annotate CHANGELOG.md @ 9:d64fe390f3c9 draft

"Fix test files used in Galaxy test workflow"
author althonos
date Thu, 24 Feb 2022 16:35:48 +0000
parents cebc53d02da6
children 9156eb4ee20c
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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]
9
d64fe390f3c9 "Fix test files used in Galaxy test workflow"
althonos
parents: 8
diff changeset
8 [Unreleased]: https://git.embl.de/grp-zeller/GECCO/compare/v0.8.10...master
d64fe390f3c9 "Fix test files used in Galaxy test workflow"
althonos
parents: 8
diff changeset
9
d64fe390f3c9 "Fix test files used in Galaxy test workflow"
althonos
parents: 8
diff changeset
10 ## [v0.8.10] - 2022-02-23
d64fe390f3c9 "Fix test files used in Galaxy test workflow"
althonos
parents: 8
diff changeset
11 [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
12 ### Fixed
d64fe390f3c9 "Fix test files used in Galaxy test workflow"
althonos
parents: 8
diff changeset
13 - `--antismash-sideload` flag of `gecco run` causing command to crash.
8
cebc53d02da6 "Release v0.8.9"
althonos
parents: 7
diff changeset
14
cebc53d02da6 "Release v0.8.9"
althonos
parents: 7
diff changeset
15 ## [v0.8.9] - 2022-02-22
cebc53d02da6 "Release v0.8.9"
althonos
parents: 7
diff changeset
16 [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
17 ### Removed
cebc53d02da6 "Release v0.8.9"
althonos
parents: 7
diff changeset
18 - Prediction and support for the *Other* biosynthetic type of MIBiG clusters.
7
76b1a38579bd "Release v0.8.8"
althonos
parents: 6
diff changeset
19
76b1a38579bd "Release v0.8.8"
althonos
parents: 6
diff changeset
20 ## [v0.8.8] - 2022-02-21
76b1a38579bd "Release v0.8.8"
althonos
parents: 6
diff changeset
21 [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
22 ### Fixed
76b1a38579bd "Release v0.8.8"
althonos
parents: 6
diff changeset
23 - `ClusterRefiner` filtering method for edge genes not working as intended.
76b1a38579bd "Release v0.8.8"
althonos
parents: 6
diff changeset
24 - `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
25
6
f8878bdf1e05 "Release v0.8.7"
althonos
parents: 5
diff changeset
26 ## [v0.8.7] - 2022-02-18
f8878bdf1e05 "Release v0.8.7"
althonos
parents: 5
diff changeset
27 [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
28 ### Fixed
f8878bdf1e05 "Release v0.8.7"
althonos
parents: 5
diff changeset
29 - `interpro.json` metadata file not being included in distribution files.
f8878bdf1e05 "Release v0.8.7"
althonos
parents: 5
diff changeset
30 - Missing docstring for `Protein.with_domains` method.
f8878bdf1e05 "Release v0.8.7"
althonos
parents: 5
diff changeset
31 ### Changed
f8878bdf1e05 "Release v0.8.7"
althonos
parents: 5
diff changeset
32 - Bump minimum `scikit-learn` version to `v1.0` for Python3.7+.
f8878bdf1e05 "Release v0.8.7"
althonos
parents: 5
diff changeset
33
f8878bdf1e05 "Release v0.8.7"
althonos
parents: 5
diff changeset
34 ## [v0.8.6] - 2022-02-17 - YANKED
5
169849dfb098 "Release v0.8.6"
althonos
parents: 3
diff changeset
35 [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
36 ### Added
169849dfb098 "Release v0.8.6"
althonos
parents: 3
diff changeset
37 - CLI flag for enabling region masking for contigs processed by Prodigal.
169849dfb098 "Release v0.8.6"
althonos
parents: 3
diff changeset
38 - CLI flag for controlling region distance used for edge distance filtering.
169849dfb098 "Release v0.8.6"
althonos
parents: 3
diff changeset
39 ### Changed
169849dfb098 "Release v0.8.6"
althonos
parents: 3
diff changeset
40 - `gecco.model.Gene` and `gecco.model.Protein` are now immutable data classes.
169849dfb098 "Release v0.8.6"
althonos
parents: 3
diff changeset
41 - Bump minimum `pyrodigal` version to `v0.6.4` to use region masking.
169849dfb098 "Release v0.8.6"
althonos
parents: 3
diff changeset
42 - Implement filtering for extracted clusters based on distance to the contig edge.
169849dfb098 "Release v0.8.6"
althonos
parents: 3
diff changeset
43 - Store InterPro metadata file uncompressed for version-control integration.
169849dfb098 "Release v0.8.6"
althonos
parents: 3
diff changeset
44 ### Fixed
169849dfb098 "Release v0.8.6"
althonos
parents: 3
diff changeset
45 - Mark `BGC0000930` as `Terpene` in the type classifier data.
169849dfb098 "Release v0.8.6"
althonos
parents: 3
diff changeset
46 - Progress bar messages are now in consistent format.
3
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
47
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
48 ## [v0.8.5] - 2021-11-21
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
49 [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
50 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
51 - 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
52
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
53 ## [v0.8.4] - 2021-09-26
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
54 [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
55 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
56 - `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
57 - `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
58 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
59 - 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
60
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
61 ## [v0.8.3-post1] - 2021-08-23
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
62 [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
63 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
64 - 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
65
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
66 ## [v0.8.3] - 2021-08-23
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
67 [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
68 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
69 - 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
70
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
71 ## [v0.9.0] - 2021-08-10 - **YANKED**
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
72 [v0.9.0]: https://git.embl.de/grp-zeller/GECCO/compare/v0.8.2...v0.9.0
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
73 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
74 - Retrain internal model using `--select=0.35` instead of `--select=0.25` like before.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
75 - Change default *p-value* filter from 1e-9 to 1e-5 to detect more features.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
76
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
77 ## [v0.8.2] - 2021-07-31
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
78 [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
79 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
80 - `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
81 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
82 - `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
83 - `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
84
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
85 ## [v0.8.1] - 2021-07-29
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
86 [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
87 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
88 - `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
89 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
90 - `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
91 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
92 - 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
93
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
94 ## [v0.8.0] - 2021-07-03
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
95 [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
96 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
97 - 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
98 - 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
99 - 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
100 - 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
101 - `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
102 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
103 - 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
104 - `ClusterCRF.trained` failing to open an external model.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
105 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
106 - `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
107 - Mandatory `pvalue` column to `FeatureTable` objects.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
108 - 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
109 - Warnings to `ClusterCRF.fit` when selecting uninformative features.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
110 - `--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
111 ### Removed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
112 - Outdated `gecco embed` command.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
113 - Unused `--truncate` flag from the `gecco train` CLI.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
114 - 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
115
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
116 ## [v0.7.0] - 2021-05-31
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
117 [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
118 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
119 - 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
120 - 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
121 - 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
122 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
123 - 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
124 - 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
125 ### Removed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
126 - 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
127
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
128 ## [v0.6.3] - 2021-05-10
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
129 [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
130 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
131 - HMMER annotation not properly handling inputs with multiple contigs.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
132 - 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
133 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
134 - `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
135 - `gecco.cli` delegates imports to make CLI more responsive.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
136 - `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
137 - `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
138
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
139 ## [v0.6.2] - 2021-05-04
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
140 [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
141 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
142 - `gecco cv loto` crashing because of outdated code.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
143 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
144 - 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
145 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
146 - 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
147
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
148 ## [v0.6.1] - 2021-03-15
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
149 [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
150 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
151 - 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
152 - 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
153 - 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
154 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
155 - `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
156 - 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
157 ### Removed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
158 - 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
159
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
160 ## [v0.6.0] - 2021-02-28
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
161 [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
162 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
163 - 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
164 Pfam-33.1/Tigrfam-15.0 embedding.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
165 - Updated internal InterPro catalog.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
166 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
167 - 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
168 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
169 protein IDs.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
170
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
171 ## [v0.5.5] - 2021-02-28
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
172 [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
173 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
174 - `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
175
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
176 ## [v0.5.4] - 2021-02-28
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
177 [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
178 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
179 - Replaced `verboselogs`, `coloredlogs` and `better-exceptions` with `rich`.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
180 ### Removed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
181 - `tqdm` training dependency.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
182 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
183 - `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
184 - `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
185
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
186 ## [v0.5.3] - 2021-02-21
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
187 [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
188 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
189 - Coordinates of genes in output GenBank files.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
190 - 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
191 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
192 - 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
193
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
194 ## [v0.5.2] - 2021-01-29
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
195 [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
196 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
197 - 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
198 - Validation of filtered HMMs with MD5 checksum.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
199 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
200 - Invalid coordinates of protein domains in GenBank output files.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
201 - `gecco.interpro` module not being added to wheel distribution.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
202 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
203 - Bump required `pyhmmer` version to `v0.2.1`.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
204
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
205 ## [v0.5.1] - 2021-01-15
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
206 [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
207 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
208 - `--hmm` flag being ignored in in `gecco run` command.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
209 - `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
210
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
211 ## [v0.5.0] - 2021-01-11
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
212 [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
213 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
214 - Explicit support for Python 3.9.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
215 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
216 - [`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
217 - 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
218 - `tqdm` is now a *training*-only dependency.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
219 - `gecco cv` now requires *training* dependencies.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
220
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
221 ## [v0.4.5] - 2020-11-23
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
222 [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
223 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
224 - Additional `fold` column to cross-validation table output.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
225 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
226 - 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
227 - 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
228 - `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
229
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
230 ## [v0.4.4] - 2020-09-30
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
231 [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
232 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
233 - `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
234 for stratification.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
235 - `header` keyword argument to `FeatureTable.dump` and `ClusterTable.dump`
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
236 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
237 existing table.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
238 - `__getitem__` implementation for `FeatureTable` and `ClusterTable`
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
239 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
240 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
241 - `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
242 the tables for every fold in memory.
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 - Bumped `pandas` training dependency to `v1.0`.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
245
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
246 ## [v0.4.3] - 2020-09-07
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
247 [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
248 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
249 - GenBank files being written with invalid `/cds` feature type.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
250 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
251 - 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
252 and breaks the current code.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
253
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
254 ## [v0.4.2] - 2020-08-07
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
255 [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
256 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
257 - `TypeClassifier.predict_types` using inverse type probabilities when
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
258 given several clusters to process.
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 ## [v0.4.1] - 2020-08-07
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
261 [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
262 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
263 - `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
264
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
265 ## [v0.4.0] - 2020-08-06
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
266 [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
267 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
268 - `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
269 ### Removed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
270 - `pandas` interaction from internal data model.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
271 - `ClusterCRF` code specific to cross-validation.
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 - `pandas`, `fisher` and `statsmodels` dependencies are now optional.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
274 - `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
275 table to know the types of the input BGCs.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
276
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
277 ## [v0.3.0] - 2020-08-03
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
278 [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
279 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
280 - 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
281 prediction for candidate BGCs.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
282 - `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
283 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
284 - 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
285 ### Removed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
286 - `--metric` argument to the `gecco run` CLI command.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
287
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
288 ## [v0.2.2] - 2020-07-31
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
289 [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
290 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
291 - `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
292 are translated to a sequence feature.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
293 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
294 - 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
295 in GenBank output files.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
296
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
297 ## [v0.2.1] - 2020-07-23
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
298 [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
299 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
300 - Various potential crashes in `ClusterRefiner` code.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
301 ### Removed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
302 - Uneeded feature dictionary filtering in `ClusterCRF` for models with
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
303 Fisher Exact Test feature selection.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
304
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
305 ## [v0.2.0] - 2020-07-23
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
306 [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
307 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
308 - `pandas` warning about unsorted columns in `gecco run`.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
309 ### Removed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
310 - `Gene.probability` property, replaced by `Gene.maximum_probability` and
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
311 `Gene.average_probability` properties to be explicit.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
312 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
313 - 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
314 selected with Fisher's Exact Test.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
315 - `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
316 contain any domain annotation.
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 ## [v0.1.1] - 2020-07-22
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
319 [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
320 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
321 - `ClusterCRF.predict_probabilities` to annotate a list of `Gene`.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
322 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
323 - 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
324 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
325 - `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
326 ### Docs
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
327 - 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
328 - Added documentation to `gecco` submodules missing some.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
329 - Included the `CHANGELOG.md` file to the generated docs.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
330
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
331 ## [v0.1.0] - 2020-07-17
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
332 [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
333 Initial release.
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 ## [v0.0.1] - 2018-08-13
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices"
althonos
parents:
diff changeset
336 [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
337 Proof-of-concept.