From 0b2880ffe15034d93d15a77e176199616a4632b2 Mon Sep 17 00:00:00 2001 From: Ralf Gabriels Date: Thu, 8 Aug 2024 14:15:07 +0000 Subject: [PATCH] Format changelog --- CHANGELOG.md | 210 ++++++++++++++++++++++++++++++++++++++++++++------- 1 file changed, 184 insertions(+), 26 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 292e3f9..7722932 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,4 +1,5 @@ # Changelog + All notable changes to this project will be documented in this file. The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), @@ -7,515 +8,672 @@ and this project adheres to # [3.0.6] - 2024-08-08 -- Remove old python build +### Changed + +- Debugging release issues # [3.0.5] - 2024-08-08 -- Remove old python build +### Changed + +- Debugging release issues # [3.0.4] - 2024-08-08 -- Remove old python build +### Changed + +- Debugging release issues # [3.0.3] - 2024-08-08 +### Changed + - Remove old python build # [3.0.2] - 2024-08-08 -- Remove old python build +### 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 -- Pin scipy version +### 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 -- Support for costum labels in plot +### 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 -### Changed +### Fixed + - Fix missing debug time in feature extractor # [2.2.13] - 2023-09-03 -### Changed +### 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 -### Changed +### 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 -### Changed +### Fixed + - Fixed a bug where a reinit led to issues with setting parallelism # [2.2.4] - 2023-07-06 -### Changed +### Fixed + - Fixed a bug where it checked the calibration file while this was not initialized # [2.2.3] - 2023-06-28 -### Changed +### Fixed + - Fixed a bug where missing atoms in encoding cause a crash # [2.2.2] - 2023-06-23 -### Changed +### Fixed + - Fixed a bug where isotopes are incorrectly parsed # [2.2.1] - 2023-06-18 -### Changed +### Fixed + - Fixed a bug where numpy no longer accepts dict_values, explicit list conversion # [2.2.0] - 2023-06-14 -### Changed +### Fixed + - Fixed a bug where atom counts were wrong, fixed by retraining models with new features # [2.1.9] - 2023-05-09 -### Changed +### 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 -### Changed +### Fixed + - fix setting cmd line calibration default # [2.1.6] - 2023-05-09 -### Changed +### Fixed + - fix setting GUI calibration default # [2.1.5] - 2023-05-08 -### Changed -- fix library +### 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 -### Changed +### Fixed + - dependency fix # [2.1.1] - 2023-05-08 -### Changed +### 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]` + 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 + 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`. + 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