From fd4f3bef3034320a9f5b5afecc75242f23faf6df Mon Sep 17 00:00:00 2001 From: Kelly Sovacool Date: Thu, 12 Sep 2024 17:17:42 -0400 Subject: [PATCH 1/5] docs: use dropdown for multiple versions on docs site resolves #142 --- .github/workflows/docs-mkdocs.yml | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 .github/workflows/docs-mkdocs.yml diff --git a/.github/workflows/docs-mkdocs.yml b/.github/workflows/docs-mkdocs.yml new file mode 100644 index 0000000..89b719b --- /dev/null +++ b/.github/workflows/docs-mkdocs.yml @@ -0,0 +1,25 @@ +name: docs +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/mkdocs-mike@v0.1 + with: + github-token: ${{ github.token }} From 28b37c2b6b85e35a36b9344b08abb16597edbcd0 Mon Sep 17 00:00:00 2001 From: Kelly Sovacool Date: Thu, 12 Sep 2024 17:19:36 -0400 Subject: [PATCH 2/5] ci: add release actions --- .github/workflows/draft-release.yml | 25 +++++++++++++++++++++++++ .github/workflows/post-release.yml | 17 +++++++++++++++++ 2 files changed, 42 insertions(+) create mode 100644 .github/workflows/draft-release.yml create mode 100644 .github/workflows/post-release.yml diff --git a/.github/workflows/draft-release.yml b/.github/workflows/draft-release.yml new file mode 100644 index 0000000..d643f5c --- /dev/null +++ b/.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/draft-release@v0.1 + with: + github-token: ${{ github.token }} + version-tag: ${{ github.event.inputs.version-tag }} diff --git a/.github/workflows/post-release.yml b/.github/workflows/post-release.yml new file mode 100644 index 0000000..e0e21eb --- /dev/null +++ b/.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/post-release@v0.1 + with: + github-token: ${{ github.token }} From 31fec60f12d935cf225c75223d22cbf5de27a97c Mon Sep 17 00:00:00 2001 From: Kelly Sovacool Date: Thu, 12 Sep 2024 17:21:41 -0400 Subject: [PATCH 3/5] chore: update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 74e358b..fe162fb 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -25,6 +25,7 @@ ### Misc - The singularity version is no longer specified, per request of the biowulf admins. (#139, @kelly-sovacool) +- Minor documentation updates. (#146, @kelly-sovacool) ## CARLISLE v2.5.0 From 0b61d3509688eba4bd87bf9725e0176967d4e142 Mon Sep 17 00:00:00 2001 From: Kelly Sovacool Date: Thu, 12 Sep 2024 17:27:53 -0400 Subject: [PATCH 4/5] docs: use readme for index --- README.md | 4 ++-- {resources => docs}/img/CUTandRUN_Workflow.jpeg | Bin docs/index.md | 8 +++++++- mkdocs.yml | 2 +- 4 files changed, 10 insertions(+), 4 deletions(-) rename {resources => docs}/img/CUTandRUN_Workflow.jpeg (100%) diff --git a/README.md b/README.md index 6b2a25c..49eddba 100644 --- a/README.md +++ b/README.md @@ -12,6 +12,6 @@ This snakemake pipeline is built to run on [Biowulf](https://hpc.nih.gov/). -For comments/suggestions/advice please reach out to [Samantha Chill](mailto:samantha.sevilla@nih.gov). +For comments/suggestions/advice please contact . -For detailed documentation on running the pipeline view the [documentation](https://CCBR.github.io/CARLISLE/) page. +For detailed documentation on running the pipeline view the [documentation](https://CCBR.github.io/CARLISLE/) website. diff --git a/resources/img/CUTandRUN_Workflow.jpeg b/docs/img/CUTandRUN_Workflow.jpeg similarity index 100% rename from resources/img/CUTandRUN_Workflow.jpeg rename to docs/img/CUTandRUN_Workflow.jpeg diff --git a/docs/index.md b/docs/index.md index 89f470f..c7caacb 100644 --- a/docs/index.md +++ b/docs/index.md @@ -1,3 +1,9 @@ + + +--8<-- "README.md" + + + The CARLISLE pipeline was developed in support of NIH [Dr Vassiliki Saloura's Laboratory](https://ccr.cancer.gov/staff-directory/vassiliki-saloura) and [Dr Javed Khan's Laboratory](https://ccr.cancer.gov/staff-directory/javed-khan/lab). It has been developed and tested solely on NIH [HPC Biowulf](https://hpc.nih.gov/). -![Image title](https://github.com/CCBR/CARLISLE/blob/dev/resources/img/CUTandRUN_Workflow.jpeg?raw=true) +![cut-and-run workflow](img/CUTandRUN_Workflow.jpeg) diff --git a/mkdocs.yml b/mkdocs.yml index 78a0d56..d41ab5b 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -91,7 +91,7 @@ markdown_extensions: # Page Tree nav: - - Background: index.md + - Home: index.md - Usage: - 1. Getting Started: user-guide/getting-started.md - 2. Preparing Files: user-guide/preparing-files.md From 0cef86c9a47efc33117a6f7cbd71f6fc601e1bb3 Mon Sep 17 00:00:00 2001 From: Kelly Sovacool Date: Thu, 12 Sep 2024 17:28:59 -0400 Subject: [PATCH 5/5] ci: remove old mkdocs action --- .github/workflows/build_mkdocs.yaml | 17 ----------------- 1 file changed, 17 deletions(-) delete mode 100644 .github/workflows/build_mkdocs.yaml diff --git a/.github/workflows/build_mkdocs.yaml b/.github/workflows/build_mkdocs.yaml deleted file mode 100644 index e41aadf..0000000 --- a/.github/workflows/build_mkdocs.yaml +++ /dev/null @@ -1,17 +0,0 @@ -name: mkdocs_build -on: - workflow_dispatch: - push: - paths: - - "docs/**" -jobs: - deploy: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v2 - - uses: actions/setup-python@v2 - with: - python-version: 3.9 - - run: pip install --upgrade pip - - run: pip install -r docs/requirements.txt - - run: mkdocs gh-deploy --force