Execution and Coverage Reporting#
See also
This notebook was rendered with myst-nb: tutorial_coverage.ipynb
The core component of the notebook execution API is the CoverageNotebookClient class,
which is a subclass of nbclient.client.NotebookClient,
that can additionally create code coverage analytics.
This class is called by execute_notebook(),
which returns an ExecuteResult object.
from pytest_notebook.execution import execute_notebook
from pytest_notebook.notebook import create_notebook, create_cell, dump_notebook
notebook = create_notebook(
metadata={
"kernelspec": {
"name": "python3",
"display_name": "Python 3",
}
},
cells=[
create_cell("""
from pytest_notebook import __version__
from pytest_notebook.notebook import create_notebook
print(__version__)
"""
)]
)
result = execute_notebook(notebook, with_coverage=True)
result.notebook
{'nbformat': 4,
'nbformat_minor': 5,
'metadata': {'kernelspec': {'name': 'python3', 'display_name': 'Python 3'},
'language_info': {'name': 'python',
'version': '3.9.18',
'mimetype': 'text/x-python',
'codemirror_mode': {'name': 'ipython', 'version': 3},
'pygments_lexer': 'ipython3',
'nbconvert_exporter': 'python',
'file_extension': '.py'}},
'cells': [{'id': '45ab3691',
'cell_type': 'code',
'metadata': {},
'execution_count': 1,
'source': '\nfrom pytest_notebook import __version__\nfrom pytest_notebook.notebook import create_notebook\nprint(__version__)\n',
'outputs': [{'output_type': 'stream',
'name': 'stdout',
'text': '0.10.0\n'}]}]}
result.coverage_data()
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The coverage can be limited to particular files or modules, by setting cov_source.
result = execute_notebook(
notebook, with_coverage=True, cov_source=['pytest_notebook.notebook'])
result.coverage_dict
{'/home/docs/checkouts/readthedocs.org/user_builds/pytest-notebook/envs/stable/lib/python3.9/site-packages/pytest_notebook/notebook.py': [128,
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Integration with pytest-cov#
If the pytest-cov plugin is installed,
the NBRegressionFixture will be initialised
with the settings and coverage.Coverage object, that
pytest-cov has created.
If the --nb-coverage flag is set, then nb_regression will run coverage introspection,
and merge the data back into the main Coverage object.
%load_ext pytest_notebook.ipy_magic
%%pytest --disable-warnings --color=yes --cov=pytest_notebook --nb-coverage --log-cli-level=info
import logging
try:
# Python <= 3.8
from importlib_resources import files
except ImportError:
from importlib.resources import files
from pytest_notebook import example_nbs
def test_notebook(nb_regression):
logging.getLogger(__name__).info(nb_regression)
with files(example_nbs).joinpath("coverage.ipynb") as path:
nb_regression.check(str(path))
============================= test session starts ==============================
platform linux -- Python 3.9.18, pytest-7.4.3, pluggy-1.3.0
rootdir: /tmp/tmpwvux8a11
plugins: pytest_notebook-0.10.0, anyio-4.1.0, cov-4.1.0
collected 1 item
test_ipycell.py::test_notebook
-------------------------------- live log call ---------------------------------
INFO test_ipycell:test_ipycell.py:11 NBRegressionFixture(exec_notebook=True, exec_cwd=None, exec_allow_errors=False, exec_timeout=120, coverage=True, cov_config='.coveragerc', cov_source=('pytest_notebook',), cov_merge=<coverage.control.Coverage object at 0x7f2ff9ad3160>, post_processors=('coalesce_streams',), process_resources={}, diff_replace=(), diff_ignore=('/cells/*/outputs/*/traceback',), diff_use_color=True, diff_color_words=False, force_regen=False)
INFO pytest_notebook.execution:execution.py:97 Executing notebook with kernel:
FAILED [100%]Coverage.py warning: Module pytest_notebook was previously imported, but not measured (module-not-measured)
=================================== FAILURES ===================================
________________________________ test_notebook _________________________________
nb_regression = NBRegressionFixture(exec_notebook=True, exec_cwd='/home/docs/checkouts/readthedocs.org/user_builds/pytest-notebook/env...lace=(), diff_ignore=('/cells/*/outputs/*/traceback',), diff_use_color=True, diff_color_words=False, force_regen=False)
def test_notebook(nb_regression):
logging.getLogger(__name__).info(nb_regression)
with files(example_nbs).joinpath("coverage.ipynb") as path:
> nb_regression.check(str(path))
E pytest_notebook.nb_regression.NBRegressionError:
E --- expected
E +++ obtained
E ## modified /cells/0/outputs/0/text:
E @@ -1 +1 @@
E -0.6.0
E +0.10.0
E
E ## modified /metadata/language_info/version:
E - 3.6.7
E + 3.9.18
E
E
test_ipycell.py:13: NBRegressionError
------------------------------ Captured log call -------------------------------
INFO test_ipycell:test_ipycell.py:11 NBRegressionFixture(exec_notebook=True, exec_cwd=None, exec_allow_errors=False, exec_timeout=120, coverage=True, cov_config='.coveragerc', cov_source=('pytest_notebook',), cov_merge=<coverage.control.Coverage object at 0x7f2ff9ad3160>, post_processors=('coalesce_streams',), process_resources={}, diff_replace=(), diff_ignore=('/cells/*/outputs/*/traceback',), diff_use_color=True, diff_color_words=False, force_regen=False)
INFO pytest_notebook.execution:execution.py:97 Executing notebook with kernel:
---------- coverage: platform linux, python 3.9.18-final-0 -----------
Name Stmts Miss Cover
----------------------------------------------------------------------------------------------------------------------------------------------------------------------
/home/docs/checkouts/readthedocs.org/user_builds/pytest-notebook/envs/stable/lib/python3.9/site-packages/pytest_notebook/__init__.py 1 0 100%
/home/docs/checkouts/readthedocs.org/user_builds/pytest-notebook/envs/stable/lib/python3.9/site-packages/pytest_notebook/diffing.py 87 13 85%
/home/docs/checkouts/readthedocs.org/user_builds/pytest-notebook/envs/stable/lib/python3.9/site-packages/pytest_notebook/example_nbs/__init__.py 0 0 100%
/home/docs/checkouts/readthedocs.org/user_builds/pytest-notebook/envs/stable/lib/python3.9/site-packages/pytest_notebook/execution.py 131 96 27%
/home/docs/checkouts/readthedocs.org/user_builds/pytest-notebook/envs/stable/lib/python3.9/site-packages/pytest_notebook/ipy_magic.py 80 80 0%
/home/docs/checkouts/readthedocs.org/user_builds/pytest-notebook/envs/stable/lib/python3.9/site-packages/pytest_notebook/nb_regression.py 189 109 42%
/home/docs/checkouts/readthedocs.org/user_builds/pytest-notebook/envs/stable/lib/python3.9/site-packages/pytest_notebook/notebook.py 147 77 48%
/home/docs/checkouts/readthedocs.org/user_builds/pytest-notebook/envs/stable/lib/python3.9/site-packages/pytest_notebook/plugin.py 126 90 29%
/home/docs/checkouts/readthedocs.org/user_builds/pytest-notebook/envs/stable/lib/python3.9/site-packages/pytest_notebook/post_processors.py 98 74 24%
/home/docs/checkouts/readthedocs.org/user_builds/pytest-notebook/envs/stable/lib/python3.9/site-packages/pytest_notebook/resources/__init__.py 0 0 100%
/home/docs/checkouts/readthedocs.org/user_builds/pytest-notebook/envs/stable/lib/python3.9/site-packages/pytest_notebook/utils.py 58 23 60%
----------------------------------------------------------------------------------------------------------------------------------------------------------------------
TOTAL 917 562 39%
=========================== short test summary info ============================
FAILED test_ipycell.py::test_notebook - pytest_notebook.nb_regression.NBRegressionError:
============================== 1 failed in 2.66s ===============================
This is also the case, when using the pytest file collection approach.
%%pytest --disable-warnings --color=yes --cov=pytest_notebook --log-cli-level=info
---
[pytest]
nb_coverage = True
nb_test_files = True
nb_diff_ignore =
/metadata/language_info
---
***
(dump_notebook(notebook), "test_notebook1.ipynb")
***
============================= test session starts ==============================
platform linux -- Python 3.9.18, pytest-7.4.3, pluggy-1.3.0
rootdir: /tmp/tmpxj_fub51
configfile: pytest.ini
plugins: pytest_notebook-0.10.0, anyio-4.1.0, cov-4.1.0
collected 1 item
test_notebook1.ipynb::nbregression(test_notebook1)
-------------------------------- live log call ---------------------------------
INFO pytest_notebook.execution:execution.py:97 Executing notebook with kernel: python3
INFO pytest_notebook.execution:execution.py:126 Recording coverage for notebook
INFO pytest_notebook.execution:execution.py:144 Recording coverage for notebook
INFO pytest_notebook.nb_regression:nb_regression.py:303 Merging coverage.
FAILED [100%]Coverage.py warning: Module pytest_notebook was previously imported, but not measured (module-not-measured)
=================================== FAILURES ===================================
____________________ notebook: nbregression(test_notebook1) ____________________
pytest_notebook.nb_regression.NBRegressionError:
--- expected
+++ obtained
## replaced (type changed from NoneType to int) /cells/0/execution_count:
- None
+ 1
## inserted before /cells/0/outputs/0:
+ output:
+ output_type: stream
+ name: stdout
+ text:
+ 0.10.0
----------------------------- Captured stderr call -----------------------------
Coverage.py warning: Module pytest_notebook was previously imported, but not measured (module-not-measured)
------------------------------ Captured log call -------------------------------
INFO pytest_notebook.execution:execution.py:97 Executing notebook with kernel: python3
INFO pytest_notebook.execution:execution.py:126 Recording coverage for notebook
INFO pytest_notebook.execution:execution.py:144 Recording coverage for notebook
INFO pytest_notebook.nb_regression:nb_regression.py:303 Merging coverage.
---------- coverage: platform linux, python 3.9.18-final-0 -----------
Name Stmts Miss Cover
----------------------------------------------------------------------------------------------------------------------------------------------------------------------
/home/docs/checkouts/readthedocs.org/user_builds/pytest-notebook/envs/stable/lib/python3.9/site-packages/pytest_notebook/__init__.py 1 0 100%
/home/docs/checkouts/readthedocs.org/user_builds/pytest-notebook/envs/stable/lib/python3.9/site-packages/pytest_notebook/diffing.py 87 10 89%
/home/docs/checkouts/readthedocs.org/user_builds/pytest-notebook/envs/stable/lib/python3.9/site-packages/pytest_notebook/example_nbs/__init__.py 0 0 100%
/home/docs/checkouts/readthedocs.org/user_builds/pytest-notebook/envs/stable/lib/python3.9/site-packages/pytest_notebook/execution.py 131 57 56%
/home/docs/checkouts/readthedocs.org/user_builds/pytest-notebook/envs/stable/lib/python3.9/site-packages/pytest_notebook/ipy_magic.py 80 80 0%
/home/docs/checkouts/readthedocs.org/user_builds/pytest-notebook/envs/stable/lib/python3.9/site-packages/pytest_notebook/nb_regression.py 189 102 46%
/home/docs/checkouts/readthedocs.org/user_builds/pytest-notebook/envs/stable/lib/python3.9/site-packages/pytest_notebook/notebook.py 147 74 50%
/home/docs/checkouts/readthedocs.org/user_builds/pytest-notebook/envs/stable/lib/python3.9/site-packages/pytest_notebook/plugin.py 126 77 39%
/home/docs/checkouts/readthedocs.org/user_builds/pytest-notebook/envs/stable/lib/python3.9/site-packages/pytest_notebook/post_processors.py 98 74 24%
/home/docs/checkouts/readthedocs.org/user_builds/pytest-notebook/envs/stable/lib/python3.9/site-packages/pytest_notebook/resources/__init__.py 0 0 100%
/home/docs/checkouts/readthedocs.org/user_builds/pytest-notebook/envs/stable/lib/python3.9/site-packages/pytest_notebook/utils.py 58 23 60%
----------------------------------------------------------------------------------------------------------------------------------------------------------------------
TOTAL 917 497 46%
=========================== short test summary info ============================
FAILED test_notebook1.ipynb::nbregression(test_notebook1)
========================= 1 failed, 1 warning in 2.67s =========================