add docs and release to github actions

.github/workflows/release.yml

@@ -0,0 +1,77 @@
+name: release
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.9"]
+
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: "pip"
+          cache-dependency-path: '**/setup.py'
+
+      - name: Build package
+        run: |
+          python${{ matrix.python-version }} -m pip install --upgrade pip pip-tools build setuptools setuptools_scm wheel
+          python${{ matrix.python-version }} -m build
+
+      - name: Publish package
+        uses: pypa/gh-action-pypi-publish@release/v1.5
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_TOKEN }}
+
+  docs:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.9"]
+    needs:
+      - deploy
+
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: "pip"
+          cache-dependency-path: '**/setup.py'
+
+      - name: Install dependencies
+        run: |
+          python${{ matrix.python-version }} -m pip install --upgrade pip pip-tools setuptools_scm
+          python${{ matrix.python-version }} -m piptools sync --user requirements/ubuntu-latest_py${{ matrix.python-version }}_extras.txt
+          # Using non-editable install for testing building of MANIFEST files
+          python${{ matrix.python-version }} -m pip install --no-deps .
+
+      - name: Build
+        run: |
+          cd docs_rst
+          python${{ matrix.python-version }} featurizer_summary.py > featurizer_summary.rst
+          python${{ matrix.python-version }} dataset_summary.py > dataset_summary.rst
+          sphinx-apidoc -o . -f ../matminer
+          make html
+          cp _static/* ../docs/html/_static
+          cd ../docs
+          cp -r html/* .
+          rm -r html
+          rm -r doctrees
+          touch .nojekyll
+          git add .
+          git commit -a -m "update docs"
+          git push

.github/workflows/test.yml

@@ -3,13 +3,27 @@
 # The ext package is also only tested in this workflow. Coverage is also computed based on this platform.
 name: Testing
 
-on: [ push, pull_request ]
+on:
+  push:
+    branches:
+      - main
+
+  pull_request:
+    branches:
+      - main
+
+  workflow_dispatch:
+    inputs:
+      fullTest:
+        description: "run full test"
+        required: true
+        default: false
+        type: boolean
 
 jobs:
 
   test:
     strategy:
-      max-parallel: 4
       matrix:
         python-version: ["3.8", "3.9"]
         mongodb-version: ['4.0']
@@ -20,9 +34,9 @@ jobs:
       PMG_MAPI_KEY: ${{ secrets.PMG_MAPI_KEY }}
       MPDS_KEY: ${{ secrets.MPDS_KEY }}
       CITRINATION_API_KEY: ${{ secrets.CITRINATION_API_KEY }}
-      MATMINER_DATASET_FULL_TEST: False
       RUNNING_ON_GHACTIONS: "True"
       MPLBACKEND: "Agg"
+      MATMINER_DATASET_FULL_TEST: ${{ inputs.fullTest }}
 
     steps:
     - uses: actions/checkout@v3
@@ -33,23 +47,59 @@ jobs:
         cache: "pip"
         cache-dependency-path: '**/setup.py'
 
-    - name: Start MongoDB
-      uses: supercharge/mongodb-github-action@1.6.0
-      with:
-        mongodb-version: ${{ matrix.mongodb-version }}
-
     - name: Install Python dependencies
       run: |
-        python${{ matrix.python-version }} -m pip install --upgrade pip pip-tools
+        python${{ matrix.python-version }} -m pip install --upgrade pip pip-tools build setuptools setuptools_scm wheel
         python${{ matrix.python-version }} -m piptools sync --user requirements/ubuntu-latest_py${{ matrix.python-version }}_extras.txt
         # Using non-editable install for testing building of MANIFEST files
         python${{ matrix.python-version }} -m pip install --no-deps .
 
+    - name: linting
+      run: |
+        black --version
+        black --check --diff --color matminer
+        flake8 --version
+        flake8 --count --show-source --statistics matminer
+        # exit-zero treats all errors as warnings.
+        flake8 --count --exit-zero --max-complexity=20 --statistics matminer
+        # mypy --version
+        # rm -rf .mypy_cache
+        # mypy matminer
+        # pydocstyle --count matminer
+        # pylint matminer
+
+    - name: Start MongoDB
+      uses: supercharge/mongodb-github-action@1.6.0
+      with:
+        mongodb-version: ${{ matrix.mongodb-version }}
+
     - name: Run tests
       run: |
         # Sleeping to allow mongo a bit more time to boot, avoiding connect errors
         sleep 10
-        echo "start mongo ..."
         mongo localhost/admin --eval 'db.createUser({user: "admin",pwd: "password",roles: [ { role: "root", db: "admin" } ]})'
-        echo "run tests ..."
         python${{ matrix.python-version }} -m pytest --cov=matminer matminer
+
+    - name: Build package
+      if: matrix.python-version == "3.9"
+      run: python${{ matrix.python-version }} -m build
+
+    - name: Publish distribution 📦s to Test PyPI
+      if: matrix.python-version == "3.9"
+      uses: pypa/gh-action-pypi-publish@release/v1.5
+      with:
+        skip_existing: true
+        repository_url: https://test.pypi.org/legacy/
+        user: __token__
+        password: ${{ secrets.TEST_PYPI_TOKEN }}
+
+  auto-gen-release:
+    needs:
+      - test
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_TOKEN: ${{ secrets.PAT }}
+    steps:
+      - uses: rymndhng/release-on-push-action@v0.25.0
+        with:
+          bump_version_scheme: norelease