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CHANGELOG
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v1.2.6, 01.03.2016 -- First tracked release
v1.3.0, 03.03.2016 -- Added plot module
v1.5.0, 11.03.2016 -- Changed package architecture to one submodules in modlamp
v2.0.4 17.03.2016 -- Updated docs and AA probabilities, added capability of reading sequences from numpy.ndarrays
v2.0.5 17.03.2016 -- Added new sequences dataset to be loaded: ``load_helicalAMPset()``
v2.1.0 17.03.2016 -- Added example script of usage and corrected some behaviour of core functions.
v2.1.1 22.03.2016 -- Fixed different docstrings, added methods to load and save descriptor data
v2.1.2 22.03.2016 -- New Documentation reference and file names
v2.1.3 23.03.2016 -- Added filtering methods for amino acids and descriptor values, as well as test cases
v2.1.4 31.03.2016 -- New function to query experimental data from the peptides database
v2.1.5 08.04.2016 -- Helical wheel plot function added to modlamp.plot
v2.1.6 07.06.2016 -- Saving Fasta files from descriptors, bug fixes
v2.2.0 08.06.2016 -- ML Module for SVM and RF added
v2.2.1 15.06.2016 -- PDE plot function plot_pde() added to modlab.plot
v2.2.2 17.06.2016 -- Violin plot function plot_violin() added to modlab.plot
v2.2.3 20.06.2016 -- random_selection() method to select a random number of sequences and descriptors from instance
v2.2.4 20.06.2016 -- filter_sequences() method to filter out specific sequences with corresponding values
v2.2.5 22.06.2016 -- new plot method to plot amino acid distributions: plot_aa_distr()
v2.2.6 08.07.2016 -- code refactoring according to PEP8 and simplification of core functions
v2.3.0 13.07.2016 -- new parallel calculation of auto- and cross-correlated descriptors
v2.3.1 25.07.2016 -- new sequences class Hepahelices for generating amphipathic sequences with a heparin-binding-domain
v2.4.0 22.08.2016 -- new module wetlab with class CD for analysis and plotting of circular dichroism data
v2.4.1 14.09.2016 -- new sequence class AMPngrams for generating sequences out of frequent APD3 ngrams
v2.5.0 23.09.2016 -- clarified documentation and replaced Biopython functions by own code
v2.5.1 17.10.2016 -- bug fixes in documentation
v2.6.0 17.11.2016 -- New module "analysis" with summary_plot method to show an overview of different peptide libraries
v2.6.1 29.11.2016 -- Some changes in README and setup.py to make modlAMP PyPI compatible
v2.6.2 18.12.2016 -- Updated data sets for publication, version uploaded to ETH data archive
v2.6.3 19.12.2016 -- Initial upload to PyPI
v2.6.4 11.01.2017 -- Bugfix in GlobalDescriptor.instability_index
v2.6.5 12.01.2017 -- Added 'all' option for combining all AA scales
v2.6.6 12.01.2017 -- Requirements corrected in setup.py
v2.6.7 12.01.2017 -- Requirements again corrected in setup.py
v2.7.0 16.01.2017 -- Adapted modlamp.wetlab.CD to recognize same squences instead of names for combination plots
v2.7.1 16.01.2017 -- Hydrophobic moment arrow option added to helical_wheel function
v2.7.2 19.01.2017 -- Slight visual adaptions in helical_wheel output
v2.7.3 30.01.2017 -- Small bug fix in ml module and clarification of documentation in ML module
v2.7.4 14.03.2017 -- Adapted CD plot function in wetlab to take ylim argument, bug fix in y axis label
v2.7.5 22.03.2017 -- New CD plot function to plot combined plots of all data
v2.7.6 23.03.2017 -- Added GlobalDescriptor.formula method to calculate the molecular formula of peptides, bugfix in calculate_all()
v2.7.7 28.03.2017 -- Removed sequences containing unnatural amino acids from the AMPvsUniProt dataset
v2.7.8 30.03.2017 -- Bug fixes and code simplifications in the ml module
v3.0.0 30.03.2017 -- Refactoring of modlamp.sequences module. All classes now share the method generate_sequences()
v3.0.1 13.04.2017 -- New unittests for the modlamp.ml module.
v3.1.0 04.05.2017 -- Publication referenced. Adaptions in CD descriptions and README
v3.1.1 15.05.2017 -- Bugfix in cv function and wetlab test case
v3.1.2 07.06.2017 -- Color option added in analysis plot, bugfix in .csv file reading
v3.2.0 23.06.2017 -- Bugfixes when plotting GlobalAnalysis summary, reorganization of AA probabilities in core module
v3.2.1 05.07.2017 -- Move to pypi.org
v3.2.2 14.07.2017 -- Change references to documentation and move it to http://modlamp.org
v3.2.3 11.09.2017 -- Improve Python3 compatibility, change bugs in bin scripts, optimize save_fasta method
v3.2.4 15.09.2017 -- Import bug fix
v3.3.0 27.09.2017 -- New descriptor pepArc, bugfix in AmphipathicArc, removed short sequences from AMPvsUniProt
v3.3.1 19.10.2017 -- Bugfixes in pepArc, random ACP probability added to sequences.Random
v3.3.2 21.12.2017 -- New options in pepArc, cleaning AMPngrams
v3.4.0 07.02.2018 -- New tests, removed biopython dependency, travis build and codecov added
v3.4.1 17.11.2018 -- Bugfix for installing via new pip versions
v3.4.2 10.12.2018 -- Bugfix for GlobalAnalysis if library contains sublibraries
v3.4.3 10.12.2018 -- Bugfix in installation
v4.0.0 13.02.2019 -- Migrating modlAMP to Python3!
v4.0.1 03.03.2019 -- Bugfix in calculate_profile
v4.0.2 29.03.2019 -- n-gram calculation and new tests
v4.0.3 05.05.2019 -- Bugfix in plot functions
v4.0.4 03.06.2019 -- Python3 bug fix in HelicesACP
v4.1.0 05.06.2019 -- Fully Python3 compatible
v4.1.1 15.07.2019 -- Bugfix in AA formula
v4.1.2 13.11.2019 -- Bugfix in GlobalAnalysis plot
v4.1.3 13.11.2019 -- Another bugfix in GlobalAnalysis plot
v4.1.4 29.04.2020 -- Added dunder info (all, author, version)
v4.2.0 04.06.2020 -- Compatibility with newest scikit-learn version
v4.2.1 12.06.2020 -- Bugfix in plot_aa_distr
v4.2.2 17.06.2020 -- Bugfix for Bioconda, pip internal function
v4.2.3 15.10.2020 -- Bugfix in GlobalAnalysis charge plot
v4.3.0 25.02.2021 -- Correction in GlobalDescriptor documentation and analysis bug fixed