Merge branch 'master' into workflow

.github/workflows/publish.yaml

@@ -0,0 +1,72 @@
+name: Publish on PyPI
+
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+
+jobs:
+  fix_release_deps:
+    permissions: write-all
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - uses: actions/setup-python@v4
+      with:
+        python-version: '3.12'
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip pip-tools setuptools
+
+    - name: Set configuration
+      run: |
+        git config --global user.name "${GITHUB_ACTOR}"
+        git config --global user.email "${GITHUB_ACTOR_ID}+${GITHUB_ACTOR}@users.noreply.github.com"
+
+    - name: Create requirements files
+      run: |
+        python tools/generate_requirements_txt.py
+        pip-compile -o requirements_full.txt pyproject.toml
+        git add requirements_full.txt requirements.txt
+        git commit -m "Updated requirements.txt files" || true
+
+    - name: Bump version to new tag
+      run: |
+        python -m pip install bump-my-version
+        bump-my-version bump --new-version $GITHUB_REF_NAME patch
+        git commit -am "Bump version to: $GITHUB_REF_NAME"
+
+    - name: Push back changes to main and tag
+      run: |
+        git tag --force $GITHUB_REF_NAME HEAD
+        git push --force --tags
+        git switch -C main
+        git push --set-upstream -f origin main
+
+  deploy:
+    needs: fix_release_deps
+    runs-on: ubuntu-latest
+    environment: release
+    permissions:
+      # IMPORTANT: this permission is mandatory for trusted publishing
+      id-token: write
+
+    steps:
+    - uses: actions/checkout@v3
+      with:
+        ref: ${{ github.ref_name }}
+
+    - uses: actions/setup-python@v4
+      with:
+        python-version: '3.12'
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install build setuptools>=61.2 wheel
+        python -m build --no-isolation
+
+    - name: Publish package
+      uses: pypa/gh-action-pypi-publish@release/v1

pyproject.toml

@@ -42,9 +42,28 @@ dependencies = [
 [project.urls]
 homepage = "https://github.com/FormingWorlds/JANUS"
 
+[project.optional-dependencies]
+develop = [
+  "bump-my-version",
+  "pytest"
+]
+publishing = [
+  "twine",
+  "wheel",
+  "build"
+]
+
 [tool.setuptools]
 package-dir = {"janus" = "src/janus"}
 include-package-data = true
 
 [tool.pytest.ini_options]
 testpaths = ["tests"]
+
+[tool.bumpversion]
+current_version = "24.04.04"
+
+[[tool.bumpversion.files]]
+filename = "pyproject.toml"
+search = "version = \"{current_version}\""
+replace = "version = \"{new_version}\""

tools/generate_requirements_txt.py

@@ -0,0 +1,19 @@
+from __future__ import annotations
+
+from pathlib import Path
+
+import tomllib
+
+this_script = Path(__file__)
+root = this_script.parents[1]
+pyproject = root / 'pyproject.toml'
+
+with open(pyproject, 'rb') as f:
+    metadata = tomllib.load(f)
+    dependencies = metadata['project']['dependencies']
+
+with open('requirements.txt', 'w') as f:
+    this_script_rel = this_script.relative_to(root)
+    f.write(f'# generated by {this_script_rel}\n')
+    f.write('\n'.join(dependencies))
+    f.write('\n')