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CHANGELOG.md

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Changelog

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 Semantic Versioning.

[0.7.4] - 2024-08-24

Changed

  • Added many tests for util functions

Fixed

  • Changed a nopython function to use numba compatible indexing

[0.7.3] - 2024-08-20

Changed

  • Used "not" instead of "~" in an if statement
  • Added a test for the coverage function

Fixed

  • Ensured that the coverage value returns the expected value (previously returned an empty generator)

[0.7.2] - 2024-08-17

Changed

  • Included output_file as required argument for finaletoolkit cleavage-profile.

Fixed

  • Fixed incompatible types in min function through an explicit cast of chrom_sizes to integers.

[0.7.1] - 2024-08-11

Changed

  • include chrom_sizes file as required argument for finaletoolkit cleavage-profile
  • Numpy dependency version set to <2 to avoid breaking changes from numpy 2. This will change in the future as we migrate to use numpy 2.
  • Replaced all instances of np.NaN with np.nan.

Fixed

  • Fixed minor issues with typing in finaletoolkit.genome.gaps
  • Fixed issue where data files are not packaged with FinaleToolkit

[0.7.0] - 2024-07-21

Added

  • Brief description of modules in documentation under structure page
  • Docstring
  • finaletoolkit.version module containing single-source __version__ variable
  • remove_nocov option in finaletoolkit.frag.delfi to toggle dropping two bins with low coverage. These bins are dropped in delfi_scripts but may not apply to fragment files not aligned to hg19.
  • tests for finaletoolkit.frag.delfi_merge_bins

Changed

  • finaletoolkit.frag.delfi changed to accept files aligned to almost any reference genome.
  • finaletoolkit.frag.delfi_merge_bins algorithm changed to be reference genome-agnostic and consistent with delfi_scripts
  • finaletoolkit delfi options -G, -M, and -R to drop gc-correction, merging, and remove nocov bins, respectively.

Removed

  • unused flags for finaletools delfi: -W, --window-size
  • redundant flags for finaletools delfi: -gc, --gc-correct, -m, --merge-bins

[0.6.5] - 2024-07-15

Changed

  • utils.agg_bw now supports PathLike for input
  • docstrings for frag.end_motifs.EndMotifsIntervals changed to be compatible with Sphinx

Fixed

  • added missing gzip import for utils.agg_bw

Added

  • tests for utils.agg_bw

[0.6.4] - 2024-06-04

Added

  • interval_size argument for adjust_wps

Changed

  • adjust_wps checks if median_window is larger than interval
  • remove default options from some private helper functions for better error catching/predictable behavior.

Fixed

  • wpsrelated functions and subcommands

[0.6.3] - 2024-05-31

Fixed

  • fixed writing to bed.gz files when using coverage

[0.6.2] - 2024-05-30

Fixed

  • adjusted handling of contig, start, stop for frag_generator so that coverage does not throw exceptions for genomewide intervals.

Added

  • test for single_coverage

[0.6.1] - 2024-05-26

Changed

  • add __version attribute
  • finaletoolkit --version displays package version
  • update PyPI page to include links

[0.6.0] - 2024-05-26

Fixed

  • Fixed intersect policy for cleavage_profile. Now it calls frag_generator with a policy of any.
  • Clean up some comments and docstrings
  • Fixed logging from coverage function

Added

  • Added numerous util functions
  • Added left and right options to cleavage_profile and CLI cleavage-profile.
  • Added tests for cleavage profile and WPS.

Changed

  • Minimum Python version 3.9
  • Changed filter_bam to have same filters as FinaleDB
  • utils.frag_generator raises ValueError if start or stop are specified without contig
  • Type hints changed to use literals when possible

Removed

  • Removed utils.get_contig_lengths
  • Removed data, conda_envs, and figs directories
  • Removed unused dependencies click, pybedtools, and `cython
  • Remove some unused imports from module files

[0.5.2] - 2024-05-08

Fixed

  • interval-mds CLI subcommand calculates correctly without large negative values.
  • interval-mds CLI subcommand now correctly parses tsv files.

Added

  • Most end-motif related Python functions accept Path instances as inputs for files.
  • Unit and function tests, especially for end-motif related functions.

[0.5.1] - 2024-05-03

Changed

  • All instances of finaletools have been renamed to finaletoolkit
  • All default tabular files are now TSV
  • Update contacts in TOML

Fixed

  • interval-mds and mds both calculate correctly when one motif has a frequency of 0

[0.5.0] - 2024-04-24

Added

  • Added finaletools.interval_end_motifs function to calculate end-motifs over genomic intervals. Stores results in an IntervalEndMotifs object.
  • Added CLI subcommand interval-end-motifs to calculate end-motifs over genomic intervals.
  • Added CLI subcommand interval-mds to calculate MDS over intervals from interval end-motifs table.

Changed

  • Added gc_correct option to delfi_merge_bins so that merging is possible without GC correction

Fixed

  • delfi can now be run with gc_correct=false and merge_bins=true
  • fixed cleavage_profile import in frag

[0.4.5] - 2024-04-9

Added

  • Added CHANGELOG.md

Fixed

  • Fixed bug in coverage where writing to non-bedgraph files would result in an error

[0.4.4] - 2024-04-5

Changed

  • finaletools.frag.coverage accepts Frag.gz format files
  • update CLI help messages and docstrings for coverage and DELFI to reflect current and previous changes
  • update docs

[0.4.2] - 2024-03-28

Changed

  • Updated emails in pyproject.toml