minor clean up

.gitignore

@@ -1,10 +1,8 @@
 # Misc
-cytospace
-show_small.py
-archive/
 workflow/.snakemake
 workflow/logs
 *ignore*
+archive/
 explore
 sandbox
 
@@ -14,7 +12,7 @@ sandbox
 # Documentation
 site
 
-# Code Ocean related
+# Code Ocean
 code
 results
 
@@ -25,15 +23,6 @@ lightning_logs
 checkpoints
 run.log
 
-# Data files
-data/*/*
-!data/aml/default.csv
-!data/aml/short.h5ad
-!data/bmmc/default.csv
-!data/poised/default.csv
-!data/debarcoding/default.csv
-!data/README.md
-
 # Jupyter Notebook
 .ipynb_checkpoints
 exploration/*

CONTRIBUTING.md

@@ -8,9 +8,9 @@ Contributions are welcome as we aim to continue improving the pipeline. For inst
 - Submitting a fix
 - Proposing new features
 
-## Contributing to the code, or debugging
+## Pull Requests
 
-Even though *sopa* is meant for flamingo, you can set up this repository locally for development or debugging purposes.
+To add some new code to **sopa**, you should:
 
 1. Install the dependencies.
 2. Create your personal branch from `master`.
@@ -21,8 +21,7 @@ Even though *sopa* is meant for flamingo, you can set up this repository locally
 ## Coding guidelines
 
 - Use the `black` formatter and `isort`. Their usage should be automatic as they are in the `pyproject.toml` file. Depending on your IDE, you can choose to format your code on save.
-- Follow the [PEP8](https://peps.python.org/pep-0008/) style guide. In particular, use snake_case notations (and PascalCase for classes).
+- Follow the [PEP8](https://peps.python.org/pep-0008/) style guide.
 - Provide meaningful names to all your variables and functions.
 - Document your functions and type your function inputs/outputs.
-- Create your functions in the intended file, or create one if needed. See the project layout.
 - Try as much as possible to follow the same coding style as the rest of the repository.