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v4.0.0#201

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RalfG merged 148 commits intoreleasescompomics/ms2pip:releasesfrom v4.0.0compomics/ms2pip:v4.0.0Copy head branch name to clipboardJul 17, 2024

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Commits

Commits on Feb 2, 2023

• Import exceptions module completely

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Commits on Feb 3, 2023

• Refactor process_peptides and process_spectra to avoid code duplication and to allow multiple PSMs per peptide.

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Commits on Feb 15, 2023

• Remove obsolete tests for SinglePrediction

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• Remove old feature_names code (should still be reimplemented)

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Commits on Mar 1, 2023

• Merge branch 'releases' of https://github.com/compomics/ms2pip_c into more-refactoring

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• psm_id in peprec/pred_emp

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Commits on Mar 3, 2023

• Restructured Python API and CLI (WIP)

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Commits on Mar 4, 2023

• Merge branch 'more-refactoring' of https://github.com/compomics/ms2pip_c into more-refactoring-rg

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Commits on Mar 5, 2023

• Reorder psm_id

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• Move package metadata to pyproject.tom

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Commits on Mar 6, 2023

• change return_results to MSPIP obj

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• Restructure package; remove obsolete and unused code

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• Merge branch 'more-refactoring' of https://github.com/compomics/ms2pip_c into more-refactoring

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Commits on Mar 10, 2023

• More restructuring (WIP)

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Commits on Mar 13, 2023

• Implement ProcessingResult

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Commits on Mar 17, 2023

• Update pyproject, setup.py, manifest

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• Add psm_id before filtering input; do not use yield in batch_processing

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Commits on Mar 31, 2023

• Implement psm_list throughout MS²PIP, removing peprec dataframe usage

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Commits on Apr 11, 2023

• logging for modification handling

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• Merge branch 'more-refactoring' of https://github.com/compomics/ms2pip into more-refactoring

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• put warning for modificaiton on invalid aa

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• import change

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Commits on Apr 14, 2023

• Further refactoring for 4.0:

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• Merge branch 'more-refactoring' of https://github.com/compomics/ms2pip_c into more-refactoring

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Commits on Apr 19, 2023

• bug fix invalid modification

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Commits on Apr 21, 2023

• Fix invalid modification bug in encoder

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• Merge branch 'more-refactoring' of https://github.com/compomics/ms2pip_c into more-refactoring

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Commits on Jun 8, 2023

• Remove typing of optional spectrum_utils import

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• Temporarily disable tests (outdated)

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Commits on Jun 23, 2023

• Remove match_spectra functionality

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• Reimplement predict-single, add logging option to CLI, add credits to CLI, minor fixes and improvements

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• Remove files related to old config file

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Commits on Jun 24, 2023

• Make cython_modules, models_c, feature_names, and encoder private; add download_models function (related to #200), remove unused exceptions, fix setuptools find directive

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• Add documentation; update docstrings; update citation.cff

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• Add readthedocs config

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• Add werkzeug dependency, add git-lfs to readthedocs config

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• Update readthedocs config

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Commits on Jun 25, 2023

• Update test and build workflows

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• Use setuptools for readthedocs

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• Download models if needed in predict-single

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• Tweak readthedocs workflow

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• Tweak readthedocs workflow

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Commits on Jun 27, 2023

• Add mirror plot images for docs

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• Update docs

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• Fix peak ordering bug in Result.as_spectra()

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• Update docs

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• Use ubuntu latest for build workflow

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Commits on Jun 28, 2023

• Update gh-action-pypi-publish versioning

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• Remove PyTables dependency (use parquet or feather instead?)

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• Bump version

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Commits on Jun 29, 2023

• Move cibuildwheel options to pyproject.toml

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Commits on Jul 1, 2023

• Add plot_spectra method to ProcessingResult; better handle missing optional dependency

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Commits on Aug 30, 2023

• Fix compatibility with MassModifications encoder.py; add tests

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Commits on Sep 4, 2023

• Implement get_training_data

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Commits on Sep 8, 2023

• timstof_models

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Commits on Sep 12, 2023

• add ms2pip timsTOF models

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• fix training data function

  ArthurDeclercq

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• changed model filenames

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• Merge pull request #203 from compomics/timstof_models

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• CI: Skip Python 3.12 builds for now

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• Version bump

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• Merge branch 'v4.0.0' of https://github.com/compomics/ms2pip_c into v4.0.0

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Commits on Sep 13, 2023

• Upgrade GitHub Action versions

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Commits on Sep 18, 2023

• Allow missing precursor charge in mzML

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• version bump

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Commits on Nov 27, 2023

• refactored _generate_preds_dict and _normalize_spectra for compatibilty of new constructor

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Commits on Dec 8, 2023

• refactored write_msp and added basic normalization methods

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Commits on Dec 11, 2023

• adjust: fix format issue in write_msp output

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• changed write_mgf function to use list of processingresults

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• Add annotate_spectra function to get annotated observed intensities

  RalfG

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• Update models docs

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• changed normalization for write_mgf

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Commits on Dec 13, 2023

• refactored write_csv to use list of processingresult

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• refactored write_dlib functions

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• refactored _write_dlib_entries

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Commits on Jan 13, 2024

• new ms2pip model

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• change intermediate name

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• missing brackets

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Commits on Jan 24, 2024

• Restructure get_feature_names, make feature names more logical, and add descriptions in docs

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• Docs: Fix type, extend local install instructions, add annotate-spectra usage mode.

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Commits on Jan 25, 2024

• Docs: Fix descriptions

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Commits on Feb 5, 2024

• swap old timstof model for newer class 2 included model

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• Merge pull request #210 from compomics/new_ms2pip_model

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Commits on Feb 6, 2024

• add both timsTOF models with default one

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Commits on Feb 8, 2024

• Update prediction-models.rst

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• Update prediction-models.rst

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Commits on Feb 9, 2024

• Minor formatting + docstring changes

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• add tdf support with timsrust_pyo3

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• add timsrust_pyo3 as optional dependency

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• Merge pull request #213 from compomics/tdf_support2

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Commits on Mar 5, 2024

• Update publish workflow to use trusted publising

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• Version bump

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• timsrust: Wait to add optional dependency until on PyPI; version bump

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Commits on Mar 27, 2024

• Add argument to specify PSM file type

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• Ensure spectrum dtypes

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• Add tdf optional dependency (now on PyPI)

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• Version bump

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Commits on Mar 28, 2024

• Ensure path is string before passing to timsrust_pyo3

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Commits on Apr 5, 2024

• set PSM filetype to "infer" if argument was None

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• Also allow Bruker miniTDF as spectrum file type; parse RT from MGF

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Commits on Apr 8, 2024

• Use rust for spectrum parsing; fix bug in writing correlations

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• Add workflow_dispatch trigger for test CI

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• Update dependencies; version bump

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Commits on Apr 17, 2024

• Ensure spectrum_path is string before passing to pyo_3

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• Version bump

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Commits on May 2, 2024

• Upgrade to Pydantic v2

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• Raise NotImplementedError in fasta2speclib until reimplemented for ms2pip v4

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• Version bump

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• Add macosx_arm64 to build roster

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• Update CI

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• Merge branch 'releases' of https://github.com/compomics/ms2pip_c into v4.0.0

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• Fix linting errors

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Commits on May 3, 2024

• Initial restructuring of fasta2speclib for predict-library

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Commits on May 6, 2024

• working predict_library and csv output

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Commits on May 7, 2024

• Functional .msp output

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• unset normalization defaults

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• Continue predict-library implementation; add tests

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• search_space: Add docs, better define api; restructure

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• Merge branch 'reimplement-predict-library' of https://github.com/compomics/ms2pip_c into reimplement-predict-library

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• Merge branch 'v4.0.0' of https://github.com/compomics/ms2pip_c into spectrum-output

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• Reimplement most of spectrum_output for v4.0.0

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• Remove unused imports

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Commits on May 8, 2024

• Finish DLIB; add general write_spectra function...

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• Clip negative predicted intensities; Allow psm_list with multiple runs/collections for prediction

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• Implement spectrum output for CLI functions

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• Fix linting errors

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• Merge pull request #220 from compomics/spectrum-output

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• Merge branch 'v4.0.0' of https://github.com/compomics/ms2pip_c into reimplement-predict-library

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• Implement spectrum-output for predict-library

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• Avoid memory issues by converting to Peptidoforms lazily

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• Remove obsolete tests; fix search space test imports

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• CI: Reinstate tests

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• Remove unused import; clean up test imports

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• Fix test workflow

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• Fix search_space_test

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• Merge pull request #219 from compomics/reimplement-predict-library

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• Update docs

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Commits on May 9, 2024

• Doc updates; version bump

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• predict-library: Allow fasta file to be missing from config file if provided in CLI

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• Fix build artifact upload

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• Revert fasta assignment

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Commits on Jul 1, 2024

• CI: Fix artifact download step

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• Ignore empty spectra

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Commits on Jul 8, 2024

• Add ion mobility prediction support through IM2Deep

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Commits on Jul 9, 2024

• Version bump; attempt to fix build workflow

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Commits on Jul 17, 2024

• Update docs

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• Version bump

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• Do not test for Python 3.12 (no pyOpenMS support yet)

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