Add .gitignore, .gitmodules, and update README with detailed usage instructions

.github/workflows/check-submodules-default-branch.yml

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+name: check-submodules-default-branch
+
+'on':
+  push:
+    branches:
+      - main
+      - dev
+      - thin-slots-cases
+  pull_request:
+    branches:
+      - main
+      - dev
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  check-submodules-default-branch:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository with submodules
+        uses: actions/checkout@v4
+        with:
+          submodules: recursive
+
+      - name: Validate submodules point to their configured branch
+        shell: bash
+        run: |
+          set -euo pipefail
+
+          if [[ ! -f .gitmodules ]]; then
+            echo "No .gitmodules file found. Nothing to validate."
+            exit 0
+          fi
+
+          mapfile -t submodule_entries < <(git config -f .gitmodules --get-regexp '^submodule\..*\.path$')
+
+          if [[ ${#submodule_entries[@]} -eq 0 ]]; then
+            echo "No submodules found in .gitmodules."
+            exit 0
+          fi
+
+          failed=0
+
+          for entry in "${submodule_entries[@]}"; do
+            key="${entry%% *}"
+            path="${entry#* }"
+            branch_key="${key%.path}.branch"
+            configured_branch="$(git config -f .gitmodules --get "${branch_key}" || true)"
+
+            echo ""
+            echo "Checking submodule: ${path}"
+            if [[ -n "${configured_branch}" ]]; then
+              echo "Configured branch: ${configured_branch}"
+            fi
+
+            if [[ ! -d "${path}" ]]; then
+              echo "::error title=Missing submodule directory::Submodule path '${path}' is missing in checkout"
+              failed=1
+              continue
+            fi
+
+            if ! git -C "${path}" rev-parse --is-inside-work-tree >/dev/null 2>&1; then
+              echo "::error title=Invalid submodule checkout::Path '${path}' is not a valid git repository"
+              failed=1
+              continue
+            fi
+
+            sha="$(git -C "${path}" rev-parse HEAD)"
+            echo "Pinned commit: ${sha}"
+
+            git -C "${path}" remote set-branches --add origin '*'
+            git -C "${path}" fetch --no-tags origin '+refs/heads/*:refs/remotes/origin/*' >/dev/null
+
+            if git -C "${path}" rev-parse --is-shallow-repository | grep -q true; then
+              git -C "${path}" fetch --unshallow --no-tags origin >/dev/null
+            fi
+
+            candidate_branches=()
+            if [[ -n "${configured_branch}" ]]; then
+              candidate_branches+=("${configured_branch}")
+            fi
+            if git -C "${path}" show-ref --verify --quiet refs/remotes/origin/main; then
+              candidate_branches+=("main")
+            fi
+            if git -C "${path}" show-ref --verify --quiet refs/remotes/origin/master; then
+              candidate_branches+=("master")
+            fi
+
+            if [[ ${#candidate_branches[@]} -eq 0 ]]; then
+              echo "::error title=Cannot determine branch::No configured branch or main/master found for submodule '${path}'"
+              failed=1
+              continue
+            fi
+
+            is_valid=0
+            for branch in "${candidate_branches[@]}"; do
+              if ! git -C "${path}" show-ref --verify --quiet "refs/remotes/origin/${branch}"; then
+                echo "::warning title=Missing submodule branch::Branch '${branch}' does not exist in '${path}'"
+                continue
+              fi
+              if git -C "${path}" merge-base --is-ancestor "${sha}" "origin/${branch}"; then
+                echo "OK: ${path} commit belongs to origin/${branch} history"
+                is_valid=1
+                break
+              fi
+            done
+
+            if [[ ${is_valid} -eq 0 ]]; then
+              echo "::error title=Submodule not on configured history::Submodule '${path}' points to ${sha}, which is not contained in any accepted branch: ${candidate_branches[*]}"
+              failed=1
+            fi
+          done
+
+          if [[ ${failed} -ne 0 ]]; then
+            echo ""
+            echo "One or more submodules are not aligned with their configured branch history."
+            exit 1
+          fi
+
+          echo ""
+          echo "All submodule commits are contained in their configured branch history."

.github/workflows/tests.yml

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+name: tests
+
+on:
+  push:
+    branches:
+      - main
+      - dev
+      - thin-slots-cases
+  pull_request:
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  pytest:
+    name: pytest / python ${{ matrix.python-version }}
+    runs-on: ubuntu-latest
+    timeout-minutes: 15
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10", "3.12"]
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: pip
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -r requirements.txt
+
+      - name: Run tests
+        run: python -m pytest -vv test/ --durations=0 --junitxml=pytest-results.xml
+
+      - name: Upload failed test diagnostics
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: pytest-results-${{ matrix.python-version }}
+          path: pytest-results.xml
+          if-no-files-found: warn
+
+  fdtd-integration:
+    name: fdtd integration
+    runs-on: ubuntu-latest
+    timeout-minutes: 45
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          submodules: recursive
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+          cache: pip
+
+      - name: Setup Fortran compiler
+        uses: fortran-lang/setup-fortran@v1
+        with:
+          compiler: gcc
+          version: "11"
+
+      - name: Setup Ninja
+        uses: seanmiddleditch/gha-setup-ninja@master
+
+      - name: Install HDF5
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y libhdf5-dev
+
+      - name: Install Python dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -r requirements.txt
+
+      - name: Build fdtd
+        run: |
+          cmake -S fdtd -B fdtd/build -G Ninja \
+            -DCMAKE_BUILD_TYPE=Release \
+            -DSEMBA_FDTD_ENABLE_MPI=OFF \
+            -DSEMBA_FDTD_ENABLE_MTLN=OFF \
+            -DSEMBA_FDTD_ENABLE_TEST=ON
+          cmake --build fdtd/build -j
+
+      - name: Run fdtd native tests
+        run: ctest --test-dir fdtd/build --output-on-failure
+
+      - name: Run caseMaker tests with fdtd
+        env:
+          SEMBA_EXE: ${{ github.workspace }}/fdtd/build/bin/semba-fdtd
+          OMP_NUM_THREADS: "1"
+        run: python -m pytest -vv test/ --durations=0 --junitxml=pytest-fdtd-results.xml
+
+      - name: Upload failed test diagnostics
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: fdtd-integration-results
+          path: |
+            pytest-fdtd-results.xml
+            fdtd/build/Testing/Temporary/LastTest.log
+          if-no-files-found: warn
+
+  tessellator-smoke:
+    name: tessellator embedded-surface smoke test
+    runs-on: ubuntu-latest
+    timeout-minutes: 45
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Checkout tessellator submodule
+        run: git submodule update --init tessellator
+
+      - name: Install system dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y libvtk9-dev ninja-build
+
+      - name: Export GitHub Actions cache environment variables
+        uses: actions/github-script@v7
+        with:
+          script: |
+            core.exportVariable('ACTIONS_CACHE_URL', process.env.ACTIONS_CACHE_URL || '');
+            core.exportVariable('ACTIONS_RUNTIME_TOKEN', process.env.ACTIONS_RUNTIME_TOKEN || '');
+
+      - name: Setup vcpkg
+        uses: lukka/run-vcpkg@v11
+        with:
+          vcpkgGitCommitId: eed289f6e06a5e7a5c9e6a729671b0a56af7dd69
+          runVcpkgInstall: false
+
+      - name: Build tessellator
+        run: |
+          cmake -S tessellator -B tessellator/build -G Ninja \
+            -DCMAKE_BUILD_TYPE=Release \
+            -DTESSELLATOR_ENABLE_TESTS=OFF \
+            -DTESSELLATOR_ENABLE_CGAL=OFF \
+            -DCMAKE_TOOLCHAIN_FILE="$VCPKG_ROOT/scripts/buildsystems/vcpkg.cmake"
+          cmake --build tessellator/build -j
+
+      - name: Run embedded-surface case
+        run: |
+          rm -rf /tmp/thin-slot-smoke
+          mkdir -p /tmp/thin-slot-smoke
+          cp testData/thin_slot/surface/* /tmp/thin-slot-smoke/
+          cd /tmp/thin-slot-smoke
+          "${GITHUB_WORKSPACE}/tessellator/build/bin/tessellator" \
+            -i squareInSquare.embeddedSurface.tessellator.json
+          test -f SquareInSquare.tessellator.str.vtk
+          test -f Discretize_Wire.tessellator.str.vtk
+          test -f squareInSquare.embeddedSurface.tessellator.grid.vtk

.gitignore

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+.vscode/settings.json
+__pycache__/
+*.py[cod]
+
+tmp_cases/

.gitmodules

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+[submodule "tessellator"]
+	path = tessellator
+	url = https://github.com/OpenSEMBA/tessellator.git
+	branch = 112-thin-slots-meshing
+[submodule "fdtd"]
+	path = fdtd
+	url = https://github.com/OpenSEMBA/fdtd.git
+	branch = 493-thin-slots-on-surfaces