Developer documentation

Please refer to the scanpy developer guide.

Pre-commit documentation

Pre-commit checks are fast programs that check code for errors, inconsistencies and code styles, before the code is committed. This is a brief documentation of pre-commits checks pre-sets in the scverse-template.

The following pre-commit checks for code style and format.

• black: standard code formatter in Python.

• autopep8: code formatter to conform to PEP8 style guide.

• isort: sort module imports into sections and types.

• prettier: standard code formatter for non-Python files (e.g. YAML).

• blacken-docs: black on python code in docs.

The following pre-commit checks for errors, inconsistencies and typing.

• flake8: standard check for errors in Python files.

  • flake8-tidy-imports: tidy module imports.

  • flake8-docstrings: pydocstyle extension of flake8.

  • flake8-rst-docstrings: extension of flake8-docstrings for rst docs.

  • flake8-comprehensions: write better list/set/dict comprehensions.

  • flake8-bugbear: find possible bugs and design issues in program.

  • flake8-blind-except: checks for blind, catch-all except statements.

• yesqa: remove unneccesary # noqa comments, follows additional dependencies listed above.

• autoflake: remove unused imports and variables.

• pre-commit-hooks: generic pre-commit hooks.

  • detect-private-key: checks for the existence of private keys.

  • check-ast: check whether files parse as valid python.

  • end-of-file-fixer:check files end in a newline and only a newline.

  • mixed-line-ending: checks mixed line ending.

  • trailing-whitespace: trims trailing whitespace.

  • check-case-conflict: check files that would conflict with case-insensitive file systems.

• pyupgrade: upgrade syntax for newer versions of the language.

Notes on pre-commit checks

• flake8: to ignore errors, you can add a comment # noqa to the offending line. You can also specify the error id to ignore with e.g. # noqa: E731. Check flake8 guide for reference.

• You can add or remove pre-commit checks by simply deleting relevant lines in the .pre-commit-config.yaml file. Some pre-commit checks have additional options that can be specified either in the pyproject.toml or pre-commit specific config files, such as .prettierrc.yml for prettier and .flake8 for flake8.