test

.github/workflows/issue_to_jira.yml

@@ -17,5 +17,5 @@ jobs:
       components: '[{"name": "simpeg"}]'
     secrets:
       JIRA_BASE_URL: ${{ secrets.JIRA_BASE_URL }}
-      JIRA_API_TOKEN: ${{ secrets.JIRA_API_TOKEN }}
-      JIRA_USER_EMAIL: ${{ secrets.JIRA_USER_EMAIL }}
+      JIRA_API_TOKEN: ${{ secrets.JIRA_API_TOKEN_WRITE }}
+      JIRA_USER_EMAIL: ${{ secrets.JIRA_USER_EMAIL_WRITE }}

.github/workflows/pr_jira_actions.yml

@@ -6,7 +6,6 @@ on:
 
 jobs:
   call-workflow-pr_jira_actions:
-    if: github.event.action != 'edited' || github.event.changes.title != null
     uses: MiraGeoscience/CI-tools/.github/workflows/reusable-jira-pr_actions.yml@v3
     permissions:
       contents: read

.github/workflows/python_analysis.yml

@@ -20,7 +20,7 @@ on:
 permissions: {}
 
 concurrency:
-  group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
+  group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
 
 jobs:

.github/workflows/security_scan.yml

@@ -20,7 +20,7 @@ on:
 permissions: {}
 
 concurrency:
-  group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
+  group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
 
 jobs:

.gitignore

@@ -1,4 +1,4 @@
-# Byte-compiled / optimized / DLL files
+# Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
 *$py.class

.pre-commit-config.yaml

@@ -22,7 +22,7 @@ repos:
     -   id: pycln
         args: [--config=pyproject.toml]
 -   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.15.15
+    rev: v0.15.20
     hooks:
     -   id: ruff-check
         args:
@@ -42,7 +42,7 @@ repos:
 #        ]
 #        exclude: ^(docs|simpeg_drivers-assets)/
 -   repo: https://github.com/codingjoe/relint
-    rev: 3.3.1
+    rev: 3.5.0
     hooks:
     -   id: relint
         args: [-W]  # to fail on warnings

docs/_toc.yml

@@ -44,4 +44,5 @@ chapters:
         - file: case_studies/Forrestania/python_code/unconstrained_gravity_inv_training
         - file: case_studies/Forrestania/python_code/unconstrained_magnetics_inv_training
         - file: case_studies/Forrestania/python_code/joint_grav_mag
+- file: release_notes
 - file: THIRD_PARTY_SOFTWARE

docs/plate-simulation/standalone.md

@@ -26,13 +26,14 @@ The parameters controlling the forward simulation are defined through a SimPEG f
 must ensure that the SimPEG group has been previously edited with appropriate options, including a topography object,
 a survey object and data components to simulate.
 
+Oftentimes, the user would like to model a thin plate that might push the resolution limits of the finite-volume approach taken by SimPEG.  In this case, the LeroiAir application may be used instead to model the secondary fields from a rectangular prism with a known conductivity-thickness.  To use the LeroiAir application for the forward modelling, select the ``Use LeroiAir`` checkbox.
+
 ```{figure} images/methodology/data/simpeg_group_options.png
 ---
 width: 300pt
 align: center
 ---
-Selecting the initialized forward modelling SimPEG group and naming the group that will store the plate
-simulation results.
+Selecting the initialized forward modelling SimPEG group, or optionally choosing LeroiAir for improved thin plate modelling and providing a name for the results group.
 ```
 
 - Create the required SimPEG group within Geoscience ANALYST through the

docs/release_notes.md

@@ -0,0 +1,258 @@
+# Release Notes
+
+## Release 0.5.0 (2026-06-05)
+
+### Plate Simulation
+* Create UI and Driver for the classification of EM anomalies
+* Export best match models as Maxwell plates (w/ GEOPY-2661)
+* Finalize Anglo Accelerated Development with synthetic example
+* Add documentation for plate sweep and match
+* Add summary option for plate sweep
+* Change reference of Plate from center-center to top-center
+* Plate Match: Attach figure with comparative plot of scaled obs versus simulated data
+* Make simpeg group names in plate-simulation more clear in the ui.jsons
+### Mag/Grav
+* MVI: Add small value to reference amplitude if reference are used
+* Implement MVI with PDE inversion
+* Use cyclic colormap by default for declination angle model
+* Change data groups saved for MVI as requested by users
+* Revert legacy behaviour with reference model ON by default
+### FEM/TEM
+* Implement arbitrary receiver orientations (u-v-w) for airborne EM surveys
+* Relabel ui.json for TEM using Vertical, inLine, cross-line
+* Airborne FEM coaxial do not rotate transmitter, and ppm normalization needs to be adjusted
+* Allow rotated receivers for ground EM survey
+* Remove dependency on Tx frequency for airborne FEM survey
+### Natural Sources
+* Incorporate MobileMT inversion with SimPEG (apparent conductivity only) DC/IP
+### DC/IP
+* Parallelize batch 2D inversion
+* Improve topography augmentation for DC and MT
+* Accept 2D inversion mesh (DrapeModel) in sensitivity_cutoff application
+* Add tooltips to missing IP inversion inputs
+* DC2D with single line crashes on run with n_workers set
+* Investigate edge cells recovered with DC2D inversions
+### Joint Inversion
+* Joint surveys using mvi crashes with dimension mismatch
+* PGI: Add checks for reference model present on inversion groups. Return clean GeoAppsError if not
+* Research auto-scaling strategy for cross-gradient regularization terms
+* Membership flip between iterations in PGI
+* Add PGI documentation
+### General Utilities
+* Add dip_direction to list of supported variables by plate_sweep
+* Micro-management of auto-scaling of misfits with tiles, channels and within joint inversions
+* Clip limits of topography extent based on mesh extent
+* Add datetime stamp to simpeg.log and simpeg.out file names
+* Add validator for negative on NDV values in uncertainties
+* Transfer visual parameters Core volume settings from the input mesh to the inversion mesh (if present)
+* Add optional out_group to Depth of Investigation app
+### Bugs and Maintenance
+* Update GravityUIJson with new data forms
+* Conductivity/Resistivity switcher doesn't make sense for joint mvi/mag
+* Synthetic topography for runtests is overly sampled
+* Fix capitalization in labels and tooltips of ui.json files
+* Update minimum requirement to python >=3.12, <3.14 and numpy 2.*
+* Implement direct run_commands to specific modules for forwards and inversions
+* DCIP 2D crash on line ID selection
+* PGI failure on petrophysical model with air cells
+* Inversion stalls on tiling for large problems during redistribution of clusters
+* Refactor extent property calculation for all grid objects
+* Consolidate code for plate model definition between different repos
+* Update dictionary to choose driver from run_command
+* Triangulation crash on input surface
+* Regularization parameters of sub-drivers always over-written by joint parameters
+* Inversion crash on tile mesh creation transferring data
+* Refresh screenshots of UIJsons in docs
+
+## Release 0.4.0 (2026-01-06)
+
+* Support 3D vector property group for orientation of rotated gradients
+* Add rotated_gradient to 2D inversions
+* Refactor components of inversion options
+* single entry point to run any application
+* Joint inversion: PGI
+* Migrate param-sweeps to geoapps-utils
+* Migrate plate-simulation to simpeg-drivers
+* Hook up 2D rotated gradients to batch 2D inversions
+* Investigate random failure of cross-gradient test
+* Amplitude model stuck on upper bound for MVI
+* Change default sensitivity threshold for DC inversions
+* Fix plate simulation label and tooltip
+* Speed up saving directive by keeping the file open during series
+* Change units displayed on selector of data type for V/Am^2
+* Investigate slow startup time for TEM inversion
+* Make pydantic validator issues returns clean GeoAppsError option
+* Add case study with Forestania datasets
+* Improve rotated gradient on octree change with average cell dim
+* Add files via upload
+* Add docs on rotated gradient options
+* Force use of MKL for Blas implementation
+* Bad flipping of large loop orientation
+* Refactor of the Factory classes
+* Migrate octree-creation-app to grid-app
+* Investigate double-print of Geoapps-Error
+* Can't handle topography grid with nan
+* Parallelize 1D simulations
+* Forward simulation of potential fields always forms the full J
+* Re-order parameters to mimic the order in metadata
+* Add check for negative cond/res model values
+* Lost control on reference angles for MVI
+* Add core depth to the max-min elevation of the survey
+* Detect issues with waveform and throw a custom GeoappsError if found
+* Add a copy group+object base in input file as it exists in the UIJson group
+* Failure of directives when using Futures for simulation
+* Create custom sweep UIjson for plate-simulation
+* Investigate speckly looking MVI models with rotated gradients
+* Make start/stop group optional, and use the plate-sim parameter instead if disabled
+* Missing grouping of EM data in save directive for joint inversions
+* Parallelize the Sweeps
+* Explore 2D gridding techniques for EM line data
+* Pydantic error on auto-mesh creation with Grid2D topography object
+* Crash on Zarr file shape for tiled inversions with disk storage
+* Crash on no-upper bound for MVI within a joint process
+* Improve parallel creation of 1D simulations
+* Investigate erratic corner cells when using rotated gradients
+* Add custom error for topography grid selected without data
+* Random failure of sensitivity cutoff app tests
+* Workers crash on creating misfits for large problems
+* Remove save directive for petrophysical model
+* Adjust target misfit down to account for number of NDV in data
+* PGI fails with single simulation selected
+* MT predicted channels missing [] indices
+* Break edge case for 1D inversion with negative elevation (release 4.7)
+* Save sensitivities option ignored (release 4.7)
+* Wrong normalization for MT
+* Speed up active from topography algorithm
+* Bring in doc of plate simulation
+* Remove out_group form ui.json
+* Cannot load results from Batch 2D inversion runs
+* DEVOPS-922: adjust or fix text in ui.json
+* Check for MVI Simpeg groups and raise error
+* Joint surveys fails validation if no starting/reference models chosen
+
+## Release 0.3.0 (2025-06-20)
+
+* Create spatial tiling estimator
+* Add a depth of investigation application
+* Add auto-meshing option for all inversions with default parameters
+* Fix simpeg-drivers pyproject still pointing to octree-creation-app/*
+* Auto-meshing: Round cell size to nearest 5 multiplier
+* Allow option for percentile cutoff in sensitivity based depth of investigation
+* Auto-meshing: Only use depth_code (no vertical pads) for potential fields and DC-IP inversions
+* Add UIJson group to hold octree creation parameters and update options
+* Octree mesh upside down
+* Refactor Params class with BaseData
+* Convert all of potential fields to BaseData params class
+* Faulty air cells in 2D inversion active
+* Reduce tests runtime
+* Use MetaSimulations instead of custom misfit mapping towards distributed process
+* Convert all DC/IP 3D/2D params to BaseData
+* Convert all EM params to BaseData
+* Convert both joint params to BaseData
+* Export uml from simpeg-drivers and design class structure for inversion parameters.
+* Selecting an active model instead of topography with surface survey option crashes
+* Update discretize to >=0.11.*
+* Cleanup constant files and data classes
+* Add version validation and write_default method to update version in …
+* Update SimPEG 0.21.2 to 0.23
+* Crash running 2D IP
+* Add custom Error for problem too large
+* Add UIJson class for gravity forward/inversion
+* Add option for MUMPS solver
+* Duplicated survey object when monitoring_directory is used
+* Resolve deprecation warnings with latest simpeg 0.23 and discretize 0.11
+* Create documentation for depth of investigation app
+* Fixup dependencies
+* Draft uml file for the UIJson/Params design
+* Update inversion docs to describe the auto-mesh option
+* Phi-d at Iter 0 shows as nan in the *.out file
+* Handle extra fields and deprecations in UIJson version validation
+* Clean up pydantic warnings
+* Implement structural orientation (rotated gradient) option to the inversion UI
+* Migrate em_inversion (EM1D) script to simpeg-drivers
+* Should update version when writing ui.json from simpeg-drivers options classes
+* Migrate FEM-1D from simpeg-drivers
+* Make lower bound for MVI visible=False
+* Add strike/dip option to the choice list of rotated_gradients.
+* Deprecate gradient_type
+* Fix warning about differing number of parameters between ui_json and data.
+* Relock on latest git dev revisions
+* Environment for coming pre-release
+* Fix UI json version tests (part of GEOPY-2049)
+* Rename params modules to options
+* Group models for L2 and LP
+* Add version to print screen
+* Allow IntegerData for active cell value model type
+* Use published dependencies, no git branches
+* Correctly declare dask for pip and dask-core for conda
+* Fixup dask dependency: do not lock on pypi
+* Use dask.distributed with workers as default behaviour
+* IP inversion with resistivity option does not convert the model to conductivity
+* Name of conductivity_model does not match the selection for resistivity
+* Change default auto-scaling to false
+* Bring back adjusted ui.json from Analyst to their respective repo
+* Bad referencing to transmitter id name
+* MVI name change breaks the forward
+* Fem1d title
+* Outdated inversion_type for 3D FDEM
+* Non-zero evaluation of the rotated gradient of a constant model
+* Sub-mesh reused on split data
+* Ensure backward compatibility of saved ui.json from Analyst 4.5 to 4.6
+
+## Release 0.2.0 (2025-02-07)
+
+* Octree mesh cell definition not update if rec array
+* Make the canny add_data optional on get_edges method
+* Crash on joint survey with apparent resistivity
+* Update simpeg fork to 0.21.2
+* Streamline geoapps-utils
+* Generate tutorial for Natural source EM
+* Add checks on waveform before sending to SimPEG
+* Training material for ATEM
+* Always check/closed EM loops and return warning
+* Fix handling of UBC ordered Octree cells
+* Add docs for validation
+* Allow input active cells instead of topography
+* Fix formatting of warning for LargeLoop. Use logging instead warning
+* Inversion: Allow for model vector to define norms
+* Re-order the inversion inputs following users comments
+* Add option to export sensitivities for all inversions
+* Enable cell/face weights in params
+* Fill in default ui.json tooltips for inversion parameters
+* Review stitching of predicted data on tipper inversion
+* Review log and out for cross-gradient inversion.
+* Regression: Crash with no-reference data
+* Group vector model orientation parameters as "Dip Direction & Dip"
+* Add option for cond/resis for all EM/DC methods
+* Flip upper and lower bound value for resistivity style inversions
+* Implement rescaling of misfit functions for joint inversion
+* Tipper inversion crashes on background_model if not constant
+* DC3D inversion reports disconnected cells
+* Ram/Disk option not working in simpeg through Analyst
+* Save sensitivities fails for MVI inversion in Analyst
+* Nan data values not handled by the inversion
+* Simpeg-drivers is adding a transmitter id to the transmitter always
+* Make the transmitter id name agnostic
+
+
+## Release 0.1.0 (2024-06-17)
+
+* Copy model to avoid applying double log
+* prepare distribution
+* Remove factor of half on cpu count for n_cpu=disabled
+* Fix reduced set of linter errors on simpeg-drivers
+* Regenerate env lock files (for SimPEG rc.1)
+* Enforce counter-clockwise ordering of EM large loops
+* Move params tests from geoapps to simpeg-drivers
+* Deal with negative octree cell dimensions from legacy inversions
+* Improve tiling strategy for large loop EM
+* Improve scaling of cross-gradient regularization
+* Build distribution files for geology and geophysics modules for Analyst
+* Use new dev script to create lock files
+* Fix tile ID on save directive
+* New RC distribution for Analyst 4.4
+* Import of simpeg-drivers too slow
+* Merge Release/0.1.0 to main
+* Use octree-creation-app v0.1.1
+
+ Copyright (c) 2023-2026 Mira Geoscience Ltd.