Merge optics into main

.github/workflows/release.yml

@@ -0,0 +1,58 @@
+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: ${{ matrix.python-version }}
+          cache: "pip"
+          cache-dependency-path: '**/setup.py'
+
+      - name: Install dependencies
+        run: |
+          python${{ 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${{ matrix.python-version }} -m pip install --no-deps .
+
+      - name: Build package and docs
+        run: |
+          git config --local user.email "feedback@materialsproject.org"
+          git config --local user.name "materialsproject"
+          git fetch --all --prune
+          git checkout main
+          python${{ matrix.python-version }} -m build
+          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
+
+      - name: Publish package
+        uses: pypa/gh-action-pypi-publish@release/v1.5
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_TOKEN }}

.github/workflows/test.yml

@@ -3,15 +3,33 @@
 # 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
+    paths:
+      - matminer/**
+
+  pull_request:
+    branches:
+      - main
+    paths:
+      - matminer/**
+
+  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]
+        python-version: ["3.8", "3.9"]
         mongodb-version: ['4.0']
 
     runs-on: ubuntu-latest
@@ -20,16 +38,41 @@ 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@v2
+    - uses: actions/checkout@v3
+      with:
+        fetch-depth: 0
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
+        cache: "pip"
+        cache-dependency-path: '**/setup.py'
+
+    - name: Install Python dependencies
+      run: |
+        python${{ matrix.python-version }} -m pip install --upgrade pip pip-tools setuptools 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: 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
@@ -41,10 +84,30 @@ jobs:
         # Sleeping to allow mongo a bit more time to boot, avoiding connect errors
         sleep 10
         mongo localhost/admin --eval 'db.createUser({user: "admin",pwd: "password",roles: [ { role: "root", db: "admin" } ]})'
-        python3 -m venv test_env
-        . test_env/bin/activate
-        python -m pip install --upgrade pip
-        pip install -r requirements.txt -r requirements-dev.txt -r requirements-optional.txt
-        # Using non-editable install for testing building of MANIFEST files
-        pip install .
-        pytest --cov=matminer matminer
+        python${{ matrix.python-version }} -m pytest --cov=matminer matminer
+
+    - name: Build package
+      if: matrix.python-version == 3.9
+      run: |
+        python${{ matrix.python-version }} -m pip install --upgrade pip build setuptools setuptools_scm wheel
+        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