gecco: CHANGELOG.md annotate

annotate CHANGELOG.md @ 16:042a23379d2d draft

Release v0.9.3

author	althonos
date	Fri, 13 May 2022 14:36:19 +0000
parents	64528877558f
children	e28ffe93dc69

rev	line source
3 359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	1 # Changelog
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	2 All notable changes to this project will be documented in this file.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	3
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	4 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	5 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	6
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	7 ## [Unreleased]
16 042a23379d2d Release v0.9.3 althonos parents: 15 diff changeset	8 [Unreleased]: https://git.embl.de/grp-zeller/GECCO/compare/v0.9.3...master
042a23379d2d Release v0.9.3 althonos parents: 15 diff changeset	9
042a23379d2d Release v0.9.3 althonos parents: 15 diff changeset	10
042a23379d2d Release v0.9.3 althonos parents: 15 diff changeset	11 ## [v0.9.3] - 2022-05-13
042a23379d2d Release v0.9.3 althonos parents: 15 diff changeset	12 [v0.9.3]: https://git.embl.de/grp-zeller/GECCO/compare/v0.9.2...v0.9.3
042a23379d2d Release v0.9.3 althonos parents: 15 diff changeset	13
042a23379d2d Release v0.9.3 althonos parents: 15 diff changeset	14 ### Changed
042a23379d2d Release v0.9.3 althonos parents: 15 diff changeset	15 - `--format` flag of `gecco annotate` and `gecco run` CLI commands is now made lowercase before giving value to `Bio.SeqIO`.
042a23379d2d Release v0.9.3 althonos parents: 15 diff changeset	16
042a23379d2d Release v0.9.3 althonos parents: 15 diff changeset	17 ### Fixed
042a23379d2d Release v0.9.3 althonos parents: 15 diff changeset	18 - Genes with duplicate IDs being silently ignored in `HMMER.run`.
042a23379d2d Release v0.9.3 althonos parents: 15 diff changeset	19
15 64528877558f "Release v0.9.2" althonos parents: 14 diff changeset	20
64528877558f "Release v0.9.2" althonos parents: 14 diff changeset	21 ## [v0.9.2] - 2022-04-11
64528877558f "Release v0.9.2" althonos parents: 14 diff changeset	22 [v0.9.2]: https://git.embl.de/grp-zeller/GECCO/compare/v0.9.1...v0.9.2
64528877558f "Release v0.9.2" althonos parents: 14 diff changeset	23
64528877558f "Release v0.9.2" althonos parents: 14 diff changeset	24 ### Added
64528877558f "Release v0.9.2" althonos parents: 14 diff changeset	25 - Padding of short sequences with empty genes when predicting probabilities in `ClusterCRF`.
14 56b924f62165 "Update tests files for Galaxy tool wrapper" althonos parents: 13 diff changeset	26
56b924f62165 "Update tests files for Galaxy tool wrapper" althonos parents: 13 diff changeset	27 ## [v0.9.1] - 2022-04-05
56b924f62165 "Update tests files for Galaxy tool wrapper" althonos parents: 13 diff changeset	28 [v0.9.1]: https://git.embl.de/grp-zeller/GECCO/compare/v0.9.1-alpha4...v0.9.1
56b924f62165 "Update tests files for Galaxy tool wrapper" althonos parents: 13 diff changeset	29
56b924f62165 "Update tests files for Galaxy tool wrapper" althonos parents: 13 diff changeset	30 ### Changed
56b924f62165 "Update tests files for Galaxy tool wrapper" althonos parents: 13 diff changeset	31 - Make the `genes.tsv` and `features.tsv` table contain all genes even when they come from a contig too short to be processed by the CRF sliding window.
56b924f62165 "Update tests files for Galaxy tool wrapper" althonos parents: 13 diff changeset	32 - Replaced the `--force-clusters-tsv` flag with a `--force-tsv` flag to force writing TSV tables even when no genes or clusters were found in `gecco run` or `gecco annotate`.
13 fde43648cba0 "Release v0.9.1-alpha4" althonos parents: 12 diff changeset	33
fde43648cba0 "Release v0.9.1-alpha4" althonos parents: 12 diff changeset	34 ## [v0.9.1-alpha4] - 2022-03-31
fde43648cba0 "Release v0.9.1-alpha4" althonos parents: 12 diff changeset	35 [v0.9.1-alpha4]: https://git.embl.de/grp-zeller/GECCO/compare/v0.9.1-alpha3...v0.9.1-alpha4
fde43648cba0 "Release v0.9.1-alpha4" althonos parents: 12 diff changeset	36
fde43648cba0 "Release v0.9.1-alpha4" althonos parents: 12 diff changeset	37 Retrain internal model with:
fde43648cba0 "Release v0.9.1-alpha4" althonos parents: 12 diff changeset	38 ```
fde43648cba0 "Release v0.9.1-alpha4" althonos parents: 12 diff changeset	39 $ python -m gecco -vv train --c1 0.4 --c2 0 --select 0.25 --window-size 20 \
fde43648cba0 "Release v0.9.1-alpha4" althonos parents: 12 diff changeset	40 -f mibig-2.0.proG2.Pfam-v35.0.features.tsv \
fde43648cba0 "Release v0.9.1-alpha4" althonos parents: 12 diff changeset	41 -c mibig-2.0.proG2.clusters.tsv \
14 56b924f62165 "Update tests files for Galaxy tool wrapper" althonos parents: 13 diff changeset	42 -g GECCO-data/data/embeddings/mibig-2.0.proG2.genes.tsv \
13 fde43648cba0 "Release v0.9.1-alpha4" althonos parents: 12 diff changeset	43 -o models/v0.9.1-alpha4
fde43648cba0 "Release v0.9.1-alpha4" althonos parents: 12 diff changeset	44 ```
12 e6597056a493 "Release v0.9.1-alpha3" althonos parents: 11 diff changeset	45
e6597056a493 "Release v0.9.1-alpha3" althonos parents: 11 diff changeset	46 ## [v0.9.1-alpha3] - 2022-03-23
e6597056a493 "Release v0.9.1-alpha3" althonos parents: 11 diff changeset	47 [v0.9.1-alpha3]: https://git.embl.de/grp-zeller/GECCO/compare/v0.9.1-alpha2...v0.9.1-alpha3
e6597056a493 "Release v0.9.1-alpha3" althonos parents: 11 diff changeset	48
e6597056a493 "Release v0.9.1-alpha3" althonos parents: 11 diff changeset	49 ### Added
e6597056a493 "Release v0.9.1-alpha3" althonos parents: 11 diff changeset	50 - `gecco.model.GeneTable` class to store gene coordinates independently of protein domains.
e6597056a493 "Release v0.9.1-alpha3" althonos parents: 11 diff changeset	51
e6597056a493 "Release v0.9.1-alpha3" althonos parents: 11 diff changeset	52 ### Changed
e6597056a493 "Release v0.9.1-alpha3" althonos parents: 11 diff changeset	53 - Refactored implementation of `load` and `dump` methods for `Table` classes into a dedicated base class.
e6597056a493 "Release v0.9.1-alpha3" althonos parents: 11 diff changeset	54 - `gecco run` and `gecco annotate` now output a gene table in addition to the feature and cluster tables.
e6597056a493 "Release v0.9.1-alpha3" althonos parents: 11 diff changeset	55 - `gecco train` expects a gene table instead of a GFF file for the gene coordinates.
11 40a525d0e1fe "Release v0.9.1-alpha2" althonos parents: 10 diff changeset	56
40a525d0e1fe "Release v0.9.1-alpha2" althonos parents: 10 diff changeset	57 ## [v0.9.1-alpha2] - 2022-03-23
12 e6597056a493 "Release v0.9.1-alpha3" althonos parents: 11 diff changeset	58 [v0.9.1-alpha2]: https://git.embl.de/grp-zeller/GECCO/compare/v0.9.1-alpha1...v0.9.1-alpha2
11 40a525d0e1fe "Release v0.9.1-alpha2" althonos parents: 10 diff changeset	59
40a525d0e1fe "Release v0.9.1-alpha2" althonos parents: 10 diff changeset	60 ### Fixed
40a525d0e1fe "Release v0.9.1-alpha2" althonos parents: 10 diff changeset	61 - `TypeClassifier.trained` not being able to read unknown types from type tables.
10 9156eb4ee20c "Release v0.9.1-alpha1" althonos parents: 9 diff changeset	62
9156eb4ee20c "Release v0.9.1-alpha1" althonos parents: 9 diff changeset	63 ## [v0.9.1-alpha1] - 2022-03-20
9156eb4ee20c "Release v0.9.1-alpha1" althonos parents: 9 diff changeset	64 [v0.9.1-alpha1]: https://git.embl.de/grp-zeller/GECCO/compare/v0.8.10...v0.9.1-alpha1
9156eb4ee20c "Release v0.9.1-alpha1" althonos parents: 9 diff changeset	65 Candidate release with support for a sliding window in the CRF prediction algorithm.
9 d64fe390f3c9 "Fix test files used in Galaxy test workflow" althonos parents: 8 diff changeset	66
d64fe390f3c9 "Fix test files used in Galaxy test workflow" althonos parents: 8 diff changeset	67 ## [v0.8.10] - 2022-02-23
d64fe390f3c9 "Fix test files used in Galaxy test workflow" althonos parents: 8 diff changeset	68 [v0.8.10]: https://git.embl.de/grp-zeller/GECCO/compare/v0.8.9...v0.8.10
d64fe390f3c9 "Fix test files used in Galaxy test workflow" althonos parents: 8 diff changeset	69 ### Fixed
d64fe390f3c9 "Fix test files used in Galaxy test workflow" althonos parents: 8 diff changeset	70 - `--antismash-sideload` flag of `gecco run` causing command to crash.
8 cebc53d02da6 "Release v0.8.9" althonos parents: 7 diff changeset	71
cebc53d02da6 "Release v0.8.9" althonos parents: 7 diff changeset	72 ## [v0.8.9] - 2022-02-22
cebc53d02da6 "Release v0.8.9" althonos parents: 7 diff changeset	73 [v0.8.9]: https://git.embl.de/grp-zeller/GECCO/compare/v0.8.8...v0.8.9
cebc53d02da6 "Release v0.8.9" althonos parents: 7 diff changeset	74 ### Removed
cebc53d02da6 "Release v0.8.9" althonos parents: 7 diff changeset	75 - Prediction and support for the Other biosynthetic type of MIBiG clusters.
7 76b1a38579bd "Release v0.8.8" althonos parents: 6 diff changeset	76
76b1a38579bd "Release v0.8.8" althonos parents: 6 diff changeset	77 ## [v0.8.8] - 2022-02-21
76b1a38579bd "Release v0.8.8" althonos parents: 6 diff changeset	78 [v0.8.8]: https://git.embl.de/grp-zeller/GECCO/compare/v0.8.7...v0.8.8
76b1a38579bd "Release v0.8.8" althonos parents: 6 diff changeset	79 ### Fixed
76b1a38579bd "Release v0.8.8" althonos parents: 6 diff changeset	80 - `ClusterRefiner` filtering method for edge genes not working as intended.
76b1a38579bd "Release v0.8.8" althonos parents: 6 diff changeset	81 - `gecco run` and `gecco annotate` commands crashing on missing input files instead of nicely rendering the error.
5 169849dfb098 "Release v0.8.6" althonos parents: 3 diff changeset	82
6 f8878bdf1e05 "Release v0.8.7" althonos parents: 5 diff changeset	83 ## [v0.8.7] - 2022-02-18
f8878bdf1e05 "Release v0.8.7" althonos parents: 5 diff changeset	84 [v0.8.7]: https://git.embl.de/grp-zeller/GECCO/compare/v0.8.6...v0.8.7
f8878bdf1e05 "Release v0.8.7" althonos parents: 5 diff changeset	85 ### Fixed
f8878bdf1e05 "Release v0.8.7" althonos parents: 5 diff changeset	86 - `interpro.json` metadata file not being included in distribution files.
f8878bdf1e05 "Release v0.8.7" althonos parents: 5 diff changeset	87 - Missing docstring for `Protein.with_domains` method.
f8878bdf1e05 "Release v0.8.7" althonos parents: 5 diff changeset	88 ### Changed
f8878bdf1e05 "Release v0.8.7" althonos parents: 5 diff changeset	89 - Bump minimum `scikit-learn` version to `v1.0` for Python3.7+.
f8878bdf1e05 "Release v0.8.7" althonos parents: 5 diff changeset	90
f8878bdf1e05 "Release v0.8.7" althonos parents: 5 diff changeset	91 ## [v0.8.6] - 2022-02-17 - YANKED
5 169849dfb098 "Release v0.8.6" althonos parents: 3 diff changeset	92 [v0.8.6]: https://git.embl.de/grp-zeller/GECCO/compare/v0.8.5...v0.8.6
169849dfb098 "Release v0.8.6" althonos parents: 3 diff changeset	93 ### Added
169849dfb098 "Release v0.8.6" althonos parents: 3 diff changeset	94 - CLI flag for enabling region masking for contigs processed by Prodigal.
169849dfb098 "Release v0.8.6" althonos parents: 3 diff changeset	95 - CLI flag for controlling region distance used for edge distance filtering.
169849dfb098 "Release v0.8.6" althonos parents: 3 diff changeset	96 ### Changed
169849dfb098 "Release v0.8.6" althonos parents: 3 diff changeset	97 - `gecco.model.Gene` and `gecco.model.Protein` are now immutable data classes.
169849dfb098 "Release v0.8.6" althonos parents: 3 diff changeset	98 - Bump minimum `pyrodigal` version to `v0.6.4` to use region masking.
169849dfb098 "Release v0.8.6" althonos parents: 3 diff changeset	99 - Implement filtering for extracted clusters based on distance to the contig edge.
169849dfb098 "Release v0.8.6" althonos parents: 3 diff changeset	100 - Store InterPro metadata file uncompressed for version-control integration.
169849dfb098 "Release v0.8.6" althonos parents: 3 diff changeset	101 ### Fixed
169849dfb098 "Release v0.8.6" althonos parents: 3 diff changeset	102 - Mark `BGC0000930` as `Terpene` in the type classifier data.
169849dfb098 "Release v0.8.6" althonos parents: 3 diff changeset	103 - Progress bar messages are now in consistent format.
3 359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	104
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	105 ## [v0.8.5] - 2021-11-21
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	106 [v0.8.5]: https://git.embl.de/grp-zeller/GECCO/compare/v0.8.4...v0.8.5
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	107 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	108 - Minimal compatibility support for running GECCO inside of Galaxy workflows.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	109
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	110 ## [v0.8.4] - 2021-09-26
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	111 [v0.8.4]: https://git.embl.de/grp-zeller/GECCO/compare/v0.8.3-post1...v0.8.4
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	112 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	113 - `gecco convert gbk --format bigslice` failing to run because of outdated code ([#5](https://github.com/zellerlab/GECCO/issues/5)).
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	114 - `gecco convert gbk --format bigslice` not creating files with names conforming to BiG-SLiCE expected input.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	115 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	116 - Bump minimum `pyrodigal` version to `v0.6.2` to use platform-accelerated code if supported.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	117
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	118 ## [v0.8.3-post1] - 2021-08-23
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	119 [v0.8.3-post1]: https://git.embl.de/grp-zeller/GECCO/compare/v0.8.3...v0.8.3-post1
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	120 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	121 - Wrong default value for `--threshold` being shown in `gecco run` help message.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	122
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	123 ## [v0.8.3] - 2021-08-23
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	124 [v0.8.3]: https://git.embl.de/grp-zeller/GECCO/compare/v0.8.2...v0.8.3
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	125 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	126 - Default probability threshold for segmentation to 0.3 (from 0.4).
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	127
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	128 ## [v0.8.2] - 2021-07-31
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	129 [v0.8.2]: https://git.embl.de/grp-zeller/GECCO/compare/v0.8.1...v0.8.2
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	130 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	131 - `gecco run` crashing on Python 3.6 because of missing `contextlib.nullcontext` class.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	132 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	133 - `gecco run` and `gecco annotate` will not try to count the number of profiles when given an external HMM file with the `--hmm` flag.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	134 - `PyHMMER.run` now reports the p-value of each domain in addition to the e-value as a `/note` qualifier.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	135
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	136 ## [v0.8.1] - 2021-07-29
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	137 [v0.8.1]: https://git.embl.de/grp-zeller/GECCO/compare/v0.8.0...v0.8.1
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	138 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	139 - `gecco run` now filters out unneeded features before annotating, making it easier to analyze the results of a run with a custom `--model`.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	140 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	141 - `gecco` reporting about using Pfam `v33.1` while actually using `v34.0` because of an outdated field in `gecco/hmmer/Pfam.ini`.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	142 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	143 - Missing documentation for the `strand` attribute of `gecco.model.Gene`.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	144
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	145 ## [v0.8.0] - 2021-07-03
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	146 [v0.8.0]: https://git.embl.de/grp-zeller/GECCO/compare/v0.7.0...v0.8.0
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	147 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	148 - Retrain internal model using new sequence embeddings and remove broken/duplicate BGCs from MIBiG 2.0.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	149 - Bump minimum `pyhmmer` version to `v0.4.0` to improve exception handling.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	150 - Bump minimum `pyrodigal` version to `v0.5.0` to fix sequence decoding on some platforms.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	151 - Use p-values instead of e-values to filter domains obtained with HMMER.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	152 - `gecco cv` and `gecco train` now seed the RNG with a user-defined seed before shuffling rows of training data.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	153 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	154 - Extraction of BGC compositions for the type predictor while training.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	155 - `ClusterCRF.trained` failing to open an external model.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	156 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	157 - `Domain.pvalue` attribute to access the p-value of a domain annotation.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	158 - Mandatory `pvalue` column to `FeatureTable` objects.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	159 - Support for loading several feature tables in `gecco train` and `gecco cv`.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	160 - Warnings to `ClusterCRF.fit` when selecting uninformative features.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	161 - `--correction` flag to `gecco train` and `gecco cv`, allowing to give a multiple testing correction method when computing p-values with the Fisher Exact Tests.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	162 ### Removed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	163 - Outdated `gecco embed` command.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	164 - Unused `--truncate` flag from the `gecco train` CLI.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	165 - Tigrfam domains, which is not improving performance on the new training data.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	166
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	167 ## [v0.7.0] - 2021-05-31
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	168 [v0.7.0]: https://git.embl.de/grp-zeller/GECCO/compare/v0.6.3...v0.7.0
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	169 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	170 - Support for writing an AntiSMASH sideload JSON file after a `gecco run` workflow.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	171 - Code for converting GenBank files in BiG-SLiCE compatible format with the `gecco convert` subcommand.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	172 - Documentation about using GECCO in combination with AntiSMASH or BiG-SLiCE.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	173 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	174 - Minimum Biopython version to `v1.73` for compatibility with older bioinformatics tooling.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	175 - Internal domain composition shipped in the `gecco.types` with newer composition array obtained directly from MIBiG files.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	176 ### Removed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	177 - Outdated notice about `-vvv` verbosity level in the help message of the main `gecco` command.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	178
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	179 ## [v0.6.3] - 2021-05-10
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	180 [v0.6.3]: https://git.embl.de/grp-zeller/GECCO/compare/v0.6.2...v0.6.3
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	181 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	182 - HMMER annotation not properly handling inputs with multiple contigs.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	183 - Some progress bar totals displaying as floats in the CLI.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	184 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	185 - `PyHMMER` now sets the `Z` and `domZ` values from the number of proteins given to the search pipeline.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	186 - `gecco.cli` delegates imports to make CLI more responsive.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	187 - `pkg_resources` has been replaced with `importlib.resources` and `importlib.metadata` where applicable.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	188 - `multiprocessing.cpu_count` has been replaced with `os.cpu_count` where applicable.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	189
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	190 ## [v0.6.2] - 2021-05-04
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	191 [v0.6.2]: https://git.embl.de/grp-zeller/GECCO/compare/v0.6.1...v0.6.2
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	192 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	193 - `gecco cv loto` crashing because of outdated code.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	194 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	195 - Logging-style prompt will only display if GECCO is running with `-vv` flag.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	196 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	197 - GECCO bioRxiv paper reference to `Cluster.to_seq_record` output record.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	198
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	199 ## [v0.6.1] - 2021-03-15
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	200 [v0.6.1]: https://git.embl.de/grp-zeller/GECCO/compare/v0.6.0...v0.6.1
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	201 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	202 - Progress bar not being disabled by `-q` flag in CLI.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	203 - Fallback to using HMM name if accession is not available in `PyHMMER`.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	204 - Group genes by source contig and process them separately in `PyHMMER` to avoid bogus E-values.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	205 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	206 - `psutil` dependency to get the number of physical CPU cores on the host machine.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	207 - Support for using an arbitrary mapping of positives to negatives in `gecco embed`.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	208 ### Removed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	209 - Unused and outdated `HMMER` and `DomainRow` classes from `gecco.hmmer`.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	210
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	211 ## [v0.6.0] - 2021-02-28
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	212 [v0.6.0]: https://git.embl.de/grp-zeller/GECCO/compare/v0.5.5...v0.6.0
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	213 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	214 - Updated internal model with a cleaned-up version of the MIBiG-2.0
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	215 Pfam-33.1/Tigrfam-15.0 embedding.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	216 - Updated internal InterPro catalog.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	217 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	218 - Features not being grouped together in `gecco cv` and `gecco train`
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	219 when provided with a feature table where rows were not sorted by
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	220 protein IDs.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	221
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	222 ## [v0.5.5] - 2021-02-28
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	223 [v0.5.5]: https://git.embl.de/grp-zeller/GECCO/compare/v0.5.4...v0.5.5
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	224 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	225 - `gecco cv` bug causing only the last fold to be written.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	226
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	227 ## [v0.5.4] - 2021-02-28
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	228 [v0.5.4]: https://git.embl.de/grp-zeller/GECCO/compare/v0.5.3...v0.5.4
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	229 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	230 - Replaced `verboselogs`, `coloredlogs` and `better-exceptions` with `rich`.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	231 ### Removed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	232 - `tqdm` training dependency.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	233 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	234 - `gecco annotate` command to produce a feature table from a genomic file.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	235 - `gecco embed` to embed BGCs into non-BGC regions using feature tables.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	236
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	237 ## [v0.5.3] - 2021-02-21
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	238 [v0.5.3]: https://git.embl.de/grp-zeller/GECCO/compare/v0.5.2...v0.5.3
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	239 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	240 - Coordinates of genes in output GenBank files.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	241 - Potential issue with the number of CPUs in `PyHMMER.run`.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	242 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	243 - Bump required `pyrodigal` version to `v0.4.2` to fix buffer overflow.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	244
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	245 ## [v0.5.2] - 2021-01-29
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	246 [v0.5.2]: https://git.embl.de/grp-zeller/GECCO/compare/v0.5.1...v0.5.2
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	247 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	248 - Support for downloading HMM files directly from GitHub releases assets.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	249 - Validation of filtered HMMs with MD5 checksum.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	250 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	251 - Invalid coordinates of protein domains in GenBank output files.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	252 - `gecco.interpro` module not being added to wheel distribution.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	253 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	254 - Bump required `pyhmmer` version to `v0.2.1`.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	255
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	256 ## [v0.5.1] - 2021-01-15
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	257 [v0.5.1]: https://git.embl.de/grp-zeller/GECCO/compare/v0.5.0...v0.5.1
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	258 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	259 - `--hmm` flag being ignored in in `gecco run` command.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	260 - `PyHMMER` using HMM names instead of accessions, causing issues with Pfam HMMs.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	261
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	262 ## [v0.5.0] - 2021-01-11
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	263 [v0.5.0]: https://git.embl.de/grp-zeller/GECCO/compare/v0.4.5...v0.5.0
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	264 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	265 - Explicit support for Python 3.9.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	266 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	267 - [`pyhmmer`](https://pypi.org/project/pyhmmer) is used to annotate protein sequences instead of HMMER3 binary `hmmsearch`.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	268 - HMM files are stored in binary format to speedup parsing and reduce storage size.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	269 - `tqdm` is now a training-only dependency.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	270 - `gecco cv` now requires training dependencies.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	271
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	272 ## [v0.4.5] - 2020-11-23
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	273 [v0.4.5]: https://git.embl.de/grp-zeller/GECCO/compare/v0.4.4...v0.4.5
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	274 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	275 - Additional `fold` column to cross-validation table output.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	276 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	277 - Use sequence ID instead of protein ID to extract type from cluster in `gecco cv`.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	278 - Install HMM data in pre-pressed format to make `hmmsearch` runs faster on short sequences.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	279 - `gecco.orf` was rewritten to extract genes from input sequences in parallel.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	280
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	281 ## [v0.4.4] - 2020-09-30
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	282 [v0.4.4]: https://git.embl.de/grp-zeller/GECCO/compare/v0.4.3...v0.4.4
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	283 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	284 - `gecco cv loto` command to run LOTO cross-validation using BGC types
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	285 for stratification.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	286 - `header` keyword argument to `FeatureTable.dump` and `ClusterTable.dump`
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	287 to write the table without the column header allowing to append to an
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	288 existing table.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	289 - `__getitem__` implementation for `FeatureTable` and `ClusterTable`
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	290 that returns a single row or a sub-table from a table.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	291 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	292 - `gecco cv` command now writes results iteratively instead of holding
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	293 the tables for every fold in memory.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	294 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	295 - Bumped `pandas` training dependency to `v1.0`.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	296
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	297 ## [v0.4.3] - 2020-09-07
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	298 [v0.4.3]: https://git.embl.de/grp-zeller/GECCO/compare/v0.4.2...v0.4.3
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	299 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	300 - GenBank files being written with invalid `/cds` feature type.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	301 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	302 - Blocked installation of Biopython `v1.78` or newer as it removes `Bio.Alphabet`
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	303 and breaks the current code.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	304
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	305 ## [v0.4.2] - 2020-08-07
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	306 [v0.4.2]: https://git.embl.de/grp-zeller/GECCO/compare/v0.4.1...v0.4.2
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	307 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	308 - `TypeClassifier.predict_types` using inverse type probabilities when
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	309 given several clusters to process.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	310
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	311 ## [v0.4.1] - 2020-08-07
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	312 [v0.4.1]: https://git.embl.de/grp-zeller/GECCO/compare/v0.4.0...v0.4.1
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	313 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	314 - `gecco run` command crashing on input sequences not containing any genes.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	315
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	316 ## [v0.4.0] - 2020-08-06
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	317 [v0.4.0]: https://git.embl.de/grp-zeller/GECCO/compare/v0.3.0...v0.4.0
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	318 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	319 - `gecco.model.ProductType` enum to model the biosynthetic class of a BGC.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	320 ### Removed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	321 - `pandas` interaction from internal data model.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	322 - `ClusterCRF` code specific to cross-validation.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	323 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	324 - `pandas`, `fisher` and `statsmodels` dependencies are now optional.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	325 - `gecco train` command expects a cluster table in addition to the feature
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	326 table to know the types of the input BGCs.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	327
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	328 ## [v0.3.0] - 2020-08-03
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	329 [v0.3.0]: https://git.embl.de/grp-zeller/GECCO/compare/v0.2.2...v0.3.0
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	330 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	331 - Replaced Nearest-Neighbours classifier with Random Forest to perform type
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	332 prediction for candidate BGCs.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	333 - `gecco.knn` module was renamed to implementation-agnostic name `gecco.types`.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	334 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	335 - Extraction of domain composition taking a long time in `gecco train` command.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	336 ### Removed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	337 - `--metric` argument to the `gecco run` CLI command.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	338
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	339 ## [v0.2.2] - 2020-07-31
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	340 [v0.2.2]: https://git.embl.de/grp-zeller/GECCO/compare/v0.2.1...v0.2.2
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	341 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	342 - `Domain` and `Gene` can now carry qualifiers that are used when they
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	343 are translated to a sequence feature.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	344 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	345 - InterPro names, accessions, and HMMER e-value for each annotated domain
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	346 in GenBank output files.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	347
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	348 ## [v0.2.1] - 2020-07-23
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	349 [v0.2.1]: https://git.embl.de/grp-zeller/GECCO/compare/v0.2.0...v0.2.1
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	350 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	351 - Various potential crashes in `ClusterRefiner` code.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	352 ### Removed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	353 - Uneeded feature dictionary filtering in `ClusterCRF` for models with
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	354 Fisher Exact Test feature selection.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	355
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	356 ## [v0.2.0] - 2020-07-23
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	357 [v0.2.0]: https://git.embl.de/grp-zeller/GECCO/compare/v0.1.1...v0.2.0
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	358 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	359 - `pandas` warning about unsorted columns in `gecco run`.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	360 ### Removed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	361 - `Gene.probability` property, replaced by `Gene.maximum_probability` and
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	362 `Gene.average_probability` properties to be explicit.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	363 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	364 - Internal model now uses `Pfam` and `Tigrfam` with the top 35% features
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	365 selected with Fisher's Exact Test.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	366 - `ClusterRefiner` now removes genes on `Cluster` edges if they do not
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	367 contain any domain annotation.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	368
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	369 ## [v0.1.1] - 2020-07-22
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	370 [v0.1.1]: https://git.embl.de/grp-zeller/GECCO/compare/v0.1.0...v0.1.1
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	371 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	372 - `ClusterCRF.predict_probabilities` to annotate a list of `Gene`.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	373 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	374 - BGC probability is now stored at the `Domain` level instead of at the `Gene`
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	375 level, independently of the feature extraction level used by the CRF.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	376 - `ClusterKNN` will use the model path provided to `gecco run` if any.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	377 ### Docs
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	378 - Added this changelog file to document changes in the code.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	379 - Added documentation to `gecco` submodules missing some.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	380 - Included the `CHANGELOG.md` file to the generated docs.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	381
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	382 ## [v0.1.0] - 2020-07-17
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	383 [v0.1.0]: https://git.embl.de/grp-zeller/GECCO/compare/v0.0.1...v0.1.0
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	384 Initial release.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	385
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	386 ## [v0.0.1] - 2018-08-13
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	387 [v0.0.1]: https://git.embl.de/grp-zeller/GECCO/compare/37afb97...v0.0.1
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	388 Proof-of-concept.

Mercurial > repos > althonos > gecco

annotate CHANGELOG.md @ 16:042a23379d2d draft