FIX: Discard lazy fields in template type checks

[ghisvail]

See issue #641 for context.

Types of changes

• Bug fix (non-breaking change which fixes an issue)

Summary

This PR discards lazy fields in checks performed in template updates.

I am not very happy with this change, but it's the only way I found so far to bypass this issue without major surgery of the code. Not being able to use output_file_template in a workflow is quite a bummer.

Open to other suggestions if any 🙏

Triage

from os import PathLike
from attrs import define, field
from pydra.engine import Workflow
from pydra.engine.specs import ShellSpec, SpecInfo
from pydra.engine.task import ShellCommandTask


class BackupFile(ShellCommandTask):
    """Example task performing a file backup with cp.

    If not target file is provided, it uses a default file suffixed by copy.
    """

    @define(kw_only=True)
    class InputSpec(ShellSpec):
        source_file: PathLike = field(
            metadata={"help_string": "source file", "mandatory": True, "argstr": ""}
        )

        target_file: str = field(
            metadata={"help_string": "target file", "argstr": "", "output_file_template": "{source_file}_copy"}
        )

    input_spec = SpecInfo(name="Input", bases=(InputSpec,))

    executable = "cp"


def backup(name="backup", **kwargs) -> Workflow:
    wf = Workflow(input_spec=["source_file", "target_file"], name=name, **kwargs)

    wf.add(
        BackupFile(
            name="backup_file",
            source_file=wf.lzin.source_file,
            target_file=wf.lzin.target_file,
        )
    )

    wf.set_output({"target_file": wf.backup_file.lzout.target_file})

    return wf


if __name__ == "__main__":
    from pathlib import Path
    from tempfile import TemporaryDirectory

    # Execute with standalone backup task.
    with TemporaryDirectory() as td:
        source_file = Path(td) / "source1.file"
        source_file.touch()

        task = BackupFile(source_file=source_file)
        result = task()

        print(result.output.target_file)

    # Execute backup task wrapped in a workflow.
    with TemporaryDirectory() as td:
        source_file = Path(td) / "source2.file"
        source_file.touch()

        task = backup(source_file=source_file)
        result = task()

        print(result.output.target_file)

Closes: #641

[ghisvail]

Without the fix, an exception is raised (Exception: target_file has to be str or bool, but LF('backup', 'target_file') set). With the fix, the path to the target file is printed.

[codecov]

Codecov Report

Patch coverage: 100.00% and project coverage change: -0.05 ⚠️

Comparison is base (426564e) 81.77% compared to head (4591be0) 81.72%.

❗ Current head 4591be0 differs from pull request most recent head f48eebb. Consider uploading reports for the commit f48eebb to get more accurate results

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #657      +/-   ##
==========================================
- Coverage   81.77%   81.72%   -0.05%     
==========================================
  Files          20       20              
  Lines        4400     4400              
  Branches     1264        0    -1264     
==========================================
- Hits         3598     3596       -2     
- Misses        798      804       +6     
+ Partials        4        0       -4     

Flag	Coverage Δ
unittests	81.72% <100.00%> (-0.05%)	⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
pydra/engine/helpers_file.py	86.10% <100.00%> (ø)

... and 4 files with indirect coverage changes

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[djarecka]

if this works for you we can have it temporarily, but I would not close the issue. Sorry, was planning to look at this earlier, but will try to check it this week.

[ghisvail]

Fixed by #662