feat: update gh actions workflows and add docs #11

.github/workflows/build-docs.yml

@@ -0,0 +1,40 @@
+name: docs
+
+on:
+  workflow_call:
+  workflow_dispatch:
+  pull_request:
+    branches: [ main ]
+    types: [labeled]
+
+permissions:
+  contents: write
+
+jobs:
+  build-docs:
+    runs-on: ubuntu-latest
+    if:  github.event.label.name == 'docthis'
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+      - uses: quarto-dev/quarto-actions/setup@v2
+        with:
+          version: "1.5.53"
+      - name: Install dependencies
+        run: |
+          python -m pip install .[dev]
+      - name: Build docs
+        run: |
+          make docs
+      - name: Commit rendered docs
+        uses: stefanzweifel/git-auto-commit-action@v5
+        with:
+          commit_message: "chore(docs): render docs"
+          commit_user_name: "github-actions[bot]"
+          commit_user_email: "github-actions[bot]@users.noreply.github.com"
+          commit_author: "github-actions[bot] <github-actions[bot]@users.noreply.github.com>"
+          file_pattern: "docs/ _inv/ _reference/ _freeze/"
+          push_options: "--force"
+

.github/workflows/draft.yml

@@ -0,0 +1,16 @@
+# Marks all newly opened pull requests as drafts
+name: Draft on Open
+on:
+  pull_request:
+    types: [ opened ]
+
+jobs:
+  mark-as-draft:
+    name: Mark as draft
+    if: github.event.pull_request.draft == false
+    runs-on: ubuntu-latest
+    steps:
+      - name: Mark as draft
+        uses: voiceflow/draft-pr@latest
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/publish.yml

@@ -0,0 +1,51 @@
+name: publish
+
+on:
+  workflow_call:
+  workflow_dispatch:
+
+
+jobs:
+  build:
+    name: Build distribution 📦
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.x"
+    - 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
+    needs:
+    - build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/kimmdy-reactions
+    permissions:
+      id-token: write
+    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/workflows/release.yml

@@ -1,21 +1,24 @@
 name: release-please
 on:
+  workflow_dispatch:
   push:
     branches: [ main ]
 
+permissions:
+  contents: write
+  pull-requests: write
+
 jobs:
   release:
     runs-on: ubuntu-latest
     outputs:
       created: ${{ steps.release.outputs.release_created }}
     steps:
-      - uses: google-github-actions/release-please-action@v3
+      - uses: googleapis/release-please-action@v4
         id: release
         with:
           release-type: python
-          package-name: kimmdy-reactions
-          changelog-notes-type: default
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: tag stable versions
         if: ${{ steps.release.outputs.release_created }}
         run: |
@@ -26,80 +29,10 @@ jobs:
           git push origin :stable || true
           git tag -a stable -m "Last Stable Release"
           git push origin stable
-
-  build:
+  publish:
     needs: release
     if: ${{ needs.release.outputs.created }}
-    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.x"
-    - 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
-    if: ${{ needs.release.outputs.created }}
-    needs:
-    - build
-    - release
-    runs-on: ubuntu-latest
-    environment:
-      name: pypi
-      url: https://pypi.org/p/kimmdy-reactions
-    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
-    if: ${{ needs.release.outputs.created }}
-    needs:
-    - build
-    - release
-    runs-on: ubuntu-latest
-
-    environment:
-      name: testpypi
-      url: https://test.pypi.org/p/kimmdy-reactions
-
     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/
+      id-token: write
+    uses: ./.github/workflows/publish.yml
 

.github/workflows/test-local.yml

@@ -5,7 +5,7 @@ on:
 jobs:
   test-local:
     runs-on: ubuntu-latest
-    container: riedmiki/gromacs-plumed-python:2021
+    container: riedmiki/gromacs-plumed-python:2023.5-plumed
     steps:
       - uses: actions/checkout@v3
       - name: run tox
@@ -19,4 +19,3 @@ jobs:
           name: coverage artifact
           path: htmlcov.zip
 
-

.github/workflows/test-pr.yml → .github/workflows/tests.yml

@@ -1,26 +1,27 @@
-name: test PR
+name: tests
 on:
+  workflow_call:
   workflow_dispatch:
   pull_request:
     branches: [ main ]
-    types: [labeled]
+    types: [opened, synchronize, reopened, ready_for_review]
 
 jobs:
   test:
-    if:  github.event.label.name == 'testthis' && !startsWith(github.head_ref, 'release-please-')
+    if: github.event.pull_request.draft == false
     runs-on: ubuntu-latest
-    container: riedmiki/gromacs-plumed-python:2021
+    container: riedmiki/gromacs-plumed-python:2023.5-plumed
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
+      - uses: psf/black@stable
       - name: run tox
         run: tox
       - name: zip coverage report
         if: ${{ !cancelled() }}
         run: zip -r htmlcov.zip htmlcov || true
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         if: ${{ !cancelled() }}
         with:
           name: coverage artifact
           path: htmlcov.zip
 
-

Makefile

@@ -0,0 +1,29 @@
+.PHONY: Makefile setup-docs preview docs clear-docs watch
+
+preview:
+	quarto preview
+
+watch:
+	python -m quartodoc build --watch
+
+docs:
+	python -m quartodoc build 
+	python -m quartodoc interlinks
+	quarto render
+
+setup-docs: clear-docs
+	quarto add --no-prompt machow/quartodoc
+	python -m quartodoc build --verbose
+	python -m quartodoc interlinks
+	quarto render
+
+clear-docs:
+	rm -rf docs
+	rm -rf .quarto
+	rm -rf _inv
+	rm -rf _reference
+	rm -f ./objects.json
+	rm -f _sidebar.yml
+
+format:
+	black src tests

README.md

@@ -1,15 +1,29 @@
-# Reaction template for KIMMDY
+# A collection of simple reactions for KIMMDY
+
+[![test latest release](https://github.com/graeter-group/kimmdy-reactions/actions/workflows/tests.yml/badge.svg?branch=release-please--branches--main)](https://github.com/graeter-group/kimmdy-reactions/actions/workflows/tests.yml/?branch=release-please--branches--main)
+
+## Documentation
+
+See [KIMMDY documentation](https://graeter-group.github.io/kimmdy/)
+and [documentation for these reactions](https://graeter-group.github.io/kimmdy-reactions/).
 
 ## Installation
-Should get installed together with kimmdy. If you want to install it separatly: 
 
-* Download
-* `pip install -e ./`  or for development: `pip install -r requirements.txt`
+Together with KIMMDY
+
+```bash
+pip installl kimmdy[reactions]
+```
+
+To install it separatly:
+
+```bash
+pip install kimmdy-reactions
+```
 
 ## Making your own
+
 * Implement your reaction as a subclass of `kimmdy.reaction.Reaction`
 * Register your Reaction class in the  **[options.entry_points]** section in the setup.cfg. The name you give here must match the entry in the config.yml for Kimmdy!
 
 
-
-

_extensions/machow/interlinks/.gitignore

@@ -0,0 +1,3 @@
+*.html
+*.pdf
+*_files/

_extensions/machow/interlinks/_extension.yml

@@ -0,0 +1,7 @@
+title: Interlinks
+author: Michael Chow
+version: 1.1.0
+quarto-required: ">=1.2.0"
+contributes:
+  filters:
+    - interlinks.lua