GEOPY-2384: merge geoapps 0.12.0 to develop branch by sebhmg · Pull Request #732 · MiraGeoscience/geoapps

sebhmg · 2025-08-14T02:41:46Z

GEOPY-2384 - merge geoapps 0.12.0 to develop branch

sebhmg

need to fix dependency declaration for new indirect dependencies

sebhmg · 2025-11-26T23:04:10Z


 simpeg-archive = {version = ">=0.11.0.1, <0.11.0.2", source = "pypi", allow-prereleases = true}
 #simpeg-archive = {git = "https://github.com/MiraGeoscience/simpeg.git", rev = "feature/simpeg_archive"}



issue: must force some indirect dependencies to conda, so that they are not locked on their pypi version

# Conflicts: # geoapps/block_model_creation/driver.py # geoapps/block_model_creation/params.py # geoapps/inversion/potential_fields/application.py # geoapps/utils/write_default_uijson.py # tests/data_transfer_test.py # tests/write_default_uijson_test.py

Copilot

Pull request overview

This PR merges geoapps 0.12.0 into develop, aligning the codebase with updated dependency stacks (notably SimPEG drivers “Options” APIs), updated UI/app wiring, and a Python version bump across packaging, CI, and environment lockfiles.

Changes:

Bump supported Python versions and CI matrix (docs/scripts/lockfiles updated accordingly).
Refactor multiple apps/tests to use new simpeg_drivers.*.options / *.build(...).flatten() patterns.
Replace/remove legacy drivers/params and some test/util scripts as part of the merge.

Reviewed changes

Copilot reviewed 54 out of 58 changed files in this pull request and generated 6 comments.

Show a summary per file

File	Description
tests/write_default_uijson_test.py	Removed test for default ui.json writer.
tests/run_tests/apps_run_test.py	Updated app run tests for new parameter structures/names.
tests/run_tests/apps_inversion_test.py	Updated inversion tests to new Options API and initializer usage.
tests/data_transfer_test.py	Removed data transfer/block model driver unit tests.
README.rst	Updated stated Python version (3.10 → 3.12).
README-dev.rst	Updated dev Python versions and dev workflow commands/docs.
pyproject.toml	Major dependency refresh; updated ruff target version; updated git dependencies.
package.rst	Updated stated minimum Python version (3.10+ → 3.12+).
install.bat	Updated default Python version used by installer (3.10 → 3.12).
geoapps/utils/write_default_uijson.py	Removed utility for writing default ui.json files.
geoapps/iso_surfaces/application.py	Updated surface-apps driver import/name.
geoapps/inversion/potential_fields/magnetic_vector/application.py	Migrated to new simpeg_drivers magnetic vector Options classes and base initializer handling.
geoapps/inversion/potential_fields/magnetic_scalar/application.py	Migrated to new simpeg_drivers magnetic scalar Options classes and base initializer handling.
geoapps/inversion/potential_fields/gravity/notebook.ipynb	Updated notebook LFS pointer.
geoapps/inversion/potential_fields/gravity/application.py	Migrated to new simpeg_drivers gravity Options classes and base initializer handling.
geoapps/inversion/potential_fields/init.py	Removed `flake8: noqa` marker.
geoapps/inversion/electromagnetics/notebook.ipynb	Updated notebook LFS pointer.
geoapps/inversion/electromagnetics/driver.py	Modified driver module main/entrypoint section.
geoapps/inversion/electromagnetics/application.py	Adjusted preprocessing integration to pass entities vs uuids.
geoapps/inversion/electricals/application.py	Migrated to DC/IP 3D Options classes; refactored initializer handling and params flattening.
geoapps/inversion/components/preprocessing.py	Updated active channel detection and return types (entities vs uuids).
geoapps/inversion/base_inversion_application.py	Refactored base inversion app to Options API + forward/inversion split for write-out.
geoapps/inversion/init.py	Removed old exported DRIVER_MAP / legacy imports.
geoapps/edge_detection/application.py	Updated curve-apps import path (`params` → `options`).
geoapps/contours/application.py	Updated curve-apps import path (`params` → `options`).
geoapps/block_model_creation/params.py	Removed legacy params class.
geoapps/block_model_creation/driver.py	Removed legacy driver implementation.
geoapps/block_model_creation/constants.py	Renamed expansion parameter key (`expansion_fact` → `expansion_factor`) in defaults/ui.json.
geoapps/block_model_creation/application.py	Switched to grid-apps driver/options for block model creation.
geoapps/base/dash_application.py	Migrated base dash app from BaseParams to Options; updated param flattening logic.
geoapps/base/application.py	Migrated base app params typing to Options/BaseInversionOptions.
environments/py-3.13-win-64.conda.lock.yml	Added new Python 3.13 Windows lockfile.
environments/py-3.13-win-64-dev.conda.lock.yml	Added new Python 3.13 Windows dev lockfile.
environments/py-3.13-linux-64.conda.lock.yml	Added new Python 3.13 Linux lockfile.
environments/py-3.13-linux-64-dev.conda.lock.yml	Added new Python 3.13 Linux dev lockfile.
environments/py-3.11-win-64.conda.lock.yml	Removed old Python 3.11 Windows lockfile.
environments/py-3.10-win-64.conda.lock.yml	Removed old Python 3.10 Windows lockfile.
environments/py-3.10-win-64-dev.conda.lock.yml	Removed old Python 3.10 Windows dev lockfile.
environments/env-python-3.13.yml	Updated env template to Python 3.13.
environments/env-python-3.11.yml	Removed Python 3.11 env template.
docs/environment.yml	Updated docs env Python version (3.10 → 3.12).
docs/content/installation.rst	Updated installation wording for Python 3.12.
deps-lock-config.yaml	Updated deps-lock Python versions (3.12/3.13).
.github/workflows/python_analysis.yml	Updated CI python versions and codecov reference version.

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 if __name__ == "__main__":
-    input_file = sys.argv[1]
+    # input_file = sys.argv[1]
+    input_file = r"C:\Users\dominiquef\Desktop\Tests\Temp\EM1DInversion_1756331920.json"
    inversion(input_file)


+    def __init__(self, ui_json=None, geoh5=str | Path | None | Workspace, **kwargs):
        if ui_json is not None and Path(ui_json.path).exists():
-            self.params = self._param_class(ui_json)
+            self.params = self._param_class.build(ui_json)
        else:
-            app_initializer.update(kwargs)
-            try:
-                self.params = self._param_class(**app_initializer)
-
-            except AssociationValidationError:
-                for key, value in app_initializer.items():
-                    if isinstance(value, uuid.UUID):
-                        app_initializer[key] = None
-
-                self.params = self._param_class(**app_initializer)
-            extras = {
-                key: value
-                for key, value in app_initializer.items()
-                if key not in self.params.param_names
+            if isinstance(geoh5, str | Path | None):


+            initializer = self._app_initializer.copy()
+            initializer.update(kwargs)
+
+            if isinstance(geoh5, str | Path | None):
+                geoh5 = Workspace(geoh5)
+
+            initializer["geoh5"] = geoh5


@@ -28,7 +28,7 @@
    "horizontal_padding": None,
    "bottom_padding": None,
    "depth_core": None,
-    "expansion_fact": None,
+    "expansion_factor": None,
    "new_grid": None,
    "generate_sweep": False,


 [tool.poetry.dependencies]
-python = ">=3.10, <3.13"
-
-fiona = "~1.9.2"
-gdal = "^3.6.3"
-matplotlib = "~3.8.4"  # also in simpeg and geoana
-
-dask = {version = "2025.3.*", extras = ["distributed"]}  # also in simpeg[dask]
-discretize = "0.11.*"  # also in simpeg, octree-creation-app
-numpy = "~1.26.0" # also in geoh5py, simpeg
-scipy = "~1.14.0"
-
-## dependencies for UI
-#---------------------
-dash = "^2.12"
-dash-daq = "0.5.*"
-flask = "~3.0.3"
-ipyfilechooser = "0.6.*"
-ipywidgets = "^7.8.0"
+dask = "~2025.3.0"  # also in simpeg[dask]
+discretize = "~0.12.0"  # also in simpeg, grid-apps
+distributed = "~2025.3.0"  # for dask[distributed]


    @params.setter
-    def params(self, params: BaseParams):
-        assert isinstance(params, BaseParams), (
-            f"Input parameters must be an instance of {BaseParams}"
+    def params(self, params: Options):
+        assert isinstance(params, Options | Options), (
+            f"Input parameters must be an instance of {Options} or {Options}."
        )


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…into GEOPY-2384

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…into GEOPY-2384

sebhmg requested review from Copilot and domfournier and removed request for Copilot August 14, 2025 02:41

github-actions Bot changed the title ~~Geopy 2384~~ GEOPY-2384: merge geoapps 0.12.0 to develop branch Aug 14, 2025

github-advanced-security AI found potential problems Aug 14, 2025

View reviewed changes

Comment thread .github/workflows/issue_to_jira.yml Fixed

Comment thread .github/workflows/pr_add_jira_summary.yml Fixed

Comment thread .github/workflows/python_analysis.yml Fixed

Comment thread .github/workflows/python_analysis.yml Fixed

sebhmg changed the base branch from main to develop August 14, 2025 14:55

domfournier added 7 commits August 26, 2025 13:14

Fix imports

0532cd5

Continue fiixing imports

0ef94ff

Multi fixes for inversion apps

bebec89

Remove internal block_model app. FIx test

63b8a25

Bump versions according to GEOPY-2403

7186ff6

Use name of test for geoh5

704e0d1

Re-lock with release branches

bfdea17

sebhmg commented Nov 26, 2025

View reviewed changes

sebhmg and others added 2 commits February 9, 2026 21:05

Change versions to 3.12

6b0d99a

Copilot AI review requested due to automatic review settings June 15, 2026 17:08

Copilot started reviewing on behalf of domfournier June 15, 2026 17:09 View session

Copilot AI reviewed Jun 15, 2026

View reviewed changes

domfournier and others added 11 commits June 15, 2026 15:25

Begin refactoring of EM1D driver

68dda0f

Re-lock with optional pywebview

c8ec485

Remove dependecy on pyside (Qt). Good run with gravity and susc

56f5b8a

[pre-commit.ci] auto fixes from pre-commit.com hooks

96298e3

for more information, see https://pre-commit.ci

Update pre-commit pycln

5c011fb

Use custom pylint location

2bc5cda

Fix issue with changing component

355f0e2

Update layouts, make mesh options

d10660a

Merge branch 'GEOPY-2384' of https://github.com/MiraGeoscience/geoapps …

afbe118

…into GEOPY-2384

[pre-commit.ci] auto fixes from pre-commit.com hooks

ab7617e

for more information, see https://pre-commit.ci

Fix DC inversion notebook

2c70378

domfournier added 17 commits June 18, 2026 15:10

Merge branch 'GEOPY-2384' of https://github.com/MiraGeoscience/geoapps …

d843a35

…into GEOPY-2384

Update notebooks for inversion

bddacf9

Code consolidation

926804e

Add file change to test

e2e9100

Remove BaseDriver and Params. Fix octree creation app with name changes

35fc2d7

Fix block model app.

ab9b78f

Review notebooks

a006b74

Add unit test for octree app

33143c3

Fixes for scatter plot

6fb6b3e

Get rid of more constant files

a716fcc

Refresh calculator notebook

4580faf

Review test contour app

9771c9a

Move rename app_initializer

7621803

Run the scattrer app from main

4e7da1b

Test scatter callbacks. fix imports

6c7b115

Move app initializer

51d43ce

Remove clustering app

5b91567

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GEOPY-2384: merge geoapps 0.12.0 to develop branch#732

GEOPY-2384: merge geoapps 0.12.0 to develop branch#732
sebhmg wants to merge 37 commits into
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GEOPY-2384

sebhmg commented Aug 14, 2025 •

edited

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		simpeg-archive = {version = ">=0.11.0.1, <0.11.0.2", source = "pypi", allow-prereleases = true}
		#simpeg-archive = {git = "https://github.com/MiraGeoscience/simpeg.git", rev = "feature/simpeg_archive"}

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sebhmg commented Aug 14, 2025 •

edited

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