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import sys
import runpy
import pytest
import unittest
import importlib.util
import importlib.machinery
import matplotlib.pyplot as plt
from pathlib import Path
from shutil import copyfile
TEST_IMAGE = "lenna.png"
@pytest.mark.skip(reason="docs tests often leads to errors during ci")
class TestDocumentationExamples(unittest.TestCase):
examples_path = Path("docs/source/examples")
examples_path = Path("docs/source/examples")
def run_script(self, script_name):
file_path = Path.joinpath(self.examples_path, script_name)
runpy.run_path(path_name=str(file_path), run_name="__main__")
def handle_lif(self):
lif_path = Path.joinpath(self.examples_path, "lif.py")
spec = importlib.util.spec_from_file_location("lif", lif_path)
module = importlib.util.module_from_spec(spec)
spec.loader.exec_module(module)
sys.modules["lif"] = module
def handle_image(self):
image_path = Path.joinpath(self.examples_path, TEST_IMAGE)
copyfile(str(image_path), str(Path.joinpath(Path(Path.cwd()), TEST_IMAGE)))
def setUp(self):
curr_path = Path.cwd()
if curr_path.stem == "nixpy":
self.examples_path = Path.joinpath(Path(curr_path),
"docs", "source", "examples")
elif curr_path.stem == "nixio":
self.examples_path = Path.joinpath(Path(curr_path).parent,
"docs", "source", "examples")
elif curr_path.stem == "test":
self.examples_path = Path.joinpath(Path(curr_path).parent.parent,
"docs", "source", "examples")
util_path = Path.joinpath(self.examples_path, "docutils.py")
spec = importlib.util.spec_from_file_location("docutils", util_path)
module = importlib.util.module_from_spec(spec)
spec.loader.exec_module(module)
sys.modules["docutils"] = module
# Render matplotlib plots non-blocking
plt.ion()
def tearDown(self):
plt.close("all")
plt.ioff()
if Path.exists(Path(TEST_IMAGE)):
Path.unlink(Path(TEST_IMAGE), True)
def test_annotations(self):
self.run_script("annotations.py")
# cleanup
Path.unlink(Path("annotations.nix"), True)
def test_category_data(self):
self.run_script("categoryData.py")
# cleanup
Path.unlink(Path("categoryData.nix"), True)
def test_continuous_recording(self):
self.run_script("continuousRecording.py")
# cleanup
Path.unlink(Path("continuous_recording.nix"), True)
def test_file_create(self):
self.run_script("fileCreate.py")
# cleanup
Path.unlink(Path("file_create_example.nix"), True)
def test_image_data(self):
# test will open image with an external program; does not work on windows
if sys.platform == 'linux':
# Requires PIL package and the "Lenna" image.
self.handle_image()
self.run_script("imageData.py")
# cleanup
Path.unlink(Path("image_example.nix"), True)
def test_image_with_metadata(self):
# Requires PIL package and the "Lenna" image.
self.handle_image()
self.run_script("imageWithMetadata.py")
# cleanup
Path.unlink(Path("image_with_source_example.h5"), True)
Path.unlink(Path("image_with_metadata.png"), True)
def test_irregularly_sampled_data(self):
self.run_script("irregularlySampledData.py")
# cleanup
Path.unlink(Path("irregular_data_example.nix"), True)
def test_lif(self):
self.run_script("lif.py")
def test_multiple_points(self):
self.run_script("multiple_points.py")
# cleanup
Path.unlink(Path("multiple_points.nix"), True)
def test_multiple_regions(self):
self.run_script("multiple_regions.py")
# cleanup
Path.unlink(Path("multiple_regions.nix"), True)
def test_multiple_rois(self):
# Requires PIL package and the "Lenna" image.
self.handle_image()
self.run_script("multipleROIs.py")
# cleanup
Path.unlink(Path("multiple_roi.nix"), True)
def test_range_dimension_link(self):
self.run_script("rangeDimensionLink.py")
# cleanup
Path.unlink(Path("range_link.nix"), True)
def test_regularly_sampled_data(self):
self.run_script("regularlySampledData.py")
# cleanup
Path.unlink(Path("regular_data_example.nix"), True)
def test_single_roi(self):
# test will open image with an external program; does not work on windows
if sys.platform == 'linux':
# Requires PIL package and the "Lenna" image.
self.handle_image()
self.run_script("singleROI.py")
# cleanup
Path.unlink(Path("single_roi.nix"), True)
def test_sources(self):
self.run_script("sources.py")
# cleanup
Path.unlink(Path("sources.nix"), True)
def test_spike_features(self):
# Requires scipy package and "lif.py"
self.handle_lif()
self.run_script("spikeFeatures.py")
# cleanup
Path.unlink(Path("spike_features.h5"), True)
def test_spike_tagging(self):
# Requires "lif.py"
self.handle_lif()
self.run_script("spikeTagging.py")
# cleanup
Path.unlink(Path("spike_tagging.nix"), True)
def test_tabular_data(self):
self.run_script("tabulardata.py")
# cleanup
Path.unlink(Path("dataframe.nix"), True)
def test_tagged_feature(self):
# Requires scipy package and "lif.py"
self.handle_lif()
self.run_script("taggedFeature.py")
# cleanup
Path.unlink(Path("spike_features.nix"), True)
def test_tagging_example(self):
# Requires scipy package
self.run_script("tagging_example.py")
# cleanup
Path.unlink(Path("tagging1.nix"), True)
def test_tagging_nd(self):
# not testing any nix feature
# self.run_script("tagging_nd.py")
pass
def test_untagged_feature(self):
# Requires scipy package and "lif.py"
self.handle_lif()
self.run_script("untaggedFeature.py")
# cleanup
Path.unlink(Path("untagged_feature.h5"), True)
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