Manifest JSON Writing Utility #486
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Added private helper `gempyor.utils._shutil_which` which has a `check` argument that behaves very similar in spirit to the same argument of `subprocess.run`. Corresponding docs/tests included.
Added an internal utility function to get the sha commit corresponding to the head of a given git repository. For use in creating manifest files.
Added `gempyor.manifest.write_manifest` for writing batch manifest JSON files containing metadata about the run. Also has extended functionality to store more metadata then the current required.
Move the `manifest` submodule to `batch` to consolidate future functionality. Minor edits to unit tests to account for the module name change.
TimothyWillard
requested review from
pearsonca,
jcblemai,
fang19911030,
anjalika-nande,
saraloo,
MacdonaldJoshuaCaleb and
emprzy
TimothyWillard
added
enhancement
emprzy
requested changes
Jan 24, 2025
| Examples: | ||
| >>> from pathlib import Path | ||
| >>> flepi_path = Path("~/Desktop/GitHub/HopkinsIDD/flepiMoP").expanduser() | ||
| >>> project_path = Path("~/Desktop/GitHub/HopkinsIDD/flepimop_sample").expanduser() |
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We are trying to move away from flepimop_sample, in favor of using the examples/tutorials folder in flepiMoP. Perhaps this line could read:
project_path = Path("~/Desktop/GitHub/HopkinsIDD/flepiMoP/examples/tutorials").expanduser()
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Also, should we all-caps FLEPI_PATH and PROJECT_PATH, if they are constants throughout the entirety of flepiMoP execution?
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| def _git_head(repository: Path) -> str: | ||
| """ | ||
| Get the sha commit has for the head of a git repository. |
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Is this suppposed to read "Get the sha commit hash for the ...."?
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Describe your changes.
This pull request adds:
_shutil_whichand_git_head, andwrite_manifestto the newbatchmodule for writing manifest JSON files containing batch metadata.Does this pull request make any user interface changes? If so please describe.
The user interface changes are none, this is all new functionality. Code level documentation (which is the main usage of this functionality) has been added to the docstrings.
What does your pull request address? Tag relevant issues.
This pull request was spun out of GH-394 to help address GH-365.