Pytest plugin for functional testing of data analysispipelines
pytest-pipeline is a pytest plugin for functional testing of data analysis pipelines. They are usually long-running scripts or executables with multiple input and/or output files + directories. The plugin is meant for end-to-end testing where you test for conditions before the pipeline run and after the pipeline runs (output files, checksums, etc.).
pytest-pipeline is tested against Python versions 2.7, 3.3, 3.4, 3.5, and 3.6.
pip install pytest-pipeline
For our example, we will use a super simple pipeline that writes a file and prints to stdout:
#!/usr/bin/env python from __future__ import print_function if __name__ == "__main__": with open("result.txt", "w") as result: result.write("42\n") print("Result computed")
At this point it’s just a simple script, but it should be enough to illustrate the plugin. Also, if you want to follow along, save the above file as run_pipeline.
With the pipeline above, here’s how your test would look like with pytest_pipeline:
import os import shutil import unittest from pytest_pipeline import PipelineRun, mark, utils # we can subclass `PipelineRun` to add custom methods # using `PipelineRun` as-is is also possible class MyRun(PipelineRun): # before_run-marked functions will be run before the pipeline is executed @mark.before_run def test_prep_executable(self): # copy the executable to the run directory shutil.copy2("/path/to/run_pipeline", "run_pipeline") # ensure that the file is executable assert os.access("run_pipeline", os.X_OK) # a pipeline run is treated as a test fixture run = MyRun.class_fixture(cmd="./run_pipeline", stdout="run.stdout") # the fixture is bound to a unittest.TestCase using the usefixtures mark @pytest.mark.usefixtures("run") # tests per-pipeline run are grouped in one unittest.TestCase instance class TestMyPipeline(unittest.TestCase): def test_result_md5(self): assert utils.file_md5sum("result.txt") == "50a2fabfdd276f573ff97ace8b11c5f4" def test_exit_code(self): # the run fixture is stored as the `run_fixture` attribute assert self.run_fixture.exit_code == 0 # we can check the stdout that we capture as well def test_stdout(self): assert open("run.stdout", "r").read().strip() == "Result computed"
If the test above is saved as test_demo.py, you can then run the test by executing py.test -v test_demo.py. You should see that three tests were executed and all four passed.
What just happened?
You just executed your first pipeline test. The plugin itself gives you:
- Test directory creation (one class gets one directory). By default, testdirectories are all created in the /tmp/pipeline_test directory. You can tweak this location by supplying the --base-pipeline-dir command line flag.
- Automatic execution of the pipeline. No need to import subprocess, just define the command via the PipelineRun object. We optionally captured the standard output to a file called run.stdout. Not a fan of doing disk IO? You can also set stdout and/or stderr to True and have their values captured in-memory.
- Timeout control. For long running pipelines, you can also supply a timeout argument which limits how long the pipeline process can run.
And since this is a py.test plugin, test discovery and execution is done via py.test.
Getting + giving help
Please use the issue tracker to report bugs or feature requests. You can always fork and submit a pull request as well.
Release date: 24 January 2017
- Allow stdout and/or stderr capture in-memory. This can be done by setting their respective keyword arguments to True when creating the run fixture.
Release date: 31 March 2015
- Pipeline runs are now modelled differently. Instead of a class attribute,
they are now created as pytest fixtures. This allows the pipeline runs
to be used in non-
after_rundecorator is deprecated.
- The command line flags
Release date: 25 August 2014
- First release on PyPI.
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