CHANGELOG.md

Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[3.1.1] - 2024-10-10

Changed

• Revert to linear calibration after transfer learning only

[3.1.0] - 2024-08-31

Changed

• Use scikit-learn instead of pygam for calibration

[3.0.8] - 2024-08-25

Changed

• Fix custom activation by using default implementation
• Loosen requirements

[3.0.7] - 2024-08-19

Changed

• Remove batch number parameter from GUI

[3.0.6] - 2024-08-08

Changed

• Debugging release issues

[3.0.5] - 2024-08-08

Changed

• Debugging release issues

[3.0.4] - 2024-08-08

Changed

• Debugging release issues

[3.0.3] - 2024-08-08

Changed

• Remove old python build

[3.0.2] - 2024-08-08

Changed

• Debugging release issues

[3.0.1] - 2024-08-08

Changed

• Windows release fix

[3.0.0] - 2024-08-08

Changed

• New TensorFlow versions that break support with earlier models

[2.2.38] - 2024-07-01

Changed

• Relax tensorflow version for mac

[2.2.37] - 2024-07-01

Changed

• Pin scipy version

[2.2.36] - 2024-04-14

Changed

• Set max threads

[2.2.35] - 2024-04-14

Changed

• Remove limit threads feature calc

[2.2.34] - 2024-04-13

Fixed

• Fix issue transfer learning single model mode

[2.2.33] - 2024-04-13

Changed

• Make single model mode available and the default

[2.2.32] - 2024-02-16

Changed

• Bump version

[2.2.31] - 2024-02-16

Changed

• Bump version

[2.2.30] - 2024-02-16

Changed

• Bump version with new workflows

[2.2.29] - 2024-02-16

Changed

• Bump version with .toml

[2.2.28] - 2024-02-16

Changed

• Removed dependencies (most importantly sklearn; which is optional now)

[2.2.27] - 2024-01-22

Changed

• Support for custom labels in plot

[2.2.26] - 2023-11-15

Fixed

• Fix memory usage, limit threads

[2.2.25] - 2023-11-15

Fixed

• Fixed multiprocessing

[2.2.24] - 2023-11-14

Changed

• Pass flag CCS feature extract

[2.2.23] - 2023-11-13

Changed

• Reintroduce ability to predict CCS

[2.2.22] - 2023-09-22

Fixed

• Fix pypi token GA

[2.2.21] - 2023-09-22

Fixed

• Fix non-initialized modifications

Fixed

• Allow for setting number of epochs

[2.2.20] - 2023-09-19

Fixed

• Fix selenium atom logging error

[2.2.19] - 2023-09-19

Fixed

• Fix selenium atom on AA

[2.2.18] - 2023-09-18

Fixed

• Fix wrong error except

[2.2.17] - 2023-09-18

Fixed

• Fix peptides that are too long and their modifcations

[2.2.16] - 2023-09-18

Changed

• bump version

[2.2.15] - 2023-09-18

Changed

• reduce logging (change to debug)

[2.2.14] - 2023-09-03

Fixed

• Fix missing debug time in feature extractor

[2.2.13] - 2023-09-03

Fixed

• Fix potential issues in feat extractor (uncommon AA)

[2.2.12] - 2023-08-19

Changed

• Set plotly param to false

[2.2.11] - 2023-08-19

Changed

• Remove assumption psm_utils_obj

[2.2.10] - 2023-08-19

Changed

• Add plotly diagnostic plots

[2.2.9] - 2023-08-08

Fixed

• Fix logger issue

[2.2.8] - 2023-08-08

Changed

• Activate garbage collection to clear GPU memory

[2.2.7] - 2023-08-03

Changed

• Reintroduce support for batched calculation
• Introduce batch_num_tf parameter for DeepLC that determines TF batch size

[2.2.6] - 2023-08-02

Changed

• Allow for linear piecewise calibration again
• More strict version of TF, as 2.13.0 crashes for transfer learning

[2.2.5] - 2023-08-02

Fixed

• Fixed a bug where a reinit led to issues with setting parallelism

[2.2.4] - 2023-07-06

Fixed

• Fixed a bug where it checked the calibration file while this was not initialized

[2.2.3] - 2023-06-28

Fixed

• Fixed a bug where missing atoms in encoding cause a crash

[2.2.2] - 2023-06-23

Fixed

• Fixed a bug where isotopes are incorrectly parsed

[2.2.1] - 2023-06-18

Fixed

• Fixed a bug where numpy no longer accepts dict_values, explicit list conversion

[2.2.0] - 2023-06-14

Fixed

• Fixed a bug where atom counts were wrong, fixed by retraining models with new features

[2.1.9] - 2023-05-09

Fixed

• Fixed a bug where detection of legacy csv is wrong

[2.1.8] - 2023-05-09

Changed

• remove pygam from GUI, set to true as default

[2.1.7] - 2023-05-09

Fixed

• fix setting cmd line calibration default

[2.1.6] - 2023-05-09

Fixed

• fix setting GUI calibration default

[2.1.5] - 2023-05-08

Fixed

• fix library feature

[2.1.4] - 2023-05-08

Changed

• slight refractoring

[2.1.3] - 2023-05-08

Changed

• slight refractoring

[2.1.2] - 2023-05-08

Changed

• add Arthur Declercq as contributor

[2.1.2] - 2023-05-08

Fixed

• dependency fix

[2.1.1] - 2023-05-08

Fixed

• Calibration bug fix

[2.1.0] - 2023-05-08

Changed

• Support for GUI and PSM utils
• Support for GUI and transfer learning

[2.0.4] - 2023-05-06

Changed

• Log peptide sequences that are too long

[2.0.3] - 2023-05-02

Changed

• bump version
• second try

[2.0.2] - 2023-05-02

Changed

• bump version

[2.0.1] - 2023-05-02

Changed

• bug fix for sequences > 60 AA
• bug fix non-resolved modifications

[2.0.0] - 2023-04-30

Added

• psm_utils integration
• pygam default calibrator

Changed

• additional support transfer learning
• code refractoring of feature extraction

Removed

• prediction library support
• piecewise linear calibration support

[1.2.1] - 2023-02-13

Changed

• Bump version

[1.2.0] - 2023-02-13

Added

• Support for DeepLCRetrainer

Changed

• Optimized library usage (~85% reduce in DeepLC prediction time) @markmipt

[1.1.2] - 2022-04-06

Changed

• Made Gooey an optional dependency (facilitates install on Linux). Install the optional dependencies for the graphical user interface with pip install deeplc[gui]

[1.1.1] - 2022-04-03

Added

• New native Python GUI, based on the Gooey package
• New standalone installer for Windows using PyInstaller and Inno Setup
• Added deeplc-gui entrypoint to start GUI from the command line

Changed

• CLI: Restructured help message
• Made DeepLC class API docstring consistent with CLI help message
• Docs: Moved dict_divider and split_cal explanation to README Q&A section.
• CI: Only run tests on commits to master or from a PR
• Refactoring: Cleaned up __main__.py
• Logging: Changed some loggings from DEBUG to INFO level, some from WARNING to INFO or DEBUG level

Removed

• Removed Java-based GUI in favor of new Python-based GUI

Fixed

• If run through CLI/GUI, all Tensorflow warnings are now fully suppressed
• Added --legacy_calibration CLI option to allow for old piecewise linear calibration while new pyGAM calibration method is default. --legacy_calibration is mutually exclusive with --pygam_calibration.

[1.0.1] - 2022-03-17

• Make version compatible with pip release

[1.0.0] - 2022-02-23

• Make version compatible with pip release

[1.0] - 2022-02-23

• Make pygam the default calibration method

[0.2.2] - 2022-02-17

• Bug fix where split_cal was not correctly passed
• CMD support for pygam calibration

[0.2.1] - 2022-02-03

• Scikit-learn and pygam dependency in setup

[0.2.0] - 2022-01-21

• Bug fix duplicate peptide+mod for DeepCALLC
• New feature DeepCALLC

[0.1.39] - 2022-01-12

• Version bump

[0.1.38] - 2022-01-10

• Deep(CAL)LC functionality

[0.1.37] - 2021-09-09

• Pygam as calibration function

[0.1.36] - 2021-09-09

• Update to Streamlit webserver: Use st.form and new official download button

[0.1.35] - 2021-08-09

• More elegant solution for library call as global

[0.1.34] - 2021-07-29

• Fix var call dict object

[0.1.33] - 2021-07-29

• Fix library delete call

[0.1.32] - 2021-07-29

• Temporary fix suggested by markmipt for the library

[0.1.31] - 2021-07-01

• Change logging to specified logger object instead of standard logger

[0.1.30] - 2021-06-09

• GUI: Fix small font through starting jar with cmd to increase font size
• Added testing for Python 3.9
• Relax h5py requirement to allow v3
• Fixed GitHub Action workflow for Streamlit docker image build

[0.1.29] - 2021-03-24

• Bug in writing library where a list was assumed so library only partially filled

[0.1.28] - 2021-03-17

• Make it optional to reload library

[0.1.27] - 2021-03-16

• Ignore library messages

[0.1.26] - 2021-03-15

• Force older library h5py for compatability

[0.1.25] - 2021-03-12

• Library gets appended for non-calibration peptides too

[0.1.24] - 2021-03-12

• Change the default windows install to pip instead of conda
• Change reporting of identifiers used from library

[0.1.23] - 2021-03-04

• Log the amount of identifiers in library used

[0.1.22] - 2021-03-04

• Publish PyPI and GitHub release

[0.1.21] - 2021-03-04

• Add library functionality that allows for storing and retrieving predictions (without running the model)

[0.1.20] - 2021-02-19

• Describe hyperparameters and limit CPU threads
• Additional modfications, including those exclusive to pFind
• Change calibration error to warning (since it is a warning if it is out of range...)

[0.1.18] - 2021-01-11

• Limit CPU usage by tensorflow by connecting to n_jobs

[0.1.17] - 2020-08-07

• Support for Python 3.8

[0.1.16] - 2020-05-18

• Bug fix in the calibration function
• Had to order the predicted instead of observed retention times of the calibration analytes
• Thanks to @courcelm for both finding and fixing the issue

[0.1.15] - 2020-05-15

• Different calibration function, should not contain gaps anymore
• Changed to more accurate rounding
• Changed to splitting in groups of retention time instead of groups of peptides

[0.1.14] - 2020-02-21

• Changed default model to a different data set

[0.1.13] - 2020-02-21

• Duplicate peptides charge fix

[0.1.12] - 2020-02-15

• Support for charges and spaces in peprec

[0.1.11] - 2020-02-13

• Fixes in GUI

[0.1.10] - 2020-02-10

• Include less models in package to meet PyPI 60MB size limitation

[0.1.9] - 2020-02-09

• Bugfix: Pass custom activation function

[0.1.8] - 2020-02-07

• Fixed support for averaging predictions of groups of models (ensemble) when no models were passed
• New models for ensemble

[0.1.7] - 2020-02-07

• Support for averaging predictions of groups of models (ensemble)

[0.1.6] - 2020-01-21

• Fix the latest release

[0.1.5] - 2020-01-21

• Spaces in paths to files and installation allowed
• References to other CompOmics tools removed in GUI

[0.1.5] - 2020-02-13

• Fixes in GUI

[0.1.4] - 2020-01-17

• Fix the latest release

[0.1.3] - 2020-01-17

• Fixed the .bat installer (now uses bioconda)

[0.1.2] - 2019-12-19

• Example files in GUI folder
• Unnecesary bat and sh for running GUI removed

[0.1.1] - 2019-12-18

• Switch to setuptools
• Reorder publish workflow; build wheels

[0.1.1.dev8] - 2019-12-16

• Remove xgboost dependancy

[0.1.1.dev7] - 2019-12-16

• Use dot instead of dash in versioning for bioconda

[0.1.1-dev6] - 2019-12-15

• Fix publish action branch specification (2)

[0.1.1-dev5] - 2019-12-15

• Fix publish action branch specification

[0.1.1-dev4] - 2019-12-15

• Test other trigger for publish action

[0.1.1-dev3] - 2019-12-15

• Update documentation, specify branch in publish action

[0.1.1-dev2] - 2019-12-15

• Add long description to setup.py

[0.1.1-dev1] - 2019-12-15

• Initial pre-release