feat: perform test and code coverage with pytest and pytest-cov (8a89db1b) · Commits · HIP / DataHIPy

.coveragerc

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		# .coveragerc to control coverage.py
		[run]
		branch = False
		concurrency = multiprocessing
		parallel = True
		source = bids_tools

		[report]
		# Regexes for lines to exclude from consideration
		exclude_lines =
		# Have to re-enable the standard pragma
		pragma: no cover

		# Don't complain about missing debug-only code:
		def __repr__
		if self\.debug

		# Don't complain if tests don't hit defensive assertion code:
		raise AssertionError
		raise NotImplementedError

		# Don't complain if non-runnable code isn't run:
		if 0:
		if __name__ == .__main__.:

		# Don't complain about abstract methods, they aren't run:
		@(abc\.)?abstractmethod

		ignore_errors = True

		[html]
		directory = coverage_html_report
		No newline at end of file

scripts/docker/entrypoint_pytest.sh

0 → 100755

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		#!/bin/bash

		USER=$1
		USER_ID=$2

		echo -n "Creating user $USER... "
		egrep "^$USER" /etc/passwd >/dev/null
		if [ $? -eq 0 ]; then
		echo "$USER already exists and has been recreated."
		userdel $USER
		fi

		useradd --create-home --shell /bin/bash $USER --uid $USER_ID
		if [ $? -eq 0 ]; then
		echo "done."
		else
		echo "failed."
		exit 1
		fi

		runuser -u $USER -- pytest --cov-config "/apps/bids_tools/.coveragerc" \
		--cov-report html:"/test/report/cov_html" \
		--cov-report xml:"/test/report/cov.xml" \
		--cov-report lcov:"/test/report/cov.info" \
		--cov=bids_tools -p no:cacheprovider -s "${@:3}"

test/init.py

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Empty file added.

test/cli/init.py

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Empty file added.

test/cli/test_main.py

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+318 −0

Original line number	Diff line number	Diff line
		from __future__ import absolute_import
		import os
		import pytest
		import json
		import shutil
		from bids_tools.cli.main import main


		@pytest.mark.script_launch_mode("subprocess")
		def test_main_help(script_runner):
		ret = script_runner.run("bids_tools", "-h")
		assert ret.success


		@pytest.mark.script_launch_mode("subprocess")
		def test_main_dataset_create(script_runner, dataset_path, io_path):
		# Create input data
		input_data = {
		"dataset_dirname": "NEW_BIDS_DS",
		"DatasetDescJSON": {
		"Name": "My New BIDS dataset",
		"BIDSVersion": "1.4.0",
		"License": "n/a",
		"Authors": ["Tom", "Jerry"],
		"Acknowledgements": "Overwrite test",
		"HowToAcknowledge": "n/a",
		"Funding": "Picsou",
		"ReferencesAndLinks": "n/a",
		"DatasetDOI": "n/a",
		},
		}
		# Create JSON file path for input data
		input_file = os.path.join(io_path, "create_dataset.json")
		# Write input data to file
		with open(input_file, "w") as f:
		json.dump(input_data, f, indent=4)
		# Remove dataset if it already exists to avoid conflicts
		if os.path.exists(dataset_path):
		shutil.rmtree(dataset_path)
		# Run bids_tools dataset.create command
		ret = script_runner.run(
		"bids_tools",
		"--command",
		"dataset.create",
		"--input_data",
		input_file,
		"--dataset_path",
		os.path.dirname(dataset_path),
		)
		# Check that the command ran successfully
		assert ret.success
		# Check that the dataset was created by checking for the dataset_description.json file
		assert os.path.exists(os.path.join(dataset_path, "dataset_description.json"))


		@pytest.mark.script_launch_mode("subprocess")
		def test_main_dataset_get(script_runner, dataset_path, io_path):
		# Create input data
		input_data = {"owner": "hipadmin", "path": dataset_path}
		# Create JSON file path for input data
		input_file = os.path.join(io_path, "get_dataset.json")
		# Write input data to file
		with open(input_file, "w") as f:
		json.dump(input_data, f, indent=4)
		# Output file path
		output_file = os.path.join(io_path, "get_dataset_output.json")
		# Run bids_tools dataset.get command
		ret = script_runner.run(
		"bids_tools",
		"--command",
		"dataset.get",
		"--input_data",
		input_file,
		"--output_file",
		output_file,
		"--dataset_path",
		dataset_path,
		)
		# Check that the command ran successfully
		assert ret.success
		# Check that the output file was created
		assert os.path.exists(output_file)


		@pytest.mark.script_launch_mode("subprocess")
		def test_main_datasets_get(script_runner, dataset_path, io_path):
		# Create input data
		input_data = {
		"owner": "hipadmin",
		"datasets": [{"path": dataset_path}, {"path": dataset_path}],
		}
		# Create JSON file path for input data
		input_file = os.path.join(io_path, "get_datasets.json")
		# Write input data to file
		with open(input_file, "w") as f:
		json.dump(input_data, f, indent=4)
		# Output file path
		output_file = os.path.join(io_path, "get_datasets_output.json")
		# Run bids_tools datasets.get command
		ret = script_runner.run(
		"bids_tools",
		"--command",
		"datasets.get",
		"--input_data",
		input_file,
		"--output_file",
		output_file,
		)
		# Check that the command ran successfully
		assert ret.success


		@pytest.mark.script_launch_mode("subprocess")
		def test_main_sub_import(script_runner, input_path, dataset_path, io_path):
		# Create input data
		input_data = {
		"subjects": [{"sub": "carole", "age": "25", "sex": "M", "hospital": "CHUV"}],
		"files": [
		{
		"modality": "ieeg",
		"subject": "carole",
		"path": "sub-carole/SZ1.TRC",
		"entities": {
		"sub": "carole",
		"ses": "postimp",
		"task": "stimulation",
		"acq": "1024hz",
		},
		},
		{
		"modality": "ieeg",
		"subject": "carole",
		"path": "sub-carole/SZ2.TRC",
		"entities": {
		"sub": "carole",
		"ses": "postimp",
		"task": "stimulation",
		"acq": "1024hz",
		},
		},
		{
		"modality": "T1w",
		"subject": "carole",
		"path": "sub-carole/3DT1post_deface.nii",
		"entities": {
		"sub": "carole",
		"ses": "postimp",
		"acq": "lowres",
		"ce": "gadolinium",
		},
		},
		{
		"modality": "T1w",
		"subject": "carole",
		"path": "sub-carole/3DT1post_deface_2.nii",
		"entities": {
		"sub": "carole",
		"ses": "postimp",
		"acq": "lowres",
		"ce": "gadolinium",
		},
		},
		{
		"modality": "T1w",
		"subject": "carole",
		"path": "sub-carole/3DT1pre_deface.nii",
		"entities": {"sub": "carole", "ses": "preimp", "acq": "lowres"},
		},
		],
		}
		# Create JSON file path for input data
		input_file = os.path.join(io_path, "import_sub.json")
		# Write input data to file
		with open(input_file, "w") as f:
		json.dump(input_data, f, indent=4)
		# Run bids_tools sub.import command
		ret = script_runner.run(
		"bids_tools",
		"--command",
		"sub.import",
		"--input_data",
		input_file,
		"--dataset_path",
		dataset_path,
		"--input_path",
		input_path,
		)
		# Check that the command ran successfully
		assert ret.success
		# Check that the sub-carole folder was created
		assert os.path.exists(os.path.join(dataset_path, "sub-carole"))


		@pytest.mark.script_launch_mode("subprocess")
		def test_main_sub_get(script_runner, dataset_path, io_path):
		# Create input data
		input_data = {"owner": "hipadmin", "path": dataset_path, "sub": "carole"}
		# Create JSON file path for input data
		input_file = os.path.join(io_path, "get_sub.json")
		# Write input data to file
		with open(input_file, "w") as f:
		json.dump(input_data, f, indent=4)
		# Output file path
		output_file = os.path.join(io_path, "get_sub_output.json")
		# Run bids_tools sub.get command
		ret = script_runner.run(
		"bids_tools",
		"--command",
		"sub.get",
		"--input_data",
		input_file,
		"--output_file",
		output_file,
		"--dataset_path",
		dataset_path,
		)
		# Check that the command ran successfully
		assert ret.success
		# Check that the output file was created
		assert os.path.exists(output_file)


		@pytest.mark.script_launch_mode("subprocess")
		def test_main_sub_edit_clinical(script_runner, dataset_path, io_path):
		# Create input data
		input_data = {
		"subject": "carole",
		"clinical": {"age": "30", "sex": "M", "handedness": "L", "hospital": "CHUGA"},
		}
		# Create JSON file path for input data
		input_file = os.path.join(io_path, "sub_edit_clinical.json")
		# Write input data to file
		with open(input_file, "w") as f:
		json.dump(input_data, f, indent=4)
		# Output updated participants.tsv file
		output_file = os.path.join(dataset_path, "participants.tsv")
		# Run bids_tools sub.edit.clinical command
		ret = script_runner.run(
		"bids_tools",
		"--command",
		"sub.edit.clinical",
		"--input_data",
		input_file,
		"--output_file",
		output_file,
		"--dataset_path",
		dataset_path,
		)
		# Check that the command ran successfully
		assert ret.success


		@pytest.mark.script_launch_mode("subprocess")
		def test_main_sub_delete_file(script_runner, dataset_path, io_path):
		# Create input data
		input_data = {
		"files": [
		{
		"subject": "carole",
		"modality": "Anat",
		"fullpath": "sub-carole/ses-postimp/anat/sub-carole_ses-postimp_acq-lowres_ce-gadolinium_run-02_T1w.nii",
		}
		]
		}
		# Create JSON file path for input data
		input_file = os.path.join(io_path, "delete_sub_file.json")
		# Write input data to file
		with open(input_file, "w") as f:
		json.dump(input_data, f, indent=4)
		# Run bids_tools sub.delete.file command
		ret = script_runner.run(
		"bids_tools",
		"--command",
		"sub.delete.file",
		"--input_data",
		input_file,
		"--dataset_path",
		dataset_path,
		)
		# Check that the command ran successfully
		assert ret.success
		# Check that the file was deleted
		assert not os.path.exists(
		os.path.join(
		dataset_path,
		os.path.join(
		"sub-carole",
		"ses-postimp",
		"anat",
		"sub-carole_ses-postimp_acq-lowres_ce-gadolinium_run-02_T1w.nii",
		),
		)
		)


		@pytest.mark.script_launch_mode("subprocess")
		def test_main_sub_delete(script_runner, dataset_path, io_path):
		# Create input data
		input_data = {"subject": "carole"}
		# Create JSON file path for input data
		input_file = os.path.join(io_path, "delete_sub.json")
		# Write input data to file
		with open(input_file, "w") as f:
		json.dump(input_data, f, indent=4)
		# Run bids_tools sub.delete command
		ret = script_runner.run(
		"bids_tools",
		"--command",
		"sub.delete",
		"--input_data",
		input_file,
		"--dataset_path",
		dataset_path,
		)
		# Check that the command ran successfully
		assert ret.success
		# Check that the sub-carole folder was deleted
		assert not os.path.exists(os.path.join(dataset_path, "sub-carole"))