mokapot v0.10.0

[v0.10.0] - 2023-09-11

Breaking changes

• Mokapot now uses numpy.random.Generator instead of the deprecated numpy.random.RandomState API.
  New rng arguments have been added to functions and classes that rely on randomness in lieu of setting a global random seed with np.random.seed(). Thanks @sjust-seerbio! (#55)

Changed

• Added linting with Ruff to tests and pre-commit hooks (along with others)!

Fixed

• The PepXML reader, which broke due to a Pandas update.
• Potential bug if lowercase peptide sequences were used and protein-level confidence estimates were enabled
• Multiprocessing led to the same training set being used for all splits (#104).

mokapot v0.9.1

[0.9.1] - 2022-12-14

Changed

• Cross-validation classes are now detected by looking for inheritance from the sklearn.model_selection._search.BaseSearchCV class.

Fixed

• Fixed backward compatibility issue for Python <3.10.

mokapot v0.9.0

[0.9.0] - 2022-12-02

Added

• Support for plugins, allowing mokapot to use new models.
• Added a custom Docker image with optional dependencies.

Fixed

• Confidence objects are now picklable.

Changes

• Updated GitHub Actions.
• Migrated to a full pyproject.toml setuptools build. Thanks @jspaezp!

mokapot v0.8.3

[0.8.3] - 2022-07-20

Fixed

• Fixed the reported mokapot score when group FDR is used.

mokapot v0.8.2

[0.8.2] - 2022-07-18

Bug fixes and small improvements.

Added

• mokapot.Model() objects now recored the CV fold that they were fit on. This means that they can be provided to mokapot.brew() in any order and still maintain proper cross-validation bins.

Fixed

• Resolved issue where models were required to have an intercept term.
• The PepXML parser would sometimes try and log transform features with 0's, resulting in missing values.

mokapot v0.8.1

[0.8.1] - 2022-06-24

Added

• Support for previously trained models in the brew() function and the CLI
  using the --load_models argument. Thanks @sambenfredj!

Fixed

• Using clip_nterm_methionine=True could result in peptides of length
  min_length-1.
• Links to example datasets in the documentation.

mokapot v0.8.0

[0.8.0] - 2022-03-11

Thanks to @sambenfredj, @gessulat, @tkschmidt, and @MatthewThe for
PR #44, which made these things happen!

Added

• A new command line argument, --max_workers. This allows the cross-validation folds to be computed in parallel.
• The PercolatorModel class now has an n_jobs parameter, which controls parallelization of the grid search.

Changes

• Improved speed by using multiple jobs for grid search by default.
• Parallelization within mokapot.brew() now uses joblib instead of concurrent.futures.

mokapot v0.7.4

Improved CLI documentation

Changed

• Improved documentation and added warnings for --subset_max_train. Thanks @jspaezp!

mokapot v0.7.3

This release is a small patch.

Fixed

• Fixed bug where the --keep_decoys did not work with --aggregate. Also,
  added tests to cover this. Thanks @jspaezp!

mokapot v0.7.2

Added

• --keep_decoys option to the command line interface. Thanks @jspaezp!
• Notes about setting a random seed to the Python API documentation. (Issue #30)
• Added more information about peptides that couldn't be mapped to proteins. (Issue #29)

Fixed

• Loading a saved model with mokapot.load_model() would fail because of an
  update to Pandas that introduced a new exception. We've updated mokapot
  accordingly.

Changed

• Updates to unit tests. Warnings are now treated as errors for system tests.