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Add notebook testing + fixes accordingly (#67)
* Testing: Change notebook testing to pytest-notebook (current tests were skipped). Add try-except ImportError for pyspark code. Bugfix in hist.py that broke the advanced tutorial. Enhancement: Add %%capture to pip install inside of notebooks. Enhancement: Make package install in notebooks work with paths with spaces. * Update requirements-test.txt * Update test_notebooks.py * Pickle doesn't work with tests (not really a popmon-specific feature anyway). Changed the notebook to fix the issue, left the code for reference. * Increase timeout
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,7 +1,8 @@ | ||
| flake8>=3.7.8 | ||
| pytest>=4.0.2 | ||
| nbconvert>=5.3.1 | ||
| pytest-notebook>=0.6.1 | ||
| nbconvert~=5.6.1 | ||
| jupyter_client>=5.2.3 | ||
| ipykernel>=5.1.3 | ||
| black>=19.10b0 | ||
| isort>=5.0.7 | ||
| isort>=5.0.7 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,55 +1,30 @@ | ||
| import os | ||
| import unittest | ||
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| import nbformat | ||
| import pytest | ||
| from jupyter_client.kernelspec import KernelSpecManager, NoSuchKernel | ||
| from nbconvert.preprocessors import ExecutePreprocessor | ||
| from nbconvert.preprocessors.execute import CellExecutionError | ||
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| from popmon import resources | ||
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| kernel_name = "python3" | ||
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| # check if jupyter python3 kernel can be opened. if kernel not found, skip unit tests below. | ||
| try: | ||
| km = KernelSpecManager() | ||
| km.get_kernel_spec(kernel_name) | ||
| kernel_found = True | ||
| except NoSuchKernel: | ||
| kernel_found = False | ||
| from pytest_notebook.nb_regression import NBRegressionFixture | ||
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| from popmon.resources import notebook | ||
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| class NotebookTest(unittest.TestCase): | ||
| """Unit test notebook""" | ||
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| def run_notebook(self, notebook): | ||
| """ Test notebook """ | ||
| @pytest.fixture(scope="module") | ||
| def nb_tester(): | ||
| """Test notebooks using pytest-notebook""" | ||
| nb_regression = NBRegressionFixture( | ||
| diff_ignore=( | ||
| "/metadata/language_info", | ||
| "/cells/*/execution_count", | ||
| "/cells/*/outputs/*", | ||
| ), | ||
| exec_timeout=1800, | ||
| ) | ||
| return nb_regression | ||
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| # load notebook | ||
| with open(notebook) as f: | ||
| nb = nbformat.read(f, as_version=4) | ||
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| # execute notebook | ||
| ep = ExecutePreprocessor(timeout=600, kernel_name=kernel_name) | ||
| try: | ||
| ep.preprocess(nb, {}) | ||
| status = True | ||
| except CellExecutionError: | ||
| # store if failed | ||
| status = False | ||
| executed_notebook = os.getcwd() + "/" + notebook.split("/")[-1] | ||
| with open(executed_notebook, mode="wt") as f: | ||
| nbformat.write(nb, f) | ||
| def test_notebook_basic(nb_tester): | ||
| nb_tester.check(notebook("popmon_tutorial_basic.ipynb")) | ||
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| # check status | ||
| self.assertTrue(status, "Notebook execution failed (%s)" % notebook) | ||
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| def test_notebook_advanced(nb_tester): | ||
| nb_tester.check(notebook("popmon_tutorial_advanced.ipynb")) | ||
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| @pytest.mark.filterwarnings("ignore:Session._key_changed is deprecated") | ||
| @pytest.mark.skipif(not kernel_found, reason=f"{kernel_name} kernel not found.") | ||
| class PipelineNotebookTest(NotebookTest): | ||
| """Unit test notebook""" | ||
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| def test_basic_tutorial(self): | ||
| self.run_notebook(resources.notebook("popmon_tutorial_basic.ipynb")) | ||
| def test_notebook_incremental_data(nb_tester): | ||
| nb_tester.check(notebook("popmon_tutorial_incremental_data.ipynb")) |