junifer 0.0.6.dev23__tar.gz → 0.0.6.dev44__tar.gz

{junifer-0.0.6.dev23 → junifer-0.0.6.dev44}/.github/workflows/ci.yml

@@ -93,16 +93,11 @@ jobs:
       continue-on-error: true
     - name: Install FSL
       run: |
-        curl -fsSL https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fslinstaller.py | python - -d /opt/fsl/
-        FSLOUTPUTTYPE="NIFTI_GZ"
-        FSLMULTIFILEQUIT="TRUE"
-        FSLTCLSH="/opt/fsl/bin/fsltclsh"
-        FSLWISH="/opt/fsl/bin/fslwish"
-        FSLLOCKDIR=""
-        FSLMACHINELIST=""
-        FSLREMOTECALL=""
-        FSLGECUDAQ="cuda.q"
-        echo "/opt/fsl" >> $GITHUB_PATH
+        curl -fsSL https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fslinstaller.py | python - -d /opt/fsl/ --skip_registration
+        echo "FSLDIR=/opt/fsl" >> $GITHUB_ENV
+        echo "FSLOUTPUTTYPE=NIFTI_GZ" >> $GITHUB_ENV
+        echo "FSLMULTIFILEQUIT=TRUE" >> $GITHUB_ENV
+        echo "/opt/fsl/bin" >> $GITHUB_PATH
       if: matrix.python-version == 3.11
       # Bypass FSL installation failure
       continue-on-error: true

{junifer-0.0.6.dev23 → junifer-0.0.6.dev44}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.6.dev23
+Version: 0.0.6.dev44
 Summary: JUelich NeuroImaging FEature extractoR
 Author-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
 Maintainer-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
@@ -66,6 +66,8 @@ Requires-Dist: julearn==0.3.3; extra == "docs"
 Requires-Dist: sphinx-copybutton<0.5.3,>=0.5.1; extra == "docs"
 Requires-Dist: towncrier<23.12.0,>=23.10.0; extra == "docs"
 Requires-Dist: sphinxcontrib-mermaid<0.10,>=0.8.1; extra == "docs"
+Requires-Dist: sphinxcontrib-towncrier==0.4.0a0; extra == "docs"
+Requires-Dist: setuptools-scm>=8; extra == "docs"
 
 ![Junifer logo](docs/images/junifer_logo.png "junifer logo")
 

{junifer-0.0.6.dev23 → junifer-0.0.6.dev44}/docs/Makefile

@@ -19,24 +19,14 @@ clean:
 	rm -rf auto_examples/
 	rm -rf api/generated/
 
-# For local build
-local: news
-	make _build_local; STATUS=$$?; make news_cleanup; exit $$STATUS
-
-news:
-	@echo "Generating whats_new.rst"
-	cd ../ && towncrier build --keep
-
-news_cleanup:
-	@echo "Cleaning up whats_new.rst"
-	git restore --staged whats_new.rst
-	git restore whats_new.rst
+local:
+	make _build_local; STATUS=$$?; exit $$STATUS
 
 _build_local:
 	sphinx-build "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
 
-html: news
-	make _html; STATUS=$$?; make news_cleanup; exit $$STATUS
+html:
+	make _html; STATUS=$$?; exit $$STATUS
 
 _html:
 	$(SPHINXBUILD) "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS)

{junifer-0.0.6.dev23 → junifer-0.0.6.dev44}/docs/api/api.rst

@@ -1,10 +1,10 @@
 API Functions
 =============
 
-Main API functions
-------------------
+Main Functions
+--------------
 
-.. automodule:: junifer.api
+.. automodule:: junifer.api.functions
    :members:
    :imported-members:
 

junifer-0.0.6.dev44/docs/api/cli.rst

@@ -0,0 +1,6 @@
+CLI Functions
+=============
+
+.. automodule:: junifer.cli.parser
+   :members:
+   :imported-members:

{junifer-0.0.6.dev23 → junifer-0.0.6.dev44}/docs/api/index.rst

@@ -25,6 +25,7 @@ Utilities
    stats
    pipeline
    api
+   cli
    utils
    testing
    onthefly

junifer-0.0.6.dev44/docs/changes/newsfragments/358.doc

@@ -0,0 +1 @@
+Improve Sphinx configuration and extensions by `Synchon Mandal`_

junifer-0.0.6.dev44/docs/changes/newsfragments/361.misc

@@ -0,0 +1 @@
+Refactor ``api`` sub-package and introduce new ``cli`` sub-package by `Synchon Mandal`_

{junifer-0.0.6.dev23 → junifer-0.0.6.dev44}/docs/conf.py

@@ -6,36 +6,45 @@
 # list see the documentation:
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
 
-# -- Path setup --------------------------------------------------------------
-
-# If extensions (or modules to document with autodoc) are in another directory,
-# add these directories to sys.path here. If the directory is relative to the
-# documentation root, use os.path.abspath to make it absolute, like shown here.
-#
-# import os
-# import sys
-# sys.path.insert(0, os.path.abspath('.'))
-
-import sys
+import datetime
+from functools import partial
 from pathlib import Path
 
+from setuptools_scm import get_version
+
 
 # Check if sphinx-multiversion is installed
 use_multiversion = False
 try:
     import sphinx_multiversion  # noqa: F401
+
     use_multiversion = True
 except ImportError:
     pass
 
-curdir = Path(__file__).parent
-sys.path.append((curdir / "sphinxext").as_posix())
+
+# -- Path setup --------------------------------------------------------------
+
+PROJECT_ROOT_DIR = Path(__file__).parents[1].resolve()
+get_scm_version = partial(get_version, root=PROJECT_ROOT_DIR)
 
 # -- Project information -----------------------------------------------------
 
-project = "junifer"
-copyright = "2023, Authors of junifer"
-author = "Fede Raimondo"
+github_url = "https://github.com"
+github_repo_org = "juaml"
+github_repo_name = "junifer"
+github_repo_slug = f"{github_repo_org}/{github_repo_name}"
+github_repo_url = f"{github_url}/{github_repo_slug}"
+
+project = github_repo_name
+author = f"{project} Contributors"
+copyright = f"{datetime.date.today().year}, {author}"
+
+# The version along with dev tag
+release = get_scm_version(
+    version_scheme="guess-next-dev",
+    local_scheme="no-local-version",
+)
 
 # -- General configuration ---------------------------------------------------
 
@@ -43,16 +52,19 @@ author = "Fede Raimondo"
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
+    # Built-in extensions:
     "sphinx.ext.autodoc",  # include documentation from docstrings
     "sphinx.ext.autosummary",  # generate autodoc summaries
     "sphinx.ext.doctest",  # test snippets in the documentation
+    "sphinx.ext.extlinks",  # markup to shorten external links
     "sphinx.ext.intersphinx",  # link to other projects` documentation
     "sphinx.ext.mathjax",  # math support for HTML outputs in Sphinx
+    # Third-party extensions:
     "sphinx_gallery.gen_gallery",  # HTML gallery of examples
     "numpydoc",  # support for NumPy style docstrings
-    "gh_substitutions",  # custom GitHub substitutions
     "sphinx_copybutton",  # copy button for code blocks
     "sphinxcontrib.mermaid",  # mermaid support
+    "sphinxcontrib.towncrier.ext",  # towncrier fragment support
 ]
 
 if use_multiversion:
@@ -88,11 +100,8 @@ nitpick_ignore_regex = [
 
 # -- Options for HTML output -------------------------------------------------
 
-# The theme to use for HTML and HTML Help pages. See the documentation for
-# a list of builtin themes.
-#
 html_theme = "furo"
-
+html_title = "junifer documentation"
 html_logo = "./images/junifer_logo.png"
 
 # These paths are either relative to html_static_path
@@ -146,6 +155,12 @@ intersphinx_mapping = {
     "scipy": ("https://docs.scipy.org/doc/scipy/", None),
 }
 
+# -- sphinx.ext.extlinks configuration ---------------------------------------
+
+extlinks = {
+    "gh": (f"{github_repo_url}/issues/%s", "#%s"),
+}
+
 # -- numpydoc configuration --------------------------------------------------
 
 numpydoc_show_class_members = False
@@ -197,3 +212,9 @@ smv_rebuild_tags = False
 smv_tag_whitelist = r"^v\d+\.\d+.\d+$"
 smv_branch_whitelist = r"main"
 smv_released_pattern = r"^tags/v.*$"
+
+# -- sphinxcontrib-towncrier configuration -----------------------------------
+
+towncrier_draft_autoversion_mode = "draft"
+towncrier_draft_include_empty = True
+towncrier_draft_working_directory = PROJECT_ROOT_DIR

{junifer-0.0.6.dev23 → junifer-0.0.6.dev44}/docs/whats_new.rst

@@ -6,6 +6,8 @@
 What's new
 ==========
 
+.. towncrier-draft-entries:: |release|
+
 .. towncrier release notes start
 
 Junifer 0.0.5 (2024-07-22)

{junifer-0.0.6.dev23 → junifer-0.0.6.dev44}/junifer/__init__.py

@@ -6,6 +6,7 @@
 
 from . import (
     api,
+    cli,
     configs,
     data,
     datagrabber,
@@ -24,6 +25,7 @@ from ._version import __version__
 
 __all__ = [
     "api",
+    "cli",
     "configs",
     "data",
     "datagrabber",

{junifer-0.0.6.dev23 → junifer-0.0.6.dev44}/junifer/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.6.dev23'
-__version_tuple__ = version_tuple = (0, 0, 6, 'dev23')
+__version__ = version = '0.0.6.dev44'
+__version_tuple__ = version_tuple = (0, 0, 6, 'dev44')

junifer-0.0.6.dev44/junifer/api/__init__.py

@@ -0,0 +1,11 @@
+"""Public API components."""
+
+# Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
+#          Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+from . import decorators
+from .functions import collect, list_elements, reset, run, queue
+
+
+__all__ = ["decorators", "collect", "queue", "run", "reset", "list_elements"]

{junifer-0.0.6.dev23 → junifer-0.0.6.dev44}/junifer/api/decorators.py

@@ -1,4 +1,4 @@
-"""Provide decorators for api."""
+"""Provide API decorators."""
 
 # Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
 #          Leonard Sasse <l.sasse@fz-juelich.de>

{junifer-0.0.6.dev23 → junifer-0.0.6.dev44}/junifer/api/functions.py

@@ -1,4 +1,4 @@
-"""Provide functions for cli."""
+"""Provide API functions."""
 
 # Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
 #          Leonard Sasse <l.sasse@fz-juelich.de>
@@ -11,6 +11,7 @@ import typing
 from pathlib import Path
 from typing import Dict, List, Optional, Tuple, Union
 
+from ..api.queue_context import GnuParallelLocalAdapter, HTCondorAdapter
 from ..datagrabber.base import BaseDataGrabber
 from ..markers.base import BaseMarker
 from ..markers.collection import MarkerCollection
@@ -18,9 +19,7 @@ from ..pipeline import WorkDirManager
 from ..pipeline.registry import build
 from ..preprocess.base import BasePreprocessor
 from ..storage.base import BaseFeatureStorage
-from ..utils import logger, raise_error
-from .queue_context import GnuParallelLocalAdapter, HTCondorAdapter
-from .utils import yaml
+from ..utils import logger, raise_error, yaml
 
 
 __all__ = ["run", "collect", "queue", "reset", "list_elements"]

{junifer-0.0.6.dev23 → junifer-0.0.6.dev44}/junifer/api/tests/test_functions.py

@@ -1,4 +1,4 @@
-"""Provide tests for functions."""
+"""Provide tests for API functions."""
 
 # Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
 #          Leonard Sasse <l.sasse@fz-juelich.de>
@@ -13,7 +13,7 @@ import pytest
 from ruamel.yaml import YAML
 
 import junifer.testing.registry  # noqa: F401
-from junifer.api.functions import collect, list_elements, queue, reset, run
+from junifer.api import collect, list_elements, queue, reset, run
 from junifer.datagrabber.base import BaseDataGrabber
 from junifer.pipeline.registry import build
 

junifer-0.0.6.dev44/junifer/cli/__init__.py

@@ -0,0 +1,8 @@
+"""Junifer CLI."""
+
+# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+from .cli import cli
+
+__all__ = ["cli"]

{junifer-0.0.6.dev23/junifer/api → junifer-0.0.6.dev44/junifer/cli}/cli.py

@@ -1,4 +1,4 @@
-"""Provide functions for cli."""
+"""Provide functions for CLI."""
 
 # Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
 #          Synchon Mandal <s.mandal@fz-juelich.de>
@@ -8,122 +8,26 @@ import pathlib
 import subprocess
 import sys
 from pathlib import Path
-from typing import Dict, List, Optional, Tuple, Union
+from typing import Optional, Tuple, Union
 
 import click
-import pandas as pd
 
-from ..utils.logging import (
+from ..api import functions as cli_func
+from ..utils import (
     configure_logging,
-    logger,
     raise_error,
-    warn_with_log,
+    yaml,
 )
-from .functions import collect as api_collect
-from .functions import list_elements as api_list_elements
-from .functions import queue as api_queue
-from .functions import reset as api_reset
-from .functions import run as api_run
-from .parser import parse_yaml
+from .parser import parse_elements, parse_yaml
 from .utils import (
     _get_dependency_information,
     _get_environment_information,
     _get_junifer_version,
     _get_python_information,
     _get_system_information,
-    yaml,
 )
 
 
-def _parse_elements(element: Tuple[str], config: Dict) -> Union[List, None]:
-    """Parse elements from cli.
-
-    Parameters
-    ----------
-    element : tuple of str
-        The element(s) to operate on.
-    config : dict
-        The configuration to operate using.
-
-    Returns
-    -------
-    list or None
-        The element(s) as list or None.
-
-    Raises
-    ------
-    ValueError
-        If no element is found either in the command-line options or
-        the configuration file.
-
-    Warns
-    -----
-    RuntimeWarning
-        If elements are specified both via the command-line options and
-        the configuration file.
-
-    """
-    logger.debug(f"Parsing elements: {element}")
-    # Early return None to continue with all elements
-    if len(element) == 0:
-        return None
-    # Check if the element is a file for single element;
-    # if yes, then parse elements from it
-    if len(element) == 1 and Path(element[0]).resolve().is_file():
-        elements = _parse_elements_file(Path(element[0]).resolve())
-    else:
-        # Process multi-keyed elements
-        elements = [tuple(x.split(",")) if "," in x else x for x in element]
-    logger.debug(f"Parsed elements: {elements}")
-    if elements is not None and "elements" in config:
-        warn_with_log(
-            "One or more elements have been specified in both the command "
-            "line and in the config file. The command line has precedence "
-            "over the configuration file. That is, the elements specified "
-            "in the command line will be used. The elements specified in "
-            "the configuration file will be ignored. To remove this warning, "
-            "please remove the `elements` item from the configuration file."
-        )
-    elif elements is None:
-        # Check in config
-        elements = config.get("elements", None)
-        if elements is None:
-            raise_error(
-                "The `elements` key is set in the configuration, but its value"
-                " is `None`. It is likely that there is an empty `elements` "
-                "section in the yaml configuration file."
-            )
-    return elements
-
-
-def _parse_elements_file(filepath: Path) -> List[Tuple[str, ...]]:
-    """Parse elements from file.
-
-    Parameters
-    ----------
-    filepath : pathlib.Path
-        The path to the element file.
-
-    Returns
-    -------
-    list of tuple of str
-        The element(s) as list.
-
-    """
-    # Read CSV into dataframe
-    csv_df = pd.read_csv(
-        filepath,
-        header=None,  # no header  # type: ignore
-        index_col=False,  # no index column
-        dtype=str,
-        skipinitialspace=True,  # no leading space after delimiter
-    )
-    # Remove trailing whitespace in cell entries
-    csv_df_trimmed = csv_df.apply(lambda x: x.str.strip())
-    # Convert to list of tuple of str
-    return list(map(tuple, csv_df_trimmed.to_numpy()))
-
-
 def _validate_verbose(
     ctx: click.Context, param: str, value: str
 ) -> Union[str, int]:
@@ -166,7 +70,7 @@ def _validate_verbose(
 
 @click.group()
 def cli() -> None:  # pragma: no cover
-    """CLI for JUelich NeuroImaging FEature extractoR."""
+    """JUelich NeuroImaging FEature extractoR."""
 
 
 @cli.command()
@@ -187,7 +91,7 @@ def cli() -> None:  # pragma: no cover
 def run(
     filepath: click.Path, element: Tuple[str], verbose: Union[str, int]
 ) -> None:
-    """Run command for CLI.
+    """Run feature extraction.
 
     \f
 
@@ -219,9 +123,9 @@ def run(
     if preprocessors is not None and not isinstance(preprocessors, list):
         preprocessors = [preprocessors]
     # Parse elements
-    elements = _parse_elements(element, config)
+    elements = parse_elements(element, config)
     # Perform operation
-    api_run(
+    cli_func.run(
         workdir=workdir,
         datagrabber=datagrabber,
         markers=markers,
@@ -246,7 +150,7 @@ def run(
     default="info",
 )
 def collect(filepath: click.Path, verbose: Union[str, int]) -> None:
-    """Collect command for CLI.
+    """Collect extracted features.
 
     \f
 
@@ -263,7 +167,7 @@ def collect(filepath: click.Path, verbose: Union[str, int]) -> None:
     config = parse_yaml(filepath)  # type: ignore
     storage = config["storage"]
     # Perform operation
-    api_collect(storage=storage)
+    cli_func.collect(storage=storage)
 
 
 @cli.command()
@@ -290,7 +194,7 @@ def queue(
     submit: bool,
     verbose: Union[str, int],
 ) -> None:
-    """Queue command for CLI.
+    """Queue feature extraction.
 
     \f
 
@@ -311,12 +215,12 @@ def queue(
     configure_logging(level=verbose)
     # TODO: add validation
     config = parse_yaml(filepath)  # type: ignore
-    elements = _parse_elements(element, config)
+    elements = parse_elements(element, config)
     if "queue" not in config:
         raise_error(f"No queue configuration found in {filepath}.")
     queue_config = config.pop("queue")
     kind = queue_config.pop("kind")
-    api_queue(
+    cli_func.queue(
         config=config,
         kind=kind,
         overwrite=overwrite,
@@ -329,7 +233,7 @@ def queue(
 @cli.command()
 @click.option("--long", "long_", is_flag=True)
 def wtf(long_: bool) -> None:
-    """Wtf command for CLI.
+    """WTF?!.
 
     \f
 
@@ -352,7 +256,7 @@ def wtf(long_: bool) -> None:
 @cli.command()
 @click.argument("subpkg", type=str)
 def selftest(subpkg: str) -> None:
-    """Selftest command for CLI.
+    """Selftest.
 
     \f
 
@@ -433,7 +337,7 @@ def reset(
     filepath: click.Path,
     verbose: Union[str, int],
 ) -> None:
-    """Reset command for CLI.
+    """Reset generated assets.
 
     \f
 
@@ -449,7 +353,7 @@ def reset(
     # Parse YAML
     config = parse_yaml(filepath)
     # Perform operation
-    api_reset(config)
+    cli_func.reset(config)
 
 
 @cli.command()
@@ -478,7 +382,7 @@ def list_elements(
     output_file: Optional[click.Path],
     verbose: Union[str, int],
 ) -> None:
-    """Element listing command for CLI.
+    """List elements of a dataset.
 
     \f
 
@@ -501,9 +405,9 @@ def list_elements(
     # Fetch datagrabber
     datagrabber = config["datagrabber"]
     # Parse elements
-    elements = _parse_elements(element, config)
+    elements = parse_elements(element, config)
     # Perform operation
-    listed_elements = api_list_elements(
+    listed_elements = cli_func.list_elements(
         datagrabber=datagrabber,
         elements=elements,
     )
@@ -517,7 +421,7 @@ def list_elements(
 
 @cli.group()
 def setup() -> None:  # pragma: no cover
-    """Configure commands for Junifer."""
+    """Configure external tools."""
     pass