Merge pull request #24 from quantifyearth/mwd-publish-script

Add github action to publush to pypi

Author: mdales

.github/workflows/pull-request.yml

@@ -0,0 +1,72 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: Python Pull Request CI
+
+on:
+  push:
+    branches: ["main"]
+  pull_request:
+    branches: ["main"]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    container: ghcr.io/osgeo/gdal:ubuntu-small-3.11.0
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10"]
+
+    steps:
+      - uses: actions/checkout@v5
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install system dependencies
+        run: |
+          apt-get update -qqy
+          apt-get install -y git python3-pip r-base libtirpc-dev
+
+      - name: Install R dependencies
+        run: R -e "install.packages(c('lme4', 'lmerTest'), repos='https://cran.rstudio.com/')" || true
+
+      - name: Install Python dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install 'gdal[numpy]==3.11.0'
+          python -m pip install -e .[dev,validation]
+
+      - name: Lint with pylint
+        run: python3 -m pylint .
+
+      - name: Type checking
+        run: python3 -m mypy .
+
+      - name: Test with pytest
+        run: python3 -m pytest --cov=aoh -vv
+
+      - name: Test CLI tools
+        run: |
+          aoh-calc --help
+          aoh-habitat-process --help
+          aoh-species-richness --help
+          aoh-endemism --help
+          aoh-collate-data --help
+          aoh-validate-prevalence --help
+
+      - name: Test package imports
+        run: |
+          python3 -c "import aoh; print('✅ Package imports work')"
+          python3 -c "from aoh import tidy_data; print('✅ Core functions work')"
+          python3 -c "from aoh.summaries import species_richness; print('✅ Summaries work')"
+          python3 -c "from aoh.validation import collate_data; print('✅ Validation works')"
+
+      - name: Build pip package
+        run: python3 -m build
+
+      - name: Check with twine
+        run: twine check dist/*

.github/workflows/python-package.yml

@@ -1,13 +1,14 @@
 # This workflow will install Python dependencies, run tests and lint with a variety of Python versions
 # For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
 
-name: Python CI
+name: Python Publish CI
 
 on:
-  push:
-    branches: ["main"]
-  pull_request:
-    branches: ["main"]
+  release:
+    types: [published]
+
+permissions:
+  contents: read
 
 jobs:
   build:
@@ -68,5 +69,8 @@ jobs:
       - name: Build pip package
         run: python3 -m build
 
-      - name: Check with twine
-        run: twine check dist/*
+      - name: Publish with twine
+        env:
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.TWINE_API_TOKEN }}
+        run: twine upload dist/*