junifer 0.0.5.dev242__py3-none-any.whl → 0.0.6__py3-none-any.whl

{junifer-0.0.5.dev242.dist-info → junifer-0.0.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: junifer
-Version: 0.0.5.dev242
+Version: 0.0.6
 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>
@@ -19,53 +19,57 @@ Classifier: Topic :: Software Development
 Classifier: Topic :: Scientific/Engineering
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Classifier: Operating System :: OS Independent
-Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
-Requires-Python: >=3.8
+Classifier: Programming Language :: Python :: 3.13
+Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE.md
 License-File: AUTHORS.rst
-Requires-Dist: click <8.2,>=8.1.3
-Requires-Dist: numpy <2.0.0,>=1.24.0
-Requires-Dist: scipy <=1.14.0,>=1.10.0
-Requires-Dist: datalad <1.2.0,>=1.0.0
-Requires-Dist: pandas <2.3.0,>=2.0.0
-Requires-Dist: nibabel <5.3.0,>=5.2.0
-Requires-Dist: nilearn <=0.10.4,>=0.10.3
-Requires-Dist: sqlalchemy <=2.1.0,>=2.0.25
-Requires-Dist: ruamel.yaml <0.18,>=0.17
-Requires-Dist: h5py >=3.10
-Requires-Dist: httpx[http2] ==0.26.0
-Requires-Dist: tqdm ==4.66.1
-Requires-Dist: templateflow >=23.0.0
-Requires-Dist: lapy <2.0.0,>=1.0.0
-Requires-Dist: importlib-metadata ; python_version < "3.9"
-Requires-Dist: looseversion ==1.3.0 ; python_version >= "3.12"
+Requires-Dist: click<8.2,>=8.1.3
+Requires-Dist: numpy<2.0.0,>=1.26.0
+Requires-Dist: scipy<=1.15.0,>=1.10.0
+Requires-Dist: datalad<1.2.0,>=1.0.0
+Requires-Dist: pandas<2.3.0,>=2.0.0
+Requires-Dist: nibabel<5.4.0,>=5.2.0
+Requires-Dist: nilearn<=0.10.4,>=0.10.3
+Requires-Dist: sqlalchemy<=2.1.0,>=2.0.25
+Requires-Dist: ruamel.yaml<0.19,>=0.17
+Requires-Dist: h5py>=3.10
+Requires-Dist: tqdm<4.67.0,>=4.66.1
+Requires-Dist: templateflow>=23.0.0
+Requires-Dist: lapy<2.0.0,>=1.0.0
+Requires-Dist: lazy_loader==0.4
+Requires-Dist: importlib_metadata; python_version < "3.9"
+Requires-Dist: looseversion==1.3.0; python_version >= "3.12"
+Requires-Dist: junifer_data==1.3.0
 Provides-Extra: all
-Requires-Dist: bctpy ==0.6.0 ; extra == 'all'
-Requires-Dist: neurokit2 >=0.1.7 ; extra == 'all'
+Requires-Dist: bctpy==0.6.0; extra == "all"
+Requires-Dist: neurokit2>=0.1.7; extra == "all"
 Provides-Extra: bct
-Requires-Dist: bctpy ==0.6.0 ; extra == 'bct'
+Requires-Dist: bctpy==0.6.0; extra == "bct"
+Provides-Extra: onthefly
+Requires-Dist: bctpy==0.6.0; extra == "onthefly"
+Provides-Extra: neurokit2
+Requires-Dist: neurokit2>=0.1.7; extra == "neurokit2"
 Provides-Extra: dev
-Requires-Dist: tox ; extra == 'dev'
-Requires-Dist: pre-commit ; extra == 'dev'
+Requires-Dist: tox; extra == "dev"
+Requires-Dist: pre-commit; extra == "dev"
 Provides-Extra: docs
-Requires-Dist: seaborn <0.14.0,>=0.13.0 ; extra == 'docs'
-Requires-Dist: sphinx <7.4.0,>=7.3.0 ; extra == 'docs'
-Requires-Dist: sphinx-gallery <0.17.0,>=0.15.0 ; extra == 'docs'
-Requires-Dist: furo <2024.6.0,>=2024.4.27 ; extra == 'docs'
-Requires-Dist: numpydoc <1.8.0,>=1.6.0 ; extra == 'docs'
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-Requires-Dist: towncrier <23.12.0,>=23.10.0 ; extra == 'docs'
-Requires-Dist: sphinxcontrib-mermaid <0.10,>=0.8.1 ; extra == 'docs'
-Provides-Extra: neurokit2
-Requires-Dist: neurokit2 >=0.1.7 ; extra == 'neurokit2'
-Provides-Extra: onthefly
-Requires-Dist: bctpy ==0.6.0 ; extra == 'onthefly'
+Requires-Dist: seaborn<0.14.0,>=0.13.0; extra == "docs"
+Requires-Dist: sphinx<8.1.0,>=7.3.0; extra == "docs"
+Requires-Dist: sphinx-gallery<0.18.0,>=0.17.0; extra == "docs"
+Requires-Dist: furo<2024.9.0,>=2024.4.27; extra == "docs"
+Requires-Dist: numpydoc<1.9.0,>=1.6.0; extra == "docs"
+Requires-Dist: julearn==0.3.3; extra == "docs"
+Requires-Dist: sphinx-copybutton<0.5.3,>=0.5.1; extra == "docs"
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+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"
+Dynamic: license-file
 
 ![Junifer logo](docs/images/junifer_logo.png "junifer logo")
 
@@ -108,6 +112,7 @@ The documentation is available at [https://juaml.github.io/junifer](https://juam
   * `preprocess`: Preprocessing module.
   * `storage`: Storage module.
   * `testing`: Testing components module.
+  * `typing`: Type hints module.
   * `utils`: Utilities module (e.g. logging).
 
 ## Installation

junifer-0.0.6.dist-info/RECORD

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+junifer-0.0.6.dist-info/licenses/LICENSE.md,sha256=MqCnOBu8uXsEOzRZWh9EBVfVz-kE9NkXcLCrtGXo2yU,34354
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+junifer-0.0.6.dist-info/entry_points.txt,sha256=6O8ru0BP-SP7YMUZiizFNoaZ2HvJpadO2G7nKk4PwjI,48
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+junifer-0.0.6.dist-info/RECORD,,

{junifer-0.0.5.dev242.dist-info → junifer-0.0.6.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (71.1.0)
+Generator: setuptools (78.0.2)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

junifer-0.0.6.dist-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+junifer = junifer.cli.cli:cli

junifer/api/parser.py

@@ -1,118 +0,0 @@
-"""Provide functions for parser."""
-
-# Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
-#          Synchon Mandal <s.mandal@fz-juelich.de>
-# License: AGPL
-
-import importlib
-import importlib.util
-import sys
-from pathlib import Path
-from typing import Dict, Union
-
-from ..utils.logging import logger, raise_error
-from .utils import yaml
-
-
-__all__ = ["parse_yaml"]
-
-
-def parse_yaml(filepath: Union[str, Path]) -> Dict:
-    """Parse YAML.
-
-    Parameters
-    ----------
-    filepath : str or pathlib.Path
-        The filepath to read from.
-
-    Returns
-    -------
-    dict
-        The contents represented as dictionary.
-
-    """
-    # Convert str to Path
-    if not isinstance(filepath, Path):
-        filepath = Path(filepath)
-
-    logger.info(f"Parsing yaml file: {filepath.absolute()!s}")
-    # Filepath existence check
-    if not filepath.exists():
-        raise_error(f"File does not exist: {filepath.absolute()!s}")
-    # Filepath reading
-    contents = yaml.load(filepath)
-    if "elements" in contents:
-        if contents["elements"] is None:
-            raise_error(
-                "The elements key was defined but its content is empty. "
-                "Please define the elements to operate on or remove the key."
-            )
-    # load modules
-    if "with" in contents:
-        to_load = contents["with"]
-        # Convert load modules to list
-        if not isinstance(to_load, list):
-            to_load = [to_load]
-        # Initialize list to have absolute paths for custom modules
-        final_to_load = []
-        for t_module in to_load:
-            if t_module.endswith(".py"):
-                logger.debug(f"Importing file: {t_module}")
-                # This resolves both absolute and relative paths
-                file_path = filepath.parent / t_module
-                if not file_path.exists():
-                    raise_error(
-                        f"File in 'with' section does not exist: {file_path}"
-                    )
-                spec = importlib.util.spec_from_file_location(
-                    t_module, file_path
-                )
-                module = importlib.util.module_from_spec(spec)  # type: ignore
-                sys.modules[t_module] = module
-                spec.loader.exec_module(module)  # type: ignore
-                # Add absolute path to final list
-                final_to_load.append(str(file_path.resolve()))
-            else:
-                logger.info(f"Importing module: {t_module}")
-                importlib.import_module(t_module)
-                # Add module to final list
-                final_to_load.append(t_module)
-
-        # Replace modules to be loaded so that custom modules will take the
-        # absolute path. This was not the case as found in #224. Similar thing
-        # is done with the storage URI below.
-        contents["with"] = final_to_load
-
-    # Compute path for the URI parameter in storage files that are relative
-    # This is a tricky thing that appeared in #127. The problem is that
-    # the path in the URI parameter is relative to YAML file, not to the
-    # current working directory. If we leave it as is in the contents
-    # dict, then it will be used later in the ``build`` function as is,
-    # which will be computed relative to the current working directory.
-    # The solution is to compute the absolute path and replace the
-    # relative path in the contents dict with the absolute path.
-
-    # Check if the storage file is defined
-    if "storage" in contents:
-        if "uri" in contents["storage"]:
-            # Check if the storage file is relative
-            uri_path = Path(contents["storage"]["uri"])
-            if not uri_path.is_absolute():
-                # Compute the absolute path
-                contents["storage"]["uri"] = str(
-                    (filepath.parent / uri_path).resolve()
-                )
-
-    # Allow relative path if queue env kind is venv; same motivation as above
-    if "queue" in contents:
-        if "env" in contents["queue"]:
-            if "venv" == contents["queue"]["env"]["kind"]:
-                # Check if the env name is relative
-                venv_path = Path(contents["queue"]["env"]["name"])
-                if not venv_path.is_absolute():
-                    # Compute the absolute path
-                    contents["queue"]["env"]["name"] = str(
-                        (filepath.parent / venv_path).resolve()
-                    )
-
-    return contents