clabtoolkit 0.5.0__tar.gz → 0.5.2__tar.gz

clabtoolkit-0.5.2/CITATION.cff

@@ -0,0 +1,53 @@
+cff-version: 1.2.0
+message: "If you use clabtoolkit in your work, please cite the toolkit paper below."
+type: software
+title: "clabtoolkit"
+abstract: >-
+  A Python toolkit for neuroimaging data processing and analysis, designed for
+  brain connectivity data, BIDS datasets and the file formats used in
+  neuroimaging.
+version: 0.5.2
+date-released: 2026-10-22
+license: Apache-2.0
+doi: "10.5281/zenodo.23540587"  # Zenodo concept DOI: always resolves to the latest version
+repository-code: "https://github.com/connectomicslab/clabtoolkit"
+url: "https://clabtoolkit.readthedocs.io"
+keywords:
+  - neuroimaging
+  - image-processing
+  - bids
+  - freesurfer
+  - connectivity
+authors:
+  - family-names: "Alemán-Gómez"
+    given-names: "Yasser"
+    orcid: "https://orcid.org/0000-0001-6067-8639"
+    affiliation: "Connectomics Lab, Radiology Department, CHUV – Lausanne University Hospital"
+  - family-names: "Hervé"
+    given-names: "Nino"
+    affiliation: "Connectomics Lab, Radiology Department, CHUV – Lausanne University Hospital"
+  - family-names: "Hagmann"
+    given-names: "Patric"
+    orcid: "https://orcid.org/0000-0002-2854-6561"
+    affiliation: "Connectomics Lab, Radiology Department, CHUV – Lausanne University Hospital"
+preferred-citation:
+  type: article
+  title: "CLABTOOLKIT: An Open-Source Toolkit for Routine Processing, Manipulation, and Visualization of Neuroimaging Data"
+  authors:
+    - family-names: "Alemán-Gómez"
+      given-names: "Yasser"
+      orcid: "https://orcid.org/0000-0001-6067-8639"
+      affiliation: "Connectomics Lab, Radiology Department, CHUV – Lausanne University Hospital"
+    - family-names: "Hervé"
+      given-names: "Nino"
+      affiliation: "Connectomics Lab, Radiology Department, CHUV – Lausanne University Hospital"
+    - family-names: "Hagmann"
+      given-names: "Patric"
+      orcid: "https://orcid.org/0000-0002-2854-6561"
+      affiliation: "Connectomics Lab, Radiology Department, CHUV – Lausanne University Hospital"
+  journal: "arXiv"
+  year: 2026
+  month: 7
+  doi: "10.48550/arXiv.2607.02638"
+  notes: "arXiv:2607.02638"
+  url: "https://arxiv.org/abs/2607.02638"

{clabtoolkit-0.5.0 → clabtoolkit-0.5.2}/CONTRIBUTING.rst

@@ -128,12 +128,17 @@ Deploying
 
 A reminder for the maintainers on how to deploy.
 
-1. Update the version in ``pyproject.toml``, ``clabtoolkit/__init__.py`` and ``release`` in
-   ``docs/source/conf.py``. The three must match.
+1. Update the version in ``pyproject.toml``, ``clabtoolkit/__init__.py``, ``release`` in
+   ``docs/source/conf.py``, the version line of ``DOCUMENTATION.md``, and ``version`` and
+   ``date-released`` in ``CITATION.cff``. They must all match.
 2. Move the "Unreleased" entries of ``HISTORY.rst`` under the new version and date.
 3. Commit the changes, make sure the CI is green, and push to ``main``. The distribution is
    built and published to TestPyPI.
 4. Tag the release and push the tag. Tags starting with ``v`` publish the distribution to PyPI::
 
-    $ git tag v0.4.6
-    $ git push origin v0.4.6
+    $ git tag vX.Y.Z
+    $ git push origin vX.Y.Z
+
+5. Publish a GitHub Release from the tag (Releases > Draft a new release). If the repository is
+   enabled in Zenodo, publishing the release archives that version and creates its DOI. Add the
+   DOI to ``CITATION.cff`` afterwards.

{clabtoolkit-0.5.0 → clabtoolkit-0.5.2}/DOCUMENTATION.md

@@ -4,7 +4,7 @@
 
 **clabtoolkit** is a comprehensive Python toolkit designed for neuroimaging data processing and analysis, with specialized focus on brain connectivity data, BIDS datasets, and various neuroimaging formats. Developed by Yasser Alemán-Gómez, this toolkit provides an end-to-end solution for connectomics research and surface-based brain analysis.
 
-**Version**: 0.5.0  
+**Version**: 0.5.2  
 **License**: Apache Software License 2.0  
 **Python Support**: 3.11+  
 **Documentation**: https://clabtoolkit.readthedocs.io  

{clabtoolkit-0.5.0 → clabtoolkit-0.5.2}/HISTORY.rst

@@ -2,6 +2,21 @@
 History
 =======
 
+0.5.2 (2026-10-22)
+------------------
+
+* Updated the README (absolute image URLs so they render on PyPI, new badges and ecosystem figure)
+* Added .zenodo.json so the Zenodo record has a description and complete metadata
+* Added the Zenodo DOI of the toolkit to CITATION.cff and the README
+* Replaced the LICENSE file by the unmodified Apache-2.0 text, so GitHub recognizes the license, and moved the copyright statement to a NOTICE file
+
+0.5.1 (2026-10-21)
+------------------
+
+* Added CITATION.cff, with the citation of the toolkit paper (arXiv:2607.02638), so GitHub offers "Cite this repository"
+* Included CITATION.cff in the source distribution
+* Updated the release steps of CONTRIBUTING.rst: version and date of CITATION.cff, and the GitHub release that archives the version in Zenodo
+
 0.5.0 (2026-10-21)
 ------------------
 

clabtoolkit-0.5.2/LICENSE

@@ -0,0 +1,202 @@
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{clabtoolkit-0.5.0 → clabtoolkit-0.5.2}/MANIFEST.in

@@ -1,7 +1,9 @@
 include AUTHORS.rst
+include CITATION.cff
 include CONTRIBUTING.rst
 include HISTORY.rst
 include LICENSE
+include NOTICE
 include README.rst
 include pyproject.toml
 

clabtoolkit-0.5.2/NOTICE

@@ -0,0 +1,5 @@
+clabtoolkit
+Copyright 2024-2026 Yasser Alemán-Gómez
+
+This product includes software developed at the Connectomics Lab, Radiology
+Department, CHUV - Lausanne University Hospital.

{clabtoolkit-0.5.0 → clabtoolkit-0.5.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: clabtoolkit
-Version: 0.5.0
+Version: 0.5.2
 Summary: A comprehensive toolkit for neuroimaging data processing and analysis
 Author-email: Yasser Alemán-Gómez <yasseraleman@protonmail.com>
 Maintainer-email: Yasser Alemán-Gómez <yasseraleman@protonmail.com>
@@ -24,6 +24,7 @@ Classifier: Topic :: Scientific/Engineering :: Image Processing
 Requires-Python: >=3.11
 Description-Content-Type: text/x-rst
 License-File: LICENSE
+License-File: NOTICE
 License-File: AUTHORS.rst
 Requires-Dist: nibabel>=5.3.2
 Requires-Dist: numpy>=1.23.5
@@ -69,7 +70,7 @@ Dynamic: license-file
 Connectomics Lab Toolkit
 ========================
 
-.. image:: docs/source/_static/clabtoolkit_logo.png
+.. image:: https://raw.githubusercontent.com/connectomicslab/clabtoolkit/main/docs/source/_static/clabtoolkit_logo.png
         :alt: clabtoolkit logo
         :align: center
         :width: 400
@@ -77,27 +78,48 @@ Connectomics Lab Toolkit
 
 .. image:: https://img.shields.io/pypi/v/clabtoolkit.svg
         :target: https://pypi.python.org/pypi/clabtoolkit
+        :alt: PyPI version
+
+.. image:: https://img.shields.io/pypi/pyversions/clabtoolkit.svg
+        :target: https://pypi.python.org/pypi/clabtoolkit
+        :alt: Python versions
+
+.. image:: https://img.shields.io/badge/License-Apache_2.0-blue.svg
+        :target: https://opensource.org/licenses/Apache-2.0
+        :alt: License: Apache 2.0
 
 .. image:: https://github.com/connectomicslab/clabtoolkit/actions/workflows/ci.yml/badge.svg
         :target: https://github.com/connectomicslab/clabtoolkit/actions/workflows/ci.yml
+        :alt: CI status
+
+.. image:: https://codecov.io/gh/connectomicslab/clabtoolkit/branch/main/graph/badge.svg
+        :target: https://codecov.io/gh/connectomicslab/clabtoolkit
+        :alt: Code coverage
 
 .. image:: https://readthedocs.org/projects/clabtoolkit/badge/?version=latest
         :target: https://clabtoolkit.readthedocs.io/en/latest/?version=latest
         :alt: Documentation Status
 
-.. image:: https://img.shields.io/pypi/pyversions/clabtoolkit.svg
-        :target: https://pypi.python.org/pypi/clabtoolkit
+.. image:: https://img.shields.io/badge/arXiv-2607.02638-b31b1b.svg
+        :target: https://arxiv.org/abs/2607.02638
+        :alt: arXiv
+
+.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.23540587.svg
+        :target: https://doi.org/10.5281/zenodo.23540587
+        :alt: Zenodo DOI
 
-.. image:: https://codecov.io/gh/connectomicslab/clabtoolkit/branch/main/graph/badge.svg
-        :target: https://codecov.io/gh/connectomicslab/clabtoolkit
 
+**clabtoolkit** (Connectomics Lab Toolkit) is a Python toolkit for neuroimaging data processing
+and analysis, with a focus on brain connectivity, BIDS datasets and common neuroimaging formats.
 
-A comprehensive Python toolkit for neuroimaging data processing and analysis, specifically designed for working with brain connectivity data, BIDS datasets, and various neuroimaging formats.
+It is built around a small set of objects (``Surface``, ``Parcellation``, ``Tractogram`` and
+``Connectome``) that share a common plotting layer (``BrainPlotter``), so surfaces, parcellations,
+streamlines and connectivity matrices can be loaded, processed and visualized with a consistent API.
+It is designed to work alongside libraries such as nibabel, nilearn and DIPY.
 
 * **Free software**: Apache Software License 2.0
 * **Documentation**: https://clabtoolkit.readthedocs.io
-* **Source Code**: https://github.com/connectomicslab/clabtoolkit
-* **Python versions**: 3.11+
+* **Source code**: https://github.com/connectomicslab/clabtoolkit
 
 Installation
 ------------
@@ -106,11 +128,11 @@ Install from PyPI::
 
     pip install clabtoolkit
 
-For development installation::
+For a development installation::
 
     git clone https://github.com/connectomicslab/clabtoolkit.git
     cd clabtoolkit
-    pip install -e .[dev]
+    pip install -e ".[dev]"
 
 Requirements and optional dependencies:
 
@@ -123,13 +145,16 @@ Requirements and optional dependencies:
 Features
 --------
 
-.. image:: docs/source/_static/clabtoolkit_ecosystem.png
+.. image:: https://raw.githubusercontent.com/connectomicslab/clabtoolkit/main/docs/source/_static/clabtoolkit_ecosystem.png
         :alt: clabtoolkit ecosystem
         :align: center
         :width: 700
 
-Each module has a notebook in ``usage_examples`` (``examples-<module>-methods.ipynb``)
-with runnable examples.
+Every module has a notebook with runnable examples in the
+`usage_examples <https://github.com/connectomicslab/clabtoolkit/tree/main/usage_examples>`_ folder
+(``examples-<module>-methods.ipynb``), and
+`clabtoolkit_examples.ipynb <https://github.com/connectomicslab/clabtoolkit/blob/main/usage_examples/clabtoolkit_examples.ipynb>`_
+gives an overview of the whole toolkit.
 
 **Data organization**
 
@@ -181,8 +206,6 @@ Quick Start
 -----------
 
 The examples below are self-contained: they use simulated data, so you can run them as they are.
-More examples for every module are available in the ``usage_examples`` folder
-(see ``usage_examples/clabtoolkit_examples.ipynb``).
 
 **Filter a parcellation by region name** (``keep_by_name``)
 
@@ -202,19 +225,30 @@ More examples for every module are available in the ``usage_examples`` folder
 
 To load your own parcellation, use ``cltparc.Parcellation("parc.nii.gz", color_table="lut.txt")``.
 
+.. note::
+
+   If a file called ``parc.lut`` is in the same directory as the parcellation, it is used as the
+   color table by default, so ``cltparc.Parcellation("parc.nii.gz")`` is enough. As long as they 
+   share the same base name, the LUT file will be automatically detected.
+
 **Sample an image along the streamlines of a tractogram** (``interpolate_on_tractogram``)
 
 .. code-block:: python
 
+    import os
+    import tempfile
+
     import clabtoolkit.imagetools as cltimg
     import clabtoolkit.tracttools as clttract
 
+    image_path = os.path.join(tempfile.gettempdir(), "image.nii.gz")
+
     # Simulate a reference image and a tractogram with 5 bundles
-    cltimg.simulate_image(reference=(100, 100, 70), simulated_image="/tmp/image.nii.gz")
-    tract = clttract.Tractogram.simulate_tractogram(ref_image="/tmp/image.nii.gz")
+    cltimg.simulate_image(reference=(100, 100, 70), simulated_image=image_path)
+    tract = clttract.Tractogram.simulate_tractogram(ref_image=image_path)
 
     # Sample the image at every point of every streamline
-    tract.interpolate_on_tractogram("/tmp/image.nii.gz", map_name="fa",
+    tract.interpolate_on_tractogram(image_path, map_name="fa",
                                     storage_mode="data_per_point", interp_method="linear")
 
     print(tract.list_maps()["maps_per_point"])  # ['fa']
@@ -229,52 +263,67 @@ Use ``storage_mode="data_per_streamline"`` with ``reduction="mean"`` to store a
     import clabtoolkit.surfacetools as cltsurf
     import clabtoolkit.visualizationtools as cltvis
 
+    # On a server without a display, set PYVISTA_OFF_SCREEN=true before running
+
     # Simulate a surface and a thickness map
     surf = cltsurf.Surface.simulate_surface(seed=42, shape="sphere")
     surf.simulate_map(map_name="thickness")
 
-    # Plot two views of the map and save the figure
+    # Option 1 (Surface object): plot the lateral and medial views of the map
+    surf.plot(views=["lateral", "medial"],
+              maps="thickness",
+              colorbar_title="Thickness (mm)")
+
+    # Option 2 (BrainPlotter): the same plot, with more control over colormaps and colorbars
     plotter = cltvis.BrainPlotter()
-    plotter.plot(objs2plot=surf, views=["lateral", "medial"], map_names="thickness",
-                 colormaps="viridis", colorbar=True, save_path="/tmp/thickness.png")
+    plotter.plot(objs2plot=surf,
+                 views=["lateral", "medial"],
+                 map_names="thickness",
+                 colormaps="hot",
+                 colorbar=True,
+                 colorbar_titles="Thickness (mm)")
 
 To plot your own data, load a surface with ``cltsurf.Surface("lh.pial")`` and its map with
 ``surf.load_scalar_maps("lh.thickness", maps_names="thickness")``.
 
-Contributing
-------------
+Citing
+------
 
-Contributions are welcome! Please open an issue first to discuss major changes. See
-`CONTRIBUTING.rst <CONTRIBUTING.rst>`_ for the full guidelines.
+If you use clabtoolkit in your work, please cite the toolkit paper:
 
-Testing
--------
+    Alemán-Gómez, Y., et al. CLABTOOLKIT: An Open-Source Toolkit for Routine Processing, Manipulation, and Visualization of Neuroimaging Data. arXiv:2607.02638.
+    https://arxiv.org/abs/2607.02638
 
-Run tests with::
+.. code-block:: bibtex
 
-    pytest
+    @article{aleman2026clabtoolkit,
+      title   = {CLABTOOLKIT: An Open-Source Toolkit for Routine Processing, Manipulation, and Visualization of Neuroimaging Data},
+      author  = {Alem{\'a}n-G{\'o}mez, Yasser and Herv{\'e} Nino and Hagmann, Patric},
+      journal = {arXiv preprint arXiv:2607.02638},
+      year    = {2026},
+      url     = {https://arxiv.org/abs/2607.02638}
+    }
 
-Run tests with coverage::
+The repository includes a ``CITATION.cff`` file, and every release is archived in Zenodo: the DOI
+`10.5281/zenodo.23540587 <https://doi.org/10.5281/zenodo.23540587>`_ always points to the latest
+version, and each version has its own DOI listed on that page.
+
+Contributing
+------------
 
-    pytest --cov=clabtoolkit
+Contributions are welcome! Please open an issue first to discuss major changes. See
+`CONTRIBUTING.rst <https://github.com/connectomicslab/clabtoolkit/blob/main/CONTRIBUTING.rst>`_
+for the guidelines, including how to run the test suite.
 
 Changelog
 ---------
 
-See `HISTORY.rst <HISTORY.rst>`_ for a detailed changelog.
-
-Citing
-------
-
-If you use clabtoolkit in your work, please cite the toolkit paper::
-
-    Alemán-Gómez, Y., et al. clabtoolkit. arXiv:2607.02638.
-    https://arxiv.org/abs/2607.02638
-
-The source code is available at https://github.com/connectomicslab/clabtoolkit.
+See `HISTORY.rst <https://github.com/connectomicslab/clabtoolkit/blob/main/HISTORY.rst>`_ for a
+detailed changelog.
 
 Credits
 -------
 
-Developed by Yasser Alemán-Gómez and collaborators at the Connectomics Lab. See
-`AUTHORS.rst <AUTHORS.rst>`_ for the full list.
+Developed by Yasser Alemán-Gómez and collaborators at the Connectomics Lab (Lausanne University
+Hospital, CHUV). See `AUTHORS.rst <https://github.com/connectomicslab/clabtoolkit/blob/main/AUTHORS.rst>`_
+for the full list.