v2.0.3

Update version to 2.0.3

v2.0.2

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Merged pull requests:

• Add example podp_id to quickstart #350 (liannette)

v2.0.1

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Merged pull requests:

• Enhance run_bigscape for BiG-SCAPE v2 compatibility #349 (CunliangGeng)
• Joss review - work on revisions Round 2 #348 (justinjjvanderhooft)
• Change cp command to copy directories recursively #346 (bgyori)

v2.0.0

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Merged pull requests:

• Provide example input data for the local mode #344 (liannette)
• [add] more state of the art - other methods + references #343 (rtlortega)
• joss review - updated statement of need #340 (justinjjvanderhooft)
• Fix installation depencencies for Gentoo #338 (apraga)
• add joss paper draft #331 (CunliangGeng)

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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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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)

Full Changelog

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)

Full Changelog

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)

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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)

Full Changelog

Merged pull requests:

• add names of bigscape classes #273 (CunliangGeng)

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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)

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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)

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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](ht...

v2.0.0-beta.1

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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)

v2.0.0-alpha.9

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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)

v2.0.0-alpha.8

Full Changelog

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)

v2.0.0-alpha.7

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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)

v2.0.0-alpha.6

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)

v2.0.0-alpha.5

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Merged pull requests:

• add names of bigscape classes #273 (CunliangGeng)