gecco: CHANGELOG.md annotate

annotate CHANGELOG.md @ 18:3dd71eaa2909 draft

Release v0.9.5

author	althonos
date	Wed, 10 Aug 2022 12:36:38 +0000
parents	e28ffe93dc69
children	cc91d730cc4f

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]
18 3dd71eaa2909 Release v0.9.5 althonos parents: 17 diff changeset	8 [Unreleased]: https://git.embl.de/grp-zeller/GECCO/compare/v0.9.5...master
3dd71eaa2909 Release v0.9.5 althonos parents: 17 diff changeset	9
3dd71eaa2909 Release v0.9.5 althonos parents: 17 diff changeset	10
3dd71eaa2909 Release v0.9.5 althonos parents: 17 diff changeset	11 ## [v0.9.5] - 2022-08-10
3dd71eaa2909 Release v0.9.5 althonos parents: 17 diff changeset	12 [v0.9.5]: https://git.embl.de/grp-zeller/GECCO/compare/v0.9.4...v0.9.5
3dd71eaa2909 Release v0.9.5 althonos parents: 17 diff changeset	13
3dd71eaa2909 Release v0.9.5 althonos parents: 17 diff changeset	14 ### Added
3dd71eaa2909 Release v0.9.5 althonos parents: 17 diff changeset	15 - `gecco predict` command to predict BGCs from an annotated genome.
3dd71eaa2909 Release v0.9.5 althonos parents: 17 diff changeset	16 - `Protein.with_seq` function to assign a new sequence to a protein object.
3dd71eaa2909 Release v0.9.5 althonos parents: 17 diff changeset	17
3dd71eaa2909 Release v0.9.5 althonos parents: 17 diff changeset	18 ### Fixed
3dd71eaa2909 Release v0.9.5 althonos parents: 17 diff changeset	19 - Issue with antiSMASH sideload JSON file generation in `gecco run` and `gecco predict`.
3dd71eaa2909 Release v0.9.5 althonos parents: 17 diff changeset	20 - Make `gecco.orf` handle STOP codons consistently ([#9](https://github.com/zellerlab/GECCO/issues/9)).
17 e28ffe93dc69 Release v0.9.4 althonos parents: 16 diff changeset	21
e28ffe93dc69 Release v0.9.4 althonos parents: 16 diff changeset	22
e28ffe93dc69 Release v0.9.4 althonos parents: 16 diff changeset	23 ## [v0.9.4] - 2022-05-31
e28ffe93dc69 Release v0.9.4 althonos parents: 16 diff changeset	24 [v0.9.4]: https://git.embl.de/grp-zeller/GECCO/compare/v0.9.3...v0.9.4
e28ffe93dc69 Release v0.9.4 althonos parents: 16 diff changeset	25
e28ffe93dc69 Release v0.9.4 althonos parents: 16 diff changeset	26 ### Added
e28ffe93dc69 Release v0.9.4 althonos parents: 16 diff changeset	27 - `classes_` property to `TypeClassifier` to access the `classes_` attribute of the `TypeBinarizer`.
e28ffe93dc69 Release v0.9.4 althonos parents: 16 diff changeset	28 - Alternative ORF finder `CDSFinder` which simply extracts CDS features from input sequences ([#8](https://github.com/zellerlab/GECCO/issues/8)).
e28ffe93dc69 Release v0.9.4 althonos parents: 16 diff changeset	29 - Support for annotating domains with "exclusive" HMMs to annotate genes with at most one HMM from the library.
e28ffe93dc69 Release v0.9.4 althonos parents: 16 diff changeset	30
e28ffe93dc69 Release v0.9.4 althonos parents: 16 diff changeset	31 ### Changed
e28ffe93dc69 Release v0.9.4 althonos parents: 16 diff changeset	32 - `ProductType` is not restricted to MIBiG types anymore and can support any string as a base type identifier.
e28ffe93dc69 Release v0.9.4 althonos parents: 16 diff changeset	33 - `PyrodigalFinder` now uses `multiprocessing.pool.ThreadPool` instead of custom thread code thanks to `OrfFinder.find_genes` reentrancy introduced in Pyrodigal `v1.0`.
e28ffe93dc69 Release v0.9.4 althonos parents: 16 diff changeset	34 - `PyrodigalFinder` can now be used in single / non-meta mode from the API.
e28ffe93dc69 Release v0.9.4 althonos parents: 16 diff changeset	35 - BUmped minimum `rich` version to `12.3` to use `None` total in progress bars when the size of an HMM library is unknown.
e28ffe93dc69 Release v0.9.4 althonos parents: 16 diff changeset	36
e28ffe93dc69 Release v0.9.4 althonos parents: 16 diff changeset	37 ### Fixed
e28ffe93dc69 Release v0.9.4 althonos parents: 16 diff changeset	38 - Broken MyPy type annotations in the `gecco.model` and `gecco.cli` modules.
16 042a23379d2d Release v0.9.3 althonos parents: 15 diff changeset	39
042a23379d2d Release v0.9.3 althonos parents: 15 diff changeset	40
042a23379d2d Release v0.9.3 althonos parents: 15 diff changeset	41 ## [v0.9.3] - 2022-05-13
042a23379d2d Release v0.9.3 althonos parents: 15 diff changeset	42 [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	43
042a23379d2d Release v0.9.3 althonos parents: 15 diff changeset	44 ### Changed
042a23379d2d Release v0.9.3 althonos parents: 15 diff changeset	45 - `--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	46
042a23379d2d Release v0.9.3 althonos parents: 15 diff changeset	47 ### Fixed
042a23379d2d Release v0.9.3 althonos parents: 15 diff changeset	48 - Genes with duplicate IDs being silently ignored in `HMMER.run`.
042a23379d2d Release v0.9.3 althonos parents: 15 diff changeset	49
15 64528877558f "Release v0.9.2" althonos parents: 14 diff changeset	50
64528877558f "Release v0.9.2" althonos parents: 14 diff changeset	51 ## [v0.9.2] - 2022-04-11
64528877558f "Release v0.9.2" althonos parents: 14 diff changeset	52 [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	53
64528877558f "Release v0.9.2" althonos parents: 14 diff changeset	54 ### Added
64528877558f "Release v0.9.2" althonos parents: 14 diff changeset	55 - 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	56
56b924f62165 "Update tests files for Galaxy tool wrapper" althonos parents: 13 diff changeset	57 ## [v0.9.1] - 2022-04-05
56b924f62165 "Update tests files for Galaxy tool wrapper" althonos parents: 13 diff changeset	58 [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	59
56b924f62165 "Update tests files for Galaxy tool wrapper" althonos parents: 13 diff changeset	60 ### Changed
56b924f62165 "Update tests files for Galaxy tool wrapper" althonos parents: 13 diff changeset	61 - 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	62 - 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	63
fde43648cba0 "Release v0.9.1-alpha4" althonos parents: 12 diff changeset	64 ## [v0.9.1-alpha4] - 2022-03-31
fde43648cba0 "Release v0.9.1-alpha4" althonos parents: 12 diff changeset	65 [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	66
fde43648cba0 "Release v0.9.1-alpha4" althonos parents: 12 diff changeset	67 Retrain internal model with:
fde43648cba0 "Release v0.9.1-alpha4" althonos parents: 12 diff changeset	68 ```
fde43648cba0 "Release v0.9.1-alpha4" althonos parents: 12 diff changeset	69 $ 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	70 -f mibig-2.0.proG2.Pfam-v35.0.features.tsv \
fde43648cba0 "Release v0.9.1-alpha4" althonos parents: 12 diff changeset	71 -c mibig-2.0.proG2.clusters.tsv \
14 56b924f62165 "Update tests files for Galaxy tool wrapper" althonos parents: 13 diff changeset	72 -g GECCO-data/data/embeddings/mibig-2.0.proG2.genes.tsv \
13 fde43648cba0 "Release v0.9.1-alpha4" althonos parents: 12 diff changeset	73 -o models/v0.9.1-alpha4
fde43648cba0 "Release v0.9.1-alpha4" althonos parents: 12 diff changeset	74 ```
12 e6597056a493 "Release v0.9.1-alpha3" althonos parents: 11 diff changeset	75
e6597056a493 "Release v0.9.1-alpha3" althonos parents: 11 diff changeset	76 ## [v0.9.1-alpha3] - 2022-03-23
e6597056a493 "Release v0.9.1-alpha3" althonos parents: 11 diff changeset	77 [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	78
e6597056a493 "Release v0.9.1-alpha3" althonos parents: 11 diff changeset	79 ### Added
e6597056a493 "Release v0.9.1-alpha3" althonos parents: 11 diff changeset	80 - `gecco.model.GeneTable` class to store gene coordinates independently of protein domains.
e6597056a493 "Release v0.9.1-alpha3" althonos parents: 11 diff changeset	81
e6597056a493 "Release v0.9.1-alpha3" althonos parents: 11 diff changeset	82 ### Changed
e6597056a493 "Release v0.9.1-alpha3" althonos parents: 11 diff changeset	83 - 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	84 - `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	85 - `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	86
40a525d0e1fe "Release v0.9.1-alpha2" althonos parents: 10 diff changeset	87 ## [v0.9.1-alpha2] - 2022-03-23
12 e6597056a493 "Release v0.9.1-alpha3" althonos parents: 11 diff changeset	88 [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	89
40a525d0e1fe "Release v0.9.1-alpha2" althonos parents: 10 diff changeset	90 ### Fixed
40a525d0e1fe "Release v0.9.1-alpha2" althonos parents: 10 diff changeset	91 - `TypeClassifier.trained` not being able to read unknown types from type tables.
10 9156eb4ee20c "Release v0.9.1-alpha1" althonos parents: 9 diff changeset	92
9156eb4ee20c "Release v0.9.1-alpha1" althonos parents: 9 diff changeset	93 ## [v0.9.1-alpha1] - 2022-03-20
9156eb4ee20c "Release v0.9.1-alpha1" althonos parents: 9 diff changeset	94 [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	95 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	96
d64fe390f3c9 "Fix test files used in Galaxy test workflow" althonos parents: 8 diff changeset	97 ## [v0.8.10] - 2022-02-23
d64fe390f3c9 "Fix test files used in Galaxy test workflow" althonos parents: 8 diff changeset	98 [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	99 ### Fixed
d64fe390f3c9 "Fix test files used in Galaxy test workflow" althonos parents: 8 diff changeset	100 - `--antismash-sideload` flag of `gecco run` causing command to crash.
8 cebc53d02da6 "Release v0.8.9" althonos parents: 7 diff changeset	101
cebc53d02da6 "Release v0.8.9" althonos parents: 7 diff changeset	102 ## [v0.8.9] - 2022-02-22
cebc53d02da6 "Release v0.8.9" althonos parents: 7 diff changeset	103 [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	104 ### Removed
cebc53d02da6 "Release v0.8.9" althonos parents: 7 diff changeset	105 - Prediction and support for the Other biosynthetic type of MIBiG clusters.
7 76b1a38579bd "Release v0.8.8" althonos parents: 6 diff changeset	106
76b1a38579bd "Release v0.8.8" althonos parents: 6 diff changeset	107 ## [v0.8.8] - 2022-02-21
76b1a38579bd "Release v0.8.8" althonos parents: 6 diff changeset	108 [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	109 ### Fixed
76b1a38579bd "Release v0.8.8" althonos parents: 6 diff changeset	110 - `ClusterRefiner` filtering method for edge genes not working as intended.
76b1a38579bd "Release v0.8.8" althonos parents: 6 diff changeset	111 - `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	112
6 f8878bdf1e05 "Release v0.8.7" althonos parents: 5 diff changeset	113 ## [v0.8.7] - 2022-02-18
f8878bdf1e05 "Release v0.8.7" althonos parents: 5 diff changeset	114 [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	115 ### Fixed
f8878bdf1e05 "Release v0.8.7" althonos parents: 5 diff changeset	116 - `interpro.json` metadata file not being included in distribution files.
f8878bdf1e05 "Release v0.8.7" althonos parents: 5 diff changeset	117 - Missing docstring for `Protein.with_domains` method.
f8878bdf1e05 "Release v0.8.7" althonos parents: 5 diff changeset	118 ### Changed
f8878bdf1e05 "Release v0.8.7" althonos parents: 5 diff changeset	119 - Bump minimum `scikit-learn` version to `v1.0` for Python3.7+.
f8878bdf1e05 "Release v0.8.7" althonos parents: 5 diff changeset	120
f8878bdf1e05 "Release v0.8.7" althonos parents: 5 diff changeset	121 ## [v0.8.6] - 2022-02-17 - YANKED
5 169849dfb098 "Release v0.8.6" althonos parents: 3 diff changeset	122 [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	123 ### Added
169849dfb098 "Release v0.8.6" althonos parents: 3 diff changeset	124 - CLI flag for enabling region masking for contigs processed by Prodigal.
169849dfb098 "Release v0.8.6" althonos parents: 3 diff changeset	125 - CLI flag for controlling region distance used for edge distance filtering.
169849dfb098 "Release v0.8.6" althonos parents: 3 diff changeset	126 ### Changed
169849dfb098 "Release v0.8.6" althonos parents: 3 diff changeset	127 - `gecco.model.Gene` and `gecco.model.Protein` are now immutable data classes.
169849dfb098 "Release v0.8.6" althonos parents: 3 diff changeset	128 - Bump minimum `pyrodigal` version to `v0.6.4` to use region masking.
169849dfb098 "Release v0.8.6" althonos parents: 3 diff changeset	129 - Implement filtering for extracted clusters based on distance to the contig edge.
169849dfb098 "Release v0.8.6" althonos parents: 3 diff changeset	130 - Store InterPro metadata file uncompressed for version-control integration.
169849dfb098 "Release v0.8.6" althonos parents: 3 diff changeset	131 ### Fixed
169849dfb098 "Release v0.8.6" althonos parents: 3 diff changeset	132 - Mark `BGC0000930` as `Terpene` in the type classifier data.
169849dfb098 "Release v0.8.6" althonos parents: 3 diff changeset	133 - Progress bar messages are now in consistent format.
3 359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	134
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	135 ## [v0.8.5] - 2021-11-21
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	136 [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	137 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	138 - 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	139
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	140 ## [v0.8.4] - 2021-09-26
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	141 [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	142 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	143 - `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	144 - `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	145 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	146 - 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	147
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	148 ## [v0.8.3-post1] - 2021-08-23
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	149 [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	150 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	151 - 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	152
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	153 ## [v0.8.3] - 2021-08-23
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	154 [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	155 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	156 - 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	157
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	158 ## [v0.8.2] - 2021-07-31
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	159 [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	160 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	161 - `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	162 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	163 - `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	164 - `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	165
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	166 ## [v0.8.1] - 2021-07-29
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	167 [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	168 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	169 - `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	170 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	171 - `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	172 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	173 - 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	174
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	175 ## [v0.8.0] - 2021-07-03
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	176 [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	177 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	178 - 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	179 - 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	180 - 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	181 - 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	182 - `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	183 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	184 - 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	185 - `ClusterCRF.trained` failing to open an external model.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	186 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	187 - `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	188 - Mandatory `pvalue` column to `FeatureTable` objects.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	189 - 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	190 - Warnings to `ClusterCRF.fit` when selecting uninformative features.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	191 - `--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	192 ### Removed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	193 - Outdated `gecco embed` command.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	194 - Unused `--truncate` flag from the `gecco train` CLI.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	195 - 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	196
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	197 ## [v0.7.0] - 2021-05-31
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	198 [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	199 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	200 - 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	201 - 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	202 - 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	203 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	204 - 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	205 - 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	206 ### Removed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	207 - 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	208
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	209 ## [v0.6.3] - 2021-05-10
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	210 [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	211 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	212 - HMMER annotation not properly handling inputs with multiple contigs.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	213 - 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	214 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	215 - `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	216 - `gecco.cli` delegates imports to make CLI more responsive.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	217 - `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	218 - `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	219
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	220 ## [v0.6.2] - 2021-05-04
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	221 [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	222 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	223 - `gecco cv loto` crashing because of outdated code.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	224 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	225 - 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	226 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	227 - 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	228
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	229 ## [v0.6.1] - 2021-03-15
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	230 [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	231 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	232 - 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	233 - 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	234 - 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	235 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	236 - `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	237 - 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	238 ### Removed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	239 - 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	240
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	241 ## [v0.6.0] - 2021-02-28
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	242 [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	243 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	244 - 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	245 Pfam-33.1/Tigrfam-15.0 embedding.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	246 - Updated internal InterPro catalog.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	247 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	248 - 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	249 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	250 protein IDs.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	251
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	252 ## [v0.5.5] - 2021-02-28
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	253 [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	254 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	255 - `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	256
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	257 ## [v0.5.4] - 2021-02-28
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	258 [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	259 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	260 - Replaced `verboselogs`, `coloredlogs` and `better-exceptions` with `rich`.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	261 ### Removed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	262 - `tqdm` training dependency.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	263 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	264 - `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	265 - `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	266
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	267 ## [v0.5.3] - 2021-02-21
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	268 [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	269 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	270 - Coordinates of genes in output GenBank files.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	271 - 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	272 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	273 - 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	274
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	275 ## [v0.5.2] - 2021-01-29
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	276 [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	277 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	278 - 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	279 - Validation of filtered HMMs with MD5 checksum.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	280 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	281 - Invalid coordinates of protein domains in GenBank output files.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	282 - `gecco.interpro` module not being added to wheel distribution.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	283 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	284 - Bump required `pyhmmer` version to `v0.2.1`.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	285
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	286 ## [v0.5.1] - 2021-01-15
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	287 [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	288 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	289 - `--hmm` flag being ignored in in `gecco run` command.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	290 - `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	291
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	292 ## [v0.5.0] - 2021-01-11
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	293 [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	294 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	295 - Explicit support for Python 3.9.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	296 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	297 - [`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	298 - 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	299 - `tqdm` is now a training-only dependency.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	300 - `gecco cv` now requires training dependencies.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	301
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	302 ## [v0.4.5] - 2020-11-23
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	303 [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	304 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	305 - Additional `fold` column to cross-validation table output.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	306 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	307 - 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	308 - 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	309 - `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	310
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	311 ## [v0.4.4] - 2020-09-30
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	312 [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	313 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	314 - `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	315 for stratification.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	316 - `header` keyword argument to `FeatureTable.dump` and `ClusterTable.dump`
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	317 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	318 existing table.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	319 - `__getitem__` implementation for `FeatureTable` and `ClusterTable`
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	320 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	321 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	322 - `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	323 the tables for every fold in memory.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	324 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	325 - Bumped `pandas` training dependency to `v1.0`.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	326
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	327 ## [v0.4.3] - 2020-09-07
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	328 [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	329 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	330 - GenBank files being written with invalid `/cds` feature type.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	331 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	332 - 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	333 and breaks the current code.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	334
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	335 ## [v0.4.2] - 2020-08-07
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	336 [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	337 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	338 - `TypeClassifier.predict_types` using inverse type probabilities when
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	339 given several clusters to process.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	340
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	341 ## [v0.4.1] - 2020-08-07
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	342 [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	343 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	344 - `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	345
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	346 ## [v0.4.0] - 2020-08-06
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	347 [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	348 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	349 - `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	350 ### Removed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	351 - `pandas` interaction from internal data model.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	352 - `ClusterCRF` code specific to cross-validation.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	353 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	354 - `pandas`, `fisher` and `statsmodels` dependencies are now optional.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	355 - `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	356 table to know the types of the input BGCs.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	357
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	358 ## [v0.3.0] - 2020-08-03
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	359 [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	360 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	361 - 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	362 prediction for candidate BGCs.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	363 - `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	364 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	365 - 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	366 ### Removed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	367 - `--metric` argument to the `gecco run` CLI command.
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 ## [v0.2.2] - 2020-07-31
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	370 [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	371 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	372 - `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	373 are translated to a sequence feature.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	374 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	375 - 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	376 in GenBank output files.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	377
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	378 ## [v0.2.1] - 2020-07-23
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	379 [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	380 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	381 - Various potential crashes in `ClusterRefiner` code.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	382 ### Removed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	383 - Uneeded feature dictionary filtering in `ClusterCRF` for models with
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	384 Fisher Exact Test feature selection.
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 ## [v0.2.0] - 2020-07-23
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	387 [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	388 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	389 - `pandas` warning about unsorted columns in `gecco run`.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	390 ### Removed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	391 - `Gene.probability` property, replaced by `Gene.maximum_probability` and
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	392 `Gene.average_probability` properties to be explicit.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	393 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	394 - 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	395 selected with Fisher's Exact Test.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	396 - `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	397 contain any domain annotation.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	398
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	399 ## [v0.1.1] - 2020-07-22
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	400 [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	401 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	402 - `ClusterCRF.predict_probabilities` to annotate a list of `Gene`.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	403 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	404 - 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	405 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	406 - `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	407 ### Docs
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	408 - 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	409 - Added documentation to `gecco` submodules missing some.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	410 - Included the `CHANGELOG.md` file to the generated docs.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	411
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	412 ## [v0.1.0] - 2020-07-17
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	413 [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	414 Initial release.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	415
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	416 ## [v0.0.1] - 2018-08-13
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	417 [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	418 Proof-of-concept.

Mercurial > repos > althonos > gecco

annotate CHANGELOG.md @ 18:3dd71eaa2909 draft