Merge pull request #158 from navis-org/mkdocs2

Swap docs to MkDocs
navis-org · Sep 6, 2024 · 78f5423 · 78f5423
2 parents 39df866 + e9f3648
commit 78f5423
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diff --git a/.github/workflows/build-docs.yml b/.github/workflows/build-docs.yml
@@ -0,0 +1,54 @@
+name: Docs
+
+permissions:
+  contents: write
+
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.10'
+      - name: Install system libraries
+        run: |
+          sudo apt-get update -y -qq
+          sudo apt-get install -y libdbus-1-3 libxkbcommon-x11-0 libxcb-icccm4 \
+            libxcb-image0 libxcb-keysyms1 libxcb-randr0 libxcb-render-util0 \
+            libxcb-xinerama0 libxcb-xinput0 graphviz graphviz-dev \
+            libegl1-mesa libgl1-mesa-dri libxcb-xfixes0-dev mesa-vulkan-drivers \
+            libxcb-cursor0
+      - name: Install Python dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install pathos pygraphviz neuron cloud-volume k3d scikit-image open3d
+          python -m pip install -e .[test-notebook,all,docs,flybrains,cloud-volume]
+      - name: Download test data
+        run: |
+          chmod +x download_test_data.sh
+          ./download_test_data.sh
+      - name: Download downsampled test transform
+        run: |
+          mkdir -p -- $HOME/flybrain-data
+          curl -o $HOME/flybrain-data/JRC2018F_JRCFIB2018F.h5 https://flyem.mrc-lmb.cam.ac.uk/flyconnectome/misc/JRC2018F_JRCFIB2018F.h5
+          curl -o $HOME/flybrain-data/JRC2018F_FAFB.h5 https://flyem.mrc-lmb.cam.ac.uk/flyconnectome/misc/JRC2018F_FAFB.h5
+      - name: Build and deploy docs
+        uses: coactions/setup-xvfb@v1
+        env:
+          NEUPRINT_APPLICATION_CREDENTIALS: ${{ secrets.neuprint }}
+          INSECT_BRAIN_DB_USER: ${{ secrets.insect_brain_db_user }}
+          INSECT_BRAIN_DB_PASSWORD: ${{ secrets.insect_brain_db_password }}
+          CAVE_SECRET: ${{ secrets.cave_secret }}
+          NAVIS_PLOT3D_BACKEND: plotly
+          QT_QPA_PLATFORM: offscreen
+        with:
+          run: |
+            python -c "import os;from caveclient import CAVEclient;client=CAVEclient();client.auth.save_token(os.getenv('CAVE_SECRET'))"
+            mkdocs gh-deploy --force
diff --git a/.github/workflows/notebooktest-package.yml → .github/workflows/test-tutorials.yml b/.github/workflows/notebooktest-package.yml → .github/workflows/test-tutorials.yml
@@ -1,4 +1,4 @@
-name: Notebooks
+name: Test tutorials
 
 on: [push]
 
@@ -24,19 +24,32 @@ jobs:
         sudo apt-get install -y libdbus-1-3 libxkbcommon-x11-0 libxcb-icccm4 \
           libxcb-image0 libxcb-keysyms1 libxcb-randr0 libxcb-render-util0 \
           libxcb-xinerama0 libxcb-xinput0 graphviz graphviz-dev \
-          libegl1-mesa libgl1-mesa-dri libxcb-xfixes0-dev mesa-vulkan-drivers
+          libegl1-mesa libgl1-mesa-dri libxcb-xfixes0-dev mesa-vulkan-drivers \
+          libxcb-cursor0
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
         python -m pip install pathos pygraphviz neuron cloud-volume k3d scikit-image open3d
         python -m pip install -e .[test-notebook,all]
-    - name: Run notebooks
+    - name: Download test data
+      run: |
+        chmod +x download_test_data.sh
+        ./download_test_data.sh
+    - name: Download downsampled test transform
+      run: |
+        mkdir -p -- $HOME/flybrain-data
+        curl -o $HOME/flybrain-data/JRC2018F_JRCFIB2018F.h5 https://flyem.mrc-lmb.cam.ac.uk/flyconnectome/misc/JRC2018F_JRCFIB2018F.h5
+        curl -o $HOME/flybrain-data/JRC2018F_FAFB.h5 https://flyem.mrc-lmb.cam.ac.uk/flyconnectome/misc/JRC2018F_FAFB.h5
+    - name: Run tutorials
       uses: coactions/setup-xvfb@v1
       env:
         NEUPRINT_APPLICATION_CREDENTIALS: ${{ secrets.neuprint }}
         INSECT_BRAIN_DB_USER: ${{ secrets.insect_brain_db_user }}
         INSECT_BRAIN_DB_PASSWORD: ${{ secrets.insect_brain_db_password }}
+        CAVE_SECRET: ${{ secrets.cave_secret }}
+        NAVIS_PLOT3D_BACKEND: plotly
+        QT_QPA_PLATFORM: offscreen
       with:
         run: |
-          export NAVIS_HEADLESS=TRUE
-          python tests/test_notebooks.py
+          python -c "import os;from caveclient import CAVEclient;client=CAVEclient();client.auth.save_token(os.getenv('CAVE_SECRET'))"
+          python tests/test_tutorials.py
diff --git a/.gitignore b/.gitignore
@@ -132,3 +132,7 @@ ENV/
 MANIFEST
 
 tmp/
+
+# Test data
+mmc2
+WannerAA*
diff --git a/README.md b/README.md
@@ -5,7 +5,7 @@
 NAVis is a Python 3 library for **N**euron **A**nalysis and **Vis**ualization.
 
 ## Documentation
-NAVis is on [ReadTheDocs](http://navis.readthedocs.io/ "NAVis ReadTheDocs").
+Visit our documentation [here](https://navis-org.github.io/navis/ "NAVis Documentation")!
 
 ## Features
 * **polyglot**: work and convert between neuron skeletons, meshes, dotprops and images

diff --git a/docs/Makefile b/docs/Makefile
diff --git a/docs/_static/NBLAST_score_mat_inv.png b/docs/_static/NBLAST_score_mat_inv.png
diff --git a/...urce/tutorials/figures/b3d_screenshot.jpg → docs/_static/b3d_screenshot.jpg b/...urce/tutorials/figures/b3d_screenshot.jpg → docs/_static/b3d_screenshot.jpg
diff --git a/docs/_static/barcode.afdesign b/docs/_static/barcode.afdesign
diff --git a/docs/_static/barcode.png b/docs/_static/barcode.png
diff --git a/docs/_static/blender_console.png b/docs/_static/blender_console.png
diff --git a/docs/_static/blender_logo.png b/docs/_static/blender_logo.png
diff --git a/docs/_static/blender_pip.png b/docs/_static/blender_pip.png
diff --git a/docs/source/tutorials/figures/k3d_viewer.png → docs/_static/k3d_viewer.png b/docs/source/tutorials/figures/k3d_viewer.png → docs/_static/k3d_viewer.png
diff --git a/docs/_static/logo_new_banner.png b/docs/_static/logo_new_banner.png
diff --git a/docs/_static/neuprint_logo.png b/docs/_static/neuprint_logo.png
diff --git a/docs/_static/octarine_viewer.png b/docs/_static/octarine_viewer.png
diff --git a/docs/_static/pickle.png b/docs/_static/pickle.png
diff --git a/docs/_static/plotly_orbital.png b/docs/_static/plotly_orbital.png
diff --git a/docs/source/tutorials/figures/rotation.gif → docs/_static/rotation.gif b/docs/source/tutorials/figures/rotation.gif → docs/_static/rotation.gif
diff --git a/...source/tutorials/figures/vispy_viewer.png → docs/_static/vispy_viewer.png b/...source/tutorials/figures/vispy_viewer.png → docs/_static/vispy_viewer.png