Adding PDF Building

.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

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/).**

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:

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
+mkdocs-mermaid2-plugin
+mkdocs-with-pdf