From 6c8bca0541dc4f1c6201d62bf4d75cb4592ad409 Mon Sep 17 00:00:00 2001
From: natsukium <tomoya.otabi@gmail.com>
Date: Tue, 21 May 2024 09:14:28 +0900
Subject: [PATCH 1/2] python311Packages.biopandas: format with nixfmt

---
 .../python-modules/biopandas/default.nix      | 35 ++++++++-----------
 1 file changed, 14 insertions(+), 21 deletions(-)

diff --git a/pkgs/development/python-modules/biopandas/default.nix b/pkgs/development/python-modules/biopandas/default.nix
index d33a9faf44031..a828d92c19c3b 100644
--- a/pkgs/development/python-modules/biopandas/default.nix
+++ b/pkgs/development/python-modules/biopandas/default.nix
@@ -1,12 +1,13 @@
-{ lib
-, buildPythonPackage
-, fetchFromGitHub
-, looseversion
-, mmtf-python
-, nose
-, numpy
-, pandas
-, pythonRelaxDepsHook
+{
+  lib,
+  buildPythonPackage,
+  fetchFromGitHub,
+  looseversion,
+  mmtf-python,
+  nose,
+  numpy,
+  pandas,
+  pythonRelaxDepsHook,
 }:
 
 buildPythonPackage rec {
@@ -21,13 +22,9 @@ buildPythonPackage rec {
     hash = "sha256-PRdemBo+bB2xJWmF2NylFTfNwEEo67i6XSaeDAFmQ/c=";
   };
 
-  nativeBuildInputs = [
-    pythonRelaxDepsHook
-  ];
+  nativeBuildInputs = [ pythonRelaxDepsHook ];
 
-  pythonRelaxDeps = [
-    "looseversion"
-  ];
+  pythonRelaxDeps = [ "looseversion" ];
 
   propagatedBuildInputs = [
     numpy
@@ -36,9 +33,7 @@ buildPythonPackage rec {
     looseversion
   ];
 
-  nativeCheckInputs = [
-    nose
-  ];
+  nativeCheckInputs = [ nose ];
 
   checkPhase = ''
     runHook preCheck
@@ -48,9 +43,7 @@ buildPythonPackage rec {
     runHook postCheck
   '';
 
-  pythonImportsCheck = [
-    "biopandas"
-  ];
+  pythonImportsCheck = [ "biopandas" ];
 
   meta = {
     description = "Working with molecular structures in pandas DataFrames";

From d487914932a906c67481cbb9c83f16122eed146e Mon Sep 17 00:00:00 2001
From: natsukium <tomoya.otabi@gmail.com>
Date: Tue, 21 May 2024 09:15:15 +0900
Subject: [PATCH 2/2] python311Packages.biopandas: 0.4.1 -> 0.5.0

Diff:
https://github.com/BioPandas/biopandas/compare/refs/tags/v0.4.1...v0.5.0

Changelog:
https://github.com/BioPandas/biopandas/releases/tag/refs/tags/v0.5.0
---
 .../python-modules/biopandas/default.nix      | 34 ++++++++++++-------
 1 file changed, 21 insertions(+), 13 deletions(-)

diff --git a/pkgs/development/python-modules/biopandas/default.nix b/pkgs/development/python-modules/biopandas/default.nix
index a828d92c19c3b..b947164f1d882 100644
--- a/pkgs/development/python-modules/biopandas/default.nix
+++ b/pkgs/development/python-modules/biopandas/default.nix
@@ -2,46 +2,54 @@
   lib,
   buildPythonPackage,
   fetchFromGitHub,
+  setuptools,
   looseversion,
   mmtf-python,
-  nose,
   numpy,
   pandas,
+  pynose,
+  pytestCheckHook,
   pythonRelaxDepsHook,
 }:
 
 buildPythonPackage rec {
   pname = "biopandas";
-  version = "0.4.1";
-  format = "setuptools";
+  version = "0.5.0";
+  pyproject = true;
 
   src = fetchFromGitHub {
     owner = "BioPandas";
     repo = "biopandas";
     rev = "refs/tags/v${version}";
-    hash = "sha256-PRdemBo+bB2xJWmF2NylFTfNwEEo67i6XSaeDAFmQ/c=";
+    hash = "sha256-1c78baBBsDyvAWrNx5mZI/Q75wyXv0DAwAdWm3EwX/I=";
   };
 
   nativeBuildInputs = [ pythonRelaxDepsHook ];
 
   pythonRelaxDeps = [ "looseversion" ];
 
-  propagatedBuildInputs = [
+  build-system = [ setuptools ];
+
+  dependencies = [
     numpy
     pandas
     mmtf-python
     looseversion
   ];
 
-  nativeCheckInputs = [ nose ];
-
-  checkPhase = ''
-    runHook preCheck
-
-    nosetests
+  nativeCheckInputs = [
+    pynose
+    pytestCheckHook
+  ];
 
-    runHook postCheck
-  '';
+  disabledTests = [
+    # require network access
+    "test_mmcif_pdb_conversion"
+    "test_fetch_pdb"
+    "test_write_mmtf_bp"
+    "test_write_mmtf"
+    "test_b_factor_shift"
+  ];
 
   pythonImportsCheck = [ "biopandas" ];