subprocess", "ipython", "littleutils", "pytest", "rich ; python_version >= \"3.11\""]
 
 [[package]]
 name = "fastjsonschema"
@@ -891,7 +872,6 @@ description = "Fastest Python implementation of JSON schema"
 optional = false
 python-versions = "*"
 groups = ["dev", "docs", "test"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "fastjsonschema-2.21.2-py3-none-any.whl", hash = "sha256:1c797122d0a86c5cace2e54bf4e819c36223b552017172f32c5c024a6b77e463"},
     {file = "fastjsonschema-2.21.2.tar.gz", hash = "sha256:b1eb43748041c880796cd077f1a07c3d94e93ae84bba5ed36800a33554ae05de"},
@@ -907,7 +887,6 @@ description = "A platform independent file lock."
 optional = false
 python-versions = ">=3.10"
 groups = ["dev"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "filelock-3.20.0-py3-none-any.whl", hash = "sha256:339b4732ffda5cd79b13f4e2711a31b0365ce445d95d243bb996273d072546a2"},
     {file = "filelock-3.20.0.tar.gz", hash = "sha256:711e943b4ec6be42e1d4e6690b48dc175c822967466bb31c0c293f34334c13f4"},
@@ -920,7 +899,6 @@ description = "the modular source code checker: pep8 pyflakes and co"
 optional = false
 python-versions = ">=3.9"
 groups = ["dev"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "flake8-7.3.0-py2.py3-none-any.whl", hash = "sha256:b9696257b9ce8beb888cdbe31cf885c90d31928fe202be0889a7cdafad32f01e"},
     {file = "flake8-7.3.0.tar.gz", hash = "sha256:fe044858146b9fc69b551a4b490d69cf960fcb78ad1edcb84e7fbb1b4a8e3872"},
@@ -938,7 +916,6 @@ description = "A plugin for flake8 finding likely bugs and design problems in yo
 optional = false
 python-versions = ">=3.8.1"
 groups = ["dev"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "flake8_bugbear-24.12.12-py3-none-any.whl", hash = "sha256:1b6967436f65ca22a42e5373aaa6f2d87966ade9aa38d4baf2a1be550767545e"},
     {file = "flake8_bugbear-24.12.12.tar.gz", hash = "sha256:46273cef0a6b6ff48ca2d69e472f41420a42a46e24b2a8972e4f0d6733d12a64"},
@@ -958,7 +935,7 @@ description = "Tools to manipulate font files"
 optional = true
 python-versions = ">=3.9"
 groups = ["main"]
-markers = "(python_version <= \"3.11\" or python_version >= \"3.12\") and extra == \"gel\""
+markers = "extra == \"gel\""
 files = [
     {file = "fonttools-4.60.1-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:9a52f254ce051e196b8fe2af4634c2d2f02c981756c6464dc192f1b6050b4e28"},
     {file = "fonttools-4.60.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:c7420a2696a44650120cdd269a5d2e56a477e2bfa9d95e86229059beb1c19e15"},
@@ -1021,17 +998,17 @@ files = [
 ]
 
 [package.extras]
-all = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "lxml (>=4.0)", "lz4 (>=1.7.4.2)", "matplotlib", "munkres", "pycairo", "scipy", "skia-pathops (>=0.5.0)", "sympy", "uharfbuzz (>=0.23.0)", "unicodedata2 (>=15.1.0)", "xattr", "zopfli (>=0.1.4)"]
+all = ["brotli (>=1.0.1) ; platform_python_implementation == \"CPython\"", "brotlicffi (>=0.8.0) ; platform_python_implementation != \"CPython\"", "lxml (>=4.0)", "lz4 (>=1.7.4.2)", "matplotlib", "munkres ; platform_python_implementation == \"PyPy\"", "pycairo", "scipy ; platform_python_implementation != \"PyPy\"", "skia-pathops (>=0.5.0)", "sympy", "uharfbuzz (>=0.23.0)", "unicodedata2 (>=15.1.0) ; python_version <= \"3.12\"", "xattr ; sys_platform == \"darwin\"", "zopfli (>=0.1.4)"]
 graphite = ["lz4 (>=1.7.4.2)"]
-interpolatable = ["munkres", "pycairo", "scipy"]
+interpolatable = ["munkres ; platform_python_implementation == \"PyPy\"", "pycairo", "scipy ; platform_python_implementation != \"PyPy\""]
 lxml = ["lxml (>=4.0)"]
 pathops = ["skia-pathops (>=0.5.0)"]
 plot = ["matplotlib"]
 repacker = ["uharfbuzz (>=0.23.0)"]
 symfont = ["sympy"]
-type1 = ["xattr"]
-unicode = ["unicodedata2 (>=15.1.0)"]
-woff = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "zopfli (>=0.1.4)"]
+type1 = ["xattr ; sys_platform == \"darwin\""]
+unicode = ["unicodedata2 (>=15.1.0) ; python_version <= \"3.12\""]
+woff = ["brotli (>=1.0.1) ; platform_python_implementation == \"CPython\"", "brotlicffi (>=0.8.0) ; platform_python_implementation != \"CPython\"", "zopfli (>=0.1.4)"]
 
 [[package]]
 name = "gprof2dot"
@@ -1040,7 +1017,6 @@ description = "Generate a dot graph from the output of several profilers."
 optional = false
 python-versions = ">=3.8"
 groups = ["test"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "gprof2dot-2025.4.14-py3-none-any.whl", hash = "sha256:0742e4c0b4409a5e8777e739388a11e1ed3750be86895655312ea7c20bd0090e"},
     {file = "gprof2dot-2025.4.14.tar.gz", hash = "sha256:35743e2d2ca027bf48fa7cba37021aaf4a27beeae1ae8e05a50b55f1f921a6ce"},
@@ -1053,7 +1029,7 @@ description = "Lightweight in-process concurrent programming"
 optional = false
 python-versions = ">=3.9"
 groups = ["docs"]
-markers = "(python_version <= \"3.11\" or python_version >= \"3.12\") and (platform_machine == \"aarch64\" or platform_machine == \"ppc64le\" or platform_machine == \"x86_64\" or platform_machine == \"amd64\" or platform_machine == \"AMD64\" or platform_machine == \"win32\" or platform_machine == \"WIN32\")"
+markers = "platform_machine == \"aarch64\" or platform_machine == \"ppc64le\" or platform_machine == \"x86_64\" or platform_machine == \"amd64\" or platform_machine == \"AMD64\" or platform_machine == \"win32\" or platform_machine == \"WIN32\""
 files = [
     {file = "greenlet-3.2.4-cp310-cp310-macosx_11_0_universal2.whl", hash = "sha256:8c68325b0d0acf8d91dde4e6f930967dd52a5302cd4062932a6b2e7c2969f47c"},
     {file = "greenlet-3.2.4-cp310-cp310-manylinux2014_aarch64.manylinux_2_17_aarch64.whl", hash = "sha256:94385f101946790ae13da500603491f04a76b6e4c059dab271b3ce2e283b2590"},
@@ -1122,7 +1098,6 @@ description = "File identification library for Python"
 optional = false
 python-versions = ">=3.9"
 groups = ["dev"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "identify-2.6.15-py2.py3-none-any.whl", hash = "sha256:1181ef7608e00704db228516541eb83a88a9f94433a8c80bb9b5bd54b1d81757"},
     {file = "identify-2.6.15.tar.gz", hash = "sha256:e4f4864b96c6557ef2a1e1c951771838f4edc9df3a72ec7118b338801b11c7bf"},
@@ -1142,7 +1117,7 @@ files = [
     {file = "idna-3.11-py3-none-any.whl", hash = "sha256:771a87f49d9defaf64091e6e6fe9c18d4833f140bd19464795bc32d966ca37ea"},
     {file = "idna-3.11.tar.gz", hash = "sha256:795dafcc9c04ed0c1fb032c2aa73654d8e8c5023a7df64a53f39190ada629902"},
 ]
-markers = {main = "(python_version <= \"3.11\" or python_version >= \"3.12\") and extra == \"download\"", docs = "python_version <= \"3.11\" or python_version >= \"3.12\"", test = "python_version <= \"3.11\" or python_version >= \"3.12\""}
+markers = {main = "extra == \"download\""}
 
 [package.extras]
 all = ["flake8 (>=7.1.1)", "mypy (>=1.11.2)", "pytest (>=8.3.2)", "ruff (>=0.6.2)"]
@@ -1154,7 +1129,6 @@ description = "Getting image size from png/jpeg/jpeg2000/gif file"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 groups = ["docs"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "imagesize-1.4.1-py2.py3-none-any.whl", hash = "sha256:0d8d18d08f840c19d0ee7ca1fd82490fdc3729b7ac93f49870406ddde8ef8d8b"},
     {file = "imagesize-1.4.1.tar.gz", hash = "sha256:69150444affb9cb0d5cc5a92b3676f0b2fb7cd9ae39e947a5e11a36b4497cd4a"},
@@ -1167,7 +1141,6 @@ description = "Read metadata from Python packages"
 optional = false
 python-versions = ">=3.9"
 groups = ["docs"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "importlib_metadata-8.7.0-py3-none-any.whl", hash = "sha256:e5dd1551894c77868a30651cef00984d50e1002d06942a7101d34870c5f02afd"},
     {file = "importlib_metadata-8.7.0.tar.gz", hash = "sha256:d13b81ad223b890aa16c5471f2ac3056cf76c5f10f82d6f9292f0b415f389000"},
@@ -1177,12 +1150,12 @@ files = [
 zipp = ">=3.20"
 
 [package.extras]
-check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"]
+check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1) ; sys_platform != \"cygwin\""]
 cover = ["pytest-cov"]
 doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
 enabler = ["pytest-enabler (>=2.2)"]
 perf = ["ipython"]
-test = ["flufl.flake8", "importlib_resources (>=1.3)", "jaraco.test (>=5.4)", "packaging", "pyfakefs", "pytest (>=6,!=8.1.*)", "pytest-perf (>=0.9.2)"]
+test = ["flufl.flake8", "importlib_resources (>=1.3) ; python_version < \"3.9\"", "jaraco.test (>=5.4)", "packaging", "pyfakefs", "pytest (>=6,!=8.1.*)", "pytest-perf (>=0.9.2)"]
 type = ["pytest-mypy"]
 
 [[package]]
@@ -1192,7 +1165,6 @@ description = "brain-dead simple config-ini parsing"
 optional = false
 python-versions = ">=3.10"
 groups = ["test"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "iniconfig-2.3.0-py3-none-any.whl", hash = "sha256:f631c04d2c48c52b84d0d0549c99ff3859c98df65b3101406327ecc7d53fbf12"},
     {file = "iniconfig-2.3.0.tar.gz", hash = "sha256:c76315c77db068650d49c5b56314774a7804df16fee4402c1f19d6d15d8c4730"},
@@ -1205,7 +1177,6 @@ description = "IPython Kernel for Jupyter"
 optional = false
 python-versions = ">=3.10"
 groups = ["docs", "test"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "ipykernel-7.1.0-py3-none-any.whl", hash = "sha256:763b5ec6c5b7776f6a8d7ce09b267693b4e5ce75cb50ae696aaefb3c85e1ea4c"},
     {file = "ipykernel-7.1.0.tar.gz", hash = "sha256:58a3fc88533d5930c3546dc7eac66c6d288acde4f801e2001e65edc5dc9cf0db"},
@@ -1240,7 +1211,6 @@ description = "IPython: Productive Interactive Computing"
 optional = false
 python-versions = ">=3.10"
 groups = ["docs", "test"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "ipython-8.37.0-py3-none-any.whl", hash = "sha256:ed87326596b878932dbcb171e3e698845434d8c61b8d8cd474bf663041a9dcf2"},
     {file = "ipython-8.37.0.tar.gz", hash = "sha256:ca815841e1a41a1e6b73a0b08f3038af9b2252564d01fc405356d34033012216"},
@@ -1262,7 +1232,7 @@ typing_extensions = {version = ">=4.6", markers = "python_version < \"3.12\""}
 [package.extras]
 all = ["ipython[black,doc,kernel,matplotlib,nbconvert,nbformat,notebook,parallel,qtconsole]", "ipython[test,test-extra]"]
 black = ["black"]
-doc = ["docrepr", "exceptiongroup", "intersphinx_registry", "ipykernel", "ipython[test]", "matplotlib", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "sphinxcontrib-jquery", "tomli", "typing_extensions"]
+doc = ["docrepr", "exceptiongroup", "intersphinx_registry", "ipykernel", "ipython[test]", "matplotlib", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "sphinxcontrib-jquery", "tomli ; python_version < \"3.11\"", "typing_extensions"]
 kernel = ["ipykernel"]
 matplotlib = ["matplotlib"]
 nbconvert = ["nbconvert"]
@@ -1280,7 +1250,6 @@ description = "An autocompletion tool for Python that can be used for text edito
 optional = false
 python-versions = ">=3.6"
 groups = ["docs", "test"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "jedi-0.19.2-py2.py3-none-any.whl", hash = "sha256:a8ef22bde8490f57fe5c7681a3c83cb58874daf72b4784de3cce5b6ef6edb5b9"},
     {file = "jedi-0.19.2.tar.gz", hash = "sha256:4770dc3de41bde3966b02eb84fbcf557fb33cce26ad23da12c742fb50ecb11f0"},
@@ -1301,7 +1270,6 @@ description = "A very fast and expressive template engine."
 optional = false
 python-versions = ">=3.7"
 groups = ["docs"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "jinja2-3.1.6-py3-none-any.whl", hash = "sha256:85ece4451f492d0c13c5dd7c13a64681a86afae63a5f347908daf103ce6d2f67"},
     {file = "jinja2-3.1.6.tar.gz", hash = "sha256:0137fb05990d35f1275a587e9aee6d56da821fc83491a0fb838183be43f66d6d"},
@@ -1320,7 +1288,6 @@ description = "An implementation of JSON Schema validation for Python"
 optional = false
 python-versions = ">=3.9"
 groups = ["dev", "docs", "test"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "jsonschema-4.25.1-py3-none-any.whl", hash = "sha256:3fba0169e345c7175110351d456342c364814cfcf3b964ba4587f22915230a63"},
     {file = "jsonschema-4.25.1.tar.gz", hash = "sha256:e4a9655ce0da0c0b67a085847e00a3a51449e1157f4f75e9fb5aa545e122eb85"},
@@ -1343,7 +1310,6 @@ description = "The JSON Schema meta-schemas and vocabularies, exposed as a Regis
 optional = false
 python-versions = ">=3.9"
 groups = ["dev", "docs", "test"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "jsonschema_specifications-2025.9.1-py3-none-any.whl", hash = "sha256:98802fee3a11ee76ecaca44429fda8a41bff98b00a0f2838151b113f210cc6fe"},
     {file = "jsonschema_specifications-2025.9.1.tar.gz", hash = "sha256:b540987f239e745613c7a9176f3edb72b832a4ac465cf02712288397832b5e8d"},
@@ -1359,7 +1325,6 @@ description = "A defined interface for working with a cache of jupyter notebooks
 optional = false
 python-versions = ">=3.9"
 groups = ["docs"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "jupyter_cache-1.0.1-py3-none-any.whl", hash = "sha256:9c3cafd825ba7da8b5830485343091143dff903e4d8c69db9349b728b140abf6"},
     {file = "jupyter_cache-1.0.1.tar.gz", hash = "sha256:16e808eb19e3fb67a223db906e131ea6e01f03aa27f49a7214ce6a5fec186fb9"},
@@ -1388,7 +1353,6 @@ description = "Jupyter protocol implementation and client libraries"
 optional = false
 python-versions = ">=3.8"
 groups = ["docs", "test"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "jupyter_client-8.6.3-py3-none-any.whl", hash = "sha256:e8a19cc986cc45905ac3362915f410f3af85424b4c0905e94fa5f2cb08e8f23f"},
     {file = "jupyter_client-8.6.3.tar.gz", hash = "sha256:35b3a0947c4a6e9d589eb97d7d4cd5e90f910ee73101611f01283732bd6d9419"},
@@ -1403,7 +1367,7 @@ traitlets = ">=5.3"
 
 [package.extras]
 docs = ["ipykernel", "myst-parser", "pydata-sphinx-theme", "sphinx (>=4)", "sphinx-autodoc-typehints", "sphinxcontrib-github-alt", "sphinxcontrib-spelling"]
-test = ["coverage", "ipykernel (>=6.14)", "mypy", "paramiko", "pre-commit", "pytest (<8.2.0)", "pytest-cov", "pytest-jupyter[client] (>=0.4.1)", "pytest-timeout"]
+test = ["coverage", "ipykernel (>=6.14)", "mypy", "paramiko ; sys_platform == \"win32\"", "pre-commit", "pytest (<8.2.0)", "pytest-cov", "pytest-jupyter[client] (>=0.4.1)", "pytest-timeout"]
 
 [[package]]
 name = "jupyter-core"
@@ -1412,7 +1376,6 @@ description = "Jupyter core package. A base package on which Jupyter projects re
 optional = false
 python-versions = ">=3.10"
 groups = ["dev", "docs", "test"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "jupyter_core-5.9.1-py3-none-any.whl", hash = "sha256:ebf87fdc6073d142e114c72c9e29a9d7ca03fad818c5d300ce2adc1fb0743407"},
     {file = "jupyter_core-5.9.1.tar.gz", hash = "sha256:4d09aaff303b9566c3ce657f580bd089ff5c91f5f89cf7d8846c3cdf465b5508"},
@@ -1433,7 +1396,7 @@ description = "A fast implementation of the Cassowary constraint solver"
 optional = true
 python-versions = ">=3.10"
 groups = ["main"]
-markers = "(python_version <= \"3.11\" or python_version >= \"3.12\") and extra == \"gel\""
+markers = "extra == \"gel\""
 files = [
     {file = "kiwisolver-1.4.9-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:b4b4d74bda2b8ebf4da5bd42af11d02d04428b2c32846e4c2c93219df8a7987b"},
     {file = "kiwisolver-1.4.9-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:fb3b8132019ea572f4611d770991000d7f58127560c4889729248eb5852a102f"},
@@ -1545,7 +1508,6 @@ description = "Python port of markdown-it. Markdown parsing, done right!"
 optional = false
 python-versions = ">=3.8"
 groups = ["docs"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "markdown-it-py-3.0.0.tar.gz", hash = "sha256:e3f60a94fa066dc52ec76661e37c851cb232d92f9886b15cb560aaada2df8feb"},
     {file = "markdown_it_py-3.0.0-py3-none-any.whl", hash = "sha256:355216845c60bd96232cd8d8c40e8f9765cc86f46880e43a8fd22dc1a1a8cab1"},
@@ -1571,7 +1533,6 @@ description = "Safely add untrusted strings to HTML/XML markup."
 optional = false
 python-versions = ">=3.9"
 groups = ["docs"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "markupsafe-3.0.3-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:2f981d352f04553a7171b8e44369f2af4055f888dfb147d55e42d29e29e74559"},
     {file = "markupsafe-3.0.3-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:e1c1493fb6e50ab01d20a22826e57520f1284df32f2d8601fdd90b6304601419"},
@@ -1671,7 +1632,7 @@ description = "Python plotting package"
 optional = true
 python-versions = ">=3.10"
 groups = ["main"]
-markers = "(python_version <= \"3.11\" or python_version >= \"3.12\") and extra == \"gel\""
+markers = "extra == \"gel\""
 files = [
     {file = "matplotlib-3.10.7-cp310-cp310-macosx_10_12_x86_64.whl", hash = "sha256:7ac81eee3b7c266dd92cee1cd658407b16c57eed08c7421fa354ed68234de380"},
     {file = "matplotlib-3.10.7-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:667ecd5d8d37813a845053d8f5bf110b534c3c9f30e69ebd25d4701385935a6d"},
@@ -1751,7 +1712,6 @@ description = "Inline Matplotlib backend for Jupyter"
 optional = false
 python-versions = ">=3.9"
 groups = ["docs", "test"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "matplotlib_inline-0.2.1-py3-none-any.whl", hash = "sha256:d56ce5156ba6085e00a9d54fead6ed29a9c47e215cd1bba2e976ef39f5710a76"},
     {file = "matplotlib_inline-0.2.1.tar.gz", hash = "sha256:e1ee949c340d771fc39e241ea75683deb94762c8fa5f2927ec57c83c4dffa9fe"},
@@ -1770,7 +1730,6 @@ description = "McCabe checker, plugin for flake8"
 optional = false
 python-versions = ">=3.6"
 groups = ["dev"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "mccabe-0.7.0-py2.py3-none-any.whl", hash = "sha256:6c2d30ab6be0e4a46919781807b4f0d834ebdd6c6e3dca0bda5a15f863427b6e"},
     {file = "mccabe-0.7.0.tar.gz", hash = "sha256:348e0240c33b60bbdf4e523192ef919f28cb2c3d7d5c7794f74009290f236325"},
@@ -1783,7 +1742,6 @@ description = "Collection of plugins for markdown-it-py"
 optional = false
 python-versions = ">=3.10"
 groups = ["docs"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "mdit_py_plugins-0.5.0-py3-none-any.whl", hash = "sha256:07a08422fc1936a5d26d146759e9155ea466e842f5ab2f7d2266dd084c8dab1f"},
     {file = "mdit_py_plugins-0.5.0.tar.gz", hash = "sha256:f4918cb50119f50446560513a8e311d574ff6aaed72606ddae6d35716fe809c6"},
@@ -1804,7 +1762,6 @@ description = "Markdown URL utilities"
 optional = false
 python-versions = ">=3.7"
 groups = ["docs"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "mdurl-0.1.2-py3-none-any.whl", hash = "sha256:84008a41e51615a49fc9966191ff91509e3c40b939176e643fd50a5c2196b8f8"},
     {file = "mdurl-0.1.2.tar.gz", hash = "sha256:bb413d29f5eea38f31dd4754dd7377d4465116fb207585f97bf925588687c1ba"},
@@ -1817,7 +1774,6 @@ description = "Type system extensions for programs checked with the mypy type ch
 optional = false
 python-versions = ">=3.8"
 groups = ["dev"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "mypy_extensions-1.1.0-py3-none-any.whl", hash = "sha256:1be4cccdb0f2482337c4743e60421de3a356cd97508abadd57d47403e94f5505"},
     {file = "mypy_extensions-1.1.0.tar.gz", hash = "sha256:52e68efc3284861e772bbcd66823fde5ae21fd2fdb51c62a211403730b916558"},
@@ -1830,7 +1786,6 @@ description = "A Jupyter Notebook Sphinx reader built on top of the MyST markdow
 optional = false
 python-versions = ">=3.9"
 groups = ["docs"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "myst_nb-1.3.0-py3-none-any.whl", hash = "sha256:1f36af3c19964960ec4e51ac30949b6ed6df220356ffa8d60dd410885e132d7d"},
     {file = "myst_nb-1.3.0.tar.gz", hash = "sha256:df3cd4680f51a5af673fd46b38b562be3559aef1475e906ed0f2e66e4587ce4b"},
@@ -1860,7 +1815,6 @@ description = "An extended [CommonMark](https://spec.commonmark.org/) compliant
 optional = false
 python-versions = ">=3.10"
 groups = ["docs"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "myst_parser-4.0.1-py3-none-any.whl", hash = "sha256:9134e88959ec3b5780aedf8a99680ea242869d012e8821db3126d427edc9c95d"},
     {file = "myst_parser-4.0.1.tar.gz", hash = "sha256:5cfea715e4f3574138aecbf7d54132296bfd72bb614d31168f48c477a830a7c4"},
@@ -1888,7 +1842,6 @@ description = "A client library for executing notebooks. Formerly nbconvert's Ex
 optional = false
 python-versions = ">=3.9.0"
 groups = ["docs"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "nbclient-0.10.2-py3-none-any.whl", hash = "sha256:4ffee11e788b4a27fabeb7955547e4318a5298f34342a4bfd01f2e1faaeadc3d"},
     {file = "nbclient-0.10.2.tar.gz", hash = "sha256:90b7fc6b810630db87a6d0c2250b1f0ab4cf4d3c27a299b0cde78a4ed3fd9193"},
@@ -1912,7 +1865,6 @@ description = "The Jupyter Notebook format"
 optional = false
 python-versions = ">=3.8"
 groups = ["dev", "docs", "test"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "nbformat-5.10.4-py3-none-any.whl", hash = "sha256:3b48d6c8fbca4b299bf3982ea7db1af21580e4fec269ad087b9e81588891200b"},
     {file = "nbformat-5.10.4.tar.gz", hash = "sha256:322168b14f937a5d11362988ecac2a4952d3d8e3a2cbeb2319584631226d5b3a"},
@@ -1935,7 +1887,6 @@ description = "Strips outputs from Jupyter and IPython notebooks"
 optional = false
 python-versions = ">=3.8"
 groups = ["dev"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "nbstripout-0.7.1-py2.py3-none-any.whl", hash = "sha256:dfb0688b42b02ff13925e583313fc009c87342ad13b79ae0329357749aa6ed0c"},
     {file = "nbstripout-0.7.1.tar.gz", hash = "sha256:2aad3454dc13e356f2fc94917856bc44f2bed3add77e8ba9f3a78003074bcd84"},
@@ -1951,7 +1902,6 @@ description = "A py.test plugin to validate Jupyter notebooks"
 optional = false
 python-versions = ">=3.7, <4"
 groups = ["test"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "nbval-0.11.0-py2.py3-none-any.whl", hash = "sha256:307aecc866c9a1e8a13bb5bbb008a702bacfda2394dff6fe504a3108a58042a0"},
     {file = "nbval-0.11.0.tar.gz", hash = "sha256:77c95797607b0a968babd2597ee3494102d25c3ad37435debbdac0e46e379094"},
@@ -1971,7 +1921,6 @@ description = "Patch asyncio to allow nested event loops"
 optional = false
 python-versions = ">=3.5"
 groups = ["docs", "test"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "nest_asyncio-1.6.0-py3-none-any.whl", hash = "sha256:87af6efd6b5e897c81050477ef65c62e2b2f35d51703cae01aff2905b1852e1c"},
     {file = "nest_asyncio-1.6.0.tar.gz", hash = "sha256:6f172d5449aca15afd6c646851f4e31e02c598d553a667e38cafa997cfec55fe"},
@@ -1984,7 +1933,6 @@ description = "Python package for creating and manipulating graphs and networks"
 optional = false
 python-versions = ">=3.10"
 groups = ["main"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "networkx-3.4.2-py3-none-any.whl", hash = "sha256:df5d4365b724cf81b8c6a7312509d0c22386097011ad1abe274afd5e9d3bbc5f"},
     {file = "networkx-3.4.2.tar.gz", hash = "sha256:307c3669428c5362aab27c8a1260aa8f47c4e91d3891f48be0141738d8d053e1"},
@@ -2005,7 +1953,6 @@ description = "Node.js virtual environment builder"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
 groups = ["dev"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "nodeenv-1.9.1-py2.py3-none-any.whl", hash = "sha256:ba11c9782d29c27c70ffbdda2d7415098754709be8a7056d79a737cd901155c9"},
     {file = "nodeenv-1.9.1.tar.gz", hash = "sha256:6ec12890a2dab7946721edbfbcd91f3319c6ccc9aec47be7c7e6b7011ee6645f"},
@@ -2018,7 +1965,7 @@ description = "Fundamental package for array computing in Python"
 optional = false
 python-versions = ">=3.10"
 groups = ["main", "docs"]
-markers = "python_version <= \"3.11\""
+markers = "python_version == \"3.10\""
 files = [
     {file = "numpy-2.2.6-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:b412caa66f72040e6d268491a59f2c43bf03eb6c96dd8f0307829feb7fa2b6fb"},
     {file = "numpy-2.2.6-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:8e41fd67c52b86603a91c1a505ebaef50b3314de0213461c7a6e99c9a3beff90"},
@@ -2084,7 +2031,7 @@ description = "Fundamental package for array computing in Python"
 optional = false
 python-versions = ">=3.11"
 groups = ["main", "docs"]
-markers = "python_version >= \"3.12\""
+markers = "python_version >= \"3.11\""
 files = [
     {file = "numpy-2.3.4-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:e78aecd2800b32e8347ce49316d3eaf04aed849cd5b38e0af39f829a4e59f5eb"},
     {file = "numpy-2.3.4-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:7fd09cc5d65bda1e79432859c40978010622112e9194e581e3415a3eccc7f43f"},
@@ -2169,7 +2116,6 @@ description = "Sphinx extension to support docstrings in Numpy format"
 optional = false
 python-versions = ">=3.9"
 groups = ["docs"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "numpydoc-1.9.0-py3-none-any.whl", hash = "sha256:8a2983b2d62bfd0a8c470c7caa25e7e0c3d163875cdec12a8a1034020a9d1135"},
     {file = "numpydoc-1.9.0.tar.gz", hash = "sha256:5fec64908fe041acc4b3afc2a32c49aab1540cf581876f5563d68bb129e27c5b"},
@@ -2181,15 +2127,14 @@ tomli = {version = ">=1.1.0", markers = "python_version < \"3.11\""}
 
 [[package]]
 name = "opencloning-linkml"
-version = "0.4.5"
+version = "0.4.6"
 description = "A LinkML data model for OpenCloning"
 optional = false
 python-versions = "<4.0,>=3.10"
 groups = ["main"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
-    {file = "opencloning_linkml-0.4.5-py3-none-any.whl", hash = "sha256:74cc57cef349a544c48fd05eb4942c9f8de5f96b011afbd4f15ab3a3e7226df3"},
-    {file = "opencloning_linkml-0.4.5.tar.gz", hash = "sha256:58bf4eeafafae2e6e1eb7af413674c070d1915fc7c36590ace412bb9660e2d4d"},
+    {file = "opencloning_linkml-0.4.6-py3-none-any.whl", hash = "sha256:442f29c4450dedbde7fbc2b750c448de8f15243a1d6d906767e60b7c90a688c0"},
+    {file = "opencloning_linkml-0.4.6.tar.gz", hash = "sha256:79e2e71b220b80846bd9296adbe08028937647b49e96ee7a726dd12068885c4e"},
 ]
 
 [package.dependencies]
@@ -2209,7 +2154,7 @@ files = [
     {file = "packaging-25.0-py3-none-any.whl", hash = "sha256:29572ef2b1f17581046b3a2227d5c611fb25ec70ca1ba8554b24b0e69331a484"},
     {file = "packaging-25.0.tar.gz", hash = "sha256:d443872c98d677bf60f6a1f2f8c1cb748e8fe762d2bf9d3148b5599295b0fc4f"},
 ]
-markers = {main = "(python_version <= \"3.11\" or python_version >= \"3.12\") and extra == \"gel\"", dev = "python_version <= \"3.11\" or python_version >= \"3.12\"", docs = "python_version <= \"3.11\" or python_version >= \"3.12\"", test = "python_version <= \"3.11\" or python_version >= \"3.12\""}
+markers = {main = "extra == \"gel\""}
 
 [[package]]
 name = "pandas"
@@ -2218,7 +2163,6 @@ description = "Powerful data structures for data analysis, time series, and stat
 optional = false
 python-versions = ">=3.9"
 groups = ["docs"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "pandas-2.3.3-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:376c6446ae31770764215a6c937f72d917f214b43560603cd60da6408f183b6c"},
     {file = "pandas-2.3.3-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:e19d192383eab2f4ceb30b412b22ea30690c9e618f78870357ae1d682912015a"},
@@ -2319,7 +2263,6 @@ description = "A Python Parser"
 optional = false
 python-versions = ">=3.6"
 groups = ["docs", "test"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "parso-0.8.5-py2.py3-none-any.whl", hash = "sha256:646204b5ee239c396d040b90f9e272e9a8017c630092bf59980beb62fd033887"},
     {file = "parso-0.8.5.tar.gz", hash = "sha256:034d7354a9a018bdce352f48b2a8a450f05e9d6ee85db84764e9b6bd96dafe5a"},
@@ -2336,7 +2279,6 @@ description = "Utility library for gitignore style pattern matching of file path
 optional = false
 python-versions = ">=3.8"
 groups = ["dev"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "pathspec-0.12.1-py3-none-any.whl", hash = "sha256:a0d503e138a4c123b27490a4f7beda6a01c6f288df0e4a8b79c7eb0dc7b4cc08"},
     {file = "pathspec-0.12.1.tar.gz", hash = "sha256:a482d51503a1ab33b1c67a6c3813a26953dbdc71c31dacaef9a838c4e29f5712"},
@@ -2349,7 +2291,7 @@ description = "Pexpect allows easy control of interactive console applications."
 optional = false
 python-versions = "*"
 groups = ["docs", "test"]
-markers = "(python_version <= \"3.11\" or python_version >= \"3.12\") and (sys_platform != \"win32\" and sys_platform != \"emscripten\")"
+markers = "sys_platform != \"win32\" and sys_platform != \"emscripten\""
 files = [
     {file = "pexpect-4.9.0-py2.py3-none-any.whl", hash = "sha256:7236d1e080e4936be2dc3e326cec0af72acf9212a7e1d060210e70a47e253523"},
     {file = "pexpect-4.9.0.tar.gz", hash = "sha256:ee7d41123f3c9911050ea2c2dac107568dc43b2d3b0c7557a33212c398ead30f"},
@@ -2365,7 +2307,7 @@ description = "Python Imaging Library (fork)"
 optional = true
 python-versions = ">=3.10"
 groups = ["main"]
-markers = "(python_version <= \"3.11\" or python_version >= \"3.12\") and extra == \"gel\""
+markers = "extra == \"gel\""
 files = [
     {file = "pillow-12.0.0-cp310-cp310-macosx_10_10_x86_64.whl", hash = "sha256:3adfb466bbc544b926d50fe8f4a4e6abd8c6bffd28a26177594e6e9b2b76572b"},
     {file = "pillow-12.0.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:1ac11e8ea4f611c3c0147424eae514028b5e9077dd99ab91e1bd7bc33ff145e1"},
@@ -2475,7 +2417,6 @@ description = "A small Python package for determining appropriate platform-speci
 optional = false
 python-versions = ">=3.10"
 groups = ["dev", "docs", "test"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "platformdirs-4.5.0-py3-none-any.whl", hash = "sha256:e578a81bb873cbb89a41fcc904c7ef523cc18284b7e3b3ccf06aca1403b7ebd3"},
     {file = "platformdirs-4.5.0.tar.gz", hash = "sha256:70ddccdd7c99fc5942e9fc25636a8b34d04c24b335100223152c2803e4063312"},
@@ -2493,7 +2434,6 @@ description = "plugin and hook calling mechanisms for python"
 optional = false
 python-versions = ">=3.9"
 groups = ["test"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "pluggy-1.6.0-py3-none-any.whl", hash = "sha256:e920276dd6813095e9377c0bc5566d94c932c33b27a3e3945d8389c374dd4746"},
     {file = "pluggy-1.6.0.tar.gz", hash = "sha256:7dcc130b76258d33b90f61b658791dede3486c3e6bfb003ee5c9bfb396dd22f3"},
@@ -2510,7 +2450,6 @@ description = "A framework for managing and maintaining multi-language pre-commi
 optional = false
 python-versions = ">=3.9"
 groups = ["dev"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "pre_commit-4.3.0-py2.py3-none-any.whl", hash = "sha256:2b0747ad7e6e967169136edffee14c16e148a778a54e4f967921aa1ebf2308d8"},
     {file = "pre_commit-4.3.0.tar.gz", hash = "sha256:499fe450cc9d42e9d58e606262795ecb64dd05438943c62b66f6a8673da30b16"},
@@ -2530,7 +2469,6 @@ description = "A simple Python library for easily displaying tabular data in a v
 optional = false
 python-versions = ">=3.9"
 groups = ["main"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "prettytable-3.16.0-py3-none-any.whl", hash = "sha256:b5eccfabb82222f5aa46b798ff02a8452cf530a352c31bddfa29be41242863aa"},
     {file = "prettytable-3.16.0.tar.gz", hash = "sha256:3c64b31719d961bf69c9a7e03d0c1e477320906a98da63952bc6698d6164ff57"},
@@ -2549,7 +2487,6 @@ description = "Library for building powerful interactive command lines in Python
 optional = false
 python-versions = ">=3.8"
 groups = ["docs", "test"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "prompt_toolkit-3.0.52-py3-none-any.whl", hash = "sha256:9aac639a3bbd33284347de5ad8d68ecc044b91a762dc39b7c21095fcd6a19955"},
     {file = "prompt_toolkit-3.0.52.tar.gz", hash = "sha256:28cde192929c8e7321de85de1ddbe736f1375148b02f2e17edd840042b1be855"},
@@ -2565,7 +2502,6 @@ description = "Cross-platform lib for process and system monitoring."
 optional = false
 python-versions = ">=3.6"
 groups = ["docs", "test"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "psutil-7.1.2-cp313-cp313t-macosx_10_13_x86_64.whl", hash = "sha256:0cc5c6889b9871f231ed5455a9a02149e388fffcb30b607fb7a8896a6d95f22e"},
     {file = "psutil-7.1.2-cp313-cp313t-macosx_11_0_arm64.whl", hash = "sha256:8e9e77a977208d84aa363a4a12e0f72189d58bbf4e46b49aae29a2c6e93ef206"},
@@ -2589,8 +2525,8 @@ files = [
 ]
 
 [package.extras]
-dev = ["abi3audit", "black", "check-manifest", "coverage", "packaging", "pylint", "pyperf", "pypinfo", "pyreadline", "pytest", "pytest-cov", "pytest-instafail", "pytest-subtests", "pytest-xdist", "pywin32", "requests", "rstcheck", "ruff", "setuptools", "sphinx", "sphinx_rtd_theme", "toml-sort", "twine", "validate-pyproject[all]", "virtualenv", "vulture", "wheel", "wheel", "wmi"]
-test = ["pytest", "pytest-instafail", "pytest-subtests", "pytest-xdist", "pywin32", "setuptools", "wheel", "wmi"]
+dev = ["abi3audit", "black", "check-manifest", "coverage", "packaging", "pylint", "pyperf", "pypinfo", "pyreadline ; os_name == \"nt\"", "pytest", "pytest-cov", "pytest-instafail", "pytest-subtests", "pytest-xdist", "pywin32 ; os_name == \"nt\" and platform_python_implementation != \"PyPy\"", "requests", "rstcheck", "ruff", "setuptools", "sphinx", "sphinx_rtd_theme", "toml-sort", "twine", "validate-pyproject[all]", "virtualenv", "vulture", "wheel", "wheel ; os_name == \"nt\" and platform_python_implementation != \"PyPy\"", "wmi ; os_name == \"nt\" and platform_python_implementation != \"PyPy\""]
+test = ["pytest", "pytest-instafail", "pytest-subtests", "pytest-xdist", "pywin32 ; os_name == \"nt\" and platform_python_implementation != \"PyPy\"", "setuptools", "wheel ; os_name == \"nt\" and platform_python_implementation != \"PyPy\"", "wmi ; os_name == \"nt\" and platform_python_implementation != \"PyPy\""]
 
 [[package]]
 name = "ptyprocess"
@@ -2599,7 +2535,7 @@ description = "Run a subprocess in a pseudo terminal"
 optional = false
 python-versions = "*"
 groups = ["docs", "test"]
-markers = "(python_version <= \"3.11\" or python_version >= \"3.12\") and (sys_platform != \"win32\" and sys_platform != \"emscripten\")"
+markers = "sys_platform != \"win32\" and sys_platform != \"emscripten\""
 files = [
     {file = "ptyprocess-0.7.0-py2.py3-none-any.whl", hash = "sha256:4b41f3967fce3af57cc7e94b888626c18bf37a083e3651ca8feeb66d492fef35"},
     {file = "ptyprocess-0.7.0.tar.gz", hash = "sha256:5c5d0a3b48ceee0b48485e0c26037c0acd7d29765ca3fbb5cb3831d347423220"},
@@ -2612,7 +2548,6 @@ description = "Safely evaluate AST nodes without side effects"
 optional = false
 python-versions = "*"
 groups = ["docs", "test"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "pure_eval-0.2.3-py3-none-any.whl", hash = "sha256:1db8e35b67b3d218d818ae653e27f06c3aa420901fa7b081ca98cbedc874e0d0"},
     {file = "pure_eval-0.2.3.tar.gz", hash = "sha256:5f4e983f40564c576c7c8635ae88db5956bb2229d7e9237d03b3c0b0190eaf42"},
@@ -2628,7 +2563,6 @@ description = "Python style guide checker"
 optional = false
 python-versions = ">=3.9"
 groups = ["dev"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "pycodestyle-2.14.0-py2.py3-none-any.whl", hash = "sha256:dd6bf7cb4ee77f8e016f9c8e74a35ddd9f67e1d5fd4184d86c3b98e07099f42d"},
     {file = "pycodestyle-2.14.0.tar.gz", hash = "sha256:c4b5b517d278089ff9d0abdec919cd97262a3367449ea1c8b49b91529167b783"},
@@ -2641,7 +2575,7 @@ description = "C parser in Python"
 optional = false
 python-versions = ">=3.8"
 groups = ["docs", "test"]
-markers = "(python_version <= \"3.11\" or python_version >= \"3.12\") and implementation_name == \"pypy\""
+markers = "implementation_name == \"pypy\""
 files = [
     {file = "pycparser-2.23-py3-none-any.whl", hash = "sha256:e5c6e8d3fbad53479cab09ac03729e0a9faf2bee3db8208a550daf5af81a5934"},
     {file = "pycparser-2.23.tar.gz", hash = "sha256:78816d4f24add8f10a06d6f05b4d424ad9e96cfebf68a4ddc99c65c0720d00c2"},
@@ -2654,7 +2588,6 @@ description = "Data validation using Python type hints"
 optional = false
 python-versions = ">=3.9"
 groups = ["main"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "pydantic-2.12.3-py3-none-any.whl", hash = "sha256:6986454a854bc3bc6e5443e1369e06a3a456af9d339eda45510f517d9ea5c6bf"},
     {file = "pydantic-2.12.3.tar.gz", hash = "sha256:1da1c82b0fc140bb0103bc1441ffe062154c8d38491189751ee00fd8ca65ce74"},
@@ -2668,7 +2601,7 @@ typing-inspection = ">=0.4.2"
 
 [package.extras]
 email = ["email-validator (>=2.0.0)"]
-timezone = ["tzdata"]
+timezone = ["tzdata ; python_version >= \"3.9\" and platform_system == \"Windows\""]
 
 [[package]]
 name = "pydantic-core"
@@ -2677,7 +2610,6 @@ description = "Core functionality for Pydantic validation and serialization"
 optional = false
 python-versions = ">=3.9"
 groups = ["main"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "pydantic_core-2.41.4-cp310-cp310-macosx_10_12_x86_64.whl", hash = "sha256:2442d9a4d38f3411f22eb9dd0912b7cbf4b7d5b6c92c4173b75d3e1ccd84e36e"},
     {file = "pydantic_core-2.41.4-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:30a9876226dda131a741afeab2702e2d127209bde3c65a2b8133f428bc5d006b"},
@@ -2808,7 +2740,6 @@ description = "Bootstrap-based Sphinx theme from the PyData community"
 optional = false
 python-versions = ">=3.9"
 groups = ["docs"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "pydata_sphinx_theme-0.15.4-py3-none-any.whl", hash = "sha256:2136ad0e9500d0949f96167e63f3e298620040aea8f9c74621959eda5d4cf8e6"},
     {file = "pydata_sphinx_theme-0.15.4.tar.gz", hash = "sha256:7762ec0ac59df3acecf49fd2f889e1b4565dbce8b88b2e29ee06fdd90645a06d"},
@@ -2838,7 +2769,6 @@ description = "String algorithms"
 optional = false
 python-versions = ">=3.9"
 groups = ["main"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "pydivsufsort-0.0.18-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:40474ee2f071fb16b33082596b35638c2c17eb37d9c0efced8b31394d6e0cacd"},
     {file = "pydivsufsort-0.0.18-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:37c660abe0f126111e8e251391a8efc88dcbb726342e18ac230c0ba79f81c1c2"},
@@ -2884,7 +2814,6 @@ description = "Pure-python FIGlet implementation"
 optional = false
 python-versions = "*"
 groups = ["main"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "pyfiglet-0.8.post1-py2.py3-none-any.whl", hash = "sha256:d555bcea17fbeaf70eaefa48bb119352487e629c9b56f30f383e2c62dd67a01c"},
     {file = "pyfiglet-0.8.post1.tar.gz", hash = "sha256:c6c2321755d09267b438ec7b936825a4910fec696292139e664ca8670e103639"},
@@ -2897,7 +2826,6 @@ description = "passive checker of Python programs"
 optional = false
 python-versions = ">=3.9"
 groups = ["dev"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "pyflakes-3.4.0-py2.py3-none-any.whl", hash = "sha256:f742a7dbd0d9cb9ea41e9a24a918996e8170c799fa528688d40dd582c8265f4f"},
     {file = "pyflakes-3.4.0.tar.gz", hash = "sha256:b24f96fafb7d2ab0ec5075b7350b3d2d2218eab42003821c06344973d3ea2f58"},
@@ -2910,7 +2838,6 @@ description = "Pygments is a syntax highlighting package written in Python."
 optional = false
 python-versions = ">=3.8"
 groups = ["docs", "test"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "pygments-2.19.2-py3-none-any.whl", hash = "sha256:86540386c03d588bb81d44bc3928634ff26449851e99741617ecb9037ee5ec0b"},
     {file = "pygments-2.19.2.tar.gz", hash = "sha256:636cb2477cec7f8952536970bc533bc43743542f70392ae026374600add5b887"},
@@ -2926,7 +2853,7 @@ description = "pyparsing - Classes and methods to define and execute parsing gra
 optional = true
 python-versions = ">=3.9"
 groups = ["main"]
-markers = "(extra == \"gel\" or extra == \"download\") and (python_version <= \"3.11\" or python_version >= \"3.12\")"
+markers = "extra == \"gel\" or extra == \"download\""
 files = [
     {file = "pyparsing-3.2.5-py3-none-any.whl", hash = "sha256:e38a4f02064cf41fe6593d328d0512495ad1f3d8a91c4f73fc401b3079a59a5e"},
     {file = "pyparsing-3.2.5.tar.gz", hash = "sha256:2df8d5b7b2802ef88e8d016a2eb9c7aeaa923529cd251ed0fe4608275d4105b6"},
@@ -2942,7 +2869,7 @@ description = "A cross-platform clipboard module for Python. (Only handles plain
 optional = true
 python-versions = "*"
 groups = ["main"]
-markers = "(python_version <= \"3.11\" or python_version >= \"3.12\") and extra == \"clipboard\""
+markers = "extra == \"clipboard\""
 files = [
     {file = "pyperclip-1.11.0-py3-none-any.whl", hash = "sha256:299403e9ff44581cb9ba2ffeed69c7aa96a008622ad0c46cb575ca75b5b84273"},
     {file = "pyperclip-1.11.0.tar.gz", hash = "sha256:244035963e4428530d9e3a6101a1ef97209c6825edab1567beac148ccc1db1b6"},
@@ -2955,7 +2882,6 @@ description = "pytest: simple powerful testing with Python"
 optional = false
 python-versions = ">=3.9"
 groups = ["test"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "pytest-8.4.2-py3-none-any.whl", hash = "sha256:872f880de3fc3a5bdc88a11b39c9710c3497a547cfa9320bc3c5e62fbf272e79"},
     {file = "pytest-8.4.2.tar.gz", hash = "sha256:86c0d0b93306b961d58d62a4db4879f27fe25513d4b969df351abdddb3c30e01"},
@@ -2980,7 +2906,6 @@ description = "Pytest plugin for measuring coverage."
 optional = false
 python-versions = ">=3.9"
 groups = ["test"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "pytest_cov-7.0.0-py3-none-any.whl", hash = "sha256:3b8e9558b16cc1479da72058bdecf8073661c7f57f7d3c5f22a1c23507f2d861"},
     {file = "pytest_cov-7.0.0.tar.gz", hash = "sha256:33c97eda2e049a0c5298e91f519302a1334c26ac65c1a483d6206fd458361af1"},
@@ -3001,7 +2926,6 @@ description = "Pytest plugin with advanced doctest features."
 optional = false
 python-versions = ">=3.9"
 groups = ["test"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "pytest_doctestplus-1.5.0-py3-none-any.whl", hash = "sha256:e13e014bab450285b3735de27a1429d4f95bca2efc7a2becd9a863247e91ae4e"},
     {file = "pytest_doctestplus-1.5.0.tar.gz", hash = "sha256:1bfb9ecf0a5a61452abd4c2a5218450d0ddd125a2c241da9e4f7f8ccf6b779fe"},
@@ -3021,7 +2945,6 @@ description = "Profiling plugin for py.test"
 optional = false
 python-versions = ">=3.6"
 groups = ["test"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "pytest-profiling-1.8.1.tar.gz", hash = "sha256:3f171fa69d5c82fa9aab76d66abd5f59da69135c37d6ae5bf7557f1b154cb08d"},
     {file = "pytest_profiling-1.8.1-py3-none-any.whl", hash = "sha256:3dd8713a96298b42d83de8f5951df3ada3e61b3e5d2a06956684175529e17aea"},
@@ -3043,7 +2966,7 @@ files = [
     {file = "python-dateutil-2.9.0.post0.tar.gz", hash = "sha256:37dd54208da7e1cd875388217d5e00ebd4179249f90fb72437e91a35459a0ad3"},
     {file = "python_dateutil-2.9.0.post0-py2.py3-none-any.whl", hash = "sha256:a8b2bc7bffae282281c8140a97d3aa9c14da0b136dfe83f850eea9a5f7470427"},
 ]
-markers = {main = "(python_version <= \"3.11\" or python_version >= \"3.12\") and extra == \"gel\"", docs = "python_version <= \"3.11\" or python_version >= \"3.12\"", test = "python_version <= \"3.11\" or python_version >= \"3.12\""}
+markers = {main = "extra == \"gel\""}
 
 [package.dependencies]
 six = ">=1.5"
@@ -3055,7 +2978,6 @@ description = "A Fast, spec compliant Python 3.13+ tokenizer that runs on older
 optional = false
 python-versions = ">=3.8"
 groups = ["dev"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "pytokens-0.2.0-py3-none-any.whl", hash = "sha256:74d4b318c67f4295c13782ddd9abcb7e297ec5630ad060eb90abf7ebbefe59f8"},
     {file = "pytokens-0.2.0.tar.gz", hash = "sha256:532d6421364e5869ea57a9523bf385f02586d4662acbcc0342afd69511b4dd43"},
@@ -3071,7 +2993,6 @@ description = "World timezone definitions, modern and historical"
 optional = false
 python-versions = "*"
 groups = ["docs"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "pytz-2025.2-py2.py3-none-any.whl", hash = "sha256:5ddf76296dd8c44c26eb8f4b6f35488f3ccbf6fbbd7adee0b7262d43f0ec2f00"},
     {file = "pytz-2025.2.tar.gz", hash = "sha256:360b9e3dbb49a209c21ad61809c7fb453643e048b38924c765813546746e81c3"},
@@ -3084,7 +3005,6 @@ description = "YAML parser and emitter for Python"
 optional = false
 python-versions = ">=3.8"
 groups = ["dev", "docs"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "PyYAML-6.0.3-cp38-cp38-macosx_10_13_x86_64.whl", hash = "sha256:c2514fceb77bc5e7a2f7adfaa1feb2fb311607c9cb518dbc378688ec73d8292f"},
     {file = "PyYAML-6.0.3-cp38-cp38-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl", hash = "sha256:9c57bb8c96f6d1808c030b1687b9b5fb476abaa47f0db9c0101f5e9f394e97f4"},
@@ -3168,7 +3088,6 @@ description = "Python bindings for 0MQ"
 optional = false
 python-versions = ">=3.8"
 groups = ["docs", "test"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "pyzmq-27.1.0-cp310-cp310-macosx_10_15_universal2.whl", hash = "sha256:508e23ec9bc44c0005c4946ea013d9317ae00ac67778bd47519fdf5a0e930ff4"},
     {file = "pyzmq-27.1.0-cp310-cp310-manylinux2014_i686.manylinux_2_17_i686.whl", hash = "sha256:507b6f430bdcf0ee48c0d30e734ea89ce5567fd7b8a0f0044a369c176aa44556"},
@@ -3274,7 +3193,6 @@ description = "JSON Referencing + Python"
 optional = false
 python-versions = ">=3.10"
 groups = ["dev", "docs", "test"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "referencing-0.37.0-py3-none-any.whl", hash = "sha256:381329a9f99628c9069361716891d34ad94af76e461dcb0335825aecc7692231"},
     {file = "referencing-0.37.0.tar.gz", hash = "sha256:44aefc3142c5b842538163acb373e24cce6632bd54bdb01b21ad5863489f50d8"},
@@ -3292,7 +3210,6 @@ description = "Alternative regular expression module, to replace re."
 optional = false
 python-versions = ">=3.8"
 groups = ["main"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "regex-2024.11.6-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:ff590880083d60acc0433f9c3f713c51f7ac6ebb9adf889c79a261ecf541aa91"},
     {file = "regex-2024.11.6-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:658f90550f38270639e83ce492f27d2c8d2cd63805c65a13a14d36ca126753f0"},
@@ -3401,7 +3318,7 @@ files = [
     {file = "requests-2.32.5-py3-none-any.whl", hash = "sha256:2462f94637a34fd532264295e186976db0f5d453d1cdd31473c85a6a161affb6"},
     {file = "requests-2.32.5.tar.gz", hash = "sha256:dbba0bac56e100853db0ea71b82b4dfd5fe2bf6d3754a8893c3af500cec7d7cf"},
 ]
-markers = {main = "(python_version <= \"3.11\" or python_version >= \"3.12\") and extra == \"download\"", docs = "python_version <= \"3.11\" or python_version >= \"3.12\"", test = "python_version <= \"3.11\" or python_version >= \"3.12\""}
+markers = {main = "extra == \"download\""}
 
 [package.dependencies]
 certifi = ">=2017.4.17"
@@ -3420,7 +3337,6 @@ description = "Mock out responses from the requests package"
 optional = false
 python-versions = ">=3.5"
 groups = ["test"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "requests-mock-1.12.1.tar.gz", hash = "sha256:e9e12e333b525156e82a3c852f22016b9158220d2f47454de9cae8a77d371401"},
     {file = "requests_mock-1.12.1-py2.py3-none-any.whl", hash = "sha256:b1e37054004cdd5e56c84454cc7df12b25f90f382159087f4b6915aaeef39563"},
@@ -3439,7 +3355,6 @@ description = "Python bindings to Rust's persistent data structures (rpds)"
 optional = false
 python-versions = ">=3.10"
 groups = ["dev", "docs", "test"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "rpds_py-0.28.0-cp310-cp310-macosx_10_12_x86_64.whl", hash = "sha256:7b6013db815417eeb56b2d9d7324e64fcd4fa289caeee6e7a78b2e11fc9b438a"},
     {file = "rpds_py-0.28.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:1a4c6b05c685c0c03f80dabaeb73e74218c49deea965ca63f76a752807397207"},
@@ -3565,7 +3480,7 @@ description = "Fundamental algorithms for scientific computing in Python"
 optional = true
 python-versions = ">=3.10"
 groups = ["main"]
-markers = "(extra == \"express\" or extra == \"gel\") and (python_version <= \"3.11\" or python_version >= \"3.12\")"
+markers = "python_version == \"3.10\" and (extra == \"express\" or extra == \"gel\")"
 files = [
     {file = "scipy-1.15.3-cp310-cp310-macosx_10_13_x86_64.whl", hash = "sha256:a345928c86d535060c9c2b25e71e87c39ab2f22fc96e9636bd74d1dbf9de448c"},
     {file = "scipy-1.15.3-cp310-cp310-macosx_12_0_arm64.whl", hash = "sha256:ad3432cb0f9ed87477a8d97f03b763fd1d57709f1bbde3c9369b1dff5503b253"},
@@ -3621,7 +3536,7 @@ numpy = ">=1.23.5,<2.5"
 [package.extras]
 dev = ["cython-lint (>=0.12.2)", "doit (>=0.36.0)", "mypy (==1.10.0)", "pycodestyle", "pydevtool", "rich-click", "ruff (>=0.0.292)", "types-psutil", "typing_extensions"]
 doc = ["intersphinx_registry", "jupyterlite-pyodide-kernel", "jupyterlite-sphinx (>=0.19.1)", "jupytext", "matplotlib (>=3.5)", "myst-nb", "numpydoc", "pooch", "pydata-sphinx-theme (>=0.15.2)", "sphinx (>=5.0.0,<8.0.0)", "sphinx-copybutton", "sphinx-design (>=0.4.0)"]
-test = ["Cython", "array-api-strict (>=2.0,<2.1.1)", "asv", "gmpy2", "hypothesis (>=6.30)", "meson", "mpmath", "ninja", "pooch", "pytest", "pytest-cov", "pytest-timeout", "pytest-xdist", "scikit-umfpack", "threadpoolctl"]
+test = ["Cython", "array-api-strict (>=2.0,<2.1.1)", "asv", "gmpy2", "hypothesis (>=6.30)", "meson", "mpmath", "ninja ; sys_platform != \"emscripten\"", "pooch", "pytest", "pytest-cov", "pytest-timeout", "pytest-xdist", "scikit-umfpack", "threadpoolctl"]
 
 [[package]]
 name = "scipy"
@@ -3630,7 +3545,7 @@ description = "Fundamental algorithms for scientific computing in Python"
 optional = true
 python-versions = ">=3.11"
 groups = ["main"]
-markers = "extra == \"express\" and python_version >= \"3.12\" or extra == \"gel\" and python_version >= \"3.12\""
+markers = "python_version >= \"3.11\" and (extra == \"express\" or extra == \"gel\")"
 files = [
     {file = "scipy-1.16.3-cp311-cp311-macosx_10_14_x86_64.whl", hash = "sha256:40be6cf99e68b6c4321e9f8782e7d5ff8265af28ef2cd56e9c9b2638fa08ad97"},
     {file = "scipy-1.16.3-cp311-cp311-macosx_12_0_arm64.whl", hash = "sha256:8be1ca9170fcb6223cc7c27f4305d680ded114a1567c0bd2bfcbf947d1b17511"},
@@ -3701,7 +3616,7 @@ numpy = ">=1.25.2,<2.6"
 [package.extras]
 dev = ["cython-lint (>=0.12.2)", "doit (>=0.36.0)", "mypy (==1.10.0)", "pycodestyle", "pydevtool", "rich-click", "ruff (>=0.0.292)", "types-psutil", "typing_extensions"]
 doc = ["intersphinx_registry", "jupyterlite-pyodide-kernel", "jupyterlite-sphinx (>=0.19.1)", "jupytext", "linkify-it-py", "matplotlib (>=3.5)", "myst-nb (>=1.2.0)", "numpydoc", "pooch", "pydata-sphinx-theme (>=0.15.2)", "sphinx (>=5.0.0,<8.2.0)", "sphinx-copybutton", "sphinx-design (>=0.4.0)"]
-test = ["Cython", "array-api-strict (>=2.3.1)", "asv", "gmpy2", "hypothesis (>=6.30)", "meson", "mpmath", "ninja", "pooch", "pytest (>=8.0.0)", "pytest-cov", "pytest-timeout", "pytest-xdist", "scikit-umfpack", "threadpoolctl"]
+test = ["Cython", "array-api-strict (>=2.3.1)", "asv", "gmpy2", "hypothesis (>=6.30)", "meson", "mpmath", "ninja ; sys_platform != \"emscripten\"", "pooch", "pytest (>=8.0.0)", "pytest-cov", "pytest-timeout", "pytest-xdist", "scikit-umfpack", "threadpoolctl"]
 
 [[package]]
 name = "seguid"
@@ -3710,14 +3625,13 @@ description = "Sequence Globally Unique Identifier (SEGUID) Checksums for Linear
 optional = false
 python-versions = "<4.0,>=3.6"
 groups = ["main"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "seguid-0.2.1-py3-none-any.whl", hash = "sha256:10767009dcee3ee1e1227e68b047e5bde82224de1fec11162c3afc4238ca6e08"},
     {file = "seguid-0.2.1.tar.gz", hash = "sha256:cc5482aea6264d5370076a82559b7ccd0810d4e38489437a9e9118affa9762e5"},
 ]
 
 [package.extras]
-pydivsufsort = ["pydivsufsort (<=0.0.14)", "pydivsufsort (>=0.0.18)"]
+pydivsufsort = ["pydivsufsort (<=0.0.14) ; python_version < \"3.9\"", "pydivsufsort (>=0.0.18) ; python_version >= \"3.9\""]
 
 [[package]]
 name = "six"
@@ -3730,7 +3644,7 @@ files = [
     {file = "six-1.17.0-py2.py3-none-any.whl", hash = "sha256:4721f391ed90541fddacab5acf947aa0d3dc7d27b2e1e8eda2be8970586c3274"},
     {file = "six-1.17.0.tar.gz", hash = "sha256:ff70335d468e7eb6ec65b95b99d3a2836546063f63acc5171de367e834932a81"},
 ]
-markers = {main = "(python_version <= \"3.11\" or python_version >= \"3.12\") and extra == \"gel\"", docs = "python_version <= \"3.11\" or python_version >= \"3.12\"", test = "python_version <= \"3.11\" or python_version >= \"3.12\""}
+markers = {main = "extra == \"gel\""}
 
 [[package]]
 name = "snowballstemmer"
@@ -3739,7 +3653,6 @@ description = "This package provides 32 stemmers for 30 languages generated from
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*"
 groups = ["docs"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "snowballstemmer-3.0.1-py3-none-any.whl", hash = "sha256:6cd7b3897da8d6c9ffb968a6781fa6532dce9c3618a4b127d920dab764a19064"},
     {file = "snowballstemmer-3.0.1.tar.gz", hash = "sha256:6d5eeeec8e9f84d4d56b847692bacf79bc2c8e90c7f80ca4444ff8b6f2e52895"},
@@ -3752,7 +3665,6 @@ description = "A modern CSS selector implementation for Beautiful Soup."
 optional = false
 python-versions = ">=3.9"
 groups = ["docs"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "soupsieve-2.8-py3-none-any.whl", hash = "sha256:0cc76456a30e20f5d7f2e14a98a4ae2ee4e5abdc7c5ea0aafe795f344bc7984c"},
     {file = "soupsieve-2.8.tar.gz", hash = "sha256:e2dd4a40a628cb5f28f6d4b0db8800b8f581b65bb380b97de22ba5ca8d72572f"},
@@ -3765,7 +3677,6 @@ description = "Python documentation generator"
 optional = false
 python-versions = ">=3.10"
 groups = ["docs"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "sphinx-8.1.3-py3-none-any.whl", hash = "sha256:09719015511837b76bf6e03e42eb7595ac8c2e41eeb9c29c5b755c6b677992a2"},
     {file = "sphinx-8.1.3.tar.gz", hash = "sha256:43c1911eecb0d3e161ad78611bc905d1ad0e523e4ddc202a58a821773dc4c927"},
@@ -3802,7 +3713,6 @@ description = "A clean book theme for scientific explanations and documentation
 optional = false
 python-versions = ">=3.9"
 groups = ["docs"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "sphinx_book_theme-1.1.4-py3-none-any.whl", hash = "sha256:843b3f5c8684640f4a2d01abd298beb66452d1b2394cd9ef5be5ebd5640ea0e1"},
     {file = "sphinx_book_theme-1.1.4.tar.gz", hash = "sha256:73efe28af871d0a89bd05856d300e61edce0d5b2fbb7984e84454be0fedfe9ed"},
@@ -3824,7 +3734,6 @@ description = "sphinxcontrib-applehelp is a Sphinx extension which outputs Apple
 optional = false
 python-versions = ">=3.9"
 groups = ["docs"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "sphinxcontrib_applehelp-2.0.0-py3-none-any.whl", hash = "sha256:4cd3f0ec4ac5dd9c17ec65e9ab272c9b867ea77425228e68ecf08d6b28ddbdb5"},
     {file = "sphinxcontrib_applehelp-2.0.0.tar.gz", hash = "sha256:2f29ef331735ce958efa4734873f084941970894c6090408b079c61b2e1c06d1"},
@@ -3842,7 +3751,6 @@ description = "sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp
 optional = false
 python-versions = ">=3.9"
 groups = ["docs"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "sphinxcontrib_devhelp-2.0.0-py3-none-any.whl", hash = "sha256:aefb8b83854e4b0998877524d1029fd3e6879210422ee3780459e28a1f03a8a2"},
     {file = "sphinxcontrib_devhelp-2.0.0.tar.gz", hash = "sha256:411f5d96d445d1d73bb5d52133377b4248ec79db5c793ce7dbe59e074b4dd1ad"},
@@ -3860,7 +3768,6 @@ description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML h
 optional = false
 python-versions = ">=3.9"
 groups = ["docs"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "sphinxcontrib_htmlhelp-2.1.0-py3-none-any.whl", hash = "sha256:166759820b47002d22914d64a075ce08f4c46818e17cfc9470a9786b759b19f8"},
     {file = "sphinxcontrib_htmlhelp-2.1.0.tar.gz", hash = "sha256:c9e2916ace8aad64cc13a0d233ee22317f2b9025b9cf3295249fa985cc7082e9"},
@@ -3878,7 +3785,6 @@ description = "A sphinx extension which renders display math in HTML via JavaScr
 optional = false
 python-versions = ">=3.5"
 groups = ["docs"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "sphinxcontrib-jsmath-1.0.1.tar.gz", hash = "sha256:a9925e4a4587247ed2191a22df5f6970656cb8ca2bd6284309578f2153e0c4b8"},
     {file = "sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl", hash = "sha256:2ec2eaebfb78f3f2078e73666b1415417a116cc848b72e5172e596c871103178"},
@@ -3894,7 +3800,6 @@ description = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp d
 optional = false
 python-versions = ">=3.9"
 groups = ["docs"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "sphinxcontrib_qthelp-2.0.0-py3-none-any.whl", hash = "sha256:b18a828cdba941ccd6ee8445dbe72ffa3ef8cbe7505d8cd1fa0d42d3f2d5f3eb"},
     {file = "sphinxcontrib_qthelp-2.0.0.tar.gz", hash = "sha256:4fe7d0ac8fc171045be623aba3e2a8f613f8682731f9153bb2e40ece16b9bbab"},
@@ -3912,7 +3817,6 @@ description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs
 optional = false
 python-versions = ">=3.9"
 groups = ["docs"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "sphinxcontrib_serializinghtml-2.0.0-py3-none-any.whl", hash = "sha256:6e2cb0eef194e10c27ec0023bfeb25badbbb5868244cf5bc5bdc04e4464bf331"},
     {file = "sphinxcontrib_serializinghtml-2.0.0.tar.gz", hash = "sha256:e9d912827f872c029017a53f0ef2180b327c3f7fd23c87229f7a8e8b70031d4d"},
@@ -3930,7 +3834,6 @@ description = "Database Abstraction Library"
 optional = false
 python-versions = ">=3.7"
 groups = ["docs"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "SQLAlchemy-2.0.44-cp37-cp37m-macosx_10_9_x86_64.whl", hash = "sha256:471733aabb2e4848d609141a9e9d56a427c0a038f4abf65dd19d7a21fd563632"},
     {file = "SQLAlchemy-2.0.44-cp37-cp37m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:48bf7d383a35e668b984c805470518b635d48b95a3c57cb03f37eaa3551b5f9f"},
@@ -4027,7 +3930,6 @@ description = "Extract data from python stack frames and tracebacks for informat
 optional = false
 python-versions = "*"
 groups = ["docs", "test"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "stack_data-0.6.3-py3-none-any.whl", hash = "sha256:d5558e0c25a4cb0853cddad3d77da9891a08cb85dd9f9f91b9f8cd66e511e695"},
     {file = "stack_data-0.6.3.tar.gz", hash = "sha256:836a778de4fec4dcd1dcd89ed8abff8a221f58308462e1c4aa2a3cf30148f0b9"},
@@ -4048,7 +3950,6 @@ description = "Pretty-print tabular data"
 optional = false
 python-versions = ">=3.7"
 groups = ["docs"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "tabulate-0.9.0-py3-none-any.whl", hash = "sha256:024ca478df22e9340661486f85298cff5f6dcdba14f3813e8830015b9ed1948f"},
     {file = "tabulate-0.9.0.tar.gz", hash = "sha256:0095b12bf5966de529c0feb1fa08671671b3368eec77d7ef7ab114be2c068b3c"},
@@ -4064,6 +3965,7 @@ description = "A lil' TOML parser"
 optional = false
 python-versions = ">=3.8"
 groups = ["dev", "docs", "test"]
+markers = "python_version == \"3.10\""
 files = [
     {file = "tomli-2.3.0-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:88bd15eb972f3664f5ed4b57c1634a97153b4bac4479dcb6a495f41921eb7f45"},
     {file = "tomli-2.3.0-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:883b1c0d6398a6a9d29b508c331fa56adbcdff647f6ace4dfca0f50e90dfd0ba"},
@@ -4108,7 +4010,6 @@ files = [
     {file = "tomli-2.3.0-py3-none-any.whl", hash = "sha256:e95b1af3c5b07d9e643909b5abbec77cd9f1217e6d0bca72b0234736b9fb1f1b"},
     {file = "tomli-2.3.0.tar.gz", hash = "sha256:64be704a875d2a59753d80ee8a533c3fe183e3f06807ff7dc2232938ccb01549"},
 ]
-markers = {dev = "python_version < \"3.11\"", docs = "python_version < \"3.11\"", test = "python_full_version <= \"3.11.0a6\""}
 
 [[package]]
 name = "tornado"
@@ -4117,7 +4018,6 @@ description = "Tornado is a Python web framework and asynchronous networking lib
 optional = false
 python-versions = ">=3.9"
 groups = ["docs", "test"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "tornado-6.5.2-cp39-abi3-macosx_10_9_universal2.whl", hash = "sha256:2436822940d37cde62771cff8774f4f00b3c8024fe482e16ca8387b8a2724db6"},
     {file = "tornado-6.5.2-cp39-abi3-macosx_10_9_x86_64.whl", hash = "sha256:583a52c7aa94ee046854ba81d9ebb6c81ec0fd30386d96f7640c96dad45a03ef"},
@@ -4140,7 +4040,6 @@ description = "Traitlets Python configuration system"
 optional = false
 python-versions = ">=3.8"
 groups = ["dev", "docs", "test"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "traitlets-5.14.3-py3-none-any.whl", hash = "sha256:b74e89e397b1ed28cc831db7aea759ba6640cb3de13090ca145426688ff1ac4f"},
     {file = "traitlets-5.14.3.tar.gz", hash = "sha256:9ed0579d3502c94b4b3732ac120375cda96f923114522847de4b3bb98b96b6b7"},
@@ -4161,7 +4060,7 @@ files = [
     {file = "typing_extensions-4.15.0-py3-none-any.whl", hash = "sha256:f0fa19c6845758ab08074a0cfa8b7aecb71c999ca73d62883bc25cc018c4e548"},
     {file = "typing_extensions-4.15.0.tar.gz", hash = "sha256:0cea48d173cc12fa28ecabc3b837ea3cf6f38c6d1136f85cbaaf598984861466"},
 ]
-markers = {main = "python_version <= \"3.11\" or python_version >= \"3.12\"", dev = "python_version >= \"3.12\" and python_version < \"3.13\" or python_version <= \"3.11\"", docs = "python_version <= \"3.11\" or python_version >= \"3.12\"", test = "python_version >= \"3.12\" and python_version < \"3.13\" or python_version <= \"3.11\""}
+markers = {dev = "python_version <= \"3.12\"", test = "python_version <= \"3.12\""}
 
 [[package]]
 name = "typing-inspection"
@@ -4170,7 +4069,6 @@ description = "Runtime typing introspection tools"
 optional = false
 python-versions = ">=3.9"
 groups = ["main"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "typing_inspection-0.4.2-py3-none-any.whl", hash = "sha256:4ed1cacbdc298c220f1bd249ed5287caa16f34d44ef4e9c3d0cbad5b521545e7"},
     {file = "typing_inspection-0.4.2.tar.gz", hash = "sha256:ba561c48a67c5958007083d386c3295464928b01faa735ab8547c5692e87f464"},
@@ -4186,7 +4084,6 @@ description = "Provider of IANA time zone data"
 optional = false
 python-versions = ">=2"
 groups = ["docs"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "tzdata-2025.2-py2.py3-none-any.whl", hash = "sha256:1a403fada01ff9221ca8044d701868fa132215d84beb92242d9acd2147f667a8"},
     {file = "tzdata-2025.2.tar.gz", hash = "sha256:b60a638fcc0daffadf82fe0f57e53d06bdec2f36c4df66280ae79bce6bd6f2b9"},
@@ -4203,10 +4100,10 @@ files = [
     {file = "urllib3-2.5.0-py3-none-any.whl", hash = "sha256:e6b01673c0fa6a13e374b50871808eb3bf7046c4b125b216f6bf1cc604cff0dc"},
     {file = "urllib3-2.5.0.tar.gz", hash = "sha256:3fc47733c7e419d4bc3f6b3dc2b4f890bb743906a30d56ba4a5bfa4bbff92760"},
 ]
-markers = {main = "(python_version <= \"3.11\" or python_version >= \"3.12\") and extra == \"download\"", docs = "python_version <= \"3.11\" or python_version >= \"3.12\"", test = "python_version <= \"3.11\" or python_version >= \"3.12\""}
+markers = {main = "extra == \"download\""}
 
 [package.extras]
-brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)"]
+brotli = ["brotli (>=1.0.9) ; platform_python_implementation == \"CPython\"", "brotlicffi (>=0.8.0) ; platform_python_implementation != \"CPython\""]
 h2 = ["h2 (>=4,<5)"]
 socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"]
 zstd = ["zstandard (>=0.18.0)"]
@@ -4218,7 +4115,6 @@ description = "Virtual Python Environment builder"
 optional = false
 python-versions = ">=3.8"
 groups = ["dev"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "virtualenv-20.35.4-py3-none-any.whl", hash = "sha256:c21c9cede36c9753eeade68ba7d523529f228a403463376cf821eaae2b650f1b"},
     {file = "virtualenv-20.35.4.tar.gz", hash = "sha256:643d3914d73d3eeb0c552cbb12d7e82adf0e504dbf86a3182f8771a153a1971c"},
@@ -4232,7 +4128,7 @@ typing-extensions = {version = ">=4.13.2", markers = "python_version < \"3.11\""
 
 [package.extras]
 docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.2,!=7.3)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"]
-test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest (>=7.4)", "pytest-env (>=0.8.2)", "pytest-freezer (>=0.4.8)", "pytest-mock (>=3.11.1)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "setuptools (>=68)", "time-machine (>=2.10)"]
+test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest (>=7.4)", "pytest-env (>=0.8.2)", "pytest-freezer (>=0.4.8) ; platform_python_implementation == \"PyPy\" or platform_python_implementation == \"GraalVM\" or platform_python_implementation == \"CPython\" and sys_platform == \"win32\" and python_version >= \"3.13\"", "pytest-mock (>=3.11.1)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "setuptools (>=68)", "time-machine (>=2.10) ; platform_python_implementation == \"CPython\""]
 
 [[package]]
 name = "wcwidth"
@@ -4241,7 +4137,6 @@ description = "Measures the displayed width of unicode strings in a terminal"
 optional = false
 python-versions = ">=3.6"
 groups = ["main", "docs", "test"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "wcwidth-0.2.14-py2.py3-none-any.whl", hash = "sha256:a7bb560c8aee30f9957e5f9895805edd20602f2d7f720186dfd906e82b4982e1"},
     {file = "wcwidth-0.2.14.tar.gz", hash = "sha256:4d478375d31bc5395a3c55c40ccdf3354688364cd61c4f6adacaa9215d0b3605"},
@@ -4254,7 +4149,6 @@ description = "A built-package format for Python"
 optional = false
 python-versions = ">=3.8"
 groups = ["main"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "wheel-0.45.1-py3-none-any.whl", hash = "sha256:708e7481cc80179af0e556bbf0cc00b8444c7321e2700b8d8580231d13017248"},
     {file = "wheel-0.45.1.tar.gz", hash = "sha256:661e1abd9198507b1409a20c02106d9670b2576e916d58f520316666abca6729"},
@@ -4270,14 +4164,13 @@ description = "Backport of pathlib-compatible object wrapper for zip files"
 optional = false
 python-versions = ">=3.9"
 groups = ["docs"]
-markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
 files = [
     {file = "zipp-3.23.0-py3-none-any.whl", hash = "sha256:071652d6115ed432f5ce1d34c336c0adfd6a884660d1e9712a256d3d3bd4b14e"},
     {file = "zipp-3.23.0.tar.gz", hash = "sha256:a07157588a12518c9d4034df3fbbee09c814741a33ff63c05fa29d26a2404166"},
 ]
 
 [package.extras]
-check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"]
+check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1) ; sys_platform != \"cygwin\""]
 cover = ["pytest-cov"]
 doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
 enabler = ["pytest-enabler (>=2.2)"]

From e95e8603b082e50b7873eab0ae1f8abf7b4d25bc Mon Sep 17 00:00:00 2001
From: Manuel Lera-Ramirez <manulera14@gmail.com>
Date: Tue, 25 Nov 2025 18:44:44 +0000
Subject: [PATCH 16/22] comment Location out

---
 src/pydna/genbank.py            | 5 +++--
 src/pydna/opencloning_models.py | 2 +-
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/src/pydna/genbank.py b/src/pydna/genbank.py
index 6cd96043..18433508 100644
--- a/src/pydna/genbank.py
+++ b/src/pydna/genbank.py
@@ -17,7 +17,8 @@
 from pydna.readers import read as _read
 
 from Bio import Entrez as _Entrez
-from Bio.SeqFeature import SimpleLocation
+
+# from Bio.SeqFeature import SimpleLocation
 from typing import Literal as _Literal, Optional as _Optional
 import re as _re
 import os as _os
@@ -179,7 +180,7 @@ def nucleotide(
         result.source = RepositoryIdSource(
             repository_id=item,
             repository_name="genbank",
-            location=SimpleLocation(seq_start, seq_stop, strand),
+            # location=SimpleLocation(seq_start, seq_stop, strand),
         )
         return result
 
diff --git a/src/pydna/opencloning_models.py b/src/pydna/opencloning_models.py
index 166870cd..c2e78cc2 100644
--- a/src/pydna/opencloning_models.py
+++ b/src/pydna/opencloning_models.py
@@ -384,7 +384,7 @@ class RepositoryIdSource(Source):
 
     repository_id: str
     repository_name: str
-    location: Location
+    # location: Location
 
 
 class RepositoryIdSourceWithSequenceFileUrl(RepositoryIdSource):

From ff396f5c6bb5def586a6af250d08957060868848 Mon Sep 17 00:00:00 2001
From: Manuel Lera-Ramirez <manulera14@gmail.com>
Date: Fri, 5 Dec 2025 17:08:19 +0000
Subject: [PATCH 17/22] fix existing genbank test and adapt to
 https://github.com/OpenCloning/OpenCloning_LinkML/pull/71

---
 poetry.lock                             | 22 ++++++++++-------
 pyproject.toml                          |  2 +-
 src/pydna/genbank.py                    | 15 ++++++++---
 src/pydna/opencloning_models.py         | 20 ++++++++-------
 tests/test_module_genbank.py            |  7 +++++-
 tests/test_module_opencloning_models.py | 33 +++++++++++++++++++++++++
 6 files changed, 75 insertions(+), 24 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 3b051b79..9f987173 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 2.1.3 and should not be changed by hand.
+# This file is automatically @generated by Poetry 2.2.1 and should not be changed by hand.
 
 [[package]]
 name = "accessible-pygments"
@@ -2127,22 +2127,26 @@ tomli = {version = ">=1.1.0", markers = "python_version < \"3.11\""}
 
 [[package]]
 name = "opencloning-linkml"
-version = "0.4.6"
+version = "0.4.8.post7.dev0+357d344"
 description = "A LinkML data model for OpenCloning"
 optional = false
-python-versions = "<4.0,>=3.10"
+python-versions = "^3.10"
 groups = ["main"]
-files = [
-    {file = "opencloning_linkml-0.4.6-py3-none-any.whl", hash = "sha256:442f29c4450dedbde7fbc2b750c448de8f15243a1d6d906767e60b7c90a688c0"},
-    {file = "opencloning_linkml-0.4.6.tar.gz", hash = "sha256:79e2e71b220b80846bd9296adbe08028937647b49e96ee7a726dd12068885c4e"},
-]
+files = []
+develop = false
 
 [package.dependencies]
-pydantic = ">=2.7.1,<3.0.0"
+pydantic = "^2.7.1"
 
 [package.extras]
 docs = ["linkml (>=1.9.2,<2.0.0)"]
 
+[package.source]
+type = "git"
+url = "https://github.com/OpenCloning/OpenCloning_LinkML"
+reference = "357d34453346ca5db7fa2c5895edc0fadd92f80a"
+resolved_reference = "357d34453346ca5db7fa2c5895edc0fadd92f80a"
+
 [[package]]
 name = "packaging"
 version = "25.0"
@@ -4186,4 +4190,4 @@ gel = ["matplotlib", "pillow", "scipy", "scipy"]
 [metadata]
 lock-version = "2.1"
 python-versions = ">=3.10,<4.0"
-content-hash = "3087cb5712ba46f202fd95cedc56096d25ff324b3c46ddf8a58de4fcd0b21392"
+content-hash = "37cf64a90a10395015d3f06e522ff21d8c08ea4cacb29a981aa52d1d2bf75f64"
diff --git a/pyproject.toml b/pyproject.toml
index dfa3fed6..a2341ec4 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -60,7 +60,7 @@ scipy = [
 ]
 seguid = ">=0.0.5"
 regex = "^2024.11.6"
-opencloning-linkml = "^0.4.5"
+opencloning-linkml = {git = "https://github.com/OpenCloning/OpenCloning_LinkML", rev = "357d34453346ca5db7fa2c5895edc0fadd92f80a"}
 [tool.poetry.extras]
 clipboard = ["pyperclip"]
 download = ["pyparsing", "requests"]
diff --git a/src/pydna/genbank.py b/src/pydna/genbank.py
index 18433508..87a47ffd 100644
--- a/src/pydna/genbank.py
+++ b/src/pydna/genbank.py
@@ -12,13 +12,13 @@
 `pydna.ini` file. See the documentation of :func:`pydna.open_config_folder`"""
 
 # from pydna.utils import memorize as _memorize
-from pydna.opencloning_models import RepositoryIdSource
+from pydna.opencloning_models import NCBISequenceSource
 from pydna.genbankrecord import GenbankRecord as _GenbankRecord
 from pydna.readers import read as _read
 
 from Bio import Entrez as _Entrez
+from Bio.SeqFeature import SimpleLocation
 
-# from Bio.SeqFeature import SimpleLocation
 from typing import Literal as _Literal, Optional as _Optional
 import re as _re
 import os as _os
@@ -176,11 +176,18 @@ def nucleotide(
         # _module_logger.info("text[:160]  %s", text[:160])
 
         result = _read(text)
+        # TODO: Address this for cases where only one is defined
+        if seq_start is not None and seq_stop is not None:
+            location = SimpleLocation(
+                int(seq_start) - 1, int(seq_stop), -1 if strand == 2 else strand
+            )
+        else:
+            location = None
 
-        result.source = RepositoryIdSource(
+        result.source = NCBISequenceSource(
             repository_id=item,
             repository_name="genbank",
-            # location=SimpleLocation(seq_start, seq_stop, strand),
+            coordinates=location,
         )
         return result
 
diff --git a/src/pydna/opencloning_models.py b/src/pydna/opencloning_models.py
index c2e78cc2..e99f4c04 100644
--- a/src/pydna/opencloning_models.py
+++ b/src/pydna/opencloning_models.py
@@ -71,8 +71,9 @@
     AnnotationReport as _AnnotationReport,
     PlannotateAnnotationReport as _PlannotateAnnotationReport,
     ReverseComplementSource as _ReverseComplementSource,
+    NCBISequenceSource as _NCBISequenceSource,
 )
-from Bio.SeqFeature import Location, LocationParserError
+from Bio.SeqFeature import Location, LocationParserError, SimpleLocation
 from Bio.Restriction.Restriction import AbstractCut
 import networkx as nx
 from typing import List
@@ -441,16 +442,19 @@ class OpenDNACollectionsSource(RepositoryIdSourceWithSequenceFileUrl):
     repository_name: str = "open_dna_collections"
 
 
-class GenomeCoordinatesSource(Source):
+class NCBISequenceSource(RepositoryIdSource):
+    TARGET_MODEL: ClassVar[Type[_NCBISequenceSource]] = _NCBISequenceSource
+    repository_name: str = "genbank"
+    coordinates: SimpleLocation | None = None
+
+
+class GenomeCoordinatesSource(NCBISequenceSource):
     TARGET_MODEL: ClassVar[Type[_GenomeCoordinatesSource]] = _GenomeCoordinatesSource
 
     assembly_accession: Optional[str] = None
-    sequence_accession: str
     locus_tag: Optional[str] = None
     gene_id: Optional[int] = None
-    start: int
-    end: int
-    strand: int
+    coordinates: SimpleLocation
 
 
 class RestrictionAndLigationSource(AssemblySource):
@@ -626,9 +630,7 @@ def add_dseqrecord(self, dseqr: "Dseqrecord"):
                 else:
                     self.add_primer(source_input.sequence)
         else:
-            self.sources.append(
-                _ManuallyTypedSource(id=get_id(dseqr), input=[], user_input="A")
-            )
+            self.sources.append(_ManuallyTypedSource(id=get_id(dseqr), input=[]))
 
     def reassign_ids(self):
         all_ids = (
diff --git a/tests/test_module_genbank.py b/tests/test_module_genbank.py
index 4e9ca824..b92bfe9c 100755
--- a/tests/test_module_genbank.py
+++ b/tests/test_module_genbank.py
@@ -5,6 +5,7 @@
 
 import pytest
 from unittest import mock
+from Bio.SeqFeature import SimpleLocation
 
 
 def test_set_email():
@@ -105,6 +106,7 @@ def test_pydna_Genbank_fresh_part(monkeypatch):
     monkeypatch.setenv("pydna_cached_funcs", "")
     import pytest
     from unittest import mock
+    from Bio import SeqIO
 
     mock_efetch = mock.MagicMock(name="mock_efetch1")
     mock_efetch().read.side_effect = open("X60065-100-110.gb", "r").read
@@ -113,8 +115,11 @@ def test_pydna_Genbank_fresh_part(monkeypatch):
     from pydna.genbank import Genbank
 
     gb = Genbank("bjornjobb@gmail.com")
-    result = gb.nucleotide("X60065.1", seq_start=1, seq_stop=10)
+    result = gb.nucleotide("X60065.1", seq_start=100, seq_stop=110)
     assert str(result.seq).lower() == "ctgaaacggac"
+    assert result.source.coordinates == SimpleLocation(99, 110, 1)
+    full_sequence = SeqIO.read("X60065.gb", "genbank")
+    assert str(result.source.coordinates.extract(full_sequence.seq)) == str(result.seq)
 
 
 def test_pydna_Genbank_fresh_partII(monkeypatch):
diff --git a/tests/test_module_opencloning_models.py b/tests/test_module_opencloning_models.py
index 93dec8be..f433a87a 100644
--- a/tests/test_module_opencloning_models.py
+++ b/tests/test_module_opencloning_models.py
@@ -14,6 +14,8 @@
     CloningStrategy,
     id_mode,
     get_id,
+    NCBISequenceSource,
+    GenomeCoordinatesSource,
 )
 from pydna.primer import Primer
 from pydna.oligonucleotide_hybridization import oligonucleotide_hybridization
@@ -569,3 +571,34 @@ def test_id_mode(self):
             self.assertEqual(get_id(dseqrecord), 456)
             self.assertRaises(ValueError, get_id, primer_wrong)
             self.assertRaises(ValueError, get_id, dseqrecord_wrong)
+
+
+class GenomeCoordinatesSourceTest(TestCase):
+    def test_coordinates_required(self):
+        with self.assertRaises(ValidationError):
+            GenomeCoordinatesSource(
+                coordinates=None,
+                repository_id="1234567890",
+                assembly_accession="1234567890",
+                locus_tag="1234567890",
+                gene_id=1234567890,
+            )
+        GenomeCoordinatesSource(
+            coordinates=SimpleLocation(1, 10),
+            repository_id="1234567890",
+            assembly_accession="1234567890",
+            locus_tag="1234567890",
+            gene_id=1234567890,
+        )
+
+
+class NCBISequenceSourceTest(TestCase):
+    def test_coordinates_not_required(self):
+        NCBISequenceSource(
+            coordinates=None,
+            repository_id="1234567890",
+        )
+        NCBISequenceSource(
+            coordinates=SimpleLocation(1, 10),
+            repository_id="1234567890",
+        )

From d3dd8a97e54d2bdb067881869f3d6f03100d2498 Mon Sep 17 00:00:00 2001
From: Manuel Lera-Ramirez <manulera14@gmail.com>
Date: Fri, 5 Dec 2025 23:20:27 +0000
Subject: [PATCH 18/22] update linkml model

---
 poetry.lock    | 8 ++++----
 pyproject.toml | 2 +-
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 9f987173..00519042 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -2127,7 +2127,7 @@ tomli = {version = ">=1.1.0", markers = "python_version < \"3.11\""}
 
 [[package]]
 name = "opencloning-linkml"
-version = "0.4.8.post7.dev0+357d344"
+version = "0.4.8.post8.dev0+75b4da2"
 description = "A LinkML data model for OpenCloning"
 optional = false
 python-versions = "^3.10"
@@ -2144,8 +2144,8 @@ docs = ["linkml (>=1.9.2,<2.0.0)"]
 [package.source]
 type = "git"
 url = "https://github.com/OpenCloning/OpenCloning_LinkML"
-reference = "357d34453346ca5db7fa2c5895edc0fadd92f80a"
-resolved_reference = "357d34453346ca5db7fa2c5895edc0fadd92f80a"
+reference = "75b4da253be0b9d62f17661c4ecf5fa1602cbf76"
+resolved_reference = "75b4da253be0b9d62f17661c4ecf5fa1602cbf76"
 
 [[package]]
 name = "packaging"
@@ -4190,4 +4190,4 @@ gel = ["matplotlib", "pillow", "scipy", "scipy"]
 [metadata]
 lock-version = "2.1"
 python-versions = ">=3.10,<4.0"
-content-hash = "37cf64a90a10395015d3f06e522ff21d8c08ea4cacb29a981aa52d1d2bf75f64"
+content-hash = "8aa1b31a211fbb38b97dcb0f91c42aaab3c9bcd4c950c556f4a8120d3f6eeb56"
diff --git a/pyproject.toml b/pyproject.toml
index a2341ec4..97c16610 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -60,7 +60,7 @@ scipy = [
 ]
 seguid = ">=0.0.5"
 regex = "^2024.11.6"
-opencloning-linkml = {git = "https://github.com/OpenCloning/OpenCloning_LinkML", rev = "357d34453346ca5db7fa2c5895edc0fadd92f80a"}
+opencloning-linkml = {git = "https://github.com/OpenCloning/OpenCloning_LinkML", rev = "75b4da253be0b9d62f17661c4ecf5fa1602cbf76"}
 [tool.poetry.extras]
 clipboard = ["pyperclip"]
 download = ["pyparsing", "requests"]

From edb1521c60dcc9686c2c1dc95efeef63626be165 Mon Sep 17 00:00:00 2001
From: Manuel Lera-Ramirez <manulera14@gmail.com>
Date: Sat, 6 Dec 2025 01:12:36 +0000
Subject: [PATCH 19/22] update linkml model and drop repository_name field

---
 poetry.lock                     |  8 ++++----
 pyproject.toml                  |  2 +-
 src/pydna/genbank.py            |  1 -
 src/pydna/opencloning_models.py | 13 -------------
 src/pydna/parsers.py            |  4 +++-
 5 files changed, 8 insertions(+), 20 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 00519042..9ecb73d4 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -2127,7 +2127,7 @@ tomli = {version = ">=1.1.0", markers = "python_version < \"3.11\""}
 
 [[package]]
 name = "opencloning-linkml"
-version = "0.4.8.post8.dev0+75b4da2"
+version = "0.4.8.post11.dev0+51cb847"
 description = "A LinkML data model for OpenCloning"
 optional = false
 python-versions = "^3.10"
@@ -2144,8 +2144,8 @@ docs = ["linkml (>=1.9.2,<2.0.0)"]
 [package.source]
 type = "git"
 url = "https://github.com/OpenCloning/OpenCloning_LinkML"
-reference = "75b4da253be0b9d62f17661c4ecf5fa1602cbf76"
-resolved_reference = "75b4da253be0b9d62f17661c4ecf5fa1602cbf76"
+reference = "51cb847cda2ffc7eebbc9d3e7b5595969463b465"
+resolved_reference = "51cb847cda2ffc7eebbc9d3e7b5595969463b465"
 
 [[package]]
 name = "packaging"
@@ -4190,4 +4190,4 @@ gel = ["matplotlib", "pillow", "scipy", "scipy"]
 [metadata]
 lock-version = "2.1"
 python-versions = ">=3.10,<4.0"
-content-hash = "8aa1b31a211fbb38b97dcb0f91c42aaab3c9bcd4c950c556f4a8120d3f6eeb56"
+content-hash = "e802a0f307a0e2e7bce549a3b1ca124f438545f01ba040ebdd41b67b80b51806"
diff --git a/pyproject.toml b/pyproject.toml
index 97c16610..291ad4f0 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -60,7 +60,7 @@ scipy = [
 ]
 seguid = ">=0.0.5"
 regex = "^2024.11.6"
-opencloning-linkml = {git = "https://github.com/OpenCloning/OpenCloning_LinkML", rev = "75b4da253be0b9d62f17661c4ecf5fa1602cbf76"}
+opencloning-linkml = {git = "https://github.com/OpenCloning/OpenCloning_LinkML", rev = "51cb847cda2ffc7eebbc9d3e7b5595969463b465"}
 [tool.poetry.extras]
 clipboard = ["pyperclip"]
 download = ["pyparsing", "requests"]
diff --git a/src/pydna/genbank.py b/src/pydna/genbank.py
index 87a47ffd..2b21e719 100644
--- a/src/pydna/genbank.py
+++ b/src/pydna/genbank.py
@@ -186,7 +186,6 @@ def nucleotide(
 
         result.source = NCBISequenceSource(
             repository_id=item,
-            repository_name="genbank",
             coordinates=location,
         )
         return result
diff --git a/src/pydna/opencloning_models.py b/src/pydna/opencloning_models.py
index e99f4c04..26129b7f 100644
--- a/src/pydna/opencloning_models.py
+++ b/src/pydna/opencloning_models.py
@@ -384,7 +384,6 @@ class RepositoryIdSource(Source):
     TARGET_MODEL: ClassVar[Type[_RepositoryIdSource]] = _RepositoryIdSource
 
     repository_id: str
-    repository_name: str
     # location: Location
 
 
@@ -401,50 +400,38 @@ class AddgeneIdSource(RepositoryIdSourceWithSequenceFileUrl):
     TARGET_MODEL: ClassVar[Type[_AddgeneIdSource]] = _AddgeneIdSource
 
     addgene_sequence_type: Optional[AddgeneSequenceType] = None
-    repository_name: str = "addgene"
 
 
 class BenchlingUrlSource(RepositoryIdSource):
     TARGET_MODEL: ClassVar[Type[_BenchlingUrlSource]] = _BenchlingUrlSource
 
-    repository_name: str = "benchling"
-
 
 class SnapGenePlasmidSource(RepositoryIdSource):
     TARGET_MODEL: ClassVar[Type[_SnapGenePlasmidSource]] = _SnapGenePlasmidSource
 
-    repository_name: str = "snapgene"
-
 
 class EuroscarfSource(RepositoryIdSource):
     TARGET_MODEL: ClassVar[Type[_EuroscarfSource]] = _EuroscarfSource
 
-    repository_name: str = "euroscarf"
-
 
 class WekWikGeneIdSource(RepositoryIdSourceWithSequenceFileUrl):
     TARGET_MODEL: ClassVar[Type[_WekWikGeneIdSource]] = _WekWikGeneIdSource
-    repository_name: str = "wekwikgene"
 
 
 class SEVASource(RepositoryIdSourceWithSequenceFileUrl):
     TARGET_MODEL: ClassVar[Type[_SEVASource]] = _SEVASource
-    repository_name: str = "seva"
 
 
 class IGEMSource(RepositoryIdSourceWithSequenceFileUrl):
     TARGET_MODEL: ClassVar[Type[_IGEMSource]] = _IGEMSource
-    repository_name: str = "igem"
 
 
 class OpenDNACollectionsSource(RepositoryIdSourceWithSequenceFileUrl):
     TARGET_MODEL: ClassVar[Type[_OpenDNACollectionsSource]] = _OpenDNACollectionsSource
-    repository_name: str = "open_dna_collections"
 
 
 class NCBISequenceSource(RepositoryIdSource):
     TARGET_MODEL: ClassVar[Type[_NCBISequenceSource]] = _NCBISequenceSource
-    repository_name: str = "genbank"
     coordinates: SimpleLocation | None = None
 
 
diff --git a/src/pydna/parsers.py b/src/pydna/parsers.py
index 9d0e7dc7..44af05f2 100644
--- a/src/pydna/parsers.py
+++ b/src/pydna/parsers.py
@@ -202,7 +202,9 @@ def parse(data, ds=True):
 
                     result = _Dseqrecord.from_SeqRecord(s)
                     result.source = UploadedFileSource(
-                        file_name=path, sequence_file_format="genbank", index_in_file=0
+                        file_name=str(path),  # we use str to handle PosixPath
+                        sequence_file_format="genbank",
+                        index_in_file=0,
                     )
                     sequences.append(result)
                     # sequences.append(_GenbankFile.from_SeqRecord(s, path=path))

From 6a29aa9a7ed9a87e16a386158b5719bf8c905703 Mon Sep 17 00:00:00 2001
From: Manuel Lera-Ramirez <manulera14@gmail.com>
Date: Sat, 6 Dec 2025 01:33:25 +0000
Subject: [PATCH 20/22] add location serializer to GenomeCoordinatesSource

---
 src/pydna/opencloning_models.py         |  4 ++++
 tests/test_module_opencloning_models.py | 10 ++++++++++
 2 files changed, 14 insertions(+)

diff --git a/src/pydna/opencloning_models.py b/src/pydna/opencloning_models.py
index 26129b7f..b1ea6549 100644
--- a/src/pydna/opencloning_models.py
+++ b/src/pydna/opencloning_models.py
@@ -443,6 +443,10 @@ class GenomeCoordinatesSource(NCBISequenceSource):
     gene_id: Optional[int] = None
     coordinates: SimpleLocation
 
+    @field_serializer("coordinates")
+    def serialize_coordinates(self, coordinates: SimpleLocation) -> str:
+        return SequenceLocationStr.from_biopython_location(coordinates)
+
 
 class RestrictionAndLigationSource(AssemblySource):
     restriction_enzymes: list[AbstractCut]
diff --git a/tests/test_module_opencloning_models.py b/tests/test_module_opencloning_models.py
index f433a87a..2bf8b8e7 100644
--- a/tests/test_module_opencloning_models.py
+++ b/tests/test_module_opencloning_models.py
@@ -591,6 +591,16 @@ def test_coordinates_required(self):
             gene_id=1234567890,
         )
 
+    def test_serialize_coordinates(self):
+        source = GenomeCoordinatesSource(
+            coordinates=SimpleLocation(0, 10),
+            repository_id="1234567890",
+            assembly_accession="1234567890",
+            locus_tag="1234567890",
+            gene_id=1234567890,
+        )
+        self.assertEqual(source.model_dump()["coordinates"], "1..10")
+
 
 class NCBISequenceSourceTest(TestCase):
     def test_coordinates_not_required(self):

From a2feb173168b285ae2a621d04e6ab5510da21bd2 Mon Sep 17 00:00:00 2001
From: Manuel Lera-Ramirez <manulera14@gmail.com>
Date: Sat, 6 Dec 2025 02:26:13 +0000
Subject: [PATCH 21/22] update opencloning-linkml to released version

---
 poetry.lock    | 268 ++++++++++++++++++++++++-------------------------
 pyproject.toml |   2 +-
 2 files changed, 135 insertions(+), 135 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 9ecb73d4..ba6af5bf 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -2127,26 +2127,22 @@ tomli = {version = ">=1.1.0", markers = "python_version < \"3.11\""}
 
 [[package]]
 name = "opencloning-linkml"
-version = "0.4.8.post11.dev0+51cb847"
+version = "0.4.9"
 description = "A LinkML data model for OpenCloning"
 optional = false
-python-versions = "^3.10"
+python-versions = "<4.0,>=3.10"
 groups = ["main"]
-files = []
-develop = false
+files = [
+    {file = "opencloning_linkml-0.4.9-py3-none-any.whl", hash = "sha256:1adcaffacf167c90475b23c4e134093db369af73be27d2b9ac9ab3cfeb39a7f1"},
+    {file = "opencloning_linkml-0.4.9.tar.gz", hash = "sha256:a243d1875df0bf7b3c9487770cd64c0db25c84254a292e2dcea94d9598e9717c"},
+]
 
 [package.dependencies]
-pydantic = "^2.7.1"
+pydantic = ">=2.7.1,<3.0.0"
 
 [package.extras]
 docs = ["linkml (>=1.9.2,<2.0.0)"]
 
-[package.source]
-type = "git"
-url = "https://github.com/OpenCloning/OpenCloning_LinkML"
-reference = "51cb847cda2ffc7eebbc9d3e7b5595969463b465"
-resolved_reference = "51cb847cda2ffc7eebbc9d3e7b5595969463b465"
-
 [[package]]
 name = "packaging"
 version = "25.0"
@@ -2587,19 +2583,19 @@ files = [
 
 [[package]]
 name = "pydantic"
-version = "2.12.3"
+version = "2.12.5"
 description = "Data validation using Python type hints"
 optional = false
 python-versions = ">=3.9"
 groups = ["main"]
 files = [
-    {file = "pydantic-2.12.3-py3-none-any.whl", hash = "sha256:6986454a854bc3bc6e5443e1369e06a3a456af9d339eda45510f517d9ea5c6bf"},
-    {file = "pydantic-2.12.3.tar.gz", hash = "sha256:1da1c82b0fc140bb0103bc1441ffe062154c8d38491189751ee00fd8ca65ce74"},
+    {file = "pydantic-2.12.5-py3-none-any.whl", hash = "sha256:e561593fccf61e8a20fc46dfc2dfe075b8be7d0188df33f221ad1f0139180f9d"},
+    {file = "pydantic-2.12.5.tar.gz", hash = "sha256:4d351024c75c0f085a9febbb665ce8c0c6ec5d30e903bdb6394b7ede26aebb49"},
 ]
 
 [package.dependencies]
 annotated-types = ">=0.6.0"
-pydantic-core = "2.41.4"
+pydantic-core = "2.41.5"
 typing-extensions = ">=4.14.1"
 typing-inspection = ">=0.4.2"
 
@@ -2609,129 +2605,133 @@ timezone = ["tzdata ; python_version >= \"3.9\" and platform_system == \"Windows
 
 [[package]]
 name = "pydantic-core"
-version = "2.41.4"
+version = "2.41.5"
 description = "Core functionality for Pydantic validation and serialization"
 optional = false
 python-versions = ">=3.9"
 groups = ["main"]
 files = [
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+    {file = "pydantic_core-2.41.5.tar.gz", hash = "sha256:08daa51ea16ad373ffd5e7606252cc32f07bc72b28284b6bc9c6df804816476e"},
 ]
 
 [package.dependencies]
@@ -4190,4 +4190,4 @@ gel = ["matplotlib", "pillow", "scipy", "scipy"]
 [metadata]
 lock-version = "2.1"
 python-versions = ">=3.10,<4.0"
-content-hash = "e802a0f307a0e2e7bce549a3b1ca124f438545f01ba040ebdd41b67b80b51806"
+content-hash = "e61b9384d308d904eb18f19078b77c56f72956510622199095ff2f820a67d4c9"
diff --git a/pyproject.toml b/pyproject.toml
index 291ad4f0..0b07fea0 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -60,7 +60,7 @@ scipy = [
 ]
 seguid = ">=0.0.5"
 regex = "^2024.11.6"
-opencloning-linkml = {git = "https://github.com/OpenCloning/OpenCloning_LinkML", rev = "51cb847cda2ffc7eebbc9d3e7b5595969463b465"}
+opencloning-linkml = "^0.4.9"
 [tool.poetry.extras]
 clipboard = ["pyperclip"]
 download = ["pyparsing", "requests"]

From 6f25090ec653e38219021aa46fa4440f888e958c Mon Sep 17 00:00:00 2001
From: Manuel Lera-Ramirez <manulera14@gmail.com>
Date: Sat, 6 Dec 2025 02:33:23 +0000
Subject: [PATCH 22/22] add utility to get coordinates in the format used for
 the NCBI API

---
 src/pydna/opencloning_models.py         | 8 ++++++++
 tests/test_module_opencloning_models.py | 9 +++++++++
 2 files changed, 17 insertions(+)

diff --git a/src/pydna/opencloning_models.py b/src/pydna/opencloning_models.py
index b1ea6549..a3708dbf 100644
--- a/src/pydna/opencloning_models.py
+++ b/src/pydna/opencloning_models.py
@@ -200,6 +200,14 @@ def from_start_and_end(
     ):
         return cls.from_biopython_location(create_location(start, end, seq_len, strand))
 
+    def get_ncbi_format_coordinates(self) -> str:
+        """Return start, end, strand in the same format as the NCBI eutils API (1-based, inclusive)"""
+        return (
+            self.to_biopython_location().start + 1,
+            self.to_biopython_location().end,
+            self.to_biopython_location().strand,
+        )
+
 
 class ConfiguredBaseModel(BaseModel):
     model_config = ConfigDict(
diff --git a/tests/test_module_opencloning_models.py b/tests/test_module_opencloning_models.py
index 2bf8b8e7..67667faf 100644
--- a/tests/test_module_opencloning_models.py
+++ b/tests/test_module_opencloning_models.py
@@ -224,6 +224,15 @@ class DummyModel(BaseModel):
         DummyModel(location="1..3")
         DummyModel(location=SequenceLocationStr("1..3"))
 
+    def test_get_ncbi_format_coordinates(self):
+        self.assertEqual(
+            SequenceLocationStr("1..3").get_ncbi_format_coordinates(), (1, 3, 1)
+        )
+        self.assertEqual(
+            SequenceLocationStr("complement(1..3)").get_ncbi_format_coordinates(),
+            (1, 3, -1),
+        )
+
 
 class SourceTest(TestCase):
     def test_to_pydantic_model(self):