📝 Docs: Create CHANGELOG.md using git-changelog (#38)

* 📝 Docs: add git-changelog to dev dependencies, create toml config, and generate CHANGELOG.md file

* 📝 Docs(README.md): Update README with information about changelog.

* 📝 Docs: Add the changelog.md file into the sphinx docs

* 🎨 Format(docs/index.md): add title to avoid blank spcae and move changelog to the last part of the project support section

* ✨ Feat(docs): add makefile to autmate the clean and build of the docs, and update the docs README with this change

* 🙈 Docs: add docs/sections_readme to gitignore

* Remove commit from Fix imports PR in CHANGELOG.md

Co-authored-by: Henry Webel <[email protected]>

* Remove commit from Remove Python restrictions PR in CHANGELOG.md

Co-authored-by: Henry Webel <[email protected]>

* 📝 Docs: update CHANGELOG and .git-changelog.toml with the 0.1.0 release

* 📝 Docs(docs/README.md): Include commands from the makefile in the README just in case users cannot run the makefile

* 📝 Docs(CHANGELOG.md): change header to release notes

* ✅ Test: try github action to generate changelogf from release

* ✅ Test: create an indep file to test the changelog on the feature branch

* ✅ Test: update ga file to test changelog

* 🐛 Fix(.github/workflows/changelog-test.yml): set commit and push to false to prevent error

* 🐛 Fix(.github/workflows/changelog-test.yml): add header to keep it in the generated changelog

* 📝 Docs: update CHANGELOG.md using the changelog-from-release tool and update the github action to automate it after every release

* 🔥 Refactor: delete .git-changelog.toml and update README with the new tool to create changelog

* 🎨 Style: fix linting of the changelog header

* ➖ Refactor: remove git-changelog dev dependency

---------

Co-authored-by: Henry Webel <[email protected]>

Author: sayalaruano

.github/workflows/cdci.yml

@@ -51,6 +51,27 @@ jobs:
       - name: Run tests
         run: python -m pytest tests
 
+  changelog:
+    name: Update changelog
+    if: github.event_name == 'release' && github.event.action == 'published'
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout main branch
+        uses: actions/checkout@v4
+        with:
+          ref: main 
+
+      - name: Update CHANGELOG.md
+        uses: rhysd/changelog-from-release/action@v3
+        with:
+          file: CHANGELOG.md
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          header: |
+            # Release Notes
+
+            All notable changes to this project are documented in this file. It was automatically generated with
+            the [changelog-from-release](https://github.com/rhysd/changelog-from-release) tool.
+
   publish:
     name: Publish package
     if: startsWith(github.ref, 'refs/tags')

.gitignore

@@ -166,3 +166,4 @@ cython_debug/
 test_results/
 docs/api_examples/outputs/
 docs/api_examples/iframe_figures/
+docs/sections_readme/

CHANGELOG.md

@@ -0,0 +1,113 @@
+# Release Notes
+
+All notable changes to this project are documented in this file. It was automatically generated with 
+the [changelog-from-release](https://github.com/rhysd/changelog-from-release) tool.
+
+<a id="v0.1.0"></a>
+# [v0.1.0](https://github.com/Multiomics-Analytics-Group/vuecore/releases/tag/v0.1.0) - 2025-09-18
+
+## What's Changed
+* :sparkles: first rudementary API documentation by [@enryH](https://github.com/enryH) in [#9](https://github.com/Multiomics-Analytics-Group/vuecore/pull/9)
+* Add logo by [@sayalaruano](https://github.com/sayalaruano) in [#10](https://github.com/Multiomics-Analytics-Group/vuecore/pull/10)
+* Refactor vuecore library with an initial example for scatter plot by [@sayalaruano](https://github.com/sayalaruano) in [#11](https://github.com/Multiomics-Analytics-Group/vuecore/pull/11)
+* Remove_python_restriction by [@enryH](https://github.com/enryH) in [#15](https://github.com/Multiomics-Analytics-Group/vuecore/pull/15)
+* :wrench:  set up sync of notebooks to py:percent format (manually) by [@enryH](https://github.com/enryH) in [#17](https://github.com/Multiomics-Analytics-Group/vuecore/pull/17)
+* Update logo by [@sayalaruano](https://github.com/sayalaruano) in [#19](https://github.com/Multiomics-Analytics-Group/vuecore/pull/19)
+* Update scatter plot to align with the Plotly API by [@sayalaruano](https://github.com/sayalaruano) in [#21](https://github.com/Multiomics-Analytics-Group/vuecore/pull/21)
+* ✨ Feat: Add scripts, test, and example for line plot by [@sayalaruano](https://github.com/sayalaruano) in [#20](https://github.com/Multiomics-Analytics-Group/vuecore/pull/20)
+* 🧑‍💻 Dev: add PR templates for general contributions and add new plots by [@sayalaruano](https://github.com/sayalaruano) in [#22](https://github.com/Multiomics-Analytics-Group/vuecore/pull/22)
+* Update readme, license, and contributing by [@sayalaruano](https://github.com/sayalaruano) in [#24](https://github.com/Multiomics-Analytics-Group/vuecore/pull/24)
+* :wrench: configure the plotly renderer on Read The Docs by [@enryH](https://github.com/enryH) in [#18](https://github.com/Multiomics-Analytics-Group/vuecore/pull/18)
+* ✨ Feat: Add scripts, test, and example for bar plot  by [@sayalaruano](https://github.com/sayalaruano) in [#26](https://github.com/Multiomics-Analytics-Group/vuecore/pull/26)
+* File formats enum by [@sayalaruano](https://github.com/sayalaruano) in [#27](https://github.com/Multiomics-Analytics-Group/vuecore/pull/27)
+* ✨ Feat: Add scripts, test, and example for box plot by [@sayalaruano](https://github.com/sayalaruano) in [#30](https://github.com/Multiomics-Analytics-Group/vuecore/pull/30)
+* Add script to split readme and organize documentation by [@sayalaruano](https://github.com/sayalaruano) in [#29](https://github.com/Multiomics-Analytics-Group/vuecore/pull/29)
+* ✅ Enable pytest on github action by [@sayalaruano](https://github.com/sayalaruano) in [#28](https://github.com/Multiomics-Analytics-Group/vuecore/pull/28)
+* ✨ Create Base Plotly Schema by [@sayalaruano](https://github.com/sayalaruano) in [#31](https://github.com/Multiomics-Analytics-Group/vuecore/pull/31)
+* ✨Factory function for user-facing plot functions by [@sayalaruano](https://github.com/sayalaruano) in [#33](https://github.com/Multiomics-Analytics-Group/vuecore/pull/33)
+* ✨Factory function for building plotly plot functions by [@sayalaruano](https://github.com/sayalaruano) in [#34](https://github.com/Multiomics-Analytics-Group/vuecore/pull/34)
+* 📝 Docs: Update contributing guidelines by [@sayalaruano](https://github.com/sayalaruano) in [#37](https://github.com/Multiomics-Analytics-Group/vuecore/pull/37)
+* ✨ Feat: Add scripts, test, and example for violin plot by [@sayalaruano](https://github.com/sayalaruano) in [#39](https://github.com/Multiomics-Analytics-Group/vuecore/pull/39)
+* ✨ Feat: Add scripts, test, and example for histogram plot by [@sayalaruano](https://github.com/sayalaruano) in [#41](https://github.com/Multiomics-Analytics-Group/vuecore/pull/41)
+* 📝 Docs(src/vuecore/README.md): Add Readme to explain the project structure and workflow by [@sayalaruano](https://github.com/sayalaruano) in [#42](https://github.com/Multiomics-Analytics-Group/vuecore/pull/42)
+
+## New Contributors
+* [@sayalaruano](https://github.com/sayalaruano) made their first contribution in [#10](https://github.com/Multiomics-Analytics-Group/vuecore/pull/10)
+
+**Full Changelog**: https://github.com/Multiomics-Analytics-Group/vuecore/compare/v0.0.5...v0.1.0
+
+[Changes][v0.1.0]
+
+
+<a id="v0.0.5"></a>
+# [v0.0.5](https://github.com/Multiomics-Analytics-Group/vuecore/releases/tag/v0.0.5) - 2025-01-31
+
+## What's Changed
+* :truck: move PCA plot from acore normalization example by [@enryH](https://github.com/enryH) in [#8](https://github.com/Multiomics-Analytics-Group/vuecore/pull/8)
+
+
+**Full Changelog**: https://github.com/Multiomics-Analytics-Group/vuecore/compare/v0.0.4...v0.0.5
+
+[Changes][v0.0.5]
+
+
+<a id="v0.0.4"></a>
+# [v0.0.4](https://github.com/Multiomics-Analytics-Group/vuecore/releases/tag/v0.0.4) - 2025-01-29
+
+## What's Changed
+* :truck: add functionality from acore by [@enryH](https://github.com/enryH) in [#7](https://github.com/Multiomics-Analytics-Group/vuecore/pull/7)
+
+
+**Full Changelog**: https://github.com/Multiomics-Analytics-Group/vuecore/compare/v0.0.3...v0.0.4
+
+[Changes][v0.0.4]
+
+
+<a id="v0.0.3"></a>
+# [v0.0.3](https://github.com/Multiomics-Analytics-Group/vuecore/releases/tag/v0.0.3) - 2024-12-18
+
+- fix import error (file was not renamed correctly)
+**Full Changelog**: https://github.com/Multiomics-Analytics-Group/vuecore/compare/v0.0.2...v0.0.3
+
+[Changes][v0.0.3]
+
+
+<a id="v0.0.2"></a>
+# [v0.0.2](https://github.com/Multiomics-Analytics-Group/vuecore/releases/tag/v0.0.2) - 2024-12-17
+
+Prepare for use in acore api examples: format and fix imports
+
+## What's Changed
+* :format: format with black by [@enryH](https://github.com/enryH) in [#5](https://github.com/Multiomics-Analytics-Group/vuecore/pull/5)
+* Fix imports by [@enryH](https://github.com/enryH) in [#3](https://github.com/Multiomics-Analytics-Group/vuecore/pull/3)
+
+
+**Full Changelog**: https://github.com/Multiomics-Analytics-Group/vuecore/compare/v0.0.1...v0.0.2
+
+[Changes][v0.0.2]
+
+
+<a id="v0.0.1"></a>
+# [v0.0.1](https://github.com/Multiomics-Analytics-Group/vuecore/releases/tag/v0.0.1) - 2024-11-29
+
+First release to have a development version on PyPI. All plots and their dependencies needs to be tested.
+
+## What's Changed
+* Mk pkg by [@enryH](https://github.com/enryH) in [#1](https://github.com/Multiomics-Analytics-Group/vuecore/pull/1)
+
+## New Contributors
+* [@enryH](https://github.com/enryH) made their first contribution in [#1](https://github.com/Multiomics-Analytics-Group/vuecore/pull/1)
+
+**Full Changelog**: https://github.com/Multiomics-Analytics-Group/vuecore/commits/v0.0.1
+
+[Changes][v0.0.1]
+
+
+[v0.1.0]: https://github.com/Multiomics-Analytics-Group/vuecore/compare/v0.0.5...v0.1.0
+[v0.0.5]: https://github.com/Multiomics-Analytics-Group/vuecore/compare/v0.0.4...v0.0.5
+[v0.0.4]: https://github.com/Multiomics-Analytics-Group/vuecore/compare/v0.0.3...v0.0.4
+[v0.0.3]: https://github.com/Multiomics-Analytics-Group/vuecore/compare/v0.0.2...v0.0.3
+[v0.0.2]: https://github.com/Multiomics-Analytics-Group/vuecore/compare/v0.0.1...v0.0.2
+[v0.0.1]: https://github.com/Multiomics-Analytics-Group/vuecore/tree/v0.0.1
+
+<!-- Generated by https://github.com/rhysd/changelog-from-release v3.9.0 -->

README.md

@@ -61,7 +61,11 @@ Full details for both licenses can be found in the [LICENSE][vuecore-license] fi
 
 ## Contributing
 
-VueCore is an open-source project, and we welcome contributions of all kinds via GitHub issues and pull requests. You can report bugs, suggest improvements, propose new features, or implement changes. Please follow the guidelines in the [CONTRIBUTING](CONTRIBUTING.md) file to ensure that your contribution is easily integrated into the project.
+VueCore is an open-source project, and we welcome contributions of all kinds via GitHub issues and pull requests. You can report bugs, suggest improvements, propose new features, or implement changes. 
+
+We follow the [Conventional Commits][conventional-commits] specification for commit messages and use the [changelog-from-release][changelog-from-release-repo] tool to automatically generate the [CHANGELOG](CHANGELOG.md).
+
+Please follow the guidelines in the [CONTRIBUTING](CONTRIBUTING.md) file to ensure that your contribution is easily integrated into the project.
 
 ## Credits and acknowledgements
 
@@ -82,6 +86,8 @@ We appreciate your feedback! If you have any comments, suggestions, or run into
 [pulls]: https://github.com/Multiomics-Analytics-Group/vuecore/pulls
 [vuegen]: https://github.com/Multiomics-Analytics-Group/vuegen
 [acore]: https://github.com/Multiomics-Analytics-Group/acore
+[conventional-commits]: https://www.conventionalcommits.org/
+[changelog-from-release-repo]: https://github.com/rhysd/changelog-from-release
 [Mona]: https://multiomics-analytics-group.github.io/
 [Biosustain]: https://www.biosustain.dtu.dk/
 [new-issue]:https://github.com/Multiomics-Analytics-Group/vuecore/issues/new

docs/Makefile

@@ -0,0 +1,17 @@
+# List of directories to remove
+CLEAN_BUILD_DIRS = _build jupyter_execute
+CLEAN_DIRS = $(CLEAN_BUILD_DIRS) downloaded reference sections_readme
+
+.PHONY: clean clean_build
+
+# Removes the specified directories
+clean:
+	rm -rf $(CLEAN_DIRS)
+
+clean_build:
+	rm -rf $(CLEAN_BUILD_DIRS)
+
+build:
+	sphinx-apidoc --force --implicit-namespaces --module-first -o reference ../src/vuecore
+	python split_readme.py
+	sphinx-build -n -W --keep-going -b html ./ ./_build/

docs/README.md

@@ -2,33 +2,40 @@
 
 In order to build the docs you need to
 
-1. install sphinx and additional support packages
-2. build the package reference files
-3. run sphinx to create a local html version
+1. Install sphinx and additional support packages
+2. Build the package reference files
+3. Run sphinx to create a local html version
 
 The documentation is build using readthedocs automatically.
 
 Install the docs dependencies of the package (as speciefied in toml):
 
 ```bash
 # in main folder
-# pip install ".[docs]"
-poetry install --with docs
+pip install ".[docs]"
 ```
 
 ## Build docs using Sphinx command line tools
 
-Command to be run from `path/to/docs`, i.e. from within the `docs` package folder:
+We use `sphinx-apidoc` to create the API reference files from the source code and 
+`sphinx-build` to create the html files. Also, we use a custom script `split_readme.py` to
+split the main `README.md` file into smaller sections for inclusion in the docs.
 
-Options:
+We provide a [Makefile](https://github.com/Multiomics-Analytics-Group/vuecore/blob/HEAD/docs/Makefile) 
+to simplify the cleaning and building process, which you can run from the `docs` folder:
 
-- `--separate` to build separate pages for each (sub-)module
+```bash
+# pwd: docs
+make clean
+make build
+```
+
+Alternatevely, you can run these commands manually each at a time, as follows:
 
 ```bash
 # pwd: docs
-# apidoc
 sphinx-apidoc --force --implicit-namespaces --module-first -o reference ../src/vuecore
-# build docs
+python split_readme.py
 sphinx-build -n -W --keep-going -b html ./ ./_build/
 ```
 

docs/index.md

@@ -1,3 +1,4 @@
+## VueCore Documentation
 <!-- https://myst-parser.readthedocs.io/en/latest/faq/index.html
 #include-a-file-from-outside-the-docs-folder-like-readme-md -->
 
@@ -42,6 +43,7 @@ reference/vuecore
 sections_readme/contributing
 sections_readme/credits
 sections_readme/contact
+sections_readme/changelog
 ```
 
 ```{toctree}

docs/split_readme.py

@@ -103,7 +103,7 @@ def process_readme(readme_path, output_dir):
         else:
             raise ValueError(f"Section '{section_title}' not found in README")
 
-    # Include CONTRIBUTING.md with its own link references
+    # Copy CONTRIBUTING.md with its own link references to the output directory
     contrib_path = readme_path.parent / "CONTRIBUTING.md"
     try:
         raw_contrib = contrib_path.read_text()
@@ -121,6 +121,15 @@ def process_readme(readme_path, output_dir):
     except FileNotFoundError as e:
         raise FileNotFoundError(f"CONTRIBUTING.md not found at {contrib_path}") from e
 
+    # Copy CHANGELOG.md to the output directory
+    changelog_path = readme_path.parent / "CHANGELOG.md"
+    try:
+        raw_changelog = changelog_path.read_text()
+        (output_dir / "changelog.md").write_text(raw_changelog)
+        print("Generated changelog.md")
+    except FileNotFoundError as e:
+        raise FileNotFoundError(f"CHANGELOG.md not found at {changelog_path}") from e
+
 
 if __name__ == "__main__":
     default_readme = Path(__file__).resolve().parent.parent / "README.md"