From 6c7a87e595f6b64169cbc011be9c3313a52f460f Mon Sep 17 00:00:00 2001 From: m-jahn Date: Mon, 13 Apr 2026 14:33:31 +0200 Subject: [PATCH 1/2] feat: change deployment to pixi, added news article --- .gitattributes | 2 + .github/workflows/deploy.yml | 12 +- .github/workflows/test-deploy.yml | 12 +- .gitignore | 3 + README.md | 11 +- blog/2026-04-13-catalog/index.md | 16 + environment.yaml | 7 - pixi.lock | 754 ++++++++++++++++++++++++++++++ pixi.toml | 15 + 9 files changed, 801 insertions(+), 31 deletions(-) create mode 100644 .gitattributes create mode 100644 blog/2026-04-13-catalog/index.md delete mode 100644 environment.yaml create mode 100644 pixi.lock create mode 100644 pixi.toml diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 0000000..997504b --- /dev/null +++ b/.gitattributes @@ -0,0 +1,2 @@ +# SCM syntax highlighting & preventing 3-way merges +pixi.lock merge=binary linguist-language=YAML linguist-generated=true -diff diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml index 1bbadfa..c5c0b9a 100644 --- a/.github/workflows/deploy.yml +++ b/.github/workflows/deploy.yml @@ -14,20 +14,14 @@ jobs: steps: - uses: actions/checkout@v6 - - name: Setup conda - uses: conda-incubator/setup-miniconda@v3 + - uses: prefix-dev/setup-pixi@v0 with: - channels: conda-forge - environment-file: environment.yaml - miniforge-version: latest + cache: true - name: Generate page - shell: bash -l {0} env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - run: | - python src/scripts/generate_page.py - python src/scripts/generate_workflow_md.py + run: pixi run generate-page - name: Upload page data uses: actions/upload-artifact@v4 diff --git a/.github/workflows/test-deploy.yml b/.github/workflows/test-deploy.yml index 2420c96..0eb1686 100644 --- a/.github/workflows/test-deploy.yml +++ b/.github/workflows/test-deploy.yml @@ -12,20 +12,14 @@ jobs: steps: - uses: actions/checkout@v6 - - name: Setup conda - uses: conda-incubator/setup-miniconda@v3 + - uses: prefix-dev/setup-pixi@v0 with: - channels: conda-forge - environment-file: environment.yaml - miniforge-version: latest + cache: true - name: Generate page - shell: bash -l {0} env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - run: | - python src/scripts/generate_page.py - python src/scripts/generate_workflow_md.py + run: pixi run generate-page - name: Upload page data uses: actions/upload-artifact@v4 diff --git a/.gitignore b/.gitignore index 9c03b07..7e93612 100644 --- a/.gitignore +++ b/.gitignore @@ -20,3 +20,6 @@ docs/workflows/all_workflows/*.md npm-debug.log* yarn-debug.log* yarn-error.log* +# pixi environments +.pixi/* +!.pixi/config.toml diff --git a/README.md b/README.md index 1c57f68..23dbb7f 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@ # mpusp.github.io [![Deploy to GitHub Pages](https://github.com/MPUSP/mpusp.github.io/actions/workflows/deploy.yml/badge.svg)](https://github.com/MPUSP/mpusp.github.io/actions/workflows/deploy.yml) -[![GitHub last commit](https://img.shields.io/github/last-commit/MPUSP/mpusp-github-io)](https://github.com/MPUSP/mpusp.github.io/actions/workflows/deploy.yml) +[![GitHub last commit](https://img.shields.io/github/last-commit/MPUSP/mpusp.github.io)](https://github.com/MPUSP/mpusp.github.io/commits/main) A homepage for the bioinformatic platform of the Max-Planck-Unit for the Science of Pathogens ([MPUSP](www.mpusp.mpg.de)). This website is built using [Docusaurus](https://docusaurus.io/), a modern static website generator. @@ -22,17 +22,16 @@ The website is automatically updated and built once per week, and on pull reques ### Dependencies -To develop the page locally, create a conda environment with the required packages: +To develop the page locally, use [pixi](https://pixi.prefix.dev) to set up the local environment from the `pixi.toml` file: ```bash -conda create -n docusaurus -c conda-forge python pygithub jinja2 nodejs -conda activate docusaurus +pixi shell ``` -To create a test page, run: +The `pixi.toml` file has predefined tasks to fetch data and generate content for the website: ```bash -npm create-docusaurus@latest docusaurus-test classic +pixi run generate-page ``` ### Local Development diff --git a/blog/2026-04-13-catalog/index.md b/blog/2026-04-13-catalog/index.md new file mode 100644 index 0000000..a3e47c0 --- /dev/null +++ b/blog/2026-04-13-catalog/index.md @@ -0,0 +1,16 @@ +--- +slug: new-catalog-features +title: New features for the Snakemake Workflow Catalog +authors: [michael] +tags: [announcements] +--- + +The [Snakemake Workflow Catalog](https://snakemake.github.io/snakemake-workflow-catalog) is rolling out **two new features**! + +1. The Catalog now supports automatic rendering of **Tube Maps** using [snakevision](https://github.com/OpenOmics/snakevision). Tube maps will automatically show up on your workflow page if the workflow has an executable test case in `.test` ([details](https://snakemake.github.io/snakemake-workflow-catalog/docs/about/adding_workflows)). + +2. The Catalog will automatically render a **Workflow Parameter Table** if your workflow repo contains a `workflow/schemas/config.schema.y(a)ml` or `config/schemas/config.schema.y(a)ml` ([details](docs/about/adding_workflows)). No need to manually maintain a table of parameters on your workflow page anymore. + +Here's an [example for a workflow](https://snakemake.github.io/snakemake-workflow-catalog/docs/workflows/MPUSP/snakemake-simple-mapping.html) with a tube map and a parameter table, `MPUSP/snakemake-simple-mapping`. + + diff --git a/environment.yaml b/environment.yaml deleted file mode 100644 index f8fcb04..0000000 --- a/environment.yaml +++ /dev/null @@ -1,7 +0,0 @@ -name: python env -channels: - - conda-forge -dependencies: - - python>=3.12 - - pygithub>=2.5 - - jinja2>=3.1 diff --git a/pixi.lock b/pixi.lock new file mode 100644 index 0000000..2ff28d8 --- /dev/null +++ b/pixi.lock @@ -0,0 +1,754 @@ +version: 6 +environments: + default: + channels: + - url: https://conda.anaconda.org/conda-forge/ + - url: https://conda.anaconda.org/bioconda/ + options: + pypi-prerelease-mode: if-necessary-or-explicit + packages: + linux-64: + - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-20_gnu.conda + - 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