Add first version of pytest infrastructure

Includes first fixtures and tagging approach
Also update first pytest test (cosserat curve) to use new approaches

Author: davidrudlstorfer

.github/actions/run_tests/action.yml

@@ -49,5 +49,4 @@ runs:
         coverage html
         coverage report
         coverage-badge -o htmlcov/coverage.svg
-        coverage run --rcfile=${{ inputs.coverage_config }} -m pytest pytest_testing_cosserat_curve.py
-        coverage report
+        pytest

pyproject.toml

@@ -39,6 +39,7 @@ dependencies = [
   "numpy-quaternion",
   "pre-commit",
   "pytest",
+  "pytest-cov",
   "pyvista",
   "pyvista_utils@git+https://github.com/isteinbrecher/pyvista_utils.git@main",
   "scipy",
@@ -55,3 +56,11 @@ CI-CD = [
   "cubitpy@git+https://github.com/imcs-compsim/cubitpy.git@main",
   "setuptools" # Needed for coverage-badge
 ]
+
+[tool.pytest.ini_options]
+addopts = "-p pytest_cov --cov-report=term --cov-report=html --cov-fail-under=30 --cov=meshpy/ --cov=tutorial/ --cov-append"
+markers = [
+  "fourc_arborx: tests in combination with 4C and ArborX",
+  "cubitpy: tests in combination with CubitPy",
+  "performance: performance tests of MeshPy"
+]

tests/conftest.py

@@ -0,0 +1,137 @@
+# -*- coding: utf-8 -*-
+# -----------------------------------------------------------------------------
+# MeshPy: A beam finite element input generator
+#
+# MIT License
+#
+# Copyright (c) 2018-2024
+#     Ivo Steinbrecher
+#     Institute for Mathematics and Computer-Based Simulation
+#     Universitaet der Bundeswehr Muenchen
+#     https://www.unibw.de/imcs-en
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+# -----------------------------------------------------------------------------
+"""Testing framework infrastructure."""
+
+import os
+from pathlib import Path
+
+import pytest
+from _pytest.config import Config
+from _pytest.config.argparsing import Parser
+
+
+def pytest_addoption(parser: Parser) -> None:
+    """Add custom command line options to pytest.
+
+    Args:
+        parser: Pytest parser
+    """
+
+    parser.addoption(
+        "--4C_ArborX",
+        action="store_true",
+        default=False,
+        help="Execute 4C and ArborX based tests.",
+    )
+
+    parser.addoption(
+        "--CubitPy",
+        action="store_true",
+        default=False,
+        help="Execute CubitPy based tests.",
+    )
+
+    parser.addoption(
+        "--performance",
+        action="store_true",
+        default=False,
+        help="Execute performance tests.",
+    )
+
+
+def pytest_collection_modifyitems(config: Config, items: list) -> None:
+    """Filter tests based on their markers and provided command line options.
+
+    Currently configured options:
+        `pytest`: execute tests with no markers
+        `pytest --4C_ArborX`: execute tests with the `fourc_arborx` marker
+        `pytest --CubitPy`: execute tests with the `cubitpy` marker
+        `pytest --performance`: execute tests with the `performance` marker
+
+    Args:
+        config: Pytest config
+        items: Pytest list of tests
+    """
+
+    selected_tests = []
+
+    # loop over all collected tests
+    for item in items:
+        # Get all set markers for current test (e.g. `fourc_arborx`, `cubitpy`, `performance`)
+        markers = [marker.name for marker in item.iter_markers()]
+
+        if config.getoption("--4C_ArborX") and "fourc_arborx" in markers:
+            selected_tests.append(item)
+
+        if config.getoption("--CubitPy") and "cubitpy" in markers:
+            selected_tests.append(item)
+
+        if config.getoption("--performance") and "performance" in markers:
+            selected_tests.append(item)
+
+        if not markers:
+            selected_tests.append(item)
+
+    deselected_tests = list(set(items) - set(selected_tests))
+
+    items[:] = selected_tests
+    config.hook.pytest_deselected(items=deselected_tests)
+
+
+@pytest.fixture(scope="session")
+def reference_file_directory() -> Path:
+    """Provide the path to the reference file directory.
+
+    Returns:
+        Path: A Path object representing the full path to the reference file directory.
+    """
+
+    testing_path = os.path.abspath(os.path.dirname(__file__))
+    return Path(testing_path) / "reference-files"
+
+
+@pytest.fixture(scope="function")
+def current_test_name(request: pytest.FixtureRequest) -> str:
+    """Return the name of the current pytest test.
+
+    Args:
+        request: The pytest request object.
+
+    Returns:
+        str: The name of the current pytest test.
+    """
+
+    return request.node.name
+
+
+@pytest.fixture
+def compare_result_file(reference, result, rtol, atol):
+    raise NotImplementedError

tests/pytest_testing_cosserat_curve.py renamed to tests/test_cosserat_curve.py

@@ -34,7 +34,6 @@
 import os
 
 import numpy as np
-import pytest
 import pyvista as pv
 import quaternion
 
@@ -50,30 +49,27 @@
 from .utils import (
     compare_test_result_pytest,
     compare_vtk_pytest,
-    get_pytest_test_name,
-    testing_input,
-    testing_temp,
 )
 
 
-def load_cosserat_curve_from_file():
+def load_cosserat_curve_from_file(reference_file_directory):
     """Load the centerline coordinates from the reference files and create the
     Cosserat curve."""
     coordinates = np.loadtxt(
-        os.path.join(testing_input, "test_cosserat_curve_centerline.txt"),
+        os.path.join(reference_file_directory, "test_cosserat_curve_centerline.txt"),
         comments="#",
         delimiter=",",
         unpack=False,
     )
     return CosseratCurve(coordinates)
 
 
-def create_beam_solid_input_file():
+def create_beam_solid_input_file(reference_file_directory):
     """Create a beam and solid input file for testing purposes."""
 
     mpy.import_mesh_full = True
     mesh = InputFile(
-        dat_file=os.path.join(testing_input, "test_cosserat_curve_mesh.dat")
+        dat_file=os.path.join(reference_file_directory, "test_cosserat_curve_mesh.dat")
     )
     create_beam_mesh_helix(
         mesh,
@@ -89,10 +85,12 @@ def create_beam_solid_input_file():
     return mesh
 
 
-def test_cosserat_curve_translate_and_rotate():
+def test_cosserat_curve_translate_and_rotate(
+    reference_file_directory, current_test_name
+):
     """Test that a curve can be loaded, rotated and transformed."""
 
-    curve = load_cosserat_curve_from_file()
+    curve = load_cosserat_curve_from_file(reference_file_directory)
 
     # Translate the curve so that the start is at the origin
     curve.translate(-curve.centerline_interpolation(5.0))
@@ -113,7 +111,7 @@ def test_cosserat_curve_translate_and_rotate():
     def load_compare(name):
         """Load the compare files and return a numpy array."""
         return np.loadtxt(
-            os.path.join(testing_input, f"{get_pytest_test_name()}_{name}.txt")
+            os.path.join(reference_file_directory, f"{current_test_name}_{name}.txt")
         )
 
     assert np.allclose(sol_half_pos, load_compare("pos_half_ref"), rtol=1e-14)
@@ -127,25 +125,27 @@ def load_compare(name):
     )
 
 
-def test_cosserat_curve_vtk_representation():
+def test_cosserat_curve_vtk_representation(
+    tmp_path, reference_file_directory, current_test_name
+):
     """Test the vtk representation of the Cosserat curve."""
 
-    result_name = os.path.join(testing_temp, get_pytest_test_name() + ".vtu")
-    curve = load_cosserat_curve_from_file()
+    result_name = os.path.join(tmp_path, current_test_name + ".vtu")
+    curve = load_cosserat_curve_from_file(reference_file_directory)
     pv.UnstructuredGrid(curve.get_pyvista_polyline()).save(result_name)
     compare_vtk_pytest(
-        os.path.join(testing_input, get_pytest_test_name() + ".vtu"),
+        os.path.join(reference_file_directory, current_test_name + ".vtu"),
         result_name,
         rtol=1e-8,
         atol=1e-8,
     )
 
 
-def test_cosserat_curve_project_point():
+def test_cosserat_curve_project_point(reference_file_directory):
     """Test that the project point function works as expected."""
 
     # Load the curve
-    curve = load_cosserat_curve_from_file()
+    curve = load_cosserat_curve_from_file(reference_file_directory)
 
     # Translate the curve so that the start is at the origin
     curve.translate(-curve.centerline_interpolation(0.0))
@@ -158,16 +158,16 @@ def test_cosserat_curve_project_point():
     assert np.allclose(t_ref, curve.project_point([-5, 1, 1], t0=4.0), rtol=rtol)
 
 
-def test_cosserat_mesh_transformation():
+def test_cosserat_mesh_transformation(reference_file_directory, current_test_name):
     """Test that the get_mesh_transformation function works as expected."""
 
-    curve = load_cosserat_curve_from_file()
+    curve = load_cosserat_curve_from_file(reference_file_directory)
     pos, rot = curve.get_centerline_position_and_rotation(0)
     rot = Rotation.from_quaternion(quaternion.as_float_array(rot))
     curve.translate(-pos)
     curve.translate([1, 2, 3])
 
-    mesh = create_beam_solid_input_file()
+    mesh = create_beam_solid_input_file(reference_file_directory)
     pos, rot = get_mesh_transformation(
         curve,
         mesh.nodes,
@@ -184,7 +184,8 @@ def test_cosserat_mesh_transformation():
 
     def load_result(name):
         with open(
-            os.path.join(testing_input, f"{get_pytest_test_name()}_{name}.json"), "r"
+            os.path.join(reference_file_directory, f"{current_test_name}_{name}.json"),
+            "r",
         ) as f:
             return np.array(json.load(f))
 
@@ -198,19 +199,19 @@ def load_result(name):
     assert np.allclose(rot_ref, rot_np, rtol=1e-14)
 
 
-def test_cosserat_curve_mesh_warp():
+def test_cosserat_curve_mesh_warp(reference_file_directory):
     """Warp a balloon along a centerline."""
 
     # Load the curve
-    curve = load_cosserat_curve_from_file()
+    curve = load_cosserat_curve_from_file(reference_file_directory)
     pos, rot = curve.get_centerline_position_and_rotation(0)
     rot = Rotation.from_quaternion(quaternion.as_float_array(rot))
     curve.translate(-pos)
     curve.translate([1, 2, 3])
 
     # Warp the mesh. The reference coordinate system is rotated such that z axis is the longitudinal direction,
     # and x and y are the first and second cross-section basis vectors respectively.
-    mesh = create_beam_solid_input_file()
+    mesh = create_beam_solid_input_file(reference_file_directory)
     warp_mesh_along_curve(
         mesh,
         curve,
@@ -226,18 +227,20 @@ def test_cosserat_curve_mesh_warp():
     )
 
 
-def test_cosserat_curve_mesh_warp_transform_boundary_conditions():
+def test_cosserat_curve_mesh_warp_transform_boundary_conditions(
+    reference_file_directory,
+):
     """Test the transform boundary creation function."""
 
     # Load the curve
-    curve = load_cosserat_curve_from_file()
+    curve = load_cosserat_curve_from_file(reference_file_directory)
     pos, rot = curve.get_centerline_position_and_rotation(0)
     rot = Rotation.from_quaternion(quaternion.as_float_array(rot))
     curve.translate(-pos)
     curve.translate([1, 2, 3])
 
     # Load the mesh
-    mesh = create_beam_solid_input_file()
+    mesh = create_beam_solid_input_file(reference_file_directory)
 
     # Apply the transform boundary conditions
     create_transform_boundary_conditions(