How To Use

1. Insert description here.
2. Rename repo with a 4 digit year-of-initiation prefix, e.g., "2022-". Convention is to use hyphens between words and all lower case.
3. Create a conda environment for this project. First modify conda-env.yml to include the relevant repositories and dependencies needed; also give the environment a good name (e.g., similar or same as this repo) - the default is "project-env". Then create the environment (see below).
4. If you do not want to work in a development container, skip to "Local Installation" to use a conda environment on your local machine.
5. Otherwise, a Docker dev container template for VS Code is provided in the .devcontainer/ folder. This creates a miniconda container and installs the environment specified in conda-env.yml into the default IPython kernel in the container. To use:
   • Change the UID and GID in .devcontainer/Dockerfile if needed.
   • Change the name of the conda environment (default="project-env") in the conda-env.yml and files in .devcontainer/.
   • Install the "Dev Containers" Extension in VS Code.
   • First git clone this repo, then open the folder in the container by selecting "Dev Containers: Open Folder in Container" from the Command Palette.
   • From a terminal in VS Code, run $ bash .devcontainer/start_jupyter.sh to launch a Jupyter server (forwarded on port 1234 by default) from the head of the repo. The default kernel contains the conda-env.yml packages but is not renamed.

Local Installation

Set up the conda environment for this project. You will need to install the environment in your Jupyter to use it (third command below). Change the name of the conda environment (default="project-env") in the conda-env.yml if you wish.

$ conda env create -f conda-env.yml
$ conda activate project-env
$ python -m ipykernel install --user --name=project-env

It is also useful to export the entire conda environment for posterity, especially if not working in a development container.

$ conda env export > environment.yml

Contributors

Update the CITATION.cff file to enable appropriate citations.

The logo for this repository (logo.png) was generated using Google Gemini (Imagen 3) on Nov. 28, 2024 with the prompt "Create a logo for a GitHub repository that is a coding template."

Versioning

• Use the public-template to create a fresh repo to release the code and details after a manuscript is published, tag the release, then use zenodo to capture changes to future changes/releases made to that repo. This serves as the primary public facing repo.
• In addition, create a "published" branch on this repo to correspond to when the associated paper is published. This is retained as the primary private repo where future work can be tested. Subsequent branches, such as "revision-YYYY-MM-DD" can be created later and similarly reflected in the public-template version if revisions are necessary.

Associated Publications

LINK TO MANUSCIPT