diff --git a/CHANGELOG.md b/CHANGELOG.md
index 1218a98d..6be34738 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,28 @@
 # Changelog
 
+## [v2.0.0-alpha.3](https://github.com/NPLinker/nplinker/tree/v2.0.0-alpha.3) (2024-07-11)
+
+[Full Changelog](https://github.com/NPLinker/nplinker/compare/v2.0.0-alpha.2...v2.0.0-alpha.3)
+
+**Implemented enhancements:**
+
+- Data size warnings / checks when installing and using nplinker package [\#237](https://github.com/NPLinker/nplinker/issues/237)
+
+**Closed issues:**
+
+- Podp: not all genome IDs are in antismashDB [\#242](https://github.com/NPLinker/nplinker/issues/242)
+- refactoring scoring \(tracker issue\) [\#205](https://github.com/NPLinker/nplinker/issues/205)
+- ensure that IDs are unique [\#146](https://github.com/NPLinker/nplinker/issues/146)
+- refactor `__eq__` and `__hash__` methods [\#136](https://github.com/NPLinker/nplinker/issues/136)
+- Missing mibig BGC [\#86](https://github.com/NPLinker/nplinker/issues/86)
+
+**Merged pull requests:**
+
+- fix tabular file header detection [\#264](https://github.com/NPLinker/nplinker/pull/264) ([CunliangGeng](https://github.com/CunliangGeng))
+- simplify error check in unit tests [\#263](https://github.com/NPLinker/nplinker/pull/263) ([CunliangGeng](https://github.com/CunliangGeng))
+- add warning for failed antismash downloads [\#262](https://github.com/NPLinker/nplinker/pull/262) ([CunliangGeng](https://github.com/CunliangGeng))
+- check disk space before downloading [\#261](https://github.com/NPLinker/nplinker/pull/261) ([CunliangGeng](https://github.com/CunliangGeng))
+
 ## [v2.0.0-alpha.2](https://github.com/NPLinker/nplinker/tree/v2.0.0-alpha.2) (2024-06-20)
 
 [Full Changelog](https://github.com/NPLinker/nplinker/compare/v2.0.0-alpha.1...v2.0.0-alpha.2)
diff --git a/CITATION.cff b/CITATION.cff
index be558c62..53573bec 100644
--- a/CITATION.cff
+++ b/CITATION.cff
@@ -45,7 +45,7 @@ authors:
   -
     given-names:  Marnix
     family-names:  Medema
-version: "2.0.0-alpha.2"
+version: "2.0.0-alpha.3"
 repository-code: "https://github.com/NPLinker/nplinker"
 keywords:
   - Genome
diff --git a/pyproject.toml b/pyproject.toml
index 3cb31aa5..36caca3a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "nplinker"
-version = "2.0.0-alpha.2"
+version = "2.0.0-alpha.3"
 description = "Natural Products Linker"
 readme = "README.md"
 requires-python = ">=3.9"
diff --git a/src/nplinker/__init__.py b/src/nplinker/__init__.py
index 02bb3205..d99ec6dd 100644
--- a/src/nplinker/__init__.py
+++ b/src/nplinker/__init__.py
@@ -7,7 +7,7 @@
 
 __author__ = "Cunliang Geng"
 __email__ = "c.geng@esciencecenter.nl"
-__version__ = "2.0.0-alpha.2"
+__version__ = "2.0.0-alpha.3"
 
 
 __all__ = ["NPLinker", "setup_logging"]