diff --git a/.github/workflows/python-build.yaml b/.github/workflows/python-build.yaml new file mode 100644 index 0000000..19c21e5 --- /dev/null +++ b/.github/workflows/python-build.yaml @@ -0,0 +1,95 @@ +name: Publish Python 🐍 distribution 📦 to PyPI and TestPyPI + +on: push + +jobs: + build: + name: Build distribution 📦 + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v4 + - name: Set up Python + uses: actions/setup-python@v4 + with: + python-version: "3.12" + - name: Install pypa/build + run: >- + python3 -m + pip install + build + --user + - name: Build a binary wheel and a source tarball + run: python3 -m build + - name: Store the distribution packages + uses: actions/upload-artifact@v4 + with: + name: python-package-distributions + path: dist/ + + publish-to-pypi: + name: >- + Publish Python 🐍 distribution 📦 to PyPI + if: startsWith(github.ref, 'refs/tags/') # only publish to PyPI on tag pushes + needs: + - build + runs-on: ubuntu-latest + environment: + name: pypi + url: https://pypi.org/p/MEDS-transforms # Replace with your PyPI project name + permissions: + id-token: write # IMPORTANT: mandatory for trusted publishing + + steps: + - name: Download all the dists + uses: actions/download-artifact@v4 + with: + name: python-package-distributions + path: dist/ + + - name: Publish distribution 📦 to PyPI + uses: pypa/gh-action-pypi-publish@release/v1 + + github-release: + name: >- + Sign the Python 🐍 distribution 📦 with Sigstore + and upload them to GitHub Release + needs: + - publish-to-pypi + runs-on: ubuntu-latest + + permissions: + contents: write # IMPORTANT: mandatory for making GitHub Releases + id-token: write # IMPORTANT: mandatory for sigstore + + steps: + - name: Download all the dists + uses: actions/download-artifact@v4 + with: + name: python-package-distributions + path: dist/ + + - name: Sign the dists with Sigstore + uses: sigstore/gh-action-sigstore-python@v2.1.1 + with: + inputs: >- + ./dist/*.tar.gz + ./dist/*.whl + - name: Create GitHub Release + env: + GITHUB_TOKEN: ${{ github.token }} + run: >- + gh release create + '${{ github.ref_name }}' + --repo '${{ github.repository }}' + --notes "" + - name: Upload artifact signatures to GitHub Release + env: + GITHUB_TOKEN: ${{ github.token }} + # Upload to GitHub Release using the `gh` CLI. + # `dist/` contains the built packages, and the + # sigstore-produced signatures and certificates. + run: >- + gh release upload + '${{ github.ref_name }}' dist/** + --repo '${{ github.repository }}' diff --git a/.github/workflows/tests.yaml b/.github/workflows/tests.yaml index 908adc5..34443b6 100644 --- a/.github/workflows/tests.yaml +++ b/.github/workflows/tests.yaml @@ -33,9 +33,14 @@ jobs: #---------------------------------------------- - name: Run tests run: | - pytest -v --doctest-modules --cov=src -s + pytest -v --doctest-modules --cov=src --junitxml=junit.xml -s - name: Upload coverage to Codecov uses: codecov/codecov-action@v4.0.1 with: token: ${{ secrets.CODECOV_TOKEN }} + - name: Upload test results to Codecov + if: ${{ !cancelled() }} + uses: codecov/test-results-action@v1 + with: + token: ${{ secrets.CODECOV_TOKEN }} diff --git a/README.md b/README.md index 9838043..35cad6d 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,7 @@ # MEDS Transforms +[![codecov](https://codecov.io/gh/mmcdermott/MEDS_transforms/graph/badge.svg?token=5RORKQOZF9)](https://codecov.io/gh/mmcdermott/MEDS_transforms) + This repository contains a set of functions and scripts for extraction to and transformation/pre-processing of MEDS-formatted data.