Merge pull request #45 from CCBR/docs-actions

set up docs site with mkdocs/mike

.github/workflows/auto-format.yml

@@ -0,0 +1,35 @@
+name: auto-format
+
+on:
+  workflow_dispatch:
+  pull_request:
+
+env:
+  GH_TOKEN: ${{ github.token }}
+
+jobs:
+  auto-format:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+        if: github.event_name == 'pull_request'
+        with:
+          fetch-depth: 0
+          ref: ${{ github.event.pull_request.head.ref }}
+
+      - uses: actions/checkout@v4
+        if: github.event_name == 'push'
+        with:
+          fetch-depth: 0
+
+      - name: format
+        uses: pre-commit/[email protected]
+        continue-on-error: true
+
+      - name: commit & push
+        run: |
+          git config --global user.name "github-actions[bot]"
+          git config --global user.email "41898282+github-actions[bot]@users.noreply.github.com"
+          git add .
+          git commit -m "ci: 🤖 format everything with pre-commit" && git push || echo "nothing to commit"

.github/workflows/docs-mkdocs.yml

@@ -0,0 +1,28 @@
+name: docs
+# this workflow requires:
+#  - an mkdocs config file (`mkdocs.yml`)
+#  - website dependencies in `docs/requirements.txt`
+on:
+  workflow_dispatch:
+  release:
+    types:
+      - published
+  push:
+    branches:
+      - main
+    paths:
+      - "docs/**"
+      - "**.md"
+      - .github/workflows/docs-mkdocs.yml
+      - mkdocs.yml
+
+jobs:
+  mkdocs:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - uses: CCBR/actions/[email protected]
+        with:
+          github-token: ${{ github.token }}

.github/workflows/draft-release.yml

@@ -0,0 +1,25 @@
+name: draft-release
+
+on:
+  workflow_dispatch:
+    inputs:
+      version-tag:
+        description: |
+          Semantic version tag for next release.
+          If not provided, it will be determined based on conventional commit history.
+          Example: v2.5.11
+        required: false
+        type: string
+        default: ""
+
+jobs:
+  draft-release:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0 # required to include tags
+      - uses: CCBR/actions/[email protected]
+        with:
+          github-token: ${{ github.token }}
+          version-tag: ${{ github.event.inputs.version-tag }}

.github/workflows/post-release.yml

@@ -0,0 +1,17 @@
+name: post-release
+
+on:
+  release:
+    types:
+      - published
+
+jobs:
+  cleanup:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - uses: CCBR/actions/[email protected]
+        with:
+          github-token: ${{ github.token }}

.gitignore

@@ -44,3 +44,6 @@ results/
 
 # user-specific dev files
 *KLS*
+
+# mkdocs
+/site

CHANGELOG.md

@@ -4,6 +4,7 @@
 - Run spooker on workflow completion.
 - Print the recommended citation in bibtex format with `crispin --citation`. (#32, @kelly-sovacool)
 - Fix citation information (#38, @kelly-sovacool)
+- Improve the documentation website with a dropdown menu to select which version to view. The latest release is shown by default. (#45, @kelly-sovacool)
 
 ## CRUISE 0.1.1
 

README.md

@@ -42,10 +42,10 @@ crispin run --mode slurm -profile test,biowulf
 
 To run CRISPIN on your own data, you'll need to create a sample sheet.
 Take a look at the example:
-[assets/samplesheet_test_biowulf.csv](assets/samplesheet_test_biowulf.csv).
+[assets/samplesheet_test_biowulf.csv](https://github.com/CCBR/CRISPIN/tree/main/assets/samplesheet_test_biowulf.csv).
 
 You'll also need to select an appropriate library for your dataset.
-CRISPIN is bundled with several libraries in [assets/lib](assets/lib),
+CRISPIN is bundled with several libraries in [assets/lib](https://github.com/CCBR/CRISPIN/tree/main/assets/lib),
 or you can download your own.
 Once you've created a samplesheet with paths to your fastq files,
 run crispin with the `--input` option to specify the path to your sample sheet
@@ -61,7 +61,7 @@ Come across a **bug**? Open an [issue](https://github.com/CCBR/CRISPIN/issues) a
 
 Have a **question**? Ask it in [discussions](https://github.com/CCBR/CRISPIN/discussions).
 
-Want to **contribute** to this project? Check out the [contributing guidelines](docs/CONTRIBUTING.md).
+Want to **contribute** to this project? Check out the [contributing guidelines](https://github.com/CCBR/CRISPIN/tree/main/docs/CONTRIBUTING.md).
 
 ## References
 

docs/requirements.txt

@@ -8,3 +8,5 @@ mkdocs-git-revision-date-plugin==0.3.2
 mkdocs-material==9.1.6
 #https://pypi.org/project/mkdocs-material-extensions/
 mkdocs-material-extensions==1.1.1
+#https://github.com/jimporter/mike
+mike

mkdocs.yml

@@ -64,8 +64,6 @@ markdown_extensions:
       permalink: true
   - pymdownx.arithmatex:
       generic: true
-  - pymdownx.betterem:
-      smart_enable: all
   - pymdownx.caret
   - pymdownx.critic
   - pymdownx.details
@@ -97,5 +95,4 @@ nav:
   - Developer Guide:
       - How to contribute: contributing.md
       - Release guide: release-guide.md
-  - Contributors: contributors.md
   - Changelog: changelog.md