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CHANGELOG.md

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Changelog

0.44.0

Fixed

  • Maybe fixed the issue where nothing actually gets installed?

[0.43.0]

Changed

  • Updated deps, including updating to numpy 2.0 and numba 0.60.0

0.42.0

Changed

  • Renamed the doc folder docs
  • Altered noxfile.py to reflect the poetry -> pdm change

Fixed

  • Apparently I moved the init_logging function at one point and forgot to update everything else

0.41.0

Changed

  • Replaced use of poetry as package manager with pdm

0.40.0

Changed

  • At this point, lots. More structural pattern matching, lots of typing fixes for mypy
  • Removed black as formatter, using ruff
  • Moved ruff config to its own file

0.31.0

Changed

  • Anndata now uses gene symbols instead of ensembl geneids for var_names

0.30.1 and 0.30.2 - 2023-08-15

Fixed

  • removed some testing code

0.30.0 - 2023-08-15

Changed

  • No longer save the results of run as a loom file - save it directly as an anndata object
  • replaced more "if...elif...else" with pattern matching
  • ExInCounter.readtranscriptmodels now returns the number of features and number of chromosome examined because that is all that was being used

0.29.0 - 2023-08-07

Fixed

  • LOOKS LIKE VELOCYTO IS BACK ON THE MENU, BOYS!

Changed

  • Updated to require Python 3.10 as minimum version
  • Updated to use Typer 0.9.0
  • Updated dependencies
  • Pulled a lot out of velocyto.commands._run() into separate functions
  • Removed ability to add UMAP and cluster info to the loom file - that will be regenerated in other software, so why?

0.28.0 - 2023-02-24

Changed

  • Code cleanup and improvements thanks to sourcery

0.27.0 - 2023-02-23

Changed

  • Pass the actual "samtools_memory" value to samtools instead of checking the amount of memory available.
    • Also change to passing the argument as a string, allowing for the use of a prefix instead of requireing memory to be defined in megabytes.

0.26.0 - 2023-02-22

Changed

  • Various code cleanups
  • Add ruff as package linter

0.20.0, 0.21.0, 0.22.0, 0.23.0, 0.24.0, and 0.25.0

Changed

  • Various. No longer sure but a lot.

0.19.1 - 2022-06-30

Fixed

  • Fixed version issues

0.19.0 - 2022-06-29

Changed

  • Removed dumping all imports into init.py and then just importing the entire module (which lead to circular imports) and am importing as needed
  • removed wildcard importing
  • removed unused imports
  • commented out a lot of unused assigned variables

Fixed

  • lots of changes to fix things flagged by flake8

0.18.0 - 2022-06-29

Changed

  • Black formatting
  • Replaced setup.py with pyproject.toml
  • remove distutils from build
  • lock requirements and versions