Merge pull request netneurolab#144 from liuzhenqi77/improvements

[ENH] Various improvements
liuzhenqi77 · Nov 20, 2024 · 107e2fe · 107e2fe
2 parents 2c4d288 + 8d56d14
commit 107e2fe
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Showing 17 changed files with 254 additions and 49 deletions.
diff --git a/.codecov.yml b/.codecov.yml
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -13,6 +13,7 @@ permissions:
 
 jobs:
   deploy_page:
+    if: github.repository_owner == 'netneurolab'
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4

diff --git a/.github/workflows/tests.yml → .github/workflows/tests-basic.yml b/.github/workflows/tests.yml → .github/workflows/tests-basic.yml
@@ -6,6 +6,8 @@ on:
     branches:
       - main
   pull_request:
+    branches:
+      - main
 
 jobs:
   check_style:
@@ -24,9 +26,9 @@ jobs:
             python -m pip install --upgrade pip
             python -m pip install ruff
       - name: Run style checks
-        run: ruff check .
+        run: ruff check --output-format=github .
 
-  run_tests:
+  run_basic_tests:
     needs: check_style
     runs-on: ${{ matrix.os }}
     strategy:
@@ -44,21 +46,14 @@ jobs:
           python-version: ${{ matrix.python-version }}
       - name: Display Python version
         run: python -c "import sys; print(sys.version)"
-      - name: Install dependencies
+      - name: Install netneurotools
         run: |
           python -m pip install --upgrade pip
-          python -m pip install pytest pytest-cov
-          python -m pip install -r requirements.txt
-      - name: Install netneurotools
-        run: python -m pip install .
+          python -m pip install '.[test]'
       - name: Print netneurotools version
         run: python -c "import netneurotools; print(netneurotools.__version__)" 
       - name: Run tests
-        run: pytest --doctest-modules --cov=netneurotools --cov-report=xml --junitxml=junit/test-results.xml --verbose --pyargs netneurotools
-      - name: Upload coverage
-        uses: codecov/codecov-action@v5
-        with:
-          files: coverage.xml
+        run: pytest --doctest-modules --junitxml=junit/test-results.xml --verbose -m "not (fetcher or pyvista or pysurfer)" netneurotools
       - name: Upload pytest test results
         uses: actions/upload-artifact@v4
         with:

diff --git a/.github/workflows/tests-datasets-fetcher.yml b/.github/workflows/tests-datasets-fetcher.yml
@@ -0,0 +1,46 @@
+name: netneurotools-tests
+
+on: 
+  workflow_dispatch:
+  push:
+    branches:
+      - main
+    paths:
+      - 'netneurotools/datasets/**'
+  pull_request:
+    branches:
+      - main
+    paths:
+      - 'netneurotools/datasets/**'
+
+jobs:
+  run_fetcher_tests:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: ['ubuntu-latest']
+        python-version: ['3.9', '3.10', '3.11', '3.12', '3.13']
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Display Python version
+        run: python -c "import sys; print(sys.version)"
+      - name: Install netneurotools
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install '.[test]'
+      - name: Print netneurotools version
+        run: python -c "import netneurotools; print(netneurotools.__version__)" 
+      - name: Run tests
+        run: pytest --doctest-modules --junitxml=junit/test-results.xml --verbose -m fetcher netneurotools
+      - name: Upload pytest test results
+        uses: actions/upload-artifact@v4
+        with:
+          name: pytest-results-${{ matrix.os }}-${{ matrix.python-version }}
+          path: junit/test-results.xml
diff --git a/.github/workflows/tests-plotting-pyvista.yml b/.github/workflows/tests-plotting-pyvista.yml
@@ -0,0 +1,46 @@
+name: netneurotools-tests
+
+on: 
+  workflow_dispatch:
+  push:
+    branches:
+      - main
+    paths:
+      - 'netneurotools/plotting/pyvista_plotters.py'
+  pull_request:
+    branches:
+      - main
+    paths:
+      - 'netneurotools/plotting/pyvista_plotters.py'
+
+jobs:
+  run_pyvista_tests:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: ['ubuntu-latest']
+        python-version: ['3.9', '3.10', '3.11', '3.12']
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Display Python version
+        run: python -c "import sys; print(sys.version)"
+      - name: Install netneurotools
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install '.[test,pyvista]'
+      - name: Print netneurotools version
+        run: python -c "import netneurotools; print(netneurotools.__version__)" 
+      - name: Run tests
+        run: pytest --doctest-modules --junitxml=junit/test-results.xml --verbose -m pyvista netneurotools
+      - name: Upload pytest test results
+        uses: actions/upload-artifact@v4
+        with:
+          name: pytest-results-${{ matrix.os }}-${{ matrix.python-version }}
+          path: junit/test-results.xml
diff --git a/docs/conf.py b/docs/conf.py
@@ -115,6 +115,7 @@
     'scipy': ('https://docs.scipy.org/doc/scipy/reference', None),
     'sklearn': ('https://scikit-learn.org/stable', None),
     'pandas': ('https://pandas.pydata.org/pandas-docs/stable', None),
+    'pyvista': ('https://docs.pyvista.org/', None),
 }
 
 doctest_global_setup = """\

diff --git a/examples/wip_plot_spin_test.py → examples/wip_plot_spin.py b/examples/wip_plot_spin_test.py → examples/wip_plot_spin.py
diff --git a/netneurotools/datasets/fetch_project.py b/netneurotools/datasets/fetch_project.py
@@ -189,6 +189,11 @@ def fetch_hansen_receptors(force=False, data_dir=None, verbose=1):
 
     If you used this data, please cite [1]_.
 
+    .. important::
+       If you use this dataset, please also cite the original data sources.
+       See the original publication or `neuromaps <https://netneurolab.github.io/neuromaps/listofmaps.html>`_
+       for more information.
+
     Returns
     -------
     filenames : :class:`sklearn.utils.Bunch`
@@ -208,7 +213,12 @@ def fetch_hansen_receptors(force=False, data_dir=None, verbose=1):
 
     References
     ----------
-    .. [1]
+    .. [1] Justine Y Hansen, Golia Shafiei, Ross D Markello, Kelly Smart, Sylvia
+        ML Cox, Martin N\u00f8rgaard, Vincent Beliveau, Yanjun Wu,
+        Jean-Dominique Gallezot, \u00c9tienne Aumont, and others. Mapping
+        neurotransmitter systems to the structural and functional organization
+        of the human neocortex. Nature neuroscience, 25(11):1569\u20131581,
+        2022.
     """
     dataset_name = "ds-hansen_receptors"
     _get_reference_info(dataset_name, verbose=verbose)
@@ -244,7 +254,10 @@ def fetch_hansen_genescognition(force=False, data_dir=None, verbose=1):
 
     References
     ----------
-    .. [1]
+    .. [1] Justine Y Hansen, Ross D Markello, Jacob W Vogel, Jakob Seidlitz,
+        Danilo Bzdok, and Bratislav Misic. Mapping gene transcription and
+        neurocognition across human neocortex. Nature Human Behaviour,
+        5(9):1240\u20131250, 2021.
     """
     dataset_name = "ds-hansen_genescognition"
     _get_reference_info(dataset_name, verbose=verbose)
@@ -280,7 +293,10 @@ def fetch_hansen_brainstemfc(force=False, data_dir=None, verbose=1):
 
     References
     ----------
-    .. [1]
+    .. [1] Justine Y Hansen, Simone Cauzzo, Kavita Singh, Mar\u00eda Guadalupe
+        Garc\u00eda-Gomar, James M Shine, Marta Bianciardi, and Bratislav Misic.
+        Integrating brainstem and cortical functional architectures. Nature
+        Neuroscience, pages 1\u201312, 2024.
     """
     dataset_name = "ds-hansen_brainstemfc"
     _get_reference_info(dataset_name, verbose=verbose)
@@ -316,7 +332,10 @@ def fetch_shafiei_megfmrimapping(force=False, data_dir=None, verbose=1):
 
     References
     ----------
-    .. [1]
+    .. [1] Golia Shafiei, Sylvain Baillet, and Bratislav Misic. Human
+        electromagnetic and haemodynamic networks systematically converge in
+        unimodal cortex and diverge in transmodal cortex. PLoS biology,
+        20(8):e3001735, 2022.
     """
     dataset_name = "ds-shafiei_megfmrimapping"
     _get_reference_info(dataset_name, verbose=verbose)
@@ -352,7 +371,10 @@ def fetch_shafiei_megdynamics(force=False, data_dir=None, verbose=1):
 
     References
     ----------
-    .. [1]
+    .. [1] Golia Shafiei, Ben D Fulcher, Bradley Voytek, Theodore D
+        Satterthwaite, Sylvain Baillet, and Bratislav Misic. Neurophysiological
+        signatures of cortical micro-architecture. Nature communications,
+        14(1):6000, 2023.
     """
     dataset_name = "ds-shafiei_megdynamics"
     _get_reference_info(dataset_name, verbose=verbose)
@@ -367,7 +389,7 @@ def fetch_suarez_mami(force=False, data_dir=None, verbose=1):
 
     This dataset contains
 
-    If you used this data, please cite [1]_.
+    If you used this data, please cite [1]_ and [2]_.
 
     Returns
     -------
@@ -388,7 +410,12 @@ def fetch_suarez_mami(force=False, data_dir=None, verbose=1):
 
     References
     ----------
-    .. [1]
+    .. [1] Laura E Suarez, Yossi Yovel, Martijn P van den Heuvel, Olaf Sporns,
+        Yaniv Assaf, Guillaume Lajoie, and Bratislav Misic. A connectomics-based
+        taxonomy of mammals. Elife, 11:e78635, 2022.
+    .. [2] Yaniv Assaf, Arieli Bouznach, Omri Zomet, Assaf Marom, and Yossi
+        Yovel. Conservation of brain connectivity and wiring across the
+        mammalian class. Nature Neuroscience, 23(7):805\u2013808, 2020.
     """
     dataset_name = "ds-suarez_mami"
     _get_reference_info(dataset_name, verbose=verbose)

diff --git a/netneurotools/datasets/netneurotools.bib b/netneurotools/datasets/netneurotools.bib
@@ -262,3 +262,77 @@ @article{markello2022neuromaps
   year={2022},
   publisher={Nature Publishing Group US New York}
 }
+
+@article{hansen2021mapping,
+  title={Mapping gene transcription and neurocognition across human neocortex},
+  author={Hansen, Justine Y and Markello, Ross D and Vogel, Jacob W and Seidlitz, Jakob and Bzdok, Danilo and Misic, Bratislav},
+  journal={Nature Human Behaviour},
+  volume={5},
+  number={9},
+  pages={1240--1250},
+  year={2021},
+  publisher={Nature Publishing Group UK London}
+}
+
+@article{hansen2022mapping,
+  title={Mapping neurotransmitter systems to the structural and functional organization of the human neocortex},
+  author={Hansen, Justine Y and Shafiei, Golia and Markello, Ross D and Smart, Kelly and Cox, Sylvia ML and N{\o}rgaard, Martin and Beliveau, Vincent and Wu, Yanjun and Gallezot, Jean-Dominique and Aumont, {\'E}tienne and others},
+  journal={Nature neuroscience},
+  volume={25},
+  number={11},
+  pages={1569--1581},
+  year={2022},
+  publisher={Nature Publishing Group US New York}
+}
+
+@article{hansen2024integrating,
+  title={Integrating brainstem and cortical functional architectures},
+  author={Hansen, Justine Y and Cauzzo, Simone and Singh, Kavita and Garc{\'\i}a-Gomar, Mar{\'\i}a Guadalupe and Shine, James M and Bianciardi, Marta and Misic, Bratislav},
+  journal={Nature Neuroscience},
+  pages={1--12},
+  year={2024},
+  publisher={Nature Publishing Group US New York}
+}
+
+@article{shafiei2023neurophysiological,
+  title={Neurophysiological signatures of cortical micro-architecture},
+  author={Shafiei, Golia and Fulcher, Ben D and Voytek, Bradley and Satterthwaite, Theodore D and Baillet, Sylvain and Misic, Bratislav},
+  journal={Nature communications},
+  volume={14},
+  number={1},
+  pages={6000},
+  year={2023},
+  publisher={Nature Publishing Group UK London}
+}
+
+@article{shafiei2022human,
+  title={Human electromagnetic and haemodynamic networks systematically converge in unimodal cortex and diverge in transmodal cortex},
+  author={Shafiei, Golia and Baillet, Sylvain and Misic, Bratislav},
+  journal={PLoS biology},
+  volume={20},
+  number={8},
+  pages={e3001735},
+  year={2022},
+  publisher={Public Library of Science San Francisco, CA USA}
+}
+
+@article{suarez2022connectomics,
+  title={A connectomics-based taxonomy of mammals},
+  author={Suarez, Laura E and Yovel, Yossi and van den Heuvel, Martijn P and Sporns, Olaf and Assaf, Yaniv and Lajoie, Guillaume and Misic, Bratislav},
+  journal={Elife},
+  volume={11},
+  pages={e78635},
+  year={2022},
+  publisher={eLife Sciences Publications Limited}
+}
+
+@article{assaf2020conservation,
+  title={Conservation of brain connectivity and wiring across the mammalian class},
+  author={Assaf, Yaniv and Bouznach, Arieli and Zomet, Omri and Marom, Assaf and Yovel, Yossi},
+  journal={Nature Neuroscience},
+  volume={23},
+  number={7},
+  pages={805--808},
+  year={2020},
+  publisher={Nature Publishing Group US New York}
+}