From 75c3ed6d05d16d6fb705d12dbfa3737436ac32b2 Mon Sep 17 00:00:00 2001
From: Ben Darwin <bcdarwin@gmail.com>
Date: Thu, 25 Jul 2024 12:20:55 -0400
Subject: [PATCH] python311Packages.fslpy: init at 3.21.1

---
 .../python-modules/fslpy/default.nix          | 98 +++++++++++++++++++
 pkgs/top-level/python-packages.nix            |  2 +
 2 files changed, 100 insertions(+)
 create mode 100644 pkgs/development/python-modules/fslpy/default.nix

diff --git a/pkgs/development/python-modules/fslpy/default.nix b/pkgs/development/python-modules/fslpy/default.nix
new file mode 100644
index 000000000000..0633b9b5133c
--- /dev/null
+++ b/pkgs/development/python-modules/fslpy/default.nix
@@ -0,0 +1,98 @@
+{
+  lib,
+  buildPythonPackage,
+  pythonOlder,
+  fetchFromGitLab,
+  setuptools,
+  dill,
+  h5py,
+  nibabel,
+  numpy,
+  scipy,
+  indexed-gzip,
+  pillow,
+  rtree,
+  trimesh,
+  wxpython,
+  pytestCheckHook,
+  pytest-cov-stub,
+  tomli,
+}:
+
+buildPythonPackage rec {
+  pname = "fslpy";
+  version = "3.21.1";
+  pyproject = true;
+
+  disabled = pythonOlder "3.8";
+
+  src = fetchFromGitLab {
+    domain = "git.fmrib.ox.ac.uk";
+    owner = "fsl";
+    repo = "fslpy";
+    rev = "refs/tags/${version}";
+    hash = "sha256-O0bhzu6zZeuGJqXAwlgM8qHkgtaGCmg7xSkOqbZH2eA=";
+  };
+
+  build-system = [ setuptools ];
+
+  dependencies = [
+    dill
+    h5py
+    nibabel
+    numpy
+    scipy
+  ];
+
+  optional-dependencies = {
+    extra = [
+      indexed-gzip
+      pillow
+      rtree
+      trimesh
+      wxpython
+    ];
+  };
+
+  nativeCheckInputs = [
+    pytestCheckHook
+    pytest-cov-stub
+    tomli
+  ] ++ optional-dependencies.extra;
+
+  disabledTestPaths = [
+    # tries to download data:
+    "fsl/tests/test_dicom.py"
+    # tests exit with "SystemExit: Unable to access the X Display, is $DISPLAY set properly?"
+    "fsl/tests/test_idle.py"
+    "fsl/tests/test_platform.py"
+    # require FSL's atlas library (via $FSLDIR), which has an unfree license:
+    "fsl/tests/test_atlases.py"
+    "fsl/tests/test_atlases_query.py"
+    "fsl/tests/test_parse_data.py"
+    "fsl/tests/test_scripts/test_atlasq_list_summary.py"
+    "fsl/tests/test_scripts/test_atlasq_ohi.py"
+    "fsl/tests/test_scripts/test_atlasq_query.py"
+    # requires FSL (unfree and not in Nixpkgs):
+    "fsl/tests/test_fslsub.py"
+    "fsl/tests/test_run.py"
+    "fsl/tests/test_wrappers"
+  ];
+
+  pythonImportsCheck = [
+    "fsl"
+    "fsl.data"
+    "fsl.scripts"
+    "fsl.transform"
+    "fsl.utils"
+    "fsl.wrappers"
+  ];
+
+  meta = {
+    description = "FSL Python library";
+    homepage = "https://git.fmrib.ox.ac.uk/fsl/fslpy";
+    changelog = "https://git.fmrib.ox.ac.uk/fsl/fslpy/-/blob/main/CHANGELOG.rst";
+    license = lib.licenses.asl20;
+    maintainers = with lib.maintainers; [ bcdarwin ];
+  };
+}
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index b033b1a3ad23..fe906ad5911f 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -4782,6 +4782,8 @@ self: super: with self; {
 
   fschat = callPackage ../development/python-modules/fschat { };
 
+  fslpy = callPackage ../development/python-modules/fslpy { };
+
   fsspec-xrootd = callPackage ../development/python-modules/fsspec-xrootd { };
 
   fsspec = callPackage ../development/python-modules/fsspec { };