Reorganizing repo for major redesign

.github/workflows/create-dist.bat

@@ -1,4 +1,4 @@
-cd pulmtln
+cd tulip
 md "dist\"
 xcopy "build\bin\Release\" "dist\" /e
 cd ..

.github/workflows/ubuntu-builds-and-tests.yml

@@ -1,12 +1,12 @@
-name: "Ubuntu | Build and tests"
+name: "Ubuntu | Tulip build and tests"
 
 permissions:
   actions: write
 
 on:
   push:
     branches:
-      - master
+      - main
       - dev
   pull_request:
     branches:
@@ -15,7 +15,7 @@ on:
   workflow_dispatch:
 
 env:
-  PULMTLN_TOP_DIR: pulmtln
+  TULIP_TOP_DIR: tulip
   MFEM_TOP_DIR: mfem
 
 jobs:
@@ -30,33 +30,37 @@ jobs:
     runs-on: ${{ matrix.os }}
 
     steps:
-    - name: checkout PULMTLN
+    - name: checkout TULIP
       uses: actions/checkout@v3
       with:
-        path: ${{ env.PULMTLN_TOP_DIR }}
+        path: ${{ env.TULIP_TOP_DIR }}
         ssh-key: ${{secrets.PULMTLN_SSH_KEY}}
         submodules: 'recursive'
 
     - name: getcmake
       uses: lukka/get-cmake@latest
 
-    - name: Setup vcpkg (it does not install any package yet)
+    - name: Install system packages
+      run: bash ${{ env.TULIP_TOP_DIR }}/scripts/install-packages.sh
+
+    - name: Setup vcpkg
       uses: lukka/run-vcpkg@v11
       with:
-        vcpkgGitCommitId: 42bb0d9e8d4cf33485afb9ee2229150f79f61a1f
-        vcpkgJsonGlob: 'pulmtln/vcpkg.json'
-      
-    - name: Configuring PULMTLN
-      env: 
-        MFEM_PACKAGE: ${{ github.workspace }}/${{env.MFEM_TOP_DIR}}/build
+        vcpkgGitCommitId: eed289f6e06a5e7a5c9e6a729671b0a56af7dd69
+        vcpkgJsonGlob: 'tulip/vcpkg.json'
+
+    - name: Configure TULIP
+      env:
+        MFEM_PACKAGE: ${{ github.workspace }}/${{ env.MFEM_TOP_DIR }}/build
       run: |
-        cmake --preset "gnu" -S pulmtln -B pulmtln/build
-    
-    - name: Building PULMTLN
+        cmake --preset "gnu" -S ${{ env.TULIP_TOP_DIR }} -B ${{ env.TULIP_TOP_DIR }}/build
+
+    - name: Build TULIP
       run: |
-        cmake --build pulmtln/build/ 
+        cmake --build ${{ env.TULIP_TOP_DIR }}/build --parallel 2
 
-    - name: test PULMTLN
-      run: cd pulmtln && build/bin/pulmtln_tests
+    - name: Test TULIP
+      run: |
+        ctest --test-dir ${{ env.TULIP_TOP_DIR }}/build --output-on-failure
 
 

.github/workflows/windows-automated-releases.yml

@@ -7,11 +7,11 @@ permissions:
 on:
   push:
     branches:
-      - master
+      - main
       - feature/automate-release
 
 env:
-  PULMTLN_TOP_DIR: pulmtln
+  TULIP_TOP_DIR: tulip
   MFEM_TOP_DIR: mfem
 
 
@@ -32,10 +32,10 @@ jobs:
       with:
         access_token: ${{ github.token }}
 
-    - name: checkout PULMTLN
+    - name: checkout TULIP
       uses: actions/checkout@v4
       with:
-        path: ${{ env.PULMTLN_TOP_DIR }}
+        path: ${{ env.TULIP_TOP_DIR }}
 
     - name: getcmake
       uses: lukka/get-cmake@latest
@@ -44,7 +44,7 @@ jobs:
       uses: lukka/run-vcpkg@v11
       with:
         vcpkgGitCommitId: 120deac3062162151622ca4860575a33844ba10b
-        vcpkgJsonGlob: 'pulmtln/vcpkg.json'
+        vcpkgJsonGlob: 'tulip/vcpkg.json'
 
     - name: cache MFEM
       uses: actions/cache@v3
@@ -79,29 +79,29 @@ jobs:
     # - name: Setup tmate session
     #   uses: mxschmitt/action-tmate@v3
 
-    - name: Configuring PULMTLN
+    - name: Configuring TULIP
       env:
         MFEM_PACKAGE: ${{ github.workspace }}/${{env.MFEM_TOP_DIR}}/build
       run: |
-        cmake --preset "msbuild-vcpkg" -S pulmtln -B pulmtln/build
+        cmake --preset "msbuild-vcpkg" -S tulip -B tulip/build
 
-    - name: Building PULMTLN
+    - name: Building TULIP
       run: |
-        cmake --build pulmtln/build/ --config Release
+        cmake --build tulip/build/ --config Release
 
-    # - name: Configuring and building PULMTLN
+    # - name: Configuring and building TULIP
     #   uses: lukka/run-cmake@v10
     #   id: runcmake
 
     #   with:
-    #     cmakeListsTxtPath: '${{ github.workspace }}/pulmtln/CMakeLists.txt'
+    #     cmakeListsTxtPath: '${{ github.workspace }}/tulip/CMakeLists.txt'
     #     configurePreset: 'msbuild-vcpkg'
     #     configurePresetAdditionalArgs: '[`-DCMAKE_PREFIX_PATH=../mfem`]'
     #     buildPreset: 'msbuild-vcpkg'
     #     buildPresetAdditionalArgs: '[`--config Release`]'
 
-    - name: test PULMTLN
-      run: cd pulmtln && build/bin/Release/pulmtln_tests.exe
+    - name: test TULIP
+      run: cd tulip && build/bin/Release/tulip_tests.exe
 
     - name: Get current date
       id: date
@@ -110,11 +110,11 @@ jobs:
     - name: Create dist folder
       shell: bash
       run: |
-        ${{ env.PULMTLN_TOP_DIR }}/.github/workflows/create-dist.bat
+        ${{ env.TULIP_TOP_DIR }}/.github/workflows/create-dist.bat
 
     - name: Create .tar file
       run: |
-        cd pulmtln && tar -czvf tulip-windows.tar.gz dist/*
+        cd tulip && tar -czvf tulip-windows.tar.gz dist/*
 
 
     - name: Generating release
@@ -125,4 +125,4 @@ jobs:
         prerelease: false
         title: "${{ steps.date.outputs.date }} Windows TULIP"
         files: |
-          pulmtln/tulip-windows.tar.gz
+          tulip/tulip-windows.tar.gz

.github/workflows/windows-builds-and-tests.yml

@@ -1,12 +1,12 @@
-name: "Windows | Build and tests"
+name: "Windows | Tulip build and tests"
 
 permissions:
   actions: write
 
 on:
   push:
     branches:
-      - master
+      - main
       - dev
   pull_request:
     branches:
@@ -15,7 +15,7 @@ on:
   workflow_dispatch:
 
 env:
-  PULMTLN_TOP_DIR: pulmtln
+  TULIP_TOP_DIR: tulip
   MFEM_TOP_DIR: mfem
 
 jobs:
@@ -35,10 +35,10 @@ jobs:
       with:
         access_token: ${{ github.token }}
 
-    - name: checkout PULMTLN
+    - name: checkout TULIP
       uses: actions/checkout@v3
       with:
-        path: ${{ env.PULMTLN_TOP_DIR }}
+        path: ${{ env.TULIP_TOP_DIR }}
         ssh-key: ${{secrets.PULMTLN_SSH_KEY}}
 
     - name: getcmake
@@ -47,8 +47,8 @@ jobs:
     - name: Setup vcpkg (it does not install any package yet)
       uses: lukka/run-vcpkg@v11
       with:
-        vcpkgGitCommitId: 120deac3062162151622ca4860575a33844ba10b
-        vcpkgJsonGlob: 'pulmtln/vcpkg.json'
+        vcpkgGitCommitId: eed289f6e06a5e7a5c9e6a729671b0a56af7dd69
+        vcpkgJsonGlob: 'tulip/vcpkg.json'
 
     - name: cache MFEM 
       uses: actions/cache@v3
@@ -64,7 +64,7 @@ jobs:
         repository: opensemba/mfem
         path: ${{ env.MFEM_TOP_DIR }}
 
-    - name: build MFEM
+    - name: Build MFEM
       if: steps.mfem-cache.outputs.cache-hit != 'true'
       uses: mfem/github-actions/build-mfem@v2.4
       env:
@@ -80,28 +80,17 @@ jobs:
         metis-dir: ${{ env.METIS_TOP_DIR }}
         mfem-dir: ${{ env.MFEM_TOP_DIR }}
 
-    - name: Configuring PULMTLN
+    - name: Configure TULIP
       env: 
         MFEM_PACKAGE: ${{ github.workspace }}/${{env.MFEM_TOP_DIR}}/build
       run: |
-        cmake --preset "msbuild-vcpkg" -S pulmtln -B pulmtln/build
+        cmake --preset "msbuild-vcpkg" -S tulip -B tulip/build
 
-    - name: Building PULMTLN
+    - name: Build TULIP
       run: |
-        cmake --build pulmtln/build/ --config Release
-
-    # - name: Configuring and building PULMTLN
-    #   uses: lukka/run-cmake@v10
-    #   id: runcmake
-
-    #   with:
-    #     cmakeListsTxtPath: '${{ github.workspace }}/pulmtln/CMakeLists.txt'
-    #     configurePreset: 'msbuild-vcpkg'
-    #     configurePresetAdditionalArgs: '[`-DCMAKE_PREFIX_PATH=../mfem`]'
-    #     buildPreset: 'msbuild-vcpkg'
-    #     buildPresetAdditionalArgs: '[`--config Release`]'
-
-    - name: test PULMTLN
-      run: cd pulmtln && build/bin/Release/pulmtln_tests.exe
-
+        cmake --build tulip/build/ --config Release
+
+    - name: Test TULIP
+      run: |
+        ctest --test-dir ${{ env.TULIP_TOP_DIR }}/build -C Release --output-on-failure        
 

.gitignore

@@ -1,6 +1,6 @@
 .vs/
 out/
-build/
+build*/
 builds/
 ParaView/
 tmp_cases/
@@ -11,8 +11,6 @@ CMakeSettings.json
 .vscode/c_cpp_properties.json
 
 
-/*.msh
-
 *.csv
 *.gf
 mesh.mesh
@@ -61,11 +59,27 @@ __pycache__/
 
 /CMakeUserPresets.json
 
-/to_from_JSONFile_test.pulmtln.out.json
+/to_from_JSONFile_test.tulip.out.json
 /Results
 /mfem-build
 /testData/lansink2024_single_wire/lansink2024_single_wire.areas.json
 /testData/lansink2024_fdtd_cell/calculations.py
 /testData/lansink2024/inCellPotentials.out.json
 /XMLGoogleTestResults.xml
 *.inCellPotentials.out.json
+*.FCStd1
+*.pyc
+.vscode/
+.pytest_cache/
+.idea/
+tmpFolder/
+venv/
+gmshDoc/
+vcpkg_installed/
+
+*.msh
+*.vtk
+*.areas.json
+build
+Testing/Temporary/CTestCostData.txt
+Testing/Temporary/LastTest.log

.gitmodules

@@ -1,7 +1,4 @@
 [submodule "external/mfem-geg"]
 	path = external/mfem-geg
 	url = https://github.com/OpenSEMBA/mfem.git
-	ignore = dirty
-[submodule "external/step2gmsh"]
-	path = external/step2gmsh
-	url = https://github.com/OpenSEMBA/step2gmsh.git
+	ignore = dirty