All notable changes to this project will be documented in this file.
The format is based on Keep a Changelog, and this project adheres to a type of CalVer.
version -> vYYYY.BUILD where BUILD is a lexicographically increasing number: i.e. 1001, 1002, ..., 1999, 22000
- changed ratio to a float (#42)
- use pixi v0.34 for dev env/docker build
- bumped minimum polars to 1.10.0
- minimum python version bumped to 3.9
- override runtime executables with env vars (#31)
- proper exit code when nothing to process (#37)
- remove erroneous debug print (#28)
- change python reqs to >=3.8
- upgraded pixi to v0.28.2
- upgraded pixi to v0.18 for pyproject.toml support
- fix(#25)
- actually fix(#17)
- Docker container uses pixi for tighter control (actual lock file)
- warn user if there is a permission error on local directory
- #22
- #21
This release followed a major refactor and some things may be missing from the changelog. Please see the documentation for up to date usage instructions.
- sphinx-based documentation website
- a log file produced in
./pipelinewhich includes all subproccess output - added polars to dependencies to improve tabulated data operations
- made at least one test case for all commands
- hidden
checkscommand to invoke pre-run checks on demand for debugging
- new version scheme of YYYY.BUILD
- pycashier will proceed even if a sample fails
- output is less verbose
- combine is now receipt and includes headers and basic calculations
- headers are included in all final tsvs
- visual indicator of work when running counts on files (#18)
- filename regex for merge is less stringent (#17)
- won't fail if unneeded program is missing (#16)
- updated ci pipeline to incorporate test prior to a tagged release
- remove
|type operator for python <3.10 compatibility (#13) - ensure init-check is run (#14)
- sample parameter for all subcommands
- added some broad input/output tests
- global parameters (i.e. threads or samples to fallback on)
- update python version requirements to >=3.8,<3.11
- updated conda lock file for docker and pinned based images to sha256 for reproducibility
- stop merge if both R1 and R2 not found
- removed extra whitespace in single cell output tsv
- added warning about broken symlinks (especially for docker) (#12)
- typechecking w/Mypy
- pinned docker image base to stable tag
- made init check dependent on command run (fixes #10)
- ignore hidden files in input directory (fixes #9)
- simplified detection of PE reads
- several UI changes for clarity and simplicity
- check for config file and exit if it doesn't exist
- separate
rich.console.Consolefor stderr outputs - automated docker build and switched to ghcr.io
- new
-y/--yesflag to skip prompts
- switch project management to pdm
- improved merge error message
- made docker build multi-stage to reduce footprint
- updated ci to use python action instead of poetry
- Fixed(#8)
- refactored cli source for simplicity
- project now adheres to CalVer
- Encourage user to increase thread count
- Drop
justformaketo streamline development
- Docker image instructions
- Use wider format help on bigger terminals
- Dockerfile
- Fix #8 to allow .fastq.gz in input directory
- Swapped
rich-clickforclick-rich-help
Pycashiernow manages version withbumpver
- Dropped yaml-based config for toml
- This CHANGELOG
- Combine command to simply combine output tsv's into one file
- Length offset to filter sequences post-clustering
- Option to
--skip-trimmingin extract - Config file to improve UX
- Entire CLI was redesigned around click/rich
- When performing adapter trimming the min/max length is set to length +/- Levenshtein distance
- Sample Queue table is formatted inline with new CLI
- Dropped regex in "extract" in favor of simple string matching
- Merge can take unzipped fastqs now