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Changelog

v2.0.0-alpha.8 (2025-01-23)

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Closed issues:

  • Replace square NPLinker logo by one used for Slack (with NPLinker text) #288

Merged pull requests:

v2.0.0-alpha.7 (2024-11-28)

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Closed issues:

  • Incorrect precursor m/z when loading MGF file from GNPS #282
  • Use bigscape version in loaders #271

Merged pull requests:

v2.0.0-alpha.6 (2024-09-17)

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Merged pull requests:

v2.0.0-alpha.5 (2024-08-22)

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Merged pull requests:

v2.0.0-alpha.4 (2024-07-29)

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Implemented enhancements:

  • Select subset of the data #265

Closed issues:

  • Fix code scanning alert - Token-Permissions #268
  • support bigscape v2 #216
  • Abstraction of run_bigscape function #115

Merged pull requests:

v2.0.0-alpha.3 (2024-07-11)

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Implemented enhancements:

  • Data size warnings / checks when installing and using nplinker package #237

Closed issues:

  • Podp: not all genome IDs are in antismashDB #242
  • refactoring scoring (tracker issue) #205
  • ensure that IDs are unique #146
  • refactor __eq__ and __hash__ methods #136
  • Missing mibig BGC #86

Merged pull requests:

v2.0.0-alpha.2 (2024-06-20)

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Closed issues:

  • improvement on docs #232
  • writing tutorials and docs for preparing data #204

Merged pull requests:

v2.0.0-alpha.1 (2024-03-25)

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Fixed bugs:

  • Fix failing tests #96

Closed issues:

  • Fix dev setup issues #222
  • Running NPLinker tutorial #213
  • Exception: Failed to find *ANY* strains, missing strain_mappings.csv? #170
  • Add schema validation #165
  • Refactor initialisation of project root and data folders [Track issue] #163
  • http 404 error from test_nplinker_local.py #156
  • implement the function to generate strain mappings file #154
  • implement the function to generate refseq id ↔ BGC id mapping file #153
  • change csv to json for strain mappings file #152
  • change csv to json for genome status file #151
  • generate strain mappings file for PODP data #150
  • how is strain_mappings.csv generated? #148
  • Strain generation, loading and mapping #147
  • Refactor DatasetLoader class #145
  • Use UUID for singleton molecular family? #144
  • KeyError: 'cluster' Extract MIBIG data #140
  • Use the refactored antismash downloader in PODPDownloader class #137
  • remove _strain_dict_index from StrainCollection class #134
  • Rename Downloader class to PODPDownloader #133
  • Exception: Failed to find *ANY* strains, missing strain_mappings.csv? #130
  • error when loading local data #129
  • nplinker library download #128
  • Hardware Requirements: #124
  • replace load_gcfs function #122
  • Refactor Downloader class to have a specific PoDP downloader #121
  • PODP mode and local data mode #117
  • Create StrainMappingLoader #116
  • Refactor GCF loading process #114
  • Change strains in StrainCollection to be a set instead of list #113
  • Implement comparison operator for StrainCollection class #110
  • Include strains again in objects loaded from Metabolomics #109
  • check if this function is still needed or forward to the proper implementation #108
  • Implement GNPS loading functionality on DatasetLoader layer #107
  • Rename MibigBGC to BGC in MibigBGCLoader #106
  • Remove strain assignment from BGC loaders? #104
  • Use unique and fixed GCF identifier in scoring #103
  • Move test files to subfolders #99
  • Create antismash_downloader module #98
  • Fix instructions for zsh shell #95
  • MiBIG v3.x support #94
  • Implement removing the strain also from self._lookup indices. [Bug] #90
  • Improve GNPS format detection #89
  • PoDP RefSeq accession is used as antiSMASH accession #76
  • Documentation on readthedocs.io #74

Merged pull requests:

v1.3.2 (2022-08-12)

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v1.3.1 (2022-08-05)

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Closed issues:

  • Important: Stop committing until restructuring is done #73
  • Explore tutorials/modules are relevant to develop the dashboard #68

Merged pull requests:

v1.3.0 (2022-07-21)

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Implemented enhancements:

  • Packaging #15

Closed issues:

  • Create independent repo for webapp? #72
  • Restructure repo with python template from eScience Center #71
  • Update wiki page #64
  • something goes wrong in the step for "MetcalfScoring.setup preprocessing dataset" #57
  • Parsing strains in GNPS FBMN output needs to be more flexible #50
  • Rosetta Score issue #39
  • Loading FBMN-GNPS and Bigscape output data into NPLinker error. #35
  • Remove requirements.txt file #6
  • Matching compound names from GNPS to MiBIG #3

Merged pull requests:

v1.2.0 (2022-06-07)

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Closed issues:

  • WebApp shows no data in tables #63
  • "Error in server loaded hook UnicodeDecodeError" #60
  • Error in loading from PoDP: MSV000078839 #58
  • Linking molfams #54

Merged pull requests:

v1.1.3 (2021-11-26)

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v1.1.2 (2021-09-23)

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Closed issues:

  • Turning MIBiG on in BiG-SCAPE run of NPLinker #55

v1.1.1 (2021-09-13)

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Closed issues:

  • Add a changelog and tag Docker images #52
  • GCF/BGC data does appear correctly in results #49

Merged pull requests:

v1.1 (2021-09-04)

Full Changelog

Implemented enhancements:

  • Error when loading Crüsemann data #38

Fixed bugs:

  • large-scale sample run error #43

Closed issues:

  • Add Licence #48
  • Allowing other websocket to connect to proxy server? #47
  • KeyError in strains.py #46
  • Internal Server Error with tutorial data #45
  • Error loading tutorial data #44
  • rosetta scoring: check for knownclusterblast .txt files at start of scoring process #34

Merged pull requests:

v1.0 (2021-03-19)

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Merged pull requests:

last_version_with_plots (2021-02-15)

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Closed issues:

  • Write log output to file #37

v.0.1 (2020-12-11)

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Implemented enhancements:

  • Input options #14
  • More general annotations #12

Closed issues:

  • metadata #2
  • MiBIG #1

scoring_jun2020 (2020-05-29)

Full Changelog

Implemented enhancements:

  • Generate null distributions for the different scoring functions #9

Fixed bugs:

  • NP-optimised Metcalf score crashes #24

Closed issues:

  • Restrict NPLinker strain object to data set population #27

Merged pull requests:

* This Changelog was automatically generated by github_changelog_generator