Update repo to be Benchling training resouces page

README.md

@@ -1,67 +1,17 @@
-# Template for a static website using Sphinx and GitHub Pages
+# Static website for Benchling materials at DTU Biosustain
 
-## Instructions
+### Description
 
-### 1. Create new repository based on this template
+This repo builds a static website using Sphinx.
+The website contains training material and guides for researchers at DTU Biosustain, to familiarise themselves with Benchling.
 
-Create a template based on 
-[this repository](https://github.com/enryH/notes_template)
-by clicking on the "Use this template" button,
-see instructions
-[here](https://docs.github.com/en/repositories/creating-and-managing-repositories/creating-a-repository-from-a-template#creating-a-repository-from-a-template)
 
-- now you are already publish the site which looks identical to the template site
- (see it here)
-- jump to step 5 to do that directly.
+### Edit files
 
-### 2. Open in GitHub Codespaces (or locally)
-
-- go to [github.com/codespaces](https://github.com/codespaces)
-- create a new codespace using the forked repository
-
-> If you are done, remember to delete the codespace to not see your free credit or money
-> wasted. Also inactive (stopped) codespaces use storage for the last 30 days.
-
-### 3. Edit files
-
-- update in `conf.py` at least the author, project and copyright information at the top
-  - also update two urls to your repository:
-   ```json
-    "github_url": "https://github.com/enryh/",
-    "repository_url": "https://github.com/enryh/notes_template",
-    ```
 - write something about you in `about.md`
 - write articles in `folder_topic/article_topic.md`
 - update the `index.md` file to include new files
 - use [pandoc](https://pandoc.org/try/) to convert your previous files into markdown or
   reStructuredText
 
-### 4. Build the site locally
-
-> Have look at `.github/workflows/build_website.yaml` to see how the site is built
-> if you are interested.
-
-- Open a terminal (GitHub Codespaces)
-- install required packages from [`requirements.txt`](requirements.txt):
-  ```bash
-  pip install -r requirements.txt
-  ```
-- build the site (you could set an alias if you want):
-  ```bash
-  sphinx-build -n -W --keep-going -b html ./ ./_build/
-  ```
-  in case the command is not found, try:
-  ```bash
-   python -m sphinx -n -W --keep-going -b html ./ ./_build/
-  ```
-- open the site in a browser:
-  - install ["Live Preview" extension](https://marketplace.visualstudio.com/items?itemName=ms-vscode.live-server) in Visual Studio Code
-  - open the `_build/index.html` file in the browser (right-click, "Show Preview")
-
-### 5. Publish the site
-
-Follow 
-[these instructions](https://docs.github.com/en/pages/getting-started-with-github-pages/configuring-a-publishing-source-for-your-github-pages-site) 
-to publish the website using GitHub Pages.
 
-- Select the `gh-pages` branch as the source for the GitHub Pages site (currently step 7)

about.md

@@ -1,10 +1,28 @@
 # About
 
-> The Informatics Platform
+Welcome to our Benchling training resources page! 
+
+We hope that here you will find the information you need to start using Benchling and master it. The resources will introduce you to various Benchling functionalities, modules and custom-built (Biosustain-specific) extensions so that you can quickly get up to speed and start using the platform! 
+
+For additonal resources, you can always visit the official Benchling support page: https://help.benchling.com/hc/en-us 
+
+
+> Our goal
+
+Through these training resources, we're here to:
+
+- Smooth out the learning curve so you can dive right into using new tools without headaches
+- Make capturing your scientific data easier — everything in one central spot, easy to find when you need it
+- Get metadata organized and standardized so everything stays clear and consistent
+- Boost data findability for the long haul — your data should be easy to locate years down the line!
+- Empower you to explore your collected data like a pro
+
+Let’s make data work for you, not the other way around!
+
+
+> The Team
+
+We are the software and data enthusiasts at the Novo Nordisk Foundation Center for Biosustainability! Here you will find more information about the team: https://www.biosustain.dtu.dk/technologies/informatics
 
-The objectives of the Informatic Platform (IP) team is to
-- Standardize, automate and accelerate data processes and analyses 
-- Improve data findability, accessibility, interoperability, (re)usability
-- Build an industry level platform that covers the entire data lifecycle from raw data to insights
 
 

conf.py

@@ -1,29 +1,31 @@
-# Configuration file for the Sphinx documentation builder.
+# Configuration file for Sphinx documentation builder.
 #
-# This file only contains a selection of the most common options. For a full
-# list see the documentation:
+# This file contains a selection of the most common options for setting up a website using a Sphinx template. 
+# See the full documentation here:
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
 
 # -- Project information -----------------------------------------------------
 
-project = "Data Science Platform notes template"
-copyright = "2024, DTU Biosustain, Informatics Platform, DSP"
-author = "Henry Webel"
+project = "Benchling materials for DTU Biosustain"
+copyright = "2024, DTU Biosustain, Informatics Platform, Research Data Management Team"
+author = "Ester Milesi"
 
 
 # -- General configuration ---------------------------------------------------
 
-
+# Enable MyST-NB, which allows Sphinx to render Markdown files with notebook (Jupyter) support.
+# Enable "sphinx_new_tab_link", which automatically makes links open in a new tab.
 extensions = [
-    "myst_nb",
+    "myst_nb", 
     # "sphinx_design", # https://sphinx-design.readthedocs.io/en/sbt-theme/
     # "sphinx_copybutton", # https://sphinx-copybutton.readthedocs.io/
     "sphinx_new_tab_link",
 ]
 
 templates_path = ["_templates"]
-# As we can use percent notebooks and markdowns files, we need to exclude some files
-# additinally to the default ones (add to the list if needed)
+# Website pages can only be built from percent notebooks and markdowns files.
+# We need to exclude some files/patterns included in the repository.
+
 exclude_patterns = [
     "_build",
     "Thumbs.db",
@@ -37,9 +39,9 @@
 ]
 
 
-# -- Notebook related settings -----------------------------------------------
+# -- Jupiter Notebook related settings -----------------------------------------------
 
-# add notebooks
+# add notebooks (myst-nb extension)
 #  https://myst-nb.readthedocs.io/en/latest/computation/execute.html
 nb_execution_mode = "auto"
 
@@ -70,35 +72,36 @@
 # browse available themes: https://sphinx-themes.org/
 
 
-# The theme to use for HTML and HTML Help pages.  See the documentation for
-# a list of builtin themes.
-# See:
+# The theme to use for HTML and HTML Help pages.  
+# See the documentation for a list of existing themes:
 # https://github.com/executablebooks/MyST-NB/blob/master/docs/conf.py
-# html_title = ""
-#OLD THEME html_theme = "sphinx_book_theme"
-#NEW THEME
+
+#OLD THEME "sphinx_book_theme"
+
+#THEME (AND LOGO) 
+
+#_static directory is typically where Sphinx expects custom static assets like images
 html_theme = 'press'
-# html_theme = "sphinx_book_theme" # alternative
-# html_logo = "_static/logo-wide.svg"
+# html_logo = "_static/logo-wide.svg" #check where is _static
 # html_favicon = "_static/logo-square.svg"
 
-#OLD THEME options
+# THEME options
 html_theme_options = {
-    # "github_url": "https://github.com/enryh/",
-    # "repository_url": "https://github.com/enryh/notes_template",
-    # # "repository_branch": "main",
-    # # "home_page_in_toc": True,
-    # # "path_to_docs": "docs",
-    # "show_navbar_depth": 1,
-    # # "use_edit_page_button": True,
+    "github_url": "https://github.com/emilesi",
+    "repository_url": "https://github.com/emilesi/My-GitHub-Website",
+    "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,
+    "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,