v1.0.4

What's Changed

• 123 docs fix link to notebook in colab link by @BioGeek in #124
• Feat separate winnow predict filtered dataset outputs by @JemmaLDaniel in #131
• Refactor Calibrator Saving to Use Single Pickle File by @JemmaLDaniel in #126
• Feat download general model from HuggingFace as the default when loading a calibrator by @JemmaLDaniel in #130
• Refactor: move Prosit beam filtering out of data loading by @JemmaLDaniel in #132
• Feat Prosit missingness support by @JemmaLDaniel in #133
• fix: add spectrum_id to both output dataframes for winnow predict command by @JemmaLDaniel in #135
• chore: rename input columns to new instanovo column names by @JemmaLDaniel in #134
• Refactor switch jaxtyping to numpy by @JemmaLDaniel in #127
• docs: change calibrator docstrings to describe the MLP classifier by @JemmaLDaniel in #149
• CI: Add Test Coverage Reporting by @JemmaLDaniel in #129
• CI: Migrate coverage badge to Gist-based dynamic system by @JemmaLDaniel in #150
• docs: add config file for PR agent by @BioGeek in #152
• Docs: use a valid commit example in contributing section by @JemmaLDaniel in #153
• chore: support emoji rendering for mkdocs by @JemmaLDaniel in #155
• Docs: remove stray quotation mark from contributing section by @JemmaLDaniel in #154
• Implement Typer + Hydra Configuration Architecture by @JemmaLDaniel in #147
• docs: small typo and commit style fixes to docs and README by @JemmaLDaniel in #156
• Update Prosit cysteine handling and standardise residue terminology by @JemmaLDaniel in #158
• fix: specify residue_remapping in Winnow data loader by @JemmaLDaniel in #161
• Chore update script logs by @JemmaLDaniel in #165
• Chore train and predict sample with cli by @JemmaLDaniel in #164
• fix: add safety checks for string peptides before computing number of matches in database-grounded FDR calculation by @JemmaLDaniel in #166
• Feat improve instanovo data loader by @JemmaLDaniel in #159
• Refactor generalise prosit features by @JemmaLDaniel in #168
• docs: update documentation to latest changes and fix format errors by @JemmaLDaniel in #169
• refactor: compute precursor mass at runtime from precursor charge and precursor m/z columns by @JemmaLDaniel in #163
• Feat: compute-features command by @JemmaLDaniel in #171
• Feat allow mgf files for instanovo data loader by @JemmaLDaniel in #172
• chore(deps): bump the uv group across 1 directory with 4 updates by @dependabot[bot] in #170
• chore(deps): bump the uv group across 1 directory with 2 updates by @dependabot[bot] in #175
• Fix AIchor Docker image compatibility for non-root users by @JemmaLDaniel in #177
• Chore upgrade dependencies by @JemmaLDaniel in #176
• chore(deps): bump pytest from 9.0.2 to 9.0.3 in the uv group across 1 directory by @dependabot[bot] in #189
• chore(deps): bump nbconvert from 7.17.0 to 7.17.1 in the uv group across 1 directory by @dependabot[bot] in #196
• fix: add utils folder to setuptools package list by @JemmaLDaniel in #199
• chore: update example data to HeLa Single Shot sample data + make train-sample calibrator by @JemmaLDaniel in #200
• chore: update getting started notebook by @JemmaLDaniel in #201
• chore: remove requirements.txt by @JemmaLDaniel in #203
• chore: bump version of lxml to 6.1.0 for security patch by @JemmaLDaniel in #202
• docs: update documentation to refer to new example datasets and minor changes to README by @JemmaLDaniel in #204

New Contributors

• @dependabot[bot] made their first contribution in #170

Full Changelog: v1.0.3...v1.0.4

v1.0.3

What's Changed

• build: bump version to v1.0.3 by @BioGeek in #122

Full Changelog: v1.0.2...v1.0.3

v1.0.2

What's Changed

• ci: normalize package name to canonical name by @BioGeek in #120

Full Changelog: v1.0.1...v1.0.2

v1.0.1

What's Changed

• ci: change project name to winnow_fdr to match PyPI name by @BioGeek in #118

Full Changelog: v1.0.0...v1.0.1

v1.0.0

What's Changed

• fix: filter out sequences longer than 30 in first and second beam prediction by @JemmaLDaniel in #54
• feat: add z-score over beam results to beam features by @JemmaLDaniel in #52
• feat: add fdr metrics into metadata table for bayes and database-grounded classes by @JemmaLDaniel in #48
• fix: filter out first beam sequences longer than 30 amino acids by @JemmaLDaniel in #55
• Feat create a train and predict script by @JemmaLDaniel in #51
• fix: fix database-ground confidence-cutoff by @JemmaLDaniel in #64
• fix: drop top predictions when computing fdr threshold by @JemmaLDaniel in #63
• Feat: change from logistic regression to MLP classifier by @JemmaLDaniel in #68
• Fix confidence cutoff to consistently select leftmost root by @JemmaLDaniel in #66
• chore: add license by @JemmaLDaniel in #83
• Fix add graceful error handling by @JemmaLDaniel in #82
• Feat dockerise for AIchor by @JemmaLDaniel in #76
• feat: add unit tests by @JemmaLDaniel in #81
• CI: run tests on merge into main by @JemmaLDaniel in #100
• fix: set irt predictor seed to 42 by default by @JemmaLDaniel in #93
• chore: add external dataset modifications to residue masses dict by @JemmaLDaniel in #92
• fix: only save an irt predictor model when available by @JemmaLDaniel in #94
• feat: add q-value support by @JemmaLDaniel in #95
• refactor: enforce same FDR calculation methods between database-grounded and non-parametric methods by @JemmaLDaniel in #103
• Feat: use non-parametric FDR estimation by @JemmaLDaniel in #69
• feat: add casanovo dataset loader by @JemmaLDaniel in #75
• feat: add early stopping to the calibrator by @JemmaLDaniel in #104
• refactor: implement DatasetLoader interface for data loading by @JemmaLDaniel in #73
• feat: create winnow example notebook by @JemmaLDaniel in #84
• 96 add mkdocs by @JemmaLDaniel in #97
• fix: make scripts folder a package by @BioGeek in #109
• refactor: explicitly specify packages for setuptools by @BioGeek in #111
• docs: fix workflow image URL in README by @BioGeek in #113
• publish the winnow_fdr package to pypi by @BioGeek in #115
• docs: add link to preprint in notebook and README by @BioGeek in #116

New Contributors

• @BioGeek made their first contribution in #109

Full Changelog: v1.0.0a...v1.0.0

v1.0.0a

What's Changed

• Port code from IN repo by @amabinsta in #1
• 11 implement to csv method to calibrationdataset class by @JemmaLDaniel in #12
• add bug and feat issue templates by @JemmaLDaniel in #16
• add pre-commit config by @JemmaLDaniel in #15
• fix: correct type hint for compute_ion_identifications by @JemmaLDaniel in #23
• resolve dependencies by @JemmaLDaniel in #17
• Implement alternative fdr scoring metrics by @JemmaLDaniel in #13
• Fix confidence cutoff bug by @amabinsta in #26
• fix: fix indexing errors for chimeric and beam features by @JemmaLDaniel in #21
• create winnow cli by @amabinsta in #35
• fix: swap numpyro beta parameters to correct ones by @JemmaLDaniel in #44
• docs: update README with project overview, installation instructions,… by @amabinsta in #39
• fix: prevent division by zero in compute_fdr by @JemmaLDaniel in #38
• feat: add a to_parquet method for metadata saving by @JemmaLDaniel in #37
• feat: add GitHub Actions workflows by @amabinsta in #40
• feat: improve issue templates by @amabinsta in #42
• adapt winnow to work with new instanovo by @JemmaLDaniel in #33

New Contributors

• @amabinsta made their first contribution in #1
• @JemmaLDaniel made their first contribution in #12

Full Changelog: https://github.com/instadeepai/winnow/commits/v1.0.0a