annotate CHANGELOG.md @ 8:cebc53d02da6 draft

"Release v0.8.9"
author althonos
date Tue, 22 Feb 2022 16:04:07 +0000
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1 # Changelog
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2 All notable changes to this project will be documented in this file.
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3
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4 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
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5 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
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6
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7 ## [Unreleased]
8
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8 [Unreleased]: https://git.embl.de/grp-zeller/GECCO/compare/v0.8.9...master
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9
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10 ## [v0.8.9] - 2022-02-22
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11 [v0.8.9]: https://git.embl.de/grp-zeller/GECCO/compare/v0.8.8...v0.8.9
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12 ### Removed
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13 - Prediction and support for the *Other* biosynthetic type of MIBiG clusters.
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14
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15 ## [v0.8.8] - 2022-02-21
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16 [v0.8.8]: https://git.embl.de/grp-zeller/GECCO/compare/v0.8.7...v0.8.8
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17 ### Fixed
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18 - `ClusterRefiner` filtering method for edge genes not working as intended.
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19 - `gecco run` and `gecco annotate` commands crashing on missing input files instead of nicely rendering the error.
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21 ## [v0.8.7] - 2022-02-18
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22 [v0.8.7]: https://git.embl.de/grp-zeller/GECCO/compare/v0.8.6...v0.8.7
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23 ### Fixed
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24 - `interpro.json` metadata file not being included in distribution files.
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25 - Missing docstring for `Protein.with_domains` method.
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26 ### Changed
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27 - Bump minimum `scikit-learn` version to `v1.0` for Python3.7+.
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28
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29 ## [v0.8.6] - 2022-02-17 - YANKED
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30 [v0.8.6]: https://git.embl.de/grp-zeller/GECCO/compare/v0.8.5...v0.8.6
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31 ### Added
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32 - CLI flag for enabling region masking for contigs processed by Prodigal.
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33 - CLI flag for controlling region distance used for edge distance filtering.
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34 ### Changed
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35 - `gecco.model.Gene` and `gecco.model.Protein` are now immutable data classes.
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36 - Bump minimum `pyrodigal` version to `v0.6.4` to use region masking.
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37 - Implement filtering for extracted clusters based on distance to the contig edge.
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38 - Store InterPro metadata file uncompressed for version-control integration.
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39 ### Fixed
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40 - Mark `BGC0000930` as `Terpene` in the type classifier data.
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41 - Progress bar messages are now in consistent format.
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42
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43 ## [v0.8.5] - 2021-11-21
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44 [v0.8.5]: https://git.embl.de/grp-zeller/GECCO/compare/v0.8.4...v0.8.5
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45 ### Added
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46 - Minimal compatibility support for running GECCO inside of Galaxy workflows.
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47
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48 ## [v0.8.4] - 2021-09-26
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49 [v0.8.4]: https://git.embl.de/grp-zeller/GECCO/compare/v0.8.3-post1...v0.8.4
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50 ### Fixed
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51 - `gecco convert gbk --format bigslice` failing to run because of outdated code ([#5](https://github.com/zellerlab/GECCO/issues/5)).
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52 - `gecco convert gbk --format bigslice` not creating files with names conforming to BiG-SLiCE expected input.
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53 ### Changed
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54 - Bump minimum `pyrodigal` version to `v0.6.2` to use platform-accelerated code if supported.
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55
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56 ## [v0.8.3-post1] - 2021-08-23
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57 [v0.8.3-post1]: https://git.embl.de/grp-zeller/GECCO/compare/v0.8.3...v0.8.3-post1
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58 ### Fixed
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59 - Wrong default value for `--threshold` being shown in `gecco run` help message.
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60
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61 ## [v0.8.3] - 2021-08-23
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62 [v0.8.3]: https://git.embl.de/grp-zeller/GECCO/compare/v0.8.2...v0.8.3
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63 ### Changed
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64 - Default probability threshold for segmentation to 0.3 (from 0.4).
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65
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66 ## [v0.9.0] - 2021-08-10 - **YANKED**
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67 [v0.9.0]: https://git.embl.de/grp-zeller/GECCO/compare/v0.8.2...v0.9.0
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68 ### Changed
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69 - Retrain internal model using `--select=0.35` instead of `--select=0.25` like before.
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70 - Change default *p-value* filter from 1e-9 to 1e-5 to detect more features.
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71
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72 ## [v0.8.2] - 2021-07-31
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73 [v0.8.2]: https://git.embl.de/grp-zeller/GECCO/compare/v0.8.1...v0.8.2
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74 ### Fixed
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75 - `gecco run` crashing on Python 3.6 because of missing `contextlib.nullcontext` class.
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76 ### Changed
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77 - `gecco run` and `gecco annotate` will not try to count the number of profiles when given an external HMM file with the `--hmm` flag.
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78 - `PyHMMER.run` now reports the *p-value* of each domain in addition to the *e-value* as a `/note` qualifier.
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79
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80 ## [v0.8.1] - 2021-07-29
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81 [v0.8.1]: https://git.embl.de/grp-zeller/GECCO/compare/v0.8.0...v0.8.1
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82 ### Changed
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83 - `gecco run` now filters out unneeded features before annotating, making it easier to analyze the results of a run with a custom `--model`.
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84 ### Fixed
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85 - `gecco` reporting about using Pfam `v33.1` while actually using `v34.0` because of an outdated field in `gecco/hmmer/Pfam.ini`.
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86 ### Added
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87 - Missing documentation for the `strand` attribute of `gecco.model.Gene`.
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88
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89 ## [v0.8.0] - 2021-07-03
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90 [v0.8.0]: https://git.embl.de/grp-zeller/GECCO/compare/v0.7.0...v0.8.0
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91 ### Changed
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92 - Retrain internal model using new sequence embeddings and remove broken/duplicate BGCs from MIBiG 2.0.
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93 - Bump minimum `pyhmmer` version to `v0.4.0` to improve exception handling.
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94 - Bump minimum `pyrodigal` version to `v0.5.0` to fix sequence decoding on some platforms.
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95 - Use p-values instead of e-values to filter domains obtained with HMMER.
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96 - `gecco cv` and `gecco train` now seed the RNG with a user-defined seed before shuffling rows of training data.
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97 ### Fixed
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98 - Extraction of BGC compositions for the type predictor while training.
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99 - `ClusterCRF.trained` failing to open an external model.
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100 ### Added
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101 - `Domain.pvalue` attribute to access the p-value of a domain annotation.
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102 - Mandatory `pvalue` column to `FeatureTable` objects.
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103 - Support for loading several feature tables in `gecco train` and `gecco cv`.
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104 - Warnings to `ClusterCRF.fit` when selecting uninformative features.
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105 - `--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.
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106 ### Removed
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107 - Outdated `gecco embed` command.
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108 - Unused `--truncate` flag from the `gecco train` CLI.
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109 - Tigrfam domains, which is not improving performance on the new training data.
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110
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111 ## [v0.7.0] - 2021-05-31
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112 [v0.7.0]: https://git.embl.de/grp-zeller/GECCO/compare/v0.6.3...v0.7.0
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113 ### Added
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114 - Support for writing an AntiSMASH sideload JSON file after a `gecco run` workflow.
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115 - Code for converting GenBank files in BiG-SLiCE compatible format with the `gecco convert` subcommand.
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116 - Documentation about using GECCO in combination with AntiSMASH or BiG-SLiCE.
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117 ### Changed
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118 - Minimum Biopython version to `v1.73` for compatibility with older bioinformatics tooling.
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119 - Internal domain composition shipped in the `gecco.types` with newer composition array obtained directly from MIBiG files.
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120 ### Removed
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121 - Outdated notice about `-vvv` verbosity level in the help message of the main `gecco` command.
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122
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123 ## [v0.6.3] - 2021-05-10
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124 [v0.6.3]: https://git.embl.de/grp-zeller/GECCO/compare/v0.6.2...v0.6.3
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125 ### Fixed
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126 - HMMER annotation not properly handling inputs with multiple contigs.
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127 - Some progress bar totals displaying as floats in the CLI.
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128 ### Changed
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129 - `PyHMMER` now sets the `Z` and `domZ` values from the number of proteins given to the search pipeline.
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130 - `gecco.cli` delegates imports to make CLI more responsive.
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131 - `pkg_resources` has been replaced with `importlib.resources` and `importlib.metadata` where applicable.
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132 - `multiprocessing.cpu_count` has been replaced with `os.cpu_count` where applicable.
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133
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134 ## [v0.6.2] - 2021-05-04
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135 [v0.6.2]: https://git.embl.de/grp-zeller/GECCO/compare/v0.6.1...v0.6.2
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136 ### Fixed
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137 - `gecco cv loto` crashing because of outdated code.
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138 ### Changed
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139 - Logging-style prompt will only display if GECCO is running with `-vv` flag.
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140 ### Added
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141 - GECCO bioRxiv paper reference to `Cluster.to_seq_record` output record.
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142
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143 ## [v0.6.1] - 2021-03-15
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144 [v0.6.1]: https://git.embl.de/grp-zeller/GECCO/compare/v0.6.0...v0.6.1
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145 ### Fixed
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146 - Progress bar not being disabled by `-q` flag in CLI.
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147 - Fallback to using HMM name if accession is not available in `PyHMMER`.
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148 - Group genes by source contig and process them separately in `PyHMMER` to avoid bogus E-values.
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149 ### Added
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150 - `psutil` dependency to get the number of physical CPU cores on the host machine.
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151 - Support for using an arbitrary mapping of positives to negatives in `gecco embed`.
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152 ### Removed
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153 - Unused and outdated `HMMER` and `DomainRow` classes from `gecco.hmmer`.
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154
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155 ## [v0.6.0] - 2021-02-28
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156 [v0.6.0]: https://git.embl.de/grp-zeller/GECCO/compare/v0.5.5...v0.6.0
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157 ### Changed
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158 - Updated internal model with a cleaned-up version of the MIBiG-2.0
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159 Pfam-33.1/Tigrfam-15.0 embedding.
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160 - Updated internal InterPro catalog.
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161 ### Fixed
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162 - Features not being grouped together in `gecco cv` and `gecco train`
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althonos
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163 when provided with a feature table where rows were not sorted by
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althonos
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164 protein IDs.
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165
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166 ## [v0.5.5] - 2021-02-28
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167 [v0.5.5]: https://git.embl.de/grp-zeller/GECCO/compare/v0.5.4...v0.5.5
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168 ### Fixed
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169 - `gecco cv` bug causing only the last fold to be written.
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170
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171 ## [v0.5.4] - 2021-02-28
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172 [v0.5.4]: https://git.embl.de/grp-zeller/GECCO/compare/v0.5.3...v0.5.4
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173 ### Changed
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174 - Replaced `verboselogs`, `coloredlogs` and `better-exceptions` with `rich`.
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althonos
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175 ### Removed
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althonos
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176 - `tqdm` training dependency.
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althonos
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177 ### Added
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178 - `gecco annotate` command to produce a feature table from a genomic file.
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althonos
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179 - `gecco embed` to embed BGCs into non-BGC regions using feature tables.
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180
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181 ## [v0.5.3] - 2021-02-21
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182 [v0.5.3]: https://git.embl.de/grp-zeller/GECCO/compare/v0.5.2...v0.5.3
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183 ### Fixed
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184 - Coordinates of genes in output GenBank files.
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althonos
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185 - Potential issue with the number of CPUs in `PyHMMER.run`.
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186 ### Changed
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187 - Bump required `pyrodigal` version to `v0.4.2` to fix buffer overflow.
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188
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189 ## [v0.5.2] - 2021-01-29
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190 [v0.5.2]: https://git.embl.de/grp-zeller/GECCO/compare/v0.5.1...v0.5.2
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191 ### Added
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192 - Support for downloading HMM files directly from GitHub releases assets.
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193 - Validation of filtered HMMs with MD5 checksum.
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194 ### Fixed
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althonos
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195 - Invalid coordinates of protein domains in GenBank output files.
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althonos
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196 - `gecco.interpro` module not being added to wheel distribution.
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197 ### Changed
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198 - Bump required `pyhmmer` version to `v0.2.1`.
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199
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200 ## [v0.5.1] - 2021-01-15
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201 [v0.5.1]: https://git.embl.de/grp-zeller/GECCO/compare/v0.5.0...v0.5.1
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202 ### Fixed
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althonos
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203 - `--hmm` flag being ignored in in `gecco run` command.
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204 - `PyHMMER` using HMM names instead of accessions, causing issues with Pfam HMMs.
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205
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206 ## [v0.5.0] - 2021-01-11
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207 [v0.5.0]: https://git.embl.de/grp-zeller/GECCO/compare/v0.4.5...v0.5.0
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208 ### Added
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209 - Explicit support for Python 3.9.
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210 ### Changed
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211 - [`pyhmmer`](https://pypi.org/project/pyhmmer) is used to annotate protein sequences instead of HMMER3 binary `hmmsearch`.
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212 - HMM files are stored in binary format to speedup parsing and reduce storage size.
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213 - `tqdm` is now a *training*-only dependency.
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214 - `gecco cv` now requires *training* dependencies.
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215
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216 ## [v0.4.5] - 2020-11-23
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217 [v0.4.5]: https://git.embl.de/grp-zeller/GECCO/compare/v0.4.4...v0.4.5
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218 ### Added
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219 - Additional `fold` column to cross-validation table output.
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220 ### Changed
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221 - Use sequence ID instead of protein ID to extract type from cluster in `gecco cv`.
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222 - Install HMM data in pre-pressed format to make `hmmsearch` runs faster on short sequences.
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223 - `gecco.orf` was rewritten to extract genes from input sequences in parallel.
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224
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225 ## [v0.4.4] - 2020-09-30
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226 [v0.4.4]: https://git.embl.de/grp-zeller/GECCO/compare/v0.4.3...v0.4.4
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227 ### Added
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228 - `gecco cv loto` command to run LOTO cross-validation using BGC types
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229 for stratification.
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230 - `header` keyword argument to `FeatureTable.dump` and `ClusterTable.dump`
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althonos
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231 to write the table without the column header allowing to append to an
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232 existing table.
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233 - `__getitem__` implementation for `FeatureTable` and `ClusterTable`
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234 that returns a single row or a sub-table from a table.
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235 ### Fixed
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236 - `gecco cv` command now writes results iteratively instead of holding
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althonos
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237 the tables for every fold in memory.
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althonos
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238 ### Changed
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239 - Bumped `pandas` training dependency to `v1.0`.
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240
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241 ## [v0.4.3] - 2020-09-07
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242 [v0.4.3]: https://git.embl.de/grp-zeller/GECCO/compare/v0.4.2...v0.4.3
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243 ### Fixed
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althonos
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244 - GenBank files being written with invalid `/cds` feature type.
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althonos
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245 ### Changed
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246 - Blocked installation of Biopython `v1.78` or newer as it removes `Bio.Alphabet`
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247 and breaks the current code.
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248
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249 ## [v0.4.2] - 2020-08-07
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250 [v0.4.2]: https://git.embl.de/grp-zeller/GECCO/compare/v0.4.1...v0.4.2
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251 ### Fixed
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althonos
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252 - `TypeClassifier.predict_types` using inverse type probabilities when
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althonos
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253 given several clusters to process.
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254
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255 ## [v0.4.1] - 2020-08-07
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256 [v0.4.1]: https://git.embl.de/grp-zeller/GECCO/compare/v0.4.0...v0.4.1
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257 ### Fixed
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althonos
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258 - `gecco run` command crashing on input sequences not containing any genes.
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259
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althonos
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260 ## [v0.4.0] - 2020-08-06
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261 [v0.4.0]: https://git.embl.de/grp-zeller/GECCO/compare/v0.3.0...v0.4.0
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262 ### Added
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263 - `gecco.model.ProductType` enum to model the biosynthetic class of a BGC.
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althonos
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264 ### Removed
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althonos
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265 - `pandas` interaction from internal data model.
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althonos
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266 - `ClusterCRF` code specific to cross-validation.
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althonos
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267 ### Changed
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268 - `pandas`, `fisher` and `statsmodels` dependencies are now optional.
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althonos
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269 - `gecco train` command expects a cluster table in addition to the feature
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althonos
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270 table to know the types of the input BGCs.
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271
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272 ## [v0.3.0] - 2020-08-03
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273 [v0.3.0]: https://git.embl.de/grp-zeller/GECCO/compare/v0.2.2...v0.3.0
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274 ### Changed
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275 - Replaced Nearest-Neighbours classifier with Random Forest to perform type
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althonos
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276 prediction for candidate BGCs.
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althonos
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277 - `gecco.knn` module was renamed to implementation-agnostic name `gecco.types`.
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althonos
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278 ### Fixed
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althonos
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279 - Extraction of domain composition taking a long time in `gecco train` command.
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althonos
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280 ### Removed
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althonos
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281 - `--metric` argument to the `gecco run` CLI command.
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282
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283 ## [v0.2.2] - 2020-07-31
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284 [v0.2.2]: https://git.embl.de/grp-zeller/GECCO/compare/v0.2.1...v0.2.2
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285 ### Changed
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286 - `Domain` and `Gene` can now carry qualifiers that are used when they
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althonos
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287 are translated to a sequence feature.
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288 ### Added
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289 - InterPro names, accessions, and HMMER e-value for each annotated domain
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290 in GenBank output files.
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291
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292 ## [v0.2.1] - 2020-07-23
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293 [v0.2.1]: https://git.embl.de/grp-zeller/GECCO/compare/v0.2.0...v0.2.1
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294 ### Fixed
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295 - Various potential crashes in `ClusterRefiner` code.
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296 ### Removed
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297 - Uneeded feature dictionary filtering in `ClusterCRF` for models with
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298 Fisher Exact Test feature selection.
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299
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300 ## [v0.2.0] - 2020-07-23
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301 [v0.2.0]: https://git.embl.de/grp-zeller/GECCO/compare/v0.1.1...v0.2.0
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302 ### Fixed
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303 - `pandas` warning about unsorted columns in `gecco run`.
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304 ### Removed
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305 - `Gene.probability` property, replaced by `Gene.maximum_probability` and
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306 `Gene.average_probability` properties to be explicit.
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307 ### Changed
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308 - Internal model now uses `Pfam` and `Tigrfam` with the top 35% features
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309 selected with Fisher's Exact Test.
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310 - `ClusterRefiner` now removes genes on `Cluster` edges if they do not
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311 contain any domain annotation.
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312
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313 ## [v0.1.1] - 2020-07-22
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314 [v0.1.1]: https://git.embl.de/grp-zeller/GECCO/compare/v0.1.0...v0.1.1
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315 ### Added
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316 - `ClusterCRF.predict_probabilities` to annotate a list of `Gene`.
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317 ### Changed
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318 - BGC probability is now stored at the `Domain` level instead of at the `Gene`
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319 level, independently of the feature extraction level used by the CRF.
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320 - `ClusterKNN` will use the model path provided to `gecco run` if any.
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321 ### Docs
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322 - Added this changelog file to document changes in the code.
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323 - Added documentation to `gecco` submodules missing some.
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324 - Included the `CHANGELOG.md` file to the generated docs.
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325
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326 ## [v0.1.0] - 2020-07-17
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327 [v0.1.0]: https://git.embl.de/grp-zeller/GECCO/compare/v0.0.1...v0.1.0
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328 Initial release.
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329
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330 ## [v0.0.1] - 2018-08-13
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331 [v0.0.1]: https://git.embl.de/grp-zeller/GECCO/compare/37afb97...v0.0.1
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332 Proof-of-concept.