Skip to content

Support using container entrypoints for shell tasks #822

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
wants to merge 8 commits into
base: main
Choose a base branch
from

removed circular import issue checking for container entrypoint

b913f30
Select commit
Loading
Failed to load commit list.
Open

Support using container entrypoints for shell tasks #822

removed circular import issue checking for container entrypoint
b913f30
Select commit
Loading
Failed to load commit list.
Codecov / codecov/patch failed Jun 21, 2025 in 1s

16.07% of diff hit (target 80.00%)

View this Pull Request on Codecov

16.07% of diff hit (target 80.00%)

Annotations

Check warning on line 39 in pydra/compose/shell/builder.py

See this annotation in the file changed.

@codecov codecov / codecov/patch

pydra/compose/shell/builder.py#L39

Added line #L39 was not covered by tests

Check warning on line 41 in pydra/compose/shell/builder.py

See this annotation in the file changed.

@codecov codecov / codecov/patch

pydra/compose/shell/builder.py#L41

Added line #L41 was not covered by tests

Check warning on line 45 in pydra/compose/shell/builder.py

See this annotation in the file changed.

@codecov codecov / codecov/patch

pydra/compose/shell/builder.py#L45

Added line #L45 was not covered by tests

Check warning on line 259 in pydra/compose/shell/task.py

See this annotation in the file changed.

@codecov codecov / codecov/patch

pydra/compose/shell/task.py#L259

Added line #L259 was not covered by tests

Check warning on line 299 in pydra/compose/shell/task.py

See this annotation in the file changed.

@codecov codecov / codecov/patch

pydra/compose/shell/task.py#L299

Added line #L299 was not covered by tests

Check warning on line 302 in pydra/compose/shell/task.py

See this annotation in the file changed.

@codecov codecov / codecov/patch

pydra/compose/shell/task.py#L301-L302

Added lines #L301 - L302 were not covered by tests

Check warning on line 238 in pydra/environments/base.py

See this annotation in the file changed.

@codecov codecov / codecov/patch

pydra/environments/base.py#L238

Added line #L238 was not covered by tests

Check warning on line 241 in pydra/environments/base.py

See this annotation in the file changed.

@codecov codecov / codecov/patch

pydra/environments/base.py#L240-L241

Added lines #L240 - L241 were not covered by tests

Check warning on line 243 in pydra/environments/base.py

See this annotation in the file changed.

@codecov codecov / codecov/patch

pydra/environments/base.py#L243

Added line #L243 was not covered by tests

Check warning on line 245 in pydra/environments/base.py

See this annotation in the file changed.

@codecov codecov / codecov/patch

pydra/environments/base.py#L245

Added line #L245 was not covered by tests

Check warning on line 249 in pydra/environments/base.py

See this annotation in the file changed.

@codecov codecov / codecov/patch

pydra/environments/base.py#L247-L249

Added lines #L247 - L249 were not covered by tests

Check warning on line 33 in pydra/environments/docker.py

See this annotation in the file changed.

@codecov codecov / codecov/patch

pydra/environments/docker.py#L33

Added line #L33 was not covered by tests

Check warning on line 19 in pydra/environments/native.py

See this annotation in the file changed.

@codecov codecov / codecov/patch

pydra/environments/native.py#L19

Added line #L19 was not covered by tests

Check warning on line 35 in pydra/environments/singularity.py

See this annotation in the file changed.

@codecov codecov / codecov/patch

pydra/environments/singularity.py#L35

Added line #L35 was not covered by tests

Check warning on line 513 in pydra/environments/tests/test_environments.py

See this annotation in the file changed.

@codecov codecov / codecov/patch

pydra/environments/tests/test_environments.py#L513

Added line #L513 was not covered by tests

Check warning on line 515 in pydra/environments/tests/test_environments.py

See this annotation in the file changed.

@codecov codecov / codecov/patch

pydra/environments/tests/test_environments.py#L515

Added line #L515 was not covered by tests

Check warning on line 523 in pydra/environments/tests/test_environments.py

See this annotation in the file changed.

@codecov codecov / codecov/patch

pydra/environments/tests/test_environments.py#L519-L523

Added lines #L519 - L523 were not covered by tests

Check warning on line 525 in pydra/environments/tests/test_environments.py

See this annotation in the file changed.

@codecov codecov / codecov/patch

pydra/environments/tests/test_environments.py#L525

Added line #L525 was not covered by tests

Check warning on line 529 in pydra/environments/tests/test_environments.py

See this annotation in the file changed.

@codecov codecov / codecov/patch

pydra/environments/tests/test_environments.py#L528-L529

Added lines #L528 - L529 were not covered by tests

Check warning on line 536 in pydra/environments/tests/test_environments.py

See this annotation in the file changed.

@codecov codecov / codecov/patch

pydra/environments/tests/test_environments.py#L536

Added line #L536 was not covered by tests

Check warning on line 539 in pydra/environments/tests/test_environments.py

See this annotation in the file changed.

@codecov codecov / codecov/patch

pydra/environments/tests/test_environments.py#L538-L539

Added lines #L538 - L539 were not covered by tests

Check warning on line 543 in pydra/environments/tests/test_environments.py

See this annotation in the file changed.

@codecov codecov / codecov/patch

pydra/environments/tests/test_environments.py#L542-L543

Added lines #L542 - L543 were not covered by tests

Check warning on line 546 in pydra/environments/tests/test_environments.py

See this annotation in the file changed.

@codecov codecov / codecov/patch

pydra/environments/tests/test_environments.py#L545-L546

Added lines #L545 - L546 were not covered by tests

Check warning on line 548 in pydra/environments/tests/test_environments.py

See this annotation in the file changed.

@codecov codecov / codecov/patch

pydra/environments/tests/test_environments.py#L548

Added line #L548 was not covered by tests

Check warning on line 550 in pydra/environments/tests/test_environments.py

See this annotation in the file changed.

@codecov codecov / codecov/patch

pydra/environments/tests/test_environments.py#L550

Added line #L550 was not covered by tests