add github actions

.github/workflows/main.yml

@@ -0,0 +1,164 @@
+name: main
+on:
+  workflow_dispatch:
+  pull_request:
+  push:
+    branches:
+      - master
+    paths-ignore:
+      - ".github/**"
+      - "!.github/workflows/main.yml"
+      - "docs/**"
+      - "*.md"
+      - ".git*"
+
+jobs:
+  clean:
+    runs-on: ubuntu-latest
+    container:
+      image: condaforge/mambaforge
+      volumes:
+        - ${{ github.workspace }}:/github/workspace
+    steps:
+      - name: Checkout
+        uses: actions/checkout@master
+      - name: Install dependencies
+        run: mamba install -c fastai -c conda-forge nbdev nbstripout
+      - name: Clean notebooks
+        run: nbdev_clean_nbs
+      - name: Strip notebook outputs
+        run: find . -name "*.ipynb" | xargs nbstripout
+      - name: Check if git status is clean
+        run: |
+          if [ ! -z "$(git status --porcelain)" ]; then
+              echo "Notebooks are not cleaned! They still contain outputs and/or metadata."
+              echo "You probably forgot to clear the notebook outputs before pushing."
+              echo "Please make sure all pre-commit hooks are properly installed to prevent this issue."
+              false;
+          fi
+
+  diff:
+    runs-on: ubuntu-latest
+    container:
+      image: condaforge/mambaforge
+      volumes:
+        - ${{ github.workspace }}:/github/workspace
+    steps:
+      - name: Checkout
+        uses: actions/checkout@master
+      - name: Install dependencies
+        run: mamba install -c fastai -c conda-forge nbdev
+      - name: Check for no diff between notebooks and library
+        run: |
+          if [ ! -z "$(nbdev_diff_nbs)" ]; then
+              echo "Python library does not match backing notebooks (diff between notebooks and library detected). "
+              echo "You probably forgot to re-generate the library before pushing."
+              echo "Please make sure all pre-commit hooks are properly installed to prevent this issue."
+              false;
+          fi
+
+  test:
+    runs-on: ubuntu-latest
+#   needs:
+#     - docker
+    container:
+      image: flaport/sax
+      volumes:
+        - ${{ github.workspace }}:/github/workspace
+    steps:
+      - name: Checkout
+        uses: actions/checkout@master
+      - name: Test notebooks
+        run: nbdev_test_nbs | tee nbdev_test_nbs.log
+      - name: Expose 'nbdev_test_nbs.log' as artifact
+        uses: actions/upload-artifact@master
+        with:
+          name: nbdev_test_nbs.log
+          path: /github/workspace/nbdev_test_nbs.log
+
+  run:
+    runs-on: ubuntu-latest
+    needs:
+      - clean
+      - diff
+#     - docker
+    container:
+      image: flaport/sax
+      volumes:
+        - ${{ github.workspace }}:/github/workspace
+    steps:
+      - name: Checkout
+        uses: actions/checkout@master
+      - name: Run notebooks
+        run: find . -name "*.ipynb" | grep -v ipynb_checkpoints | xargs -I {} papermill -k python3 {} {}
+      - name: Expose 'nbs' as artifact
+        uses: actions/upload-artifact@master
+        with:
+          name: nbs
+          path: /github/workspace/nbs
+      - name: Expose 'examples' as artifact
+        uses: actions/upload-artifact@master
+        with:
+          name: examples
+          path: /github/workspace/examples
+      - name: Expose 'index.ipynb' as artifact
+        uses: actions/upload-artifact@master
+        with:
+          name: index.ipynb
+          path: /github/workspace/index.ipynb
+
+  docs:
+    runs-on: ubuntu-latest
+    needs:
+      - run
+    container:
+      image: flaport/sax
+      volumes:
+        - ${{ github.workspace }}:/github/workspace
+    steps:
+      - name: Checkout
+        uses: actions/checkout@master
+      - name: Download 'nbs' artifact
+        uses: actions/download-artifact@master
+        with:
+          name: nbs
+          path: ./nbs
+      - name: Download 'examples' artifact
+        uses: actions/download-artifact@master
+        with:
+          name: examples
+          path: ./examples
+      - name: Download 'index.ipynb' artifact
+        uses: actions/download-artifact@master
+        with:
+          name: index.ipynb
+          path: ./index.ipynb
+      - name: Build docs
+        run: nbdev_build_docs
+      - name: Store artifacts
+        uses: actions/upload-artifact@master
+        with:
+          name: docs
+          path: /github/workspace/docs
+
+  pages:
+    runs-on: ubuntu-latest
+    needs:
+      - docs
+    container:
+      image: flaport/sax
+      volumes:
+        - ${{ github.workspace }}:/github/workspace
+    steps:
+      - name: Checkout
+        uses: actions/checkout@master
+      - name: Download 'docs' artifact
+        uses: actions/download-artifact@master
+        with:
+          name: docs
+          path: /github/workspace/docs
+      - name: Deploy
+        uses: JamesIves/github-pages-deploy-action@4.1.7
+        with:
+          branch: pages
+          folder: docs

Dockerfile

@@ -1,8 +1,10 @@
 FROM condaforge/mambaforge:4.11.0-0
 
 COPY environment.yml /environment.yml
+RUN sed -i "s/^[ ]*-[ ]*sax=\+.*//g" environment.yml
 RUN mamba env update -n base -f /environment.yml
 RUN conda run -n base python -m ipykernel install --user --name base --display-name base
+RUN conda run -n base python -m ipykernel install --user --name sax --display-name sax
 RUN rm -rf /environment.yml
 
 COPY docs/nbdev_showdoc.patch /nbdev_showdoc.patch
@@ -12,6 +14,3 @@ RUN rm -rf /nbdev_showdoc.patch
 ADD . /sax
 RUN pip install /sax
 RUN rm -rf /sax
-
-RUN conda create -n sax --clone base
-RUN conda run -n sax python -m ipykernel install --user --name sax --display-name sax

environment.yml

@@ -29,11 +29,12 @@ dependencies:
   - pre-commit==2.17.0
   - pyright==0.0.13
   - pytables==3.7.0
+  - pytest==6.2.5
   - pyyaml==6.0
   - scipy==1.7.3
   - shapely==1.8.0
   - tqdm==4.62.3
-  - twine==0.0.0
+  - twine==3.7.1
   - pip:
     - flax==0.4.0
     - jax==0.2.27