v2.1.0

What's Changed

• Asyncable functions by @JoshLoecker in #258

Full Changelog: v2.0.2...v2.1.0

v2.0.2

What's Changed

• chore: bump zFPKM>=1.1.1 by @JoshLoecker in #256

Full Changelog: v2.0.1...v2.0.2

v2.0.1

What's Changed

• Update Jupyter Notebook by @JoshLoecker in #254

Full Changelog: v2.0.0...v2.0.1

v2.0.0

Version 2.0

Note

This change list was copied from the Pull Request
The list of "What's Changed" does not include all changes as the diff-viewer in GitHub was unable to compute changes from the previous version; thus, a local-merge was created, and this hides changes
You can view #252 for the list of changes in its entirety

This is a massive pull request that contains a huge variety of features, improvements, bug fixes, and changes. While these are too numerous to list, the main components include:

• Per-data-type input and output controls
  • It is now possible to specify exactly where input and output files should be read from and saved to
  • This adds some complexity and verbose-ness to each function, but significantly reduces COMO's strictness for file-level organization
• Refactored iMAT integration to fix negative-values being placed in middle-expression bin
• Fixed FPKM calculations to be on a per-gene basis instead of per-sample
• Use Stouffer's method to integrate z-scores
• Better handling of incorrect data from remote APIs (e.g., BioDBNet and MyGene.info)
• Added integration with Salmon gene quantification and its TPM calculations
• Added and updated type hints on significant portions of public (and most private) APIs for easier understanding of what is needed for input and output files/data
• Better error and warning messages, plus better error handling

What's Changed

• Revert mistaken merge by @JoshLoecker in #209
• chore(deps): bump astral-sh/ruff-action from 2 to 3 by @dependabot[bot] in #213
• chore(deps): bump astral-sh/setup-uv from 4 to 5 by @dependabot[bot] in #212
• Version 2.0 by @JoshLoecker in #252

Full Changelog: 1.11.1...v2.0.0

v1.12.0-dev4

Test GitHub PyPi publishing workflow

v1.12.0-dev3

Test GitHub PyPi publishing workflow

v1.12.0-dev1

Test PyPi publishing workflow

v1.12.0-dev2

Test GitHub PyPi publishing workflow

1.11.1

What's Changed

• fix: do not make Solver private by @JoshLoecker in #191
• Add boundary column by @JoshLoecker in #196
• Write zFPKM Graphs by @JoshLoecker in #197
• Modify column names by @JoshLoecker in #198
• Set Troppo Source by @JoshLoecker in #202
• chore(deps): bump astral-sh/ruff-action from 1 to 2 by @dependabot in #201
• chore(deps): bump astral-sh/setup-uv from 3 to 4 by @dependabot in #200
• hotfix: allow setting solvers through troppo; update actions by @JoshLoecker in #203

Full Changelog: 1.11.0...1.11.1

1.11.0

What's Changed

• Bump docker/build-push-action from 5 to 6 by @dependabot in #183
• Purge R code by @JoshLoecker in #187

Full Changelog: v1.10.0-main...1.11.0