Setting up the basic structure of the website and adding the github a…

…ctions to build the pages etc.

.github/workflows/github-actions.yml

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+# This is a basic workflow for the Actions
+
+name: CI
+
+# Controls when the workflow will run
+on:
+  # Triggers the workflow on push or pull request events but only for the "main" (or "master") branch
+  push:
+    branches: 
+      - master
+      - main
+  pull_request:
+    branches: 
+      - master
+      - main
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# 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 "deploy"
+  deploy:
+    # The type of runner that the job will run on
+    runs-on: ubuntu-latest
+
+    # 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
+      - uses: actions/setup-python@v5
+        with:
+          python-version: 3.x
+      - run: pip install mkdocstrings mkdocs-embed-external-markdown feedparser mkdocs-gen-files markdown-exec[ansi] markdown-include mkdocs-open-in-new-tab markdown-extra 
+      - run:  mkdocs gh-deploy --force

docs/index.md

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+# Welcome to the course "QM/MM - best practices" 
+
+The aim of this ONLINE course is to give an intro to classical Molecular Dynamics (MD) simulations and the combined Quantum Mechanical and Molecular Mechanics (QM/MM) simulations. We will start from scratch by setting a MD simulation, in the first half-day of the course, and then use this system to setup a QM/MM simulation. Regarding the software, we will use VMD, NAMD, ORCA, and GAUSSIAN for the full QM/MM protocol. We will also provide users with a set of best practices to improve the performance of their simulations. 
+

mkdocs.yml

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+site_name: QM/MM - best practices
+site_url: https://hpc2n.github.io/course-qmmm
+site_description: Material for the course QM/MM - best practices
+site_dir: site.build
+theme:
+  name: readthedocs
+  locale: en
+  logo: images/hpc2n-qmmm.png
+    #  static_templates:
+    #- sitemap.html
+  include_sidebar: true
+  font:
+    code: Robot Mono
+  features:
+    - toc.follow
+    - toc.integrate
+    - navigation.top
+    - navigation.sections
+    - search.suggest
+    - search.highlight
+    - content.tabs.link
+    - content.code.annotation
+    - content.code.copy
+  tabs: true
+  language: en
+extra_css:
+  - css/extra.css
+    #extra_javascript:
+    #  - js/popper.min.js
+    #  - js/tippy-bundle.umd.js
+    #  - js/clipboard.js
+
+nav:
+  - Home: index.md
+  - Introduction: intro.md
+  - Classical MD simulations: class.md
+    - NAMD+VMD: namdvmd.md
+    - GAUSSIAN/ORCA: gaussianorca.md  
+  - QM/MM simulations: qmmm.md
+    - NAMD+VMD: namdvmd.md
+    - GAUSSIAN/ORCA: gaussianorca.md
+  - Summary: summary.md
+plugins:
+  - search
+  - external-markdown
+  - mkdocstrings
+  - markdown-exec
+  - open-in-new-tab
+
+markdown_extensions:
+  - pymdownx.highlight:
+      anchor_linenums: true
+      line_spans: __span
+      pygments_lang_class: true
+  - pymdownx.inlinehilite
+  - pymdownx.snippets
+  - admonition
+  - pymdownx.arithmatex:
+      generic: true
+  - footnotes
+  - smarty
+  - pymdownx.details
+  - pymdownx.superfences
+  - codehilite
+  - pymdownx.mark
+  - pymdownx.caret
+  - pymdownx.tilde
+  - pymdownx.tabbed
+  - attr_list
+  - md_in_html
+  - tables
+  - toc:
+      permalink: true
+      separator: "__"
+

requirements.txt

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+mkdocs==1.6.0
+mkdocstrings==0.25.1
+mkdocs-embed-external-markdown==3.0.2
+feedparser==6.0.11
+mkdocs-gen-files==0.5.0
+markdown-exec[ansi]==1.8.3
+markdown-include==0.8.1
+mkdocs-open-in-new-tab==1.0.3
+markdown-extra==1.0.1