gecco: CHANGELOG.md annotate

annotate CHANGELOG.md @ 22:a41a2bcb0b91 draft default tip

Release v0.9.8

author	althonos
date	Fri, 09 Jun 2023 11:26:07 +0000
parents	6ba37b7dea42
children

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]
22 a41a2bcb0b91 Release v0.9.8 althonos parents: 21 diff changeset	8 [Unreleased]: https://github.com/zellerlab/GECCO/compare/v0.9.8...master
a41a2bcb0b91 Release v0.9.8 althonos parents: 21 diff changeset	9
a41a2bcb0b91 Release v0.9.8 althonos parents: 21 diff changeset	10
a41a2bcb0b91 Release v0.9.8 althonos parents: 21 diff changeset	11 ## [v0.9.8] - 2023-06-09
a41a2bcb0b91 Release v0.9.8 althonos parents: 21 diff changeset	12 [v0.9.8]: https://github.com/zellerlab/GECCO/compare/v0.9.7...v0.9.8
a41a2bcb0b91 Release v0.9.8 althonos parents: 21 diff changeset	13
a41a2bcb0b91 Release v0.9.8 althonos parents: 21 diff changeset	14 ### Fixed
a41a2bcb0b91 Release v0.9.8 althonos parents: 21 diff changeset	15 - `ClusterTable.from_clusters` extracting cluster IDs in the wrong column.
a41a2bcb0b91 Release v0.9.8 althonos parents: 21 diff changeset	16 - Deprecation warnings in `polars.read_csv` and `polars.write_csv` with recent `polars` versions.
a41a2bcb0b91 Release v0.9.8 althonos parents: 21 diff changeset	17 - Deprecation warnings in `importlib_resources` with recent Python versions.
21 6ba37b7dea42 Release v0.9.7 althonos parents: 19 diff changeset	18
6ba37b7dea42 Release v0.9.7 althonos parents: 19 diff changeset	19
6ba37b7dea42 Release v0.9.7 althonos parents: 19 diff changeset	20 ## [v0.9.7] - 2023-05-26
6ba37b7dea42 Release v0.9.7 althonos parents: 19 diff changeset	21 [v0.9.7]: https://github.com/zellerlab/GECCO/compare/v0.9.6...v0.9.7
6ba37b7dea42 Release v0.9.7 althonos parents: 19 diff changeset	22
6ba37b7dea42 Release v0.9.7 althonos parents: 19 diff changeset	23 ### Added
6ba37b7dea42 Release v0.9.7 althonos parents: 19 diff changeset	24 - Command line option to annotate proteins using bitscore cutoffs from HMMs.
6ba37b7dea42 Release v0.9.7 althonos parents: 19 diff changeset	25 - Command line option to disentangle overlapping domains after HMM annotation.
6ba37b7dea42 Release v0.9.7 althonos parents: 19 diff changeset	26
6ba37b7dea42 Release v0.9.7 althonos parents: 19 diff changeset	27 ### Changed
6ba37b7dea42 Release v0.9.7 althonos parents: 19 diff changeset	28 - Bump `pyhmmer` dependency to `v0.8.0`.
6ba37b7dea42 Release v0.9.7 althonos parents: 19 diff changeset	29 - Bump `pyrodigal` dependency to `v2.1.0`.
6ba37b7dea42 Release v0.9.7 althonos parents: 19 diff changeset	30 - Rewrite `gecco.model` to use `polars` for managing tabular data.
6ba37b7dea42 Release v0.9.7 althonos parents: 19 diff changeset	31 - Replace `pandas` dependencies with `polars`
6ba37b7dea42 Release v0.9.7 althonos parents: 19 diff changeset	32 - Update `gecco run` to skip type classification for tasks without an assigned cluster type.
6ba37b7dea42 Release v0.9.7 althonos parents: 19 diff changeset	33
6ba37b7dea42 Release v0.9.7 althonos parents: 19 diff changeset	34 ### Fixed
6ba37b7dea42 Release v0.9.7 althonos parents: 19 diff changeset	35 - `Cluster.to_seq_record` crashing when called on a cluster with `types` attribute unset.
6ba37b7dea42 Release v0.9.7 althonos parents: 19 diff changeset	36 - Progress bar resetting when performing domain annotation with multiple HMMs.
6ba37b7dea42 Release v0.9.7 althonos parents: 19 diff changeset	37
6ba37b7dea42 Release v0.9.7 althonos parents: 19 diff changeset	38 ### Removed
6ba37b7dea42 Release v0.9.7 althonos parents: 19 diff changeset	39 - Support for Python 3.7.
19 cc91d730cc4f Fix syntax of Galaxy script for GECCO althonos parents: 18 diff changeset	40
cc91d730cc4f Fix syntax of Galaxy script for GECCO althonos parents: 18 diff changeset	41
cc91d730cc4f Fix syntax of Galaxy script for GECCO althonos parents: 18 diff changeset	42 ## [v0.9.6] - 2023-01-11
cc91d730cc4f Fix syntax of Galaxy script for GECCO althonos parents: 18 diff changeset	43 [v0.9.6]: https://github.com/zellerlab/GECCO/compare/v0.9.5...v0.9.6
cc91d730cc4f Fix syntax of Galaxy script for GECCO althonos parents: 18 diff changeset	44
cc91d730cc4f Fix syntax of Galaxy script for GECCO althonos parents: 18 diff changeset	45 ### Added
cc91d730cc4f Fix syntax of Galaxy script for GECCO althonos parents: 18 diff changeset	46 - Gene Ontology annotations to `gecco.interpro` local metadata.
cc91d730cc4f Fix syntax of Galaxy script for GECCO althonos parents: 18 diff changeset	47 - Reference to Gene Ontology terms and derived functions to `gecco.model.Domain` objects.
cc91d730cc4f Fix syntax of Galaxy script for GECCO althonos parents: 18 diff changeset	48 - Gene color based on predicted function in `gecco.model.Gene.to_seq_feature`.
cc91d730cc4f Fix syntax of Galaxy script for GECCO althonos parents: 18 diff changeset	49
cc91d730cc4f Fix syntax of Galaxy script for GECCO althonos parents: 18 diff changeset	50 ### Fixed
cc91d730cc4f Fix syntax of Galaxy script for GECCO althonos parents: 18 diff changeset	51 - Missing `gzip` import in the CLI preventing usage of gzip-compressed inputs.
cc91d730cc4f Fix syntax of Galaxy script for GECCO althonos parents: 18 diff changeset	52 - Invalid coordinates of domains found in reverse-strand genes.
cc91d730cc4f Fix syntax of Galaxy script for GECCO althonos parents: 18 diff changeset	53 - Detection of entry points with `importlib.metadata` on older Python versions.
cc91d730cc4f Fix syntax of Galaxy script for GECCO althonos parents: 18 diff changeset	54
cc91d730cc4f Fix syntax of Galaxy script for GECCO althonos parents: 18 diff changeset	55 ### Changed
cc91d730cc4f Fix syntax of Galaxy script for GECCO althonos parents: 18 diff changeset	56 - `bgc_id` columns of cluster tables are renamed `cluster_id`.
cc91d730cc4f Fix syntax of Galaxy script for GECCO althonos parents: 18 diff changeset	57 - `gecco.model.ProductType` is renamed to `gecco.model.ClusterType`.
cc91d730cc4f Fix syntax of Galaxy script for GECCO althonos parents: 18 diff changeset	58 - Bumped `pyrodigal` dependency to `v2.0`.
cc91d730cc4f Fix syntax of Galaxy script for GECCO althonos parents: 18 diff changeset	59 - Bumped `pyhmmer` dependency to `v0.7`.
18 3dd71eaa2909 Release v0.9.5 althonos parents: 17 diff changeset	60
3dd71eaa2909 Release v0.9.5 althonos parents: 17 diff changeset	61
3dd71eaa2909 Release v0.9.5 althonos parents: 17 diff changeset	62 ## [v0.9.5] - 2022-08-10
19 cc91d730cc4f Fix syntax of Galaxy script for GECCO althonos parents: 18 diff changeset	63 [v0.9.5]: https://github.com/zellerlab/GECCO/compare/v0.9.4...v0.9.5
18 3dd71eaa2909 Release v0.9.5 althonos parents: 17 diff changeset	64
3dd71eaa2909 Release v0.9.5 althonos parents: 17 diff changeset	65 ### Added
3dd71eaa2909 Release v0.9.5 althonos parents: 17 diff changeset	66 - `gecco predict` command to predict BGCs from an annotated genome.
3dd71eaa2909 Release v0.9.5 althonos parents: 17 diff changeset	67 - `Protein.with_seq` function to assign a new sequence to a protein object.
3dd71eaa2909 Release v0.9.5 althonos parents: 17 diff changeset	68
3dd71eaa2909 Release v0.9.5 althonos parents: 17 diff changeset	69 ### Fixed
3dd71eaa2909 Release v0.9.5 althonos parents: 17 diff changeset	70 - Issue with antiSMASH sideload JSON file generation in `gecco run` and `gecco predict`.
3dd71eaa2909 Release v0.9.5 althonos parents: 17 diff changeset	71 - 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	72
e28ffe93dc69 Release v0.9.4 althonos parents: 16 diff changeset	73
e28ffe93dc69 Release v0.9.4 althonos parents: 16 diff changeset	74 ## [v0.9.4] - 2022-05-31
19 cc91d730cc4f Fix syntax of Galaxy script for GECCO althonos parents: 18 diff changeset	75 [v0.9.4]: https://github.com/zellerlab/GECCO/compare/v0.9.3...v0.9.4
17 e28ffe93dc69 Release v0.9.4 althonos parents: 16 diff changeset	76
e28ffe93dc69 Release v0.9.4 althonos parents: 16 diff changeset	77 ### Added
e28ffe93dc69 Release v0.9.4 althonos parents: 16 diff changeset	78 - `classes_` property to `TypeClassifier` to access the `classes_` attribute of the `TypeBinarizer`.
e28ffe93dc69 Release v0.9.4 althonos parents: 16 diff changeset	79 - 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	80 - 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	81
e28ffe93dc69 Release v0.9.4 althonos parents: 16 diff changeset	82 ### Changed
e28ffe93dc69 Release v0.9.4 althonos parents: 16 diff changeset	83 - `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	84 - `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	85 - `PyrodigalFinder` can now be used in single / non-meta mode from the API.
e28ffe93dc69 Release v0.9.4 althonos parents: 16 diff changeset	86 - 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	87
e28ffe93dc69 Release v0.9.4 althonos parents: 16 diff changeset	88 ### Fixed
e28ffe93dc69 Release v0.9.4 althonos parents: 16 diff changeset	89 - Broken MyPy type annotations in the `gecco.model` and `gecco.cli` modules.
16 042a23379d2d Release v0.9.3 althonos parents: 15 diff changeset	90
042a23379d2d Release v0.9.3 althonos parents: 15 diff changeset	91
042a23379d2d Release v0.9.3 althonos parents: 15 diff changeset	92 ## [v0.9.3] - 2022-05-13
19 cc91d730cc4f Fix syntax of Galaxy script for GECCO althonos parents: 18 diff changeset	93 [v0.9.3]: https://github.com/zellerlab/GECCO/compare/v0.9.2...v0.9.3
16 042a23379d2d Release v0.9.3 althonos parents: 15 diff changeset	94
042a23379d2d Release v0.9.3 althonos parents: 15 diff changeset	95 ### Changed
042a23379d2d Release v0.9.3 althonos parents: 15 diff changeset	96 - `--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	97
042a23379d2d Release v0.9.3 althonos parents: 15 diff changeset	98 ### Fixed
042a23379d2d Release v0.9.3 althonos parents: 15 diff changeset	99 - Genes with duplicate IDs being silently ignored in `HMMER.run`.
042a23379d2d Release v0.9.3 althonos parents: 15 diff changeset	100
15 64528877558f "Release v0.9.2" althonos parents: 14 diff changeset	101
64528877558f "Release v0.9.2" althonos parents: 14 diff changeset	102 ## [v0.9.2] - 2022-04-11
19 cc91d730cc4f Fix syntax of Galaxy script for GECCO althonos parents: 18 diff changeset	103 [v0.9.2]: https://github.com/zellerlab/GECCO/compare/v0.9.1...v0.9.2
15 64528877558f "Release v0.9.2" althonos parents: 14 diff changeset	104
64528877558f "Release v0.9.2" althonos parents: 14 diff changeset	105 ### Added
64528877558f "Release v0.9.2" althonos parents: 14 diff changeset	106 - 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	107
56b924f62165 "Update tests files for Galaxy tool wrapper" althonos parents: 13 diff changeset	108 ## [v0.9.1] - 2022-04-05
19 cc91d730cc4f Fix syntax of Galaxy script for GECCO althonos parents: 18 diff changeset	109 [v0.9.1]: https://github.com/zellerlab/GECCO/compare/v0.9.1-alpha4...v0.9.1
14 56b924f62165 "Update tests files for Galaxy tool wrapper" althonos parents: 13 diff changeset	110
56b924f62165 "Update tests files for Galaxy tool wrapper" althonos parents: 13 diff changeset	111 ### Changed
56b924f62165 "Update tests files for Galaxy tool wrapper" althonos parents: 13 diff changeset	112 - 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	113 - 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	114
fde43648cba0 "Release v0.9.1-alpha4" althonos parents: 12 diff changeset	115 ## [v0.9.1-alpha4] - 2022-03-31
19 cc91d730cc4f Fix syntax of Galaxy script for GECCO althonos parents: 18 diff changeset	116 [v0.9.1-alpha4]: https://github.com/zellerlab/GECCO/compare/v0.9.1-alpha3...v0.9.1-alpha4
13 fde43648cba0 "Release v0.9.1-alpha4" althonos parents: 12 diff changeset	117
fde43648cba0 "Release v0.9.1-alpha4" althonos parents: 12 diff changeset	118 Retrain internal model with:
fde43648cba0 "Release v0.9.1-alpha4" althonos parents: 12 diff changeset	119 ```
fde43648cba0 "Release v0.9.1-alpha4" althonos parents: 12 diff changeset	120 $ 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	121 -f mibig-2.0.proG2.Pfam-v35.0.features.tsv \
fde43648cba0 "Release v0.9.1-alpha4" althonos parents: 12 diff changeset	122 -c mibig-2.0.proG2.clusters.tsv \
14 56b924f62165 "Update tests files for Galaxy tool wrapper" althonos parents: 13 diff changeset	123 -g GECCO-data/data/embeddings/mibig-2.0.proG2.genes.tsv \
13 fde43648cba0 "Release v0.9.1-alpha4" althonos parents: 12 diff changeset	124 -o models/v0.9.1-alpha4
fde43648cba0 "Release v0.9.1-alpha4" althonos parents: 12 diff changeset	125 ```
12 e6597056a493 "Release v0.9.1-alpha3" althonos parents: 11 diff changeset	126
e6597056a493 "Release v0.9.1-alpha3" althonos parents: 11 diff changeset	127 ## [v0.9.1-alpha3] - 2022-03-23
19 cc91d730cc4f Fix syntax of Galaxy script for GECCO althonos parents: 18 diff changeset	128 [v0.9.1-alpha3]: https://github.com/zellerlab/GECCO/compare/v0.9.1-alpha2...v0.9.1-alpha3
12 e6597056a493 "Release v0.9.1-alpha3" althonos parents: 11 diff changeset	129
e6597056a493 "Release v0.9.1-alpha3" althonos parents: 11 diff changeset	130 ### Added
e6597056a493 "Release v0.9.1-alpha3" althonos parents: 11 diff changeset	131 - `gecco.model.GeneTable` class to store gene coordinates independently of protein domains.
e6597056a493 "Release v0.9.1-alpha3" althonos parents: 11 diff changeset	132
e6597056a493 "Release v0.9.1-alpha3" althonos parents: 11 diff changeset	133 ### Changed
e6597056a493 "Release v0.9.1-alpha3" althonos parents: 11 diff changeset	134 - 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	135 - `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	136 - `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	137
40a525d0e1fe "Release v0.9.1-alpha2" althonos parents: 10 diff changeset	138 ## [v0.9.1-alpha2] - 2022-03-23
19 cc91d730cc4f Fix syntax of Galaxy script for GECCO althonos parents: 18 diff changeset	139 [v0.9.1-alpha2]: https://github.com/zellerlab/GECCO/compare/v0.9.1-alpha1...v0.9.1-alpha2
11 40a525d0e1fe "Release v0.9.1-alpha2" althonos parents: 10 diff changeset	140
40a525d0e1fe "Release v0.9.1-alpha2" althonos parents: 10 diff changeset	141 ### Fixed
40a525d0e1fe "Release v0.9.1-alpha2" althonos parents: 10 diff changeset	142 - `TypeClassifier.trained` not being able to read unknown types from type tables.
10 9156eb4ee20c "Release v0.9.1-alpha1" althonos parents: 9 diff changeset	143
9156eb4ee20c "Release v0.9.1-alpha1" althonos parents: 9 diff changeset	144 ## [v0.9.1-alpha1] - 2022-03-20
19 cc91d730cc4f Fix syntax of Galaxy script for GECCO althonos parents: 18 diff changeset	145 [v0.9.1-alpha1]: https://github.com/zellerlab/GECCO/compare/v0.8.10...v0.9.1-alpha1
10 9156eb4ee20c "Release v0.9.1-alpha1" althonos parents: 9 diff changeset	146 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	147
d64fe390f3c9 "Fix test files used in Galaxy test workflow" althonos parents: 8 diff changeset	148 ## [v0.8.10] - 2022-02-23
19 cc91d730cc4f Fix syntax of Galaxy script for GECCO althonos parents: 18 diff changeset	149 [v0.8.10]: https://github.com/zellerlab/GECCO/compare/v0.8.9...v0.8.10
9 d64fe390f3c9 "Fix test files used in Galaxy test workflow" althonos parents: 8 diff changeset	150 ### Fixed
d64fe390f3c9 "Fix test files used in Galaxy test workflow" althonos parents: 8 diff changeset	151 - `--antismash-sideload` flag of `gecco run` causing command to crash.
8 cebc53d02da6 "Release v0.8.9" althonos parents: 7 diff changeset	152
cebc53d02da6 "Release v0.8.9" althonos parents: 7 diff changeset	153 ## [v0.8.9] - 2022-02-22
19 cc91d730cc4f Fix syntax of Galaxy script for GECCO althonos parents: 18 diff changeset	154 [v0.8.9]: https://github.com/zellerlab/GECCO/compare/v0.8.8...v0.8.9
8 cebc53d02da6 "Release v0.8.9" althonos parents: 7 diff changeset	155 ### Removed
cebc53d02da6 "Release v0.8.9" althonos parents: 7 diff changeset	156 - Prediction and support for the Other biosynthetic type of MIBiG clusters.
7 76b1a38579bd "Release v0.8.8" althonos parents: 6 diff changeset	157
76b1a38579bd "Release v0.8.8" althonos parents: 6 diff changeset	158 ## [v0.8.8] - 2022-02-21
19 cc91d730cc4f Fix syntax of Galaxy script for GECCO althonos parents: 18 diff changeset	159 [v0.8.8]: https://github.com/zellerlab/GECCO/compare/v0.8.7...v0.8.8
7 76b1a38579bd "Release v0.8.8" althonos parents: 6 diff changeset	160 ### Fixed
76b1a38579bd "Release v0.8.8" althonos parents: 6 diff changeset	161 - `ClusterRefiner` filtering method for edge genes not working as intended.
76b1a38579bd "Release v0.8.8" althonos parents: 6 diff changeset	162 - `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	163
6 f8878bdf1e05 "Release v0.8.7" althonos parents: 5 diff changeset	164 ## [v0.8.7] - 2022-02-18
19 cc91d730cc4f Fix syntax of Galaxy script for GECCO althonos parents: 18 diff changeset	165 [v0.8.7]: https://github.com/zellerlab/GECCO/compare/v0.8.6...v0.8.7
6 f8878bdf1e05 "Release v0.8.7" althonos parents: 5 diff changeset	166 ### Fixed
f8878bdf1e05 "Release v0.8.7" althonos parents: 5 diff changeset	167 - `interpro.json` metadata file not being included in distribution files.
f8878bdf1e05 "Release v0.8.7" althonos parents: 5 diff changeset	168 - Missing docstring for `Protein.with_domains` method.
f8878bdf1e05 "Release v0.8.7" althonos parents: 5 diff changeset	169 ### Changed
f8878bdf1e05 "Release v0.8.7" althonos parents: 5 diff changeset	170 - Bump minimum `scikit-learn` version to `v1.0` for Python3.7+.
f8878bdf1e05 "Release v0.8.7" althonos parents: 5 diff changeset	171
f8878bdf1e05 "Release v0.8.7" althonos parents: 5 diff changeset	172 ## [v0.8.6] - 2022-02-17 - YANKED
19 cc91d730cc4f Fix syntax of Galaxy script for GECCO althonos parents: 18 diff changeset	173 [v0.8.6]: https://github.com/zellerlab/GECCO/compare/v0.8.5...v0.8.6
5 169849dfb098 "Release v0.8.6" althonos parents: 3 diff changeset	174 ### Added
169849dfb098 "Release v0.8.6" althonos parents: 3 diff changeset	175 - CLI flag for enabling region masking for contigs processed by Prodigal.
169849dfb098 "Release v0.8.6" althonos parents: 3 diff changeset	176 - CLI flag for controlling region distance used for edge distance filtering.
169849dfb098 "Release v0.8.6" althonos parents: 3 diff changeset	177 ### Changed
169849dfb098 "Release v0.8.6" althonos parents: 3 diff changeset	178 - `gecco.model.Gene` and `gecco.model.Protein` are now immutable data classes.
169849dfb098 "Release v0.8.6" althonos parents: 3 diff changeset	179 - Bump minimum `pyrodigal` version to `v0.6.4` to use region masking.
169849dfb098 "Release v0.8.6" althonos parents: 3 diff changeset	180 - Implement filtering for extracted clusters based on distance to the contig edge.
169849dfb098 "Release v0.8.6" althonos parents: 3 diff changeset	181 - Store InterPro metadata file uncompressed for version-control integration.
169849dfb098 "Release v0.8.6" althonos parents: 3 diff changeset	182 ### Fixed
169849dfb098 "Release v0.8.6" althonos parents: 3 diff changeset	183 - Mark `BGC0000930` as `Terpene` in the type classifier data.
169849dfb098 "Release v0.8.6" althonos parents: 3 diff changeset	184 - Progress bar messages are now in consistent format.
3 359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	185
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	186 ## [v0.8.5] - 2021-11-21
19 cc91d730cc4f Fix syntax of Galaxy script for GECCO althonos parents: 18 diff changeset	187 [v0.8.5]: https://github.com/zellerlab/GECCO/compare/v0.8.4...v0.8.5
3 359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	188 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	189 - 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	190
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	191 ## [v0.8.4] - 2021-09-26
19 cc91d730cc4f Fix syntax of Galaxy script for GECCO althonos parents: 18 diff changeset	192 [v0.8.4]: https://github.com/zellerlab/GECCO/compare/v0.8.3-post1...v0.8.4
3 359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	193 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	194 - `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	195 - `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	196 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	197 - 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	198
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	199 ## [v0.8.3-post1] - 2021-08-23
19 cc91d730cc4f Fix syntax of Galaxy script for GECCO althonos parents: 18 diff changeset	200 [v0.8.3-post1]: https://github.com/zellerlab/GECCO/compare/v0.8.3...v0.8.3-post1
3 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 - 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	203
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	204 ## [v0.8.3] - 2021-08-23
19 cc91d730cc4f Fix syntax of Galaxy script for GECCO althonos parents: 18 diff changeset	205 [v0.8.3]: https://github.com/zellerlab/GECCO/compare/v0.8.2...v0.8.3
3 359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	206 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	207 - 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	208
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	209 ## [v0.8.2] - 2021-07-31
19 cc91d730cc4f Fix syntax of Galaxy script for GECCO althonos parents: 18 diff changeset	210 [v0.8.2]: https://github.com/zellerlab/GECCO/compare/v0.8.1...v0.8.2
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 - `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	213 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	214 - `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	215 - `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	216
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	217 ## [v0.8.1] - 2021-07-29
19 cc91d730cc4f Fix syntax of Galaxy script for GECCO althonos parents: 18 diff changeset	218 [v0.8.1]: https://github.com/zellerlab/GECCO/compare/v0.8.0...v0.8.1
3 359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	219 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	220 - `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	221 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	222 - `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	223 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	224 - 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	225
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	226 ## [v0.8.0] - 2021-07-03
19 cc91d730cc4f Fix syntax of Galaxy script for GECCO althonos parents: 18 diff changeset	227 [v0.8.0]: https://github.com/zellerlab/GECCO/compare/v0.7.0...v0.8.0
3 359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	228 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	229 - 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	230 - 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	231 - 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	232 - 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	233 - `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	234 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	235 - 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	236 - `ClusterCRF.trained` failing to open an external model.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	237 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	238 - `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	239 - Mandatory `pvalue` column to `FeatureTable` objects.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	240 - 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	241 - Warnings to `ClusterCRF.fit` when selecting uninformative features.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	242 - `--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	243 ### Removed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	244 - Outdated `gecco embed` command.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	245 - Unused `--truncate` flag from the `gecco train` CLI.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	246 - 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	247
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	248 ## [v0.7.0] - 2021-05-31
19 cc91d730cc4f Fix syntax of Galaxy script for GECCO althonos parents: 18 diff changeset	249 [v0.7.0]: https://github.com/zellerlab/GECCO/compare/v0.6.3...v0.7.0
3 359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	250 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	251 - 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	252 - 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	253 - 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	254 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	255 - 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	256 - 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	257 ### Removed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	258 - 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	259
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	260 ## [v0.6.3] - 2021-05-10
19 cc91d730cc4f Fix syntax of Galaxy script for GECCO althonos parents: 18 diff changeset	261 [v0.6.3]: https://github.com/zellerlab/GECCO/compare/v0.6.2...v0.6.3
3 359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	262 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	263 - HMMER annotation not properly handling inputs with multiple contigs.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	264 - 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	265 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	266 - `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	267 - `gecco.cli` delegates imports to make CLI more responsive.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	268 - `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	269 - `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	270
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	271 ## [v0.6.2] - 2021-05-04
19 cc91d730cc4f Fix syntax of Galaxy script for GECCO althonos parents: 18 diff changeset	272 [v0.6.2]: https://github.com/zellerlab/GECCO/compare/v0.6.1...v0.6.2
3 359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	273 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	274 - `gecco cv loto` crashing because of outdated code.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	275 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	276 - 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	277 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	278 - 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	279
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	280 ## [v0.6.1] - 2021-03-15
19 cc91d730cc4f Fix syntax of Galaxy script for GECCO althonos parents: 18 diff changeset	281 [v0.6.1]: https://github.com/zellerlab/GECCO/compare/v0.6.0...v0.6.1
3 359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	282 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	283 - 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	284 - 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	285 - 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	286 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	287 - `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	288 - 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	289 ### Removed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	290 - 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	291
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	292 ## [v0.6.0] - 2021-02-28
19 cc91d730cc4f Fix syntax of Galaxy script for GECCO althonos parents: 18 diff changeset	293 [v0.6.0]: https://github.com/zellerlab/GECCO/compare/v0.5.5...v0.6.0
3 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 - 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	296 Pfam-33.1/Tigrfam-15.0 embedding.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	297 - Updated internal InterPro catalog.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	298 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	299 - 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	300 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	301 protein IDs.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	302
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	303 ## [v0.5.5] - 2021-02-28
19 cc91d730cc4f Fix syntax of Galaxy script for GECCO althonos parents: 18 diff changeset	304 [v0.5.5]: https://github.com/zellerlab/GECCO/compare/v0.5.4...v0.5.5
3 359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	305 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	306 - `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	307
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	308 ## [v0.5.4] - 2021-02-28
19 cc91d730cc4f Fix syntax of Galaxy script for GECCO althonos parents: 18 diff changeset	309 [v0.5.4]: https://github.com/zellerlab/GECCO/compare/v0.5.3...v0.5.4
3 359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	310 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	311 - Replaced `verboselogs`, `coloredlogs` and `better-exceptions` with `rich`.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	312 ### Removed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	313 - `tqdm` training dependency.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	314 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	315 - `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	316 - `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	317
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	318 ## [v0.5.3] - 2021-02-21
19 cc91d730cc4f Fix syntax of Galaxy script for GECCO althonos parents: 18 diff changeset	319 [v0.5.3]: https://github.com/zellerlab/GECCO/compare/v0.5.2...v0.5.3
3 359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	320 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	321 - Coordinates of genes in output GenBank files.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	322 - 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	323 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	324 - 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	325
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	326 ## [v0.5.2] - 2021-01-29
19 cc91d730cc4f Fix syntax of Galaxy script for GECCO althonos parents: 18 diff changeset	327 [v0.5.2]: https://github.com/zellerlab/GECCO/compare/v0.5.1...v0.5.2
3 359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	328 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	329 - 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	330 - Validation of filtered HMMs with MD5 checksum.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	331 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	332 - Invalid coordinates of protein domains in GenBank output files.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	333 - `gecco.interpro` module not being added to wheel distribution.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	334 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	335 - Bump required `pyhmmer` version to `v0.2.1`.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	336
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	337 ## [v0.5.1] - 2021-01-15
19 cc91d730cc4f Fix syntax of Galaxy script for GECCO althonos parents: 18 diff changeset	338 [v0.5.1]: https://github.com/zellerlab/GECCO/compare/v0.5.0...v0.5.1
3 359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	339 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	340 - `--hmm` flag being ignored in in `gecco run` command.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	341 - `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	342
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	343 ## [v0.5.0] - 2021-01-11
19 cc91d730cc4f Fix syntax of Galaxy script for GECCO althonos parents: 18 diff changeset	344 [v0.5.0]: https://github.com/zellerlab/GECCO/compare/v0.4.5...v0.5.0
3 359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	345 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	346 - Explicit support for Python 3.9.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	347 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	348 - [`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	349 - 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	350 - `tqdm` is now a training-only dependency.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	351 - `gecco cv` now requires training dependencies.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	352
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	353 ## [v0.4.5] - 2020-11-23
19 cc91d730cc4f Fix syntax of Galaxy script for GECCO althonos parents: 18 diff changeset	354 [v0.4.5]: https://github.com/zellerlab/GECCO/compare/v0.4.4...v0.4.5
3 359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	355 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	356 - Additional `fold` column to cross-validation table output.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	357 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	358 - 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	359 - 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	360 - `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	361
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	362 ## [v0.4.4] - 2020-09-30
19 cc91d730cc4f Fix syntax of Galaxy script for GECCO althonos parents: 18 diff changeset	363 [v0.4.4]: https://github.com/zellerlab/GECCO/compare/v0.4.3...v0.4.4
3 359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	364 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	365 - `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	366 for stratification.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	367 - `header` keyword argument to `FeatureTable.dump` and `ClusterTable.dump`
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	368 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	369 existing table.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	370 - `__getitem__` implementation for `FeatureTable` and `ClusterTable`
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	371 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	372 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	373 - `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	374 the tables for every fold in memory.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	375 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	376 - Bumped `pandas` training dependency to `v1.0`.
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 ## [v0.4.3] - 2020-09-07
19 cc91d730cc4f Fix syntax of Galaxy script for GECCO althonos parents: 18 diff changeset	379 [v0.4.3]: https://github.com/zellerlab/GECCO/compare/v0.4.2...v0.4.3
3 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 - GenBank files being written with invalid `/cds` feature type.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	382 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	383 - 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	384 and breaks the current code.
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 ## [v0.4.2] - 2020-08-07
19 cc91d730cc4f Fix syntax of Galaxy script for GECCO althonos parents: 18 diff changeset	387 [v0.4.2]: https://github.com/zellerlab/GECCO/compare/v0.4.1...v0.4.2
3 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 - `TypeClassifier.predict_types` using inverse type probabilities when
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	390 given several clusters to process.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	391
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	392 ## [v0.4.1] - 2020-08-07
19 cc91d730cc4f Fix syntax of Galaxy script for GECCO althonos parents: 18 diff changeset	393 [v0.4.1]: https://github.com/zellerlab/GECCO/compare/v0.4.0...v0.4.1
3 359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	394 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	395 - `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	396
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	397 ## [v0.4.0] - 2020-08-06
19 cc91d730cc4f Fix syntax of Galaxy script for GECCO althonos parents: 18 diff changeset	398 [v0.4.0]: https://github.com/zellerlab/GECCO/compare/v0.3.0...v0.4.0
3 359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	399 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	400 - `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	401 ### Removed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	402 - `pandas` interaction from internal data model.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	403 - `ClusterCRF` code specific to cross-validation.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	404 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	405 - `pandas`, `fisher` and `statsmodels` dependencies are now optional.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	406 - `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	407 table to know the types of the input BGCs.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	408
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	409 ## [v0.3.0] - 2020-08-03
19 cc91d730cc4f Fix syntax of Galaxy script for GECCO althonos parents: 18 diff changeset	410 [v0.3.0]: https://github.com/zellerlab/GECCO/compare/v0.2.2...v0.3.0
3 359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	411 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	412 - 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	413 prediction for candidate BGCs.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	414 - `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	415 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	416 - 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	417 ### Removed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	418 - `--metric` argument to the `gecco run` CLI command.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	419
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	420 ## [v0.2.2] - 2020-07-31
19 cc91d730cc4f Fix syntax of Galaxy script for GECCO althonos parents: 18 diff changeset	421 [v0.2.2]: https://github.com/zellerlab/GECCO/compare/v0.2.1...v0.2.2
3 359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	422 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	423 - `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	424 are translated to a sequence feature.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	425 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	426 - 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	427 in GenBank output files.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	428
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	429 ## [v0.2.1] - 2020-07-23
19 cc91d730cc4f Fix syntax of Galaxy script for GECCO althonos parents: 18 diff changeset	430 [v0.2.1]: https://github.com/zellerlab/GECCO/compare/v0.2.0...v0.2.1
3 359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	431 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	432 - Various potential crashes in `ClusterRefiner` code.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	433 ### Removed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	434 - Uneeded feature dictionary filtering in `ClusterCRF` for models with
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	435 Fisher Exact Test feature selection.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	436
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	437 ## [v0.2.0] - 2020-07-23
19 cc91d730cc4f Fix syntax of Galaxy script for GECCO althonos parents: 18 diff changeset	438 [v0.2.0]: https://github.com/zellerlab/GECCO/compare/v0.1.1...v0.2.0
3 359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	439 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	440 - `pandas` warning about unsorted columns in `gecco run`.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	441 ### Removed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	442 - `Gene.probability` property, replaced by `Gene.maximum_probability` and
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	443 `Gene.average_probability` properties to be explicit.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	444 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	445 - 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	446 selected with Fisher's Exact Test.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	447 - `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	448 contain any domain annotation.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	449
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	450 ## [v0.1.1] - 2020-07-22
19 cc91d730cc4f Fix syntax of Galaxy script for GECCO althonos parents: 18 diff changeset	451 [v0.1.1]: https://github.com/zellerlab/GECCO/compare/v0.1.0...v0.1.1
3 359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	452 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	453 - `ClusterCRF.predict_probabilities` to annotate a list of `Gene`.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	454 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	455 - 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	456 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	457 - `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	458 ### Docs
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	459 - 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	460 - Added documentation to `gecco` submodules missing some.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	461 - Included the `CHANGELOG.md` file to the generated docs.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	462
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	463 ## [v0.1.0] - 2020-07-17
19 cc91d730cc4f Fix syntax of Galaxy script for GECCO althonos parents: 18 diff changeset	464 [v0.1.0]: https://github.com/zellerlab/GECCO/compare/v0.0.1...v0.1.0
3 359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	465 Initial release.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	466
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	467 ## [v0.0.1] - 2018-08-13
19 cc91d730cc4f Fix syntax of Galaxy script for GECCO althonos parents: 18 diff changeset	468 [v0.0.1]: https://github.com/zellerlab/GECCO/compare/37afb97...v0.0.1
3 359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	469 Proof-of-concept.

Mercurial > repos > althonos > gecco

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