From fd303e8ec93ff376ea81b2597e6ed7608a203c2c Mon Sep 17 00:00:00 2001
From: Gaetan Lepage <gaetan@glepage.com>
Date: Mon, 21 Apr 2025 19:37:00 +0200
Subject: [PATCH] python312Packages.pymoo: cleanup, fix build

---
 .../python-modules/pymoo/default.nix          | 89 ++++++++++++-------
 1 file changed, 57 insertions(+), 32 deletions(-)

diff --git a/pkgs/development/python-modules/pymoo/default.nix b/pkgs/development/python-modules/pymoo/default.nix
index 7f9b6c6908b6..6f4d59689c50 100644
--- a/pkgs/development/python-modules/pymoo/default.nix
+++ b/pkgs/development/python-modules/pymoo/default.nix
@@ -2,22 +2,37 @@
   lib,
   buildPythonPackage,
   fetchFromGitHub,
+
+  # build-system
+  cython,
   setuptools,
-  pytestCheckHook,
-  writeText,
+
+  # dependencies
   autograd,
   cma,
-  cython,
   deprecated,
   dill,
   matplotlib,
+  numpy,
+  scipy,
+
+  # tests
+  pytestCheckHook,
   nbformat,
   notebook,
   numba,
-  numpy,
-  scipy,
+  pythonAtLeast,
+  writeText,
 }:
 
+let
+  pymoo_data = fetchFromGitHub {
+    owner = "anyoptimization";
+    repo = "pymoo-data";
+    rev = "33f61a78182ceb211b95381dd6d3edee0d2fc0f3";
+    hash = "sha256-iGWPepZw3kJzw5HKV09CvemVvkvFQ38GVP+BAryBSs0=";
+  };
+in
 buildPythonPackage rec {
   pname = "pymoo";
   version = "0.6.1.3";
@@ -30,27 +45,32 @@ buildPythonPackage rec {
     hash = "sha256-CbeJwv51lu4cABgGieqy/8DCDJCb8wOPPVqUHk8Jb7E=";
   };
 
-  pymoo_data = fetchFromGitHub {
-    owner = "anyoptimization";
-    repo = "pymoo-data";
-    rev = "33f61a78182ceb211b95381dd6d3edee0d2fc0f3";
-    hash = "sha256-iGWPepZw3kJzw5HKV09CvemVvkvFQ38GVP+BAryBSs0=";
-  };
-
-  pythonRelaxDeps = [ "cma" ];
-  pythonRemoveDeps = [ "alive-progress" ];
-
   postPatch = ''
     substituteInPlace pymoo/util/display/display.py \
       --replace-fail "from pymoo.util.display.progress import ProgressBar" "" \
-      --replace-fail "ProgressBar() if progress else None" \
-                "print('Missing alive_progress needed for progress=True!') if progress else None"
+      --replace-fail \
+        "ProgressBar() if progress else None" \
+        "print('Missing alive_progress needed for progress=True!') if progress else None"
+
+    substituteInPlace pymoo/algorithms/soo/nonconvex/es.py \
+      --replace-fail "np.math.ceil" "np.ceil"
+    substituteInPlace pymoo/util/mnn.py \
+      --replace-fail "np.product" "np.prod"
+
+    substituteInPlace pymoo/config.py \
+      --replace-fail \
+        "https://raw.githubusercontent.com/anyoptimization/pymoo-data/main/" \
+        "file://${pymoo_data}/"
   '';
 
+  pythonRelaxDeps = [ "cma" ];
+  pythonRemoveDeps = [ "alive-progress" ];
+
   build-system = [
     setuptools
     cython
   ];
+
   dependencies = [
     autograd
     cma
@@ -62,10 +82,6 @@ buildPythonPackage rec {
   ];
 
   preCheck = ''
-    substituteInPlace pymoo/config.py \
-      --replace-fail "https://raw.githubusercontent.com/anyoptimization/pymoo-data/main/" \
-                "file://$pymoo_data/"
-
     # Some tests require a grad backend to be configured, this is a hacky way to do so.
     # The choice must be either "jax.numpy" or "autograd.numpy"
     echo 'from pymoo.gradient import activate; activate("autograd.numpy")' >> tests/conftest.py
@@ -78,15 +94,24 @@ buildPythonPackage rec {
   ];
   # Select some lightweight tests
   pytestFlagsArray = [ "-m 'not long'" ];
-  disabledTests = [
-    # ModuleNotFoundError: No module named 'pymoo.cython.non_dominated_sorting'
-    "test_fast_non_dominated_sorting"
-    "test_efficient_non_dominated_sort"
-    "test_dominance_degree_non_dominated_sort"
+  disabledTests =
+    [
+      # ModuleNotFoundError: No module named 'pymoo.cython.non_dominated_sorting'
+      "test_fast_non_dominated_sorting"
+      "test_efficient_non_dominated_sort"
+      "test_dominance_degree_non_dominated_sort"
 
-    # sensitive to float precision
-    "test_cd_and_pcd"
-  ];
+      # sensitive to float precision
+      "test_cd_and_pcd"
+
+      # TypeError: 'NoneType' object is not subscriptable
+      "test_dascomp"
+      "test_mw"
+    ]
+    ++ lib.optionals (pythonAtLeast "3.13") [
+      # AttributeError: 'ZDT3' object has no attribute 'elementwise'
+      "test_kktpm_correctness"
+    ];
   disabledTestPaths = [
     # sensitive to float precision
     "tests/algorithms/test_no_modfication.py"
@@ -98,10 +123,10 @@ buildPythonPackage rec {
 
   pythonImportsCheck = [ "pymoo" ];
 
-  meta = with lib; {
+  meta = {
     description = "Multi-objective Optimization in Python";
     homepage = "https://pymoo.org/";
-    license = licenses.asl20;
-    maintainers = with maintainers; [ veprbl ];
+    license = lib.licenses.asl20;
+    maintainers = with lib.maintainers; [ veprbl ];
   };
 }