JelmerBot · JelmerBot · Dec 16, 2025 · Nov 24, 2025 · Nov 24, 2025 · Nov 25, 2025
diff --git a/.github/workflows/_build_wheels.yml b/.github/workflows/_build_wheels.yml
@@ -8,16 +8,18 @@ jobs:
     permissions:
       contents: read
     runs-on: ${{ 
-      (matrix.platform == 'macosx' && matrix.arch == 'x64' && 'macosx-15-intel') ||
-      (matrix.platform == 'macosx' && matrix.arch == 'arm64' && 'macosx-latest') ||
+      (matrix.platform == 'macosx' && matrix.arch == 'arm64' && 'macos-latest') ||
       (matrix.platform == 'win' && matrix.arch == 'x64' && 'windows-latest') ||
-      (matrix.platform == 'win' && matrix.arch == 'arm64' && 'windows-11-arm64') ||
-      (endsWith(matrix.platform, 'linux') && matrix.arch == 'x64' && 'ubuntu-latest') || 
-      (endsWith(matrix.platform, 'linux') && matrix.arch == 'arm64' && 'ubuntu-24.04-arm64') }}
+      (endsWith(matrix.platform, 'linux') && matrix.arch == 'x64' && 'ubuntu-latest')}}
     strategy:
       matrix:
-        arch: [x64]                                        # add arm64 and macosx when repo goes public
-        platform: [manylinux, win]                         # no scikit-learn wheels for musllinux
+        include:                                           # no scikit-learn wheels for musllinux
+          - platform: win                                  # arm64 runners not readily available
+            arch: x64                                      # macos-x64 is deprecated by Apple
+          - platform: manylinux
+            arch: x64
+          - platform: macosx
+            arch: arm64
 
     steps:
       - uses: actions/checkout@v5
@@ -32,14 +34,14 @@ jobs:
         run: | 
           brew install libomp
           echo "OpenMP_ROOT=$(brew --prefix libomp)" >> $GITHUB_ENV
-          echo "MACOSX_DEPLOYMENT_TARGET=${{ matrix.arch == 'arm64' && '14.0' || '13.0' }}" >> $GITHUB_ENV
+          echo "MACOSX_DEPLOYMENT_TARGET=${{ matrix.arch == 'arm64' && '15.0' || '13.0' }}" >> $GITHUB_ENV
 
       - name: Build wheels
         uses: pypa/cibuildwheel@v3.3.0
         env:
           CIBW_ARCHS: "native"
           CIBW_BUILD: "*${{ matrix.platform }}*"
-          CIBW_SKIP: "*314*"                               # no scikit-learn wheels for Python 3.14(t) (yet)
+          CIBW_SKIP: "*t-${{ matrix.platform }}*"          # skip free-threading builds
           CIBW_BUILD_VERBOSITY : "1"                       # show build output for debugging
           PIP_ONLY_BINARY: ":all:"                         # avoid compiling dependencies
           CIBW_ENVIRONMENT_PASS_LINUX: "PIP_ONLY_BINARY"   # also in the manylinux container

diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml
@@ -23,7 +23,7 @@ jobs:
     steps:
       - uses: actions/checkout@v5
       - name: Install linters
-        run: pip install black[jupyter]==25.1 
+        run: pip install black[jupyter]==25.1
       - uses: wearerequired/lint-action@v2
         with:
           black: true

diff --git a/README.md b/README.md
@@ -1,13 +1,15 @@
 [![PyPi version](https://badge.fury.io/py/plscan.svg)](https://badge.fury.io/py/plscan)
+![Conda version](https://anaconda.org/conda-forge/plscan/badges/version.svg)
+[![Repository DOI](https://zenodo.org/badge/xxx.svg)](https://zenodo.org/doi/xxx/zenodo.yyy)
 
 # Persistent Leaf Spatial Clustering for Applications with Noise
 
 This library provides a new clustering algorithm based on HDBSCAN*. The primary
 advantages of PLSCAN over the standard ``hdbscan`` library are:
 
  - PLSCAN automatically finds the optimal minimum cluster size.
- - PLSCAN can easily use all available cores to speed up computation;
- - PLSCAN has much faster implementations of tree condensing and cluster extraction;
+ - PLSCAN can easily use all available cores to speed up computation.
+ - PLSCAN has much faster implementations of tree condensing and cluster extraction.
  - PLSCAN does not rely on JIT compilation.
 
 To use PLSCAN, you only need to set the ``min_samples`` parameter. This
@@ -130,6 +132,14 @@ Also update the `~/.zshrc` config file with:
 export OpenMP_ROOT=$(brew --prefix)/opt/libomp
 ```
 
+or pass `OpenMP_ROOT` as cmake argument:
+
+```bash
+pip install --no-deps --no-build-isolation \
+  -C cmake.args="-DOpenMP_ROOT=$(brew --prefix)/opt/libomp" \
+  -ve .
+```
+
 ### Windows
 
 The default MSVC C++ compiler on windows does not support
@@ -160,7 +170,19 @@ with the optional Clang compiler support enabled.
 
 ## Citing
 
-TODO
+When using this work, please cite our (upcoming) preprint:
+
+```bibtex
+@article{bot2025plscan,
+  title         = {Persistent Multiscale Density-based Clustering},
+  author        = {Dani{\"{e}}l M. Bot and Leland McInnes and Jan Aerts},
+  year          = {2025},
+  month         = {12},
+  archiveprefix = {arXiv},
+  eprint        = {TODO},
+  primaryclass  = {cs.CL}
+}
+```
 
 ## Licensing
 

diff --git a/docs/_paper_figures.ipynb b/docs/_paper_figures.ipynb
diff --git a/docs/_trial_barcodes.ipynb b/docs/_trial_barcodes.ipynb
diff --git a/docs/_trial_persistence_pruning.ipynb b/docs/_trial_persistence_pruning.ipynb
diff --git a/docs/demo_computational_performance.ipynb b/docs/demo_computational_performance.ipynb
diff --git a/docs/demo_parameter_sensitivity.ipynb b/docs/demo_parameter_sensitivity.ipynb
diff --git a/docs/demo_selection_strategies.ipynb b/docs/demo_selection_strategies.ipynb
diff --git a/docs/images/benchmark_time.pdf b/docs/images/benchmark_time.pdf
diff --git a/docs/images/leaf_tree_explainer_1.pdf b/docs/images/leaf_tree_explainer_1.pdf
diff --git a/docs/images/leaf_tree_explainer_2.pdf b/docs/images/leaf_tree_explainer_2.pdf
diff --git a/docs/images/parameter_sensitivity_articles_1442_5.pdf b/docs/images/parameter_sensitivity_articles_1442_5.pdf
diff --git a/docs/images/parameter_sensitivity_articles_1442_80.pdf b/docs/images/parameter_sensitivity_articles_1442_80.pdf
diff --git a/docs/images/parameter_sensitivity_audioset.pdf b/docs/images/parameter_sensitivity_audioset.pdf
diff --git a/docs/images/parameter_sensitivity_authorship.pdf b/docs/images/parameter_sensitivity_authorship.pdf
diff --git a/docs/images/parameter_sensitivity_boxplot.pdf b/docs/images/parameter_sensitivity_boxplot.pdf
diff --git a/docs/images/parameter_sensitivity_cardiotocography.pdf b/docs/images/parameter_sensitivity_cardiotocography.pdf
diff --git a/docs/images/parameter_sensitivity_cell_cycle_237.pdf b/docs/images/parameter_sensitivity_cell_cycle_237.pdf
diff --git a/docs/images/parameter_sensitivity_cifar_10.pdf b/docs/images/parameter_sensitivity_cifar_10.pdf
diff --git a/docs/images/parameter_sensitivity_ecoli.pdf b/docs/images/parameter_sensitivity_ecoli.pdf
diff --git a/docs/images/parameter_sensitivity_elegans.pdf b/docs/images/parameter_sensitivity_elegans.pdf
diff --git a/docs/images/parameter_sensitivity_fashion_mnist.pdf b/docs/images/parameter_sensitivity_fashion_mnist.pdf
diff --git a/docs/images/parameter_sensitivity_header.pdf b/docs/images/parameter_sensitivity_header.pdf
diff --git a/docs/images/parameter_sensitivity_iris.pdf b/docs/images/parameter_sensitivity_iris.pdf
diff --git a/docs/images/parameter_sensitivity_mfeat_factors.pdf b/docs/images/parameter_sensitivity_mfeat_factors.pdf
diff --git a/docs/images/parameter_sensitivity_mfeat_karhunen.pdf b/docs/images/parameter_sensitivity_mfeat_karhunen.pdf
diff --git a/docs/images/parameter_sensitivity_mnist.pdf b/docs/images/parameter_sensitivity_mnist.pdf
diff --git a/docs/images/parameter_sensitivity_newsgroups.pdf b/docs/images/parameter_sensitivity_newsgroups.pdf
diff --git a/docs/images/parameter_sensitivity_scaled.pdf b/docs/images/parameter_sensitivity_scaled.pdf
diff --git a/docs/images/parameter_sensitivity_semeion.pdf b/docs/images/parameter_sensitivity_semeion.pdf
diff --git a/docs/images/parameter_sensitivity_violinplot.pdf b/docs/images/parameter_sensitivity_violinplot.pdf
diff --git a/docs/images/parameter_sensitivity_yeast_galactose.pdf b/docs/images/parameter_sensitivity_yeast_galactose.pdf
diff --git a/docs/images/plscan_cluster_layers.pdf b/docs/images/plscan_cluster_layers.pdf
diff --git a/docs/images/plscan_condensed_trees.pdf b/docs/images/plscan_condensed_trees.pdf
diff --git a/docs/images/plscan_density_smoothing.pdf b/docs/images/plscan_density_smoothing.pdf
diff --git a/docs/images/plscan_density_smoothing_data.pdf b/docs/images/plscan_density_smoothing_data.pdf
diff --git a/docs/images/plscan_larger_layers.pdf b/docs/images/plscan_larger_layers.pdf
diff --git a/docs/images/plscan_leaf_tree.pdf b/docs/images/plscan_leaf_tree.pdf
diff --git a/docs/images/plscan_parameter_example.pdf b/docs/images/plscan_parameter_example.pdf
diff --git a/docs/images/plscan_persistence_trace.pdf b/docs/images/plscan_persistence_trace.pdf
diff --git a/docs/index.rst b/docs/index.rst
@@ -36,7 +36,7 @@
 
    local_development
 
-|PyPI version|
+|PyPI version| |Conda version| |DOI badge|
 
 Persistent Leaves Spatial Clustering of Applications with Noise
 ===============================================================
@@ -126,7 +126,20 @@ strengths.
 Citing
 ------
 
-TODO
+When using this work, please cite our (upcoming) preprint:
+
+.. code-block:: bibtex
+
+   @article{bot2025plscan,
+      title         = {Persistent Multiscale Density-based Clustering},
+      author        = {Dani{\"{e}}l M. Bot and Leland McInnes and Jan Aerts},
+      year          = {2025},
+      month         = {12},
+      archiveprefix = {arXiv},
+      eprint        = {TODO},
+      primaryclass  = {cs.CL}
+   }
+
 
 Licensing
 ---------
@@ -135,4 +148,7 @@ The ``plscan`` package has a 3-Clause BSD license.
 
 .. |PyPI version| image:: https://badge.fury.io/py/plscan.svg
    :target: https://badge.fury.io/py/plscan
-
+.. |Conda version| image:: https://anaconda.org/conda-forge/plscan/badges/version.svg
+   :target: https://anaconda.org/conda-forge/plscan
+.. |DOI badge| image:: https://zenodo.org/badge/xxx.svg
+   :target: https://zenodo.org/doi/xxx/zenodo.yyy
diff --git a/docs/lib/plotting.py b/docs/lib/plotting.py
@@ -7,7 +7,10 @@
 
 # LaTeX font sizes on 10pt document:
 # https://latex-tutorial.com/changing-font-size/
-fontsize = dict(tiny=5, script=7, footnote=8, small=9, normal=10)
+# for the pre-print template!
+# fontsize = dict(tiny=5, script=7, footnote=8, small=9, normal=10)
+# for the journal template!
+fontsize = dict(tiny=6, script=8, footnote=9, small=10, normal=10.95)
 
 
 def configure_matplotlib():
@@ -38,16 +41,24 @@ def configure_matplotlib():
             "savefig.format": "png",
             "font.family": "serif",
             "text.usetex": True,
+            # For the pre-print template:
+            # "text.latex.preamble": dedent(
+            #     r"""
+            #     \usepackage[english]{babel}
+            #     \usepackage[T1]{fontenc}
+            #     \usepackage[varqu,varl]{inconsolata}
+            #     \usepackage[
+            #         theoremfont,trueslanted,largesc,p,
+            #         amsthm,smallerops
+            #     ]{newpx}
+            #     \usepackage[scr=rsfso]{mathalpha}
+            #     \usepackage[stretch=10,shrink=10,tracking,spacing,kerning,babel]{microtype}
+            #     """
+            # ),
+            # For the journal template:
             "text.latex.preamble": dedent(
                 r"""
                 \usepackage[english]{babel}
-                \usepackage[T1]{fontenc}
-                \usepackage[varqu,varl]{inconsolata}
-                \usepackage[
-                    theoremfont,trueslanted,largesc,p,
-                    amsthm,smallerops
-                ]{newpx}
-                \usepackage[scr=rsfso]{mathalpha}
                 \usepackage[stretch=10,shrink=10,tracking,spacing,kerning,babel]{microtype}
                 """
             ),
@@ -61,7 +72,8 @@ def sized_fig(width=0.5, aspect=0.618, dpi=None):
     """Create a figure with width as fraction of A4 page."""
     if dpi is None:
         dpi = 150
-    page_width_inch = 6.9305
+    # page_width_inch = 6.93050  # For the pre-print template
+    page_width_inch = 6.00117  # For the journal template
     w = width * page_width_inch
     h = aspect * w
     return plt.figure(figsize=(w, h), dpi=dpi)

diff --git a/docs/local_development.rst b/docs/local_development.rst
@@ -50,6 +50,14 @@ Also update the ``~/.zshrc`` config file with:
 
   export OpenMP_ROOT=$(brew --prefix)/opt/libomp
 
+or pass `OpenMP_ROOT` as cmake argument:
+
+.. code-block:: bash
+
+  pip install --no-deps --no-build-isolation \
+    -C cmake.args="-DOpenMP_ROOT=$(brew --prefix)/opt/libomp" \
+    -ve .
+
 Windows
 -------
 

diff --git a/docs/using_multiple_components.ipynb b/docs/using_multiple_components.ipynb
@@ -45,7 +45,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 6,
    "id": "c91190a6",
    "metadata": {},
    "outputs": [
@@ -64,7 +64,7 @@
     "from sklearn.neighbors import NearestNeighbors\n",
     "\n",
     "knn = NearestNeighbors(n_neighbors=50).fit(X).kneighbors(X)\n",
-    "c = PLSCAN(metric='precomputed').fit(knn)\n",
+    "c = PLSCAN(metric=\"precomputed\").fit(knn)\n",
     "\n",
     "plt.scatter(*X.T, c=c.labels_ % 10, s=1, linewidth=0, cmap=\"tab10\")\n",
     "plt.axis(\"off\")\n",
@@ -83,7 +83,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 7,
    "id": "2e0b7ea7",
    "metadata": {},
    "outputs": [
@@ -105,7 +105,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 8,
    "id": "148fdcbc",
    "metadata": {},
    "outputs": [

diff --git a/pyproject.toml b/pyproject.toml
@@ -20,13 +20,14 @@ dependencies = [
     "scikit-learn>=1.6,<2",
 ]
 classifiers = [
-    "Development Status :: 4 - Beta",
+    "Development Status :: 5 - Production/Stable",
     "Programming Language :: C++",
     "Programming Language :: Python :: 3",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
     "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
     "Operating System :: OS Independent",
     "Intended Audience :: Science/Research",
     "Intended Audience :: Developers",
@@ -36,7 +37,14 @@ classifiers = [
 
 [project.optional-dependencies]
 tests = ["pytest", "networkx", "pandas"]
-docs = ["furo", "sphinx", "pandoc", "nbsphinx", "sphinx-copybutton"]
+docs = [
+    "furo",
+    "sphinx",
+    "pandoc",
+    "nbsphinx",
+    "sphinx-copybutton",
+    "sphinx_autodoc_typehints",
+]
 
 [project.urls]
 Documentation = "https://JelmerBot.github.io/plscan"
@@ -48,7 +56,7 @@ minimum-version = "0.4"
 build-dir = "build/{wheel_tag}"
 wheel.py-api = "cp312"
 wheel.exclude = ["**.h", "**.cpp", "**/CMakeLists.txt"]
-sdist.exclude = [".*", ".*/", "docs/data/", "docs/lib/", "docs/images/"]
+sdist.exclude = [".*", ".*/", "docs/"]
 metadata.version.provider = "scikit_build_core.metadata.setuptools_scm"
 
 [tool.setuptools_scm]

diff --git a/src/plscan/sklearn.py b/src/plscan/sklearn.py
@@ -476,8 +476,11 @@ def cluster_layers(
 
         """
         check_is_fitted(self, "_persistence_trace")
+        # Pad persistence with zero so maxima at the edges can be detected as peaks
         x, y = self._persistence_trace
-        peaks = find_peaks(y, height=height, threshold=threshold, **kwargs)[0]
+        zero = np.array([0], dtype=y.dtype)
+        signal = np.hstack((zero, y, zero))
+        peaks = find_peaks(signal, height=height, threshold=threshold, **kwargs)[0] - 1
 
         if min_size is not None:
             peaks = peaks[x[peaks] >= min_size]

diff --git a/tests/baseline_images/test_plots/condensed_tree.png b/tests/baseline_images/test_plots/condensed_tree.png
diff --git a/tests/baseline_images/test_plots/condensed_tree_args.png b/tests/baseline_images/test_plots/condensed_tree_args.png
diff --git a/tests/baseline_images/test_plots/condensed_tree_dens.png b/tests/baseline_images/test_plots/condensed_tree_dens.png
diff --git a/tests/baseline_images/test_plots/condensed_tree_dist.png b/tests/baseline_images/test_plots/condensed_tree_dist.png
diff --git a/tests/baseline_images/test_plots/condensed_tree_rank.png b/tests/baseline_images/test_plots/condensed_tree_rank.png
diff --git a/tests/baseline_images/test_plots/leaf_tree.png b/tests/baseline_images/test_plots/leaf_tree.png
diff --git a/tests/baseline_images/test_plots/leaf_tree_args.png b/tests/baseline_images/test_plots/leaf_tree_args.png
diff --git a/tests/baseline_images/test_plots/persistence_trace.png b/tests/baseline_images/test_plots/persistence_trace.png
diff --git a/tests/baseline_images/test_plots/persistence_trace_args.png b/tests/baseline_images/test_plots/persistence_trace_args.png