feat: Add SBE 911+ HEX reader support

[eleanorfrajka]

Summary

• Extends SbeHexReader to handle SBE 911plus/917plus .hex files alongside the existing SBE37 family, using a single-class family-dispatch architecture.
• Adds detect_sbe_hex_family(), a new * key = value header parser, and an index-keyed xmlcon channel-map reader that correctly handles dual T/C and all 8 auxiliary voltage channels.
• Implements a table-driven dataset builder using seabirdscientific's frequency converters (convert_temperature_frequency, convert_pressure_digiquartz, convert_conductivity, convert_sbe43_oxygen), fixing ctdproc's hardcoded channel wiring.
• Constructs the time coordinate from System UpLoad Time + scan index × sample_interval (derived from Number of Scans Averaged / 24 Hz), since 911+ files carry no per-scan "date time" column.
• Fixes 7 silent failure traps in the existing SBE37 path (zero-substitution fallbacks, swallowed calibration parse errors, first-index-wins sensor deduplication).
• Corrects mislabelling: FluoroWetlabECO_AFL_FL_Sensor output is fluorescence, not chlorophyll.
• Commits a trimmed real-cruise fixture (MIXSED2_000.hex, 500 scans, + .xmlcon) and adds an end-to-end integration test against it.

Variables produced for a full 911+ configuration (dual T/C, 8 aux channels)

temp, cond, press, temp2, cond2, oxygen, oxygen_ml_l, fluorescence, turbidity, altimeter, transmissometer, volt0_raw (user polynomial / UVP6), volt3_raw (pH raw voltage), nmea_latitude, nmea_longitude

Sensors declared NotInUse are skipped with a logged explanation. Sensors present in the xmlcon but without a conversion implementation store raw voltage and log a warning rather than silently disappearing.

Breaking changes

• SbeHexReader.format_name() changes from "SeaBird SBE37 HEX" to "SeaBird SBE HEX". Any downstream code that hardcodes the old string to identify this reader will need updating.
• Calibration-coefficient fallbacks that previously substituted zeros (temperature compensation, T/P in conductivity conversion) now raise ValueError instead. Files that previously loaded with wrong silent substitutions will now error; fix: supply the correct xmlcon.
• SBE37SM is no longer the silent fallback for an unrecognised SBE37 device type — it now raises ValueError. The 911+ path never uses this code.

Test plan

• pytest tests/readers/test_sbe_hex_reader.py -v — all tests pass
• Added multiple versions of *hex/*xmlcon files to tests/readers/fixtures/ for SBE911+

Test fixtures added

All .hex files are trimmed to ~500 scans (header preserved verbatim). MIXSED2_000.hex is the primary end-to-end fixture; the others exercise specific xmlcon configurations.

File	Family	CTD SN	Seasave	Voltage words	Notes
m84_3_287_short.hex	911+	1294	7.20c	5	Old XMLCON (pre-7.22, no Coefficients[@equation] wrapper)
64PE426_000_1_short.hex	911+	1294	7.21d	2	2 volt words suppressed
msm_021_1_168_short.hex	911+	1294	7.21f	4
MSM72_002_2_short.hex	911+	1717	7.22	3	1 volt word suppressed
M104_154_01_short.hex	911+	5283	7.22.4	5	PAR + SPAR sensors
PS129_014_01_short.hex	911+	1374	7.23.1	4	Southern Ocean (55°S)
P503_358_short.hex	911+	1294	7.25.0.151	4
M166_025_1_short.hex	911+	1294	7.26.7.107	2	2 volt words suppressed
m212_005_short.hex	911+	4145	7.26.7.121	4
msm_142_1_056_short.hex	911+	4823	7.26.7.121	4
MIXSED2_000.hex	911+	4798	7.26.7.121	4	Primary end-to-end fixture; full cruise file

[Copilot]

Pull request overview

Adds Sea-Bird SBE 911plus/917plus .hex support to the existing SBE HEX reader path, expands parameter/mapping metadata for newly produced variables, and introduces multiple real-world fixtures plus integration tests to validate end-to-end decoding and calibration.

Changes:

• Extend SbeHexReader/sbe_hex_reader to detect and parse SBE911+ HEX + XMLCON configurations and build calibrated datasets.
• Add/adjust parameter metadata and mappings (notably par, plus updated oxygen/salinity metadata).
• Add new SBE911+ fixtures and integration tests; adjust reader completeness tests to ignore helper dataclasses.

Reviewed changes

Copilot reviewed 30 out of 31 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
seasenselib/readers/sbe_hex_reader.py	Implements/extends SBE911+ parsing, XMLCON mapping, and dataset construction.
tests/readers/test_sbe_hex_reader.py	Adds extensive SBE911+ unit/integration tests and updates existing expectations.
tests/test_readers_completeness.py	Excludes helper dataclasses from “reader class” enforcement.
seasenselib/parameters.py	Adds par and updates parameter metadata (incl. oxygen, fluorescence, salinity).
seasenselib/knowledge/pipeline/metadata_enrichment/parameters_metadata.json	Mirrors metadata updates for enrichment pipeline.
seasenselib/knowledge/pipeline/mapping/mappings_default.json	Adds default name mappings for par.
seasenselib/knowledge/pipeline/mapping/allowed_parameters.json	Adds par to allowed parameters.
tests/readers/fixtures/*.hex, tests/readers/fixtures/*.XMLCON, tests/readers/fixtures/*.xmlcon	Adds real-world SBE911+ fixtures for test coverage.
.gitignore	Ignores .coverage file.

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