diff --git a/README.md b/README.md index 32da005..540c6d4 100644 --- a/README.md +++ b/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) diff --git a/about.md b/about.md index caf8bd6..6cb6b6e 100644 --- a/about.md +++ b/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 diff --git a/conf.py b/conf.py index 887eff3..55faab4 100644 --- a/conf.py +++ b/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,