Update version to 2.0.0-alpha.1

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.3.2
+current_version = 2.0.0-alpha.1
 
 [comment]
 comment = The contents of this file cannot be merged with that of setup.cfg until https://github.com/c4urself/bump2version/issues/185 is resolved
@@ -14,4 +14,4 @@ replace = version = "{new_version}"
 
 [bumpversion:file:CITATION.cff]
 search = version: "{current_version}"
-replace = version: "{new_version}"
+replace = version: "{new_version}"

CHANGELOG.md

@@ -1,5 +1,164 @@
 # Changelog
 
+## [v2.0.0-alpha.1](https://github.com/NPLinker/nplinker/tree/v2.0.0-alpha.1) (2024-03-25)
+
+[Full Changelog](https://github.com/NPLinker/nplinker/compare/v1.3.2...v2.0.0-alpha.1)
+
+**Fixed bugs:**
+
+- Fix failing tests [\#96](https://github.com/NPLinker/nplinker/issues/96)
+
+**Closed issues:**
+
+- Fix dev setup issues [\#222](https://github.com/NPLinker/nplinker/issues/222)
+- Running NPLinker tutorial [\#213](https://github.com/NPLinker/nplinker/issues/213)
+- Exception: Failed to find \*ANY\* strains, missing strain\_mappings.csv? [\#170](https://github.com/NPLinker/nplinker/issues/170)
+- Add schema validation [\#165](https://github.com/NPLinker/nplinker/issues/165)
+- Refactor initialisation of project root and data folders \[Track issue\] [\#163](https://github.com/NPLinker/nplinker/issues/163)
+- http 404 error from `test_nplinker_local.py` [\#156](https://github.com/NPLinker/nplinker/issues/156)
+- implement the function to generate strain mappings file [\#154](https://github.com/NPLinker/nplinker/issues/154)
+- implement the function to generate `refseq id ↔ BGC id` mapping file [\#153](https://github.com/NPLinker/nplinker/issues/153)
+- change csv to json for strain mappings file [\#152](https://github.com/NPLinker/nplinker/issues/152)
+- change csv to json for genome status file [\#151](https://github.com/NPLinker/nplinker/issues/151)
+- generate strain mappings file for PODP data [\#150](https://github.com/NPLinker/nplinker/issues/150)
+- how is `strain_mappings.csv` generated? [\#148](https://github.com/NPLinker/nplinker/issues/148)
+- Strain generation, loading and mapping [\#147](https://github.com/NPLinker/nplinker/issues/147)
+- Refactor `DatasetLoader` class  [\#145](https://github.com/NPLinker/nplinker/issues/145)
+- Use UUID for singleton molecular family? [\#144](https://github.com/NPLinker/nplinker/issues/144)
+- KeyError: 'cluster' Extract MIBIG data [\#140](https://github.com/NPLinker/nplinker/issues/140)
+- Use the refactored antismash downloader in `PODPDownloader` class [\#137](https://github.com/NPLinker/nplinker/issues/137)
+- remove `_strain_dict_index` from `StrainCollection` class [\#134](https://github.com/NPLinker/nplinker/issues/134)
+- Rename `Downloader` class to `PODPDownloader` [\#133](https://github.com/NPLinker/nplinker/issues/133)
+- Exception: Failed to find \*ANY\* strains, missing strain\_mappings.csv? [\#130](https://github.com/NPLinker/nplinker/issues/130)
+- error when loading local data [\#129](https://github.com/NPLinker/nplinker/issues/129)
+- nplinker library download [\#128](https://github.com/NPLinker/nplinker/issues/128)
+- Hardware Requirements: [\#124](https://github.com/NPLinker/nplinker/issues/124)
+- replace load\_gcfs function [\#122](https://github.com/NPLinker/nplinker/issues/122)
+- Refactor `Downloader` class to have a specific PoDP downloader [\#121](https://github.com/NPLinker/nplinker/issues/121)
+- PODP mode and local data mode [\#117](https://github.com/NPLinker/nplinker/issues/117)
+- Create StrainMappingLoader [\#116](https://github.com/NPLinker/nplinker/issues/116)
+- Refactor GCF loading process [\#114](https://github.com/NPLinker/nplinker/issues/114)
+- Change `strains` in `StrainCollection` to be a `set` instead of `list` [\#113](https://github.com/NPLinker/nplinker/issues/113)
+- Implement comparison operator for `StrainCollection` class [\#110](https://github.com/NPLinker/nplinker/issues/110)
+- Include `strains` again in objects loaded from Metabolomics [\#109](https://github.com/NPLinker/nplinker/issues/109)
+- check if this function is still needed or forward to the proper implementation [\#108](https://github.com/NPLinker/nplinker/issues/108)
+- Implement GNPS loading functionality on `DatasetLoader` layer [\#107](https://github.com/NPLinker/nplinker/issues/107)
+- Rename `MibigBGC` to `BGC` in MibigBGCLoader [\#106](https://github.com/NPLinker/nplinker/issues/106)
+- Remove strain assignment from BGC loaders? [\#104](https://github.com/NPLinker/nplinker/issues/104)
+- Use unique and fixed GCF identifier in scoring [\#103](https://github.com/NPLinker/nplinker/issues/103)
+- Move test files to subfolders [\#99](https://github.com/NPLinker/nplinker/issues/99)
+- Create `antismash_downloader` module [\#98](https://github.com/NPLinker/nplinker/issues/98)
+- Fix instructions for zsh shell [\#95](https://github.com/NPLinker/nplinker/issues/95)
+- MiBIG v3.x support [\#94](https://github.com/NPLinker/nplinker/issues/94)
+- Implement removing the strain also from self.\_lookup indices. \[Bug\] [\#90](https://github.com/NPLinker/nplinker/issues/90)
+- Improve GNPS format detection [\#89](https://github.com/NPLinker/nplinker/issues/89)
+- PoDP RefSeq accession is used as antiSMASH accession [\#76](https://github.com/NPLinker/nplinker/issues/76)
+- Documentation on readthedocs.io [\#74](https://github.com/NPLinker/nplinker/issues/74)
+
+**Merged pull requests:**
+
+- move dependencies to pyproject.toml file [\#233](https://github.com/NPLinker/nplinker/pull/233) ([CunliangGeng](https://github.com/CunliangGeng))
+- Add user tutorials  [\#231](https://github.com/NPLinker/nplinker/pull/231) ([CunliangGeng](https://github.com/CunliangGeng))
+- update dev env settings for vscode [\#230](https://github.com/NPLinker/nplinker/pull/230) ([CunliangGeng](https://github.com/CunliangGeng))
+- update readme files [\#228](https://github.com/NPLinker/nplinker/pull/228) ([CunliangGeng](https://github.com/CunliangGeng))
+- enable github actions for PRs on all branches [\#227](https://github.com/NPLinker/nplinker/pull/227) ([CunliangGeng](https://github.com/CunliangGeng))
+- update dependencies [\#226](https://github.com/NPLinker/nplinker/pull/226) ([CunliangGeng](https://github.com/CunliangGeng))
+- remove unused mkdocs settings [\#225](https://github.com/NPLinker/nplinker/pull/225) ([CunliangGeng](https://github.com/CunliangGeng))
+- Fix github actions for large file storage [\#224](https://github.com/NPLinker/nplinker/pull/224) ([CunliangGeng](https://github.com/CunliangGeng))
+- Fix dev setup [\#223](https://github.com/NPLinker/nplinker/pull/223) ([adraismawur](https://github.com/adraismawur))
+- Add API documentation [\#221](https://github.com/NPLinker/nplinker/pull/221) ([CunliangGeng](https://github.com/CunliangGeng))
+- Restructure codebase [\#220](https://github.com/NPLinker/nplinker/pull/220) ([CunliangGeng](https://github.com/CunliangGeng))
+- setup docs with Mkdocs [\#218](https://github.com/NPLinker/nplinker/pull/218) ([CunliangGeng](https://github.com/CunliangGeng))
+- fix docstrings [\#217](https://github.com/NPLinker/nplinker/pull/217) ([CunliangGeng](https://github.com/CunliangGeng))
+- add class DatasetArranger [\#215](https://github.com/NPLinker/nplinker/pull/215) ([CunliangGeng](https://github.com/CunliangGeng))
+- use git large file for large zip files [\#214](https://github.com/NPLinker/nplinker/pull/214) ([CunliangGeng](https://github.com/CunliangGeng))
+- Update strain mappings generator [\#212](https://github.com/NPLinker/nplinker/pull/212) ([CunliangGeng](https://github.com/CunliangGeng))
+- Update global variables [\#211](https://github.com/NPLinker/nplinker/pull/211) ([CunliangGeng](https://github.com/CunliangGeng))
+- Update mibig downloader [\#210](https://github.com/NPLinker/nplinker/pull/210) ([CunliangGeng](https://github.com/CunliangGeng))
+- Update config template and validations [\#209](https://github.com/NPLinker/nplinker/pull/209) ([CunliangGeng](https://github.com/CunliangGeng))
+- Update utils [\#208](https://github.com/NPLinker/nplinker/pull/208) ([CunliangGeng](https://github.com/CunliangGeng))
+- Redesign the template of nplinker config file [\#206](https://github.com/NPLinker/nplinker/pull/206) ([CunliangGeng](https://github.com/CunliangGeng))
+- Refactor config loader [\#203](https://github.com/NPLinker/nplinker/pull/203) ([CunliangGeng](https://github.com/CunliangGeng))
+- refactor initiation of paths to metabolomics files [\#202](https://github.com/NPLinker/nplinker/pull/202) ([CunliangGeng](https://github.com/CunliangGeng))
+- update logics of loading mibig data [\#201](https://github.com/NPLinker/nplinker/pull/201) ([CunliangGeng](https://github.com/CunliangGeng))
+- remove filtering of common strains during loading [\#200](https://github.com/NPLinker/nplinker/pull/200) ([CunliangGeng](https://github.com/CunliangGeng))
+- remove loading of optional data [\#199](https://github.com/NPLinker/nplinker/pull/199) ([CunliangGeng](https://github.com/CunliangGeng))
+- deprecate the method `_load_class_info` [\#198](https://github.com/NPLinker/nplinker/pull/198) ([CunliangGeng](https://github.com/CunliangGeng))
+- Update loading of genomics data [\#197](https://github.com/NPLinker/nplinker/pull/197) ([CunliangGeng](https://github.com/CunliangGeng))
+- Update logics of loading metabolomics data [\#196](https://github.com/NPLinker/nplinker/pull/196) ([CunliangGeng](https://github.com/CunliangGeng))
+- remove unused `mgf.py` and its test file [\#194](https://github.com/NPLinker/nplinker/pull/194) ([CunliangGeng](https://github.com/CunliangGeng))
+- refactor `Spectrum` class [\#193](https://github.com/NPLinker/nplinker/pull/193) ([CunliangGeng](https://github.com/CunliangGeng))
+- Remove class `SingletonFamily` and MF attribute `id` [\#192](https://github.com/NPLinker/nplinker/pull/192) ([CunliangGeng](https://github.com/CunliangGeng))
+- Enable filtering of singleton molecular families [\#191](https://github.com/NPLinker/nplinker/pull/191) ([CunliangGeng](https://github.com/CunliangGeng))
+- enable parallel testing using pytest-xdist [\#190](https://github.com/NPLinker/nplinker/pull/190) ([CunliangGeng](https://github.com/CunliangGeng))
+- refactor class GCF [\#189](https://github.com/NPLinker/nplinker/pull/189) ([CunliangGeng](https://github.com/CunliangGeng))
+- refactor class `MolecularFamily` [\#188](https://github.com/NPLinker/nplinker/pull/188) ([CunliangGeng](https://github.com/CunliangGeng))
+- remove deprecated functions of loading metabolomics data [\#187](https://github.com/NPLinker/nplinker/pull/187) ([CunliangGeng](https://github.com/CunliangGeng))
+- rename `genomics.py` to `utils.py` [\#186](https://github.com/NPLinker/nplinker/pull/186) ([CunliangGeng](https://github.com/CunliangGeng))
+- update the process of loading genomics data [\#185](https://github.com/NPLinker/nplinker/pull/185) ([CunliangGeng](https://github.com/CunliangGeng))
+- remove deprecated functions of loading genomics data [\#184](https://github.com/NPLinker/nplinker/pull/184) ([CunliangGeng](https://github.com/CunliangGeng))
+- rename `strains.py` to `strain.py` [\#183](https://github.com/NPLinker/nplinker/pull/183) ([CunliangGeng](https://github.com/CunliangGeng))
+- return list for `get_bgcs` methods of BGC loaders [\#182](https://github.com/NPLinker/nplinker/pull/182) ([CunliangGeng](https://github.com/CunliangGeng))
+- Enable GCF loader to filter singleton GCFs [\#181](https://github.com/NPLinker/nplinker/pull/181) ([CunliangGeng](https://github.com/CunliangGeng))
+- refactor filtering of user specified strains [\#178](https://github.com/NPLinker/nplinker/pull/178) ([CunliangGeng](https://github.com/CunliangGeng))
+- Update ruff rules to ignore unused imports in `__init__.py` files [\#177](https://github.com/NPLinker/nplinker/pull/177) ([CunliangGeng](https://github.com/CunliangGeng))
+- change linter and formatter to ruff [\#176](https://github.com/NPLinker/nplinker/pull/176) ([CunliangGeng](https://github.com/CunliangGeng))
+- Add or update `__init__.py` [\#174](https://github.com/NPLinker/nplinker/pull/174) ([CunliangGeng](https://github.com/CunliangGeng))
+- Add magic method `__add__` [\#173](https://github.com/NPLinker/nplinker/pull/173) ([CunliangGeng](https://github.com/CunliangGeng))
+- Fix download bugs [\#172](https://github.com/NPLinker/nplinker/pull/172) ([CunliangGeng](https://github.com/CunliangGeng))
+- allow GCF loader to filter mibig-only GCF objects [\#171](https://github.com/NPLinker/nplinker/pull/171) ([CunliangGeng](https://github.com/CunliangGeng))
+- Refactor gnps classes [\#169](https://github.com/NPLinker/nplinker/pull/169) ([CunliangGeng](https://github.com/CunliangGeng))
+- Refactor loading genomics [\#168](https://github.com/NPLinker/nplinker/pull/168) ([CunliangGeng](https://github.com/CunliangGeng))
+- Add schema validation for json data [\#167](https://github.com/NPLinker/nplinker/pull/167) ([CunliangGeng](https://github.com/CunliangGeng))
+-  Create functions to extract/get/generate strain mappings [\#166](https://github.com/NPLinker/nplinker/pull/166) ([CunliangGeng](https://github.com/CunliangGeng))
+- preparations for issue 154  [\#164](https://github.com/NPLinker/nplinker/pull/164) ([CunliangGeng](https://github.com/CunliangGeng))
+- change class method to static method [\#161](https://github.com/NPLinker/nplinker/pull/161) ([CunliangGeng](https://github.com/CunliangGeng))
+- Handle 404 NOT FOUND error for `download_and_extract_antismash_data` [\#160](https://github.com/NPLinker/nplinker/pull/160) ([gcroci2](https://github.com/gcroci2))
+- Handle unavailable GNPS service [\#159](https://github.com/NPLinker/nplinker/pull/159) ([CunliangGeng](https://github.com/CunliangGeng))
+- Issue152 replace csv with json for strain mappings file [\#158](https://github.com/NPLinker/nplinker/pull/158) ([CunliangGeng](https://github.com/CunliangGeng))
+- Issue151 use json for genome status file [\#157](https://github.com/NPLinker/nplinker/pull/157) ([CunliangGeng](https://github.com/CunliangGeng))
+- 153 bgc mappings generation [\#155](https://github.com/NPLinker/nplinker/pull/155) ([CunliangGeng](https://github.com/CunliangGeng))
+- clean up loader and downloader [\#149](https://github.com/NPLinker/nplinker/pull/149) ([CunliangGeng](https://github.com/CunliangGeng))
+- refactor: move non-download functionalities out of `PODPDownloader` - `_run_bigscape` [\#143](https://github.com/NPLinker/nplinker/pull/143) ([gcroci2](https://github.com/gcroci2))
+- Use unique string IDs [\#142](https://github.com/NPLinker/nplinker/pull/142) ([CunliangGeng](https://github.com/CunliangGeng))
+- fix indentation bug in autodocsting [\#141](https://github.com/NPLinker/nplinker/pull/141) ([CunliangGeng](https://github.com/CunliangGeng))
+- Refactor `__eq__` and `__hash__` methods [\#139](https://github.com/NPLinker/nplinker/pull/139) ([CunliangGeng](https://github.com/CunliangGeng))
+- refactor: use refactored antismash downloader module in `PODPDownloader` class [\#138](https://github.com/NPLinker/nplinker/pull/138) ([gcroci2](https://github.com/gcroci2))
+- Refactor StrainCollection class [\#135](https://github.com/NPLinker/nplinker/pull/135) ([CunliangGeng](https://github.com/CunliangGeng))
+- Rename `Downloader` class to `POPDownloader` [\#132](https://github.com/NPLinker/nplinker/pull/132) ([gcroci2](https://github.com/gcroci2))
+- Refactor Strain class [\#131](https://github.com/NPLinker/nplinker/pull/131) ([CunliangGeng](https://github.com/CunliangGeng))
+- refactor: create antismash downloader module and move there inherent code [\#127](https://github.com/NPLinker/nplinker/pull/127) ([gcroci2](https://github.com/gcroci2))
+- Add bgc-genome mapping to BGC loaders [\#126](https://github.com/NPLinker/nplinker/pull/126) ([CunliangGeng](https://github.com/CunliangGeng))
+- Change `GCF.strains` back to attribute [\#125](https://github.com/NPLinker/nplinker/pull/125) ([CunliangGeng](https://github.com/CunliangGeng))
+- add comments for loading process of strain mapping [\#123](https://github.com/NPLinker/nplinker/pull/123) ([CunliangGeng](https://github.com/CunliangGeng))
+- refactor GCF loading process [\#120](https://github.com/NPLinker/nplinker/pull/120) ([CunliangGeng](https://github.com/CunliangGeng))
+- Improved test coverage for loader [\#118](https://github.com/NPLinker/nplinker/pull/118) ([hechth](https://github.com/hechth))
+- rename MibigBGC to BGC in docstrings [\#112](https://github.com/NPLinker/nplinker/pull/112) ([CunliangGeng](https://github.com/CunliangGeng))
+- Implement comparison operator for `StrainCollection` class [\#111](https://github.com/NPLinker/nplinker/pull/111) ([hechth](https://github.com/hechth))
+- Fix local test error [\#105](https://github.com/NPLinker/nplinker/pull/105) ([CunliangGeng](https://github.com/CunliangGeng))
+- Refactor GCF class [\#102](https://github.com/NPLinker/nplinker/pull/102) ([CunliangGeng](https://github.com/CunliangGeng))
+- Refactor BGC data model [\#101](https://github.com/NPLinker/nplinker/pull/101) ([CunliangGeng](https://github.com/CunliangGeng))
+- Move test files to subfolders and update pytest's conftest.py [\#100](https://github.com/NPLinker/nplinker/pull/100) ([CunliangGeng](https://github.com/CunliangGeng))
+- docs: add quotes in package installation for zsh shell [\#97](https://github.com/NPLinker/nplinker/pull/97) ([gcroci2](https://github.com/gcroci2))
+- Refactored GNPS downloading and file extraction code [\#93](https://github.com/NPLinker/nplinker/pull/93) ([hechth](https://github.com/hechth))
+- Refactor BGC data loader [\#92](https://github.com/NPLinker/nplinker/pull/92) ([CunliangGeng](https://github.com/CunliangGeng))
+- Initial refactoring of Metabolomics data loading [\#91](https://github.com/NPLinker/nplinker/pull/91) ([hechth](https://github.com/hechth))
+- static typing [\#88](https://github.com/NPLinker/nplinker/pull/88) ([CunliangGeng](https://github.com/CunliangGeng))
+- Refactor mibig related code [\#87](https://github.com/NPLinker/nplinker/pull/87) ([CunliangGeng](https://github.com/CunliangGeng))
+- Add download extract utils [\#85](https://github.com/NPLinker/nplinker/pull/85) ([CunliangGeng](https://github.com/CunliangGeng))
+- Refactor AA prediction [\#84](https://github.com/NPLinker/nplinker/pull/84) ([CunliangGeng](https://github.com/CunliangGeng))
+- Check metcalf and IOKR scoring [\#83](https://github.com/NPLinker/nplinker/pull/83) ([CunliangGeng](https://github.com/CunliangGeng))
+- add dev branch to github actions [\#82](https://github.com/NPLinker/nplinker/pull/82) ([CunliangGeng](https://github.com/CunliangGeng))
+- add DATA\_DIR for sharing test data dir [\#81](https://github.com/NPLinker/nplinker/pull/81) ([CunliangGeng](https://github.com/CunliangGeng))
+- Initial refactoring on scoring methods [\#80](https://github.com/NPLinker/nplinker/pull/80) ([hechth](https://github.com/hechth))
+- Implemented some tests for the metabolomics side [\#79](https://github.com/NPLinker/nplinker/pull/79) ([hechth](https://github.com/hechth))
+- Refactored `genomics.py` and `metabolomics.py` by moving classes into individual files [\#78](https://github.com/NPLinker/nplinker/pull/78) ([hechth](https://github.com/hechth))
+- Refine github actions [\#77](https://github.com/NPLinker/nplinker/pull/77) ([CunliangGeng](https://github.com/CunliangGeng))
+
+## [v1.3.2](https://github.com/NPLinker/nplinker/tree/v1.3.2) (2022-08-12)
+
+[Full Changelog](https://github.com/NPLinker/nplinker/compare/v1.3.1...v1.3.2)
+
 ## [v1.3.1](https://github.com/NPLinker/nplinker/tree/v1.3.1) (2022-08-05)
 
 [Full Changelog](https://github.com/NPLinker/nplinker/compare/v1.3.0...v1.3.1)

CITATION.cff

@@ -45,7 +45,7 @@ authors:
   -
     given-names:  Marnix
     family-names:  Medema
-version: "1.3.2"
+version: "2.0.0-alpha.1"
 repository-code: "https://github.com/NPLinker/nplinker"
 keywords:
   - Genome

pyproject.toml

@@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "nplinker"
-version = "1.3.2"
+version = "2.0.0-alpha.1"
 description = "Natural Products Linker"
 readme = "README.md"
 requires-python = ">=3.9"

src/nplinker/__init__.py

@@ -5,4 +5,4 @@
 
 __author__ = "Cunliang Geng"
 __email__ = "[email protected]"
-__version__ = "1.3.2"
+__version__ = "2.0.0-alpha.1"