diff --git a/.github/workflows/link_check.yml b/.github/workflows/link_check.yml new file mode 100644 index 000000000..a277d543b --- /dev/null +++ b/.github/workflows/link_check.yml @@ -0,0 +1,18 @@ +# from: https://github.com/gaurav-nelson/github-action-markdown-link-check + +name: Check Markdown links + +# Controls when the workflow will run +on: + # Triggers the workflow on push or pull request events but only for the master branch + push: + branches: [ master ] + pull_request: + branches: [ master ] + +jobs: + markdown-link-check: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@master + - uses: gaurav-nelson/github-action-markdown-link-check@v1 \ No newline at end of file diff --git a/docs/ReDU.md b/docs/ReDU.md index 058838fcd..0cdcfe2c2 100644 --- a/docs/ReDU.md +++ b/docs/ReDU.md @@ -5,7 +5,7 @@ ## "What is ReDU?" **Finding and reusing data is hard.** ReDU aims to make that easier. **[ReDU](https://redu.ucsd.edu/)** is a community-minded approach to find and reuse public data containing tandem MS data at the repository scale. ReDU is the bridge between the Global Natural Product Social Molecular Networking Analysis Platform [(GNPS)](https://gnps.ucsd.edu/ProteoSAFe/static/gnps-splash.jsp) and [MassIVE](https://massive.ucsd.edu/ProteoSAFe/static/massive.jsp), a public data repository for mass spectrometry data. The key to making this work is a systemic way of capturing basic information about each file contributed to ReDU (*i.e.* sample information aka metadata). Using the sample information, users can select public data for re-analysis in GNPS or provide their own data along with public data to perform co-analysis. Our aim is to empower researchers to put their data in the context of public data as well as explore questions using public data at the repository scale. -![image](https://github.com/mwang87/ReDU-MS2-Documentation/tree/master/docs/images/image_doc.png) +![image](https://github.com/mwang87/ReDU-MS2-Documentation/raw/master/docs/images/image_doc.png) !!! question "How do I contribute to ReDU?" **This is a community effort and everyone is encouraged to participate by submitting their own data and sample information [instructions](https://mwang87.github.io/ReDU-MS2-Documentation/HowtoContribute/).** diff --git a/mkdocs.yml b/mkdocs.yml index 2fb992c85..d71ff4440 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -114,6 +114,10 @@ plugins: - git-revision-date-localized: type: datetime - mermaid2 + - with-pdf: + output_path: documentation.pdf + show_anchors: true + markdown_extensions: - toc: diff --git a/requirements.txt b/requirements.txt index 5bc560166..42b2bc3f6 100644 --- a/requirements.txt +++ b/requirements.txt @@ -5,4 +5,5 @@ pymdown-extensions>=7.0 mkdocs-material-extensions>=1.0 mkdocs-git-revision-date-localized-plugin mkdocs-git-authors-plugin -mkdocs-mermaid2-plugin \ No newline at end of file +mkdocs-mermaid2-plugin +mkdocs-with-pdf