v2.0.2 (2026-03-30)
Merged pull requests:
v2.0.1 (2026-03-14)
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 (2026-01-28)
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)
v2.0.0-beta.1 (2025-06-05)
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 (2025-03-25)
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 (2025-01-23)
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 (2024-11-28)
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 (2024-09-17)
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 (2024-08-22)
Merged pull requests:
- add names of bigscape classes #273 (CunliangGeng)
v2.0.0-alpha.4 (2024-07-29)
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)
v2.0.0-alpha.3 (2024-07-11)
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)
v2.0.0-alpha.2 (2024-06-20)
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
molfamtomfto 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_strainsto 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)
v2.0.0-alpha.1 (2024-03-25)
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.pyand its test file #194 (CunliangGeng) - refactor
Spectrumclass #193 (CunliangGeng) - Remove class
SingletonFamilyand MF attributeid#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.pytoutils.py#186 (CunliangGeng) - update the process of loading genomics data #185 (CunliangGeng)
- remove deprecated functions of loading genomics data #184 (CunliangGeng)
- rename
strains.pytostrain.py#183 (CunliangGeng) - return list for
get_bgcsmethods of BGC loaders #182 (CunliangGeng) - Enable GCF loader to filter singleton GCFs #181 (CunliangGeng)
- refactor filtering of user specified strains #178 (CunliangGeng)
- Update ruff rules to ignore unused imports in
__init__.pyfiles #177 (CunliangGeng) - change linter and formatter to ruff #176 (CunliangGeng)
- Add or update
__init__.py#174 (CunliangGeng) - Add magic method
__add__#173 (CunliangGeng) - Fix download bugs #172 (CunliangGeng)
- allow GCF loader to filter mibig-only GCF objects #171 (CunliangGeng)
- Refactor gnps classes #169 (CunliangGeng)
- Refactor loading genomics #168 (CunliangGeng)
- Add schema validation for json data #167 (CunliangGeng)
- Create functions to extract/get/generate strain mappings #166 (CunliangGeng)
- preparations for issue 154 #164 (CunliangGeng)
- change class method to static method #161 (CunliangGeng)
- Handle 404 NOT FOUND error for
download_and_extract_antismash_data#160 (gcroci2) - Handle unavailable GNPS service #159 (CunliangGeng)
- Issue152 replace csv with json for strain mappings file #158 (CunliangGeng)
- Issue151 use json for genome status file #157 (CunliangGeng)
- 153 bgc mappings generation #155 (CunliangGeng)
- clean up loader and downloader #149 (CunliangGeng)
- refactor: move non-download functionalities out of
PODPDownloader-_run_bigscape#143 (gcroci2) - Use unique string IDs #142 (CunliangGeng)
- fix indentation bug in autodocsting #141 (CunliangGeng)
- Refactor
__eq__and__hash__methods #139 (CunliangGeng) - refactor: use refactored antismash downloader module in
PODPDownloaderclass #138 (gcroci2) - Refactor StrainCollection class #135 (CunliangGeng)
- Rename
Downloaderclass toPOPDownloader#132 (gcroci2) - Refactor Strain class #131 (CunliangGeng)
- refactor: create antismash downloader module and move there inherent code #127 (gcroci2)
- Add bgc-genome mapping to BGC loaders #126 (CunliangGeng)
- Change
GCF.strainsback to attribute #125 (CunliangGeng) - add comments for loading process of strain mapping #123 (CunliangGeng)
- refactor GCF loading process #120 (CunliangGeng)
- Improved test coverage for loader #118 (hechth)
- rename MibigBGC to BGC in docstrings #112 (CunliangGeng)
- Implement comparison operator for
StrainCollectionclass #111 (hechth) - Fix local test error #105 (CunliangGeng)
- Refactor GCF class #102 (CunliangGeng)
- Refactor BGC data model #101 (CunliangGeng)
- Move test files to subfolders and update pytest's conftest.py #100 (CunliangGeng)
- docs: add quotes in package installation for zsh shell #97 (gcroci2)
- Refactored GNPS downloading and file extraction code #93 (hechth)
- Refactor BGC data loader #92 (CunliangGeng)
- Initial refactoring of Metabolomics data loading #91 (hechth)
- static typing #88 (CunliangGeng)
- Refactor mibig related code #87 (CunliangGeng)
- Add download extract utils #85 (CunliangGeng)
- Refactor AA prediction #84 (CunliangGeng)
- Check metcalf and IOKR scoring #83 (CunliangGeng)
- add dev branch to github actions #82 (CunliangGeng)
- add DATA_DIR for sharing test data dir #81 (CunliangGeng)
- Initial refactoring on scoring methods #80 (hechth)
- Implemented some tests for the metabolomics side #79 (hechth)
- Refactored
genomics.pyandmetabolomics.pyby moving classes into individual files #78 (hechth) - Refine github actions #77 (CunliangGeng)
v1.3.2 (2022-08-12)
v1.3.1 (2022-08-05)
Merged pull requests:
- Refine install script and upgrade python syntax #75 (CunliangGeng)
v1.3.0 (2022-07-21)
Merged pull requests:
- Bump numpy from 1.21.0 to 1.22.0 #70 (dependabot[bot])
- NpclassScore expand notebooks #69 (louwenjjr)
v1.2.0 (2022-06-07)
Merged pull requests:
- Bump httpx from 0.16.1 to 0.23.0 #66 (dependabot[bot])
- Expand documentation #65 (louwenjjr)
- Bump numpy from 1.20.1 to 1.21.0 #62 (dependabot[bot])
- NPClassScore scoring #61 (louwenjjr)
- Bump pillow from 8.3.2 to 9.0.0 #59 (dependabot[bot])
v1.1.3 (2021-11-26)
v1.1.2 (2021-09-23)
v1.1.1 (2021-09-13)
Merged pull requests:
- Bump pillow from 8.2.0 to 8.3.2 #53 (dependabot[bot])
v1.1 (2021-09-04)
Merged pull requests:
- Bump pillow from 8.1.1 to 8.2.0 #42 (dependabot[bot])
v1.0 (2021-03-19)
Merged pull requests:
- Bump pillow from 8.1.0 to 8.1.1 #40 (dependabot[bot])
last_version_with_plots (2021-02-15)
v.0.1 (2020-12-11)
scoring_jun2020 (2020-05-29)
Merged pull requests:
- Bump bleach from 3.0.2 to 3.1.1 #30 (dependabot[bot])
- Hack to resolve GenBank accession to RefSeq accession #29 (grimur)
- Rosetta #28 (sdrogers)
- Bump notebook from 5.7.0 to 5.7.8 #26 (dependabot[bot])
- Merging webapp back into master #25 (andrewramsay)
- Additional link expectancy calculations. #20 (florian-huber)
- get_links function now takes Spectrum, MolecularFamily, or GCF object… #19 (florian-huber)
- Added some expectancy/probability calculations #18 (florian-huber)
- Update of tests for updated matrix multiplication functions #17 (florian-huber)
- Added functions and clearer code structure #16 (florian-huber)
- Additional DataLinks and LinkProbabilty classes #8 (florian-huber)
- Updating metcalf_scoring to use a faster numpy-based method. #7 (andrewramsay)
- 2to3 changes #5 (andrewramsay)
- simple multiprocessing for scoring #4 (andrewramsay)
* This Changelog was automatically generated by github_changelog_generator