replace bumpversion with make update-version command

- remove bumpversion
- add command update-version to Makefile
- update the use of make command

.github/workflows/publish_gh_release.yml

@@ -41,10 +41,9 @@ jobs:
     - name: Upgrade pip and install dependencies
       run: |
         python3 -m pip install --upgrade pip
-        pip install bump2version
     - name: Update package version and change log
       run: |
-        bumpversion --current-version ${{ inputs.current_version }}  --new-version ${{ inputs.new_version }} fake
+        make update-version CURRENT_VERSION=${{ inputs.current_version }} NEW_VERSION=${{ inputs.new_version }} 
         docker run --rm -v "$(pwd)":/usr/local/src/your-app \
           githubchangeloggenerator/github-changelog-generator \
           -u ${{ github.repository_owner }} \

Makefile

@@ -1,4 +1,4 @@
-.PHONY: clean clean-build clean-pyc clean-test release build
+.PHONY: clean clean-build clean-pyc clean-test release build update-version
 
 help:
 	@echo "clean - remove all build, test, coverage and Python artifacts"
@@ -8,6 +8,7 @@ help:
 	@echo "release - upload package to pypi"
 	@echo "build - build package"
 	@echo "update - update pip, build, twine packages"
+	@echo "update-version - update NPLinker version. Usage: make update-version CURRENT_VERSION=0.1.0 NEW_VERSION=0.2.0"
 
 clean: clean-build clean-pyc clean-test
 
@@ -44,3 +45,32 @@ venv:
 
 clean-venv:
 	rm -rf venv
+
+
+# Define the files to update version
+FILES := src/nplinker/__init__.py pyproject.toml CITATION.cff
+
+# Rule to update the version in the specified files
+update-version:
+ifndef CURRENT_VERSION
+	$(error CURRENT_VERSION is not provided. Usage: make update-version CURRENT_VERSION=0.1.0 NEW_VERSION=0.2.0)
+endif
+ifndef NEW_VERSION
+	$(error NEW_VERSION is not provided. Usage: make update-version CURRENT_VERSION=0.1.0 NEW_VERSION=0.2.0)
+endif
+	@for file in $(FILES); do \
+		if ! grep -qE "__version__ = \"$(CURRENT_VERSION)\"|version = \"$(CURRENT_VERSION)\"|version: \"$(CURRENT_VERSION)\"" $$file; then \
+			echo "Error: Current version $(CURRENT_VERSION) not found in $$file"; \
+			exit 1; \
+		fi; \
+	done
+
+	@echo "Updating version from $(CURRENT_VERSION) to $(NEW_VERSION) for following files:"
+	@for file in $(FILES); do \
+		echo "  $$file"; \
+		sed -i '' 's/__version__ = "$(CURRENT_VERSION)"/__version__ = "$(NEW_VERSION)"/' $$file; \
+		sed -i '' 's/version = "$(CURRENT_VERSION)"/version = "$(NEW_VERSION)"/' $$file; \
+		sed -i '' 's/version: "$(CURRENT_VERSION)"/version: "$(NEW_VERSION)"/' $$file; \
+	done
+	@echo "Version update complete."
+	@find . -name "*.bak" -type f -delete

README.dev.md

@@ -154,14 +154,10 @@ All these mike operations will be recorded as git commits of branch `gh-pages`.
 
 ## Versioning
 
-Bumping the version across all files is done with [bumpversion](https://github.com/c4urself/bump2version), e.g.
+Updating the version of the NPLinker package is done with make command `update-version`, e.g.
 
 ```shell
-bumpversion major
-bumpversion minor
-bumpversion patch
-
-bumpversion --current-version 2.0.0 --new-version 2.1.0 fakepart
+make update-version CURRENT_VERSION=0.0.1 NEW_VERSION=0.0.2
 ```
 
 ## Making a release

project_setup.md

@@ -55,7 +55,7 @@ help you decide which tool to use for packaging.
 ## Package version number
 
 - We recommend using [semantic versioning](https://guide.esciencecenter.nl/#/best_practices/releases?id=semantic-versioning).
-- For convenience, the package version is stored in a single place: `nplinker/.bumpversion.cfg`.
+- You can update the version using make command, e.g. `make update-version CURRENT_VERSION=0.0.1 NEW_VERSION=0.0.2`.
 - Don't forget to update the version number before [making a release](https://guide.esciencecenter.nl/#/best_practices/releases)!
 
 ## Logging

pyproject.toml

@@ -46,7 +46,6 @@ dependencies = [
 dev = [
     # packaging
     "build",
-    "bump2version",
     "wheel",
     # formatting and linting
     "ruff",