Merge pull request #37 from DasLab/feat/github-actions-packaging

Add release workflow for publishing to PyPI via Github Actions

.github/workflows/release.yml

@@ -0,0 +1,118 @@
+name: Publish Python package to PyPI and TestPyPI
+
+on: push
+
+jobs:
+  build:
+    name: Build distribution package
+    runs-on: "ubuntu-latest"
+
+    steps:
+    - name: Checkout source
+      uses: actions/checkout@v4
+
+    - name: Set up Python 3.7
+      uses: actions/setup-python@v4
+      with:
+        python-version: "3.7"
+
+    - 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@v3
+      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/arnie
+    permissions:
+      id-token: write  # IMPORTANT: mandatory for trusted publishing
+
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v3
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Publish distribution to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+
+  publish-to-testpypi:
+    name: Publish Python distribution to TestPyPI
+    needs:
+    - build
+    runs-on: ubuntu-latest
+
+    environment:
+      name: testpypi
+      url: https://test.pypi.org/p/arnie
+
+    permissions:
+      id-token: write  # IMPORTANT: mandatory for trusted publishing
+
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v3
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Publish distribution to TestPyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        repository-url: https://test.pypi.org/legacy/
+
+  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@v3
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Sign the dists with Sigstore
+      uses: sigstore/gh-action-sigstore-python@v1.2.3
+      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 }}'

README.md

@@ -35,6 +35,11 @@ Hannah Wayment-Steele
 
 `RNAGraph`: DEPRECATED, see https://github.com/DasLab/RiboGraphViz/ for current version of the code. Code to process and visualize secondary structures as graph objects.
 
+## Install:
+`arnie` is [available on PyPI](https://pypi.org/projectarnie/).
+
+`pip install arnie`
+
 ## Setup:
 
 1. To use Arnie, you will create a file that contains the paths to the software packages that Arnie is wrapping. See [`docs/setup_doc.md`](docs/setup_doc.md) for installation instructions and troubleshooting tips, as well as instructions for setting up the arnie file.

pyproject.toml

@@ -1,7 +1,7 @@
 
 [project]
 name = "arnie"
-version = "0.1.5"
+version = "0.1.6"
 authors = [
   { name="Das Lab", email="thedaslab@stanford.edu" },
 ]