deeplc - v3.1.9

Changed

• When no calibration peptides are present, just fit a model that returns the original predicted value

- Python
Published by github-actions[bot] 8 months ago

deeplc - v3.1.8

Changed

• Allow for much smaller peptides in feature calculation

- Python
Published by github-actions[bot] about 1 year ago

deeplc - v3.1.7

Changed

• Log warnings in obtaining atoms only once

- Python
Published by github-actions[bot] about 1 year ago

deeplc - v3.1.6

Changed

• Remove unimod, replace with psm_utils

- Python
Published by github-actions[bot] about 1 year ago

deeplc - v3.1.5

Changed

• Bump minimal requirements python version

- Python
Published by github-actions[bot] about 1 year ago

deeplc - v3.1.3

Changed

• Bioconda fix import

- Python
Published by github-actions[bot] over 1 year ago

deeplc - v3.1.2

Changed

• Remove dependencies

- Python
Published by github-actions[bot] over 1 year ago

deeplc - v3.1.1

Changed

• Revert to linear calibration after transfer learning only

- Python
Published by github-actions[bot] over 1 year ago

deeplc - v3.1.0

Changed

• Use scikit-learn instead of pygam for calibration

- Python
Published by github-actions[bot] over 1 year ago

deeplc - v3.0.8

Changed

• Fix custom activation by using default implementation
• Loosen requirements

- Python
Published by github-actions[bot] over 1 year ago

deeplc - v3.0.7

Changed

• Remove batch number parameter from GUI

- Python
Published by github-actions[bot] over 1 year ago

deeplc - v3.0.6

Changed

• Debugging release issues

- Python
Published by github-actions[bot] over 1 year ago

deeplc - v2.2.36

- Python
Published by github-actions[bot] almost 2 years ago

deeplc - v2.2.35

- Python
Published by github-actions[bot] almost 2 years ago

deeplc - v2.2.34

- Python
Published by github-actions[bot] almost 2 years ago

deeplc - v2.2.33

- Python
Published by github-actions[bot] almost 2 years ago

deeplc - v2.2.27

- Python
Published by github-actions[bot] about 2 years ago

deeplc - v2.2.26

- Python
Published by github-actions[bot] over 2 years ago

deeplc - v2.2.25

- Python
Published by github-actions[bot] over 2 years ago

deeplc - v2.2.24

- Python
Published by github-actions[bot] over 2 years ago

deeplc - v2.2.23

- Python
Published by github-actions[bot] over 2 years ago

deeplc - v2.2.22

- Python
Published by github-actions[bot] over 2 years ago

deeplc - v2.2.20

- Python
Published by github-actions[bot] over 2 years ago

deeplc - v2.2.19

- Python
Published by github-actions[bot] over 2 years ago

deeplc - v2.2.18

- Python
Published by github-actions[bot] over 2 years ago

deeplc - v2.2.16

- Python
Published by github-actions[bot] over 2 years ago

deeplc - v2.2.14

- Python
Published by github-actions[bot] over 2 years ago

deeplc - v2.2.12

- Python
Published by github-actions[bot] over 2 years ago

deeplc - v2.2.11

- Python
Published by github-actions[bot] over 2 years ago

deeplc - v2.2.10

- Python
Published by github-actions[bot] over 2 years ago

deeplc - v2.2.9

- Python
Published by github-actions[bot] over 2 years ago

deeplc - v2.2.8

- Python
Published by github-actions[bot] over 2 years ago

deeplc - v2.2.7

- Python
Published by github-actions[bot] over 2 years ago

deeplc - v2.2.6

- Python
Published by github-actions[bot] over 2 years ago

deeplc - v2.2.5

- Python
Published by github-actions[bot] over 2 years ago

deeplc - v2.2.4

- Python
Published by github-actions[bot] over 2 years ago

deeplc - v2.2.3

- Python
Published by github-actions[bot] over 2 years ago

deeplc - v2.2.2

- Python
Published by github-actions[bot] over 2 years ago

deeplc - v2.2.1

- Python
Published by github-actions[bot] over 2 years ago

deeplc - v2.2.0

- Python
Published by github-actions[bot] over 2 years ago

deeplc - v2.1.9

- Python
Published by github-actions[bot] over 2 years ago

deeplc - v2.1.8

Fix the argument parser for the GUI and command line.

- Python
Published by RobbinBouwmeester almost 3 years ago

deeplc - v2.1.6

- Python
Published by github-actions[bot] almost 3 years ago

deeplc - v2.1.5

Support for PSM utils in the GUI.

- Python
Published by RobbinBouwmeester almost 3 years ago

deeplc - v2.1.1

- Python
Published by github-actions[bot] almost 3 years ago

deeplc - v2.1.0

- Python
Published by github-actions[bot] almost 3 years ago

deeplc - v2.0.4

• Log peptide sequences that are too long
• bug fix for sequences > 60 AA
• bug fix non-resolved modifications
• psm_utils integration
• pygam default calibrator
• additional support transfer learning
• code refractoring of feature extraction
• prediction library support
• piecewise linear calibration support

- Python
Published by RobbinBouwmeester almost 3 years ago

deeplc - v1.1.2

Changed

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

- Python
Published by github-actions[bot] almost 4 years ago

deeplc - v1.1.1

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.

- Python
Published by github-actions[bot] almost 4 years ago

deeplc - v1.0.1

• Make version compatible with pip release

- Python
Published by github-actions[bot] almost 4 years ago

deeplc - v1.0.0

• Make version compatible with pip release

[1.0] - 2022-02-23

• Make pygam the default calibration method

- Python
Published by github-actions[bot] about 4 years ago

deeplc - v0.2.2

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

- Python
Published by github-actions[bot] about 4 years ago

deeplc - v0.2.1

• Scikit-learn and pygam dependency in setup

- Python
Published by github-actions[bot] about 4 years ago

deeplc - v0.2.0

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

- Python
Published by github-actions[bot] about 4 years ago

deeplc - v0.1.39

• Version bump

- Python
Published by github-actions[bot] about 4 years ago

deeplc - v0.1.38

• Deep(CAL)LC functionality

- Python
Published by github-actions[bot] about 4 years ago

deeplc - v0.1.37

• Pygam as calibration function

- Python
Published by github-actions[bot] about 4 years ago

deeplc - v0.1.36

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

- Python
Published by github-actions[bot] over 4 years ago

deeplc - v0.1.35

• More elegant solution for library call as global

- Python
Published by github-actions[bot] over 4 years ago

deeplc - v0.1.34

• Fix var call dict object

- Python
Published by github-actions[bot] over 4 years ago

deeplc - v0.1.33

• Fix library delete call

- Python
Published by github-actions[bot] over 4 years ago

deeplc - v0.1.32

• Temporary fix suggested by markmipt for the library

- Python
Published by github-actions[bot] over 4 years ago

deeplc - v0.1.31

• Change logging to specified logger object instead of standard logger

- Python
Published by github-actions[bot] over 4 years ago

deeplc - v0.1.30

• 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

- Python
Published by github-actions[bot] over 4 years ago

deeplc - v0.1.29

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

- Python
Published by github-actions[bot] almost 5 years ago

deeplc - v0.1.28

• Make it optional to reload library

- Python
Published by github-actions[bot] almost 5 years ago

deeplc - v0.1.27

• Ignore library messages

- Python
Published by github-actions[bot] almost 5 years ago

deeplc - v0.1.26

• Force older library h5py for compatability

- Python
Published by github-actions[bot] almost 5 years ago

deeplc - v0.1.25

• Library gets appended for non-calibration peptides too

- Python
Published by github-actions[bot] almost 5 years ago

deeplc - v0.1.24

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

- Python
Published by github-actions[bot] almost 5 years ago

deeplc - v0.1.23

• Log the amount of identifiers in library used

- Python
Published by github-actions[bot] almost 5 years ago

deeplc - v0.1.22

• Publish PyPI and GitHub release

- Python
Published by github-actions[bot] almost 5 years ago

deeplc - v0.1.20

• 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...)

- Python
Published by github-actions[bot] about 5 years ago

deeplc - v0.1.18

• Limit CPU usage by tensorflow by connecting to n_jobs

- Python
Published by github-actions[bot] about 5 years ago

deeplc - v0.1.17

• Support for Python 3.8

- Python
Published by github-actions[bot] over 5 years ago

deeplc - 0.1.16

• 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

- Python
Published by github-actions[bot] almost 6 years ago

deeplc - 0.1.15

• 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

- Python
Published by github-actions[bot] almost 6 years ago

deeplc - 0.1.14

• Changed default model to a different data set

- Python
Published by github-actions[bot] almost 6 years ago

deeplc - 0.1.13

• Duplicate peptides charge fix

- Python
Published by github-actions[bot] about 6 years ago

deeplc - 0.1.12

• Support for charges and spaces in peprec

- Python
Published by github-actions[bot] about 6 years ago

deeplc - 0.1.11

• Fixes in GUI

- Python
Published by github-actions[bot] about 6 years ago

deeplc - 0.1.10

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

- Python
Published by github-actions[bot] about 6 years ago

deeplc - 0.1.9

- Python
Published by github-actions[bot] about 6 years ago

deeplc - 0.1.8

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

- Python
Published by github-actions[bot] about 6 years ago

deeplc - 0.1.7

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

- Python
Published by github-actions[bot] about 6 years ago

deeplc - 0.1.6

• Fix the latest release

- Python
Published by github-actions[bot] about 6 years ago

deeplc - 0.1.4

• Fix the latest release

- Python
Published by github-actions[bot] about 6 years ago

deeplc - 0.1.2

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

- Python
Published by github-actions[bot] about 6 years ago

deeplc - 0.1.1

• Switch to setuptools
• Reorder publish workflow; build wheels

- Python
Published by github-actions[bot] about 6 years ago