github actions added

.github/workflows/build_main.yaml

@@ -0,0 +1,54 @@
+name: Build schemas
+
+# when main changed rebuild the products (schemas and documentations) and updates the build folder
+on:
+  push:
+    branches: [ main ]
+
+permissions: write-all
+
+jobs:
+  build-and-publish:
+    name: Build main branch
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [ '3.9' ]
+    steps:
+
+      - uses: actions/checkout@v3
+        with:
+          persist-credentials: false # otherwise, the token used is the GITHUB_TOKEN, instead of your personal access token.
+          fetch-depth: 0 # otherwise, there would be errors pushing refs to the destination repository.
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install Poetry
+        run: |
+          curl -sSL https://install.python-poetry.org | python3 -
+
+      - name: Install dependencies
+        run: |
+          poetry install
+
+      - name: Generate merged schemas
+        run: |
+          cp src/cell_annotation_schema/schema/cell_annotation_schema.yaml build/general_schema.yaml
+          gen-linkml src/cell_annotation_schema/schema/BICAN/BICAN_schema.yaml --output build/BICAN_schema.yaml --mergeimports --format yaml --no-materialize-attributes
+          gen-linkml src/cell_annotation_schema/schema/CAP/CAP_schema.yaml --output build/CAP_schema.yaml --mergeimports --format yaml --no-materialize-attributes
+
+
+      - name: Commit files
+        run: |
+          git config --local user.email "github-actions[bot]@users.noreply.github.com"
+          git config --local user.name "github-actions[bot]"
+          git diff --quiet && git diff --staged --quiet || git commit -a -m "Main branch build"
+
+      - name: Push changes
+        uses: ad-m/github-push-action@master
+        with:
+          github_token: ${{ secrets.P_TOKEN }}
+          branch: ${{ github.head_ref }}

.github/workflows/nightly_snapshot.yaml

@@ -0,0 +1,56 @@
+name: Nightly Snapshot
+
+on:
+  schedule:
+  - cron: "59 23 * * *"
+  workflow_dispatch:
+
+permissions:
+  contents: write
+
+jobs:
+  tag:
+    name: Make snapshot release
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [ '3.9' ]
+    steps:
+      - name: Get current date
+        id: date
+        run: echo "date=$(date +'%Y-%m-%d')" >> $GITHUB_OUTPUT
+
+      - name: Checkout Repository
+        uses: actions/checkout@v3
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install Poetry
+        run: |
+          curl -sSL https://install.python-poetry.org | python3 -
+
+      - name: Install dependencies
+        run: |
+          poetry install
+
+      - name: Generate merged schemas
+        run: |
+          cp src/cell_annotation_schema/schema/cell_annotation_schema.yaml build/general_schema.yaml
+          gen-linkml src/cell_annotation_schema/schema/BICAN/BICAN_schema.yaml --output build/BICAN_schema.yaml --mergeimports --format yaml --no-materialize-attributes
+          gen-linkml src/cell_annotation_schema/schema/CAP/CAP_schema.yaml --output build/CAP_schema.yaml --mergeimports --format yaml --no-materialize-attributes
+
+      - name: Make Snapshot
+        uses: ncipollo/release-action@v1
+        with:
+          artifacts: "build/general_schema.yaml,
+          build/BICAN_schema.yaml,build/CAP_schema.yaml"
+          body: "Nightly snapshot release. Draft only, please use a stable release instead."
+          allowUpdates: true
+          draft: true
+          makeLatest: false
+          name: "${{ steps.date.outputs.date }} SNAPSHOT"
+          removeArtifacts: true
+          tag: "snapshot"

.github/workflows/pypi-publish.yaml

@@ -23,14 +23,31 @@ jobs:
           pipx install poetry
           poetry self add "poetry-dynamic-versioning[plugin]"
 
-      # - name: Install dependencies
-      #   run: poetry install --no-interaction
+      - name: Install dependencies
+        run: poetry install --no-interaction
+
+      - name: Generate merged schemas
+        run: |
+          cp src/cell_annotation_schema/schema/cell_annotation_schema.yaml build/general_schema.yaml
+          gen-linkml src/cell_annotation_schema/schema/BICAN/BICAN_schema.yaml --output build/BICAN_schema.yaml --mergeimports --format yaml --no-materialize-attributes
+          gen-linkml src/cell_annotation_schema/schema/CAP/CAP_schema.yaml --output build/CAP_schema.yaml --mergeimports --format yaml --no-materialize-attributes
+
+      - name: Package release assets
+        run: |
+          mkdir -p src/cell_annotation_schema/schemas
+          touch src/cas_schema/schemas/__init__.py
+          cp build/general_schema.yaml src/cell_annotation_schema/schemas
+          cp build/BICAN_schema.yaml src/cell_annotation_schema/schemas
+          cp build/CAP_schema.yaml src/cell_annotation_schema/schemas
+
+      - name: Update package version
+        run: |
+          sed -i 's/__version__/${{  github.ref_name }}/g' pyproject.toml
 
       - name: Build source and wheel archives
         run: poetry build
 
-      - name: Publish distribution 📦 to PyPI
-        uses: pypa/gh-action-pypi-publish@v1.2.2
+      - name: Publish Package
+        uses: pypa/gh-action-pypi-publish@release/v1
         with:
-          user: __token__
-          password: ${{ secrets.PYPI_PASSWORD }}
+          password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/pypi-test-publish.yaml

@@ -0,0 +1,54 @@
+---
+name: Publish Python Package
+
+on:
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+jobs:
+  build-n-publish:
+    name: Build and publish Python 🐍 distributions 📦 to PyPI
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.9
+
+      - name: Install Poetry
+        run: |
+          pipx install poetry
+          poetry self add "poetry-dynamic-versioning[plugin]"
+
+      - name: Install dependencies
+        run: poetry install --no-interaction
+
+      - name: Generate merged schemas
+        run: |
+          cp src/cell_annotation_schema/schema/cell_annotation_schema.yaml build/general_schema.yaml
+          gen-linkml src/cell_annotation_schema/schema/BICAN/BICAN_schema.yaml --output build/BICAN_schema.yaml --mergeimports --format yaml --no-materialize-attributes
+          gen-linkml src/cell_annotation_schema/schema/CAP/CAP_schema.yaml --output build/CAP_schema.yaml --mergeimports --format yaml --no-materialize-attributes
+
+      - name: Package release assets
+        run: |
+          mkdir -p src/cell_annotation_schema/schemas
+          touch src/cas_schema/schemas/__init__.py
+          cp build/general_schema.yaml src/cell_annotation_schema/schemas
+          cp build/BICAN_schema.yaml src/cell_annotation_schema/schemas
+          cp build/CAP_schema.yaml src/cell_annotation_schema/schemas
+
+      - name: Update package version
+        run: |
+          sed -i 's/__version__/${{  github.ref_name }}/g' pyproject.toml
+
+      - name: Build source and wheel archives
+        run: poetry build
+
+      - name: Publish Package
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/
+          password: ${{ secrets.TEST_PYPI_API_TOKEN }}

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "cell_annotation_schema"
-version = "1.1.0"
+version = "__version__"
 description = "General, open-standard schema for cell annotations"
 authors = ["Huseyin Kir <[email protected]>"]
 license = "GNU GPL v3.0"