From 64f50cb59549d81b4be2e555838596435245ee2e Mon Sep 17 00:00:00 2001
From: Michael Baudis <675030+mbaudis@users.noreply.github.com>
Date: Mon, 30 Oct 2023 06:25:31 +0100
Subject: [PATCH] mkdocs workflow & config first try

---
 .DS_Store                          | Bin 0 -> 6148 bytes
 .github/.DS_Store                  | Bin 0 -> 6148 bytes
 .github/workflows/make-mkdocs.yaml |  21 ++++++++++
 README.md                          |   9 ++++-
 docs/beacon-queries.md             |   3 ++
 mkdocs.yml                         |  62 ++++++++++++++++++++++++++++-
 6 files changed, 92 insertions(+), 3 deletions(-)
 create mode 100644 .DS_Store
 create mode 100644 .github/.DS_Store
 create mode 100644 .github/workflows/make-mkdocs.yaml
 create mode 100644 docs/beacon-queries.md

diff --git a/.DS_Store b/.DS_Store
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diff --git a/.github/.DS_Store b/.github/.DS_Store
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diff --git a/.github/workflows/make-mkdocs.yaml b/.github/workflows/make-mkdocs.yaml
new file mode 100644
index 0000000..b334545
--- /dev/null
+++ b/.github/workflows/make-mkdocs.yaml
@@ -0,0 +1,21 @@
+name: mk-docs 
+on:
+  push:
+    branches:
+      - main
+      - master
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+        with:
+          python-version: 3.x
+      - run: pip install mkdocs-material 
+      - run: pip install mkdocs-macros-plugin
+      - run: pip install pymdown-extensions
+      - run: pip install mkdocs-mermaid2-plugin
+      - run: pip install mdx_gh_links
+      - run: pip install mkdocs-with-pdf
+      - run: mkdocs gh-deploy --force
diff --git a/README.md b/README.md
index 3d37058..fdc5426 100644
--- a/README.md
+++ b/README.md
@@ -1,2 +1,7 @@
-# cnv-reference-resources
-Data &amp; tools for hCNV analysis with a focus on the distributed normal
+# hCNV Reference Resources
+##### Data &amp; tools for hCNV analysis with a focus on the distributed normal
+
+The site was started as a project of the [ELIXIR hCNV Community](https://cnvar.org)
+at the [Biohackathon Europe 2023](https://biohackathon-europe.org):
+
+    [A "batteries-included" open reference resource for human genomic copy number variants (CNV)](https://github.com/elixir-europe/biohackathon-projects-2023/tree/main/1)
\ No newline at end of file
diff --git a/docs/beacon-queries.md b/docs/beacon-queries.md
new file mode 100644
index 0000000..9fcab84
--- /dev/null
+++ b/docs/beacon-queries.md
@@ -0,0 +1,3 @@
+# Beacon CNV Queries
+
+==TBD==
\ No newline at end of file
diff --git a/mkdocs.yml b/mkdocs.yml
index c97182f..3009473 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -1 +1,61 @@
-site_name: My Docs
+site_name: hCNV Reference Resources
+site_description: 'Data &amp; tools for hCNV analysis with a focus on the distributed normal'
+site_author: Michael Baudis
+repo_name: 'cnv-reference-resources'
+repo_url: https://github.com/hCNV/cnv-reference-resources
+edit_uri: edit/main/docs/
+
+###############################################################################
+
+nav:
+  - Home: /
+  - Topic Pages:
+    - Input Data: data-resources
+    - Parameters &amp; Mappings: parameters-and-mappings
+    - Beacon Queries: beacon-queries
+  - Biohack 2023 Page: https://github.com/elixir-europe/biohackathon-projects-2023/tree/main/1
+  - Beacon Documentation: 'https://docs.genomebeacons.org'
+
+###############################################################################
+
+markdown_extensions:
+  - toc:
+      toc_depth: 2-3
+      permalink: true
+  - admonition
+  - attr_list
+  - footnotes
+  - md_in_html
+  - pymdownx.critic
+  - pymdownx.caret
+  - pymdownx.details
+  - pymdownx.keys
+  - pymdownx.magiclink:
+      hide_protocol: true
+  - pymdownx.mark
+  - pymdownx.tilde
+  - pymdownx.saneheaders
+  - pymdownx.superfences:
+      custom_fences:
+        - name: mermaid
+          class: mermaid
+          format: !!python/name:mermaid2.fence_mermaid   
+  - pymdownx.tabbed:
+      alternate_style: true
+  - pymdownx.tasklist:
+      custom_checkbox: true
+  - tables
+  - mdx_gh_links:
+      user: hCNV
+      repo: hcnv.github.io
+  - pymdownx.emoji:
+        emoji_index: !!python/name:materialx.emoji.twemoji
+        emoji_generator: !!python/name:materialx.emoji.to_svg
+
+###############################################################################
+
+theme:
+  name: material
+plugins:
+    - search
+    - macros