Keep the Febus G1 sample window and fix two coordinate bugs it exposed

[d-chambers]

Description

Reading a directory of Febus G1 BSL files surfaced a cluster of problems, found while investigating why spool.get_contents()['start_time'] came back as a float column rather than datetime64. Four are in the Febus G1 readers and the index; a fifth, found during review, is in coordinate merging and is the reason the new coordinate is worth having at all.

The start_time/end_time attrs were epoch-second floats. The G1 HDF5 attr map copied the root start_time/end_time header attrs straight into patch attrs. Both are bit-identical to start_times[0] and end_times[-1], so they only restated the time datasets as untyped floats. They are now dropped, which is what the sibling A1 text path already does via attr_exclude. This also removes the confusing follow-on where those columns went NaN for every merged row under spool.chunk(..., conflict='drop') — they were per-file values that could not survive a merge. A test asserts the information is still recoverable from the coords, which is what justifies deleting rather than retyping them.

The per-sample acquisition window was discarded. The readers built the time coord from start_times and ignored the end_times dataset entirely, so a BSL patch presented as instantaneous samples when each value is really an average over a window — ~600 s in the data that prompted this, ~0.85 s in the test file, with a short dead gap before the next sample. Patches now carry a non-dimensional sample_span coord mapped to time holding that length.

The span is stored rather than the raw end_times on purpose. start_times and end_times are both near-regular, so each snaps to a CoordRange independently and they land on slightly different steps; differencing the two snapped coords turns the real per-sample jitter into a linear drift. Differencing the raw arrays first keeps it exact, and doing so in float seconds is more precise than differencing after the round to datetime64[ns].

formatVersion collided with a reserved index column. It was mapped to a format_version attr, so every index build warned Skipping reserved attr name 'format_version' and the attr was left unqueryable. The same value is already reported as source_version, so the redundant mapping is removed.

A stepless numeric coord's step became an int64 sentinel. In SQLIndexBackend._add_envelope_objects the envelope column was assigned as a bare object array, letting pandas re-infer the dtype. When no numeric coord in a result carries a step, that array holds only Timedeltas and None, so it inferred timedelta64 and turned the numeric nulls into NaT; pd.to_numeric in _pivot_coords then mapped those to -9223372036854775808. It is data-dependent rather than chunk-specific — chunking just tends to produce a small result where nothing anchors the column to a numeric dtype. Assigning an explicit object-dtype Series keeps the nulls as NaN. _env_min/_env_max shared the hazard.

Merging replaced associated coords with the dimension coord. _get_merged_coords used dim where it meant coord_name, so every coordinate mapped to the merge dimension had the dimension coord's values concatenated in place of its own. This is pre-existing and already corrupts temperature on any multi-file Febus G1 spool — after a chunk it comes back as datetime64 copies of time rather than temperatures. It would have silently destroyed sample_span in the same way, so the new coordinate is not meaningful without this fix. Snapping is now applied only to the dimension coordinate, since only it defines contiguity. It is a separate commit if you would rather it went in on its own.

Notes

• sample_span is new user-visible state on Febus G1 HDF5 patches (both BSL and MTX, which share the coord builder). It slices with select and survives chunk/merge like temperature.
• It is deliberately not named time_span: a coord whose name starts with a dimension name shadows the {dim}_{suffix} envelope convention, and update_coords(time_span_min=...) died with an internal ValueError: too many values to unpack where other names raise a clean CoordError.
• INDEX_VERSION is intentionally not bumped — history shows it tracks schema changes, not reader metadata, and bumping would force every user to rebuild every index for a Febus-only change. Anyone with an existing index over Febus G1 data should rebuild it to pick up sample_span and drop the removed attrs.
• The reader now raises a named error when start_times and end_times disagree in shape; previously a truncated or mid-write file raised an opaque broadcast error, and a length-1 end_times broadcast silently into garbage spans.
• start_time/end_time were removed from the VENDOR_ATTRS allowlist in test_common_io.py; no reader emits them now, so leaving them would have let them back in unnoticed.
• One limitation worth knowing: a span array regular enough to look like a range is still normalized to a CoordRange by get_coord_manager, so exactness is guaranteed at the constructor but not through the coord manager. The comment says so rather than claiming more.

Changelog

• fixed: The Febus G1 HDF5 readers no longer copy the redundant start_time and end_time header floats into patch attrs, where they restated the time coordinate as epoch seconds.
• added: Febus G1 HDF5 patches now carry a sample_span coordinate giving the length of each sample's acquisition window.
• fixed: The Febus G1 HDF5 readers no longer emit a format_version attr, which collided with a reserved index column and warned on every index build.
• fixed: The Febus G1 HDF5 readers now raise a clear error when a file's start_times and end_times datasets disagree in length.
• fixed: A numeric coordinate with no step no longer reports that step as a large negative integer instead of a null when no other numeric coordinate in the result carries one.
• fixed: Merging patches along a dimension no longer replaces the values of coordinates associated with that dimension, such as temperature, with the dimension coordinate's own values.

Checklist

I have:

• filled in the Changelog section above (see docs/contributing/general_guidelines.qmd).

I have (if applicable):

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

Summary by CodeRabbit

• Documentation

  • Expanded FEBUS format documentation with acquisition-window and timing-coordinate details.

• Bug Fixes

  • Added reliable sample_span timing coordinates for FEBUS G1 data.
  • Added validation for inconsistent timing datasets.
  • Prevented missing envelope values from being misinterpreted as timestamps.
  • Preserved associated coordinate values and data types during coordinate merges.
  • Preserved floating-point null values when loading indexed data.
  • Removed redundant timing and format metadata from patch attributes while retaining scan metadata.

[coderabbitai]

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📝 Walkthrough

Walkthrough

The PR adds Febus sample_span coordinates from raw acquisition windows, validates timing arrays, and removes redundant timing attributes. It also preserves associated coordinate values during merging and prevents null numeric index values from temporal dtype coercion.

Changes

Febus timing coordinates

Layer / File(s)	Summary
Febus coordinate construction dascore/io/febus/core.py, dascore/io/febus/g1utils.py, tests/test_io/test_common_io.py	Febus documentation describes acquisition windows and sample_span. HDF5 coordinate construction validates start and end arrays and derives spans from their exact differences. Redundant timing and format attributes are excluded.
Febus timing validation tests/test_io/test_febus/test_febusbsl.py, tests/test_io/test_febus/test_febusg1.py	Tests cover sample spans, unsnapped timing differences, malformed files, attribute removal, metadata recovery, sliced reads, and MTX scan metadata.

Coordinate manager merging

Layer / File(s)	Summary
Coordinate merge behavior dascore/utils/coordmanager.py, tests/test_utils/test_coordmanager_utils.py	Coordinate merging retrieves each named coordinate independently and snaps only the dimension coordinate. Tests verify that associated values and dtypes remain unchanged.

Index null-step handling

Layer / File(s)	Summary
Index envelope dtype preservation dascore/io/index/backend.py, tests/test_io/test_index/test_index_edge_cases.py	Envelope columns use explicit object dtype. Regression coverage verifies that stepless numeric coordinates retain float64 null steps after backend queries.

Possibly related PRs

• DASDAE/dascore#644: Both PRs modify coordinate retrieval and construction in related code paths.
• DASDAE/dascore#748: Both PRs address temporal null handling and datetime/timedelta coordinate behavior.
• DASDAE/dascore#757: Both PRs modify envelope-column handling in the index backend.

Suggested labels: IO

Mergeability Score: ⚪ Minimal · up to e957f

This PR updates Febus G1 time metadata, preserves sample acquisition spans, and fixes coordinate and index handling; no actionable merge-blocking risk remains after normal checks and review.

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Description check	✅ Passed	The description clearly explains the problems, changes, tests, documentation, changelog, and remaining optional checklist items.
Title check	✅ Passed	The title clearly identifies the primary Febus G1 sample-window change and related coordinate fixes.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
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Actionable comments posted: 1

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Inline comments:
In `@tests/test_utils/test_coordmanager_utils.py`:
- Around line 54-70: Strengthen test_merge_keeps_associated_coord_values by
assigning distinct quality values to cm2, introducing a small gap between the
managers, and invoking merge_coord_managers with a non-None snap_tolerance.
Assert that the merged quality values are the concatenation of each manager’s
own values, preserve the expected dtype, and verify the merged time dimension
mapping.

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• dascore/io/febus/core.py
• dascore/io/febus/g1utils.py
• dascore/io/index/backend.py
• dascore/utils/coordmanager.py
• tests/test_io/test_common_io.py
• tests/test_io/test_febus/test_febusbsl.py
• tests/test_io/test_febus/test_febusg1.py
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• tests/test_io/test_common_io.py

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✅ All modified and coverable lines are covered by tests.
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[d-chambers]

Good catch on the merge test — both points were right.

The two managers carried identical quality values (cm2 was derived from cm1 by offsetting time only), so concatenating the first manager's values twice would have passed. They now differ by a constant.

The more useful half was the snapping path: without a snap_tolerance, _snap_coords returns immediately, so the part of the change that restricts snapping to the dimension coordinate was never exercised. The test now merges with snap_tolerance=1.3 and an offset that lands inside it.

Verified the strengthened test catches each half of the fix independently:

• reverting coord_map[coord_name] to coord_map[dim] → AssertionError on the values
• dropping the coord_name == dim guard around snapping → CoordMergeError, since a stepless coord has no step to build a tolerance from

Pushed in e957f1d.