From ed61fe8783d08732c8ccc88004de87ea0f78466c Mon Sep 17 00:00:00 2001
From: Gaetan Lepage <gaetan@glepage.com>
Date: Sat, 20 Dec 2025 10:45:36 +0000
Subject: [PATCH] python3Packages.meeko: 0.6.1 -> 0.7.1

Diff: https://github.com/forlilab/Meeko/compare/v0.6.1...v0.7.1

Changelog: https://github.com/forlilab/Meeko/releases/tag/v0.7.1
---
 .../python-modules/meeko/default.nix          | 61 ++++++++++++++++---
 1 file changed, 52 insertions(+), 9 deletions(-)

diff --git a/pkgs/development/python-modules/meeko/default.nix b/pkgs/development/python-modules/meeko/default.nix
index f9f7c60f045a..4e5488582859 100644
--- a/pkgs/development/python-modules/meeko/default.nix
+++ b/pkgs/development/python-modules/meeko/default.nix
@@ -1,31 +1,39 @@
 {
   lib,
+  stdenv,
   buildPythonPackage,
   fetchFromGitHub,
+
+  # build-system
+  setuptools,
+
+  # dependencies
   gemmi,
   numpy,
-  pytestCheckHook,
-  pythonOlder,
   rdkit,
   scipy,
+
+  # tests
+  pytestCheckHook,
 }:
 
 buildPythonPackage rec {
   pname = "meeko";
-  version = "0.6.1";
-  format = "setuptools";
-
-  disabled = pythonOlder "3.5";
+  version = "0.7.1";
+  pyproject = true;
 
   src = fetchFromGitHub {
     owner = "forlilab";
     repo = "Meeko";
     tag = "v${version}";
-    hash = "sha256-ViIBiczwxTwraYn8UnFAZFCFT28v3WEYm04W2YpU/4g=";
+    hash = "sha256-ObGUUNzfK2k37uJ/aY3DHf9BlJ1nzqTe6tHvV2rj1og=";
   };
 
-  propagatedBuildInputs = [
-    # setup.py only requires numpy but others are needed at runtime
+  build-system = [
+    setuptools
+  ];
+
+  dependencies = [
     gemmi
     numpy
     rdkit
@@ -34,6 +42,41 @@ buildPythonPackage rec {
 
   nativeCheckInputs = [ pytestCheckHook ];
 
+  disabledTests = [
+    # Require internet connection
+    "test_add_variants"
+    "test_build_noncovalent_CC"
+
+    # AssertionError: assert {'chosen_by_d...ond': [], ...} == {'chosen_by_d...ond': [], ...}
+    "test_polymer_encoding_decoding"
+  ]
+  ++ lib.optionals stdenv.hostPlatform.isDarwin [
+    # AssertionError: assert 'altloc' in 'updated 1 h positions but deleted 11
+    "test_AHHY_all_static_residues"
+    "test_AHHY_flex_residues"
+    "test_AHHY_flexibilize_then_parameterize"
+    "test_AHHY_mk_prep_and_export"
+    "test_AHHY_mutate_residues"
+    "test_AHHY_padding"
+    "test_disulfide_adjacent"
+    "test_disulfides"
+    "test_export_sidechains_no_idxmap"
+    "test_insertion_code"
+    "test_just_three_padded_mol"
+    "test_monomer_encoding_decoding"
+    "test_pdbqt_writing_from_decoded_polymer"
+    "test_rdkit_molsetup_encoding_decoding"
+    "test_residue_chem_templates_encoding_decoding"
+    "test_residue_padder_encoding_decoding"
+    "test_residue_template_encoding_decoding"
+    "test_stitch_polymer"
+    "test_write_pdb_1igy"
+    "test_write_pdb_AHHY"
+
+    # RuntimeError: Updated 1 H positions but deleted 10
+    "test_altloc"
+  ];
+
   pythonImportsCheck = [ "meeko" ];
 
   meta = {