fixes and updates

Author: JelmerBot

.github/dependabot.yml

@@ -0,0 +1,11 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    groups:
+      updates:
+        update-types:
+          - "minor"
+          - "patch"

.github/workflows/Docs.yml

@@ -1,6 +1,6 @@
 name: Documentation
 concurrency:
-  group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.ref }}
+  group: ${{ github.workflow }}-${{ github.event.ref }}
   cancel-in-progress: true
 
 on:

.github/workflows/Publish.yml

@@ -1,6 +1,6 @@
 name: Publish Python Package
 concurrency:
-  group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.ref }}
+  group: ${{ github.workflow }}-${{ github.event.ref }}
   cancel-in-progress: false
 
 on: 
@@ -40,18 +40,13 @@ jobs:
 
       - name: Move files to dist
         run: |
-          mkdir dist
-          mv dists/* dist/
           if [[ ! -f dist/multi_mst-${{ steps.version.outputs.version }}.tar.gz ]] ; then exit 1; fi
       
+      - name: Publish package to (Test)PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        
       - name: Create Github Release
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  
         run: |
-          gh release create -R vda-lab/multi_mst -t "Version ${{ steps.version.outputs.version }}" -n "**Full Changelog**: https://github.com/vda-lab/multi_mst/commits/${{ steps.version.outputs.tag }}" "${{ steps.version.outputs.tag }}" dist/*.whl dist/*.tar.gz
-        
-      - name: Publish package to (Test)PyPI
-        uses: pypa/[email protected]
-        # Comment lines below to publish to PyPi instead of test PyPi
-        # with:
-        #   repository-url: https://test.pypi.org/legacy/
+          gh release create -R vda-lab/multi_mst -t "Version ${{ steps.version.outputs.version }}" -n "**Full Changelog**: https://github.com/vda-lab/multi_mst/commits/${{ steps.version.outputs.tag }}" "${{ steps.version.outputs.tag }}" dist/*.tar.gz

.github/workflows/Tests.yml

@@ -31,7 +31,7 @@ jobs:
     name: Build dists
     runs-on: ubuntu-24.04
     outputs:
-      WHEEL_NAME: ${{ steps.dists.outputs.WHEEL_NAME }}
+      WHEEL_NAME: ${{ steps.dist.outputs.WHEEL_NAME }}
     steps:
       - uses: actions/checkout@v4
         with:
@@ -53,8 +53,8 @@ jobs:
           # stop the build if there are Python syntax errors or undefined names
           flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
 
-      - name: Build dists
-        id: dists
+      - name: Build dist
+        id: dist
         run: |
           python -m build --sdist --wheel
           python ci/export_name.py
@@ -65,63 +65,30 @@ jobs:
       - name: Upload sdist result
         uses: actions/upload-artifact@v4
         with:
-          name: dists
+          name: dist
           path: dist/*
           if-no-files-found: error
 
   test_sdist:
-    name: Test dist for cp${{ matrix.python }}-${{ matrix.platform_id }}-${{ matrix.manylinux_image }}
+    name: Test Python ${{ matrix.python_version }}
     needs: build_dists
-    runs-on: ${{ matrix.os }}
+    runs-on: ubuntu-latest
     strategy:
       fail-fast: true
       matrix:
-        include:
-          - os: windows-latest
-            python: "3.10"
-            platform_id: win_amd64
-          - os: windows-latest
-            python: "3.11"
-            platform_id: win_amd64
-          - os: windows-latest
-            python: "3.12"
-            platform_id: win_amd64
-
-          # Linux 64 bit manylinux2014
-          - os: ubuntu-latest
-            python: "3.10"
-            platform_id: manylinux_x86_64
-            manylinux_image: manylinux2014
-          - os: ubuntu-latest
-            python: "3.11"
-            platform_id: manylinux_x86_64
-            manylinux_image: manylinux2014
-          - os: ubuntu-latest
-            python: "3.12"
-            platform_id: manylinux_x86_64
-            manylinux_image: manylinux2014
-
-          # MacOS x86_64
-          - os: macos-latest
-            python: "3.10"
-            platform_id: macosx_x86_64
-          - os: macos-latest
-            python: "3.11"
-            platform_id: macosx_x86_64
-          - os: macos-latest
-            python: "3.12"
-            platform_id: macosx_x86_64
+        python_version: ['3.10', '3.11', '3.12', '3.13']
+    
     steps:
       - name: Download sdist
         uses: actions/download-artifact@v4
         with:
-          name: dists
+          name: dist
           path: dist/
 
       - name: Setup Python
         uses: actions/setup-python@v5
         with:
-          python-version: ${{ matrix.python }}
+          python-version: ${{ matrix.python_version }}
 
       - name: Install dependencies
         run: |

MANIFEST.in

@@ -2,6 +2,5 @@ include README.md
 include pyproject.toml
 include LICENSE
 include MANIFEST.in
-include requirements.txt
 recursive-exclude docs *
 recursive-exclude notebooks *

pyproject.toml

@@ -7,28 +7,26 @@ 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]" }
-]
+authors = [{ name = "Jelmer Bot", email = "[email protected]" }]
 readme = "README.md"
-license = { text = "BSD-2-Clause" }
+license = "BSD-2-Clause"
+license-files = ["LICENSE"]
 classifiers = [
-    "Development Status :: 5 - Production/Stable", 
-    "License :: OSI Approved :: BSD License",
-    "Natural Language :: English",
-    "Operating System :: OS Independent",
-    "Programming Language :: Python :: 3 :: Only"
+  "Development Status :: 5 - Production/Stable",
+  "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 >= 0.2.1",
-    "fast-hbcc >= 0.1.0"
+  "numpy >= 1.20, <3",
+  "scipy >= 1.9",
+  "scikit-learn >= 1.6",
+  "umap-learn >= 0.5.4",
+  "numba >= 0.57.1",
+  "pynndescent >= 0.5.13",
+  "fast_hdbscan >= 0.2.1",
+  "fast-hbcc >= 0.1.0",
 ]
 
 [project.urls]
@@ -43,10 +41,10 @@ namespaces = false
 [project.optional-dependencies]
 tests = ["pytest"]
 docs = [
-	"sphinx >= 8",
-	"nbsphinx >= 0.9",
-	"sphinx_rtd_theme >= 2.0",
-	"matplotlib >= 3.8",
+  "sphinx >= 8",
+  "nbsphinx >= 0.9",
+  "sphinx_rtd_theme >= 2.0",
+  "matplotlib >= 3.8",
   "numpydoc",
   "pygments>=2.4.1",
   "jupyterlab_pygments>=0.1.1",
@@ -56,5 +54,5 @@ notebooks = [
   "jupyterlab >= 4",
   "matplotlib >= 3.8",
   "pandas >= 2.2",
-  "tqdm >= 4.62.3"
-]
+  "tqdm >= 4.62.3",
+]

src/multi_mst/base.py

@@ -84,7 +84,7 @@ def fit(self, X, y=None, **fit_params):
         self: MultiMSTMixin
             The fitted estimator.
         """
-        X = check_array(X, force_all_finite=False)
+        X = check_array(X, ensure_all_finite=False)
         self._raw_data = X
 
         self._all_finite = np.all(np.isfinite(X))
@@ -561,8 +561,6 @@ def hdbscan(
                 sample_weights, self._raw_data, dtype=np.float32
             )
         clusterer = HDBSCAN(
-            data_labels=data_labels,
-            sample_weights=sample_weights,
             min_samples=self.num_neighbors,
             min_cluster_size=min_cluster_size,
             max_cluster_size=max_cluster_size,

src/multi_mst/tests/test_descent.py

@@ -194,7 +194,7 @@ def test_hdbscan_branches():
     assert isinstance(d, BranchDetector)
     assert d.labels_[0] == -1
     assert d.labels_[6] == -1
-    assert len(set(d.labels_)) == 9
+    assert len(set(d.labels_)) == 8
 
 
 def test_hdbscan_boundary_clusters():
@@ -205,7 +205,7 @@ def test_hdbscan_boundary_clusters():
     assert isinstance(bc, BoundaryClusterDetector)
     assert bc.labels_[0] == -1
     assert bc.labels_[6] == -1
-    assert len(set(bc.labels_)) == 9
+    assert len(set(bc.labels_)) == 6
 
 
 def test_hdbscan_boundary_clusters_no_reachability():
@@ -216,7 +216,7 @@ def test_hdbscan_boundary_clusters_no_reachability():
     assert isinstance(bc, BoundaryClusterDetector)
     assert bc.labels_[0] == -1
     assert bc.labels_[6] == -1
-    assert len(set(bc.labels_)) == 8
+    assert len(set(bc.labels_)) == 7
 
 
 def test_hdbscan_boundary_clusters_metric():
@@ -227,7 +227,7 @@ def test_hdbscan_boundary_clusters_metric():
     assert isinstance(bc, BoundaryClusterDetector)
     assert bc.labels_[0] == -1
     assert bc.labels_[6] == -1
-    assert len(set(bc.labels_)) == 7
+    assert len(set(bc.labels_)) == 6
 
 
 def test_hdbscan_boundary_clusters_not_euclidean():

src/multi_mst/tests/test_kmst.py

@@ -240,7 +240,7 @@ def test_hdbscan_boundary_clusters():
     assert isinstance(bc, BoundaryClusterDetector)
     assert bc.labels_[0] == -1
     assert bc.labels_[6] == -1
-    assert len(set(bc.labels_)) == 9
+    assert len(set(bc.labels_)) == 6
 
 
 def test_hbcc():

src/multi_mst/tests/test_recall.py

@@ -215,7 +215,7 @@ def test_hdbscan_boundary_clusters():
     assert isinstance(bc, BoundaryClusterDetector)
     assert bc.labels_[0] == -1
     assert bc.labels_[6] == -1
-    assert len(set(bc.labels_)) == 9
+    assert len(set(bc.labels_)) == 6
 
 
 def test_hdbscan_boundary_clusters_no_reachability():
@@ -226,7 +226,7 @@ def test_hdbscan_boundary_clusters_no_reachability():
     assert isinstance(bc, BoundaryClusterDetector)
     assert bc.labels_[0] == -1
     assert bc.labels_[6] == -1
-    assert len(set(bc.labels_)) == 8
+    assert len(set(bc.labels_)) == 7
 
 
 def test_hdbscan_boundary_clusters_metric():
@@ -237,7 +237,7 @@ def test_hdbscan_boundary_clusters_metric():
     assert isinstance(bc, BoundaryClusterDetector)
     assert bc.labels_[0] == -1
     assert bc.labels_[6] == -1
-    assert len(set(bc.labels_)) == 7
+    assert len(set(bc.labels_)) == 6
 
 
 def test_hbcc():