added mkdocs

.github/workflows/docs_ci.yaml

@@ -0,0 +1,32 @@
+# This is a basic workflow to help you get started with Actions
+
+name: MKDocs
+
+# Controls when the action will run. Triggers the workflow on push or pull request
+# events but only for the main branch
+on:
+  push:
+    branches: [main]
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  # This workflow contains a single job called "build"
+  build:
+    # The type of runner that the job will run on
+    runs-on: ubuntu-latest
+
+    permissions:
+      contents: write
+      packages: write
+      attestations: write
+      id-token: write
+
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: '0'
+      - uses: tercen/actions/mkdocs@main
+        with:
+          committers_api_key: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/docs_release.yaml

@@ -0,0 +1,34 @@
+# This is a basic workflow to help you get started with Actions
+
+name: MKDocs release
+
+# Controls when the action will run. Triggers the workflow on push or pull request
+# events but only for the main branch
+on:
+  push:
+    tags:
+      - '[0-9]+.[0-9]+.[0-9]+'
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  # This workflow contains a single job called "build"
+  build:
+    # The type of runner that the job will run on
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+      packages: write
+      attestations: write
+      id-token: write
+
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: '0'
+      - uses: tercen/actions/mkdocs@main
+        with:
+          set_default: "true"
+          tag: ${GITHUB_REF##*/}
+          committers_api_key: ${{ secrets.GITHUB_TOKEN }}

.gitignore

@@ -0,0 +1,3 @@
+site/
+.idea
+.vscode

docs/index.md

@@ -0,0 +1,2 @@
+# Home
+

docs/stylesheets/extra.css

@@ -0,0 +1,5 @@
+:root {
+    --md-primary-fg-color:        #006a7f;
+    --md-primary-fg-color--light: #8bbed1;
+    --md-primary-fg-color--dark:  #1e5051;
+}

mkdocs.yml

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+site_name: FlowJo Report
+docs_dir: docs/
+site_url: https://tercen.com
+repo_url: https://github.com/tercen/iteos_flowjo_reported_stats_template
+repo_name: tercen/iteos_flowjo_reported_stats_template
+edit_uri: edit/main/docs/
+site_author: "Tercen Authors"
+site_description: "Doc for FlowJo Report Pipeline"
+use_directory_urls: true
+
+copyright: Copyright © 2024 Tercen
+
+theme:
+  name: material
+  # custom_dir: .docs/overrides/
+  font: false
+  favicon: https://tercen.com/_assets/brand/fav.png
+  logo: ./images/Tercen Logo white_vert_B.png
+  icon:
+    repo: fontawesome/brands/github
+  palette:
+    primary: custom
+  features:
+    - content.tabs.link
+    - instant
+    - navigation.footer
+    - navigation.path
+    - navigation.sections
+    #    - navigation.expand
+    - navigation.tabs
+    #    - navigation.tabs.sticky
+    - navigation.top
+    - navigation.tracking
+    - search.highlight
+    - search.share
+    - search.suggest
+    - tabs
+    - content.code.annotate
+    - content.code.copy
+    - content.action.edit
+    - content.action.view
+extra_css:
+  - stylesheets/extra.css
+plugins:
+  - search
+  - git-committers:
+      repository: tercen/iteos_flowjo_reported_stats_template
+      branch: main
+  - git-revision-date-localized:
+      enable_creation_date: true
+      type: timeago
+  #  - exclude:
+  #      glob:
+  #        - README.md
+  #        - "*.gotmpl"
+  #        - "*.gotmpl.md"
+  #  - awesome-pages
+  # - macros:
+  #     module_name: .docs/macros/includes/main
+  - minify:
+      minify_html: true
+      minify_js: true
+      htmlmin_opts:
+        remove_comments: true
+      #js_files: []
+  # - redirects:
+  #     redirect_maps:
+  #       README.md: Getting-Started/intro.md
+  - mike:
+      # these fields are all optional; the defaults are as below...
+      version_selector: true # set to false to leave out the version selector
+      css_dir: css # the directory to put the version selector's CSS
+      javascript_dir: js # the directory to put the version selector's JS
+      canonical_version:
+        null # the version for <link rel="canonical">; `null`
+      # uses the version specified via `mike deploy`
+markdown_extensions:
+  - admonition
+  - attr_list
+  - def_list
+  - footnotes
+  - meta
+  - toc:
+      permalink: true
+  - tables
+  - pymdownx.details
+  - pymdownx.emoji:
+      emoji_index: !!python/name:material.extensions.emoji.twemoji
+      emoji_generator: !!python/name:material.extensions.emoji.to_svg
+  - pymdownx.highlight:
+      anchor_linenums: true
+      use_pygments: true
+      linenums: true
+  - pymdownx.inlinehilite
+  - pymdownx.keys
+  - pymdownx.magiclink
+  - pymdownx.mark
+  - pymdownx.snippets
+  - pymdownx.tasklist:
+      custom_checkbox: true
+  - pymdownx.superfences
+  - pymdownx.tabbed
+extra:
+  version:
+    provider: mike
+
+
+
+
+
+
+
+
+#nav:
+#  - Home: index.md
+#  - Getting started:
+#      - Guidelines: intro_guidelines.md
+#      - Getting started:
+#          - Core concepts: getting-started_core-concepts.md
+#          - Setting up Tercen Studio:    getting-started_setup-tercen-studio.md
+#      - R Operator development:
+#          - General workflow: operator-dev_intro.md
+#          - "Walkthrough example: R operator": operator-dev_create.md
+#          - Deploying an R operator:   operator-dev_deploy.md
+#          - Improving an operator:   operator-dev_improve.md