Fix febus format empty file #492

d-chambers · 2025-02-28T00:50:49Z

Description

This PR fixes an issue in the Febus data format which causes dascore to identify empty hdf5 files as febus format.

Checklist

I have (if applicable):

referenced the GitHub issue this PR closes.
documented the new feature with docstrings or appropriate doc page.
included a test. See testing guidelines.
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added the "ready_for_review" tag once the PR is ready to be reviewed.

Summary by CodeRabbit

Bug Fixes
- Refined version display logic to ensure version information is only presented when complete instrument details are available.
Tests
- Expanded test coverage by adding scenarios that verify proper error handling when processing empty input files.

coderabbitai · 2025-02-28T00:51:08Z

Walkthrough

This pull request updates the Febus version string retrieval logic and expands the test suite. In the Febus utility, the conditional check now requires both a valid Febus flag and non-empty instrument keys before returning a version string. Meanwhile, new tests were introduced that create an empty HDF5 file fixture and verify that calling the format retrieval function on such a file raises an appropriate error.

Changes

File	Summary
dascore/.../utils.py	Modified `_get_febus_version_str` to require non-empty `inst_keys` along with `is_febus` before returning the version string.
tests/.../test_io_core.py	Added a new pytest fixture `empty_h5_path` to create an empty HDF5 file and a test `test_empty_hdf5_no_format` to assert error raising on it.

Sequence Diagram(s)

sequenceDiagram
    participant Caller
    participant VersionFunc as _get_febus_version_str
    Caller->>VersionFunc: Call with (inst_keys, is_febus)
    alt inst_keys is non-empty and is_febus is true
        VersionFunc-->>Caller: Return version string
    else Condition not met
        VersionFunc-->>Caller: No version string returned
    end

sequenceDiagram
    participant Test
    participant FileFixture as empty_h5_path
    participant DC as dc.get_format
    Test->>FileFixture: Create an empty HDF5 file
    Test->>DC: Call get_format(empty HDF5 file)
    DC-->>Test: Raise UnknownFiberFormatError

Poem

Hi, I'm a happy rabbit on the run,
Hopping through fixes just for fun.
Now our Febus check needs more than a glance,
And empty files get met with a testy chance.
Code carrots abound—let’s celebrate each one!
🥕🐇

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📥 Commits

Reviewing files that changed from the base of the PR and between 1dbb10e and 6648cc5.

📒 Files selected for processing (2)

dascore/io/febus/utils.py (1 hunks)
tests/test_io/test_io_core.py (3 hunks)

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🔇 Additional comments (4)

dascore/io/febus/utils.py (1)

78-78: Good fix for the empty file detection.

This change ensures that empty HDF5 files aren't incorrectly identified as Febus format files by checking that inst_keys is not empty before determining a file is in Febus format. This addresses the PR's main objective.

tests/test_io/test_io_core.py (3)

10-10: Added necessary import for the new test fixture.

The h5py import is required for creating the empty HDF5 test file.

264-271: Well-designed test fixture for creating empty HDF5 files.

This fixture creates an empty HDF5 file that will be used to verify the fix for the Febus format detection issue. The class scope is appropriate as the file can be reused across tests.

291-295: Effective test case that verifies the fix.

This test ensures that the empty HDF5 file correctly raises an UnknownFiberFormatError instead of being incorrectly identified as a Febus format file, which directly addresses the issue described in the PR objective.

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codecov · 2025-02-28T00:54:17Z

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 99.85%. Comparing base (1dbb10e) to head (6648cc5).
Report is 2 commits behind head on master.

Additional details and impacted files

@@           Coverage Diff           @@
##           master     #492   +/-   ##
=======================================
  Coverage   99.85%   99.85%           
=======================================
  Files         118      118           
  Lines        9696     9696           
=======================================
  Hits         9682     9682           
  Misses         14       14

Flag	Coverage Δ
unittests	`99.85% <100.00%> (ø)`

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

☔ View full report in Codecov by Sentry.
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d-chambers added 2 commits February 27, 2025 14:05

work on adding neubrex

557343b

fix febus format issue

6648cc5

d-chambers added bug Something isn't working IO Work for reading/writing different formats labels Feb 28, 2025

d-chambers merged commit 045cbbb into master Feb 28, 2025
19 checks passed

d-chambers deleted the fix_febus_format_empty_file branch February 28, 2025 18:38

coderabbitai bot mentioned this pull request Sep 3, 2025

Loosen instrument naming requirement for febus files #525

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