Voxel headmodel

.github/workflows/build_docs.yml

@@ -4,6 +4,7 @@ on:
   push:
     branches:
       - main
+      - dev
 
 # cancel job if a new push to main occurs while running
 concurrency:
@@ -16,41 +17,55 @@ jobs:
     defaults:
       run:
         shell: bash -el {0}
-    strategy:
-      max-parallel: 5
 
     steps:
-      - uses: actions/checkout@v4
+      - name: Checkout git repository 
+        uses: actions/checkout@v4
 
       - name: Setup headless display
-        uses: pyvista/setup-headless-display-action@v2
+        uses: pyvista/setup-headless-display-action@v3
 
-      - name: Create conda environment
-        uses: mamba-org/setup-micromamba@v1
+      - name: Setup Miniforge
+        uses: conda-incubator/setup-miniconda@v3
         with:
-          environment-file: environment_dev.yml
-          micromamba-version: 'latest'
-          cache-environment: true
+          miniforge-version: latest
+          activate-environment: cedalion
 
-      - name: Conda info
-        run: conda info
+      - name: Get Date
+        id: get-date
+        run: echo "today=$(/bin/date -u '+%Y%m%d')" >> $GITHUB_OUTPUT
+        shell: bash
+
+      - name: Cache Conda env
+        uses: actions/cache@v4
+        with:
+          path: ${{ env.CONDA }}/envs
+          key:
+            conda-${{ runner.os }}--${{ runner.arch }}--${{
+            steps.get-date.outputs.today }}-${{
+            hashFiles('environment_dev.yml') }}-${{ env.CACHE_NUMBER }}
+        env:
+          # Increase this value to reset cache if environment_dev.yml has not changed
+          CACHE_NUMBER: 0
+        id: cache
+
+      - name: Update environment
+        run: conda env update -n cedalion -f environment_dev.yml
+        if: steps.cache.outputs.cache-hit != 'true'
 
       - name: Install cedalion
-        run: |
-           python -m pip install -e . --no-deps --force-reinstall
+        run: python -m pip install -e . --no-deps --force-reinstall
 
       - name: Install nirfaster
-        run: |
-           bash install_nirfaster.sh CPU
+        run: bash install_nirfaster.sh CPU
         shell: bash
 
       - name: Building docs
-        run: |
-          ./scripts/build_docs.sh docs
+        run: ./scripts/build_docs.sh docs
 
       - name: Save website as an artifact
         uses: actions/upload-artifact@v4
         with:
-          name: docs
+          name: docs-${{ github.ref_name }}
           path: docs/_build/html
-          retention-days: 14
+          retention-days: 2

.github/workflows/run_tests.yml

@@ -13,24 +13,43 @@ jobs:
         shell: bash -l {0}
 
     steps:
-      - uses: actions/checkout@v4
+      - name: Checkout git repository 
+        uses: actions/checkout@v4
 
-      - name: Create conda environment
-        uses: mamba-org/setup-micromamba@v1
+      - name: Setup Miniforge
+        uses: conda-incubator/setup-miniconda@v3
         with:
-          environment-file: environment_dev.yml
-          micromamba-version: 'latest'
-          cache-environment: true
+          miniforge-version: latest
+          activate-environment: cedalion
+
+      - name: Get Date
+        id: get-date
+        run: echo "today=$(/bin/date -u '+%Y%m%d')" >> $GITHUB_OUTPUT
+        shell: bash
+
+      - name: Cache Conda env
+        uses: actions/cache@v4
+        with:
+          path: ${{ env.CONDA }}/envs
+          key:
+            conda-${{ runner.os }}--${{ runner.arch }}--${{
+            steps.get-date.outputs.today }}-${{
+            hashFiles('environment_dev.yml') }}-${{ env.CACHE_NUMBER }}
+        env:
+          # Increase this value to reset cache if environment_dev.yml has not changed
+          CACHE_NUMBER: 0
+        id: cache
+
+      - name: Update environment
+        run: conda env update -n cedalion -f environment_dev.yml
+        if: steps.cache.outputs.cache-hit != 'true'
 
       - name: Install cedalion
-        run: |
-           python -m pip install -e . --no-deps --force-reinstall
+        run: python -m pip install -e . --no-deps --force-reinstall
 
       - name: Install nirfaster
-        run: |
-           bash install_nirfaster.sh CPU
+        run: bash install_nirfaster.sh CPU
         shell: bash
 
       - name: Running Tests
-        run: |
-           python -m pytest --verbose
+        run: python -m pytest --verbose

.gitignore

@@ -167,9 +167,11 @@ src/cedalion/_version.py
 
 # rendered example notebooks
 docs/examples/*.ipynb
+docs/examples/*/*.ipynb
 
 # API documentation from sphinx-apidoc
 docs/api/*
+_autosummary*/
 
 # vscode settings
 .vscode/

.pre-commit-config.yaml

@@ -4,11 +4,13 @@ repos:
 # Ruff
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.
-  rev: v0.5.4
+  rev: v0.7.0
   hooks:
-    # Run the linter.
     - id: ruff
       files: ^src/cedalion/
-    # Run the formatter.
-    #- id: ruff-format
-    #  files: ^src/cedalion/
+- repo: https://github.com/kynan/nbstripout
+  rev: 0.7.1
+  hooks:
+    - id: nbstripout
+      files: ^examples/
+

README.md

@@ -12,7 +12,7 @@ multimodal fNIRS signals.
 
 The [documentation](https://doc.ibs.tu-berlin.de/cedalion/doc/dev) contains
 [installation instructions](https://doc.ibs.tu-berlin.de/cedalion/doc/dev/getting_started/installation.html) as
-well as several [example notebooks](https://doc.ibs.tu-berlin.de/cedalion/doc/dev/examples/index.html)
+well as several [example notebooks](https://doc.ibs.tu-berlin.de/cedalion/doc/dev/examples.html)
 that illustrate the functionality of the toolbox.
 For discussions and help you can visit the [cedalion forum on openfnirs.org](https://openfnirs.org/community/cedalion/)