From 87e495ef4ff7d15382f1297ea7f2656e93756cad Mon Sep 17 00:00:00 2001
From: Martin Weinelt <hexa@darmstadt.ccc.de>
Date: Mon, 27 Feb 2023 02:14:32 +0100
Subject: [PATCH] python3Packages.nibabel: 4.0.2 -> 5.0.1

https://github.com/nipy/nibabel/releases/tag/5.0.0
https://github.com/nipy/nibabel/releases/tag/5.0.1
---
 .../python-modules/nibabel/default.nix        | 70 ++++++++++++++++---
 1 file changed, 60 insertions(+), 10 deletions(-)

diff --git a/pkgs/development/python-modules/nibabel/default.nix b/pkgs/development/python-modules/nibabel/default.nix
index 54b92a17871b..2c1f0b2ae27c 100644
--- a/pkgs/development/python-modules/nibabel/default.nix
+++ b/pkgs/development/python-modules/nibabel/default.nix
@@ -1,31 +1,81 @@
 { lib
 , buildPythonPackage
 , fetchPypi
-, isPy27
-, packaging
-, pytestCheckHook
-, nose
+, pythonOlder
+, hatchling
+, hatch-vcs
 , numpy
-, h5py
+, packaging
+, importlib-resources
 , pydicom
+, pillow
+, h5py
 , scipy
+, git
+, pytest-doctestplus
+, pytest-httpserver
+, pytest-xdist
+, pytestCheckHook
 }:
 
 buildPythonPackage rec {
   pname = "nibabel";
-  version = "4.0.2";
-  disabled = isPy27;
+  version = "5.0.1";
+  format = "pyproject";
+
+  disabled = pythonOlder "3.8";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "sha256-RcSbU0k1G0X2wEWpGqArTw02dob/MoRjLvlaxluTB4Y=";
+    hash = "sha256-SvZQFbTMmZQEyvA04cFcGrZ1h5XCXWkH/3T127/p9D4=";
   };
 
-  propagatedBuildInputs = [ numpy scipy h5py packaging pydicom ];
+  nativeBuildInputs = [
+    hatchling
+    hatch-vcs
+  ];
+
+  propagatedBuildInputs = [
+    numpy
+    packaging
+  ] ++ lib.optionals (pythonOlder "3.9") [
+    importlib-resources
+  ];
+
+  passthru.optional-dependencies = rec {
+    all = dicom
+      ++ dicomfs
+      ++ minc2
+      ++ spm
+      ++ zstd;
+    dicom = [
+      pydicom
+    ];
+    dicomfs = [
+      pillow
+    ] ++ dicom;
+    minc2 = [
+      h5py
+    ];
+    spm = [
+      scipy
+    ];
+    zstd = [
+      # TODO: pyzstd
+    ];
+  };
 
   nativeCheckInputs = [
+    git
+    pytest-doctestplus
+    pytest-httpserver
+    pytest-xdist
     pytestCheckHook
-  ];
+  ] ++ passthru.optional-dependencies.all;
+
+  preCheck = ''
+    export PATH=$out/bin:$PATH
+  '';
 
   disabledTests = [
     # https://github.com/nipy/nibabel/issues/951