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deepmodeling / dpdispatcher

generate HPC scheduler systems jobs input scripts and submit these scripts to HPC systems and poke until they finish
https://docs.deepmodeling.com/projects/dpdispatcher/
GNU Lesser General Public License v3.0
45 stars 57 forks source link

feat: allow copying files to remote with LocalContext #487

Closed njzjz closed 2 months ago

njzjz commented 2 months ago

Fix #486.

Summary by CodeRabbit

coderabbitai[bot] commented 2 months ago

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Commits Files that changed from the base of the PR and between 7a69737725de718f091aaf55891e8b8a556575ee and 3204a17daf8641f751c3e99dcabdfd4bbfd4f784.
Walkthrough ## Walkthrough The changes involve modifications to the file handling process within the `Local` context type. The documentation has been updated to reflect a shift from copying files to using symlinks, enhancing efficiency. Additionally, the codebase has been improved with new attributes and methods to support this change, and a new test class has been introduced to validate local context submissions. ## Changes | File | Change Summary | |----------------------------------------|-----------------------------------------------------------------------------------------------------| | doc/context.md | Updated documentation to reflect the change from copying files to symlinking in the `Local` context. | | dpdispatcher/contexts/local_context.py | Added `symlink` attribute, introduced `_copy_from_local_to_remote` method, and added `machine_subfields` method. | | tests/test_run_submission.py | Introduced `TestLocalContextCopy` class for testing local context submissions with a new test method. | ## Sequence Diagram(s) ```mermaid sequenceDiagram participant User participant LocalContext participant RemoteSystem User->>LocalContext: Submit Job LocalContext->>RemoteSystem: Symlink files RemoteSystem->>LocalContext: Confirm Symlink LocalContext->>RemoteSystem: Execute Job RemoteSystem-->>LocalContext: Job Completion LocalContext-->>User: Return Results ``` ## Assessment against linked issues | Objective | Addressed | Explanation | |---------------------------------------------------------------------------|-----------|--------------------------------------------------| | #486: Address the "sed: can't read script" error when using LocalContext | ✅ | |

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codecov[bot] commented 2 months ago

Codecov Report

Attention: Patch coverage is 79.16667% with 5 lines in your changes missing coverage. Please review.

Project coverage is 47.80%. Comparing base (c8e9b20) to head (3204a17). Report is 2 commits behind head on master.

Files with missing lines Patch % Lines
dpdispatcher/contexts/local_context.py 77.27% 5 Missing :warning:

:exclamation: There is a different number of reports uploaded between BASE (c8e9b20) and HEAD (3204a17). Click for more details.

HEAD has 1 upload less than BASE | Flag | BASE (c8e9b20) | HEAD (3204a17) | |------|------|------| ||15|14|
Additional details and impacted files ```diff @@ Coverage Diff @@ ## master #487 +/- ## =========================================== - Coverage 60.13% 47.80% -12.33% =========================================== Files 39 39 Lines 3845 3857 +12 =========================================== - Hits 2312 1844 -468 - Misses 1533 2013 +480 ```

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