Merge branch 'NPLinker:dev' into output_files

CHANGELOG.md

@@ -1,5 +1,21 @@
 # Changelog
 
+## [v2.0.0-alpha.7](https://github.com/NPLinker/nplinker/tree/v2.0.0-alpha.7) (2024-11-28)
+
+[Full Changelog](https://github.com/NPLinker/nplinker/compare/v2.0.0-alpha.6...v2.0.0-alpha.7)
+
+**Closed issues:**
+
+- Incorrect precursor m/z when loading MGF file from GNPS [\#282](https://github.com/NPLinker/nplinker/issues/282)
+- Use bigscape version in loaders [\#271](https://github.com/NPLinker/nplinker/issues/271)
+
+**Merged pull requests:**
+
+- remove default config file to make all settings explicit [\#287](https://github.com/NPLinker/nplinker/pull/287) ([CunliangGeng](https://github.com/CunliangGeng))
+- add support of mibig v4.0 [\#286](https://github.com/NPLinker/nplinker/pull/286) ([CunliangGeng](https://github.com/CunliangGeng))
+- fix the resolving of genbank and jgi IDs [\#285](https://github.com/NPLinker/nplinker/pull/285) ([CunliangGeng](https://github.com/CunliangGeng))
+- Precursor m/z value fix [\#283](https://github.com/NPLinker/nplinker/pull/283) ([liannette](https://github.com/liannette))
+
 ## [v2.0.0-alpha.6](https://github.com/NPLinker/nplinker/tree/v2.0.0-alpha.6) (2024-09-17)
 
 [Full Changelog](https://github.com/NPLinker/nplinker/compare/v2.0.0-alpha.5...v2.0.0-alpha.6)

CITATION.cff

@@ -45,7 +45,7 @@ authors:
   -
     given-names:  Marnix
     family-names:  Medema
-version: "2.0.0-alpha.6"
+version: "2.0.0-alpha.7"
 repository-code: "https://github.com/NPLinker/nplinker"
 keywords:
   - Genome

README.md

@@ -16,7 +16,8 @@
 | Citation data consistency          | [![cffconvert](https://github.com/NPLinker/nplinker/actions/workflows/cffconvert.yml/badge.svg)](https://github.com/NPLinker/nplinker/actions/workflows/cffconvert.yml) |
 
 
-# Natural Products Linker (NPLinker)
+![NPLinker Logo](./docs/images/NPLinker_standard_black.svg)
+
 NPLinker is a python framework for data mining microbial natural products by integrating genomics and metabolomics data.
 
 Original paper: [Ranking microbial metabolomic and genomic links in the NPLinker framework using complementary scoring functions](https://doi.org/10.1371/journal.pcbi.1008920).

docs/concepts/config_file.md

@@ -4,13 +4,9 @@
 --8<-- "src/nplinker/data/nplinker.toml"
 ```
 
+## Example Configuration
 
-## Default Configurations
-The default configurations are automatically used by NPLinker if you don't set them in your config file.
-
-```toml
---8<-- "src/nplinker/nplinker_default.toml"
-```
+For a full example of a configuration file, see [here](../quickstart.md#3-prepare-config-file).
 
 ## Config loader