use pyproject.toml

.github/workflows/Docs.yml

@@ -8,14 +8,14 @@ on:
     branches:
     - main
     paths:
-      - 'doc/**'
+      - 'docs/**'
       - 'multi_mst/*.py'
       - '.github/workflows/Docs.yml'
   workflow_dispatch:
 
 jobs:
   pages:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
     environment:
       name: github-pages
       url: ${{ steps.deployment.outputs.page_url }}
@@ -27,30 +27,20 @@ jobs:
         with:
           fetch-depth: 0
 
-      - uses: actions/setup-python@v5
-        name: Install python
-        with: 
-          python-version: "3.10"
-          cache: 'pip'
-
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip
           sudo apt-get install -y pandoc
-          pip install -e .
 
       - name: Prepare Examples
         run: |
           cd notebooks
           for FILE in *.ipynb; do 
-            cp $FILE ../doc
+            cp $FILE ../docs
           done
           cd ..
 
       - id: deployment
         uses: sphinx-notes/pages@v3
         with:
           cache: True
-          checkout: False
-          documentation_path: ./doc
-          requirements_path: ./doc/requirements.txt
+          checkout: False

.github/workflows/Publish.yml

@@ -12,7 +12,7 @@ on:
 jobs:
   publish_pypi:
     name: Publish to PyPi
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
     permissions:
       # IMPORTANT: this permission is mandatory for trusted publishing
       id-token: write

.github/workflows/Tests.yml

@@ -8,7 +8,7 @@ on:
     branches:
       - main
     paths-ignore:
-      - 'doc/**'
+      - 'docs/**'
       - 'notebooks/**'
       - 'README.md'
       - '.gitignore'
@@ -18,7 +18,7 @@ on:
     branches:
       - main
     paths-ignore:
-      - 'doc/**'
+      - 'docs/**'
       - 'notebooks/**'
       - 'README.md'
       - '.gitignore'
@@ -29,7 +29,7 @@ on:
 jobs:
   build_dists:
     name: Build dists
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
     outputs:
       WHEEL_NAME: ${{ steps.dists.outputs.WHEEL_NAME }}
     steps:
@@ -46,7 +46,6 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install -r requirements.txt
           pip install twine flake8 build
 
       - name: Lint with flake8

.gitignore

@@ -26,7 +26,7 @@ MANIFEST
 .pytest_cache/
 
 # Sphinx documentation
-doc/_build/
+docs/_build/
 
 # Jupyter Notebook
 .ipynb_checkpoints

doc/make.bat → docs/make.bat

@@ -1,35 +1,35 @@
-@ECHO OFF
-
-pushd %~dp0
-
-REM Command file for Sphinx documentation
-
-if "%SPHINXBUILD%" == "" (
-	set SPHINXBUILD=sphinx-build
-)
-set SOURCEDIR=.
-set BUILDDIR=_build
-
-%SPHINXBUILD% >NUL 2>NUL
-if errorlevel 9009 (
-	echo.
-	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
-	echo.installed, then set the SPHINXBUILD environment variable to point
-	echo.to the full path of the 'sphinx-build' executable. Alternatively you
-	echo.may add the Sphinx directory to PATH.
-	echo.
-	echo.If you don't have Sphinx installed, grab it from
-	echo.https://www.sphinx-doc.org/
-	exit /b 1
-)
-
-if "%1" == "" goto help
-
-%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
-goto end
-
-:help
-%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
-
-:end
-popd
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

pyproject.toml

@@ -1,3 +1,56 @@
 [build-system]
-requires = ["setuptools >= 40.6.0", "wheel"]
+requires = ["setuptools"]
 build-backend = "setuptools.build_meta"
+
+[project]
+name = "multi_mst"
+version = "0.2.0"
+description = "Minimum spanning tree based manifold approximations."
+keywords = ["dimensionality reduction", "clustering", "minimum spanning tree"]
+authors = [
+  {name= "Jelmer Bot", email = "[email protected]" }
+]
+readme = "README.md"
+license = { text = "BSD-2-Clause" }
+classifiers = [
+    "Development Status :: 5 - Production/Stable", 
+    "License :: OSI Approved :: BSD License",
+    "Natural Language :: English",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3 :: Only"
+]
+requires-python = ">=3.10"
+dependencies = [
+    "numpy >= 1.20, <3",
+    "scipy >= 1.9",
+    "scikit-learn >= 1.1",
+    "umap-learn >= 0.5.4",
+    "numba >= 0.57.1",
+    "pynndescent >= 0.5.13",
+    "fast_hdbscan @ git+https://github.com/TutteInstitute/fast_hdbscan.git@main#egg=fast_hdbscan",
+    "fast_hbcc @ git+https://github.com/vda-lab/fast_hbcc.git@main#egg=fast_hbcc"
+]
+
+[project.urls]
+Homepage = "https://github.com/vda-lab/multi_mst"
+Issues = "https://github.com/vda-lab/multi_mst/issues"
+
+[tool.setuptools.packages.find]
+where = ["src"]
+include = ["multi_mst*"]
+namespaces = false
+
+[project.optional-dependencies]
+tests = ["pytest"]
+docs = [
+	"sphinx >= 8",
+	"nbsphinx >= 0.9",
+	"sphinx_rtd_theme >= 2.0",
+	"matplotlib >= 3.8"
+]
+notebooks = [
+  "jupyterlab >= 4",
+  "matplotlib >= 3.8",
+  "pandas >= 2.2",
+  "tqdm >= 4.62.3"
+]