gecco: CHANGELOG.md annotate

annotate CHANGELOG.md @ 3:359232b58f6a draft

"Update Galaxy tool wrapper to follow the IUC best practices"

author	althonos
date	Sun, 21 Nov 2021 19:47:22 +0000
parents
children	169849dfb098

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]
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	8 [Unreleased]: https://git.embl.de/grp-zeller/GECCO/compare/v0.8.5...master
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	9
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	10 ## [v0.8.5] - 2021-11-21
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	11 [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	12 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	13 - 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	14
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	15 ## [v0.8.4] - 2021-09-26
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	16 [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	17 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	18 - `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	19 - `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	20 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	21 - 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	22
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	23 ## [v0.8.3-post1] - 2021-08-23
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	24 [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	25 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	26 - 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	27
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	28 ## [v0.8.3] - 2021-08-23
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	29 [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	30 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	31 - 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	32
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	33 ## [v0.9.0] - 2021-08-10 - YANKED
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	34 [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	35 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	36 - 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	37 - 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	38
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	39 ## [v0.8.2] - 2021-07-31
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	40 [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	41 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	42 - `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	43 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	44 - `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	45 - `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	46
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	47 ## [v0.8.1] - 2021-07-29
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	48 [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	49 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	50 - `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	51 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	52 - `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	53 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	54 - 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	55
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	56 ## [v0.8.0] - 2021-07-03
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	57 [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	58 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	59 - 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	60 - 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	61 - 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	62 - 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	63 - `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	64 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	65 - 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	66 - `ClusterCRF.trained` failing to open an external model.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	67 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	68 - `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	69 - Mandatory `pvalue` column to `FeatureTable` objects.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	70 - 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	71 - Warnings to `ClusterCRF.fit` when selecting uninformative features.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	72 - `--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	73 ### Removed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	74 - Outdated `gecco embed` command.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	75 - Unused `--truncate` flag from the `gecco train` CLI.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	76 - 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	77
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	78 ## [v0.7.0] - 2021-05-31
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	79 [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	80 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	81 - 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	82 - 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	83 - 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	84 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	85 - 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	86 - 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	87 ### Removed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	88 - 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	89
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	90 ## [v0.6.3] - 2021-05-10
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	91 [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	92 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	93 - HMMER annotation not properly handling inputs with multiple contigs.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	94 - 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	95 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	96 - `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	97 - `gecco.cli` delegates imports to make CLI more responsive.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	98 - `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	99 - `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	100
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	101 ## [v0.6.2] - 2021-05-04
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	102 [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	103 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	104 - `gecco cv loto` crashing because of outdated code.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	105 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	106 - 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	107 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	108 - 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	109
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	110 ## [v0.6.1] - 2021-03-15
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	111 [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	112 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	113 - 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	114 - 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	115 - 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	116 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	117 - `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	118 - 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	119 ### Removed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	120 - 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	121
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	122 ## [v0.6.0] - 2021-02-28
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	123 [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	124 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	125 - 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	126 Pfam-33.1/Tigrfam-15.0 embedding.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	127 - Updated internal InterPro catalog.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	128 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	129 - 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	130 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	131 protein IDs.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	132
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	133 ## [v0.5.5] - 2021-02-28
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	134 [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	135 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	136 - `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	137
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	138 ## [v0.5.4] - 2021-02-28
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	139 [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	140 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	141 - Replaced `verboselogs`, `coloredlogs` and `better-exceptions` with `rich`.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	142 ### Removed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	143 - `tqdm` training dependency.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	144 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	145 - `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	146 - `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	147
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	148 ## [v0.5.3] - 2021-02-21
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	149 [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	150 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	151 - Coordinates of genes in output GenBank files.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	152 - 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	153 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	154 - 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	155
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	156 ## [v0.5.2] - 2021-01-29
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	157 [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	158 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	159 - 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	160 - Validation of filtered HMMs with MD5 checksum.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	161 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	162 - Invalid coordinates of protein domains in GenBank output files.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	163 - `gecco.interpro` module not being added to wheel distribution.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	164 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	165 - Bump required `pyhmmer` version to `v0.2.1`.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	166
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	167 ## [v0.5.1] - 2021-01-15
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	168 [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	169 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	170 - `--hmm` flag being ignored in in `gecco run` command.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	171 - `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	172
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	173 ## [v0.5.0] - 2021-01-11
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	174 [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	175 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	176 - Explicit support for Python 3.9.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	177 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	178 - [`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	179 - 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	180 - `tqdm` is now a training-only dependency.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	181 - `gecco cv` now requires training dependencies.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	182
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	183 ## [v0.4.5] - 2020-11-23
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	184 [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	185 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	186 - Additional `fold` column to cross-validation table output.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	187 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	188 - 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	189 - 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	190 - `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	191
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	192 ## [v0.4.4] - 2020-09-30
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	193 [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	194 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	195 - `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	196 for stratification.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	197 - `header` keyword argument to `FeatureTable.dump` and `ClusterTable.dump`
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	198 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	199 existing table.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	200 - `__getitem__` implementation for `FeatureTable` and `ClusterTable`
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	201 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	202 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	203 - `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	204 the tables for every fold in memory.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	205 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	206 - Bumped `pandas` training dependency to `v1.0`.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	207
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	208 ## [v0.4.3] - 2020-09-07
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	209 [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	210 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	211 - GenBank files being written with invalid `/cds` feature type.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	212 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	213 - 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	214 and breaks the current code.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	215
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	216 ## [v0.4.2] - 2020-08-07
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	217 [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	218 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	219 - `TypeClassifier.predict_types` using inverse type probabilities when
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	220 given several clusters to process.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	221
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	222 ## [v0.4.1] - 2020-08-07
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	223 [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	224 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	225 - `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	226
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	227 ## [v0.4.0] - 2020-08-06
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	228 [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	229 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	230 - `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	231 ### Removed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	232 - `pandas` interaction from internal data model.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	233 - `ClusterCRF` code specific to cross-validation.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	234 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	235 - `pandas`, `fisher` and `statsmodels` dependencies are now optional.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	236 - `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	237 table to know the types of the input BGCs.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	238
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	239 ## [v0.3.0] - 2020-08-03
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	240 [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	241 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	242 - 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	243 prediction for candidate BGCs.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	244 - `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	245 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	246 - 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	247 ### Removed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	248 - `--metric` argument to the `gecco run` CLI command.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	249
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	250 ## [v0.2.2] - 2020-07-31
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	251 [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	252 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	253 - `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	254 are translated to a sequence feature.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	255 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	256 - 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	257 in GenBank output files.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	258
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	259 ## [v0.2.1] - 2020-07-23
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	260 [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	261 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	262 - Various potential crashes in `ClusterRefiner` code.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	263 ### Removed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	264 - Uneeded feature dictionary filtering in `ClusterCRF` for models with
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	265 Fisher Exact Test feature selection.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	266
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	267 ## [v0.2.0] - 2020-07-23
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	268 [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	269 ### Fixed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	270 - `pandas` warning about unsorted columns in `gecco run`.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	271 ### Removed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	272 - `Gene.probability` property, replaced by `Gene.maximum_probability` and
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	273 `Gene.average_probability` properties to be explicit.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	274 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	275 - 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	276 selected with Fisher's Exact Test.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	277 - `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	278 contain any domain annotation.
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 ## [v0.1.1] - 2020-07-22
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	281 [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	282 ### Added
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	283 - `ClusterCRF.predict_probabilities` to annotate a list of `Gene`.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	284 ### Changed
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	285 - 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	286 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	287 - `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	288 ### Docs
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	289 - 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	290 - Added documentation to `gecco` submodules missing some.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	291 - Included the `CHANGELOG.md` file to the generated docs.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	292
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	293 ## [v0.1.0] - 2020-07-17
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	294 [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	295 Initial release.
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 ## [v0.0.1] - 2018-08-13
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: diff changeset	298 [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	299 Proof-of-concept.

Mercurial > repos > althonos > gecco

annotate CHANGELOG.md @ 3:359232b58f6a draft