From c8c874cb3977d0b797950684bd0d2015221056fd Mon Sep 17 00:00:00 2001
From: Sharlatan Hellseher <sharlatanus@gmail.com>
Date: Tue, 23 Sep 2025 13:12:28 +0100
Subject: [PATCH] gnu: python-hdbscan: Update to 0.8.40.

* gnu/packages/machine-learning.scm (python-hdbscan): Update to 0.8.40.
[arguments] <test-flags>: Ignore 3 test files.
<phases>: Add 'pre-check.
[native-inputs]: Remove python-nose, python-pandas, python-networkx, and
python-wheel; add python-numpy.

Change-Id: I38813d1cc16d4e90b5f0875dc93728bb42f4fa5d
---
 gnu/packages/machine-learning.scm | 33 +++++++++++++++++++------------
 1 file changed, 20 insertions(+), 13 deletions(-)

diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 353db595b5c..66fb27428ee 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -2275,32 +2275,39 @@ for scientific computing and data science (e.g. BLAS and OpenMP).")
 (define-public python-hdbscan
   (package
     (name "python-hdbscan")
-    (version "0.8.33")
+    (version "0.8.40")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "hdbscan" version))
        (sha256
-        (base32 "03gr70ys1zrnp15pxzhichvrdj5bj88p6p5k0wj8vx251rgvryjp"))))
+        (base32 "05wask431fm78n1227dhvwsmlnys9d95vxjz0y8hbvmy2zzq7qy9"))))
     (build-system pyproject-build-system)
     (arguments
      (list
+      #:test-flags
+      ;; XXX: Test files which fail during test collection.
+      #~(list "--ignore=hdbscan/tests/test_branches.py"
+              "--ignore=hdbscan/tests/test_hdbscan.py"
+              "--ignore=hdbscan/tests/test_rsl.py")
       #:phases
       #~(modify-phases %standard-phases
+          (add-before 'check 'pre-check
+            (lambda _
+              (delete-file "hdbscan/tests/__init__.py")))
           (add-before 'check 'build-extensions
             (lambda _
               (invoke "python" "setup.py" "build_ext" "--inplace"))))))
-    (propagated-inputs (list python-joblib
-                             python-numpy
-                             python-scikit-learn
-                             python-scipy))
-    (native-inputs (list python-cython
-                         python-nose
-                         python-pytest
-                         python-pandas
-                         python-networkx
-                         python-setuptools
-                         python-wheel))
+    (native-inputs
+     (list python-cython
+           python-numpy
+           python-pytest
+           python-setuptools))
+    (propagated-inputs
+     (list python-joblib
+           python-numpy
+           python-scikit-learn
+           python-scipy))
     (home-page "https://github.com/scikit-learn-contrib/hdbscan")
     (synopsis "High performance implementation of HDBSCAN clustering")
     (description "HDBSCAN - Hierarchical Density-Based Spatial Clustering of