Merge pull request #24 from turbomam/23-make-a-cumulative-branch

make a cumulative branch for repo cleanup and build process streamlining

Author: turbomam

.github/workflows/deploy-docs.yaml

@@ -1,43 +1,49 @@
----
-name: Auto-deployment of mixs Documentation
+name: Deploy documentation to GitHub Pages
+
 on:
   push:
     branches: [main]
+  workflow_dispatch:
+
+permissions:
+  contents: write
+  pages: write
+  id-token: write
+
+concurrency: deploy-${{ github.ref }}
 
 jobs:
-  build-docs:
+  deploy:
     runs-on: ubuntu-latest
+
     steps:
       - name: Checkout
         uses: actions/checkout@v4
         with:
-          fetch-depth: 0  # otherwise, you will failed to push refs to dest repo
+          fetch-depth: 0
 
-      - name: Set up Python 3.
-        uses: actions/setup-python@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.9
-
-      - name: Install Poetry.
-        uses: snok/[email protected]
+          python-version: '3.10'
 
-      - name: Install dependencies.
-        run: poetry install -E docs
+      - name: Install Poetry
+        uses: snok/install-poetry@v1
 
-      - name: Setup Node.js
-        uses: actions/setup-node@v2
-        with:
-          node-version: '14' # Choose the desired Node.js version
-
-      - name: Add Node.js to the system path
-        run: |
-          echo 'export PATH=$HOME/.npm-global/bin:$PATH' >> $GITHUB_ENV
+      - name: Install dependencies
+        run: make install
 
-      - name: Build documentation.
+      - name: Generate documentation
         run: |
+          make clean
           mkdir -p docs
           touch docs/.nojekyll
           make gendoc
-          ([ ! -f docs/about.md ] && cp src/docs/about.md docs/) || true
-          poetry run mkdocs build --clean
-          make mkd-gh-deploy
+          poetry run mkdocs build -d site
+
+      - name: Deploy to GitHub Pages
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./site
+          publish_branch: gh-pages

.github/workflows/lint-linkml.yml renamed to .github/workflows/lint-linkml.yaml

@@ -15,27 +15,25 @@ jobs:
     name: LinkML Linting
     runs-on: ubuntu-latest
     steps:
-      - name: Check out repository
+      - name: Checkout
         uses: actions/checkout@v4
 
       # Fixed: Specify exact Python version instead of using undefined matrix variable
-      - name: Set up Python 3.11
+      - name: Set up Python 3.10
         uses: actions/setup-python@v5
         with:
-          python-version: '3.11'
-          # Removed cache here since Poetry isn't installed yet
+          python-version: '3.10'
 
-      # Install Poetry first before trying to use it
       - name: Install Poetry
-        run: pipx install poetry
+        uses: snok/install-poetry@v1
 
       # Now we can configure Poetry cache
       - name: Configure Poetry cache
         run: poetry config cache-dir ~/.cache/poetry
 
-      # Install dependencies with Poetry
+      # Install dependencies using Makefile
       - name: Install dependencies
-        run: poetry install --no-interaction --no-root
+        run: make install
 
       # Run the LinkML linting command
       - name: Run LinkML Linting

.github/workflows/lint-yaml.yaml

@@ -2,7 +2,8 @@
 name: Yamllint GitHub Action
 
 on:
-- pull_request
+  pull_request:
+  workflow_dispatch:
 
 jobs:
   yamllint:

.github/workflows/main.yaml

@@ -4,34 +4,30 @@
 ---
 name: Build and test mixs
 
-on: [pull_request]
+on: 
+  pull_request:
+  workflow_dispatch:
 
 jobs:
   test:
 
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.9", "3.10"]
+        python-version: ["3.10"]
 
     steps:
 
-      - name: Check out repository
+      - name: Checkout
         uses: actions/checkout@v4
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
       - name: Install Poetry
-        uses: snok/install-poetry@v1.3
+        uses: snok/install-poetry@v1
 
-      - name: Install dependencies
-        run: poetry install --no-interaction --no-root
-
-      - name: Install project
-        run: poetry install --no-interaction
-
-      - name: Run test suite
-        run: make test
+      - name: Run release SOP
+        run: make install clean all all-contrib test

.github/workflows/pypi-publish.yaml

@@ -4,6 +4,7 @@ name: Publish Python Package
 on:
   release:
     types: [created]
+  workflow_dispatch:
 
 jobs:
   build-n-publish:
@@ -14,18 +15,18 @@ jobs:
       - uses: actions/checkout@v4
 
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.9
+          python-version: '3.10'
 
       - name: Install Poetry
-        run: |
-          pip install poetry
-          poetry self add "poetry-dynamic-versioning[plugin]"
-        # uses: snok/[email protected]
-        # with:
-        #   virtualenvs-create: true
-        #   virtualenvs-in-project: true
+        uses: snok/install-poetry@v1
+        with:
+          virtualenvs-create: true
+          virtualenvs-in-project: true
+      
+      - name: Add poetry-dynamic-versioning plugin
+        run: poetry self add "poetry-dynamic-versioning[plugin]"
 
       # - name: Install dependencies
       #   run: poetry install --no-interaction

.github/workflows/test_pages_build.yaml

@@ -6,31 +6,36 @@ on:
       - opened
       - reopened
       - synchronize
+  workflow_dispatch:
 
 concurrency: preview-${{ github.ref }}
 
 jobs:
   run:
     runs-on: ubuntu-latest
+    permissions:
+      contents: write
+      pull-requests: write
     steps:
       - name: Checkout
         uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
-      - name: Install Poetry
-        run: pipx install poetry
-
       - name: Set up Python 3
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.9
+          python-version: '3.10'
+
+      - name: Install Poetry
+        uses: snok/install-poetry@v1
 
       - name: Install dependencies
-        run: poetry install
+        run: make install
 
       - name: Generate web-based documentation
         run: |
+          make clean
           mkdir -p docs
           touch docs/.nojekyll
           make gendoc

.gitignore

@@ -135,10 +135,20 @@ dmypy.json
 # Pyre type checker
 .pyre/
 
-# Excel files dumped in project/excel
+# Project-specific generated files
+/docs/
+/project/docs/
+/tmp/
 project/excel
+/site
+linting-results*
 
-.DS_Store
+# Local development files
+/local/*
+!/local/.gitkeep
 
+# IDE files
 .vscode/
-linting-results*
+
+# OS files
+.DS_Store

.linkmllint.yaml

@@ -4,7 +4,22 @@ rules:
     level: error
     exclude_type:
       - enum_definition
+    exclude:
+      - combination_classes
+      - sequencing
+      - environment
+      - nucleic acid sequence source
+      - investigation
   standard_naming:
     level: error
     exclude_type:
       - permissible_value
+    exclude:
+      - HACCP_term
+      - IFSAC_category
+      - air_PM_concen
+      - ferm_pH
+      - microb_start_taxID
+      - soil_pH
+      - spikein_AMR
+      - water_pH