junifer 0.0.3.dev188__tar.gz → 0.0.4__tar.gz

junifer-0.0.4/.github/dependabot.yml

@@ -0,0 +1,10 @@
+# Set update schedule for GitHub Actions
+
+version: 2
+updates:
+
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      # Check for updates to GitHub Actions every week
+      interval: "weekly"

{junifer-0.0.3.dev188 → junifer-0.0.4}/.github/workflows/ci-docs.yml

@@ -15,7 +15,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
     steps:
       - run: 'echo "No build required"'
       - name: Create mock coverage.xml file
@@ -40,11 +40,12 @@ jobs:
           echo '</package>' >> coverage.xml
           echo '</packages>' >> coverage.xml
           echo '</coverage>' >> coverage.xml
-        if: matrix.python-version == 3.10
+        if: matrix.python-version == 3.11
       - name: Upload mock coverage to Codecov
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v4
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
-          fail_ci_if_error: true
+          # Allow coverage upload failure
+          fail_ci_if_error: false
           flags: docs
-        if: success() && matrix.python-version == 3.10
+        if: success() && matrix.python-version == 3.11

{junifer-0.0.3.dev188 → junifer-0.0.4}/.github/workflows/ci.yml

@@ -16,7 +16,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
 
     steps:
     - name: Set up system
@@ -29,11 +29,11 @@ jobs:
         git config --global user.email "runner@github.com"
         git config --global user.name "GitHub Runner"
     - name: Checkout repository
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         submodules: true
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install Python dependencies
@@ -65,18 +65,53 @@ jobs:
         curl -O https://afni.nimh.nih.gov/pub/dist/bin/misc/@update.afni.binaries
         sudo tcsh @update.afni.binaries -package linux_ubuntu_16_64 -bindir /afni
         echo "/afni" >> $GITHUB_PATH
-      if: matrix.python-version == 3.10
+      if: matrix.python-version == 3.11
     - name: Check AFNI
       run: |
         echo "Using AFNI : $(afni --version)"
-      if: matrix.python-version == 3.10
+      if: matrix.python-version == 3.11
+    - name: Install ANTs
+      run: |
+        sudo apt-get install -y -qq unzip
+        curl -fsSL -o ants.zip https://github.com/ANTsX/ANTs/releases/download/v2.5.1/ants-2.5.1-ubuntu-22.04-X64-gcc.zip
+        unzip ants.zip -d /opt
+        mv /opt/ants-2.5.1/bin/* /opt/ants-2.5.1
+        rm ants.zip
+        echo "/opt/ants-2.5.1" >> $GITHUB_PATH
+      if: matrix.python-version == 3.11
+    - name: Check ANTs
+      run: |
+        echo "Using ANTs : $(antsRegistration --version)"
+      if: matrix.python-version == 3.11
+    - name: Install FSL
+      run: |
+        sudo apt-get install -y -qq python3
+        curl -fsSL https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fslinstaller.py | python3 - -d /opt/fsl-6.0.6.4 -V 6.0.6.4
+        FSLOUTPUTTYPE="NIFTI_GZ"
+        FSLMULTIFILEQUIT="TRUE"
+        FSLTCLSH="/opt/fsl-6.0.6.4/bin/fsltclsh"
+        FSLWISH="/opt/fsl-6.0.6.4/bin/fslwish"
+        FSLLOCKDIR=""
+        FSLMACHINELIST=""
+        FSLREMOTECALL=""
+        FSLGECUDAQ="cuda.q"
+        echo "/opt/fsl-6.0.6.4" >> $GITHUB_PATH
+      if: matrix.python-version == 3.11
+      # Bypass FSL installation failure
+      continue-on-error: true
+    - name: Check FSL
+      run: |
+        echo "Using FSL : $(flirt -version)"
+      if: matrix.python-version == 3.11
+      # Bypass FSL installation failure
+      continue-on-error: true
     - name: Test with tox
       run: |
         tox
     - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         fail_ci_if_error: true
         flags: junifer
-      if: success() && matrix.python-version == 3.10
+      if: success() && matrix.python-version == 3.11

{junifer-0.0.3.dev188 → junifer-0.0.4}/.github/workflows/docs-preview.yml

@@ -20,14 +20,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - name: Checkout source
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         fetch-depth: 0
         submodules: true
-    - name: Set up Python 3.10
-      uses: actions/setup-python@v4
+    - name: Set up Python 3.11
+      uses: actions/setup-python@v5
       with:
-        python-version: '3.10'
+        python-version: '3.11'
     - name: Check for sudo
       shell: bash
       run: |
@@ -39,11 +39,25 @@ jobs:
         $SUDO apt-get update -qq
         $SUDO apt-get install git-annex-standalone
         python -m pip install --upgrade pip setuptools wheel
-        python -m pip install -e .[docs]
+        python -m pip install -e ".[docs,neurokit2]"
     - name: Configure git for datalad
       run: |
         git config --global user.email "runner@github.com"
         git config --global user.name "GITHUB CI Runner"
+    - name: Install ANTs
+      run: |
+        echo "++ Add universe repo"
+        sudo add-apt-repository -y universe
+
+        echo "++ Update package manager info"
+        sudo apt-get update -qq
+
+        echo "++ Downloading ANTs"
+        curl -fsSL -o ants.zip https://github.com/ANTsX/ANTs/releases/download/v2.5.1/ants-2.5.1-ubuntu-22.04-X64-gcc.zip
+        unzip ants.zip -d /opt
+        mv /opt/ants-2.5.1/bin/* /opt/ants-2.5.1
+        rm ants.zip
+        echo "/opt/ants-2.5.1" >> $GITHUB_PATH
     - name: Test build docs
       run: |
         BUILDDIR=_build/main make -C docs/ local

{junifer-0.0.3.dev188 → junifer-0.0.4}/.github/workflows/docs.yml

@@ -14,15 +14,15 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - name: Checkout source
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         # require all of history to see all tagged versions' docs
         fetch-depth: 0
         submodules: true
-    - name: Set up Python 3.10
-      uses: actions/setup-python@v4
+    - name: Set up Python 3.11
+      uses: actions/setup-python@v5
       with:
-        python-version: '3.10'
+        python-version: '3.11'
     - name: Check for sudo
       shell: bash
       run: |
@@ -34,16 +34,30 @@ jobs:
         $SUDO apt-get update -qq
         $SUDO apt-get install git-annex-standalone
         python -m pip install --upgrade pip setuptools wheel
-        python -m pip install -e .[docs]
+        python -m pip install -e ".[docs,neurokit2]"
         python -m pip install git+https://github.com/dls-controls/sphinx-multiversion@only-arg
     - name: Configure git for datalad
       run: |
         git config --global user.email "runner@github.com"
         git config --global user.name "GITHUB CI Runner"
+    - name: Install ANTs
+      run: |
+        echo "++ Add universe repo"
+        sudo add-apt-repository -y universe
+
+        echo "++ Update package manager info"
+        sudo apt-get update -qq
+
+        echo "++ Downloading ANTs"
+        curl -fsSL -o ants.zip https://github.com/ANTsX/ANTs/releases/download/v2.5.1/ants-2.5.1-ubuntu-22.04-X64-gcc.zip
+        unzip ants.zip -d /opt
+        mv /opt/ants-2.5.1/bin/* /opt/ants-2.5.1
+        rm ants.zip
+        echo "/opt/ants-2.5.1" >> $GITHUB_PATH
     - name: Checkout gh-pages
       # As we already did a deploy of gh-pages above, it is guaranteed to be there
       # so check it out so we can selectively build docs below
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
           ref: gh-pages
           path: docs/_build

{junifer-0.0.3.dev188 → junifer-0.0.4}/.github/workflows/lint.yml

@@ -8,16 +8,16 @@ jobs:
   lint:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Install Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: "3.11"
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          python -m pip install tox ruff
+          python -m pip install tox "ruff>=0.1.0"
       - name: Run ruff
-        run: ruff check --format=github .
+        run: ruff check --output-format=github .
       - name: Run codespell
         run: tox -e codespell

{junifer-0.0.3.dev188 → junifer-0.0.4}/.github/workflows/pypi.yml

@@ -11,25 +11,20 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - name: Checkout source
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         fetch-depth: 0
         submodules: true
-    - name: Set up Python 3.10
-      uses: actions/setup-python@v4
+    - name: Set up Python 3.11
+      uses: actions/setup-python@v5
       with:
-        python-version: '3.10'
+        python-version: '3.11'
     - name: Install build
       run:
         pip install build
     - name: Build a binary wheel and a source tarball
       run:
         python -m build --sdist --wheel --outdir dist/ .
-    # - name: Publish distribution 📦 to Test PyPI
-    #   uses: pypa/gh-action-pypi-publish@master
-    #   with:
-    #     password: ${{ secrets.testpypi_token }}
-    #     repository_url: https://test.pypi.org/legacy/
     - name: Publish distribution 📦 to PyPI
       uses: pypa/gh-action-pypi-publish@release/v1
       with:

{junifer-0.0.3.dev188 → junifer-0.0.4}/.pre-commit-config.yaml

@@ -4,7 +4,7 @@ ci:
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.5.0
     hooks:
       - id: check-ast
       - id: check-docstring-first
@@ -17,23 +17,24 @@ repos:
       - id: trailing-whitespace
         args: [--markdown-linebreak-ext=md]
   - repo: https://github.com/abravalheri/validate-pyproject
-    rev: v0.12.2
+    rev: v0.16
     hooks:
       - id: validate-pyproject
   - repo: https://github.com/psf/black
-    rev: 23.3.0
+    rev: 24.1.1
     hooks:
       - id: black
         exclude: ^(docs/|examples/|tools/)
         args: [--check]
-  - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.0.267
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.1.15
     hooks:
       - id: ruff
+        types_or: [python, jupyter]
         exclude: ^(__init__.py)
-        args: [--format, grouped, --show-fixes]
+        args: [--output-format, grouped, --show-fixes]
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.4
+    rev: v2.2.6
     hooks:
       - id: codespell
         exclude: ^(.github/|docs/)

{junifer-0.0.3.dev188 → junifer-0.0.4}/PKG-INFO

@@ -1,13 +1,14 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.3.dev188
+Version: 0.0.4
 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>
 License: AGPL-3.0-only
-Project-URL: homepage, https://juaml.github.io/junifer
-Project-URL: documentation, https://juaml.github.io/junifer
-Project-URL: repository, https://github.com/juaml/junifer
+Project-URL: Changelog, https://juaml.github.io/junifer/main/whats_new.html
+Project-URL: Documentation, https://juaml.github.io/junifer
+Project-URL: Homepage, https://juaml.github.io/junifer
+Project-URL: Source, https://github.com/juaml/junifer
 Keywords: neuroimaging
 Classifier: Development Status :: 4 - Beta
 Classifier: Intended Audience :: Science/Research
@@ -22,13 +23,48 @@ 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
 Description-Content-Type: text/markdown
-Provides-Extra: dev
-Provides-Extra: docs
-Provides-Extra: onthefly
 License-File: LICENSE.md
 License-File: AUTHORS.rst
+Requires-Dist: click<8.2,>=8.1.3
+Requires-Dist: numpy<1.27,>=1.24
+Requires-Dist: scipy<=1.11.4,>=1.9.0
+Requires-Dist: datalad<0.20,>=0.15.4
+Requires-Dist: pandas<2.2,>=1.4.0
+Requires-Dist: nibabel<5.11,>=3.2.0
+Requires-Dist: nilearn<=0.10.2,>=0.9.0
+Requires-Dist: sqlalchemy<=2.1.0,>=1.4.27
+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: importlib_metadata; python_version < "3.10"
+Requires-Dist: looseversion==1.3.0; python_version >= "3.12"
+Provides-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"
+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"
+Provides-Extra: docs
+Requires-Dist: seaborn<0.13,>=0.11.2; extra == "docs"
+Requires-Dist: sphinx<7.3,>=5.3.0; extra == "docs"
+Requires-Dist: sphinx-gallery<0.15.0,>=0.11.0; extra == "docs"
+Requires-Dist: furo<2023.10.0,>=2022.9.29; extra == "docs"
+Requires-Dist: numpydoc<1.6,>=1.5.0; extra == "docs"
+Requires-Dist: julearn<0.4,>=0.3.0; extra == "docs"
+Requires-Dist: sphinx-copybutton<0.5.3,>=0.5.1; extra == "docs"
+Requires-Dist: towncrier<23.7,>=22.12.0; extra == "docs"
+Requires-Dist: sphinxcontrib-mermaid<0.10,>=0.8.1; extra == "docs"
 
 ![Junifer logo](docs/images/junifer_logo.png "junifer logo")
 
@@ -43,10 +79,12 @@ 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)
+[![FAIR checklist badge](https://fairsoftwarechecklist.net/badge.svg)](https://fairsoftwarechecklist.net/v0.2?f=31&a=32113&i=32322&r=133)
 
 ## 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.
 
@@ -69,7 +107,7 @@ The documentation is available at [https://juaml.github.io/junifer](https://juam
   * `preprocess`: Preprocessing module.
   * `storage`: Storage module.
   * `testing`: Testing components module.
-  * `utils`: Utilities module (e.g. logging)
+  * `utils`: Utilities module (e.g. logging).
 
 ## Installation
 
@@ -85,14 +123,29 @@ You can also install via `conda`, like so:
 conda install -c conda-forge junifer
 ```
 
+### Optional dependencies
+
+`junifer` supports a few optional dependencies to enable certain features. You can
+install them by specifying a comma separated list within square brackets, like so:
+
+```
+pip install "junifer[bct,dev]"
+```
+
+* `bct` installs [bctpy](https://github.com/aestrivex/bctpy) to enable use of `onthefly` module.
+* `neurokit2` installs [neurokit2](https://github.com/neuropsychology/NeuroKit) to enable use of [complexity markers](https://juaml.github.io/junifer/main/api/markers.html#module-junifer.markers.complexity).
+* `all` includes all of the above.
+* `dev` installs packages needed for development.
+* `docs` installs packages needed for building documentation.
+
 ## 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 +157,7 @@ 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.dev188 → junifer-0.0.4}/README.md

@@ -11,10 +11,12 @@
 [![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)
+[![FAIR checklist badge](https://fairsoftwarechecklist.net/badge.svg)](https://fairsoftwarechecklist.net/v0.2?f=31&a=32113&i=32322&r=133)
 
 ## 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.
 
@@ -37,7 +39,7 @@ The documentation is available at [https://juaml.github.io/junifer](https://juam
   * `preprocess`: Preprocessing module.
   * `storage`: Storage module.
   * `testing`: Testing components module.
-  * `utils`: Utilities module (e.g. logging)
+  * `utils`: Utilities module (e.g. logging).
 
 ## Installation
 
@@ -53,14 +55,29 @@ You can also install via `conda`, like so:
 conda install -c conda-forge junifer
 ```
 
+### Optional dependencies
+
+`junifer` supports a few optional dependencies to enable certain features. You can
+install them by specifying a comma separated list within square brackets, like so:
+
+```
+pip install "junifer[bct,dev]"
+```
+
+* `bct` installs [bctpy](https://github.com/aestrivex/bctpy) to enable use of `onthefly` module.
+* `neurokit2` installs [neurokit2](https://github.com/neuropsychology/NeuroKit) to enable use of [complexity markers](https://juaml.github.io/junifer/main/api/markers.html#module-junifer.markers.complexity).
+* `all` includes all of the above.
+* `dev` installs packages needed for development.
+* `docs` installs packages needed for building documentation.
+
 ## 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 +89,7 @@ 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/conda-env.yml

@@ -0,0 +1,33 @@
+name: junifer-dev
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - python>=3.10,<=3.11
+  - click=8.1.*
+  - numpy>=1.22,<1.27
+  - pandas>=1.4.0,<2.2
+  - nibabel>=3.2.0,<5.2
+  - nilearn>=0.9.0,<=0.10.1
+  - sqlalchemy>=1.4.27,<= 2.0.21
+  - ruamel.yaml=0.17.*
+  - h5py>=3.8,<=3.9
+  - seaborn>=0.11,<=0.13
+  - sphinx>=5.3,<7.3
+  - sphinx-gallery>=0.11.0,<0.15.0
+  - furo>=2022.9.29,<2023.10.0
+  - numpydoc>=1.5.0,<1.6
+  - sphinx-copybutton>=0.5.1,<0.5.3
+  - towncrier>=22.12.0,<23.7
+  - sphinxcontrib-mermaid>=0.8.1,<0.10
+  - tox
+  - ipykernel
+  - pytest-cov
+  - pytest
+  - black
+  - ruff
+  - codespell
+  - pip
+  - pip:
+    - datalad>=0.15.4,<0.20
+    - julearn==0.3.0

{junifer-0.0.3.dev188 → junifer-0.0.4}/docs/api/api.rst

@@ -15,3 +15,11 @@ Decorators
 .. automodule:: junifer.api.decorators
    :members:
    :imported-members:
+
+
+Queue Context
+-------------
+
+.. automodule:: junifer.api.queue_context
+   :members:
+   :imported-members:

{junifer-0.0.3.dev188 → junifer-0.0.4}/docs/api/data.rst

@@ -4,6 +4,7 @@ Parcellations
 .. automodule:: junifer.data.parcellations
    :members:
 
+
 Coordinates
 ===========
 
@@ -16,3 +17,10 @@ Masks
 
 .. automodule:: junifer.data.masks
    :members:
+
+
+Template Spaces
+===============
+
+.. automodule:: junifer.data.template_spaces
+   :members:

junifer-0.0.4/docs/api/markers.rst

@@ -0,0 +1,14 @@
+Markers
+=======
+
+.. automodule:: junifer.markers
+   :members:
+   :imported-members:
+
+
+Complexity
+----------
+
+.. automodule:: junifer.markers.complexity
+   :members:
+   :imported-members: