Update environment files and github workflows

.github/workflows/build_docs.yaml

@@ -1,57 +1,58 @@
-name: build_documentation
+name: Build and Deploy Docs
 
-# build the documentation for a new release
 on:
-  release:
-    types: created
-
-# # for debugging
-# on: [push, pull_request]
+  push:
+    paths:
+      - "doc/*.md"   # Trigger on changes to any markdown file
+      - "torch_em/**/*.py"   # Optionally include changes in Python files
+    branches:
+      - main        # Run the workflow only on pushes to the main branch
+  workflow_dispatch:
 
 # security: restrict permissions for CI jobs.
 permissions:
   contents: read
 
-# NOTE: importing of napari fails with CI and I am not quite sure why
-# I tried to adjust it based on the napari CI tests, but that didn't seem to help
-
-# https://github.com/napari/napari/blob/main/.github/workflows/test_comprehensive.yml
 jobs:
-  # Build the documentation and upload the static HTML files as an artifact.
   build:
+    name: Build Documentation
     runs-on: ubuntu-latest
+
     steps:
-      - name: Checkout
-        uses: actions/checkout@v4
+    - name: Checkout Code
+      uses: actions/checkout@v4
+
+    - name: Set up Micromamba
+      uses: mamba-org/setup-micromamba@v2
+      with:
+        micromamba-version: "latest"
+        environment-file: environment.yaml
+        init-shell: bash
+        cache-environment: true
+        post-cleanup: 'all'
+
+    - name: Install package
+      shell: bash -l {0}
+      run: pip install -e .
 
-      - name: Setup miniconda
-        uses: conda-incubator/setup-miniconda@v2
-        with:
-          activate-environment: sam
-          mamba-version: "*"
-          auto-update-conda: true
-          environment-file: .github/doc_env.yaml
-          python-version: ${{ matrix.python-version }}
-          auto-activate-base: false
-        env:
-          ACTIONS_ALLOW_UNSECURE_COMMANDS: true
+    - name: Install pdoc
+      shell: bash -l {0}
+      run: pip install pdoc
 
-      - name: Install package
-        shell: bash -l {0}
-        run: pip install --no-deps -e .
+    - name: Generate Documentation
+      shell: bash -l {0}
+      run: pdoc synapse_net/ -d google -o doc/
 
-      # We use a custom build script for pdoc itself, ideally you just run `pdoc -o docs/ ...` here.
-      - name: Run pdoc
-        shell: bash -l {0}
-        run: python build_doc.py --out
+    - name: Verify Documentation Output
+      run: ls -la doc/
 
-      - uses: actions/upload-pages-artifact@v1
-        with:
-          path: tmp/
+    - name: Upload Documentation Artifact
+      uses: actions/upload-pages-artifact@v3
+      with:
+        path: doc/
 
-  # Deploy the artifact to GitHub pages.
-  # This is a separate job so that only actions/deploy-pages has the necessary permissions.
   deploy:
+    name: Deploy Documentation
     needs: build
     runs-on: ubuntu-latest
     permissions:
@@ -61,5 +62,5 @@ jobs:
       name: github-pages
       url: ${{ steps.deployment.outputs.page_url }}
     steps:
-      - id: deployment
-        uses: actions/deploy-pages@v2
+      - name: Deploy to GiHub Pages
+        uses: actions/deploy-pages@v4

.github/workflows/test.yaml

@@ -20,7 +20,7 @@ jobs:
       - name: Setup micromamba
         uses: mamba-org/setup-micromamba@v1
         with:
-          environment-file: environment_cpu.yaml
+          environment-file: environment.yaml
           create-args: >-
             python=${{ matrix.python-version }}
 

environment.yaml

@@ -0,0 +1,16 @@
+channels:
+    - conda-forge
+name:
+    torch-em-dev
+dependencies:
+    - affogato
+    - bioimageio.spec
+    - bioimageio.core
+    - imagecodecs
+    - python-elf
+    - pytorch
+    - tensorboard
+    - tifffile
+    - torchvision
+    - tqdm
+    - kornia

environment_cpu.yaml → environment_cpu_win.yaml

@@ -9,6 +9,9 @@ dependencies:
     - bioimageio.core >=0.6.0
     - cpuonly
     - imagecodecs
+    # This pin is necessary because later nifty versions have import errors on windows.
+    - nifty =1.2.1=*_4
+    - protobuf <5
     - python-elf
     - pytorch >=2.0
     - tensorboard

environment_gpu.yaml → environment_gpu_win.yaml

@@ -9,6 +9,9 @@ dependencies:
     - bioimageio.spec >=0.5.0
     - bioimageio.core >=0.6.0
     - imagecodecs
+    # This pin is necessary because later nifty versions have import errors on windows.
+    - nifty =1.2.1=*_4
+    - protobuf <5
     - python-elf
     - pytorch >=2.0
     - pytorch-cuda>=11.7  # you may need to update the pytorch version to match your system