junifer 0.0.3.dev186__tar.gz → 0.0.4.dev8__tar.gz

{junifer-0.0.3.dev186 → junifer-0.0.4.dev8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.3.dev186
+Version: 0.0.4.dev8
 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>
@@ -43,10 +43,11 @@ License-File: AUTHORS.rst
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg?style=flat-square)](https://github.com/psf/black)
 [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/charliermarsh/ruff/main/assets/badge/v2.json)](https://github.com/charliermarsh/ruff)
 [![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit)](https://github.com/pre-commit/pre-commit)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.8176570.svg)](https://doi.org/10.5281/zenodo.8176570)
 
 ## About
 
-junifer is a data handling and feature extraction library targeted towards neuroimaging data specifically functional MRI data.
+`junifer` is a data handling and feature extraction library targeted towards neuroimaging data specifically functional MRI data.
 
 It is currently being developed and maintained at the [Applied Machine Learning](https://www.fz-juelich.de/en/inm/inm-7/research-groups/applied-machine-learning-aml) group at [Forschungszentrum Juelich](https://www.fz-juelich.de/en), Germany. Although the library is designed for people working at [Institute of Neuroscience and Medicine - Brain and Behaviour (INM-7)](https://www.fz-juelich.de/en/inm/inm-7), it is designed to be as modular as possible thus enabling others to extend it easily.
 
@@ -87,12 +88,12 @@ conda install -c conda-forge junifer
 
 ## Citation
 
-If you use junifer in a scientific publication, we would appreciate if you cite our work. Currently, we do not have a publication, so feel free to use the project [URL](https://juaml.github.io/junifer).
+If you use `junifer` in a scientific publication, we would appreciate if you cite our work. Currently, we do not have a publication, so feel free to use the project's [Zenodo URL](https://doi.org/10.5281/zenodo.8176569).
 
 ## Funding
 
 We thank the [Helmholtz Imaging Platform](https://helmholtz-imaging.de/) and
-[SMHB](https://www.fz-juelich.de/en/smhb) for supporting development of Junifer.
+[SMHB](https://www.fz-juelich.de/en/smhb) for supporting development of `junifer`.
 (The funding sources had no role in the design, implementation and evaluation of the pipeline.)
 
 ## Contribution
@@ -104,7 +105,7 @@ Contributions are welcome and greatly appreciated. Please read the [guidelines](
 junifer is released under the AGPL v3 license:
 
 junifer, FZJuelich AML neuroimaging feature extraction library.
-Copyright (C) 2022, authors of junifer.
+Copyright (C) 2023, authors of junifer.
 
 This program is free software: you can redistribute it and/or modify
 it under the terms of the GNU Affero General Public License as published by

{junifer-0.0.3.dev186 → junifer-0.0.4.dev8}/README.md

@@ -11,10 +11,11 @@
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg?style=flat-square)](https://github.com/psf/black)
 [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/charliermarsh/ruff/main/assets/badge/v2.json)](https://github.com/charliermarsh/ruff)
 [![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit)](https://github.com/pre-commit/pre-commit)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.8176570.svg)](https://doi.org/10.5281/zenodo.8176570)
 
 ## About
 
-junifer is a data handling and feature extraction library targeted towards neuroimaging data specifically functional MRI data.
+`junifer` is a data handling and feature extraction library targeted towards neuroimaging data specifically functional MRI data.
 
 It is currently being developed and maintained at the [Applied Machine Learning](https://www.fz-juelich.de/en/inm/inm-7/research-groups/applied-machine-learning-aml) group at [Forschungszentrum Juelich](https://www.fz-juelich.de/en), Germany. Although the library is designed for people working at [Institute of Neuroscience and Medicine - Brain and Behaviour (INM-7)](https://www.fz-juelich.de/en/inm/inm-7), it is designed to be as modular as possible thus enabling others to extend it easily.
 
@@ -55,12 +56,12 @@ conda install -c conda-forge junifer
 
 ## Citation
 
-If you use junifer in a scientific publication, we would appreciate if you cite our work. Currently, we do not have a publication, so feel free to use the project [URL](https://juaml.github.io/junifer).
+If you use `junifer` in a scientific publication, we would appreciate if you cite our work. Currently, we do not have a publication, so feel free to use the project's [Zenodo URL](https://doi.org/10.5281/zenodo.8176569).
 
 ## Funding
 
 We thank the [Helmholtz Imaging Platform](https://helmholtz-imaging.de/) and
-[SMHB](https://www.fz-juelich.de/en/smhb) for supporting development of Junifer.
+[SMHB](https://www.fz-juelich.de/en/smhb) for supporting development of `junifer`.
 (The funding sources had no role in the design, implementation and evaluation of the pipeline.)
 
 ## Contribution
@@ -72,7 +73,7 @@ Contributions are welcome and greatly appreciated. Please read the [guidelines](
 junifer is released under the AGPL v3 license:
 
 junifer, FZJuelich AML neuroimaging feature extraction library.
-Copyright (C) 2022, authors of junifer.
+Copyright (C) 2023, authors of junifer.
 
 This program is free software: you can redistribute it and/or modify
 it under the terms of the GNU Affero General Public License as published by

junifer-0.0.4.dev8/docs/changes/newsfragments/247.doc

@@ -0,0 +1 @@
+Add Zenodo badge in ``README`` and improve general documentation by `Synchon Mandal`_

{junifer-0.0.3.dev186 → junifer-0.0.4.dev8}/docs/contribution.rst

@@ -2,8 +2,8 @@
 
 .. _contribution_guidelines:
 
-Contributing to junifer
-=======================
+Contributing
+============
 
 Setting up the local development environment
 --------------------------------------------

{junifer-0.0.3.dev186 → junifer-0.0.4.dev8}/docs/maintaining.rst

@@ -30,58 +30,58 @@ before proceeding.
 
 #. Make sure you are in sync with the main branch.
 
-.. code-block:: bash
+   .. code-block:: bash
 
-    git checkout main
-    git pull --rebase origin main
+       git checkout main
+       git pull --rebase origin main
 
 #. Run the following to check changelog is properly generated:
 
-.. code-block:: bash
+   .. code-block:: bash
 
-   towncrier build --draft
+      towncrier build --draft
 
 #. Then, run:
 
-.. code-block:: bash
+   .. code-block:: bash
 
-   towncrier
+      towncrier
 
-to generate the proper changelog that should be reflected in
-``docs/whats_new.rst``.
+   to generate the proper changelog that should be reflected in
+   ``docs/whats_new.rst``.
 
 #. Commit the changes, make a PR and merge via a merge commit.
 
 #. Make sure you are in sync with the main branch.
 
-.. code-block:: bash
+   .. code-block:: bash
 
-    git checkout main
-    git pull --rebase origin main
+       git checkout main
+       git pull --rebase origin main
 
 #. Create tag (replace ``X.Y.Z`` with the proper version) on the merged PR's
    merge commit.
 
-.. code-block:: bash
+   .. code-block:: bash
 
-    git tag -a vX.Y.Z -m "Release X.Y.Z"
+       git tag -a vX.Y.Z -m "Release X.Y.Z"
 
 #. Check that the build system is creating the proper version
 
-.. code-block:: bash
+   .. code-block:: bash
 
-    SETUPTOOLS_SCM_DEBUG=1 python -m build --source --binary --out-dir dist/ .
+       SETUPTOOLS_SCM_DEBUG=1 python -m build --outdir dist/ .
 
 #. Push the tag
 
-.. code-block:: bash
+   .. code-block:: bash
 
-    git push origin --follow-tags
+       git push origin --follow-tags
 
 #. Optional: bump the *MAJOR* or *MINOR* segment of next release (replace
    ``D.E.0`` with the proper version).
 
-.. code-block:: bash
+   .. code-block:: bash
 
-    git tag -a vD.E.0.dev -m "Set next release to D.E.0"
-    git push origin --follow-tags
+       git tag -a vD.E.0.dev -m "Set next release to D.E.0"
+       git push origin --follow-tags

{junifer-0.0.3.dev186 → junifer-0.0.4.dev8}/docs/whats_new.rst

@@ -8,6 +8,91 @@ What's new
 
 .. towncrier release notes start
 
+Junifer 0.0.3 (2023-07-21)
+---------------------------------
+
+Bugfixes
+^^^^^^^^
+
+- Enable YAML 1.2 support and allow multiline strings in YAML which would not
+  work earlier by `Synchon Mandal`_ (:gh:`223`)
+- Handle ``datalad.IncompleteResultsError`` exception for partial clone in
+  :class:`.DataladDataGrabber` by `Synchon Mandal`_ (:gh:`235`)
+
+
+API Changes
+^^^^^^^^^^^
+
+- Expose ``types`` parameter for :class:`.DataladAOMICID1000`,
+  :class:`.DataladAOMICPIOP1`, :class:`.DataladAOMICPIOP2` and
+  :class:`.JuselessUCLA` by `Synchon Mandal`_ (:gh:`132`)
+- Rename ``junifer.testing.datagrabbers.SPMAuditoryTestingDatagrabber`` to
+  :class:`.SPMAuditoryTestingDataGrabber` and
+  ``junifer.testing.datagrabbers.OasisVBMTestingDatagrabber`` to
+  :class:`.OasisVBMTestingDataGrabber` by `Synchon Mandal`_ (:gh:`222`)
+- Add :meth:`.BaseFeatureStorage.read` method for storage-like objects by
+  `Synchon Mandal`_ (:gh:`236`)
+
+
+Improved Documentation
+^^^^^^^^^^^^^^^^^^^^^^
+
+- Improve general prose, formatting and code blocks in docs and set line length
+  for ``.rst`` files to 80 by `Synchon Mandal`_ (:gh:`220`)
+- Update ``julearn`` example under ``examples`` by `Synchon Mandal`_
+  (:gh:`242`)
+
+
+Enhancements
+^^^^^^^^^^^^
+
+- Change validation of ``types`` against ``patterns`` to allow a subset of
+  ``patterns``'s types to be used for ``DataGrabber`` data fetch by `Synchon
+  Mandal`_ (:gh:`132`)
+- Rename instances of "Datagrabber" to "DataGrabber" especially in
+  ``junifer.testing`` to be consistent by `Synchon Mandal`_ (:gh:`222`)
+- Use ``ruamel.yaml`` instead of ``pyyaml`` as YAML I/O library by `Synchon
+  Mandal`_ (:gh:`223`)
+- Adopt ``DataGrabber`` consistently throughout codebase to match with the
+  documentation by `Synchon Mandal`_ (:gh:`226`)
+- Adopt ``DataReader`` consistently throughout codebase to match with the
+  documentation by `Synchon Mandal`_ (:gh:`227`)
+- Enable ``stdout`` and ``stderr`` capture for AFNI commands by `Synchon
+  Mandal`_ (:gh:`234`)
+- Adapt :meth:`.HDF5FeatureStorage.read_df` due to addition of
+  :meth:`.HDF5FeatureStorage.read` by `Synchon Mandal`_ (:gh:`236`)
+
+
+Features
+^^^^^^^^
+
+- Add ``AICHA v1`` and ``AICHA v2`` parcellations to ``junifer.data`` by
+  `Synchon Mandal`_ (:gh:`173`)
+- Add ``Shen 2013``, ``Shen 2015`` and ``Shen 2019`` parcellations to
+  ``junifer.data`` by `Synchon Mandal`_ (:gh:`184`)
+- Add ``Yan 2023`` parcellation to ``junifer.data`` by `Synchon Mandal`_
+  (:gh:`225`)
+- Introduce :mod:`.onthefly` sub-module and :func:`.read_transform` for quick
+  transform operations on stored data by `Synchon Mandal`_ (:gh:`237`)
+
+
+Misc
+^^^^
+
+- Consistent docstrings for pytest fixtures used in the test suite by `Synchon
+  Mandal`_ (:gh:`228`)
+- Adopt ``ruff`` as the only linter for the codebase by `Synchon Mandal`_
+  (:gh:`229`)
+- Improve ``codespell`` support by fixing typos in documentation by `Synchon
+  Mandal`_ (:gh:`230`)
+- Adopt ``pre-commit`` for adding and managing git pre-commit hooks by
+  `Synchon Mandal`_ (:gh:`232`)
+- Improve docstrings and code style and parametrize remaining tests for
+  ``junifer.data.parcellations`` by `Synchon Mandal`_ (:gh:`238`)
+- Bump ``numpy`` version constraint to ``>=1.24,<1.26`` by `Synchon Mandal`_
+  (:gh:`241`)
+
+
 Junifer 0.0.2 (2023-03-31)
 --------------------------
 
@@ -140,15 +225,9 @@ Features
   when used as ``method`` in markers by `Fede Raimondo`_ (:gh:`190`)
 
 
-junifer 0.0.1 (2022-12-20)
+Junifer 0.0.1 (2022-12-20)
 --------------------------
 
-API Changes
-^^^^^^^^^^^
-
-- Change the ``single_output`` default parameter in storage classes from
-  ``False`` to ``True`` by `Fede Raimondo`_ (:gh:`134`)
-
 Bugfixes
 ^^^^^^^^
 
@@ -168,6 +247,14 @@ Bugfixes
 - Fix a bug in which the generated DAG for HTCondor will not work by
   `Fede Raimondo`_ (:gh:`143`)
 
+
+API Changes
+^^^^^^^^^^^
+
+- Change the ``single_output`` default parameter in storage classes from
+  ``False`` to ``True`` by `Fede Raimondo`_ (:gh:`134`)
+
+
 Improved Documentation
 ^^^^^^^^^^^^^^^^^^^^^^
 
@@ -181,6 +268,7 @@ Improved Documentation
 - Change documentation template to furo. Fix references and standardize
   documentation by `Fede Raimondo`_ (:gh:`114`)
 
+
 Enhancements
 ^^^^^^^^^^^^
 
@@ -217,6 +305,7 @@ Enhancements
 - Refactor :class:`.PipelineStepMixin` to improve its implementation and
   validation for pipeline steps by `Synchon Mandal`_ (:gh:`152`)
 
+
 Features
 ^^^^^^^^
 
@@ -283,6 +372,7 @@ Features
 - Implement :class:`.ALFFParcels` and :class:`.ALFFSpheres` markers by
   `Fede Raimondo`_ (:gh:`35`)
 
+
 Misc
 ^^^^
 

junifer-0.0.4.dev8/junifer/_version.py

@@ -0,0 +1,4 @@
+# file generated by setuptools_scm
+# don't change, don't track in version control
+__version__ = version = '0.0.4.dev8'
+__version_tuple__ = version_tuple = (0, 0, 4, 'dev8')

{junifer-0.0.3.dev186 → junifer-0.0.4.dev8}/junifer/data/masks.py

@@ -213,7 +213,7 @@ def get_mask(
     all_masks = []
     for t_mask in true_masks:
         if isinstance(t_mask, dict):
-            mask_name = list(t_mask.keys())[0]
+            mask_name = next(iter(t_mask.keys()))
             mask_params = t_mask[mask_name]
         else:
             mask_name = t_mask

{junifer-0.0.3.dev186 → junifer-0.0.4.dev8}/junifer/data/tests/test_masks.py

@@ -411,7 +411,7 @@ def test_get_mask_multiple(
         computed = get_mask(masks=junifer_masks, target_data=input["BOLD"])
 
         masks_names = [
-            list(x.keys())[0] if isinstance(x, dict) else x for x in masks
+            next(iter(x.keys())) if isinstance(x, dict) else x for x in masks
         ]
 
         mask_funcs = [

{junifer-0.0.3.dev186 → junifer-0.0.4.dev8}/junifer/markers/tests/test_collection.py

@@ -197,7 +197,7 @@ def test_marker_collection_storage(tmp_path: Path) -> None:
 
     features = storage.list_features()
     assert len(features) == 3
-    feature_md5 = list(features.keys())[0]
+    feature_md5 = next(iter(features.keys()))
     t_feature = storage.read_df(feature_md5=feature_md5)
     fname = "gmd_schaefer100x7_mean"
     t_data = out[fname]["VBM_GM"]["data"]  # type: ignore

{junifer-0.0.3.dev186 → junifer-0.0.4.dev8}/junifer/storage/pandas_base.py

@@ -114,7 +114,8 @@ class PandasBaseFeatureStorage(BaseFeatureStorage):
         if len(elem_idx) == 1:
             # Create normal index for vector
             index = pd.Index(
-                data=list(elem_idx.values())[0], name=list(elem_idx.keys())[0]
+                data=next(iter(elem_idx.values())),
+                name=next(iter(elem_idx.keys())),
             )
         else:
             # Create multiindex for timeseries

{junifer-0.0.3.dev186 → junifer-0.0.4.dev8}/junifer/storage/tests/test_hdf5.py

@@ -175,7 +175,7 @@ def test_store_metadata_and_list_features(tmp_path: Path) -> None:
     # List the stored features
     features = storage.list_features()
     # Get the first MD5
-    feature_md5 = list(features.keys())[0]
+    feature_md5 = next(iter(features.keys()))
     # Check the MD5
     assert meta_md5 == feature_md5
 

{junifer-0.0.3.dev186 → junifer-0.0.4.dev8}/junifer/storage/tests/test_sqlite.py

@@ -335,7 +335,7 @@ def test_store_df_and_read_df(tmp_path: Path) -> None:
     with pytest.raises(ValueError, match="Only one"):
         storage.read_df(feature_name="wrong_name", feature_md5="wrong_md5")
     # Get MD5 hash of features
-    feature_md5 = list(features.keys())[0]
+    feature_md5 = next(iter(features.keys()))
     assert "feature_md5" == feature_md5
     # Check for key
     assert "BOLD_markername" == features[feature_md5]["name"]
@@ -373,7 +373,7 @@ def test_store_metadata(tmp_path: Path) -> None:
         meta_md5=meta_md5, element=element_to_store, meta=meta_to_store
     )
     features = storage.list_features()
-    feature_md5 = list(features.keys())[0]
+    feature_md5 = next(iter(features.keys()))
     assert meta_md5 == feature_md5
 
 
@@ -474,7 +474,7 @@ def test_store_matrix(tmp_path: Path) -> None:
     stored_names = [f"{i}~{j}" for i in row_names for j in col_names]
 
     features = storage.list_features()
-    feature_md5 = list(features.keys())[0]
+    feature_md5 = next(iter(features.keys()))
     assert "BOLD_fc" == features[feature_md5]["name"]
 
     read_df = storage.read_df(feature_md5=feature_md5)
@@ -498,7 +498,7 @@ def test_store_matrix(tmp_path: Path) -> None:
         for j in range(data.shape[1])
     ]
     features = storage.list_features()
-    feature_md5 = list(features.keys())[0]
+    feature_md5 = next(iter(features.keys()))
     assert "BOLD_fc" == features[feature_md5]["name"]
     read_df = storage.read_df(feature_md5=feature_md5)
     assert list(read_df.columns) == stored_names
@@ -563,7 +563,7 @@ def test_store_matrix(tmp_path: Path) -> None:
     ]
 
     features = storage.list_features()
-    feature_md5 = list(features.keys())[0]
+    feature_md5 = next(iter(features.keys()))
     assert "BOLD_fc" == features[feature_md5]["name"]
     read_df = storage.read_df(feature_md5=feature_md5)
     assert list(read_df.columns) == stored_names
@@ -595,7 +595,7 @@ def test_store_matrix(tmp_path: Path) -> None:
     ]
 
     features = storage.list_features()
-    feature_md5 = list(features.keys())[0]
+    feature_md5 = next(iter(features.keys()))
     assert "BOLD_fc" == features[feature_md5]["name"]
     read_df = storage.read_df(feature_md5=feature_md5)
     assert list(read_df.columns) == stored_names
@@ -632,7 +632,7 @@ def test_store_matrix(tmp_path: Path) -> None:
     ]
 
     features = storage.list_features()
-    feature_md5 = list(features.keys())[0]
+    feature_md5 = next(iter(features.keys()))
     assert "BOLD_fc" == features[feature_md5]["name"]
     read_df = storage.read_df(feature_md5=feature_md5)
     assert list(read_df.columns) == stored_names
@@ -663,7 +663,7 @@ def test_store_matrix(tmp_path: Path) -> None:
     ]
 
     features = storage.list_features()
-    feature_md5 = list(features.keys())[0]
+    feature_md5 = next(iter(features.keys()))
     assert "BOLD_fc" == features[feature_md5]["name"]
     read_df = storage.read_df(feature_md5=feature_md5)
     assert list(read_df.columns) == stored_names

{junifer-0.0.3.dev186 → junifer-0.0.4.dev8}/junifer.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.3.dev186
+Version: 0.0.4.dev8
 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>
@@ -43,10 +43,11 @@ License-File: AUTHORS.rst
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg?style=flat-square)](https://github.com/psf/black)
 [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/charliermarsh/ruff/main/assets/badge/v2.json)](https://github.com/charliermarsh/ruff)
 [![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit)](https://github.com/pre-commit/pre-commit)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.8176570.svg)](https://doi.org/10.5281/zenodo.8176570)
 
 ## About
 
-junifer is a data handling and feature extraction library targeted towards neuroimaging data specifically functional MRI data.
+`junifer` is a data handling and feature extraction library targeted towards neuroimaging data specifically functional MRI data.
 
 It is currently being developed and maintained at the [Applied Machine Learning](https://www.fz-juelich.de/en/inm/inm-7/research-groups/applied-machine-learning-aml) group at [Forschungszentrum Juelich](https://www.fz-juelich.de/en), Germany. Although the library is designed for people working at [Institute of Neuroscience and Medicine - Brain and Behaviour (INM-7)](https://www.fz-juelich.de/en/inm/inm-7), it is designed to be as modular as possible thus enabling others to extend it easily.
 
@@ -87,12 +88,12 @@ conda install -c conda-forge junifer
 
 ## Citation
 
-If you use junifer in a scientific publication, we would appreciate if you cite our work. Currently, we do not have a publication, so feel free to use the project [URL](https://juaml.github.io/junifer).
+If you use `junifer` in a scientific publication, we would appreciate if you cite our work. Currently, we do not have a publication, so feel free to use the project's [Zenodo URL](https://doi.org/10.5281/zenodo.8176569).
 
 ## Funding
 
 We thank the [Helmholtz Imaging Platform](https://helmholtz-imaging.de/) and
-[SMHB](https://www.fz-juelich.de/en/smhb) for supporting development of Junifer.
+[SMHB](https://www.fz-juelich.de/en/smhb) for supporting development of `junifer`.
 (The funding sources had no role in the design, implementation and evaluation of the pipeline.)
 
 ## Contribution
@@ -104,7 +105,7 @@ Contributions are welcome and greatly appreciated. Please read the [guidelines](
 junifer is released under the AGPL v3 license:
 
 junifer, FZJuelich AML neuroimaging feature extraction library.
-Copyright (C) 2022, authors of junifer.
+Copyright (C) 2023, authors of junifer.
 
 This program is free software: you can redistribute it and/or modify
 it under the terms of the GNU Affero General Public License as published by

{junifer-0.0.3.dev186 → junifer-0.0.4.dev8}/junifer.egg-info/SOURCES.txt

@@ -56,30 +56,7 @@ docs/api/testing.rst
 docs/api/utils.rst
 docs/changes/contributors.inc
 docs/changes/newsfragments/.gitignore
-docs/changes/newsfragments/132.change
-docs/changes/newsfragments/132.enh
-docs/changes/newsfragments/173.feature
-docs/changes/newsfragments/184.feature
-docs/changes/newsfragments/220.doc
-docs/changes/newsfragments/222.change
-docs/changes/newsfragments/222.enh
-docs/changes/newsfragments/223.bugfix
-docs/changes/newsfragments/223.enh
-docs/changes/newsfragments/225.feature
-docs/changes/newsfragments/226.enh
-docs/changes/newsfragments/227.enh
-docs/changes/newsfragments/228.misc
-docs/changes/newsfragments/229.misc
-docs/changes/newsfragments/230.misc
-docs/changes/newsfragments/232.misc
-docs/changes/newsfragments/234.enh
-docs/changes/newsfragments/235.bugfix
-docs/changes/newsfragments/236.change
-docs/changes/newsfragments/236.enh
-docs/changes/newsfragments/237.feature
-docs/changes/newsfragments/238.misc
-docs/changes/newsfragments/241.misc
-docs/changes/newsfragments/242.doc
+docs/changes/newsfragments/247.doc
 docs/extending/coordinates.rst
 docs/extending/datagrabber.rst
 docs/extending/extension.rst

junifer-0.0.3.dev186/docs/changes/newsfragments/132.change

@@ -1 +0,0 @@
-Expose ``types`` parameter for :class:`.DataladAOMICID1000`, :class:`.DataladAOMICPIOP1`, :class:`.DataladAOMICPIOP2` and :class:`.JuselessUCLA` by `Synchon Mandal`_

junifer-0.0.3.dev186/docs/changes/newsfragments/132.enh

@@ -1 +0,0 @@
-Change validation of ``types`` against ``patterns`` to allow a subset of ``patterns``'s types to be used for ``DataGrabber`` data fetch by `Synchon Mandal`_

junifer-0.0.3.dev186/docs/changes/newsfragments/173.feature

@@ -1 +0,0 @@
-Add ``AICHA v1`` and ``AICHA v2`` parcellations to ``junifer.data`` by `Synchon Mandal`_

junifer-0.0.3.dev186/docs/changes/newsfragments/184.feature

@@ -1 +0,0 @@
-Add ``Shen 2013``, ``Shen 2015`` and ``Shen 2019`` parcellations to ``junifer.data`` by `Synchon Mandal`_

junifer-0.0.3.dev186/docs/changes/newsfragments/220.doc

@@ -1 +0,0 @@
-Improve general prose, formatting and code blocks in docs and set line length for ``.rst`` files to 80 by `Synchon Mandal`_

junifer-0.0.3.dev186/docs/changes/newsfragments/222.change

@@ -1 +0,0 @@
-Rename ``junifer.testing.datagrabbers.SPMAuditoryTestingDatagrabber`` to :class:`.SPMAuditoryTestingDataGrabber` and ``junifer.testing.datagrabbers.OasisVBMTestingDatagrabber`` to :class:`.OasisVBMTestingDataGrabber` by `Synchon Mandal`_

junifer-0.0.3.dev186/docs/changes/newsfragments/222.enh

@@ -1 +0,0 @@
-Rename instances of "Datagrabber" to "DataGrabber" especially in ``junifer.testing`` to be consistent by `Synchon Mandal`_

junifer-0.0.3.dev186/docs/changes/newsfragments/223.bugfix

@@ -1 +0,0 @@
-Enable YAML 1.2 support and allow multiline strings in YAML which would not work earlier by `Synchon Mandal`_

junifer-0.0.3.dev186/docs/changes/newsfragments/223.enh

@@ -1 +0,0 @@
-Use ``ruamel.yaml`` instead of ``pyyaml`` as YAML I/O library by `Synchon Mandal`_

junifer-0.0.3.dev186/docs/changes/newsfragments/225.feature

@@ -1 +0,0 @@
-Add ``Yan 2023`` parcellation to ``junifer.data`` by `Synchon Mandal`_

junifer-0.0.3.dev186/docs/changes/newsfragments/226.enh

@@ -1 +0,0 @@
-Adopt ``DataGrabber`` consistently throughout codebase to match with the documentation by `Synchon Mandal`_

junifer-0.0.3.dev186/docs/changes/newsfragments/227.enh

@@ -1 +0,0 @@
-Adopt ``DataReader`` consistently throughout codebase to match with the documentation by `Synchon Mandal`_

junifer-0.0.3.dev186/docs/changes/newsfragments/228.misc

@@ -1 +0,0 @@
-Consistent docstrings for pytest fixtures used in the test suite by `Synchon Mandal`_

junifer-0.0.3.dev186/docs/changes/newsfragments/229.misc

@@ -1 +0,0 @@
-Adopt ``ruff`` as the only linter for the codebase by `Synchon Mandal`_

junifer-0.0.3.dev186/docs/changes/newsfragments/230.misc

@@ -1 +0,0 @@
-Improve ``codespell`` support by fixing typos in documentation by `Synchon Mandal`_

junifer-0.0.3.dev186/docs/changes/newsfragments/232.misc

@@ -1 +0,0 @@
-Adopt ``pre-commmit`` for adding and managing git pre-commit hooks by `Synchon Mandal`_

junifer-0.0.3.dev186/docs/changes/newsfragments/234.enh

@@ -1 +0,0 @@
-Enable ``stdout`` and ``stderr`` capture for AFNI commands by `Synchon Mandal`_

junifer-0.0.3.dev186/docs/changes/newsfragments/235.bugfix

@@ -1 +0,0 @@
-Handle ``datalad.IncompleteResultsError`` exception for partial clone in :class:`.DataladDataGrabber` by `Synchon Mandal`_

junifer-0.0.3.dev186/docs/changes/newsfragments/236.change

@@ -1 +0,0 @@
-Add :meth:`.BaseFeatureStorage.read` method for storage-like objects by `Synchon Mandal`_

junifer-0.0.3.dev186/docs/changes/newsfragments/236.enh

@@ -1 +0,0 @@
-Adapt :meth:`.HDF5FeatureStorage.read_df` due to addition of :meth:`.HDF5FeatureStorage.read` by `Synchon Mandal`_

junifer-0.0.3.dev186/docs/changes/newsfragments/237.feature

@@ -1 +0,0 @@
-Introduce :mod:`.onthefly` sub-module and :func:`.read_transform` for quick transform operations on stored data by `Synchon Mandal`_

junifer-0.0.3.dev186/docs/changes/newsfragments/238.misc

@@ -1 +0,0 @@
-Improve docstrings and code style and parametrize remaining tests for ``junifer.data.parcellations`` by `Synchon Mandal`_

junifer-0.0.3.dev186/docs/changes/newsfragments/241.misc

@@ -1 +0,0 @@
-Bump ``numpy`` version constraint to ``>=1.24,<1.26`` by `Synchon Mandal`_

junifer-0.0.3.dev186/docs/changes/newsfragments/242.doc

@@ -1 +0,0 @@
-Update ``julearn`` example under ``examples`` by `Synchon Mandal`_

junifer-0.0.3.dev186/junifer/_version.py

@@ -1,4 +0,0 @@
-# file generated by setuptools_scm
-# don't change, don't track in version control
-__version__ = version = '0.0.3.dev186'
-__version_tuple__ = version_tuple = (0, 0, 3, 'dev186')