From e689678cbedf46d794b4ab93b019980ef7e9131d Mon Sep 17 00:00:00 2001
From: Synchon Mandal <synchon@protonmail.com>
Date: Wed, 17 Dec 2025 11:26:16 +0100
Subject: [PATCH 01/32] update: add yaml dep and config

---
 julio/_yaml.py | 16 +++++++++++
 pyproject.toml |  1 +
 uv.lock        | 72 ++++++++++++++++++++++++++++++++++++++++++++++++++
 3 files changed, 89 insertions(+)
 create mode 100644 julio/_yaml.py

diff --git a/julio/_yaml.py b/julio/_yaml.py
new file mode 100644
index 0000000..732ca75
--- /dev/null
+++ b/julio/_yaml.py
@@ -0,0 +1,16 @@
+"""Provide YAML config definition for junifer use."""
+
+# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+from ruamel.yaml import YAML
+
+
+__all__ = ["yaml"]
+
+
+# Configure YAML class once for further use
+yaml = YAML()
+yaml.default_flow_style = False
+yaml.allow_unicode = True
+yaml.indent(mapping=2, sequence=4, offset=2)
diff --git a/pyproject.toml b/pyproject.toml
index 7fe3fda..5017ba0 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -39,6 +39,7 @@ dependencies = [
     "datalad>=1.0.0,<1.3.0",
     "lazy_loader==0.4",
     "structlog>=25.0.0,<26.0.0",
+    "ruamel.yaml>=0.17,<0.19",
 ]
 dynamic = ["version"]
 
diff --git a/uv.lock b/uv.lock
index 8b60db2..bbd033a 100644
--- a/uv.lock
+++ b/uv.lock
@@ -488,6 +488,7 @@ dependencies = [
     { name = "click" },
     { name = "datalad" },
     { name = "lazy-loader" },
+    { name = "ruamel-yaml" },
     { name = "structlog" },
 ]
 
@@ -505,6 +506,7 @@ requires-dist = [
     { name = "datalad", specifier = ">=1.0.0,<1.3.0" },
     { name = "lazy-loader", specifier = "==0.4" },
     { name = "pre-commit", marker = "extra == 'dev'" },
+    { name = "ruamel-yaml", specifier = ">=0.17,<0.19" },
     { name = "ruff", marker = "extra == 'dev'" },
     { name = "structlog", specifier = ">=25.0.0,<26.0.0" },
     { name = "towncrier", marker = "extra == 'dev'" },
@@ -942,6 +944,76 @@ wheels = [
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 ]
 
+[[package]]
+name = "ruamel-yaml"
+version = "0.18.16"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "ruamel-yaml-clib", marker = "python_full_version < '3.14' and platform_python_implementation == 'CPython'" },
+]
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+name = "ruamel-yaml-clib"
+version = "0.2.15"
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+]
+
 [[package]]
 name = "ruff"
 version = "0.14.8"

From c023dcea31d69a8e3f66b99ec04ec22209f03d71 Mon Sep 17 00:00:00 2001
From: Synchon Mandal <synchon@protonmail.com>
Date: Wed, 17 Dec 2025 11:28:12 +0100
Subject: [PATCH 02/32] update: add h5io, tqdm as deps and _utils.py

---
 julio/_utils.py | 398 ++++++++++++++++++++++++++++++++++++++++++++++++
 pyproject.toml  |   2 +
 uv.lock         | 220 +++++++++++++++++++++++++-
 3 files changed, 617 insertions(+), 3 deletions(-)
 create mode 100644 julio/_utils.py

diff --git a/julio/_utils.py b/julio/_utils.py
new file mode 100644
index 0000000..099b2f1
--- /dev/null
+++ b/julio/_utils.py
@@ -0,0 +1,398 @@
+"""Utilities for julio."""
+
+# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+import pathlib
+import re
+from pathlib import Path
+from typing import Any
+
+import click
+import datalad.api as dl
+import structlog
+from h5io import read_hdf5, write_hdf5
+from tqdm import tqdm
+
+from ._yaml import yaml
+
+
+__all__ = ["PathOrURL", "is_julio_registry", "process_features"]
+
+logger = structlog.get_logger()
+
+# The following is taken from:
+# https://validators.readthedocs.io/en/latest/_modules/validators/url.html#url
+# and based on:
+# https://gist.github.com/dperini/729294
+ip_middle_octet = r"(?:\.(?:1?\d{1,2}|2[0-4]\d|25[0-5]))"
+ip_last_octet = r"(?:\.(?:[1-9]\d?|1\d\d|2[0-4]\d|25[0-4]))"
+
+regex = re.compile(
+    "^"
+    # protocol identifier
+    "(?:(?:https?|ftp)://)"
+    # user:pass authentication
+    r"(?:\S+(?::\S*)?@)?"
+    "(?:"
+    "(?P<private_ip>"
+    # IP address exclusion
+    # private & local networks
+    "(?:(?:10|127)" + ip_middle_octet + "{2}" + ip_last_octet + ")|"
+    r"(?:(?:169\.254|192\.168)" + ip_middle_octet + ip_last_octet + ")|"
+    r"(?:172\.(?:1[6-9]|2\d|3[0-1])" + ip_middle_octet + ip_last_octet + "))"
+    "|"
+    # IP address dotted notation octets
+    # excludes loopback network 0.0.0.0
+    # excludes reserved space >= 224.0.0.0
+    # excludes network & broadcast addresses
+    # (first & last IP address of each class)
+    "(?P<public_ip>"
+    r"(?:[1-9]\d?|1\d\d|2[01]\d|22[0-3])"
+    "" + ip_middle_octet + "{2}"
+    "" + ip_last_octet + ")"
+    "|"
+    # host name
+    "(?:(?:[a-z\u00a1-\uffff0-9]-?)*[a-z\u00a1-\uffff0-9]+)"
+    # domain name
+    r"(?:\.(?:[a-z\u00a1-\uffff0-9]-?)*[a-z\u00a1-\uffff0-9]+)*"
+    # TLD identifier
+    r"(?:\.(?:[a-z\u00a1-\uffff]{2,}))"
+    ")"
+    # port number
+    r"(?::\d{2,5})?"
+    # resource path
+    r"(?:/\S*)?"
+    # query string
+    r"(?:\?\S*)?"
+    "$",
+    re.UNICODE | re.IGNORECASE,
+)
+
+pattern = re.compile(regex)
+
+
+class PathOrURLParamType(click.ParamType):
+    name = "path_or_url"
+
+    def convert(self, value, param, ctx):
+        # URL
+        if value.startswith("http"):
+            if pattern.match(value) is not None:
+                return value
+            else:
+                self.fail(f"{value!r} is not a valid url.", param, ctx)
+        # Path
+        try:
+            p = click.Path(
+                exists=True,
+                readable=True,
+                writable=True,
+                file_okay=False,
+                path_type=pathlib.Path,
+            ).convert(value, param, ctx)
+        except click.BadParameter as e:
+            self.fail(f"{e}", param, ctx)
+        else:
+            return p
+
+
+PathOrURL = PathOrURLParamType()
+
+
+def is_julio_registry(ds: dl.Dataset) -> bool:
+    """Check if the dataset is a julio registry.
+
+    Parameters
+    ----------
+    ds : dl.Dataset
+        Dataset to check.
+
+    Returns
+    -------
+    bool
+        True if the dataset is a julio registry, False otherwise.
+
+    """
+    if (ds.pathobj / "registry-config.yml").is_file():
+        return True
+    return False
+
+
+def _make_absolute_path(path: str, base_path: Path) -> str:
+    """Make a path absolute.
+
+    Parameters
+    ----------
+    path : str
+        Path to make absolute.
+    base_path : Path
+        Base path to use.
+
+    Returns
+    -------
+    str
+        Absolute path.
+
+    """
+    log = logger.bind(cmd="make_absolute_path", path=str(path))
+    log.debug("Making path absolute")
+    path = Path(path)
+    if not path.is_absolute():
+        path = base_path / path
+    log.debug("Made path absolute")
+    return str(path.resolve())
+
+
+def _adjust_paths(data: dict, yaml_path: Path) -> dict:
+    """Adjust paths in the data dictionary.
+
+    Parameters
+    ----------
+    data : dict
+        Data dictionary to adjust.
+    yaml_path : Path
+        Path to the YAML file.
+
+    Returns
+    -------
+    dict
+        Adjusted data dictionary.
+
+    """
+    log = logger.bind(cmd="adjust_paths", path=str(yaml_path.resolve()))
+    log.debug("Adjusting paths")
+    if "workdir" in data:
+        if isinstance(data["workdir"], str):
+            data["workdir"] = _make_absolute_path(
+                data["workdir"], yaml_path.parent
+            )
+        else:
+            data["workdir"]["path"] = _make_absolute_path(
+                data["workdir"]["path"], yaml_path.parent
+            )
+    if "with" in data:
+        if not isinstance(data["with"], list):
+            data["with"] = list(data["with"])
+        mods = []
+        for w in data["with"]:
+            if w.endswith(".py"):
+                mods.append(_make_absolute_path(w, yaml_path.parent))
+            else:
+                mods.append(w)
+        data["with"] = mods
+    data["storage"]["uri"] = _make_absolute_path(
+        data["storage"]["uri"], yaml_path.parent
+    )
+    log.debug("Adjusted paths")
+    return data
+
+
+def _parse_yaml(yaml_path: Path) -> dict:
+    """Parse the junifer YAML.
+
+    Parameters
+    ----------
+    yaml_path : Path
+        Path to the junifer YAML.
+
+    Returns
+    -------
+    dict
+        Parsed YAML content.
+
+    Raises
+    ------
+    RuntimeError
+        If the YAML file is invalid or
+        storage file does not exist.
+
+    """
+    log = logger.bind(cmd="parse_yaml", path=str(yaml_path.resolve()))
+    log.debug("Parsing junifer YAML")
+    contents = yaml.load(yaml_path)
+    # Validate mandatory sections
+    mandatory = ("workdir", "datagrabber", "markers", "storage")
+    for s in mandatory:
+        if s not in contents.keys():
+            raise RuntimeError(
+                f"`{s}` section not defined in {yaml_path.resolve()!s}"
+            )
+    # Validate optional sections
+    optional = ("with", "preprocess", "queue")
+    for k in contents.keys():
+        if k not in mandatory + optional:
+            raise RuntimeError(
+                f"Unknown section `{k}` in {yaml_path.resolve()!s}"
+            )
+    # Validate storage
+    if "uri" not in contents["storage"]:
+        raise RuntimeError(
+            f"`uri` missing from `storage` section in {yaml_path.resolve()!s}"
+        )
+    # Replace relative file paths with absolute
+    contents = _adjust_paths(contents, yaml_path)
+    # Validate storage file exists
+    if not Path(contents["storage"]["uri"]).exists():
+        raise RuntimeError(
+            f"Storage file does not exist: {contents['storage']['uri']}"
+        )
+    # Remove elements key if empty
+    if "elements" in contents:
+        if contents["elements"] is None:
+            _ = contents.pop("elements")
+    log.debug("Parsed junifer YAML")
+    return contents
+
+
+def _feature_yaml_from_meta(data: dict, feature: str) -> dict:
+    """Generate a feature YAML from metadata.
+
+    Parameters
+    ----------
+    data : dict
+        Dictionary containing the HDF5 metadata.
+    feature : str
+        MD5 hash of the feature.
+
+    Returns
+    -------
+    dict
+        Feature YAML.
+
+    """
+    y: dict[str, Any] = {}
+    y["workdir"] = ""
+    if "with" in data:
+        y["with"] = data["with"].copy()
+    # Set datagrabber
+    y["datagrabber"] = data["datagrabber"].copy()
+    a = y["datagrabber"].pop("class")
+    y["datagrabber"]["kind"] = a
+    if a not in ("PatternDataGrabber", "PatternDataladDataGrabber"):
+        _ = y["datagrabber"].pop("uri")
+        _ = y["datagrabber"].pop("rootdir")
+        _ = y["datagrabber"].pop("patterns")
+        _ = y["datagrabber"].pop("replacements")
+        _ = y["datagrabber"].pop("confounds_format")
+        _ = y["datagrabber"].pop("partial_pattern_ok")
+        for k in data[
+            "datagrabber"
+        ].keys():  # use data instead of y to avoid .copy()
+            if k.startswith("datalad"):
+                _ = y["datagrabber"].pop(k)
+    # Set preprocess
+    if "preprocess" in data:
+        y["preprocess"] = data["preprocess"].copy()
+        b = y["preprocess"].pop("class")
+        y["preprocess"]["kind"] = b
+    # Set markers
+    y["markers"] = []
+    y["markers"].append(data["marker"].copy())
+    c = y["markers"][0].pop("class")
+    y["markers"][0]["kind"] = c
+    if y["markers"][0]["masks"] is None:
+        _ = y["markers"][0].pop("masks")
+    # Set storage
+    y["storage"] = {
+        "kind": "HDF5FeatureStorage",
+        "uri": "",
+    }
+    # Set queue
+    y["queue"] = {
+        "jobname": data["name"],
+        "kind": "",
+    }
+    return y
+
+
+def _process_hdf5(data: dict, ds: dl.Dataset) -> dl.Dataset:
+    """Read and write HDF5 data.
+
+    Parameters
+    ----------
+    data : dict
+        Dictionary containing the HDF5 data.
+    ds : dl.Dataset
+        Dataset to add features to.
+
+    Returns
+    -------
+    dl.Dataset
+        Dataset with features added.
+
+    """
+    log = logger.bind(cmd="process_hdf5", path=data["storage"]["uri"])
+    log.debug("Processing HDF5 file")
+    metadata = read_hdf5(
+        fname=data["storage"]["uri"],
+        title="meta",
+        slash="ignore",
+    )
+    feature_dir = ds.pathobj / "features"
+    feature_dir.mkdir(exist_ok=True)
+    for k, v in tqdm(metadata.items(), desc="Processing features"):
+        # Metadata
+        meta_path = feature_dir / f"feature-{k}-meta.yaml"
+        yaml.dump(v, stream=meta_path.open("w"))
+        # YAML
+        yaml_data = _feature_yaml_from_meta(v, k)
+        yaml_path = feature_dir / f"feature-{k}.yml"
+        yaml.dump(yaml_data, stream=yaml_path.open("w"))
+        # Data
+        data = read_hdf5(fname=data["storage"]["uri"], title=k, slash="ignore")
+        data_path = feature_dir / f"feature-{k}.h5"
+        write_hdf5(
+            fname=str(data_path.resolve()),
+            data=data,
+            overwrite=True,
+            title=k,
+            slash="error",
+            use_json=False,
+        )
+    log.debug("Processed HDF5 file")
+    return ds
+
+
+def process_features(yaml_path: Path, ds: dl.Dataset) -> dl.Dataset:
+    """Parse the junifer YAML and add features to the dataset.
+
+    Parameters
+    ----------
+    yaml_path : Path
+        Path to the junifer YAML.
+    ds : dl.Dataset
+        Dataset to add features to.
+
+    Returns
+    -------
+    dl.Dataset
+        Dataset with features added.
+
+    Raises
+    ------
+    RuntimeError
+        If the storage file does not exist or
+        is not a valid format.
+
+    """
+    log = logger.bind(cmd="process_features", path=str(yaml_path.resolve()))
+    log.debug("Processing features")
+    data = _parse_yaml(yaml_path)
+    if data["storage"]["uri"].endswith(".hdf5"):
+        ds = _process_hdf5(data, ds)
+    elif data["storage"]["uri"].endswith(".sqlite"):
+        # TODO(synchon): add support for SQLite
+        pass
+    else:
+        raise RuntimeError(
+            "Unsupported storage format extension: "
+            f"{Path(data['storage']['uri']).suffix}"
+        )
+    ds.save(
+        message=f"[julio] add features for {yaml_path.name}",
+        on_failure="stop",
+        result_renderer="disabled",
+    )
+    log.debug("Processed features")
+    return ds
diff --git a/pyproject.toml b/pyproject.toml
index 5017ba0..332697c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -40,6 +40,8 @@ dependencies = [
     "lazy_loader==0.4",
     "structlog>=25.0.0,<26.0.0",
     "ruamel.yaml>=0.17,<0.19",
+    "h5io@git+https://github.com/juaml/h5io@600d9e25c625b11520d86b08f9f0b761f71b0542",
+    "tqdm>=4.66.1,<4.67.0",
 ]
 dynamic = ["version"]
 
diff --git a/uv.lock b/uv.lock
index bbd033a..abdd7d9 100644
--- a/uv.lock
+++ b/uv.lock
@@ -367,6 +367,67 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/76/91/7216b27286936c16f5b4d0c530087e4a54eead683e6b0b73dd0c64844af6/filelock-3.20.0-py3-none-any.whl", hash = "sha256:339b4732ffda5cd79b13f4e2711a31b0365ce445d95d243bb996273d072546a2", size = 16054, upload-time = "2025-10-08T18:03:48.35Z" },
 ]
 
+[[package]]
+name = "h5io"
+version = "0.1.7"
+source = { git = "https://github.com/juaml/h5io?rev=600d9e25c625b11520d86b08f9f0b761f71b0542#600d9e25c625b11520d86b08f9f0b761f71b0542" }
+dependencies = [
+    { name = "h5py" },
+    { name = "numpy", version = "2.2.6", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.11'" },
+    { name = "numpy", version = "2.3.5", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.11'" },
+]
+
+[[package]]
+name = "h5py"
+version = "3.15.1"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "numpy", version = "2.2.6", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.11'" },
+    { name = "numpy", version = "2.3.5", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.11'" },
+]
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 name = "humanize"
 version = "4.14.0"
@@ -487,9 +548,11 @@ source = { editable = "." }
 dependencies = [
     { name = "click" },
     { name = "datalad" },
+    { name = "h5io" },
     { name = "lazy-loader" },
     { name = "ruamel-yaml" },
     { name = "structlog" },
+    { name = "tqdm" },
 ]
 
 [package.optional-dependencies]
@@ -504,6 +567,7 @@ dev = [
 requires-dist = [
     { name = "click", specifier = ">=8.1.3,<8.2" },
     { name = "datalad", specifier = ">=1.0.0,<1.3.0" },
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     { name = "ruamel-yaml", specifier = ">=0.17,<0.19" },
@@ -511,6 +575,7 @@ requires-dist = [
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     { name = "towncrier", marker = "extra == 'dev'" },
     { name = "tox", marker = "extra == 'dev'" },
+    { name = "tqdm", specifier = ">=4.66.1,<4.67.0" },
 ]
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+]
+
 [[package]]
 name = "packaging"
 version = "25.0"
@@ -1173,14 +1387,14 @@ wheels = [
 
 [[package]]
 name = "tqdm"
-version = "4.67.1"
+version = "4.66.6"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "colorama", marker = "sys_platform == 'win32'" },
 ]
-sdist = { url = "https://files.pythonhosted.org/packages/a8/4b/29b4ef32e036bb34e4ab51796dd745cdba7ed47ad142a9f4a1eb8e0c744d/tqdm-4.67.1.tar.gz", hash = "sha256:f8aef9c52c08c13a65f30ea34f4e5aac3fd1a34959879d7e59e63027286627f2", size = 169737, upload-time = "2024-11-24T20:12:22.481Z" }
+sdist = { url = "https://files.pythonhosted.org/packages/e9/34/bef135b27fe1864993a5284ad001157ee9b5538e859ac90f5b0e8cc8c9ec/tqdm-4.66.6.tar.gz", hash = "sha256:4bdd694238bef1485ce839d67967ab50af8f9272aab687c0d7702a01da0be090", size = 169533, upload-time = "2024-10-28T12:49:58.611Z" }
 wheels = [
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From c51aab6bc3331a4adaddf54602edbdba85af2315 Mon Sep 17 00:00:00 2001
From: Synchon Mandal <synchon@protonmail.com>
Date: Wed, 17 Dec 2025 11:28:59 +0100
Subject: [PATCH 03/32] feat(cli): introduce add command

---
 julio/_cli.py | 40 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)

diff --git a/julio/_cli.py b/julio/_cli.py
index 42a922e..d61ac29 100644
--- a/julio/_cli.py
+++ b/julio/_cli.py
@@ -7,12 +7,14 @@
 import logging.config
 import pathlib
 import sys
+from pathlib import Path
 
 import click
 import datalad
 import structlog
 
 from . import _functions as cli_func
+from . import _utils as cli_utils
 
 
 __all__ = ["cli", "create"]
@@ -152,3 +154,41 @@ def create(
         click.echo(f"{err}", err=True)
     else:
         click.echo("Success")
+
+
+@cli.command
+@click.argument(
+    "yaml_path",
+    type=click.Path(
+        exists=True,
+        readable=True,
+        writable=True,
+        dir_okay=False,
+        path_type=pathlib.Path,
+    ),
+    metavar="<yaml>",
+)
+@click.option(
+    "-r",
+    "--registry",
+    default=None,
+    type=cli_utils.PathOrURL,
+    metavar="<registry>",
+    help="Path to registry; if not passed, use current directory",
+)
+@click.option("-v", "--verbose", count=True, type=int)
+def add(
+    yaml_path: click.Path,
+    registry: click.Path,
+    verbose: int,
+) -> None:
+    """Add feature(s) registry."""
+    _set_log_config(verbose)
+    try:
+        cli_func.add(
+            yaml_path, registry if registry is not None else Path(".")
+        )
+    except RuntimeError as err:
+        click.echo(f"{err}", err=True)
+    else:
+        click.echo("Success")

From 32b2e8d999c7a90c5c2ab4b023927a5a46a98bc6 Mon Sep 17 00:00:00 2001
From: Synchon Mandal <synchon@protonmail.com>
Date: Wed, 17 Dec 2025 11:30:01 +0100
Subject: [PATCH 04/32] feat(functions): introduce add command

---
 julio/_functions.py | 56 ++++++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 55 insertions(+), 1 deletion(-)

diff --git a/julio/_functions.py b/julio/_functions.py
index 8f5ce90..7cc4a73 100644
--- a/julio/_functions.py
+++ b/julio/_functions.py
@@ -3,14 +3,17 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
+import tempfile
 from pathlib import Path
 
 import datalad.api as dl
 import structlog
 from datalad.support.exceptions import IncompleteResultsError
 
+from ._utils import is_julio_registry, process_features
 
-__all__ = ["create"]
+
+__all__ = ["add", "create"]
 
 
 logger = structlog.get_logger()
@@ -54,3 +57,54 @@ def create(registry_path: Path):
         on_failure="stop",
         result_renderer="disabled",
     )
+
+
+def add(yaml_path: Path, registry_path: str | Path) -> None:
+    """Add feature(s) from `yaml_path` to the registry at `registry_path`.
+
+    Parameters
+    ----------
+    yaml_path : pathlib.Path
+        Path to the junifer YAML.
+    registry_path : str or pathlib.Path
+        Path to the existing julio registry.
+
+    Raises
+    ------
+    RuntimeError
+        If there is a problem cloning a remote registry or
+        if the dataset is not a julio registry.
+
+    """
+    log = logger.bind(
+        cmd="create",
+        path=registry_path if str else str(registry_path.resolve()),
+    )
+    if isinstance(registry_path, str):
+        log.debug("Cloning remote registry")
+        with tempfile.TemporaryDirectory() as tmpdir:
+            log.debug(f"Temporary directory created at {tmpdir}")
+            try:
+                ds = dl.clone(
+                    source=registry_path,
+                    path=tmpdir,
+                    on_failure="stop",
+                    result_renderer="disabled",
+                )
+            except IncompleteResultsError as e:
+                raise RuntimeError(
+                    f"Failed to clone dataset: {e.failed}"
+                ) from e
+            else:
+                log.debug("Remote registry cloned successfully")
+            if not is_julio_registry(ds):
+                raise RuntimeError(
+                    f"Dataset at {ds.path} is not a julio registry"
+                )
+            process_features(yaml_path, ds)
+            # TODO: push changes to remote
+    else:
+        ds = dl.Dataset(registry_path)
+        if not is_julio_registry(ds):
+            raise RuntimeError(f"Dataset at {ds.path} is not a julio registry")
+        process_features(yaml_path, ds)

From 4c6a294993228849616934521bf0749fb6b701d2 Mon Sep 17 00:00:00 2001
From: Synchon Mandal <synchon@protonmail.com>
Date: Wed, 17 Dec 2025 11:30:29 +0100
Subject: [PATCH 05/32] chore(functions): update create

---
 julio/_functions.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/julio/_functions.py b/julio/_functions.py
index 7cc4a73..21dff5e 100644
--- a/julio/_functions.py
+++ b/julio/_functions.py
@@ -19,7 +19,7 @@
 logger = structlog.get_logger()
 
 
-def create(registry_path: Path):
+def create(registry_path: Path) -> None:
     """Create a registry at `registry_path`.
 
     Parameters
@@ -49,7 +49,7 @@ def create(registry_path: Path):
             path=str(registry_path.resolve()),
         )
     # Add config file
-    conf_path = Path(ds.path) / "registry-config.yml"
+    conf_path = ds.pathobj / "registry-config.yml"
     conf_path.touch()
     ds.save(
         conf_path,

From ff90bd8b9010bf4d90ffa65efcbe2ffb0e775036 Mon Sep 17 00:00:00 2001
From: Synchon Mandal <synchon@protonmail.com>
Date: Mon, 2 Mar 2026 16:43:46 +0100
Subject: [PATCH 06/32] update(utils): improve feature yaml generation

---
 julio/_utils.py | 42 ++++++++++++++++++++----------------------
 1 file changed, 20 insertions(+), 22 deletions(-)

diff --git a/julio/_utils.py b/julio/_utils.py
index 099b2f1..832d00c 100644
--- a/julio/_utils.py
+++ b/julio/_utils.py
@@ -245,15 +245,13 @@ def _parse_yaml(yaml_path: Path) -> dict:
     return contents
 
 
-def _feature_yaml_from_meta(data: dict, feature: str) -> dict:
+def _generate_feature_yaml(meta: dict) -> dict:
     """Generate a feature YAML from metadata.
 
     Parameters
     ----------
-    data : dict
-        Dictionary containing the HDF5 metadata.
-    feature : str
-        MD5 hash of the feature.
+    meta : dict
+        Feature metadata as dictionary.
 
     Returns
     -------
@@ -263,36 +261,36 @@ def _feature_yaml_from_meta(data: dict, feature: str) -> dict:
     """
     y: dict[str, Any] = {}
     y["workdir"] = ""
-    if "with" in data:
-        y["with"] = data["with"].copy()
+    if "with" in meta:
+        y["with"] = meta["with"].copy()
     # Set datagrabber
-    y["datagrabber"] = data["datagrabber"].copy()
+    y["datagrabber"] = meta["datagrabber"].copy()
     a = y["datagrabber"].pop("class")
     y["datagrabber"]["kind"] = a
     if a not in ("PatternDataGrabber", "PatternDataladDataGrabber"):
-        _ = y["datagrabber"].pop("uri")
-        _ = y["datagrabber"].pop("rootdir")
-        _ = y["datagrabber"].pop("patterns")
-        _ = y["datagrabber"].pop("replacements")
-        _ = y["datagrabber"].pop("confounds_format")
-        _ = y["datagrabber"].pop("partial_pattern_ok")
-        for k in data[
+        y["datagrabber"].pop("uri")
+        y["datagrabber"].pop("rootdir")
+        y["datagrabber"].pop("patterns")
+        y["datagrabber"].pop("replacements")
+        y["datagrabber"].pop("confounds_format")
+        y["datagrabber"].pop("partial_pattern_ok")
+        for k in meta[
             "datagrabber"
         ].keys():  # use data instead of y to avoid .copy()
             if k.startswith("datalad"):
-                _ = y["datagrabber"].pop(k)
+                y["datagrabber"].pop(k)
     # Set preprocess
-    if "preprocess" in data:
-        y["preprocess"] = data["preprocess"].copy()
+    if "preprocess" in meta:
+        y["preprocess"] = meta["preprocess"].copy()
         b = y["preprocess"].pop("class")
         y["preprocess"]["kind"] = b
     # Set markers
     y["markers"] = []
-    y["markers"].append(data["marker"].copy())
+    y["markers"].append(meta["marker"].copy())
     c = y["markers"][0].pop("class")
     y["markers"][0]["kind"] = c
     if y["markers"][0]["masks"] is None:
-        _ = y["markers"][0].pop("masks")
+        y["markers"][0].pop("masks")
     # Set storage
     y["storage"] = {
         "kind": "HDF5FeatureStorage",
@@ -300,7 +298,7 @@ def _feature_yaml_from_meta(data: dict, feature: str) -> dict:
     }
     # Set queue
     y["queue"] = {
-        "jobname": data["name"],
+        "jobname": meta["name"],
         "kind": "",
     }
     return y
@@ -336,7 +334,7 @@ def _process_hdf5(data: dict, ds: dl.Dataset) -> dl.Dataset:
         meta_path = feature_dir / f"feature-{k}-meta.yaml"
         yaml.dump(v, stream=meta_path.open("w"))
         # YAML
-        yaml_data = _feature_yaml_from_meta(v, k)
+        yaml_data = _generate_feature_yaml(v)
         yaml_path = feature_dir / f"feature-{k}.yml"
         yaml.dump(yaml_data, stream=yaml_path.open("w"))
         # Data

From 6e06fa0f85d154508aac032161c15127a257f0df Mon Sep 17 00:00:00 2001
From: Synchon Mandal <synchon@protonmail.com>
Date: Mon, 2 Mar 2026 16:47:43 +0100
Subject: [PATCH 07/32] update(utils): improve feature meta yaml generation

---
 julio/_utils.py | 84 +++++++++++++++++++++++++++++++++++++++++++++++--
 1 file changed, 81 insertions(+), 3 deletions(-)

diff --git a/julio/_utils.py b/julio/_utils.py
index 832d00c..584a3dc 100644
--- a/julio/_utils.py
+++ b/julio/_utils.py
@@ -5,6 +5,8 @@
 
 import pathlib
 import re
+import sys
+from datetime import datetime
 from pathlib import Path
 from typing import Any
 
@@ -305,6 +307,74 @@ def _generate_feature_yaml(meta: dict) -> dict:
 
 
 def _process_hdf5(data: dict, ds: dl.Dataset) -> dl.Dataset:
+def _generate_meta_yaml(
+    meta: dict,
+    data: dict,
+    md5: str,
+    mappings: dict,
+    dataset_display_name: str | None,
+) -> dict:
+    """Generate a feature meta YAML from data.
+
+    Parameters
+    ----------
+    meta : dict
+        Feature metadata as dictionary.
+    data : dict
+        Feature data as dictionary.
+    md5 : str
+        Feature MD5.
+    mappings : dict
+        Registry mappings as dictionary.
+    dataset_display_name : str or None
+        Dataset display name.
+
+    Returns
+    -------
+    dict
+        Feature meta YAML.
+
+    """
+    y: dict[str, Any] = {}
+    y["md5"] = md5
+    y["name"] = meta["name"]
+    y["added_on"] = datetime.utcnow().strftime("%Y-%m-%d %H:%M:%S")
+    ndata = data["data"]
+    y["data"] = {
+        "shape": ndata.shape,
+        "size": ndata.size,
+        "dtype": str(ndata.dtype),
+        "nbytes": sys.getsizeof(ndata),
+    }
+    y["samples"] = len(data["element"])
+    mm = {}
+    for k, v in meta["marker"].items():
+        if k not in ("class", "on", "name"):
+            mm[k] = v
+    y["marker_meta"] = mm
+    sm = {}
+    for k, v in data.items():
+        if k not in ("data", "element"):
+            sm[k] = v
+    y["storage_meta"] = sm
+    tags = []
+    for i in mappings["datagrabbers"]:
+        if meta["datagrabber"]["class"] == i["class"]:
+            tags.extend(i["tags"])
+            y["dataset"] = {
+                "name": i["class"],
+                "description": i["description"],
+                "display_name": i["display_name"]
+                if dataset_display_name is None
+                else dataset_display_name,
+            }
+    for i in mappings["markers"]:
+        if meta["marker"]["class"] == i["class"]:
+            tags.extend(i["tags"])
+    y["tags"] = list(set(tags))
+    return y
+
+
     """Read and write HDF5 data.
 
     Parameters
@@ -330,9 +400,6 @@ def _process_hdf5(data: dict, ds: dl.Dataset) -> dl.Dataset:
     feature_dir = ds.pathobj / "features"
     feature_dir.mkdir(exist_ok=True)
     for k, v in tqdm(metadata.items(), desc="Processing features"):
-        # Metadata
-        meta_path = feature_dir / f"feature-{k}-meta.yaml"
-        yaml.dump(v, stream=meta_path.open("w"))
         # YAML
         yaml_data = _generate_feature_yaml(v)
         yaml_path = feature_dir / f"feature-{k}.yml"
@@ -348,6 +415,17 @@ def _process_hdf5(data: dict, ds: dl.Dataset) -> dl.Dataset:
             slash="error",
             use_json=False,
         )
+        # Metadata
+        config_path = ds.pathobj / "registry-config.yml"
+        meta_data = _generate_meta_yaml(
+            meta=v,
+            data=data,
+            md5=k,
+            mappings=yaml.load(stream=config_path.open("r"))["mappings"],
+            dataset_display_name=dataset_display_name,
+        )
+        meta_path = feature_dir / f"feature-{k}-meta.yml"
+        yaml.dump(meta_data, stream=meta_path.open("w"))
     log.debug("Processed HDF5 file")
     return ds
 

From 7b2f8ce3ef494c19b8ea2afc89d5ac8475aafa4e Mon Sep 17 00:00:00 2001
From: Synchon Mandal <synchon@protonmail.com>
Date: Mon, 2 Mar 2026 16:49:20 +0100
Subject: [PATCH 08/32] update(utils): improve storage hdf5 processing

---
 julio/_utils.py | 19 +++++++++++++------
 1 file changed, 13 insertions(+), 6 deletions(-)

diff --git a/julio/_utils.py b/julio/_utils.py
index 584a3dc..6cd84b5 100644
--- a/julio/_utils.py
+++ b/julio/_utils.py
@@ -306,7 +306,6 @@ def _generate_feature_yaml(meta: dict) -> dict:
     return y
 
 
-def _process_hdf5(data: dict, ds: dl.Dataset) -> dl.Dataset:
 def _generate_meta_yaml(
     meta: dict,
     data: dict,
@@ -375,14 +374,21 @@ def _generate_meta_yaml(
     return y
 
 
+def _process_hdf5(
+    data: dict,
+    ds: dl.Dataset,
+    dataset_display_name: str | None,
+) -> dl.Dataset:
     """Read and write HDF5 data.
 
     Parameters
     ----------
     data : dict
-        Dictionary containing the HDF5 data.
+        Parsed YAML as dictionary.
     ds : dl.Dataset
         Dataset to add features to.
+    dataset_display_name : str or None
+        Dataset display name.
 
     Returns
     -------
@@ -456,10 +462,11 @@ def process_features(yaml_path: Path, ds: dl.Dataset) -> dl.Dataset:
     log.debug("Processing features")
     data = _parse_yaml(yaml_path)
     if data["storage"]["uri"].endswith(".hdf5"):
-        ds = _process_hdf5(data, ds)
-    elif data["storage"]["uri"].endswith(".sqlite"):
-        # TODO(synchon): add support for SQLite
-        pass
+        ds = _process_hdf5(
+            data=data,
+            ds=ds,
+            dataset_display_name=dataset_display_name,
+        )
     else:
         raise RuntimeError(
             "Unsupported storage format extension: "

From 13f688a9b34d7ba52ad0ca5d6f8f07dd9a3f5619 Mon Sep 17 00:00:00 2001
From: Synchon Mandal <synchon@protonmail.com>
Date: Mon, 2 Mar 2026 16:55:12 +0100
Subject: [PATCH 09/32] update(functions): add dataset_display_name to add

---
 julio/_functions.py | 53 +++++++++++++++++++++++++++++++++++++++++++--
 1 file changed, 51 insertions(+), 2 deletions(-)

diff --git a/julio/_functions.py b/julio/_functions.py
index 21dff5e..7ca3560 100644
--- a/julio/_functions.py
+++ b/julio/_functions.py
@@ -59,7 +59,11 @@ def create(registry_path: Path) -> None:
     )
 
 
-def add(yaml_path: Path, registry_path: str | Path) -> None:
+def add(
+    yaml_path: Path,
+    registry_path: str | Path,
+    dataset_display_name: str | None,
+) -> None:
     """Add feature(s) from `yaml_path` to the registry at `registry_path`.
 
     Parameters
@@ -68,6 +72,8 @@ def add(yaml_path: Path, registry_path: str | Path) -> None:
         Path to the junifer YAML.
     registry_path : str or pathlib.Path
         Path to the existing julio registry.
+    dataset_display_name : str or None
+        Dataset display name.
 
     Raises
     ------
@@ -77,7 +83,50 @@ def add(yaml_path: Path, registry_path: str | Path) -> None:
 
     """
     log = logger.bind(
-        cmd="create",
+        cmd="add",
+        path=registry_path if str else str(registry_path.resolve()),
+    )
+    if isinstance(registry_path, str):
+        log.debug("Cloning remote registry")
+        with tempfile.TemporaryDirectory() as tmpdir:
+            log.debug(f"Temporary directory created at {tmpdir}")
+            # Clone the remote registry
+            try:
+                ds = dl.clone(
+                    source=registry_path,
+                    path=tmpdir,
+                    on_failure="stop",
+                    result_renderer="disabled",
+                )
+            except IncompleteResultsError as e:
+                raise RuntimeError(
+                    f"Failed to clone dataset: {e.failed}"
+                ) from e
+            else:
+                log.debug("Remote registry cloned successfully")
+            if not is_julio_registry(ds):
+                raise RuntimeError(
+                    f"Dataset at {ds.path} is not a julio registry"
+                )
+            # Add features
+            process_features(yaml_path, ds, dataset_display_name)
+            # Push changes to remote registry
+            try:
+                ds = dl.push(
+                    on_failure="stop",
+                    result_renderer="disabled",
+                )
+            except IncompleteResultsError as e:
+                raise RuntimeError(
+                    f"Failed to push dataset: {e.failed}"
+                ) from e
+            else:
+                log.debug("Pushed changes to remote registry successfully")
+    else:
+        ds = dl.Dataset(registry_path)
+        if not is_julio_registry(ds):
+            raise RuntimeError(f"Dataset at {ds.path} is not a julio registry")
+        process_features(yaml_path, ds, dataset_display_name)
         path=registry_path if str else str(registry_path.resolve()),
     )
     if isinstance(registry_path, str):

From 8b1b0197eefbd6bb9e7935d49df89fa7724266f2 Mon Sep 17 00:00:00 2001
From: Synchon Mandal <synchon@protonmail.com>
Date: Mon, 2 Mar 2026 17:01:53 +0100
Subject: [PATCH 10/32] update(functions): copy default registry-config.yml in
 create

---
 julio/_functions.py       |   5 +-
 julio/registry-config.yml | 293 ++++++++++++++++++++++++++++++++++++++
 2 files changed, 297 insertions(+), 1 deletion(-)
 create mode 100644 julio/registry-config.yml

diff --git a/julio/_functions.py b/julio/_functions.py
index 7ca3560..2b0b980 100644
--- a/julio/_functions.py
+++ b/julio/_functions.py
@@ -50,7 +50,10 @@ def create(registry_path: Path) -> None:
         )
     # Add config file
     conf_path = ds.pathobj / "registry-config.yml"
-    conf_path.touch()
+    shutil.copy(
+        src=Path(__file__).parent / "registry-config.yml",
+        dst=conf_path,
+    )
     ds.save(
         conf_path,
         message="[julio] add registry configuration",
diff --git a/julio/registry-config.yml b/julio/registry-config.yml
new file mode 100644
index 0000000..bde863f
--- /dev/null
+++ b/julio/registry-config.yml
@@ -0,0 +1,293 @@
+mappings:
+
+  datagrabbers:
+
+    - class: HCP1200
+      display_name: WU-Minn HCP1200
+      tags:
+        - HCP1200
+      description: HCP1200 3T/7T MR scans from young healthy adults twins and non-twin siblings (ages 22-35)
+
+    - class: DataladHCP1200
+      display_name: WU-Minn HCP1200
+      tags:
+        - HCP1200
+      description: HCP1200 3T/7T MR scans from young healthy adults twins and non-twin siblings (ages 22-35)
+
+    - class: DataladAOMICID1000
+      display_name: AOMIC ID1000
+      tags:
+        - AOMIC
+        - ID1000
+      description: Amsterdam Open MRI Collection (AOMIC) ID1000 3T MR scans from 928 participants
+
+    - class: DataladAOMICPIOP1
+      display_name: AOMIC PIOP1
+      tags:
+        - AOMIC
+        - PIOP1
+      description: Amsterdam Open MRI Collection (AOMIC) PIOP1 3T MR scans from 216 participants
+
+    - class: DataladAOMICPIOP2
+      display_name: AOMIC PIOP2
+      tags:
+        - AOMIC
+        - PIOP2
+      description: Amsterdam Open MRI Collection (AOMIC) PIOP2 3T MR scans from 226 participants
+
+    - class: DMCC13Benchmark
+      display_name: DMCC13 Benchmark
+      tags:
+        - DMCC
+      description: Dual Mechanisms of Cognitive Control data for 13 subjects used as a benchmark dataset for comparing preprocessing pipelines
+
+    - class: JuselessDataladAOMICID1000VBM
+      display_name: AOMIC ID1000 VBM
+      tags:
+        - AOMIC
+        - ID1000
+        - CAT
+      description: AOMIC ID1000 VBM data
+
+    - class: JuselessDataladCamCANVBM
+      display_name: CamCAN VBM
+      tags:
+        - CamCAN
+        - CAT
+      description: Cambridge Centre for Ageing Neuroscience (CamCAN) VBM data
+
+    - class: JuselessDataladIXIVBM
+      display_name: IXI VBM
+      tags:
+        - IXI
+        - CAT
+      description: IXI VBM data
+
+    - class: JuselessUCLA
+      display_name: UCLA
+      tags:
+        - UCLA
+      description: UCLA data on juseless.imm7.de
+
+    - class: JuselessDataladUKBVBM
+      display_name: UK Biobank VBM
+      tags:
+        - UK Biobank
+        - CAT
+      description: UK Biobank VBM data, computed using CAT12.8 by Felix
+
+  markers:
+
+    - class: ParcelAggregation
+      display_name: Aggregation
+      tags:
+        - fMRI
+        - Aggregation
+        - Parcellation
+      description: Signal extraction from Region of Interests (ROIs) based on deterministic atlas, computed using specific aggregation function
+
+    - class: SphereAggregation
+      display_name: Aggregation
+      tags:
+        - fMRI
+        - Aggregation
+        - Coordinates
+      description: Signal extraction from Region of Interests (ROIs) based on spherical region around coordinates, computed using specific aggregation function
+
+    - class: MapsAggregation
+      display_name: Aggregation
+      tags:
+        - fMRI
+        - Aggregation
+        - Maps
+      description: Signal extraction from Region of Interests (ROIs) based on probabilistic atlas, computed using specific aggregation function
+
+    - class: FunctionalConnectivityParcels
+      display_name: Functional Connectivity
+      tags:
+        - fMRI
+        - FC
+        - Parcellation
+      description: Functional connectivity computed on parcellations
+
+    - class: FunctionalConnectivitySpheres
+      display_name: Functional Connectivity
+      tags:
+        - fMRI
+        - FC
+        - Coordinates
+      description: Functional connectivity computed on coordinates
+
+    - class: FunctionalConnectivityMaps
+      display_name: Functional Connectivity
+      tags:
+        - fMRI
+        - FC
+        - Maps
+      description: Functional connectivity computed on maps
+
+    - class: ALFFParcels
+      display_name: ALFF / fALFF
+      tags:
+        - fMRI
+        - ALFF/fALFF
+        - Parcellation
+      description: Amplitude of low-frequency fluctuations (ALFF) and fractional ALFF (fALFF) computed on parcellations
+
+    - class: ALFFSpheres
+      display_name: ALFF / fALFF
+      tags:
+        - fMRI
+        - ALFF/fALFF
+        - Coordinates
+      description: Amplitude of low-frequency fluctuations (ALFF) and fractional ALFF (fALFF) computed on coordinates
+
+    - class: ALFFMaps
+      display_name: ALFF / fALFF
+      tags:
+        - fMRI
+        - ALFF/fALFF
+        - Maps
+      description: Amplitude of low-frequency fluctuations (ALFF) and fractional ALFF (fALFF) computed on maps
+
+    - class: ReHoParcels
+      display_name: Regional Homogeneity
+      tags:
+        - fMRI
+        - ReHo
+        - Parcellation
+      description: Regional homogeneity computed on parcellations
+
+    - class: ReHoSpheres
+      display_name: Regional Homogeneity
+      tags:
+        - fMRI
+        - ReHo
+        - Coordinates
+      description: Regional homogeneity computed on coordinates
+
+    - class: ReHoMaps
+      display_name: Regional Homogeneity
+      tags:
+        - fMRI
+        - ReHo
+        - Maps
+      description: Regional homogeneity computed on maps
+
+    - class: EdgeCentricFCParcels
+      display_name: Edge Functional Connectivity
+      tags:
+        - fMRI
+        - Edge FC
+        - Parcellation
+      description: Edge-centric functional connectivity computed on parcellation
+
+    - class: EdgeCentricFCSpheres
+      display_name: Edge Functional Connectivity
+      tags:
+        - fMRI
+        - Edge FC
+        - Coordinates
+      description: Edge-centric functional connectivity computed on coordinates
+
+    - class: EdgeCentricFCMaps
+      display_name: Edge Functional Connectivity
+      tags:
+        - fMRI
+        - Edge FC
+        - Maps
+      description: Edge-centric functional connectivity computed on maps
+
+    - class: CrossParcellationFC
+      display_name: Cross-parcellation functional connectivity
+      tags:
+        - fMRI
+        - FC
+        - Parcellation
+      description: Cross-parcellation functional connectivity computed on two parcellations
+
+    - class: TemporalSNRParcels
+      display_name: Temporal signal-to-noise ratio
+      tags:
+        - fMRI
+        - tSNR
+        - Parcellation
+      description: Temporal signal-to-noise (tSNR) ratio computed on parcellation
+
+    - class: TemporalSNRSpheres
+      display_name: Temporal signal-to-noise ratio
+      tags:
+        - fMRI
+        - tSNR
+        - Coordinates
+      description: Temporal signal-to-noise (tSNR) ratio computed on coordinates
+
+    - class: TemporalSNRMaps
+      display_name: Temporal signal-to-noise ratio
+      tags:
+        - fMRI
+        - tSNR
+        - Maps
+      description: Temporal signal-to-noise (tSNR) ratio computed on maps
+
+    - class: RSSETSMarker
+      display_name: Root sum of squares of edgewise timeseries
+      tags:
+        - fMRI
+        - Parcellation
+      description: Root sum of squares of edgewise timeseries computed on parcellation
+
+    - class: HurstExponent
+      display_name: Hurst Exponent of timeseries
+      tags:
+        - fMRI
+        - Entropy
+        - Parcellation
+      description: Entropy measure using Hurst Exponent of timeseries
+
+    - class: MultiscaleEntropyAUC
+      display_name: AUC of Multiscale Entropy of timeseries
+      tags:
+        - fMRI
+        - Entropy
+        - Parcellation
+      description: Area under the curve of Multiscale Entropy measure of timeseries
+
+    - class: PermEntropy
+      display_name: Permutation Entropy of timeseries
+      tags:
+        - fMRI
+        - Entropy
+        - Parcellation
+      description: Permutation Entropy measure of timeseries
+
+    - class: RangeEntropy
+      display_name: Range Entropy of timeseries
+      tags:
+        - fMRI
+        - Entropy
+        - Parcellation
+      description: Range Entropy measure of timeseries
+
+    - class: RangeEntropyAUC
+      display_name: AUC of Range Entropy of timeseries
+      tags:
+        - fMRI
+        - Entropy
+        - Parcellation
+      description: Area under the curve of Range Entropy measure of timeseries
+
+    - class: SampleEntropy
+      display_name: Sample Entropy of timeseries
+      tags:
+        - fMRI
+        - Entropy
+        - Parcellation
+      description: Sample Entropy measure of timeseries
+
+    - class: BrainPrint
+      display_name: BrainPrint measure
+      tags:
+        - sMRI
+        - BrainPrint
+      description: Computed BrainPrint measure from FreeSurfer-derived surface data

From eab51df91091c1a449c571d58698bf2f17b54205 Mon Sep 17 00:00:00 2001
From: Synchon Mandal <synchon@protonmail.com>
Date: Mon, 2 Mar 2026 17:04:33 +0100
Subject: [PATCH 11/32] update(cli): add dataset_display_name in create

---
 julio/_cli.py | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

diff --git a/julio/_cli.py b/julio/_cli.py
index d61ac29..1700ae7 100644
--- a/julio/_cli.py
+++ b/julio/_cli.py
@@ -176,17 +176,28 @@ def create(
     metavar="<registry>",
     help="Path to registry; if not passed, use current directory",
 )
+@click.option(
+    "-d",
+    "--dataset-display-name",
+    default=None,
+    type=str,
+    metavar="<dataset-display-name>",
+    help="Dataset display name; if not passed, will use the name from YAML",
+)
 @click.option("-v", "--verbose", count=True, type=int)
 def add(
     yaml_path: click.Path,
     registry: click.Path,
+    dataset_display_name: str,
     verbose: int,
 ) -> None:
     """Add feature(s) registry."""
     _set_log_config(verbose)
     try:
         cli_func.add(
-            yaml_path, registry if registry is not None else Path(".")
+            yaml_path=yaml_path,
+            registry_path=registry if registry is not None else Path("."),
+            dataset_display_name=dataset_display_name,
         )
     except RuntimeError as err:
         click.echo(f"{err}", err=True)

From 35ef2e4036fe4756fc11baa18f2d02634ee001ab Mon Sep 17 00:00:00 2001
From: Synchon Mandal <synchon@protonmail.com>
Date: Mon, 2 Mar 2026 17:07:55 +0100
Subject: [PATCH 12/32] chore(utils): code clean up

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

diff --git a/julio/_utils.py b/julio/_utils.py
index 6cd84b5..8450fd9 100644
--- a/julio/_utils.py
+++ b/julio/_utils.py
@@ -139,11 +139,11 @@ def _make_absolute_path(path: str, base_path: Path) -> str:
     """
     log = logger.bind(cmd="make_absolute_path", path=str(path))
     log.debug("Making path absolute")
-    path = Path(path)
-    if not path.is_absolute():
-        path = base_path / path
+    path_p = Path(path)
+    if not path_p.is_absolute():
+        path_p = base_path / path_p
     log.debug("Made path absolute")
-    return str(path.resolve())
+    return str(path_p.resolve())
 
 
 def _adjust_paths(data: dict, yaml_path: Path) -> dict:
@@ -242,7 +242,7 @@ def _parse_yaml(yaml_path: Path) -> dict:
     # Remove elements key if empty
     if "elements" in contents:
         if contents["elements"] is None:
-            _ = contents.pop("elements")
+            contents.pop("elements")
     log.debug("Parsed junifer YAML")
     return contents
 

From decd53eb75f45e86af8f56a7afcf4d017725f8fd Mon Sep 17 00:00:00 2001
From: Synchon Mandal <synchon@protonmail.com>
Date: Mon, 2 Mar 2026 17:08:14 +0100
Subject: [PATCH 13/32] update(utils): add dataset_display_name in
 process_features

---
 julio/_utils.py | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/julio/_utils.py b/julio/_utils.py
index 8450fd9..0ac61e8 100644
--- a/julio/_utils.py
+++ b/julio/_utils.py
@@ -436,7 +436,11 @@ def _process_hdf5(
     return ds
 
 
-def process_features(yaml_path: Path, ds: dl.Dataset) -> dl.Dataset:
+def process_features(
+    yaml_path: Path,
+    ds: dl.Dataset,
+    dataset_display_name: str | None,
+) -> dl.Dataset:
     """Parse the junifer YAML and add features to the dataset.
 
     Parameters
@@ -445,6 +449,8 @@ def process_features(yaml_path: Path, ds: dl.Dataset) -> dl.Dataset:
         Path to the junifer YAML.
     ds : dl.Dataset
         Dataset to add features to.
+    dataset_display_name : str or None
+        Dataset display name.
 
     Returns
     -------

From c67881feecfe1b2900ffee0310ca933b9d0162d9 Mon Sep 17 00:00:00 2001
From: Synchon Mandal <synchon@protonmail.com>
Date: Mon, 2 Mar 2026 17:34:54 +0100
Subject: [PATCH 14/32] update(tests): add test for add

---
 julio/tests/feature.yml       |  22 ++++++++++++++++++++++
 julio/tests/store.hdf5        | Bin 0 -> 29466 bytes
 julio/tests/test_functions.py |  23 ++++++++++++++++++++++-
 3 files changed, 44 insertions(+), 1 deletion(-)
 create mode 100644 julio/tests/feature.yml
 create mode 100644 julio/tests/store.hdf5

diff --git a/julio/tests/feature.yml b/julio/tests/feature.yml
new file mode 100644
index 0000000..75b85a9
--- /dev/null
+++ b/julio/tests/feature.yml
@@ -0,0 +1,22 @@
+datagrabber:
+  kind: DMCC13Benchmark
+  types:
+    - BOLD
+  sessions:
+    - ses-wave1bas
+  tasks:
+    - Rest
+  phase_encodings:
+    - AP
+  runs:
+    - "1"
+
+markers:
+  - kind: FunctionalConnectivitySpheres
+    coords: DMNBuckner
+    radius: 5.0
+    name: fc_spheres
+
+storage:
+  kind: HDF5FeatureStorage
+  uri: ./store.hdf5
diff --git a/julio/tests/store.hdf5 b/julio/tests/store.hdf5
new file mode 100644
index 0000000000000000000000000000000000000000..67eea961680f9c61fb753d48f3adbc36acefe7ec
GIT binary patch
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diff --git a/julio/tests/test_functions.py b/julio/tests/test_functions.py
index 978fb8a..166f4a8 100644
--- a/julio/tests/test_functions.py
+++ b/julio/tests/test_functions.py
@@ -8,7 +8,7 @@
 
 import pytest
 
-from julio import create
+from julio import add, create
 
 
 def test_create(tmp_path: Path) -> None:
@@ -27,3 +27,24 @@ def test_create(tmp_path: Path) -> None:
     with pytest.raises(RuntimeError):
         create(registry_path)
     shutil.rmtree(registry_path)
+
+
+def test_add(tmp_path: Path) -> None:
+    """Test feature addition.
+
+    Parameters
+    ----------
+    tmp_path : Path
+        Pytest fixture that provides a temporary directory.
+
+    """
+    registry_path = tmp_path / "test_registry"
+    create(registry_path)
+    add(
+        yaml_path=Path(__file__).parent / "feature.yml",
+        registry_path=registry_path,
+        dataset_display_name=None,
+    )
+    f_dir = registry_path / "features"
+    assert f_dir.is_dir()
+    shutil.rmtree(registry_path)

From 2043da42fb07baccc25362d541b462f038d7bc12 Mon Sep 17 00:00:00 2001
From: Synchon Mandal <synchon@protonmail.com>
Date: Mon, 2 Mar 2026 17:35:55 +0100
Subject: [PATCH 15/32] chore: add workdir section in tests/feature.yml

---
 julio/tests/feature.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/julio/tests/feature.yml b/julio/tests/feature.yml
index 75b85a9..55378f4 100644
--- a/julio/tests/feature.yml
+++ b/julio/tests/feature.yml
@@ -1,3 +1,5 @@
+workdir: ./junifer-temp
+
 datagrabber:
   kind: DMCC13Benchmark
   types:

From 5b928fc04556f5760b5610f1d46a258e4b836090 Mon Sep 17 00:00:00 2001
From: Synchon Mandal <synchon@protonmail.com>
Date: Tue, 3 Mar 2026 11:41:30 +0100
Subject: [PATCH 16/32] fix(tests): make add test work

---
 julio/tests/test_functions.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/julio/tests/test_functions.py b/julio/tests/test_functions.py
index 166f4a8..d56c0bf 100644
--- a/julio/tests/test_functions.py
+++ b/julio/tests/test_functions.py
@@ -6,6 +6,7 @@
 import shutil
 from pathlib import Path
 
+import datalad.api as dl
 import pytest
 
 from julio import add, create
@@ -47,4 +48,5 @@ def test_add(tmp_path: Path) -> None:
     )
     f_dir = registry_path / "features"
     assert f_dir.is_dir()
+    dl.drop(".", reckless="kill", dataset=dl.Dataset(registry_path))
     shutil.rmtree(registry_path)

From fba578883c73147eafa83bb0ce08e81541c3dca1 Mon Sep 17 00:00:00 2001
From: Synchon Mandal <synchon@protonmail.com>
Date: Tue, 3 Mar 2026 11:48:26 +0100
Subject: [PATCH 17/32] chore(functions): fix statements

---
 julio/_functions.py | 30 ------------------------------
 1 file changed, 30 deletions(-)

diff --git a/julio/_functions.py b/julio/_functions.py
index 2b0b980..cfcd375 100644
--- a/julio/_functions.py
+++ b/julio/_functions.py
@@ -130,33 +130,3 @@ def add(
         if not is_julio_registry(ds):
             raise RuntimeError(f"Dataset at {ds.path} is not a julio registry")
         process_features(yaml_path, ds, dataset_display_name)
-        path=registry_path if str else str(registry_path.resolve()),
-    )
-    if isinstance(registry_path, str):
-        log.debug("Cloning remote registry")
-        with tempfile.TemporaryDirectory() as tmpdir:
-            log.debug(f"Temporary directory created at {tmpdir}")
-            try:
-                ds = dl.clone(
-                    source=registry_path,
-                    path=tmpdir,
-                    on_failure="stop",
-                    result_renderer="disabled",
-                )
-            except IncompleteResultsError as e:
-                raise RuntimeError(
-                    f"Failed to clone dataset: {e.failed}"
-                ) from e
-            else:
-                log.debug("Remote registry cloned successfully")
-            if not is_julio_registry(ds):
-                raise RuntimeError(
-                    f"Dataset at {ds.path} is not a julio registry"
-                )
-            process_features(yaml_path, ds)
-            # TODO: push changes to remote
-    else:
-        ds = dl.Dataset(registry_path)
-        if not is_julio_registry(ds):
-            raise RuntimeError(f"Dataset at {ds.path} is not a julio registry")
-        process_features(yaml_path, ds)

From d94634fba595d0e314bfba0f43c6fbdf3a930afc Mon Sep 17 00:00:00 2001
From: Synchon Mandal <synchon@protonmail.com>
Date: Tue, 3 Mar 2026 11:52:19 +0100
Subject: [PATCH 18/32] chore(functions): add missing shutil import

---
 julio/_functions.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/julio/_functions.py b/julio/_functions.py
index cfcd375..b3b26ea 100644
--- a/julio/_functions.py
+++ b/julio/_functions.py
@@ -3,6 +3,7 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
+import shutil
 import tempfile
 from pathlib import Path
 

From e21248257009028f0db65543d454e26ef3ea0156 Mon Sep 17 00:00:00 2001
From: Synchon Mandal <synchon@protonmail.com>
Date: Tue, 3 Mar 2026 11:56:08 +0100
Subject: [PATCH 19/32] chore: add missing package import

---
 julio/__init__.pyi | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/julio/__init__.pyi b/julio/__init__.pyi
index 575fb65..d72d57e 100644
--- a/julio/__init__.pyi
+++ b/julio/__init__.pyi
@@ -1,5 +1,6 @@
 __all__ = [
+    "add",
     "create",
 ]
 
-from ._functions import create
+from ._functions import add, create

From c99073bd373fed96aee144e97948156f61ffa00b Mon Sep 17 00:00:00 2001
From: Synchon Mandal <synchon@protonmail.com>
Date: Tue, 10 Mar 2026 11:54:17 +0100
Subject: [PATCH 20/32] chore(functions): add no cover pragma for add

---
 julio/_functions.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/julio/_functions.py b/julio/_functions.py
index b3b26ea..0c26d81 100644
--- a/julio/_functions.py
+++ b/julio/_functions.py
@@ -90,7 +90,7 @@ def add(
         cmd="add",
         path=registry_path if str else str(registry_path.resolve()),
     )
-    if isinstance(registry_path, str):
+    if isinstance(registry_path, str): # pragma: no cover
         log.debug("Cloning remote registry")
         with tempfile.TemporaryDirectory() as tmpdir:
             log.debug(f"Temporary directory created at {tmpdir}")

From 33187c87f4124823e910ffe0624071f62e458d6c Mon Sep 17 00:00:00 2001
From: Synchon Mandal <synchon@protonmail.com>
Date: Tue, 10 Mar 2026 12:07:30 +0100
Subject: [PATCH 21/32] tests(functions): improve test for add

---
 julio/tests/test_functions.py | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/julio/tests/test_functions.py b/julio/tests/test_functions.py
index d56c0bf..bac98b7 100644
--- a/julio/tests/test_functions.py
+++ b/julio/tests/test_functions.py
@@ -50,3 +50,10 @@ def test_add(tmp_path: Path) -> None:
     assert f_dir.is_dir()
     dl.drop(".", reckless="kill", dataset=dl.Dataset(registry_path))
     shutil.rmtree(registry_path)
+    # Check for invalid dataset
+    with pytest.raises(RuntimeError):
+        add(
+            yaml_path=Path(__file__).parent / "feature.yml",
+            registry_path=tmp_path,
+            dataset_display_name=None,
+        )

From 424f5e1b4f762f182297598165b19824d1047d7d Mon Sep 17 00:00:00 2001
From: Synchon Mandal <synchon@protonmail.com>
Date: Wed, 11 Mar 2026 13:25:51 +0100
Subject: [PATCH 22/32] update: improve tests for add

---
 julio/tests/invalid_store.yml          | 24 ++++++++++++++++
 julio/tests/test_functions.py          | 36 ++++++++++++++++--------
 julio/tests/{feature.yml => valid.yml} |  0
 julio/tests/valid_extra.yml            | 38 ++++++++++++++++++++++++++
 4 files changed, 87 insertions(+), 11 deletions(-)
 create mode 100644 julio/tests/invalid_store.yml
 rename julio/tests/{feature.yml => valid.yml} (100%)
 create mode 100644 julio/tests/valid_extra.yml

diff --git a/julio/tests/invalid_store.yml b/julio/tests/invalid_store.yml
new file mode 100644
index 0000000..f9c1043
--- /dev/null
+++ b/julio/tests/invalid_store.yml
@@ -0,0 +1,24 @@
+workdir: ./junifer-temp
+
+datagrabber:
+  kind: DMCC13Benchmark
+  types:
+    - BOLD
+  sessions:
+    - ses-wave1bas
+  tasks:
+    - Rest
+  phase_encodings:
+    - AP
+  runs:
+    - "1"
+
+markers:
+  - kind: FunctionalConnectivitySpheres
+    coords: DMNBuckner
+    radius: 5.0
+    name: fc_spheres
+
+storage:
+  kind: HDF5FeatureStorage
+  uri: ./store.sqlite
diff --git a/julio/tests/test_functions.py b/julio/tests/test_functions.py
index bac98b7..c6ba23c 100644
--- a/julio/tests/test_functions.py
+++ b/julio/tests/test_functions.py
@@ -4,6 +4,7 @@
 # License: AGPL
 
 import shutil
+from contextlib import AbstractContextManager, nullcontext
 from pathlib import Path
 
 import datalad.api as dl
@@ -30,30 +31,43 @@ def test_create(tmp_path: Path) -> None:
     shutil.rmtree(registry_path)
 
 
-def test_add(tmp_path: Path) -> None:
+@pytest.mark.parametrize(
+    "yml, expect",
+    [
+        ("valid.yml", nullcontext()),
+        ("invalid_store.yml", pytest.raises(RuntimeError)),
+        ("valid_extra.yml", nullcontext()),
+    ],
+)
+def test_add(tmp_path: Path, yml: str, expect: AbstractContextManager) -> None:
     """Test feature addition.
 
     Parameters
     ----------
     tmp_path : Path
         Pytest fixture that provides a temporary directory.
+    yml : str
+        The parametrized YAML file name.
+    expect : typing.ContextManager
+        The parametrized ContextManager object.
 
     """
     registry_path = tmp_path / "test_registry"
     create(registry_path)
-    add(
-        yaml_path=Path(__file__).parent / "feature.yml",
-        registry_path=registry_path,
-        dataset_display_name=None,
-    )
-    f_dir = registry_path / "features"
-    assert f_dir.is_dir()
-    dl.drop(".", reckless="kill", dataset=dl.Dataset(registry_path))
-    shutil.rmtree(registry_path)
+    with expect:
+        add(
+            yaml_path=Path(__file__).parent / yml,
+            registry_path=registry_path,
+            dataset_display_name=None,
+        )
+        f_dir = registry_path / "features"
+        assert f_dir.is_dir()
+        dl.drop(".", reckless="kill", dataset=dl.Dataset(registry_path))
+        shutil.rmtree(registry_path)
     # Check for invalid dataset
     with pytest.raises(RuntimeError):
         add(
-            yaml_path=Path(__file__).parent / "feature.yml",
+            yaml_path=Path(__file__).parent / yml,
             registry_path=tmp_path,
             dataset_display_name=None,
         )
diff --git a/julio/tests/feature.yml b/julio/tests/valid.yml
similarity index 100%
rename from julio/tests/feature.yml
rename to julio/tests/valid.yml
diff --git a/julio/tests/valid_extra.yml b/julio/tests/valid_extra.yml
new file mode 100644
index 0000000..3f3c5b6
--- /dev/null
+++ b/julio/tests/valid_extra.yml
@@ -0,0 +1,38 @@
+workdir: ./junifer-temp
+
+with:
+  - math
+
+datagrabber:
+  kind: PatternDataladDataGrabber
+  uri: https://github.com/OpenNeuroDatasets/ds003720.git
+  types:
+    - BOLD
+  patterns:
+    BOLD:
+      pattern: "{subject}/func/{subject}_task-{task}_{session}_bold.nii"
+      space: MNI152NLin2009cAsym
+  replacements:
+    - subject
+    - task
+    - session
+
+preprocess:
+  - kind: Smoothing
+    using: nilearn
+    on:
+      - BOLD
+    smoothing_params:
+      fwhm: fast
+
+markers:
+  - kind: FunctionalConnectivitySpheres
+    coords: DMNBuckner
+    radius: 5.0
+    name: fc_spheres
+    masks:
+      - compute_epi_mask
+
+storage:
+  kind: HDF5FeatureStorage
+  uri: ./store.hdf5

From 0b2e020eb6b157dcbf1bfbbd219767400b32b2e2 Mon Sep 17 00:00:00 2001
From: Synchon Mandal <synchon@protonmail.com>
Date: Wed, 11 Mar 2026 13:28:10 +0100
Subject: [PATCH 23/32] chore: add and update no cover pragma

---
 julio/_functions.py | 2 +-
 julio/_utils.py     | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/julio/_functions.py b/julio/_functions.py
index 0c26d81..1f63a60 100644
--- a/julio/_functions.py
+++ b/julio/_functions.py
@@ -90,7 +90,7 @@ def add(
         cmd="add",
         path=registry_path if str else str(registry_path.resolve()),
     )
-    if isinstance(registry_path, str): # pragma: no cover
+    if isinstance(registry_path, str):  # pragma: no cover
         log.debug("Cloning remote registry")
         with tempfile.TemporaryDirectory() as tmpdir:
             log.debug(f"Temporary directory created at {tmpdir}")
diff --git a/julio/_utils.py b/julio/_utils.py
index 0ac61e8..23b8ed5 100644
--- a/julio/_utils.py
+++ b/julio/_utils.py
@@ -74,7 +74,7 @@
 pattern = re.compile(regex)
 
 
-class PathOrURLParamType(click.ParamType):
+class PathOrURLParamType(click.ParamType):  # pragma : no cover
     name = "path_or_url"
 
     def convert(self, value, param, ctx):

From 97cbc184c6b0dae2036eee3103f833c55641bea4 Mon Sep 17 00:00:00 2001
From: Synchon Mandal <synchon@protonmail.com>
Date: Wed, 11 Mar 2026 13:29:22 +0100
Subject: [PATCH 24/32] chore: update tox.ini

---
 tox.ini | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/tox.ini b/tox.ini
index f46a1e7..8eea918 100644
--- a/tox.ini
+++ b/tox.ini
@@ -49,4 +49,8 @@ skip_install = false
 deps =
     pytest-cov
 commands =
-    pytest --cov={envsitepackagesdir}/julio --cov-report=xml --cov-report=term --cov-config=pyproject.toml {envsitepackagesdir}/julio
+    pytest --cov={envsitepackagesdir}/julio \
+           --cov-report=xml \
+           --cov-report=term-missing \
+           --cov-config=pyproject.toml \
+           {envsitepackagesdir}/julio

From bbf525af1bbdfacf1673858595e90fd8a5d28285 Mon Sep 17 00:00:00 2001
From: Synchon Mandal <synchon@protonmail.com>
Date: Wed, 11 Mar 2026 13:32:38 +0100
Subject: [PATCH 25/32] chore: fix no cover pragma

---
 julio/_utils.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/julio/_utils.py b/julio/_utils.py
index 23b8ed5..c49d2ac 100644
--- a/julio/_utils.py
+++ b/julio/_utils.py
@@ -74,7 +74,7 @@
 pattern = re.compile(regex)
 
 
-class PathOrURLParamType(click.ParamType):  # pragma : no cover
+class PathOrURLParamType(click.ParamType):  # pragma: no cover
     name = "path_or_url"
 
     def convert(self, value, param, ctx):

From f288050050233a356b1ac65fe9d6e88d5fa495bf Mon Sep 17 00:00:00 2001
From: Synchon Mandal <synchon@protonmail.com>
Date: Wed, 11 Mar 2026 13:34:42 +0100
Subject: [PATCH 26/32] chore: update valid_extra.yml

---
 julio/tests/extra.py        | 0
 julio/tests/valid_extra.yml | 5 ++++-
 2 files changed, 4 insertions(+), 1 deletion(-)
 create mode 100644 julio/tests/extra.py

diff --git a/julio/tests/extra.py b/julio/tests/extra.py
new file mode 100644
index 0000000..e69de29
diff --git a/julio/tests/valid_extra.yml b/julio/tests/valid_extra.yml
index 3f3c5b6..14e8dd0 100644
--- a/julio/tests/valid_extra.yml
+++ b/julio/tests/valid_extra.yml
@@ -1,7 +1,10 @@
-workdir: ./junifer-temp
+workdir:
+  path: ./junifer-temp
+  cleanup: true
 
 with:
   - math
+  - ./extra.py
 
 datagrabber:
   kind: PatternDataladDataGrabber

From 355e1737bddfc852ae4ca46eeb6a48061041f6f9 Mon Sep 17 00:00:00 2001
From: Synchon Mandal <synchon@protonmail.com>
Date: Wed, 11 Mar 2026 13:56:17 +0100
Subject: [PATCH 27/32] update: improve tests for add

---
 julio/tests/invalid_mandatory_section.yml | 22 +++++++++++++++++++
 julio/tests/invalid_section.yml           | 26 +++++++++++++++++++++++
 julio/tests/missing_storage_uri.yml       | 23 ++++++++++++++++++++
 julio/tests/test_functions.py             |  5 ++++-
 4 files changed, 75 insertions(+), 1 deletion(-)
 create mode 100644 julio/tests/invalid_mandatory_section.yml
 create mode 100644 julio/tests/invalid_section.yml
 create mode 100644 julio/tests/missing_storage_uri.yml

diff --git a/julio/tests/invalid_mandatory_section.yml b/julio/tests/invalid_mandatory_section.yml
new file mode 100644
index 0000000..75b85a9
--- /dev/null
+++ b/julio/tests/invalid_mandatory_section.yml
@@ -0,0 +1,22 @@
+datagrabber:
+  kind: DMCC13Benchmark
+  types:
+    - BOLD
+  sessions:
+    - ses-wave1bas
+  tasks:
+    - Rest
+  phase_encodings:
+    - AP
+  runs:
+    - "1"
+
+markers:
+  - kind: FunctionalConnectivitySpheres
+    coords: DMNBuckner
+    radius: 5.0
+    name: fc_spheres
+
+storage:
+  kind: HDF5FeatureStorage
+  uri: ./store.hdf5
diff --git a/julio/tests/invalid_section.yml b/julio/tests/invalid_section.yml
new file mode 100644
index 0000000..34b01bb
--- /dev/null
+++ b/julio/tests/invalid_section.yml
@@ -0,0 +1,26 @@
+invalid:
+
+workdir: ./junifer-temp
+
+datagrabber:
+  kind: DMCC13Benchmark
+  types:
+    - BOLD
+  sessions:
+    - ses-wave1bas
+  tasks:
+    - Rest
+  phase_encodings:
+    - AP
+  runs:
+    - "1"
+
+markers:
+  - kind: FunctionalConnectivitySpheres
+    coords: DMNBuckner
+    radius: 5.0
+    name: fc_spheres
+
+storage:
+  kind: HDF5FeatureStorage
+  uri: ./store.hdf5
diff --git a/julio/tests/missing_storage_uri.yml b/julio/tests/missing_storage_uri.yml
new file mode 100644
index 0000000..b2af8ca
--- /dev/null
+++ b/julio/tests/missing_storage_uri.yml
@@ -0,0 +1,23 @@
+workdir: ./junifer-temp
+
+datagrabber:
+  kind: DMCC13Benchmark
+  types:
+    - BOLD
+  sessions:
+    - ses-wave1bas
+  tasks:
+    - Rest
+  phase_encodings:
+    - AP
+  runs:
+    - "1"
+
+markers:
+  - kind: FunctionalConnectivitySpheres
+    coords: DMNBuckner
+    radius: 5.0
+    name: fc_spheres
+
+storage:
+  kind: HDF5FeatureStorage
diff --git a/julio/tests/test_functions.py b/julio/tests/test_functions.py
index c6ba23c..fbbccb6 100644
--- a/julio/tests/test_functions.py
+++ b/julio/tests/test_functions.py
@@ -35,8 +35,11 @@ def test_create(tmp_path: Path) -> None:
     "yml, expect",
     [
         ("valid.yml", nullcontext()),
-        ("invalid_store.yml", pytest.raises(RuntimeError)),
         ("valid_extra.yml", nullcontext()),
+        ("invalid_store.yml", pytest.raises(RuntimeError)),
+        ("invalid_mandatory_section.yml", pytest.raises(RuntimeError)),
+        ("invalid_section.yml", pytest.raises(RuntimeError)),
+        ("missing_storage_uri.yml", pytest.raises(RuntimeError)),
     ],
 )
 def test_add(tmp_path: Path, yml: str, expect: AbstractContextManager) -> None:

From a8784cc58785c3c0732953ba9a3b4e37d6121d86 Mon Sep 17 00:00:00 2001
From: Synchon Mandal <synchon@protonmail.com>
Date: Wed, 11 Mar 2026 14:22:00 +0100
Subject: [PATCH 28/32] chore: lint

---
 julio/tests/extra.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/julio/tests/extra.py b/julio/tests/extra.py
index e69de29..88eba52 100644
--- a/julio/tests/extra.py
+++ b/julio/tests/extra.py
@@ -0,0 +1 @@
+"""Placeholder module for test."""

From 5d2018c53556a61dbae8ec3635541ec4c09f1fc5 Mon Sep 17 00:00:00 2001
From: Synchon Mandal <synchon@protonmail.com>
Date: Wed, 11 Mar 2026 14:28:40 +0100
Subject: [PATCH 29/32] chore: add changelog

---
 changelog.d/3.added.md | 1 +
 1 file changed, 1 insertion(+)
 create mode 100644 changelog.d/3.added.md

diff --git a/changelog.d/3.added.md b/changelog.d/3.added.md
new file mode 100644
index 0000000..0e55a70
--- /dev/null
+++ b/changelog.d/3.added.md
@@ -0,0 +1 @@
+Introduce feature files addition to registry

From bf010ab0185fe5351e02a2d4c8fd21ad8a59b3bc Mon Sep 17 00:00:00 2001
From: Synchon Mandal <synchon@protonmail.com>
Date: Fri, 29 May 2026 16:28:16 +0200
Subject: [PATCH 30/32] chore: remove ruamel.yaml and use junifer's yaml config

---
 julio/_utils.py |  3 +--
 julio/_yaml.py  | 16 ----------------
 pyproject.toml  |  1 -
 3 files changed, 1 insertion(+), 19 deletions(-)
 delete mode 100644 julio/_yaml.py

diff --git a/julio/_utils.py b/julio/_utils.py
index c49d2ac..71c05de 100644
--- a/julio/_utils.py
+++ b/julio/_utils.py
@@ -14,10 +14,9 @@
 import datalad.api as dl
 import structlog
 from h5io import read_hdf5, write_hdf5
+from junifer.utils import yaml
 from tqdm import tqdm
 
-from ._yaml import yaml
-
 
 __all__ = ["PathOrURL", "is_julio_registry", "process_features"]
 
diff --git a/julio/_yaml.py b/julio/_yaml.py
deleted file mode 100644
index 732ca75..0000000
--- a/julio/_yaml.py
+++ /dev/null
@@ -1,16 +0,0 @@
-"""Provide YAML config definition for junifer use."""
-
-# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
-# License: AGPL
-
-from ruamel.yaml import YAML
-
-
-__all__ = ["yaml"]
-
-
-# Configure YAML class once for further use
-yaml = YAML()
-yaml.default_flow_style = False
-yaml.allow_unicode = True
-yaml.indent(mapping=2, sequence=4, offset=2)
diff --git a/pyproject.toml b/pyproject.toml
index 332697c..236bb36 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -39,7 +39,6 @@ dependencies = [
     "datalad>=1.0.0,<1.3.0",
     "lazy_loader==0.4",
     "structlog>=25.0.0,<26.0.0",
-    "ruamel.yaml>=0.17,<0.19",
     "h5io@git+https://github.com/juaml/h5io@600d9e25c625b11520d86b08f9f0b761f71b0542",
     "tqdm>=4.66.1,<4.67.0",
 ]

From 3d0930ef183e66e3e2af745574a529370ff98f7d Mon Sep 17 00:00:00 2001
From: Synchon Mandal <synchon@protonmail.com>
Date: Fri, 29 May 2026 16:31:19 +0200
Subject: [PATCH 31/32] update: use junifer to parse and generate yaml

---
 julio/_utils.py | 144 +++---------------------------------------------
 1 file changed, 8 insertions(+), 136 deletions(-)

diff --git a/julio/_utils.py b/julio/_utils.py
index 71c05de..3e9ccb2 100644
--- a/julio/_utils.py
+++ b/julio/_utils.py
@@ -14,6 +14,7 @@
 import datalad.api as dl
 import structlog
 from h5io import read_hdf5, write_hdf5
+from junifer.api import generate_yaml, parse_yaml
 from junifer.utils import yaml
 from tqdm import tqdm
 
@@ -120,75 +121,6 @@ def is_julio_registry(ds: dl.Dataset) -> bool:
     return False
 
 
-def _make_absolute_path(path: str, base_path: Path) -> str:
-    """Make a path absolute.
-
-    Parameters
-    ----------
-    path : str
-        Path to make absolute.
-    base_path : Path
-        Base path to use.
-
-    Returns
-    -------
-    str
-        Absolute path.
-
-    """
-    log = logger.bind(cmd="make_absolute_path", path=str(path))
-    log.debug("Making path absolute")
-    path_p = Path(path)
-    if not path_p.is_absolute():
-        path_p = base_path / path_p
-    log.debug("Made path absolute")
-    return str(path_p.resolve())
-
-
-def _adjust_paths(data: dict, yaml_path: Path) -> dict:
-    """Adjust paths in the data dictionary.
-
-    Parameters
-    ----------
-    data : dict
-        Data dictionary to adjust.
-    yaml_path : Path
-        Path to the YAML file.
-
-    Returns
-    -------
-    dict
-        Adjusted data dictionary.
-
-    """
-    log = logger.bind(cmd="adjust_paths", path=str(yaml_path.resolve()))
-    log.debug("Adjusting paths")
-    if "workdir" in data:
-        if isinstance(data["workdir"], str):
-            data["workdir"] = _make_absolute_path(
-                data["workdir"], yaml_path.parent
-            )
-        else:
-            data["workdir"]["path"] = _make_absolute_path(
-                data["workdir"]["path"], yaml_path.parent
-            )
-    if "with" in data:
-        if not isinstance(data["with"], list):
-            data["with"] = list(data["with"])
-        mods = []
-        for w in data["with"]:
-            if w.endswith(".py"):
-                mods.append(_make_absolute_path(w, yaml_path.parent))
-            else:
-                mods.append(w)
-        data["with"] = mods
-    data["storage"]["uri"] = _make_absolute_path(
-        data["storage"]["uri"], yaml_path.parent
-    )
-    log.debug("Adjusted paths")
-    return data
-
-
 def _parse_yaml(yaml_path: Path) -> dict:
     """Parse the junifer YAML.
 
@@ -211,7 +143,7 @@ def _parse_yaml(yaml_path: Path) -> dict:
     """
     log = logger.bind(cmd="parse_yaml", path=str(yaml_path.resolve()))
     log.debug("Parsing junifer YAML")
-    contents = yaml.load(yaml_path)
+    contents = parse_yaml(yaml_path)
     # Validate mandatory sections
     mandatory = ("workdir", "datagrabber", "markers", "storage")
     for s in mandatory:
@@ -231,80 +163,15 @@ def _parse_yaml(yaml_path: Path) -> dict:
         raise RuntimeError(
             f"`uri` missing from `storage` section in {yaml_path.resolve()!s}"
         )
-    # Replace relative file paths with absolute
-    contents = _adjust_paths(contents, yaml_path)
     # Validate storage file exists
     if not Path(contents["storage"]["uri"]).exists():
         raise RuntimeError(
             f"Storage file does not exist: {contents['storage']['uri']}"
         )
-    # Remove elements key if empty
-    if "elements" in contents:
-        if contents["elements"] is None:
-            contents.pop("elements")
     log.debug("Parsed junifer YAML")
     return contents
 
 
-def _generate_feature_yaml(meta: dict) -> dict:
-    """Generate a feature YAML from metadata.
-
-    Parameters
-    ----------
-    meta : dict
-        Feature metadata as dictionary.
-
-    Returns
-    -------
-    dict
-        Feature YAML.
-
-    """
-    y: dict[str, Any] = {}
-    y["workdir"] = ""
-    if "with" in meta:
-        y["with"] = meta["with"].copy()
-    # Set datagrabber
-    y["datagrabber"] = meta["datagrabber"].copy()
-    a = y["datagrabber"].pop("class")
-    y["datagrabber"]["kind"] = a
-    if a not in ("PatternDataGrabber", "PatternDataladDataGrabber"):
-        y["datagrabber"].pop("uri")
-        y["datagrabber"].pop("rootdir")
-        y["datagrabber"].pop("patterns")
-        y["datagrabber"].pop("replacements")
-        y["datagrabber"].pop("confounds_format")
-        y["datagrabber"].pop("partial_pattern_ok")
-        for k in meta[
-            "datagrabber"
-        ].keys():  # use data instead of y to avoid .copy()
-            if k.startswith("datalad"):
-                y["datagrabber"].pop(k)
-    # Set preprocess
-    if "preprocess" in meta:
-        y["preprocess"] = meta["preprocess"].copy()
-        b = y["preprocess"].pop("class")
-        y["preprocess"]["kind"] = b
-    # Set markers
-    y["markers"] = []
-    y["markers"].append(meta["marker"].copy())
-    c = y["markers"][0].pop("class")
-    y["markers"][0]["kind"] = c
-    if y["markers"][0]["masks"] is None:
-        y["markers"][0].pop("masks")
-    # Set storage
-    y["storage"] = {
-        "kind": "HDF5FeatureStorage",
-        "uri": "",
-    }
-    # Set queue
-    y["queue"] = {
-        "jobname": meta["name"],
-        "kind": "",
-    }
-    return y
-
-
 def _generate_meta_yaml(
     meta: dict,
     data: dict,
@@ -405,8 +272,13 @@ def _process_hdf5(
     feature_dir = ds.pathobj / "features"
     feature_dir.mkdir(exist_ok=True)
     for k, v in tqdm(metadata.items(), desc="Processing features"):
+        # Add "with" and "queue" section if present in data
+        if "with" in data:
+            v["with"] = data["with"].copy()
+        if "queue" in data:
+            v["queue"] = data["queue"].copy()
         # YAML
-        yaml_data = _generate_feature_yaml(v)
+        yaml_data = generate_yaml(v)
         yaml_path = feature_dir / f"feature-{k}.yml"
         yaml.dump(yaml_data, stream=yaml_path.open("w"))
         # Data

From 817e050ed9bc8a6dfda7636ee848c438d901222f Mon Sep 17 00:00:00 2001
From: Synchon Mandal <synchon@protonmail.com>
Date: Fri, 29 May 2026 16:31:59 +0200
Subject: [PATCH 32/32] chore: improve datetime imports

---
 julio/_utils.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/julio/_utils.py b/julio/_utils.py
index 3e9ccb2..a9e8730 100644
--- a/julio/_utils.py
+++ b/julio/_utils.py
@@ -3,10 +3,10 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
+import datetime as dt
 import pathlib
 import re
 import sys
-from datetime import datetime
 from pathlib import Path
 from typing import Any
 
@@ -203,7 +203,7 @@ def _generate_meta_yaml(
     y: dict[str, Any] = {}
     y["md5"] = md5
     y["name"] = meta["name"]
-    y["added_on"] = datetime.utcnow().strftime("%Y-%m-%d %H:%M:%S")
+    y["added_on"] = dt.datetime.now(tz=dt.UTC).strftime("%Y-%m-%d %H:%M:%S")
     ndata = data["data"]
     y["data"] = {
         "shape": ndata.shape,