Full Changelog

Merged pull requests:

• Update python version and fix testing issues #329 (CunliangGeng)
• Update BiG-SCAPE v2 dependency #328 (adraismawur)
• docs: add webapp docs page #327 (gcroci2)
• improve make commands and fix some typos #325 (CunliangGeng)
• Update doc for work dir structure #322 (CunliangGeng)
• Update readme dev #320 (CunliangGeng)
• Update installation instructions to use conda #319 (CunliangGeng)
• Remove unused methods and files #318 (CunliangGeng)

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Fixed bugs:

• Fix dependency conflict #278

Closed issues:

• Fix logging file output #314
• Inconsistent BiG-SCAPE version handling causes ValueError #305
• GNPS2 results not supported #284
• Update releasing workflow #279

Merged pull requests:

• Update docs and readme #317 (CunliangGeng)
• Bump tj-actions/changed-files from 44 to 46 in /.github/workflows #313 (dependabot[bot])
• Local strain mappings #310 (rtlortega)
• Fix: Handle invalid GenBank accessions or missing RefSeq accessions in _resolve_genbank_accession() #309 (liannette)
• Fix inconsistent Bigscape version handling #306 (liannette)
• fix mkdocs warnings #304 (CunliangGeng)

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Closed issues:

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

Merged pull requests:

• move config template file outside of code folder #303 (CunliangGeng)
• remove unused or deprecated code and data #302 (CunliangGeng)
• update doc for gnps2 #301 (CunliangGeng)
• update DatasetArranger for different version of gnps #300 (CunliangGeng)
• update GNPSSpectrumLoader for gnps2 #299 (CunliangGeng)
• update GNPSMolecularFamilyLoader for gnps2 #298 (CunliangGeng)
• update GNPSFileMappingLoader for gnps2 #297 (CunliangGeng)
• Update GNPSFileMappingLoader to support GNPS2 data #296 (CunliangGeng)
• update GNPSExtractor class to support gnps2 #295 (CunliangGeng)
• update GNPSDownloader class to support gnps2 #294 (CunliangGeng)
• update gnpsformat detection function to support gnps2 #293 (CunliangGeng)
• update GNPSFormat to support gnps2 #292 (CunliangGeng)
• add gnps version as a new setting in config file #291 (CunliangGeng)
• change bigscape version setting from int to str #290 (CunliangGeng)
• remove smiles prediction #289 (CunliangGeng)
• add methods to export results in tabular format #280 (liannette)

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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:

• remove default config file to make all settings explicit #287 (CunliangGeng)
• add support of mibig v4.0 #286 (CunliangGeng)
• fix the resolving of genbank and jgi IDs #285 (CunliangGeng)
• Precursor m/z value fix #283 (liannette)

Full Changelog

Merged pull requests:

• Allow bigscape run for local mode #277 (CunliangGeng)
• Add table display for link graph #276 (CunliangGeng)
• Handle two quantification table folders of GNPS feature-based workflow #275 (CunliangGeng)
• Verify the support of WSL #274 (CunliangGeng)

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Merged pull requests:

• add names of bigscape classes #273 (CunliangGeng)

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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:

• update doc for bigscape #270 (CunliangGeng)
• add filter method to LinkGraph #269 (CunliangGeng)
• Add OSSF Scorecard action and badge #267 (CunliangGeng)
• improve docstrings #266 (CunliangGeng)
• Run bigscape v2 #251 (adraismawur)

Full Changelog

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:

• fix tabular file header detection #264 (CunliangGeng)
• simplify error check in unit tests #263 (CunliangGeng)
• add warning for failed antismash downloads #262 (CunliangGeng)
• check disk space before downloading #261 (CunliangGeng)

Full Changelog

Closed issues:

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

Merged pull requests:

• update docs #260 (CunliangGeng)
• improving type hints and usage of abc #259 (CunliangGeng)
• add pickling #258 (CunliangGeng)
• fix mypy and ruff errors #257 (CunliangGeng)
• refactor NPLinker class #256 (CunliangGeng)
• rename molfam to mf to uniform the abbreviation for MolecularFamily #255 (CunliangGeng)
• refactor MetcalfScoring methods #254 (CunliangGeng)
• use uniformed attribute name id #253 (CunliangGeng)
• Add LinkGraph to replace ObjectLink and LinkCollection #252 (CunliangGeng)
• merge DataLinks get_common_strains to ObjectLink #250 (CunliangGeng)
• merge DataLinks to MetcalfScoring class #249 (CunliangGeng)
• merge LinkFinder to MetcalfScoring class #248 (CunliangGeng)
• add abstract base class for scoring methods #247 (CunliangGeng)
• Specify config file explicitly for initializing NPLinker #246 (CunliangGeng)
• fix empty caplog #245 (CunliangGeng)
• update docs and readme #244 (CunliangGeng)
• refactor logging control #243 (CunliangGeng)
• add default output path #241 (CunliangGeng)
• rename globals.py to defaults.py #240 (CunliangGeng)
• Fix locations of attributes docstrings #239 (CunliangGeng)
• check format and typing only on changed files #238 (CunliangGeng)
• remove static typings from Returns in docstrings #236 (CunliangGeng)
• set ruff to not check docstrings of test files #235 (CunliangGeng)
• Support Bigscape v2 data #234 (adraismawur)

Full Changelog

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:

• move dependencies to pyproject.toml file #233 (CunliangGeng)
• Add user tutorials #231 (CunliangGeng)
• update dev env settings for vscode #230 (CunliangGeng)
• update readme files #228 (CunliangGeng)
• enable github actions for PRs on all branches #227 (CunliangGeng)
• update dependencies #226 (CunliangGeng)
• remove unused mkdocs settings #225 (CunliangGeng)
• Fix github actions for large file storage #224 (CunliangGeng)
• Fix dev setup #223 (adraismawur)
• Add API documentation #221 (CunliangGeng)
• Restructure codebase #220 (CunliangGeng)
• setup docs with Mkdocs #218 (CunliangGeng)
• fix docstrings #217 (CunliangGeng)
• add class DatasetArranger #215 (CunliangGeng)
• use git large file for large zip files #214 (CunliangGeng)
• Update strain mappings generator #212 (CunliangGeng)
• Update global variables #211 (CunliangGeng)
• Update mibig downloader #210 (CunliangGeng)
• Update config template and validations #209 (CunliangGeng)
• Update utils #208 (CunliangGeng)
• Redesign the template of nplinker config file #206 (CunliangGeng)
• Refactor config loader #203 (CunliangGeng)
• refactor initiation of paths to metabolomics files #202 (CunliangGeng)
• update logics of loading mibig data #201 (CunliangGeng)
• remove filtering of common strains during loading #200 (CunliangGeng)
• remove loading of optional data #199 (CunliangGeng)
• deprecate the method _load_class_info #198 (CunliangGeng)
• Update loading of genomics data #197 (CunliangGeng)
• Update logics of loading metabolomics data #196 (CunliangGeng)
• remove unused mgf.py and its test file #194 (CunliangGeng)
• refactor Spectrum class #193 (CunliangGeng)
• Remove class SingletonFamily and MF attribute id #192 (CunliangGeng)
• Enable filtering of singleton molecular families #191 (CunliangGeng)
• enable parallel testing using pytest-xdist #190 (CunliangGeng)
• refactor class GCF #189 (CunliangGeng)
• refactor class MolecularFamily #188 (CunliangGeng)
• remove deprecated functions of loading metabolomics data #187 (CunliangGeng)
• rename genomics.py to `utils.py...