python3Packages.scikitimage: 0.18.1 -> 0.18.3 (#137038)

pkgs/development/python-modules/scikit-image/add-testing-data.patch

@@ -0,0 +1,17 @@
+diff --git a/skimage/data/setup.py b/skimage/data/setup.py
+index 528e9c284ce..ba0e155559c 100644
+--- a/skimage/data/setup.py
++++ b/skimage/data/setup.py
+@@ -11,7 +11,11 @@ def configuration(parent_package='', top_path=None):
+     # further notice.
+     # Testing data and additional datasets should only
+     # be made available via pooch
+-    config.add_data_files(*legacy_datasets)
++    # Nix patch: add ALL images to facilitate testing of a fully-built package
++    from pathlib import Path
++    config.add_data_files(
++        *(path.name for path in Path(__file__).parent.glob("*") if path.suffix != ".py")
++    )
+     # It seems hard to create a consistent hash for README.txt since
+     # the line endings keep getting converted
+     config.add_data_files('README.txt')

pkgs/development/python-modules/scikit-image/default.nix

@@ -1,6 +1,7 @@
 { lib
-, fetchPypi
+, fetchFromGitHub
 , buildPythonPackage
+, python
 , cython
 , numpy
 , scipy
@@ -11,20 +12,26 @@
 , pywavelets
 , dask
 , cloudpickle
-, pytest
 , imageio
 , tifffile
+, pytestCheckHook
 }:
 
-buildPythonPackage rec {
+let
+  installedPackageRoot = "${builtins.placeholder "out"}/${python.sitePackages}";
+in buildPythonPackage rec {
   pname = "scikit-image";
   version = "0.18.3";
 
-  src = fetchPypi {
-    inherit pname version;
-    sha256 = "ecae99f93f4c5e9b1bf34959f4dc596c41f2f6b2fc407d9d9ddf85aebd3137ca";
+  src = fetchFromGitHub {
+    owner = pname;
+    repo = pname;
+    rev = "v${version}";
+    sha256 = "0a2h3bw5rkk23k4r04qc9maccg00nddssd7lfsps8nhp5agk1vyh";
   };
 
+  patches = [ ./add-testing-data.patch ];
+
   nativeBuildInputs = [ cython ];
 
   propagatedBuildInputs = [
@@ -41,14 +48,51 @@ buildPythonPackage rec {
     tifffile
   ];
 
-  checkInputs = [ pytest ];
+  checkInputs = [ pytestCheckHook ];
 
-  # No tests in archive
-  doCheck = false;
+  # (1) The package has cythonized modules, whose .so libs will appear only in the wheel, i.e. in nix store;
+  # (2) To stop Python from importing the wrong directory, i.e. the one in the build dir, not the one in nix store, `skimage` dir should be removed or renamed;
+  # (3) Therefore, tests should be run on the installed package in nix store.
+
+  # See e.g. https://discourse.nixos.org/t/cant-import-cythonized-modules-at-checkphase/14207 on why the following is needed.
+  preCheck = ''
+    rm -r skimage
+  '';
+
+  disabledTestPaths = [
+    # Requires network access (actually some data is loaded via `skimage._shared.testing.fetch` in the global scope, which calls `pytest.skip` when a network is unaccessible, leading to a pytest collection error).
+    "${installedPackageRoot}/skimage/filters/rank/tests/test_rank.py"
+  ];
+  pytestFlagsArray = [ "${installedPackageRoot}" "--pyargs" "skimage" ] ++ builtins.map (testid: "--deselect=" + testid) [
+    # These tests require network access
+    "skimage/data/test_data.py::test_skin"
+    "skimage/data/tests/test_data.py::test_skin"
+    "skimage/io/tests/test_io.py::test_imread_http_url"
+    "skimage/restoration/tests/test_rolling_ball.py::test_ndim"
+  ];
+
+  # Check cythonized modules
+  pythonImportsCheck = [
+    "skimage"
+    "skimage._shared"
+    "skimage.draw"
+    "skimage.feature"
+    "skimage.restoration"
+    "skimage.filters"
+    "skimage.future.graph"
+    "skimage.graph"
+    "skimage.io"
+    "skimage.measure"
+    "skimage.morphology"
+    "skimage.transform"
+    "skimage.util"
+    "skimage.segmentation"
+  ];
 
   meta = {
     description = "Image processing routines for SciPy";
     homepage = "https://scikit-image.org";
     license = lib.licenses.bsd3;
+    maintainers = with lib.maintainers; [ yl3dy ];
   };
 }