Run lammps extra outputs

[zjgemi]

Summary by CodeRabbit

• New Features

  • Added support for collecting and returning additional output files ("extra_outputs") in relevant operations.
  • Users can now specify extra output file patterns (including wildcards) to be captured after LAMMPS runs.

• Tests

  • Introduced a new test to verify correct handling and content of extra output files.
  • Extended existing tests to validate downloading of "extra_outputs" artifacts.

• Chores

  • Updated artifact download settings to include "extra_outputs" in the list of downloadable items.

[coderabbitai]

📝 Walkthrough

"""

Walkthrough

The changes introduce a new output artifact, "extra_outputs", to the LAMMPS run operation and its associated preparation and artifact download utilities. The code updates the output signatures, configuration arguments, and artifact mappings to support collecting and handling additional output files matching user-specified patterns. A new test covers this functionality.

Changes

File(s)	Change Summary
dpgen2/op/run_lmp.py	Extended RunLmp output to include "extra_outputs" (list of Path), updated argument parsing, and logic to collect extra output files based on user-specified patterns.
dpgen2/superop/prep_run_lmp.py	Added "extra_outputs" to PrepRunLmp output artifacts and updated artifact mapping in run step configuration.
dpgen2/utils/download_dpgen2_artifacts.py	Included "extra_outputs" in the list of artifacts to be downloaded for the "prep-run-explore" step.
tests/op/test_run_lmp.py	Added test_extra_outputs to verify correct handling and content of extra output files in RunLmp.
tests/mocked_ops.py	Added "extra_outputs" key with empty list to MockedRunLmp.execute output dictionary.
tests/utils/test_dl_dpgen2_arti.py	Extended expected artifact downloads to include "arti-extra_outputs" for the "prep-run-explore" step.

Sequence Diagram(s)

sequenceDiagram
    participant User
    participant RunLmp
    participant FileSystem

    User->>RunLmp: Execute with config (including extra_output_files)
    RunLmp->>FileSystem: Run LAMMPS and generate outputs
    RunLmp->>FileSystem: Glob for extra_output_files patterns
    FileSystem-->>RunLmp: Return matched files
    RunLmp-->>User: Return outputs (including extra_outputs)

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Suggested reviewers

• wanghan-iapcm
  """

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• tests/utils/test_dl_dpgen2_arti.py (3 hunks)

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🔇 Additional comments (3)

tests/utils/test_dl_dpgen2_arti.py (3)

126-130: LGTM! Correctly adds test expectation for new extra_outputs artifact.

The test expectation for the new "arti-extra_outputs" artifact is correctly added to the LAMMPS download test, following the same pattern as other artifacts.

---

261-265: LGTM! Consistently adds extra_outputs artifact expectation.

The test expectation for "arti-extra_outputs" is correctly added to the update finished steps test with existing steps, maintaining consistency with the artifact download pattern.

---

328-332: LGTM! Completes the test coverage for extra_outputs artifact.

The test expectation for "arti-extra_outputs" is correctly added to the update finished steps test with no existing steps, ensuring comprehensive test coverage for the new artifact.

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 84.22%. Comparing base (9062e8a) to head (93027ae).
⚠️ Report is 9 commits behind head on master.

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #299      +/-   ##
==========================================
+ Coverage   84.20%   84.22%   +0.01%     
==========================================
  Files         104      104              
  Lines        6105     6111       +6     
==========================================
+ Hits         5141     5147       +6     
  Misses        964      964              

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