GEOPY-2731: Replace InputFile for BaseUIJson class

[domfournier]

GEOPY-2731 - Replace InputFile for BaseUIJson class

[Copilot]

Pull request overview

This PR migrates curve-apps away from geoh5py.ui_json.InputFile toward the newer geoh5py.ui_json.UIJson / geoapps_utils.base.Options flow, updating both runtime drivers/apps and the test suite to build and run from UIJson-backed parameter models.

Changes:

• Updated tests and drivers to use UIJson.read()/write() and Options.build(...) instead of InputFile.read_ui_json()/write_ui_json().
• Refactored Peak Finder parameters from the legacy BaseParams pattern to an Options model and adjusted driver/app integration accordingly.
• Tweaked UI JSON assets (e.g., Peak Finder group dataType entries) and contour fixed-contour serialization behavior.

Reviewed changes

Copilot reviewed 18 out of 18 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
tests/trend_line_run_test.py	Updates Trend Lines tests to use UIJson and new build(...) calling convention.
tests/peak_finder/peak_finder_test.py	Updates Peak Finder tests to build params directly from objects/kwargs rather than UIJson string payloads.
tests/parameters_test.py	Switches validation assertions to UIJson access patterns and updated contour fixed-contour serialization expectations.
tests/edge_detection_run_test.py	Updates Edge Detection tests to use UIJson and Options.build(...).
tests/contour_test.py	Adjusts ContourParameters.build(...) invocation to match new API.
curve_apps/trend_lines/driver.py	Removes InputFile constructor support and imports in favor of Options.
curve_apps/peak_finder/peak_finder.geoh5	Removes the (LFS pointer) .geoh5 asset from the repo.
curve_apps/peak_finder/params.py	Refactors Peak Finder params into an Options model.
curve_apps/peak_finder/layout.py	Updates a layout html.Div to explicit children= with flex styling.
curve_apps/peak_finder/driver.py	Updates Peak Finder driver to use Options patterns and adds get_line_field helper.
curve_apps/peak_finder/base_dash.py	Migrates dash base application from BaseParams to Options/ui_json.flatten().
curve_apps/peak_finder/application.py	Switches CLI entrypoint to UIJson.read and PeakFinderParams.build(...); simplifies trigger handling.
curve_apps/edges/driver.py	Removes InputFile constructor support and imports in favor of Options.
curve_apps/driver.py	Removes InputFile constructor handling from BaseCurveDriver.
curve_apps/contours/options.py	Adds serializer for fixed contours to persist as comma-separated string in ui.json output.
curve_apps/contours/driver.py	Removes InputFile constructor support and imports in favor of Options.
curve_apps-assets/uijson/peak_finder.ui.json	Adds dataType: Float metadata for Peak Finder data groups.
curve_apps-assets/uijson/contours.ui.json	Removes one meshType entry from contour ui.json.

Suppressed comments (1)

curve_apps/peak_finder/application.py:1983

• In the __main__ launch-dash path, _ = peak_parameters.survey no longer "triggers computation" because PeakFinderParams.survey is now just a plain field (the computed in-memory survey copy lives on PeakFinder.survey). As written, this line is a no-op and the comment is misleading.

    if peak_parameters.launch_dash:
        with peak_parameters.geoh5.open(mode="r"):
            _ = peak_parameters.survey  # Trigger computation
            logger.info("Loaded. Launching peak finder app . . .")
            PeakFinder(peak_parameters).run()

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[codecov]

Codecov Report

❌ Patch coverage is 81.89655% with 21 lines in your changes missing coverage. Please review.
✅ Project coverage is 64.57%. Comparing base (dfec2e9) to head (ae7a8a2).

Files with missing lines	Patch %	Lines
curve_apps/peak_finder/driver.py	50.00%	6 Missing and 3 partials ⚠️
curve_apps/peak_finder/application.py	66.66%	7 Missing ⚠️
curve_apps/peak_finder/base_dash.py	72.22%	2 Missing and 3 partials ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop     #134      +/-   ##
===========================================
- Coverage    67.97%   64.57%   -3.41%     
===========================================
  Files           20       20              
  Lines         2364     2120     -244     
  Branches       325      323       -2     
===========================================
- Hits          1607     1369     -238     
+ Misses         654      651       -3     
+ Partials       103      100       -3     

Files with missing lines	Coverage Δ
curve_apps/contours/driver.py	72.41% <100.00%> (-0.92%)	⬇️
curve_apps/contours/options.py	96.87% <100.00%> (+0.26%)	⬆️
curve_apps/edges/driver.py	85.71% <100.00%> (-0.37%)	⬇️
curve_apps/peak_finder/layout.py	100.00% <ø> (ø)
curve_apps/peak_finder/params.py	90.62% <100.00%> (-3.79%)	⬇️
curve_apps/trend_lines/driver.py	79.45% <100.00%> (-0.55%)	⬇️
curve_apps/peak_finder/base_dash.py	58.87% <72.22%> (-2.37%)	⬇️
curve_apps/peak_finder/application.py	31.52% <66.66%> (+0.59%)	⬆️
curve_apps/peak_finder/driver.py	75.13% <50.00%> (-2.24%)	⬇️

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[gmcga]

Noticed a couple of small potential issues, other than that seems good!

[gmcga]

run creates a local out_group but neither stores or returns it, which will probably cause problems with the new Driver.start as it will receive result = None

[domfournier]

Technically no issue because the driver.out_group is not None. But agree that update_monitoring_directory(out_group) is already in the start

[gmcga]

Looks good