Get unit tests passing with Scan Workflows
This commit is contained in:
Julian Stirling
parent
c82523dd5b
commit
2a3a54b936
5 changed files with 149 additions and 135 deletions
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@ -11,15 +11,16 @@ import time
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from copy import copy
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import pytest
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from pydantic import BaseModel
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import labthings_fastapi as lt
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from openflexure_microscope_server.stitching import (
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STITCHING_RESOLUTION,
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BaseStitcher,
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FinalStitcher,
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PreviewStitcher,
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StitcherValidationError,
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StitchingSettings,
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)
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from ..shared_utils.lt_test_utils import LabThingsTestEnv
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@ -88,87 +89,41 @@ FINAL_EXPECTED_COMMAND = [
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FAKE_DIR,
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]
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def test_final_stitcher_command_defaults(caplog):
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"""Check the FinalStitcher stitches with expected default values.
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It should warn when default values are used as they are a fallback.
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"""
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n_logs = 0
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# Test with no dictionary data and with irrelevant dictionary data.
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with caplog.at_level(logging.WARNING):
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for data_dict in [None, {"irrelevant": "data"}]:
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stitcher = FinalStitcher(FAKE_DIR, logger=LOGGER, scan_data_dict=data_dict)
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# Should log for overlap being None and correlation_resize being None
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n_logs += 2
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assert len(caplog.records) == n_logs
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assert stitcher.command == FINAL_EXPECTED_COMMAND
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DEFAULT_SETTINGS = StitchingSettings(correlation_resize=0.5, overlap=0.1)
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def test_final_stitcher_command_tiff(caplog):
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def test_final_stitcher_command_tiff():
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"""Check that the tiff can be requested."""
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# Modify defaults
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expected_command = copy(FINAL_EXPECTED_COMMAND)
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expected_command[4] = "--stitch_tiff"
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stitcher = FinalStitcher(FAKE_DIR, logger=LOGGER, stitch_tiff=True)
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# Should log for overlap being None and correlation_resize being None
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assert len(caplog.records) == 2
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stitcher = FinalStitcher(
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FAKE_DIR, logger=LOGGER, stitching_settings=DEFAULT_SETTINGS, stitch_tiff=True
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)
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assert stitcher.command == expected_command
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def test_final_stitcher_command_set_val_directly():
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"""Check that values are set as expected when directly input."""
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# Modify defaults
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expected_command = copy(FINAL_EXPECTED_COMMAND)
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expected_command[8] = "0.36"
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expected_command[10] = "0.25"
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# Test with no data dictionary, irrelevant data, and also the wrong data
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# When wrong data is submitted, it should take the directly input data.
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dict_vals = [
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None,
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{"irrelevant": "data"},
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{"overlap": 0.2, "save_resolution": [5, 5]},
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]
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for data_dict in dict_vals:
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stitcher = FinalStitcher(
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FAKE_DIR,
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logger=LOGGER,
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overlap=0.4,
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correlation_resize=0.25,
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scan_data_dict=data_dict,
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)
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assert stitcher.command == expected_command
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def test_final_stitcher_command_set_with_dict():
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def test_final_stitcher_command_with_settings():
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"""Check that values are set as expected when set from a ScanData dictionary."""
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# Modify defaults
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expected_command = copy(FINAL_EXPECTED_COMMAND)
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expected_command[8] = "0.36"
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expected_command[10] = "0.25"
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# Check same thing works with a dictionary, resize is calculated from the saved image
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# resolution. Make 4x bigger than STITCHING_RESOLUTION to get 0.25
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resolution = [dim * 4 for dim in STITCHING_RESOLUTION]
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# Check legacy key as well as current one:
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for resolution_key in ["save_resolution", "capture resolution"]:
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stitcher = FinalStitcher(
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FAKE_DIR,
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logger=LOGGER,
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scan_data_dict={"overlap": 0.4, resolution_key: resolution},
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)
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assert stitcher.command == expected_command
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stitcher = FinalStitcher(
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FAKE_DIR,
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logger=LOGGER,
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stitching_settings=StitchingSettings(correlation_resize=0.25, overlap=0.4),
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)
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assert stitcher.command == expected_command
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def _validation_error_tester(scan_path, **kwargs):
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"""Check each type of stitcher throws a validation error for the given init args."""
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# If scan_data_dict is in the kwargs only test the scan_data_dict
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if "scan_data_dict" not in kwargs:
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with pytest.raises(StitcherValidationError):
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BaseStitcher(scan_path, **kwargs).command
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with pytest.raises(StitcherValidationError):
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PreviewStitcher(scan_path, **kwargs).command
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"""Check stitcher throws a validation error for the given init args."""
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with pytest.raises(StitcherValidationError):
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FinalStitcher(scan_path, logger=LOGGER, **kwargs).command
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BaseStitcher(scan_path, **kwargs).command
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with pytest.raises(StitcherValidationError):
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PreviewStitcher(scan_path, **kwargs).command
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def test_validation_error():
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@ -176,10 +131,23 @@ def test_validation_error():
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The stitcher should throw a validation error each attempt.
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"""
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# Tests for preview (and base) stitcher
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_validation_error_tester("/dir;rm -rf /;", overlap=".2", correlation_resize=".25")
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_validation_error_tester(FAKE_DIR, overlap=".2", correlation_resize=".25;rm -rf /;")
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_validation_error_tester(FAKE_DIR, overlap=".2;rm -rf /;", correlation_resize=".25")
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_validation_error_tester(FAKE_DIR, scan_data_dict={"overlap": ".2;rm -rf /;"})
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class EvilModel(BaseModel):
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overlap: str
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correlation_resize: str
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with pytest.raises(StitcherValidationError):
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FinalStitcher(
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FAKE_DIR,
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logger=LOGGER,
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stitching_settings=EvilModel(
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overlap=".2;rm -rf /;", correlation_resize=".25"
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),
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)
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def test_extra_arg_validation():
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@ -188,7 +156,9 @@ def test_extra_arg_validation():
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Currently extra args do not come from user input. But this makes checks more
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future-proof.
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"""
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stitcher = FinalStitcher(FAKE_DIR, logger=LOGGER)
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stitcher = FinalStitcher(
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FAKE_DIR, logger=LOGGER, stitching_settings=DEFAULT_SETTINGS
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)
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stitcher._extra_args = ["&&rm -rf /&&"]
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with pytest.raises(StitcherValidationError):
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stitcher.command
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@ -233,7 +203,9 @@ class StitchingTestThing(lt.Thing):
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@lt.action
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def run_final(self):
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"""Run the final stitcher."""
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stitcher = FinalStitcher(FAKE_DIR, logger=self.logger)
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stitcher = FinalStitcher(
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FAKE_DIR, logger=self.logger, stitching_settings=DEFAULT_SETTINGS
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)
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# Send in the argument HANG to mock-stitch and it just hang for 10s
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stitcher._extra_args = ["HANG"]
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stitcher.run()
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@ -277,9 +249,8 @@ def test_final_stitching_command(caplog, mocker):
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mocker.patch("openflexure_microscope_server.stitching.STITCHING_CMD", mock_cmd)
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with caplog.at_level(logging.INFO):
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# Input values to prevent logging
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stitcher = FinalStitcher(
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FAKE_DIR, logger=LOGGER, overlap=0.1, correlation_resize=0.5
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FAKE_DIR, logger=LOGGER, stitching_settings=DEFAULT_SETTINGS
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)
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# For the final stitcher it will always complete before returning.
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stitcher.run()
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@ -315,16 +286,17 @@ def test_final_stitching_command_cancelled(stitching_test_env, mocker):
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assert re.match(r"^Invocation [0-9a-f-]+ was cancelled", logs[-1]["message"])
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def test_final_stitching_command_error(caplog, mocker):
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def test_final_stitching_command_error(mocker):
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"""Check that ChildProcessError is raised if the final stitch errors."""
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mock_cmd = f"python {MOCK_STITCHER}"
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mocker.patch("openflexure_microscope_server.stitching.STITCHING_CMD", mock_cmd)
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with caplog.at_level(logging.INFO):
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stitcher = FinalStitcher(FAKE_DIR, logger=LOGGER)
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# Send in the argument ERROR to mock-stitch and it will raise an error rather
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# than echo.
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stitcher._extra_args = ["ERROR"]
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with pytest.raises(ChildProcessError):
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stitcher.run()
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stitcher = FinalStitcher(
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FAKE_DIR, logger=LOGGER, stitching_settings=DEFAULT_SETTINGS
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)
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# Send in the argument ERROR to mock-stitch and it will raise an error rather
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# than echo.
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stitcher._extra_args = ["ERROR"]
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with pytest.raises(ChildProcessError):
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stitcher.run()
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