From e71729c3368c7316b135ba44b5e628c5b884804c Mon Sep 17 00:00:00 2001
From: Andrew Gray <andrewg@mirageoscience.com>
Date: Mon, 14 Aug 2023 10:03:20 -0700
Subject: [PATCH 01/33] GEOPY-882 migrate provision-with-micromamba to
 setup-micromamba

---
 .github/workflows/pytest-windows.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pytest-windows.yaml b/.github/workflows/pytest-windows.yaml
index 86853dc17..248fd2ae5 100644
--- a/.github/workflows/pytest-windows.yaml
+++ b/.github/workflows/pytest-windows.yaml
@@ -43,7 +43,7 @@ jobs:
         with:
           lfs: true
       - name: Setup conda env
-        uses: mamba-org/provision-with-micromamba@main
+        uses: mamba-org/setup-micromamba@v1
         with:
           environment-file: ${{ env.CONDA_LOCK_ENV_FILE }}
           environment-name: test_env

From 27a0c5165190985938667b9b5eb8bb5aaa4e63d3 Mon Sep 17 00:00:00 2001
From: Andrew Gray <andrewg@mirageoscience.com>
Date: Mon, 14 Aug 2023 10:28:58 -0700
Subject: [PATCH 02/33] GEOPY-882 tell github action to activate the conda env
 it just created?

---
 .github/workflows/pytest-windows.yaml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/pytest-windows.yaml b/.github/workflows/pytest-windows.yaml
index 248fd2ae5..8b93fc657 100644
--- a/.github/workflows/pytest-windows.yaml
+++ b/.github/workflows/pytest-windows.yaml
@@ -47,8 +47,10 @@ jobs:
         with:
           environment-file: ${{ env.CONDA_LOCK_ENV_FILE }}
           environment-name: test_env
+          activate-environment: test_env
           cache-downloads: true
       - name: pytest
+        shell: shell: bash -l {0}
         run: |
           pytest --cov=${source_dir} --cov-report=xml --cov-branch
       - name: Codecov

From e1e63542986e2e25a89c3fced57b150add14484b Mon Sep 17 00:00:00 2001
From: Andrew Gray <andrewg@mirageoscience.com>
Date: Mon, 14 Aug 2023 11:13:56 -0700
Subject: [PATCH 03/33] GEOPY-882 remove incorrect shell

---
 .github/workflows/pytest-windows.yaml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/pytest-windows.yaml b/.github/workflows/pytest-windows.yaml
index 8b93fc657..4e31fb3ef 100644
--- a/.github/workflows/pytest-windows.yaml
+++ b/.github/workflows/pytest-windows.yaml
@@ -50,7 +50,6 @@ jobs:
           activate-environment: test_env
           cache-downloads: true
       - name: pytest
-        shell: shell: bash -l {0}
         run: |
           pytest --cov=${source_dir} --cov-report=xml --cov-branch
       - name: Codecov

From 684c9a7d455588212df6d59ce2076d80d9d62918 Mon Sep 17 00:00:00 2001
From: Andrew Gray <andrewg@mirageoscience.com>
Date: Mon, 14 Aug 2023 11:38:10 -0700
Subject: [PATCH 04/33] GEOPY-882 specify shell

---
 .github/workflows/pytest-windows.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/pytest-windows.yaml b/.github/workflows/pytest-windows.yaml
index 4e31fb3ef..b283ca92d 100644
--- a/.github/workflows/pytest-windows.yaml
+++ b/.github/workflows/pytest-windows.yaml
@@ -50,6 +50,7 @@ jobs:
           activate-environment: test_env
           cache-downloads: true
       - name: pytest
+        shell: powershell
         run: |
           pytest --cov=${source_dir} --cov-report=xml --cov-branch
       - name: Codecov

From ea3194709a5200f9f2da0f0365c625a99236df42 Mon Sep 17 00:00:00 2001
From: Andrew Gray <andrewg@mirageoscience.com>
Date: Mon, 14 Aug 2023 11:53:08 -0700
Subject: [PATCH 05/33] GEOPY-882 specify init-shell

---
 .github/workflows/pytest-windows.yaml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/pytest-windows.yaml b/.github/workflows/pytest-windows.yaml
index b283ca92d..c412410bc 100644
--- a/.github/workflows/pytest-windows.yaml
+++ b/.github/workflows/pytest-windows.yaml
@@ -47,10 +47,9 @@ jobs:
         with:
           environment-file: ${{ env.CONDA_LOCK_ENV_FILE }}
           environment-name: test_env
-          activate-environment: test_env
+          init-shell: powershell
           cache-downloads: true
       - name: pytest
-        shell: powershell
         run: |
           pytest --cov=${source_dir} --cov-report=xml --cov-branch
       - name: Codecov

From dd4a6516ee0f867c8d0ebd1b7edfb7350eca0e14 Mon Sep 17 00:00:00 2001
From: Andrew Gray <andrewg@mirageoscience.com>
Date: Wed, 20 Sep 2023 09:53:58 -0700
Subject: [PATCH 06/33] GEOPY-1058 migrate to setup-micromamba in github
 workflows

---
 .github/workflows/create_env_file.yml | 4 ++--
 .github/workflows/pytest-unix-os.yaml | 2 +-
 .github/workflows/static-analysis.yml | 2 +-
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/create_env_file.yml b/.github/workflows/create_env_file.yml
index 3d3b03bb0..387ad2cf1 100644
--- a/.github/workflows/create_env_file.yml
+++ b/.github/workflows/create_env_file.yml
@@ -34,13 +34,13 @@ jobs:
           SHORT_SHA=${GITHUB_SHA:0:8}
           echo "git_ref_suffix=${REF_NAME}-${SHORT_SHA}" >> $GITHUB_OUTPUT
       - name: Activate conda base env
-        uses: mamba-org/provision-with-micromamba@main
+        uses: mamba-org/setup-micromamba@v1
         with:
           environment-file: environments\env-python-${{ env.python_ver }}.yml
           environment-name: conda-lock
           cache-downloads: true
           cache-env: true
-          extra-specs: conda-lock
+          create-args: conda-lock
           channels: conda-forge
       - name: Create env file
         id: create-env-file
diff --git a/.github/workflows/pytest-unix-os.yaml b/.github/workflows/pytest-unix-os.yaml
index cde52eebd..e0af82f33 100644
--- a/.github/workflows/pytest-unix-os.yaml
+++ b/.github/workflows/pytest-unix-os.yaml
@@ -44,7 +44,7 @@ jobs:
         with:
           lfs: true
       - name: Setup conda env
-        uses: mamba-org/provision-with-micromamba@main
+        uses: mamba-org/setup-micromamba@v1
         with:
           environment-file: ${{ env.CONDA_LOCK_ENV_FILE }}
           environment-name: test_env
diff --git a/.github/workflows/static-analysis.yml b/.github/workflows/static-analysis.yml
index 8ef8a2124..7e9ea3933 100644
--- a/.github/workflows/static-analysis.yml
+++ b/.github/workflows/static-analysis.yml
@@ -37,7 +37,7 @@ jobs:
     steps:
       - uses: actions/checkout@v3
       - name: Setup conda env
-        uses: mamba-org/provision-with-micromamba@main
+        uses: mamba-org/setup-micromamba@v1
         with:
           environment-file: ${{ env.CONDA_LOCK_ENV_FILE }}
           environment-name: linter_env

From c2d23b68faff504af4be79f250642e746425d00f Mon Sep 17 00:00:00 2001
From: Andrew Gray <andrewg@mirageoscience.com>
Date: Fri, 29 Sep 2023 06:47:11 -0700
Subject: [PATCH 07/33] GEOPY-1083 run pylint on ubuntu

---
 .github/workflows/static-analysis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/static-analysis.yml b/.github/workflows/static-analysis.yml
index 7e9ea3933..c9c4466ce 100644
--- a/.github/workflows/static-analysis.yml
+++ b/.github/workflows/static-analysis.yml
@@ -26,7 +26,7 @@ env:
 jobs:
   pylint:
     name: pylint
-    runs-on: windows-latest
+    runs-on: ubuntu-latest
     defaults:
       run:
         shell: bash -l {0}

From 3c9b3082239008a5a2b094718628a9fd1a64f28a Mon Sep 17 00:00:00 2001
From: Andrew Gray <andrewg@mirageoscience.com>
Date: Fri, 29 Sep 2023 07:13:32 -0700
Subject: [PATCH 08/33] GEOPY-1083 static-analysys: use linux lock file

---
 .github/workflows/static-analysis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/static-analysis.yml b/.github/workflows/static-analysis.yml
index c9c4466ce..1d3a4c3ee 100644
--- a/.github/workflows/static-analysis.yml
+++ b/.github/workflows/static-analysis.yml
@@ -32,7 +32,7 @@ jobs:
         shell: bash -l {0}
     env:
       PYTHONUTF8: 1
-      CONDA_LOCK_ENV_FILE: environments/conda-py-3.9-win-64-dev.lock.yml
+      CONDA_LOCK_ENV_FILE: environments/conda-py-3.9-linux-64-dev.lock.yml
       PIP_EXTRA_INDEX_URL: https://test.pypi.org/simple/
     steps:
       - uses: actions/checkout@v3

From 4ae3b3fcefbbe0f523ac039297ffef3511bd4a94 Mon Sep 17 00:00:00 2001
From: Andrew Gray <andrewg@mirageoscience.com>
Date: Fri, 29 Sep 2023 10:30:36 -0700
Subject: [PATCH 09/33] GEOPY-1083 remove Macos from pytest for now

---
 .github/workflows/pytest-unix-os.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pytest-unix-os.yaml b/.github/workflows/pytest-unix-os.yaml
index e0af82f33..0bb98d2df 100644
--- a/.github/workflows/pytest-unix-os.yaml
+++ b/.github/workflows/pytest-unix-os.yaml
@@ -30,7 +30,7 @@ jobs:
       fail-fast: false
       matrix:
         python_ver: ['3.9', '3.10']
-        os: [ubuntu-latest, macos-latest]
+        os: [ubuntu-latest]
     runs-on: ${{ matrix.os }}
     defaults:
       run:

From ad82243e47ebff163b8cac52e545e3b8fe4639cc Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Sun, 1 Oct 2023 11:09:43 +0000
Subject: [PATCH 10/33] Bump actions/checkout from 3 to 4

Bumps [actions/checkout](https://github.com/actions/checkout) from 3 to 4.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](https://github.com/actions/checkout/compare/v3...v4)

---
updated-dependencies:
- dependency-name: actions/checkout
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 .github/workflows/create_env_file.yml | 6 +++---
 .github/workflows/pytest-unix-os.yaml | 2 +-
 .github/workflows/pytest-windows.yaml | 2 +-
 .github/workflows/static-analysis.yml | 2 +-
 4 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/create_env_file.yml b/.github/workflows/create_env_file.yml
index 387ad2cf1..5eac9037c 100644
--- a/.github/workflows/create_env_file.yml
+++ b/.github/workflows/create_env_file.yml
@@ -26,7 +26,7 @@ jobs:
       full_env_file: ${{ steps.create-env-file.outputs.full_env_file }}
       artifact: ${{ env.ARTIFACT_NAME }}.${{ steps.git-info.outputs.git_ref_suffix }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: git info
         id: git-info
         run: |
@@ -63,7 +63,7 @@ jobs:
     outputs:
       release_id: ${{ steps.create-release.outputs.release_id }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Create draft release
         id: create-release
         env:
@@ -85,7 +85,7 @@ jobs:
     if: ${{ needs.create-env-file.outputs.releaseFullEnv == true }}
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: actions/download-artifact@v3
         with:
           name: ${{ needs.create-env-file.outputs.artifact }}
diff --git a/.github/workflows/pytest-unix-os.yaml b/.github/workflows/pytest-unix-os.yaml
index 0bb98d2df..ad800e30a 100644
--- a/.github/workflows/pytest-unix-os.yaml
+++ b/.github/workflows/pytest-unix-os.yaml
@@ -40,7 +40,7 @@ jobs:
       CONDA_LOCK_ENV_FILE: environments/conda-py-${{ matrix.python_ver }}-${{ startsWith(matrix.os, 'macos') && 'osx' || 'linux' }}-64-dev.lock.yml
       PIP_EXTRA_INDEX_URL: https://test.pypi.org/simple/
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           lfs: true
       - name: Setup conda env
diff --git a/.github/workflows/pytest-windows.yaml b/.github/workflows/pytest-windows.yaml
index c412410bc..9d8dff5b5 100644
--- a/.github/workflows/pytest-windows.yaml
+++ b/.github/workflows/pytest-windows.yaml
@@ -39,7 +39,7 @@ jobs:
       CONDA_LOCK_ENV_FILE: environments/conda-py-${{ matrix.python_ver }}-win-64-dev.lock.yml
       PIP_EXTRA_INDEX_URL: https://test.pypi.org/simple/
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           lfs: true
       - name: Setup conda env
diff --git a/.github/workflows/static-analysis.yml b/.github/workflows/static-analysis.yml
index 1d3a4c3ee..99edd0f5d 100644
--- a/.github/workflows/static-analysis.yml
+++ b/.github/workflows/static-analysis.yml
@@ -35,7 +35,7 @@ jobs:
       CONDA_LOCK_ENV_FILE: environments/conda-py-3.9-linux-64-dev.lock.yml
       PIP_EXTRA_INDEX_URL: https://test.pypi.org/simple/
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Setup conda env
         uses: mamba-org/setup-micromamba@v1
         with:

From 592914b5eca7d02f7ab319df7536a76a892bf554 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 2 Oct 2023 20:39:22 +0000
Subject: [PATCH 11/33] [pre-commit.ci] pre-commit autoupdate
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/psf/black: 23.7.0 → 23.9.1](https://github.com/psf/black/compare/23.7.0...23.9.1)
- [github.com/asottile/pyupgrade: v3.10.1 → v3.13.0](https://github.com/asottile/pyupgrade/compare/v3.10.1...v3.13.0)
- [github.com/rstcheck/rstcheck: v6.1.2 → v6.2.0](https://github.com/rstcheck/rstcheck/compare/v6.1.2...v6.2.0)
---
 .pre-commit-config.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 7ede0a341..20390c8ff 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -12,7 +12,7 @@ ci:
 
 repos:
 -   repo: https://github.com/psf/black
-    rev: 23.7.0
+    rev: 23.9.1
     hooks:
     -   id: black
 -   repo: https://github.com/PyCQA/isort
@@ -29,7 +29,7 @@ repos:
 #    hooks:
 #    -   id: flake8
 -   repo: https://github.com/asottile/pyupgrade
-    rev: v3.10.1
+    rev: v3.13.0
     hooks:
     -   id: pyupgrade
         args: [--py39-plus]
@@ -83,7 +83,7 @@ repos:
     -   id: mixed-line-ending
     -   id: name-tests-test
 -   repo: https://github.com/rstcheck/rstcheck
-    rev: v6.1.2
+    rev: v6.2.0
     hooks:
     -   id: rstcheck
         exclude: ^THIRD_PARTY_SOFTWARE.rst$

From 7ba5f096b209d48c47fd85f1449736cb26cf43de Mon Sep 17 00:00:00 2001
From: Andrew Gray <andrewg@mirageoscience.com>
Date: Mon, 14 Aug 2023 10:03:20 -0700
Subject: [PATCH 12/33] GEOPY-882 migrate provision-with-micromamba to
 setup-micromamba

---
 .github/workflows/pytest-windows.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pytest-windows.yaml b/.github/workflows/pytest-windows.yaml
index 86853dc17..248fd2ae5 100644
--- a/.github/workflows/pytest-windows.yaml
+++ b/.github/workflows/pytest-windows.yaml
@@ -43,7 +43,7 @@ jobs:
         with:
           lfs: true
       - name: Setup conda env
-        uses: mamba-org/provision-with-micromamba@main
+        uses: mamba-org/setup-micromamba@v1
         with:
           environment-file: ${{ env.CONDA_LOCK_ENV_FILE }}
           environment-name: test_env

From 8876ea478f42d25ab6cfecc1a7d75eebdcaba2ba Mon Sep 17 00:00:00 2001
From: Andrew Gray <andrewg@mirageoscience.com>
Date: Mon, 14 Aug 2023 10:28:58 -0700
Subject: [PATCH 13/33] GEOPY-882 tell github action to activate the conda env
 it just created?

---
 .github/workflows/pytest-windows.yaml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/pytest-windows.yaml b/.github/workflows/pytest-windows.yaml
index 248fd2ae5..8b93fc657 100644
--- a/.github/workflows/pytest-windows.yaml
+++ b/.github/workflows/pytest-windows.yaml
@@ -47,8 +47,10 @@ jobs:
         with:
           environment-file: ${{ env.CONDA_LOCK_ENV_FILE }}
           environment-name: test_env
+          activate-environment: test_env
           cache-downloads: true
       - name: pytest
+        shell: shell: bash -l {0}
         run: |
           pytest --cov=${source_dir} --cov-report=xml --cov-branch
       - name: Codecov

From e2f28992282a74000bda8039c4f6ad02836e2fec Mon Sep 17 00:00:00 2001
From: Andrew Gray <andrewg@mirageoscience.com>
Date: Mon, 14 Aug 2023 11:13:56 -0700
Subject: [PATCH 14/33] GEOPY-882 remove incorrect shell

---
 .github/workflows/pytest-windows.yaml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/pytest-windows.yaml b/.github/workflows/pytest-windows.yaml
index 8b93fc657..4e31fb3ef 100644
--- a/.github/workflows/pytest-windows.yaml
+++ b/.github/workflows/pytest-windows.yaml
@@ -50,7 +50,6 @@ jobs:
           activate-environment: test_env
           cache-downloads: true
       - name: pytest
-        shell: shell: bash -l {0}
         run: |
           pytest --cov=${source_dir} --cov-report=xml --cov-branch
       - name: Codecov

From 2279ac466b71b9d35b596ba15b4683e9997cad65 Mon Sep 17 00:00:00 2001
From: Andrew Gray <andrewg@mirageoscience.com>
Date: Mon, 14 Aug 2023 11:38:10 -0700
Subject: [PATCH 15/33] GEOPY-882 specify shell

---
 .github/workflows/pytest-windows.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/pytest-windows.yaml b/.github/workflows/pytest-windows.yaml
index 4e31fb3ef..b283ca92d 100644
--- a/.github/workflows/pytest-windows.yaml
+++ b/.github/workflows/pytest-windows.yaml
@@ -50,6 +50,7 @@ jobs:
           activate-environment: test_env
           cache-downloads: true
       - name: pytest
+        shell: powershell
         run: |
           pytest --cov=${source_dir} --cov-report=xml --cov-branch
       - name: Codecov

From 1a824c76fa5a46899f387fc67cffe9cb761013e4 Mon Sep 17 00:00:00 2001
From: Andrew Gray <andrewg@mirageoscience.com>
Date: Mon, 14 Aug 2023 11:53:08 -0700
Subject: [PATCH 16/33] GEOPY-882 specify init-shell

---
 .github/workflows/pytest-windows.yaml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/pytest-windows.yaml b/.github/workflows/pytest-windows.yaml
index b283ca92d..c412410bc 100644
--- a/.github/workflows/pytest-windows.yaml
+++ b/.github/workflows/pytest-windows.yaml
@@ -47,10 +47,9 @@ jobs:
         with:
           environment-file: ${{ env.CONDA_LOCK_ENV_FILE }}
           environment-name: test_env
-          activate-environment: test_env
+          init-shell: powershell
           cache-downloads: true
       - name: pytest
-        shell: powershell
         run: |
           pytest --cov=${source_dir} --cov-report=xml --cov-branch
       - name: Codecov

From 0bcca1b183e2539d3320adbe260dffafb0dbca24 Mon Sep 17 00:00:00 2001
From: Andrew Gray <andrewg@mirageoscience.com>
Date: Wed, 20 Sep 2023 09:53:58 -0700
Subject: [PATCH 17/33] GEOPY-1058 migrate to setup-micromamba in github
 workflows

---
 .github/workflows/create_env_file.yml | 4 ++--
 .github/workflows/pytest-unix-os.yaml | 2 +-
 .github/workflows/static-analysis.yml | 2 +-
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/create_env_file.yml b/.github/workflows/create_env_file.yml
index 3d3b03bb0..387ad2cf1 100644
--- a/.github/workflows/create_env_file.yml
+++ b/.github/workflows/create_env_file.yml
@@ -34,13 +34,13 @@ jobs:
           SHORT_SHA=${GITHUB_SHA:0:8}
           echo "git_ref_suffix=${REF_NAME}-${SHORT_SHA}" >> $GITHUB_OUTPUT
       - name: Activate conda base env
-        uses: mamba-org/provision-with-micromamba@main
+        uses: mamba-org/setup-micromamba@v1
         with:
           environment-file: environments\env-python-${{ env.python_ver }}.yml
           environment-name: conda-lock
           cache-downloads: true
           cache-env: true
-          extra-specs: conda-lock
+          create-args: conda-lock
           channels: conda-forge
       - name: Create env file
         id: create-env-file
diff --git a/.github/workflows/pytest-unix-os.yaml b/.github/workflows/pytest-unix-os.yaml
index b4a45dbbf..0bb98d2df 100644
--- a/.github/workflows/pytest-unix-os.yaml
+++ b/.github/workflows/pytest-unix-os.yaml
@@ -44,7 +44,7 @@ jobs:
         with:
           lfs: true
       - name: Setup conda env
-        uses: mamba-org/provision-with-micromamba@main
+        uses: mamba-org/setup-micromamba@v1
         with:
           environment-file: ${{ env.CONDA_LOCK_ENV_FILE }}
           environment-name: test_env
diff --git a/.github/workflows/static-analysis.yml b/.github/workflows/static-analysis.yml
index 8ef8a2124..7e9ea3933 100644
--- a/.github/workflows/static-analysis.yml
+++ b/.github/workflows/static-analysis.yml
@@ -37,7 +37,7 @@ jobs:
     steps:
       - uses: actions/checkout@v3
       - name: Setup conda env
-        uses: mamba-org/provision-with-micromamba@main
+        uses: mamba-org/setup-micromamba@v1
         with:
           environment-file: ${{ env.CONDA_LOCK_ENV_FILE }}
           environment-name: linter_env

From c6294c80cb2c2f8f20aab5d3a184a97560b08ddd Mon Sep 17 00:00:00 2001
From: Andrew Gray <andrewg@mirageoscience.com>
Date: Fri, 29 Sep 2023 06:47:11 -0700
Subject: [PATCH 18/33] GEOPY-1083 run pylint on ubuntu

---
 .github/workflows/static-analysis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/static-analysis.yml b/.github/workflows/static-analysis.yml
index 7e9ea3933..c9c4466ce 100644
--- a/.github/workflows/static-analysis.yml
+++ b/.github/workflows/static-analysis.yml
@@ -26,7 +26,7 @@ env:
 jobs:
   pylint:
     name: pylint
-    runs-on: windows-latest
+    runs-on: ubuntu-latest
     defaults:
       run:
         shell: bash -l {0}

From fe1ed8ee25f2becb09974fbaabb471e9aa0bd5e0 Mon Sep 17 00:00:00 2001
From: Andrew Gray <andrewg@mirageoscience.com>
Date: Fri, 29 Sep 2023 07:13:32 -0700
Subject: [PATCH 19/33] GEOPY-1083 static-analysys: use linux lock file

---
 .github/workflows/static-analysis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/static-analysis.yml b/.github/workflows/static-analysis.yml
index c9c4466ce..1d3a4c3ee 100644
--- a/.github/workflows/static-analysis.yml
+++ b/.github/workflows/static-analysis.yml
@@ -32,7 +32,7 @@ jobs:
         shell: bash -l {0}
     env:
       PYTHONUTF8: 1
-      CONDA_LOCK_ENV_FILE: environments/conda-py-3.9-win-64-dev.lock.yml
+      CONDA_LOCK_ENV_FILE: environments/conda-py-3.9-linux-64-dev.lock.yml
       PIP_EXTRA_INDEX_URL: https://test.pypi.org/simple/
     steps:
       - uses: actions/checkout@v3

From d05343709b378a070fa4f8af5d15ccdb3c40c6ff Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 2 Oct 2023 20:39:22 +0000
Subject: [PATCH 20/33] [pre-commit.ci] pre-commit autoupdate
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/psf/black: 23.7.0 → 23.9.1](https://github.com/psf/black/compare/23.7.0...23.9.1)
- [github.com/asottile/pyupgrade: v3.10.1 → v3.13.0](https://github.com/asottile/pyupgrade/compare/v3.10.1...v3.13.0)
- [github.com/rstcheck/rstcheck: v6.1.2 → v6.2.0](https://github.com/rstcheck/rstcheck/compare/v6.1.2...v6.2.0)
---
 .pre-commit-config.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 7ede0a341..20390c8ff 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -12,7 +12,7 @@ ci:
 
 repos:
 -   repo: https://github.com/psf/black
-    rev: 23.7.0
+    rev: 23.9.1
     hooks:
     -   id: black
 -   repo: https://github.com/PyCQA/isort
@@ -29,7 +29,7 @@ repos:
 #    hooks:
 #    -   id: flake8
 -   repo: https://github.com/asottile/pyupgrade
-    rev: v3.10.1
+    rev: v3.13.0
     hooks:
     -   id: pyupgrade
         args: [--py39-plus]
@@ -83,7 +83,7 @@ repos:
     -   id: mixed-line-ending
     -   id: name-tests-test
 -   repo: https://github.com/rstcheck/rstcheck
-    rev: v6.1.2
+    rev: v6.2.0
     hooks:
     -   id: rstcheck
         exclude: ^THIRD_PARTY_SOFTWARE.rst$

From 51a85ba031b8bd9318e24a857a384f778ba3ba4d Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Sun, 1 Oct 2023 11:09:43 +0000
Subject: [PATCH 21/33] Bump actions/checkout from 3 to 4

Bumps [actions/checkout](https://github.com/actions/checkout) from 3 to 4.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](https://github.com/actions/checkout/compare/v3...v4)

---
updated-dependencies:
- dependency-name: actions/checkout
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 .github/workflows/create_env_file.yml | 6 +++---
 .github/workflows/pytest-unix-os.yaml | 2 +-
 .github/workflows/pytest-windows.yaml | 2 +-
 .github/workflows/static-analysis.yml | 2 +-
 4 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/create_env_file.yml b/.github/workflows/create_env_file.yml
index 387ad2cf1..5eac9037c 100644
--- a/.github/workflows/create_env_file.yml
+++ b/.github/workflows/create_env_file.yml
@@ -26,7 +26,7 @@ jobs:
       full_env_file: ${{ steps.create-env-file.outputs.full_env_file }}
       artifact: ${{ env.ARTIFACT_NAME }}.${{ steps.git-info.outputs.git_ref_suffix }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: git info
         id: git-info
         run: |
@@ -63,7 +63,7 @@ jobs:
     outputs:
       release_id: ${{ steps.create-release.outputs.release_id }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Create draft release
         id: create-release
         env:
@@ -85,7 +85,7 @@ jobs:
     if: ${{ needs.create-env-file.outputs.releaseFullEnv == true }}
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: actions/download-artifact@v3
         with:
           name: ${{ needs.create-env-file.outputs.artifact }}
diff --git a/.github/workflows/pytest-unix-os.yaml b/.github/workflows/pytest-unix-os.yaml
index 0bb98d2df..ad800e30a 100644
--- a/.github/workflows/pytest-unix-os.yaml
+++ b/.github/workflows/pytest-unix-os.yaml
@@ -40,7 +40,7 @@ jobs:
       CONDA_LOCK_ENV_FILE: environments/conda-py-${{ matrix.python_ver }}-${{ startsWith(matrix.os, 'macos') && 'osx' || 'linux' }}-64-dev.lock.yml
       PIP_EXTRA_INDEX_URL: https://test.pypi.org/simple/
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           lfs: true
       - name: Setup conda env
diff --git a/.github/workflows/pytest-windows.yaml b/.github/workflows/pytest-windows.yaml
index c412410bc..9d8dff5b5 100644
--- a/.github/workflows/pytest-windows.yaml
+++ b/.github/workflows/pytest-windows.yaml
@@ -39,7 +39,7 @@ jobs:
       CONDA_LOCK_ENV_FILE: environments/conda-py-${{ matrix.python_ver }}-win-64-dev.lock.yml
       PIP_EXTRA_INDEX_URL: https://test.pypi.org/simple/
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           lfs: true
       - name: Setup conda env
diff --git a/.github/workflows/static-analysis.yml b/.github/workflows/static-analysis.yml
index 1d3a4c3ee..99edd0f5d 100644
--- a/.github/workflows/static-analysis.yml
+++ b/.github/workflows/static-analysis.yml
@@ -35,7 +35,7 @@ jobs:
       CONDA_LOCK_ENV_FILE: environments/conda-py-3.9-linux-64-dev.lock.yml
       PIP_EXTRA_INDEX_URL: https://test.pypi.org/simple/
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Setup conda env
         uses: mamba-org/setup-micromamba@v1
         with:

From 0e79eb1392cd56f2091a5cc7bafa7157ff551278 Mon Sep 17 00:00:00 2001
From: jamiefb <jamieb@mirageoscience.com>
Date: Tue, 31 Oct 2023 15:50:12 -0700
Subject: [PATCH 22/33] add diagonal_balance to uijson

---
 geoapps/octree_creation/constants.py |  6 +++++
 geoapps/octree_creation/driver.py    | 35 +++++++++++++++++++++++-----
 geoapps/octree_creation/params.py    |  9 +++++++
 3 files changed, 44 insertions(+), 6 deletions(-)

diff --git a/geoapps/octree_creation/constants.py b/geoapps/octree_creation/constants.py
index 15b19dac7..5b26272d4 100644
--- a/geoapps/octree_creation/constants.py
+++ b/geoapps/octree_creation/constants.py
@@ -99,6 +99,12 @@
             "main": True,
             "value": 500.0,
         },
+        "diagonal_balance": {
+            "group": "Basic",
+            "label": "UBC Compatible",
+            "main": True,
+            "value": False,
+        },
         "minimum_level": {
             "enabled": True,
             "group": "Basic",
diff --git a/geoapps/octree_creation/driver.py b/geoapps/octree_creation/driver.py
index 466ad9377..322ad0e74 100644
--- a/geoapps/octree_creation/driver.py
+++ b/geoapps/octree_creation/driver.py
@@ -65,7 +65,9 @@ def octree_from_params(params: OctreeParams):
             depth_core=params.depth_core,
         )
         minimum_level = OctreeDriver.minimum_level(mesh, params.minimum_level)
-        mesh.refine(minimum_level, finalize=False)
+        mesh.refine(
+            minimum_level, finalize=False, diagonal_balance=params.diagonal_balance
+        )
 
         for label, value in params.free_parameter_dict.items():
             refinement_object = getattr(params, value["object"])
@@ -77,12 +79,12 @@ def octree_from_params(params: OctreeParams):
 
             if isinstance(refinement_object, Curve):
                 mesh = OctreeDriver.refine_tree_from_curve(
-                    mesh, refinement_object, levels
+                    mesh, refinement_object, levels, params.diagonal_balance
                 )
 
             elif isinstance(refinement_object, Surface):
                 mesh = OctreeDriver.refine_tree_from_triangulation(
-                    mesh, refinement_object, levels
+                    mesh, refinement_object, levels, params.diagonal_balance
                 )
 
             elif getattr(params, value["type"]) == "surface":
@@ -90,6 +92,7 @@ def octree_from_params(params: OctreeParams):
                     mesh,
                     refinement_object,
                     levels,
+                    params.diagonal_balance,
                     max_distance=getattr(params, value["distance"]),
                 )
 
@@ -98,6 +101,7 @@ def octree_from_params(params: OctreeParams):
                     mesh,
                     refinement_object,
                     levels,
+                    diagonal_balance=params.diagonal_balance,
                 )
 
             else:
@@ -116,6 +120,7 @@ def refine_tree_from_curve(
         mesh: TreeMesh,
         curve: Curve,
         levels: list[int] | np.ndarray,
+        diagonal_balance: bool,
         finalize: bool = False,
     ) -> TreeMesh:
         """
@@ -126,6 +131,7 @@ def refine_tree_from_curve(
         :param curve: Curve object to use for refinement.
         :param levels: Number of cells requested at each refinement level.
             Defined in reversed order from the highest octree to lowest.
+        :param diagonal_balance: Whether to balance cells along the diagonal of the tree during construction.
         :param finalize: Finalize the tree mesh after refinement.
 
         """
@@ -137,7 +143,7 @@ def refine_tree_from_curve(
 
         locations = densify_curve(curve, mesh.h[0][0])
         mesh = OctreeDriver.refine_tree_from_points(
-            mesh, locations, levels, finalize=False
+            mesh, locations, levels, diagonal_balance=diagonal_balance, finalize=False
         )
 
         if finalize:
@@ -150,6 +156,7 @@ def refine_tree_from_points(
         mesh: TreeMesh,
         points: ObjectBase | np.ndarray,
         levels: list[int] | np.ndarray,
+        diagonal_balance: bool,
         finalize: bool = False,
     ) -> TreeMesh:
         """
@@ -159,6 +166,7 @@ def refine_tree_from_points(
         :param points: Object to use for refinement.
         :param levels: Number of cells requested at each refinement level.
             Defined in reversed order from the highest octree to lowest.
+        :param diagonal_balance: Whether to balance cells along the diagonal of the tree during construction.
         :param finalize: Finalize the tree mesh after refinement.
 
         :return: Refined tree mesh.
@@ -177,7 +185,13 @@ def refine_tree_from_points(
         distance = 0
         for ii, n_cells in enumerate(levels):
             distance += n_cells * OctreeDriver.cell_size_from_level(mesh, ii)
-            mesh.refine_ball(locations, distance, mesh.max_level - ii, finalize=False)
+            mesh.refine_ball(
+                locations,
+                distance,
+                mesh.max_level - ii,
+                diagonal_balance=diagonal_balance,
+                finalize=False,
+            )
 
         if finalize:
             mesh.finalize()
@@ -189,6 +203,7 @@ def refine_tree_from_surface(
         mesh: TreeMesh,
         surface: ObjectBase,
         levels: list[int] | np.ndarray,
+        diagonal_balance: bool,
         max_distance: float = np.inf,
         finalize: bool = False,
     ) -> TreeMesh:
@@ -200,6 +215,7 @@ def refine_tree_from_surface(
         :param levels: Number of cells requested at each refinement level.
             Defined in reversed order from the highest octree to lowest.
         :param max_distance: Maximum distance from the surface to refine.
+        :param diagonal_balance: Whether to balance cells along the diagonal of the tree during construction.
         :param finalize: Finalize the tree mesh after refinement.
 
         :return: Refined tree mesh.
@@ -247,6 +263,7 @@ def refine_tree_from_surface(
                 mesh.insert_cells(
                     np.c_[xy[keeper], elevation - depth],
                     np.ones(nnz) * mesh.max_level - ind,
+                    diagonal_balance=diagonal_balance,
                     finalize=False,
                 )
 
@@ -257,7 +274,11 @@ def refine_tree_from_surface(
 
     @staticmethod
     def refine_tree_from_triangulation(
-        mesh: TreeMesh, surface, levels: list[int] | np.ndarray, finalize=False
+        mesh: TreeMesh,
+        surface,
+        levels: list[int] | np.ndarray,
+        diagonal_balance: bool,
+        finalize=False,
     ) -> TreeMesh:
         """
         Refine a tree mesh along the simplicies of a surface.
@@ -266,6 +287,7 @@ def refine_tree_from_triangulation(
         :param surface: Surface object to use for refinement.
         :param levels: Number of cells requested at each refinement level.
             Defined in reversed order from highest octree to lowest.
+        :param diagonal_balance: Whether to balance cells along the diagonal of the tree during construction.
         :param finalize: Finalize the tree mesh after refinement.
 
         :return: Refined tree mesh.
@@ -290,6 +312,7 @@ def refine_tree_from_triangulation(
                 (surface.vertices, surface.cells),
                 -ind[0] - 1,
                 paddings,
+                diagonal_balance=diagonal_balance,
                 finalize=finalize,
             )
         return mesh
diff --git a/geoapps/octree_creation/params.py b/geoapps/octree_creation/params.py
index 84ccea33d..980194239 100644
--- a/geoapps/octree_creation/params.py
+++ b/geoapps/octree_creation/params.py
@@ -31,6 +31,7 @@ def __init__(self, input_file=None, **kwargs):
         self._u_cell_size = None
         self._v_cell_size = None
         self._w_cell_size = None
+        self._diagonal_balance = None
         self._minimum_level = None
         self._horizontal_padding = None
         self._vertical_padding = None
@@ -143,6 +144,14 @@ def depth_core(self):
     def depth_core(self, val):
         self.setter_validator("depth_core", val)
 
+    @property
+    def diagonal_balance(self):
+        return self._diagonal_balance
+
+    @diagonal_balance.setter
+    def diagonal_balance(self, val):
+        self.setter_validator("diagonal_balance", val)
+
     @property
     def minimum_level(self):
         return self._minimum_level

From c483a790d4b7dc2448daccf327c6ff77077e30b3 Mon Sep 17 00:00:00 2001
From: jamiefb <jamieb@mirageoscience.com>
Date: Wed, 1 Nov 2023 11:07:57 -0700
Subject: [PATCH 23/33] test passing visually

---
 tests/run_tests/octree_creation_test.py | 68 +++++++++++++++++++++++--
 1 file changed, 65 insertions(+), 3 deletions(-)

diff --git a/tests/run_tests/octree_creation_test.py b/tests/run_tests/octree_creation_test.py
index fc9c26e33..378f58aa9 100644
--- a/tests/run_tests/octree_creation_test.py
+++ b/tests/run_tests/octree_creation_test.py
@@ -19,6 +19,7 @@
 from scipy.spatial import Delaunay
 
 from geoapps.driver_base.utils import treemesh_2_octree
+from geoapps.octree_creation import OctreeParams
 from geoapps.octree_creation.application import OctreeDriver, OctreeMesh
 from geoapps.utils.testing import get_output_workspace
 
@@ -88,6 +89,7 @@ def test_create_octree_radial(tmp_path: Path, setup_test_octree):
             treemesh,
             points,
             str2list(refinement),
+            diagonal_balance=False,
             finalize=True,
         )
         octree = treemesh_2_octree(workspace, treemesh, name="Octree_Mesh")
@@ -139,11 +141,16 @@ def test_create_octree_curve(tmp_path: Path, setup_test_octree):
     with Workspace.create(tmp_path / "testOctree.geoh5") as workspace:
         curve = Curve.create(workspace, vertices=locations)
         curve.remove_cells([-1])
-        treemesh.refine(treemesh.max_level - minimum_level + 1, finalize=False)
+        treemesh.refine(
+            treemesh.max_level - minimum_level + 1,
+            diagonal_balance=False,
+            finalize=False,
+        )
         treemesh = OctreeDriver.refine_tree_from_curve(
             treemesh,
             curve,
             str2list(refinement),
+            diagonal_balance=False,
             finalize=True,
         )
         octree = treemesh_2_octree(workspace, treemesh, name="Octree_Mesh")
@@ -191,11 +198,16 @@ def test_create_octree_surface(tmp_path: Path, setup_test_octree):
 
     with Workspace.create(tmp_path / "testOctree.geoh5") as workspace:
         points = Points.create(workspace, vertices=locations)
-        treemesh.refine(treemesh.max_level - minimum_level + 1, finalize=False)
+        treemesh.refine(
+            treemesh.max_level - minimum_level + 1,
+            diagonal_balance=False,
+            finalize=False,
+        )
         treemesh = OctreeDriver.refine_tree_from_surface(
             treemesh,
             points,
             str2list(refinement),
+            diagonal_balance=False,
             finalize=True,
         )
         octree = treemesh_2_octree(workspace, treemesh, name="Octree_Mesh")
@@ -270,11 +282,16 @@ def test_create_octree_triangulation(tmp_path: Path, setup_test_octree):
             vertices=np.c_[x.flatten(), y.flatten(), z.flatten()],
             cells=surf.simplices,
         )
-        treemesh.refine(treemesh.max_level - minimum_level + 1, finalize=False)
+        treemesh.refine(
+            treemesh.max_level - minimum_level + 1,
+            diagonal_balance=False,
+            finalize=False,
+        )
         treemesh = OctreeDriver.refine_tree_from_triangulation(
             treemesh,
             sphere,
             str2list(refinement),
+            diagonal_balance=False,
             finalize=True,
         )
         octree = treemesh_2_octree(workspace, treemesh, name="Octree_Mesh")
@@ -306,3 +323,48 @@ def test_create_octree_triangulation(tmp_path: Path, setup_test_octree):
         with Workspace(get_output_workspace(tmp_path)) as workspace:
             rec_octree = workspace.get_entity("Octree_Mesh")[0]
             compare_entities(octree, rec_octree, ignore=["_uid"])
+
+
+def test_octree_diagonal_balance(tmp_path: Path):
+    # Create temp workspace
+    with Workspace(tmp_path / "testOctree.geoh5") as workspace:
+        points = Points.create(workspace, vertices=np.array([[150, 0, 150], [0, 0, 0]]))
+
+        # Repeat the creation using the app
+        params_dict = {
+            "geoh5": workspace,
+            "objects": str(points.uid),
+            "u_cell_size": 10.0,
+            "v_cell_size": 10.0,
+            "w_cell_size": 10.0,
+            "horizontal_padding": 500.0,
+            "vertical_padding": 200.0,
+            "depth_core": 400.0,
+            "Refinement A object": points.uid,
+            "Refinement A levels": "1",
+            "Refinement A type": "radial",
+            "Refinement A distance": 200,
+        }
+
+        diag_true_params = OctreeParams(
+            **params_dict, diagonal_balance=True, ga_group_name="diag_true_mesh"
+        )
+        diag_false_params = OctreeParams(
+            **params_dict, diagonal_balance=False, ga_group_name="diag_false_mesh"
+        )
+
+        diag_true_filename = "diag_balance_true.ui.json"
+        diag_false_filename = "diag_balance_false.ui.json"
+        diag_true_params.write_input_file(
+            name=diag_true_filename, path=tmp_path, validate=False
+        )
+        diag_false_params.write_input_file(
+            name=diag_false_filename, path=tmp_path, validate=False
+        )
+
+        OctreeDriver.start(tmp_path / diag_true_filename)
+        OctreeDriver.start(tmp_path / diag_false_filename)
+
+        with workspace.open(mode="r"):
+            diag_true_results = workspace.get_entity("diag_true_mesh")
+            diag_false_results = workspace.get_entity("diag_false_mesh")

From e8961b70790d52fd4eb15d9a94da393d7a15fe9a Mon Sep 17 00:00:00 2001
From: jamiefb <jamieb@mirageoscience.com>
Date: Wed, 1 Nov 2023 13:48:04 -0700
Subject: [PATCH 24/33] update tests, add diagonal_balance to notebook

---
 geoapps/octree_creation/application.py  | 45 +++++++++++++++++++++---
 geoapps/utils/testing.py                |  2 ++
 tests/run_tests/octree_creation_test.py | 46 +++++++++++++++++++++----
 3 files changed, 83 insertions(+), 10 deletions(-)

diff --git a/geoapps/octree_creation/application.py b/geoapps/octree_creation/application.py
index d6167f700..85391769e 100644
--- a/geoapps/octree_creation/application.py
+++ b/geoapps/octree_creation/application.py
@@ -23,13 +23,23 @@
 
 from geoapps.base.application import BaseApplication
 from geoapps.base.selection import ObjectDataSelection
+from geoapps.octree_creation.constants import app_initializer
+from geoapps.octree_creation.driver import OctreeDriver
+from geoapps.octree_creation.params import OctreeParams
 from geoapps.utils import warn_module_not_found
 
-from . import OctreeParams, app_initializer
-from .driver import OctreeDriver
-
 with warn_module_not_found():
-    from ipywidgets import Dropdown, FloatText, Label, Layout, Text, VBox, Widget
+    from ipywidgets import (
+        Checkbox,
+        Dropdown,
+        FloatText,
+        IntText,
+        Label,
+        Layout,
+        Text,
+        VBox,
+        Widget,
+    )
     from ipywidgets.widgets.widget_selection import TraitError
 
 
@@ -46,6 +56,8 @@ class OctreeMesh(ObjectDataSelection):
     _depth_core = None
     _horizontal_padding = None
     _vertical_padding = None
+    _diagonal_balance = None
+    _minimum_level = None
 
     def __init__(self, ui_json=None, **kwargs):
         app_initializer.update(kwargs)
@@ -79,6 +91,9 @@ def __init__(self, ui_json=None, **kwargs):
                         Label("Padding distance"),
                         self.horizontal_padding,
                         self.vertical_padding,
+                        Label("Basic"),
+                        self.diagonal_balance,
+                        self.minimum_level,
                     ],
                     layout=Layout(border="solid"),
                 ),
@@ -180,6 +195,28 @@ def vertical_padding(self) -> FloatText:
             )
         return self._vertical_padding
 
+    @property
+    def diagonal_balance(self) -> Checkbox:
+        """
+        Widget controlling the diagonal balance.
+        """
+        if getattr(self, "_diagonal_balance", None) is None:
+            self._diagonal_balance = Checkbox(
+                description="UBC compatible",
+            )
+        return self._diagonal_balance
+
+    @property
+    def minimum_level(self) -> IntText:
+        """
+        Widget controlling the minimum refinement level.
+        """
+        if getattr(self, "_minimum_level", None) is None:
+            self._minimum_level = IntText(
+                description="Minimum refinement level",
+            )
+        return self._minimum_level
+
     @property
     def workspace(self):
         """
diff --git a/geoapps/utils/testing.py b/geoapps/utils/testing.py
index 81a5ef52e..9304aa0df 100644
--- a/geoapps/utils/testing.py
+++ b/geoapps/utils/testing.py
@@ -417,6 +417,7 @@ def topo_drape(x, y):
             mesh,
             topography,
             levels=refinement,
+            diagonal_balance=False,
             finalize=False,
         )
 
@@ -425,6 +426,7 @@ def topo_drape(x, y):
                 mesh,
                 vertices,
                 levels=[2],
+                diagonal_balance=False,
                 finalize=False,
             )
 
diff --git a/tests/run_tests/octree_creation_test.py b/tests/run_tests/octree_creation_test.py
index 378f58aa9..6066e4cca 100644
--- a/tests/run_tests/octree_creation_test.py
+++ b/tests/run_tests/octree_creation_test.py
@@ -21,6 +21,7 @@
 from geoapps.driver_base.utils import treemesh_2_octree
 from geoapps.octree_creation import OctreeParams
 from geoapps.octree_creation.application import OctreeDriver, OctreeMesh
+from geoapps.shared_utils.utils import octree_2_treemesh
 from geoapps.utils.testing import get_output_workspace
 
 # pylint: disable=redefined-outer-name
@@ -326,9 +327,10 @@ def test_create_octree_triangulation(tmp_path: Path, setup_test_octree):
 
 
 def test_octree_diagonal_balance(tmp_path: Path):
-    # Create temp workspace
-    with Workspace(tmp_path / "testOctree.geoh5") as workspace:
-        points = Points.create(workspace, vertices=np.array([[150, 0, 150], [0, 0, 0]]))
+    workspace = Workspace.create(tmp_path / "testDiagonalBalance.geoh5")
+    with workspace.open(mode="r+"):
+        point = [0, 0, 0]
+        points = Points.create(workspace, vertices=np.array([[150, 0, 150], point]))
 
         # Repeat the creation using the app
         params_dict = {
@@ -365,6 +367,38 @@ def test_octree_diagonal_balance(tmp_path: Path):
         OctreeDriver.start(tmp_path / diag_true_filename)
         OctreeDriver.start(tmp_path / diag_false_filename)
 
-        with workspace.open(mode="r"):
-            diag_true_results = workspace.get_entity("diag_true_mesh")
-            diag_false_results = workspace.get_entity("diag_false_mesh")
+    with workspace.open(mode="r"):
+        for name in ["diag_true_mesh", "diag_false_mesh"]:
+            results = []
+            treemesh = octree_2_treemesh(workspace.get_entity(name)[0])
+
+            ind = treemesh._get_containing_cell_indexes(  # pylint: disable=protected-access
+                point
+            )
+            starting_cell = treemesh[ind]
+
+            level = starting_cell._level  # pylint: disable=protected-access
+            for first_neighbor in starting_cell.neighbors:
+                neighbors = []
+                for neighbor in treemesh[first_neighbor].neighbors:
+                    if isinstance(neighbor, list):
+                        neighbors += neighbor
+                    else:
+                        neighbors.append(neighbor)
+
+                for second_neighbor in neighbors:
+                    compare_cell = treemesh[second_neighbor]
+                    if set(starting_cell.nodes) & set(compare_cell.nodes):
+                        results.append(
+                            np.abs(
+                                level
+                                - compare_cell._level  # pylint: disable=protected-access
+                            )
+                        )
+
+            if name == "diag_true_mesh":
+                assert np.all(np.array(results) < 2)
+            elif name == "diag_false_mesh":
+                values, counts = np.unique(results, return_counts=True)
+                assert (values == np.array([0, 1, 2])).all()
+                assert (counts == np.array([22, 8, 2])).all()

From 6c29f6fd57df2c60d8a671b7932fee1ad2f13fef Mon Sep 17 00:00:00 2001
From: jamiefb <jamieb@mirageoscience.com>
Date: Wed, 1 Nov 2023 13:59:30 -0700
Subject: [PATCH 25/33] update tests with diagonal balance

---
 tests/data_test.py  | 1 +
 tests/utils_test.py | 3 ++-
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/tests/data_test.py b/tests/data_test.py
index 7a2cfec7f..8f24db35a 100644
--- a/tests/data_test.py
+++ b/tests/data_test.py
@@ -81,6 +81,7 @@ def test_survey_data(tmp_path: Path):
             mesh,
             test_topo_object,
             levels=[2],
+            diagonal_balance=False,
             finalize=True,
         )
 
diff --git a/tests/utils_test.py b/tests/utils_test.py
index e1b657ee7..238dc7726 100644
--- a/tests/utils_test.py
+++ b/tests/utils_test.py
@@ -110,13 +110,14 @@ def test_drape_to_octree(tmp_path: Path):
         mesh_type="TREE",
     )
     tree = OctreeDriver.refine_tree_from_points(
-        tree, locs, levels=[4, 2], finalize=False
+        tree, locs, levels=[4, 2], diagonal_balance=False, finalize=False
     )
     topography = Points.create(ws, vertices=topo)
     tree = OctreeDriver.refine_tree_from_surface(
         tree,
         topography,
         levels=[2, 2],
+        diagonal_balance=False,
         finalize=True,
     )
     # interp and save common models into the octree

From 3c094c1667c14a0e11f4960fb208f9c928c86482 Mon Sep 17 00:00:00 2001
From: jamiefb <jamieb@mirageoscience.com>
Date: Thu, 2 Nov 2023 10:36:01 -0700
Subject: [PATCH 26/33] default diagonal_balance true; parametrize unit test

---
 geoapps/octree_creation/constants.py    |  2 +-
 geoapps/octree_creation/driver.py       |  8 +--
 tests/run_tests/octree_creation_test.py | 89 ++++++++++++-------------
 3 files changed, 46 insertions(+), 53 deletions(-)

diff --git a/geoapps/octree_creation/constants.py b/geoapps/octree_creation/constants.py
index 5b26272d4..9924744a9 100644
--- a/geoapps/octree_creation/constants.py
+++ b/geoapps/octree_creation/constants.py
@@ -103,7 +103,7 @@
             "group": "Basic",
             "label": "UBC Compatible",
             "main": True,
-            "value": False,
+            "value": True,
         },
         "minimum_level": {
             "enabled": True,
diff --git a/geoapps/octree_creation/driver.py b/geoapps/octree_creation/driver.py
index 322ad0e74..4b7765e1e 100644
--- a/geoapps/octree_creation/driver.py
+++ b/geoapps/octree_creation/driver.py
@@ -120,7 +120,7 @@ def refine_tree_from_curve(
         mesh: TreeMesh,
         curve: Curve,
         levels: list[int] | np.ndarray,
-        diagonal_balance: bool,
+        diagonal_balance: bool = True,
         finalize: bool = False,
     ) -> TreeMesh:
         """
@@ -156,7 +156,7 @@ def refine_tree_from_points(
         mesh: TreeMesh,
         points: ObjectBase | np.ndarray,
         levels: list[int] | np.ndarray,
-        diagonal_balance: bool,
+        diagonal_balance: bool = True,
         finalize: bool = False,
     ) -> TreeMesh:
         """
@@ -203,7 +203,7 @@ def refine_tree_from_surface(
         mesh: TreeMesh,
         surface: ObjectBase,
         levels: list[int] | np.ndarray,
-        diagonal_balance: bool,
+        diagonal_balance: bool = True,
         max_distance: float = np.inf,
         finalize: bool = False,
     ) -> TreeMesh:
@@ -277,7 +277,7 @@ def refine_tree_from_triangulation(
         mesh: TreeMesh,
         surface,
         levels: list[int] | np.ndarray,
-        diagonal_balance: bool,
+        diagonal_balance: bool = True,
         finalize=False,
     ) -> TreeMesh:
         """
diff --git a/tests/run_tests/octree_creation_test.py b/tests/run_tests/octree_creation_test.py
index 6066e4cca..262ce223b 100644
--- a/tests/run_tests/octree_creation_test.py
+++ b/tests/run_tests/octree_creation_test.py
@@ -326,7 +326,13 @@ def test_create_octree_triangulation(tmp_path: Path, setup_test_octree):
             compare_entities(octree, rec_octree, ignore=["_uid"])
 
 
-def test_octree_diagonal_balance(tmp_path: Path):
+@pytest.mark.parametrize(
+    "diagonal_balance, exp_values, exp_counts",
+    [(True, [0, 1], [22, 10]), (False, [0, 1, 2], [22, 8, 2])],
+)
+def test_octree_diagonal_balance(
+    tmp_path: Path, diagonal_balance, exp_values, exp_counts
+):
     workspace = Workspace.create(tmp_path / "testDiagonalBalance.geoh5")
     with workspace.open(mode="r+"):
         point = [0, 0, 0]
@@ -348,57 +354,44 @@ def test_octree_diagonal_balance(tmp_path: Path):
             "Refinement A distance": 200,
         }
 
-        diag_true_params = OctreeParams(
-            **params_dict, diagonal_balance=True, ga_group_name="diag_true_mesh"
-        )
-        diag_false_params = OctreeParams(
-            **params_dict, diagonal_balance=False, ga_group_name="diag_false_mesh"
+        params = OctreeParams(
+            **params_dict, diagonal_balance=diagonal_balance, ga_group_name="mesh"
         )
+        filename = "diag_balance.ui.json"
 
-        diag_true_filename = "diag_balance_true.ui.json"
-        diag_false_filename = "diag_balance_false.ui.json"
-        diag_true_params.write_input_file(
-            name=diag_true_filename, path=tmp_path, validate=False
-        )
-        diag_false_params.write_input_file(
-            name=diag_false_filename, path=tmp_path, validate=False
-        )
+        params.write_input_file(name=filename, path=tmp_path, validate=False)
 
-        OctreeDriver.start(tmp_path / diag_true_filename)
-        OctreeDriver.start(tmp_path / diag_false_filename)
+        OctreeDriver.start(tmp_path / filename)
 
     with workspace.open(mode="r"):
-        for name in ["diag_true_mesh", "diag_false_mesh"]:
-            results = []
-            treemesh = octree_2_treemesh(workspace.get_entity(name)[0])
-
-            ind = treemesh._get_containing_cell_indexes(  # pylint: disable=protected-access
-                point
-            )
-            starting_cell = treemesh[ind]
-
-            level = starting_cell._level  # pylint: disable=protected-access
-            for first_neighbor in starting_cell.neighbors:
-                neighbors = []
-                for neighbor in treemesh[first_neighbor].neighbors:
-                    if isinstance(neighbor, list):
-                        neighbors += neighbor
-                    else:
-                        neighbors.append(neighbor)
-
-                for second_neighbor in neighbors:
-                    compare_cell = treemesh[second_neighbor]
-                    if set(starting_cell.nodes) & set(compare_cell.nodes):
-                        results.append(
-                            np.abs(
-                                level
-                                - compare_cell._level  # pylint: disable=protected-access
-                            )
+        results = []
+        treemesh = octree_2_treemesh(workspace.get_entity("mesh")[0])
+
+        ind = treemesh._get_containing_cell_indexes(  # pylint: disable=protected-access
+            point
+        )
+        starting_cell = treemesh[ind]
+
+        level = starting_cell._level  # pylint: disable=protected-access
+        for first_neighbor in starting_cell.neighbors:
+            neighbors = []
+            for neighbor in treemesh[first_neighbor].neighbors:
+                if isinstance(neighbor, list):
+                    neighbors += neighbor
+                else:
+                    neighbors.append(neighbor)
+
+            for second_neighbor in neighbors:
+                compare_cell = treemesh[second_neighbor]
+                if set(starting_cell.nodes) & set(compare_cell.nodes):
+                    results.append(
+                        np.abs(
+                            level
+                            - compare_cell._level  # pylint: disable=protected-access
                         )
+                    )
+
+        values, counts = np.unique(results, return_counts=True)
 
-            if name == "diag_true_mesh":
-                assert np.all(np.array(results) < 2)
-            elif name == "diag_false_mesh":
-                values, counts = np.unique(results, return_counts=True)
-                assert (values == np.array([0, 1, 2])).all()
-                assert (counts == np.array([22, 8, 2])).all()
+        assert (values == np.array(exp_values)).all()
+        assert (counts == np.array(exp_counts)).all()

From c559017de03d3264a63a8939c34b760b5861e57c Mon Sep 17 00:00:00 2001
From: dominiquef <dominiquef@mirageoscience.com>
Date: Thu, 2 Nov 2023 14:11:26 -0700
Subject: [PATCH 27/33] Fix tests

---
 tests/run_tests/octree_creation_test.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/tests/run_tests/octree_creation_test.py b/tests/run_tests/octree_creation_test.py
index 262ce223b..378f18aaf 100644
--- a/tests/run_tests/octree_creation_test.py
+++ b/tests/run_tests/octree_creation_test.py
@@ -116,6 +116,7 @@ def test_create_octree_radial(tmp_path: Path, setup_test_octree):
             w_cell_size=cell_sizes[2],
             horizontal_padding=horizontal_padding,
             vertical_padding=vertical_padding,
+            diagonal_balance=False,
             depth_core=depth_core,
             **refinements,
         )
@@ -175,6 +176,7 @@ def test_create_octree_curve(tmp_path: Path, setup_test_octree):
             horizontal_padding=horizontal_padding,
             vertical_padding=vertical_padding,
             depth_core=depth_core,
+            diagonal_balance=False,
             **refinements,
         )
         app.trigger_click(None)
@@ -235,6 +237,7 @@ def test_create_octree_surface(tmp_path: Path, setup_test_octree):
             horizontal_padding=horizontal_padding,
             vertical_padding=vertical_padding,
             depth_core=depth_core,
+            diagonal_balance=False,
             **refinements,
         )
         app.trigger_click(None)

From d58c460b98edae6b224b5b9058f0649b7e13b54c Mon Sep 17 00:00:00 2001
From: dominiquef <dominiquef@mirageoscience.com>
Date: Mon, 18 Dec 2023 16:38:48 -0800
Subject: [PATCH 28/33] Create copy of models

---
 geoapps/inversion/components/models.py | 19 +++++++++++++------
 1 file changed, 13 insertions(+), 6 deletions(-)

diff --git a/geoapps/inversion/components/models.py b/geoapps/inversion/components/models.py
index 5567bf828..88b79d93e 100644
--- a/geoapps/inversion/components/models.py
+++ b/geoapps/inversion/components/models.py
@@ -115,16 +115,17 @@ def active_cells(self, active_cells):
 
     @property
     def starting(self):
-        mstart = self._starting.model
+        mstart = self._starting.model.copy()
 
         if mstart is not None and self.is_sigma:
+            mstart = mstart.copy()
             mstart = np.log(mstart)
 
         return mstart
 
     @property
     def reference(self):
-        mref = self._reference.model
+        mref = self._reference.model.copy()
 
         if self.driver.params.forward_only:
             return mref
@@ -132,11 +133,13 @@ def reference(self):
         if mref is None:
             mref = self.starting
             self.driver.params.alpha_s = 0.0
-        elif self.is_sigma & (all(mref == 0)):
-            mref = self.starting
-            self.driver.params.alpha_s = 0.0
         else:
-            mref = np.log(mref) if self.is_sigma else mref
+            mref = mref.copy()
+            if self.is_sigma & (all(mref == 0)):
+                mref = self.starting
+                self.driver.params.alpha_s = 0.0
+            else:
+                mref = np.log(mref) if self.is_sigma else mref
         return mref
 
     @property
@@ -146,6 +149,8 @@ def lower_bound(self):
         if lbound is None:
             return -np.inf
 
+        lbound = lbound.copy()
+
         if self.is_sigma:
             is_finite = np.isfinite(lbound)
             lbound[is_finite] = np.log(lbound[is_finite])
@@ -158,6 +163,7 @@ def upper_bound(self):
         if ubound is None:
             return np.inf
 
+        ubound = ubound.copy()
         if self.is_sigma:
             is_finite = np.isfinite(ubound)
             ubound[is_finite] = np.log(ubound[is_finite])
@@ -169,6 +175,7 @@ def conductivity(self):
         mstart = self._conductivity.model
 
         if mstart is not None and self.is_sigma:
+            mstart = mstart.copy()
             mstart = np.log(mstart)
 
         return mstart

From dd070365b0c609250a4fac07bb6f73ad6aa9fa84 Mon Sep 17 00:00:00 2001
From: dominiquef <dominiquef@mirageoscience.com>
Date: Mon, 18 Dec 2023 16:39:50 -0800
Subject: [PATCH 29/33] Fix issue with lagging workspace_geoh5

---
 geoapps/inversion/joint/driver.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/geoapps/inversion/joint/driver.py b/geoapps/inversion/joint/driver.py
index 6a6e9ee68..7be9f987e 100644
--- a/geoapps/inversion/joint/driver.py
+++ b/geoapps/inversion/joint/driver.py
@@ -69,6 +69,7 @@ def drivers(self) -> list[InversionDriver] | None:
                 group = self.workspace.get_entity(group.uid)[0]
                 ui_json = group.options
                 ui_json["geoh5"] = self.workspace
+                ui_json["workspace_geoh5"] = None
 
                 ifile = InputFile(ui_json=ui_json)
                 mod_name, class_name = DRIVER_MAP.get(ifile.data["inversion_type"])

From 621ff71564c675f1a9a821796fb1a1abcbfb9be3 Mon Sep 17 00:00:00 2001
From: dominiquef <dominiquef@mirageoscience.com>
Date: Wed, 3 Jan 2024 15:16:04 -0800
Subject: [PATCH 30/33] Update years

---
 LICENSE    | 2 +-
 README.rst | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/LICENSE b/LICENSE
index 63604bb9b..814813801 100644
--- a/LICENSE
+++ b/LICENSE
@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2023 Mira Geoscience
+Copyright (c) 2024 Mira Geoscience
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal
diff --git a/README.rst b/README.rst
index e03c00f88..714c8cd7d 100644
--- a/README.rst
+++ b/README.rst
@@ -79,7 +79,7 @@ License
 ^^^^^^^
 MIT License
 
-Copyright (c) 2023 Mira Geoscience
+Copyright (c) 2024 Mira Geoscience
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

From cae3ab6808ec337609110ca4940a194a2bd45d98 Mon Sep 17 00:00:00 2001
From: dominiquef <dominiquef@mirageoscience.com>
Date: Thu, 11 Jan 2024 11:31:06 -0800
Subject: [PATCH 31/33] Remove redundant copies

---
 geoapps/inversion/components/models.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/geoapps/inversion/components/models.py b/geoapps/inversion/components/models.py
index 213b80704..64a2c6b38 100644
--- a/geoapps/inversion/components/models.py
+++ b/geoapps/inversion/components/models.py
@@ -115,7 +115,7 @@ def active_cells(self, active_cells):
 
     @property
     def starting(self):
-        mstart = self._starting.model.copy()
+        mstart = self._starting.model
 
         if mstart is not None and self.is_sigma:
             mstart = mstart.copy()
@@ -125,7 +125,7 @@ def starting(self):
 
     @property
     def reference(self):
-        mref = self._reference.model.copy()
+        mref = self._reference.model
 
         if self.driver.params.forward_only:
             return mref

From c1567f5d65dbbf9345f2a17b9ba98035bd897fb0 Mon Sep 17 00:00:00 2001
From: dominiquef <dominiquef@mirageoscience.com>
Date: Mon, 29 Jan 2024 15:13:58 -0800
Subject: [PATCH 32/33] Update and fix assigned log values

---
 geoapps/inversion/components/models.py        | 52 ++++++++++---------
 .../inversion/joint/joint_surveys/driver.py   |  3 ++
 2 files changed, 30 insertions(+), 25 deletions(-)

diff --git a/geoapps/inversion/components/models.py b/geoapps/inversion/components/models.py
index 64a2c6b38..eb0043ab1 100644
--- a/geoapps/inversion/components/models.py
+++ b/geoapps/inversion/components/models.py
@@ -114,42 +114,43 @@ def active_cells(self, active_cells):
         self._active_cells = active_cells
 
     @property
-    def starting(self):
-        mstart = self._starting.model
+    def starting(self) -> np.ndarray | None:
+        if self._starting.model is None:
+            return None
+
+        mstart = self._starting.model.copy()
 
         if mstart is not None and self.is_sigma:
-            mstart = mstart.copy()
             mstart = np.log(mstart)
 
         return mstart
 
     @property
-    def reference(self):
+    def reference(self) -> np.ndarray | None:
         mref = self._reference.model
 
         if self.driver.params.forward_only:
             return mref
 
         if mref is None:
-            mref = self.starting
+            ref_model = self.starting
             self.driver.params.alpha_s = 0.0
         else:
-            mref = mref.copy()
+            ref_model = mref.copy()
             if self.is_sigma & (all(mref == 0)):
-                mref = self.starting
+                ref_model = self.starting
                 self.driver.params.alpha_s = 0.0
             else:
-                mref = np.log(mref) if self.is_sigma else mref
-        return mref
+                ref_model = np.log(ref_model) if self.is_sigma else ref_model
 
-    @property
-    def lower_bound(self):
-        lbound = self._lower_bound.model
+        return ref_model
 
-        if lbound is None:
+    @property
+    def lower_bound(self) -> np.ndarray | None:
+        if self._lower_bound.model is None:
             return -np.inf
 
-        lbound = lbound.copy()
+        lbound = self._lower_bound.model.copy()
 
         if self.is_sigma:
             is_finite = np.isfinite(lbound)
@@ -157,13 +158,12 @@ def lower_bound(self):
         return lbound
 
     @property
-    def upper_bound(self):
-        ubound = self._upper_bound.model
-
-        if ubound is None:
+    def upper_bound(self) -> np.ndarray | None:
+        if self._upper_bound.model is None:
             return np.inf
 
-        ubound = ubound.copy()
+        ubound = self._upper_bound.model.copy()
+
         if self.is_sigma:
             is_finite = np.isfinite(ubound)
             ubound[is_finite] = np.log(ubound[is_finite])
@@ -171,14 +171,16 @@ def upper_bound(self):
         return ubound
 
     @property
-    def conductivity(self):
-        mstart = self._conductivity.model
+    def conductivity(self) -> np.ndarray | None:
+        if self._conductivity.model is None:
+            return None
 
-        if mstart is not None and self.is_sigma:
-            mstart = mstart.copy()
-            mstart = np.log(mstart)
+        cond_model = self._conductivity.model.copy()
 
-        return mstart
+        if cond_model is not None and self.is_sigma:
+            cond_model = np.log(cond_model)
+
+        return cond_model
 
     def _initialize(self, driver):
         self.driver = driver
diff --git a/geoapps/inversion/joint/joint_surveys/driver.py b/geoapps/inversion/joint/joint_surveys/driver.py
index ff7acbb42..46aab255b 100644
--- a/geoapps/inversion/joint/joint_surveys/driver.py
+++ b/geoapps/inversion/joint/joint_surveys/driver.py
@@ -47,6 +47,9 @@ def validate_create_models(self):
                 norm = np.array(np.sum(projection, axis=1)).flatten()
                 model = (projection * model_local_values) / (norm + 1e-8)
 
+                if self.drivers[0].models.is_sigma:
+                    model = np.exp(model)
+
                 setattr(
                     getattr(self.models, f"_{model_type}"),
                     "model",

From e53da5c9e6d0dc316083fd94baef0755850171f7 Mon Sep 17 00:00:00 2001
From: dominiquef <dominiquef@mirageoscience.com>
Date: Tue, 30 Jan 2024 11:31:17 -0800
Subject: [PATCH 33/33] Simplify logic

---
 geoapps/inversion/components/models.py | 14 +++++---------
 1 file changed, 5 insertions(+), 9 deletions(-)

diff --git a/geoapps/inversion/components/models.py b/geoapps/inversion/components/models.py
index eb0043ab1..ef6f4e74a 100644
--- a/geoapps/inversion/components/models.py
+++ b/geoapps/inversion/components/models.py
@@ -132,16 +132,12 @@ def reference(self) -> np.ndarray | None:
         if self.driver.params.forward_only:
             return mref
 
-        if mref is None:
-            ref_model = self.starting
+        if mref is None or (self.is_sigma and all(mref == 0)):
+            mref = self.starting
             self.driver.params.alpha_s = 0.0
-        else:
-            ref_model = mref.copy()
-            if self.is_sigma & (all(mref == 0)):
-                ref_model = self.starting
-                self.driver.params.alpha_s = 0.0
-            else:
-                ref_model = np.log(ref_model) if self.is_sigma else ref_model
+
+        ref_model = mref.copy()
+        ref_model = np.log(ref_model) if self.is_sigma else ref_model
 
         return ref_model