CI: various fixes

- fix deploy docs workflow
- add flybrains to test requirements
- download required transform; note: the transform is a heavily
  downsampled version of the real thing

.github/workflows/build-docs.yml

@@ -0,0 +1,53 @@
+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
+      - 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

.github/workflows/test-tutorials.yml

@@ -35,6 +35,10 @@ jobs:
       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
     - name: Run tutorials
       uses: coactions/setup-xvfb@v1
       env:

requirements.txt

@@ -63,6 +63,7 @@ jupyter
 neuprint-python
 caveclient
 cloud-volume
+flybrains
 Shapely>=1.6.0
 
 #extra: dev

tests/test_tutorials.py

@@ -9,6 +9,8 @@
    process before the current process has finished its bootstrapping phase." error which typically
    means that the script has to be run in a `if __name__ == "__main__":` block.
    Set `capture_output=True` to see the error message.
+ - the MICrONS tutorial occasionally fails because the CAVE backend throws an error
+   (e.g. during the materialization)
 """
 
 import subprocess