Support for Base Editor Data

.github/workflows/run-tests-on-push.yml

@@ -6,9 +6,23 @@ env:
   LOG_CONFIG: test
 
 jobs:
+  run-tests-3_9-core-dependencies:
+    runs-on: ubuntu-latest
+    name: Pytest on Core Dependencies-- Python 3.9
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
+      with:
+        python-version: "3.9"
+        cache: 'pip'
+    - run: pip install --upgrade pip
+    - run: pip install poetry
+    - run: poetry install --with dev
+    - run: poetry run pytest tests/
+
   run-tests-3_9:
     runs-on: ubuntu-latest
-    name: Pytest on Python 3.9
+    name: Pytest on Optional Dependencies-- Python 3.9
     steps:
     - uses: actions/checkout@v4
     - uses: actions/setup-python@v5
@@ -20,9 +34,23 @@ jobs:
     - run: poetry install --with dev --extras server
     - run: poetry run pytest tests/ --show-capture=stdout --cov=src
 
+  run-tests-3_10-core-dependencies:
+    runs-on: ubuntu-latest
+    name: Pytest on Core Dependencies-- Python 3.10
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
+      with:
+        python-version: "3.10"
+        cache: 'pip'
+    - run: pip install --upgrade pip
+    - run: pip install poetry
+    - run: poetry install --with dev
+    - run: poetry run pytest tests/
+
   run-tests-3_10:
     runs-on: ubuntu-latest
-    name: Pytest on Python 3.10
+    name: Pytest on Optional Dependencies-- Python 3.10
     steps:
     - uses: actions/checkout@v4
     - uses: actions/setup-python@v5
@@ -34,9 +62,23 @@ jobs:
     - run: poetry install --with dev --extras server
     - run: poetry run pytest tests/ --show-capture=stdout --cov=src
 
+  run-tests-3_11-core-dependencies:
+    runs-on: ubuntu-latest
+    name: Pytest on Core Dependencies-- Python 3.11
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
+      with:
+        python-version: "3.11"
+        cache: 'pip'
+    - run: pip install --upgrade pip
+    - run: pip install poetry
+    - run: poetry install --with dev
+    - run: poetry run pytest tests/
+
   run-tests-3_11:
     runs-on: ubuntu-latest
-    name: Pytest on Python 3.11
+    name: Pytest on Optional Dependencies-- Python 3.11
     steps:
     - uses: actions/checkout@v4
     - uses: actions/setup-python@v5
@@ -50,7 +92,7 @@ jobs:
 
   run-mypy-3_10:
     runs-on: ubuntu-latest
-    name: MyPy checks on Python 3.10
+    name: MyPy on Full Codebase-- Python 3.10
     steps:
     - uses: actions/checkout@v4
     - uses: actions/setup-python@v5
@@ -64,7 +106,7 @@ jobs:
 
   run-ruff-lint:
     runs-on: ubuntu-latest
-    name: Ruff linting on Python 3.10
+    name: Ruff on Full Codebase-- Python 3.10
     steps:
     - uses: actions/checkout@v4
     - uses: actions/setup-python@v5

Dockerfile

@@ -2,7 +2,7 @@
 # python-base
 # Set up shared environment variables
 ################################
-FROM python:3.9 as python-base
+FROM python:3.9 AS python-base
 
     # Poetry
     # https://python-poetry.org/docs/configuration/#using-environment-variables
@@ -69,7 +69,7 @@ RUN samtools faidx GCF_000001405.39_GRCh38.p13_genomic.fna.gz
 # builder
 # Builds application dependencies and creates venv
 ################################
-FROM python-base as builder
+FROM python-base AS builder
 
 WORKDIR /code
 
@@ -90,7 +90,7 @@ COPY src/mavedb/server_main.py /code/main.py
 # worker
 # Worker image
 ################################
-FROM builder as worker
+FROM builder AS worker
 COPY --from=downloader /data /data
 
 # copy pre-built poetry + venv
@@ -103,7 +103,7 @@ CMD ["arq", "mavedb.worker.WorkerSettings"]
 # application
 # Application image
 ################################
-FROM builder as application
+FROM builder AS application
 COPY --from=downloader /data /data
 
 # copy pre-built poetry + venv

alembic/versions/f69b4049bc3b_add_is_base_editor_column_to_target_.py

@@ -0,0 +1,31 @@
+"""Add is_base_editor column to target_accessions
+
+Revision ID: f69b4049bc3b
+Revises: c404b6719110
+Create Date: 2025-03-02 14:06:52.217554
+
+"""
+
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = "f69b4049bc3b"
+down_revision = "c404b6719110"
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.add_column(
+        "target_accessions", sa.Column("is_base_editor", sa.Boolean(), nullable=False, server_default="false")
+    )
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_column("target_accessions", "is_base_editor")
+    # ### end Alembic commands ###

docker-compose-dev.yml

@@ -23,6 +23,7 @@ services:
       - "8002:8000"
     volumes:
       - .:/code
+      - mavedb-seqrepo-dev:/usr/local/share/seqrepo
 
   worker:
     image: mavedb-api/mavedb-worker:dev
@@ -41,6 +42,7 @@ services:
       LOG_CONFIG: dev
     volumes:
       - .:/code
+      - mavedb-seqrepo-dev:/usr/local/share/seqrepo
     depends_on:
       - db
       - redis
@@ -77,15 +79,10 @@ services:
       - mavedb-seqrepo-dev:/usr/local/share/seqrepo
 
   seqrepo:
-    image: biocommons/seqrepo:2021-01-29
+    image: biocommons/seqrepo:2024-12-20
     volumes:
       - mavedb-seqrepo-dev:/usr/local/share/seqrepo
 
-#  rabbitmq:
-#    image: rabbitmq:3.8.3
-#    ports:
-#      - "5673:5672"
-
 volumes:
   mavedb-data-dev:
   mavedb-redis-dev:

mypy_stubs/cdot/hgvs/dataproviders/fasta_seqfetcher.pyi

@@ -1,6 +1,7 @@
 from typing import Union
 
-from hgvs.dataproviders.seqfetcher import SeqFetcher
+class SeqFetcher:
+    def __init__(self, *args) -> None: ...
 
 class FastaSeqFetcher:
     def __init__(self, *args, cache: bool = True) -> None: ...

mypy_stubs/mavehgvs/variant.pyi

@@ -1,4 +1,5 @@
-from typing import Any, List, Mapping, Optional, Sequence, Tuple, Union
+from typing import Any, Callable, List, Mapping, Optional, Sequence, Tuple, Union
+from re import Match
 
 from .position import VariantPosition
 
@@ -21,3 +22,5 @@ class Variant:
     prefix: str
 
     sequence: Union[str, Tuple[str, str], List[Optional[Union[str, Tuple[str, str]]]], None]
+    is_multi_variant: Callable[..., bool]
+    fullmatch: Callable[..., Optional[Match[str]]]