Matt Stone
Matt Stone
a brief manifest including a tag and/or version for the pipeline and/or toolkit would be nice to have by default in all of our snakemake pipelines
I'm introducing a function to search a directory for a FASTQ belonging to a given sample, regardless of extension or [name formatting](https://support.illumina.com/help/BaseSpace_Sequence_Hub_OLH_009008_2/Source/Informatics/BS/NamingConvention_FASTQ-files-swBS.htm). I've added it to a new submodule, `util.files`,...
Closes #88 Closes #90 --- I am opening a feature branch to collect a number of PRs supporting the addition of a `MetricWriter`. - [x] #109 - [x] #124 -...
`pytest-cov` would be sufficient, but a codecov subscription might be nice
https://peps.python.org/pep-0585/ > Importing those from typing is deprecated. Due to [PEP 563](https://peps.python.org/pep-0563/) and the intention to minimize the runtime impact of typing, this deprecation will not generate DeprecationWarnings. Instead, type...
Unused `type: ignore` statements should get cleaned up during #126 (which adds a warning for unused type ignores) We should also circle through and review any remaining type ignores to...
I split the remaining code in #107 into two PRs to facilitate review. This PR introduces several of the assertion methods used when constructing the `MetricWriter`. (See #107 for how...
- [x] Tooling configuration should be moved out of per-tool config files and into` pyproject.toml` - [x] flake8.cfg #140 - [x] mypy.ini - [x] `dev-dependencies` [is deprecated](https://python-poetry.org/docs/managing-dependencies/) and should be...
It's more conventional to reserve `__init__.py` for imports and namespace management (i.e. with `__all__`). If this is implemented, there should likely be (approximately) one PR per module - [ ]...
It would be great if the structure of the project could be updated to be more consistent with Python packaging conventions (in before someone points out the oxymoron). Tests should...