Contributor Guide

Thank you for your interest in improving this project. This project is open-source under the BSD license and highly welcomes contributions in the form of bug reports, feature requests, and pull requests.

Here is a list of important resources for contributors:

How to add a dataloader

Overview of contributing dataloaders to ncem.

  1. Install ncem.

    Clone ncem into a local repository from development branch and install via pip.

cd target_directory
git clone https://github.com/theislab/ncem.git
git checkout development
# git pull  # use this to update your installation
cd ncem  # go into ncem directory
pip install -e .  # install
  1. Create a new dataloader in data.py

    Your dataloader should be a new class in data.py (ideally named by first author, e.g. DataLoaderZhang) and should contain the following functions _register_celldata, _register_img_celldata and _register_graph_features.

    _register_celldata creates an AnnData object called celldata of the complete dataset with feature names stored in celldata.var_names. Cell type annotations are stored in celldata.obs. celldata.uns[‘metadata’] should contain the naming conventions of files and columns in obs.

    _register_img_celldata then automatically splits the celldata into a dictionary of AnnData object with one AnnData object per image in the dataset.

    _register_graph_features can be added in case of additional graph features, e.g. disease status of images.

    Additionally, each dataloader should have a class attribute cell_type_merge_dict which provides a logic on how to merge cell types in any subsequent analysis. This can be helpful when considering datasets with fine cell type annotations and a coarser annotation is wanted.

  2. Make loader public (Optional).

    You can contribute the data loader to public ncem as code through a pull request. Note that you can also just keep the data loader in your local installation if you do not want to make it public.

# make sure you are in the top-level ncem directory from step 1
git add *
git commit  # enter your commit description
# Next make sure you are up to date with dev
git checkout development
git pull
git checkout YOUR_BRANCH_NAME
git merge development
git push  # this starts the pull request.

In any case, feel free to open an GitHub issue on on the Issue Tracker.

How to report a bug

Report bugs on the Issue Tracker.

How to request a feature

Request features on the Issue Tracker.

How to set up your development environment

You need Python 3.7+ and the following tools:

You can install them with:

$ pip install poetry nox nox-poetry

Install the package with development requirements:

$ make install

You can now run an interactive Python session, or the command-line interface:

$ poetry run python
$ poetry run ncem

How to test the project

Run the full test suite:

$ nox

List the available Nox sessions:

$ nox --list-sessions

You can also run a specific Nox session. For example, invoke the unit test suite like this:

$ nox --session=tests

Unit tests are located in the tests directory, and are written using the pytest testing framework.

How to submit changes

Open a pull request to submit changes to this project against the development branch.

Your pull request needs to meet the following guidelines for acceptance:

  • The Nox test suite must pass without errors and warnings.

  • Include unit tests. This project maintains a high code coverage.

  • If your changes add functionality, update the documentation accordingly.

To run linting and code formatting checks before committing your change, you can install pre-commit as a Git hook by running the following command:

$ nox --session=pre-commit -- install

It is recommended to open an issue before starting work on anything. This will allow a chance to talk it over with the owners and validate your approach.