python312Packages.meshio: skip failing tests (#383057)

Author: GaetanLepage

pkgs/development/python-modules/gstools/default.nix

@@ -2,37 +2,43 @@
   lib,
   buildPythonPackage,
   fetchFromGitHub,
-  setuptools,
-  setuptools-scm,
-  numpy,
+
+  # build-system
   cython,
   extension-helpers,
+  numpy,
+  setuptools,
+  setuptools-scm,
+
+  # dependencies
   hankel,
   emcee,
   meshio,
   pyevtk,
   scipy,
+
+  # tests
   pytestCheckHook,
 }:
 
 buildPythonPackage rec {
   pname = "gstools";
-  version = "1.6.0";
+  version = "1.6.1";
   pyproject = true;
 
   src = fetchFromGitHub {
     owner = "GeoStat-Framework";
     repo = "GSTools";
     tag = "v${version}";
-    hash = "sha256-QpdOARzcSRVFl/DbnE2JLBFZmTSh/fBOmzweuf+zfEs=";
+    hash = "sha256-Aieuk0Xjlut8rTZoFHcBpPtyIj/fstMrHiiKyDOpQlg=";
   };
 
   build-system = [
-    setuptools
-    setuptools-scm
-    numpy
     cython
     extension-helpers
+    numpy
+    setuptools
+    setuptools-scm
   ];
 
   dependencies = [
@@ -50,7 +56,7 @@ buildPythonPackage rec {
   meta = {
     description = "Geostatistical toolbox";
     homepage = "https://github.com/GeoStat-Framework/GSTools";
-    changelog = "https://github.com/GeoStat-Framework/GSTools/blob/${src.rev}/CHANGELOG.md";
+    changelog = "https://github.com/GeoStat-Framework/GSTools/blob/v${version}/CHANGELOG.md";
     license = lib.licenses.lgpl3Only;
     maintainers = with lib.maintainers; [ sigmanificient ];
   };

pkgs/development/python-modules/hankel/default.nix

@@ -2,11 +2,17 @@
   lib,
   buildPythonPackage,
   fetchFromGitHub,
+
+  # build-system
   setuptools,
   setuptools-scm,
+
+  # dependencies
   mpmath,
   numpy,
   scipy,
+
+  # tests
   pytestCheckHook,
   pytest-xdist,
 }:
@@ -27,22 +33,29 @@ buildPythonPackage rec {
     setuptools
     setuptools-scm
   ];
+
   dependencies = [
     mpmath
     numpy
     scipy
   ];
 
   pythonImportsCheck = [ "hankel" ];
+
   nativeCheckInputs = [
     pytestCheckHook
     pytest-xdist
   ];
 
+  disabledTests = [
+    # ValueError: Calling nonzero on 0d arrays is not allowed.
+    "test_nu0"
+  ];
+
   meta = {
     description = "Implementation of Ogata's (2005) method for Hankel transforms";
     homepage = "https://github.com/steven-murray/hankel";
-    changelog = "https://github.com/steven-murray/hankel/${src.rev}/CHANGELOG.rst";
+    changelog = "https://github.com/steven-murray/hankel/v${version}/CHANGELOG.rst";
     license = lib.licenses.mit;
     maintainers = with lib.maintainers; [ sigmanificient ];
   };

pkgs/development/python-modules/meshio/default.nix

@@ -1,47 +1,113 @@
 {
   lib,
   buildPythonPackage,
-  fetchPypi,
-  numpy,
-  netcdf4,
+  fetchFromGitHub,
+
+  # build-system
+  setuptools,
+
+  # dependencies
   h5py,
+  netcdf4,
+  numpy,
+  rich,
+
+  # tests
   exdown,
   pytestCheckHook,
-  rich,
-  setuptools,
 }:
 
 buildPythonPackage rec {
   pname = "meshio";
   version = "5.3.5";
-  format = "pyproject";
+  pyproject = true;
 
-  src = fetchPypi {
-    inherit pname version;
-    hash = "sha256-8h8Bq9nym6BuoRkwSz055hBCHP6Tud0jNig0kZ+HWG0=";
+  src = fetchFromGitHub {
+    owner = "nschloe";
+    repo = "meshio";
+    tag = "v${version}";
+    hash = "sha256-2j+5BYftCiy+g33UbsgCMWBRggGBJBx5VoEdSqQ/mV0=";
   };
 
-  nativeBuildInputs = [ setuptools ];
+  build-system = [ setuptools ];
 
-  propagatedBuildInputs = [
-    numpy
-    netcdf4
+  dependencies = [
     h5py
+    netcdf4
+    numpy
     rich
   ];
 
+  pythonImportsCheck = [ "meshio" ];
+
   nativeCheckInputs = [
     exdown
     pytestCheckHook
   ];
 
-  pythonImportsCheck = [ "meshio" ];
+  disabledTests = [
+    # RuntimeError: Not a valid Netgen mesh
+    "test_advanced"
 
-  meta = with lib; {
-    homepage = "https://github.com/nschloe/meshio";
+    # ValueError: cannot reshape array of size 12 into shape (1936876918,3)
+    "test_area"
+
+    # Error: Couldn't read file /build/source/tests/meshes/vtk/06_color_scalars.vtk as vtk
+    # Illegal VTK header
+    "test_color_scalars"
+    "test_pathlike"
+
+    # AssertionError
+    "test_comma_space"
+
+    # ValueError: could not convert string to float: 'np.float64(63.69616873214543)'
+    "test_dolfin"
+
+    # ValueError: cannot reshape array of size 1 into shape
+    "test_gmsh22"
+    "test_gmsh40"
+    "test_gmsh41"
+
+    # meshio._exceptions.ReadError: Header of ugrid file is ill-formed
+    "test_io"
+    "test_volume"
+
+    # ValueError: invalid literal for int() with base 10: 'version'
+    "test_point_cell_refs"
+
+    # Error: Couldn't read file /build/source/tests/meshes/vtu/01_raw_binary_int64.vtu as vtu
+    "test_read_from_file"
+
+    # ValueError: cannot reshape array of size 12 into shape (1936876918,3)
+    # -- or
+    # Error: Couldn't read file /build/source/tests/meshes/medit/hch_strct.4.meshb as medit
+    # Invalid code
+    # -- or
+    # AssertionError
+    # -- or
+    # Error: Couldn't read file /build/source/tests/meshes/msh/insulated-2.2.msh as either of ansys, gmsh
+    "test_reference_file"
+
+    # UnboundLocalError: cannot access local variable 'points' where it is not associated with a value
+    # -- or
+    # Error: Couldn't read file /build/source/tests/meshes/vtk/00_image.vtk as vtk
+    # Illegal VTK header
+    "test_structured"
+
+    # Error: Couldn't read file /build/source/tests/meshes/ply/bun_zipper_res4.ply as ply
+    # Expected ply
+    "test_read_pathlike"
+    "test_read_str"
+    "test_write_pathlike"
+    "test_write_str"
+  ];
+
+  meta = {
     description = "I/O for mesh files";
+    homepage = "https://github.com/nschloe/meshio";
+    changelog = "https://github.com/nschloe/meshio/blob/v${version}/CHANGELOG.md";
     mainProgram = "meshio";
-    license = licenses.mit;
-    maintainers = with maintainers; [ wd15 ];
+    license = lib.licenses.mit;
+    maintainers = with lib.maintainers; [ wd15 ];
   };
 }

pkgs/development/python-modules/sfepy/default.nix

@@ -1,41 +1,73 @@
 {
   lib,
   buildPythonPackage,
-  pythonOlder,
   fetchFromGitHub,
+  writableTmpDirAsHomeHook,
+
+  # build-system
   cmake,
   cython_0,
   ninja,
   oldest-supported-numpy,
   setuptools,
   scikit-build,
-  numpy,
-  scipy,
+
+  # dependencies
   matplotlib,
+  meshio,
+  numpy,
   pyparsing,
-  tables,
   python,
-  sympy,
-  meshio,
-  openssh,
   pyvista,
+  scipy,
+  sympy,
+  tables,
+
+  # tests
   pytest,
+  openssh,
 }:
 
 buildPythonPackage rec {
   pname = "sfepy";
-  version = "2024.1";
+  version = "2024.4";
   pyproject = true;
 
-  disabled = pythonOlder "3.8";
-
   src = fetchFromGitHub {
     owner = "sfepy";
     repo = "sfepy";
-    rev = "release_${version}";
-    hash = "sha256-r2Qx9uJmVS4ugJxrIxg2UscnYu1Qr4hEkcz66NyWGmA=";
+    tag = "release_${version}";
+    hash = "sha256-3XQqPoAM1Qw/fZ649Xk+ceaeBkZ3ypI1FSRxtYbIrxw=";
   };
 
+  postPatch = ''
+    substituteInPlace pyproject.toml \
+      --replace-fail "ninja<=1.11.1.1" "ninja" \
+      --replace-fail "numpy<2" "numpy"
+
+    substituteInPlace sfepy/solvers/optimize.py \
+      --replace-fail "nm.Inf" "nm.inf"
+
+    substituteInPlace sfepy/examples/quantum/quantum_common.py \
+      --replace-fail "NaN" "nan"
+
+    # slow tests
+    rm sfepy/tests/test_elasticity_small_strain.py
+    rm sfepy/tests/test_hyperelastic_tlul.py
+    rm sfepy/tests/test_io.py
+    rm sfepy/tests/test_linear_solvers.py
+    rm sfepy/tests/test_poly_spaces.py
+    rm sfepy/tests/test_quadratures.py
+    rm sfepy/tests/test_refine_hanging.py
+    rm sfepy/tests/test_term_call_modes.py
+    #  ValueError: invalid literal for int() with base 10: 'np.int64(3)'
+    rm sfepy/tests/test_meshio.py
+  '';
+
+  nativeBuildInputs = [
+    writableTmpDirAsHomeHook
+  ];
+
   build-system = [
     cmake
     cython_0
@@ -48,37 +80,35 @@ buildPythonPackage rec {
   dontUseCmakeConfigure = true;
 
   dependencies = [
-    numpy
-    scipy
     matplotlib
-    pyparsing
-    tables
-    sympy
     meshio
+    numpy
+    pyparsing
     pyvista
+    scipy
+    sympy
+    tables
   ];
 
-  postPatch = ''
-    # slow tests
-    rm sfepy/tests/test_io.py
-    rm sfepy/tests/test_elasticity_small_strain.py
-    rm sfepy/tests/test_term_call_modes.py
-    rm sfepy/tests/test_refine_hanging.py
-    rm sfepy/tests/test_hyperelastic_tlul.py
-    rm sfepy/tests/test_poly_spaces.py
-    rm sfepy/tests/test_linear_solvers.py
-    rm sfepy/tests/test_quadratures.py
-  '';
+  pythonRelaxDeps = [
+    "numpy"
+  ];
 
-  nativeCheckInputs = [ pytest ];
+  nativeCheckInputs = [
+    pytest
+    writableTmpDirAsHomeHook
+  ];
 
   checkPhase = ''
-    export OMPI_MCA_plm_rsh_agent=${openssh}/bin/ssh
-    export HOME=$TMPDIR
+    runHook preCheck
+
+    export OMPI_MCA_plm_rsh_agent=${lib.getExe openssh}
     mv sfepy sfepy.hidden
     mkdir -p $HOME/.matplotlib
     echo "backend: ps" > $HOME/.matplotlib/matplotlibrc
     ${python.interpreter} -c "import sfepy; sfepy.test()"
+
+    runHook postCheck
   '';
 
   meta = {