Data array refactoring: replace inheritence with specs

.github/workflows/tidy3d-python-client-tests.yml

@@ -101,6 +101,9 @@ on:
 permissions:
   contents: read
 
+env:
+  VERIFICATIONS_PY_VERSION: '3.11'
+
 jobs:
   determine-test-scope:
     runs-on: ubuntu-latest
@@ -223,6 +226,39 @@ jobs:
           echo "version_match_tests=$version_match_tests"
           echo "extras_integration_tests=$extras_integration_tests"
           echo "test_type=$test_type"
+
+
+  move-type-imports:
+    name: move-type-imports
+    needs: determine-test-scope
+    if: needs.determine-test-scope.outputs.code_quality_tests == 'true'
+    runs-on: ubuntu-latest
+    steps:
+      - name: checkout-branch
+        uses: actions/checkout@v4
+        with:
+          ref: ${{ github.event.pull_request.head.ref }}
+          repository: ${{ github.event.pull_request.head.repo.full_name }}
+          fetch-depth: 0
+          persist-credentials: false
+
+      - name: setup-python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ env.VERIFICATIONS_PY_VERSION }}
+
+      - name: install-dependencies
+        run: |
+          set -euo pipefail
+          python -m venv .venv
+          source .venv/bin/activate
+          pip install libcst
+
+      - name: verify-type-import-guards
+        run: |
+          set -euo pipefail
+          source .venv/bin/activate
+          python scripts/move_type_imports.py --mode check_on_change
 
   lint:
     needs: determine-test-scope
@@ -256,10 +292,10 @@ jobs:
           submodules: false
           persist-credentials: false
 
-      - name: set-python-3.10
+      - name: set-python
         uses: actions/setup-python@v4
         with:
-          python-version: '3.10'
+          python-version: ${{ env.VERIFICATIONS_PY_VERSION }}
 
       - name: Install mypy
         run: |
@@ -270,6 +306,27 @@ jobs:
         run: |
           mypy --config-file=pyproject.toml
 
+  ensure-common-imports:
+    name: ensure-common-imports
+    needs: determine-test-scope
+    if: needs.determine-test-scope.outputs.code_quality_tests == 'true'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 1
+          submodules: false
+          persist-credentials: false
+
+      - name: set-python-3.10
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+
+      - name: Run tidy3d._common import check
+        run: |
+          python scripts/ensure_imports_from_common.py
+
   zizmor:
     name: Run zizmor 🌈
     runs-on: ubuntu-latest
@@ -287,7 +344,7 @@ jobs:
         uses: astral-sh/setup-uv@b75a909f75acd358c2196fb9a5f1299a9a8868a4 # v6.7.0
 
       - name: Run zizmor 🌈
-        run: uvx zizmor .github/workflows/*.y* --format=sarif . > results.sarif 
+        run: uvx zizmor==1.19.0 .github/workflows/*.y* --format=sarif . > results.sarif
         env:
           GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} 
 
@@ -298,7 +355,7 @@ jobs:
           category: zizmor
 
       - name: run zizmor directly  # this gets a success or fail result
-        run: uvx zizmor  .github/workflows/*.y*
+        run: uvx zizmor==1.19.0  .github/workflows/*.y*
         env:
           GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} 
 
@@ -429,7 +486,7 @@ jobs:
 
       - name: install-depedencies
         run: |
-          uv venv $GITHUB_WORKSPACE/.venv -p 3.11
+          uv venv $GITHUB_WORKSPACE/.venv -p "$VERIFICATIONS_PY_VERSION"
           source $GITHUB_WORKSPACE/.venv/bin/activate
           uv pip install -e "$GITHUB_WORKSPACE"
 
@@ -981,8 +1038,10 @@ jobs:
       - determine-test-scope
       - local-tests
       - remote-tests
+      - move-type-imports
       - lint
       - mypy
+      - ensure-common-imports
       - verify-schema-change
       - lint-commit-messages
       - lint-branch-name
@@ -993,6 +1052,12 @@ jobs:
       - extras-integration-tests
     runs-on: ubuntu-latest
     steps:
+      - name: move-type-imports
+        if: ${{ needs.determine-test-scope.outputs.code_quality_tests == 'true' && needs.move-type-imports.result != 'success' && needs.move-type-imports.result != 'skipped' }}
+        run: |
+          echo "❌ Found imports used only for typing that are not guarded by if TYPE_CHECKING."
+          exit 1
+
       - name: check-linting-result
         if: ${{ needs.determine-test-scope.outputs.code_quality_tests == 'true' && needs.lint.result != 'success' && needs.lint.result != 'skipped' }}
         run: |
@@ -1004,6 +1069,12 @@ jobs:
         run: |
           echo "❌ Mypy type checking failed."
           exit 1
+
+      - name: check-common-imports-result
+        if: ${{ needs.determine-test-scope.outputs.code_quality_tests == 'true' && needs.ensure-common-imports.result != 'success' && needs.ensure-common-imports.result != 'skipped' }}
+        run: |
+          echo "❌ tidy3d._common import check failed."
+          exit 1
 
       - name: check-schema-change-verification
         if: ${{ needs.determine-test-scope.outputs.code_quality_tests == 'true' && needs.verify-schema-change.result != 'success' && needs.verify-schema-change.result != 'skipped' }}

.gitignore

@@ -1,6 +1,7 @@
 # Batch JSON files
 batch*.json
 *.vtu
+simulation.json
 
 # Byte-compiled / optimized / DLL files
 *$py.class

.gitmodules

@@ -1,6 +0,0 @@
-[submodule "docs/notebooks"]
-	path = docs/notebooks
-	url = git@github.com:flexcompute/tidy3d-notebooks.git
-[submodule "docs/faq"]
-	path = docs/faq
-	url = https://github.com/flexcompute/tidy3d-faq

.pre-commit-config.yaml

@@ -3,6 +3,14 @@ default_install_hook_types:
   - pre-commit
   - commit-msg
 repos:
+  - repo: local
+    hooks:
+      - id: move-type-imports
+        name: move type-only imports under TYPE_CHECKING
+        entry: poetry run python scripts/move_type_imports.py --mode fix --only-changed
+        language: system
+        pass_filenames: false
+        stages: [pre-commit]
   - repo: https://github.com/astral-sh/ruff-pre-commit
     rev: "v0.11.11"
     hooks:
@@ -20,7 +28,7 @@ repos:
         entry: bash -c 'commitlint --edit || exit 0'
   - repo: https://github.com/zizmorcore/zizmor-pre-commit
     # Zizmor version.
-    rev: v1.15.2
+    rev: v1.19.0
     hooks:
       - id: zizmor
         stages: [pre-commit]

AGENTS.md

@@ -45,5 +45,6 @@
 - Follow Conventional Commits per `.commitlintrc.json`.
 - Branch names must use an allowed prefix (`chore`, `hotfix`, `daily-chore`) or include a Jira key to satisfy CI.
 - PRs should link issues, summarize behavior changes, list the `poetry run …` checks you executed, and call out docs/schema updates.
+- Add a changelog entry under `## [Unreleased]` in `CHANGELOG.md` for user-facing changes (new features, bug fixes, breaking changes).
 
 _Reminder: update this AGENTS.md whenever workflow, tooling, or review expectations change so agents stay in sync with the repo._

CHANGELOG.md

@@ -8,11 +8,26 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ## [Unreleased]
 
 ### Added
+- Added priority attribute to `TopologyDesignRegion` to enable manual control of overlapping structures.
+- `to_mat_file()` method is now available on `ModeSimulationData` and `HeatChargeSimulationData` for exporting results to MATLAB `.mat` files.
+- Added autograd support for diagonal `AnisotropicMedium` and `CustomAnisotropicMedium` with diagonal permittivity tensor.
+- Added support of numpy 2.4
+- Added validation to `DCVoltageSource` that warns when duplicate voltage values are detected in the `voltage` array, including treating `0` and `-0` as the same value.
 
 ### Changed
+- For `HeatChargeSimulation` objects, the `plot` function now adds the simulation boundary conditions.
 
 ### Fixed
 - Fixed `AutoImpedanceSpec` validation to check path intersections against all conductors, not just filtered ones, as well as the mode plane bounds.
+- Fixed `WavePort` validation so invalid `mode_spec` errors are no longer masked by a `KeyError`.
+- Fixed adjoint gradients being treated as zero due to scale-dependent `np.allclose(..., atol=1e-8)` checks, which could skip adjoint simulations and return zero gradients.
+- Fixed interpolation handling for permittivity and conductivity gradients in CustomMedium.
+- Restored original batch-load logging by suppressing per-task “Loading simulation…” messages. 
+- Fixed output range of `tidy3d.plugins.invdes.FilterAndProject` to be between 0 and 1.
+- Cropped adjoint monitor sizes in 2D simulations to planar geometry intersection.
+- Fixed `Batch.download()` silently succeeding when background downloads fail (e.g., gzip extraction errors).
+- Handling of zero values when using `sim_data.plot_field` with `scale=dB`.
+- Fixed `intersections_plane` method in `PolySlab`, which sometimes missed vertices for planes coincident with `PolySlab` side faces.
 
 ## [2.10.0] - 2025-12-18
 

docs/api/plugins/index.rst

@@ -1,6 +1,11 @@
 Plugins
 =======
 
+.. warning::
+
+   |:warning:| The 'adjoint' plugin (legacy JAX-based adjoint plugin)
+   was deprecated in Tidy3D 'v2.7.0' and is disabled as of 'v2.9.0'.
+
 .. toctree::
    :maxdepth: 1