Feature/uijson

[domfournier]

No description provided.

[codecov]

Codecov Report

❌ Patch coverage is 86.89655% with 19 lines in your changes missing coverage. Please review.
✅ Project coverage is 86.10%. Comparing base (7238a55) to head (6be47be).

Files with missing lines	Patch %	Lines
geoapps_utils/base.py	85.55%	7 Missing and 6 partials ⚠️
geoapps_utils/run.py	86.48%	2 Missing and 3 partials ⚠️
geoapps_utils/param_sweeps/generate.py	91.66%	1 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop     #217      +/-   ##
===========================================
+ Coverage    85.70%   86.10%   +0.40%     
===========================================
  Files           19       18       -1     
  Lines         1196      950     -246     
  Branches       155      126      -29     
===========================================
- Hits          1025      818     -207     
+ Misses         129       97      -32     
+ Partials        42       35       -7     

Files with missing lines	Coverage Δ
geoapps_utils/param_sweeps/driver.py	81.60% <100.00%> (-0.21%)	⬇️
geoapps_utils/param_sweeps/generate.py	78.94% <91.66%> (+4.58%)	⬆️
geoapps_utils/run.py	88.34% <86.48%> (-4.25%)	⬇️
geoapps_utils/base.py	85.10% <85.55%> (-6.92%)	⬇️

... and 2 files with indirect coverage changes

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[Copilot]

Pull request overview

This PR updates geoapps_utils to use geoh5py’s newer UIJson API instead of InputFile/legacy params, and refactors the run + param-sweep utilities and tests to align with that shift.

Changes:

• Refactor geoapps_utils.base.Driver and geoapps_utils.run to accept/operate on UIJson (including BytesIO) and update result persistence behavior.
• Update param sweep generation/driver logic to read/write UIJson and adjust tests to use a shared uijson_path fixture.
• Update the base UI template (base.ui.json) and dependency pin/lockfiles for the geoh5py UIJson feature branch.

Reviewed changes

Copilot reviewed 29 out of 29 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
tests/uijson_run_test.py	Reworks UIJson execution tests to use UIJson + a shared fixture and validates output file expectations.
tests/param_sweeps/generate_test.py	Updates sweep generation test to use an Options subclass with a default UIJson template.
tests/param_sweeps/driver_test.py	Updates sweep driver tests to serialize from options.ui_json and use a nested model template.
tests/driver_test.py	Removes legacy driver/options tests superseded by the new base/UIJson testing approach.
tests/dataclass_test.py	Updates dataclass tests for UIJson-backed build/flatten behavior and nested model defaults.
tests/conftest.py	Adds a uijson_path fixture that materializes a UIJson file for integration-style tests.
tests/base_test.py	Adds new base-level tests around UIJson serialization, driver start, warnings, and error cases.
pyproject.toml	Pins geoh5py to the feature/uijson git rev.
geoapps_utils/run.py	Migrates run helpers to UIJson and adds support for BytesIO ui.json references.
geoapps_utils/param_sweeps/generate.py	Updates sweep file generation to read/write via UIJson.
geoapps_utils/param_sweeps/driver.py	Updates sweep trial file writing to use UIJson.set_values() + UIJson.write().
geoapps_utils/driver/params.py	Removes the legacy BaseParams implementation.
geoapps_utils/base.py	Refactors Driver.start() and Options to build from UIJson, adds deprecation plumbing for InputFile, and updates serialization/flattening.
geoapps_utils-assets/uijson/base.ui.json	Updates out_group from a primitive to a structured UIJson group object.
environments/py-3.14-win-64.conda.lock.yml	Lockfile refresh for updated dependency graph (incl. geoh5py revision).
environments/py-3.14-win-64-dev.conda.lock.yml	Dev lockfile refresh for updated dependency graph.
environments/py-3.14-linux-64.conda.lock.yml	Lockfile refresh for updated dependency graph.
environments/py-3.14-linux-64-dev.conda.lock.yml	Dev lockfile refresh for updated dependency graph.
environments/py-3.13-win-64.conda.lock.yml	Lockfile refresh for updated dependency graph.
environments/py-3.13-win-64-dev.conda.lock.yml	Dev lockfile refresh for updated dependency graph.
environments/py-3.13-linux-64.conda.lock.yml	Lockfile refresh for updated dependency graph.
environments/py-3.13-linux-64-dev.conda.lock.yml	Dev lockfile refresh for updated dependency graph.
environments/py-3.12-win-64.conda.lock.yml	Lockfile refresh for updated dependency graph.
environments/py-3.12-win-64-dev.conda.lock.yml	Dev lockfile refresh for updated dependency graph.
environments/py-3.12-linux-64.conda.lock.yml	Lockfile refresh for updated dependency graph.
environments/py-3.12-linux-64-dev.conda.lock.yml	Dev lockfile refresh for updated dependency graph.

Suppressed comments (2)

geoapps_utils/base.py:136

• isinstance(results, tuple | list) will raise TypeError at runtime for the same reason (union types are not allowed in isinstance). Use (tuple, list) or a sequence ABC instead.

                elif isinstance(results, tuple | list):

geoapps_utils/base.py:215

• isinstance(out_group, self._out_group_class | None) is invalid (| None cannot be used inside isinstance). Check None explicitly or include type(None) in a tuple of types.

        if not isinstance(out_group, self._out_group_class | None):

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