✨ first version of dsp notes

.github/workflows/build_website.yaml

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+name: deploy-website
+
+# Only run this when the master branch changes
+on:
+  pull_request:
+  push:
+    branches:
+      - main
+  workflow_dispatch:
+
+# This job installs dependencies, builds the website and pushes it to `gh-pages`
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+      - name: Install dependencies
+        run: |
+          pip install -r requirements.txt
+
+      - name: Build the site
+        run: |
+          sphinx-build -nW --keep-going -b html .  _build
+
+      # # Hide pages behind a password
+      # - uses: actions/setup-node@v3
+      # - run: npm install -g staticrypt
+      # - run: find _build/hidden -type f -name "*.html" -exec staticrypt {} TEST -o {} \;
+
+      # If we've pushed to main, push the book's HTML to github-pages
+      - if: ${{ github.ref == 'refs/heads/main' }}
+        name: GitHub Pages action
+        uses: peaceiris/actions-gh-pages@v4
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./_build
+          # cname: website.com

.gitignore

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+# Local build folder
+_build
+jupyter_execute
+
+# Hidden files
+.DS_Store
+.ipynb_checkpoints

about.md

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+# About
+
+> More information about us and our work.
+
+The Data Sciene Platform at Novo Nordisk Foundation Center for Biosustainability 
+is part of the Informatics Platform, see our aims and goals
+[here](https://www.biosustain.dtu.dk/technologies/informatics/data-science-platform). 
+
+

azure/creating_ressources.md

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+# Create Azure resources
+
+How to create azure resources in a common VNET
+
+> good first issue for Albert:)

azure/running_nextflow_on_azure.md

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+# How to run a nextflow pipleline on Azure
+
+> to be written

conf.py

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+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+
+project = "Data Science Platform notes"
+# ! update if someone adds information
+copyright = "2024, Henry Webel"
+author = "Henry Webel"
+
+
+# -- General configuration ---------------------------------------------------
+
+
+extensions = [
+    "myst_nb",
+    # "sphinx_design", # interactive webcomponents
+    # "sphinx_copybutton",
+    # "sphinx_examples",
+    "sphinx_new_tab_link",
+]
+
+templates_path = ["_templates"]
+exclude_patterns = [
+    "_build",
+    "Thumbs.db",
+    ".DS_Store",
+    "**/pandoc_ipynb/inputs/*",
+    ".nox/*",
+    "README.md",
+    "**/.ipynb_checkpoints/*",
+    "jupyter_execute",
+    "conf.py",
+]
+
+
+html_theme = "pydata_sphinx_theme"
+# html_theme = "sphinx_book_theme" # alternative
+
+
+#  https://myst-nb.readthedocs.io/en/latest/computation/execute.html
+nb_execution_mode = "auto"
+
+myst_enable_extensions = ["dollarmath", "amsmath"]
+
+# Plolty support through require javascript library
+# https://myst-nb.readthedocs.io/en/latest/render/interactive.html#plotly
+html_js_files = [
+    "https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"
+]
+
+# https://myst-nb.readthedocs.io/en/latest/configuration.html
+# Execution
+nb_execution_raise_on_error = True
+# Rendering
+nb_merge_streams = True
+
+# https://myst-nb.readthedocs.io/en/latest/authoring/custom-formats.html#write-custom-formats
+nb_custom_formats = {
+    ".py": ["jupytext.reads", {"fmt": "py:percent"}]
+}
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+# See:
+# https://github.com/executablebooks/MyST-NB/blob/master/docs/conf.py
+# html_title = ""
+html_theme = "sphinx_book_theme"
+# html_logo = "_static/logo-wide.svg"
+# html_favicon = "_static/logo-square.svg"
+html_theme_options = {
+    "github_url": "https://github.com/biosustain/",
+    "repository_url": "https://github.com/biosustain/dsp_notes",
+    # "repository_branch": "main",
+    # "home_page_in_toc": True,
+    # "path_to_docs": "docs",
+    "show_navbar_depth": 1,
+    # "use_edit_page_button": True,
+    "use_repository_button": True,
+    "use_download_button": True,
+    "launch_buttons": {
+        "colab_url": "https://colab.research.google.com"
+        #     "binderhub_url": "https://mybinder.org",
+        #     "notebook_interface": "jupyterlab",
+    },
+    "navigation_with_keys": False,
+}
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+# html_static_path = ['_static']

index.md

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+# DTU Biosustain's Data Science Platform Documentation
+
+Welcome to the documentation of the Data Science Platform at DTU Biosustain. This is a
+place to keep general notes on how to do things,
+DTU infrastructure specific trics and institute wide educational material.
+
+The Data Sciene Platform at Novo Nordisk Foundation Center for Biosustainability 
+is part of the Informatics Platform, see our aims and goals
+[here](https://www.biosustain.dtu.dk/technologies/informatics/data-science-platform). 
+
+```{toctree}
+:maxdepth: 2
+:hidden:
+
+about
+```
+
+```{toctree}
+:maxdepth: 2
+:hidden:
+:caption: Azure
+
+azure/creating_ressources
+azure/running_nextflow_on_azure
+```
+
+```{toctree}
+:maxdepth: 2
+:hidden:
+:caption: Python
+
+python/percent_notebooks
+```
+
+
+
+

jupyter_execute/conf.ipynb

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+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "86487a2c",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "zsh:1: command not found: update\r\n"
+     ]
+    }
+   ],
+   "source": [
+    "# Configuration file for the Sphinx documentation builder.\n",
+    "#\n",
+    "# This file only contains a selection of the most common options. For a full\n",
+    "# list see the documentation:\n",
+    "# https://www.sphinx-doc.org/en/master/usage/configuration.html\n",
+    "\n",
+    "# -- Project information -----------------------------------------------------\n",
+    "\n",
+    "project = \"Data Science Platform notes\"\n",
+    "! update if someone adds information\n",
+    "copyright = \"2024, Henry Webel\"\n",
+    "author = \"Henry Webel\"\n",
+    "\n",
+    "\n",
+    "# -- General configuration ---------------------------------------------------\n",
+    "\n",
+    "\n",
+    "extensions = [\n",
+    "    \"myst_nb\",\n",
+    "    # \"sphinx_design\", # interactive webcomponents\n",
+    "    # \"sphinx_copybutton\",\n",
+    "    # \"sphinx_examples\",\n",
+    "    \"sphinx_new_tab_link\",\n",
+    "]\n",
+    "\n",
+    "templates_path = [\"_templates\"]\n",
+    "exclude_patterns = [\n",
+    "    \"_build\",\n",
+    "    \"Thumbs.db\",\n",
+    "    \".DS_Store\",\n",
+    "    \"**/pandoc_ipynb/inputs/*\",\n",
+    "    \".nox/*\",\n",
+    "    \"README.md\",\n",
+    "    \"**/.ipynb_checkpoints/*\",\n",
+    "    \"jupyter_execute\",\n",
+    "]\n",
+    "\n",
+    "\n",
+    "html_theme = \"pydata_sphinx_theme\"\n",
+    "# html_theme = \"sphinx_book_theme\" # alternative\n",
+    "\n",
+    "\n",
+    "#  https://myst-nb.readthedocs.io/en/latest/computation/execute.html\n",
+    "nb_execution_mode = \"auto\"\n",
+    "\n",
+    "myst_enable_extensions = [\"dollarmath\", \"amsmath\"]\n",
+    "\n",
+    "# Plolty support through require javascript library\n",
+    "# https://myst-nb.readthedocs.io/en/latest/render/interactive.html#plotly\n",
+    "html_js_files = [\n",
+    "    \"https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js\"\n",
+    "]\n",
+    "\n",
+    "# https://myst-nb.readthedocs.io/en/latest/configuration.html\n",
+    "# Execution\n",
+    "nb_execution_raise_on_error = True\n",
+    "# Rendering\n",
+    "nb_merge_streams = True\n",
+    "\n",
+    "# https://myst-nb.readthedocs.io/en/latest/authoring/custom-formats.html#write-custom-formats\n",
+    "nb_custom_formats = {\n",
+    "    \".py\": [\"jupytext.reads\", {\"fmt\": \"py:percent\"}]\n",
+    "}\n",
+    "\n",
+    "\n",
+    "# -- Options for HTML output -------------------------------------------------\n",
+    "\n",
+    "# The theme to use for HTML and HTML Help pages.  See the documentation for\n",
+    "# a list of builtin themes.\n",
+    "# See:\n",
+    "# https://github.com/executablebooks/MyST-NB/blob/master/docs/conf.py\n",
+    "# html_title = \"\"\n",
+    "html_theme = \"sphinx_book_theme\"\n",
+    "# html_logo = \"_static/logo-wide.svg\"\n",
+    "# html_favicon = \"_static/logo-square.svg\"\n",
+    "html_theme_options = {\n",
+    "    \"github_url\": \"https://github.com/biosustain/\",\n",
+    "    \"repository_url\": \"https://github.com/biosustain/dsp_notes\",\n",
+    "    # \"repository_branch\": \"main\",\n",
+    "    # \"home_page_in_toc\": True,\n",
+    "    # \"path_to_docs\": \"docs\",\n",
+    "    \"show_navbar_depth\": 1,\n",
+    "    # \"use_edit_page_button\": True,\n",
+    "    \"use_repository_button\": True,\n",
+    "    \"use_download_button\": True,\n",
+    "    \"launch_buttons\": {\n",
+    "        \"colab_url\": \"https://colab.research.google.com\"\n",
+    "        #     \"binderhub_url\": \"https://mybinder.org\",\n",
+    "        #     \"notebook_interface\": \"jupyterlab\",\n",
+    "    },\n",
+    "    \"navigation_with_keys\": False,\n",
+    "}\n",
+    "# Add any paths that contain custom static files (such as style sheets) here,\n",
+    "# relative to this directory. They are copied after the builtin static files,\n",
+    "# so a file named \"default.css\" will overwrite the builtin \"default.css\".\n",
+    "# html_static_path = ['_static']"
+   ]
+  }
+ ],
+ "metadata": {
+  "jupytext": {
+   "cell_metadata_filter": "-all",
+   "main_language": "python",
+   "notebook_metadata_filter": "-all",
+   "text_representation": {
+    "extension": ".py",
+    "format_name": "percent"
+   }
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.12.6"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

python/percent_notebooks.py

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+# %% [markdown]
+# # Percent Notebooks in VSCode (and other editior)
+# This site is written as a jupyter notebook which is then executed and converted to html
+# by mystnb and sphinx.
+#
+# A brief example:
+# ```
+# # %% [markdown]
+# # # Heading 1
+# # Some text
+# #
+# # %%
+# # print("Hello World")
+#
+# ```
+# Find more information on
+# [jupytext's documentation](https://jupytext.readthedocs.io/en/latest/formats-scripts.html)
+
+# %%
+print("Hello World form a percent notebook")
+
+# %% [markdown]
+# This notebook was executed using `jupytext` and `mystnb` by `sphinx`.

requirements.txt

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+sphinx
+sphinx-book-theme
+myst-nb
+ipywidgets
+sphinx-new-tab-link!=0.2.2
+jupytext