From 041ea43a86f39e7c55ba3551bbe59d0ef9798c73 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 3 May 2024 14:55:53 +0200
Subject: gnu: python-pingouin: Update to 0.5.4.

* gnu/packages/python-science.scm (python-pingouin): Update to 0.5.4.
[build-system]: Use pyproject-build-system.
[arguments]: Remove custom 'check phase; add 'sklearn-compatibility phase;
skip one test.

Change-Id: I8d13f15558eadee0547f04bc4bb89a0fd0e0767b
---
 gnu/packages/python-science.scm | 23 ++++++++++++++---------
 1 file changed, 14 insertions(+), 9 deletions(-)

(limited to 'gnu')

diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 63df0ae5e4..c5e9a41ce2 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -1991,7 +1991,7 @@ (define-public python-pandas-flavor
 (define-public python-pingouin
   (package
     (name "python-pingouin")
-    (version "0.5.2")
+    (version "0.5.4")
     (source
      ;; The PyPI tarball does not contain the tests.
      (origin
@@ -2002,11 +2002,15 @@ (define-public python-pingouin
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "0czy7cpn6xx9fs6wbz6rq2lpkb1a89bzxj1anf2f9in1m5qyrh83"))))
-    (build-system python-build-system)
+         "1j3qkgvyc31604ddl952h4hwza7schg8kwkycmxvpvx7xjj7nn68"))))
+    (build-system pyproject-build-system)
     (arguments
-     `(#:phases
-       (modify-phases %standard-phases
+     (list
+      #:test-flags
+      ;; This one fails due to minor differences in accuracy
+      '(list "-k" "not test_logistic_regression")
+      #:phases
+      '(modify-phases %standard-phases
          (add-after 'unpack 'loosen-requirements
            (lambda _
              (substitute* '("requirements.txt" "setup.py")
@@ -2024,10 +2028,11 @@ (define-public python-pingouin
              (substitute* "pingouin/__init__.py"
                (("^from outdated[^\n]*") "")
                (("^warn_if_outdated[^\n]*") ""))))
-         (replace 'check
-           (lambda* (#:key tests? #:allow-other-keys)
-             (when tests?
-               (invoke "pytest")))))))
+         (add-after 'unpack 'sklearn-compatibility
+           (lambda _
+             (substitute* "pingouin/regression.py"
+               (("kwargs\\[\"penalty\"\\] = \"none\"")
+                "kwargs[\"penalty\"] = None")))))))
     (native-inputs
      (list python-pytest python-pytest-cov))
     (propagated-inputs
-- 
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