Merge pull request #88 from computational-cell-analytics/pdoc

Add workflow for deploying the docs

Author: constantinpape

.github/workflows/build_docs.yaml

@@ -0,0 +1,63 @@
+name: build_documentation
+
+# build the documentation whenever there are new commits on main
+on:
+  push:
+    branches:
+      - main
+    # TODO only build on releases once this works
+    # Alternative: only build for tags.
+    # tags:
+    #   - '*'
+
+# security: restrict permissions for CI jobs.
+permissions:
+  contents: read
+
+jobs:
+  # Build the documentation and upload the static HTML files as an artifact.
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+
+      - name: Setup miniconda
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: sam
+          mamba-version: "*"
+          auto-update-conda: true
+          environment-file: .github/workflows/doc_env.yaml
+          python-version: ${{ matrix.python-version }}
+          auto-activate-base: false
+        env:
+          ACTIONS_ALLOW_UNSECURE_COMMANDS: true
+
+      - name: Install package
+        shell: bash -l {0}
+        run: pip install --no-deps -e .
+
+      # 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: pdoc --docformat google --logo "https://raw.githubusercontent.com/computational-cell-analytics/micro-sam/master/doc/images/micro-sam-logo.png" -o docs/ micro_sam
+
+      - uses: actions/upload-pages-artifact@v1
+        with:
+          path: docs/
+
+  # Deploy the artifact to GitHub pages.
+  # This is a separate job so that only actions/deploy-pages has the necessary permissions.
+  deploy:
+    needs: build
+    runs-on: ubuntu-latest
+    permissions:
+      pages: write
+      id-token: write
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    steps:
+      - id: deployment
+        uses: actions/deploy-pages@v2

.github/workflows/doc_env.yaml

@@ -0,0 +1,16 @@
+channels:
+    - pytorch
+    - conda-forge
+name:
+    sam
+dependencies:
+    - cpuonly
+    - pdoc
+    - pooch
+    - python-elf
+    - pytorch
+    - torchvision
+    - tqdm
+    - zarr
+    - pip:
+        - git+https://github.com/facebookresearch/segment-anything.git

micro_sam/__init__.py

@@ -3,3 +3,12 @@
 .. include:: ../doc/annotation_tools.md
 .. include:: ../doc/installaiton.md
 """
+
+__all__ = [
+    "instance_segmentation",
+    "prompt_based_segmentation",
+    "prompt_generators",
+    "sample_data",
+    "util",
+    "visualization",
+]