From 52a0e458e4ff1472d2ba2f8aa551de2936bc7a40 Mon Sep 17 00:00:00 2001
From: Gaetan Lepage <gaetan@glepage.com>
Date: Sun, 16 Mar 2025 11:02:56 +0100
Subject: [PATCH 1/2] python312Packages.ezyrb: cleanup, fix build

---
 .../python-modules/ezyrb/default.nix          | 39 ++++++++++++++-----
 1 file changed, 29 insertions(+), 10 deletions(-)

diff --git a/pkgs/development/python-modules/ezyrb/default.nix b/pkgs/development/python-modules/ezyrb/default.nix
index c3506c61d2ff..f779b98cb4d2 100644
--- a/pkgs/development/python-modules/ezyrb/default.nix
+++ b/pkgs/development/python-modules/ezyrb/default.nix
@@ -2,22 +2,26 @@
   lib,
   buildPythonPackage,
   fetchFromGitHub,
-  pythonOlder,
+
+  # build-system
+  setuptools,
+
+  # dependencies
   future,
   numpy,
   scipy,
   matplotlib,
   scikit-learn,
   torch,
+
+  # tests
   pytestCheckHook,
 }:
 
 buildPythonPackage rec {
   pname = "ezyrb";
   version = "1.3.0.post2404";
-  format = "setuptools";
-
-  disabled = pythonOlder "3.7";
+  pyproject = true;
 
   src = fetchFromGitHub {
     owner = "mathLab";
@@ -26,12 +30,27 @@ buildPythonPackage rec {
     hash = "sha256-nu75Geyeu1nTLoGaohXB9pmbUWKgdgch9Z5OJqz9xKQ=";
   };
 
-  propagatedBuildInputs = [
+  # AttributeError: module 'numpy' has no attribute 'VisibleDeprecationWarning'
+  postPatch = ''
+    substituteInPlace \
+      tests/test_k_neighbors_regressor.py \
+      tests/test_linear.py \
+      tests/test_radius_neighbors_regressor.py \
+      --replace-fail \
+        "np.VisibleDeprecationWarning" \
+        "np.exceptions.VisibleDeprecationWarning"
+  '';
+
+  build-system = [
+    setuptools
+  ];
+
+  dependencies = [
     future
-    numpy
-    scipy
     matplotlib
+    numpy
     scikit-learn
+    scipy
     torch
   ];
 
@@ -44,11 +63,11 @@ buildPythonPackage rec {
     "tests/test_podae.py"
   ];
 
-  meta = with lib; {
+  meta = {
     description = "Easy Reduced Basis method";
     homepage = "https://mathlab.github.io/EZyRB/";
     downloadPage = "https://github.com/mathLab/EZyRB/releases";
-    license = licenses.mit;
-    maintainers = with maintainers; [ yl3dy ];
+    license = lib.licenses.mit;
+    maintainers = with lib.maintainers; [ yl3dy ];
   };
 }

From 98f7ced0d7adfdc2d45239f394d649d646120973 Mon Sep 17 00:00:00 2001
From: Gaetan Lepage <gaetan@glepage.com>
Date: Sun, 16 Mar 2025 11:56:21 +0100
Subject: [PATCH 2/2] python312Packages.pydmd: 2025.01.01 -> 2025.03.01

Diff: https://github.com/PyDMD/PyDMD/compare/refs/tags/2025.01.01...2025.03.01

Changelog: https://github.com/PyDMD/PyDMD/releases/tag/2025.03.01
---
 .../python-modules/pydmd/default.nix          | 108 +++++++++---------
 1 file changed, 57 insertions(+), 51 deletions(-)

diff --git a/pkgs/development/python-modules/pydmd/default.nix b/pkgs/development/python-modules/pydmd/default.nix
index d48e92fc80a8..9da1917c0a3f 100644
--- a/pkgs/development/python-modules/pydmd/default.nix
+++ b/pkgs/development/python-modules/pydmd/default.nix
@@ -1,64 +1,70 @@
 {
   lib,
-  stdenv,
   buildPythonPackage,
   fetchFromGitHub,
+
+  # build-system
   setuptools,
+  setuptools-git-versioning,
+
+  # dependencies
+  ezyrb,
   future,
+  h5netcdf,
   matplotlib,
   numpy,
-  pytestCheckHook,
-  pytest-mock,
-  pythonOlder,
   scipy,
-  ezyrb,
+  xarray,
+
+  # tests
+  pytest-mock,
+  pytestCheckHook,
 }:
 
-let
-  self = buildPythonPackage rec {
-    pname = "pydmd";
-    version = "2025.01.01";
-    pyproject = true;
+buildPythonPackage rec {
+  pname = "pydmd";
+  version = "2025.03.01";
+  pyproject = true;
 
-    disabled = pythonOlder "3.6";
-
-    src = fetchFromGitHub {
-      owner = "PyDMD";
-      repo = "PyDMD";
-      tag = version;
-      hash = "sha256-edjBr0LsfyBEi4YZiTY0GegqgESWgSFennZOi2YFhC4=";
-    };
-
-    build-system = [ setuptools ];
-
-    propagatedBuildInputs = [
-      future
-      matplotlib
-      numpy
-      scipy
-      ezyrb
-    ];
-
-    nativeCheckInputs = [
-      pytestCheckHook
-      pytest-mock
-    ];
-
-    pytestFlagsArray = [ "tests/test_dmdbase.py" ];
-
-    pythonImportsCheck = [ "pydmd" ];
-
-    passthru.tests = self.overrideAttrs (old: {
-      pytestFlagsArray = [ ];
-    });
-
-    meta = with lib; {
-      description = "Python Dynamic Mode Decomposition";
-      homepage = "https://pydmd.github.io/PyDMD/";
-      changelog = "https://github.com/PyDMD/PyDMD/releases/tag/${src.tag}";
-      license = licenses.mit;
-      maintainers = with maintainers; [ yl3dy ];
-    };
+  src = fetchFromGitHub {
+    owner = "PyDMD";
+    repo = "PyDMD";
+    tag = version;
+    hash = "sha256-2pfWW+CLSDr6tJrcLpodil/RnhLTZ5Yqw0ThTCqO0MY=";
   };
-in
-self
+
+  postPatch = ''
+    substituteInPlace pyproject.toml \
+      --replace-fail "setuptools-git-versioning>=2.0,<3" "setuptools-git-versioning"
+  '';
+
+  build-system = [
+    setuptools
+    setuptools-git-versioning
+  ];
+
+  dependencies = [
+    ezyrb
+    future
+    h5netcdf
+    matplotlib
+    numpy
+    scipy
+    xarray
+  ];
+
+  pythonImportsCheck = [ "pydmd" ];
+
+  nativeCheckInputs = [
+    pytest-mock
+    pytestCheckHook
+  ];
+
+  meta = {
+    description = "Python Dynamic Mode Decomposition";
+    homepage = "https://pydmd.github.io/PyDMD/";
+    changelog = "https://github.com/PyDMD/PyDMD/releases/tag/${src.tag}";
+    license = lib.licenses.mit;
+    maintainers = with lib.maintainers; [ yl3dy ];
+  };
+}