From 271e91217deb88a20165b5b8b4657dc01406b13b Mon Sep 17 00:00:00 2001
From: cianciosa <m4c@ornl.gov>
Date: Mon, 21 Oct 2024 13:51:34 -0400
Subject: [PATCH] Enable doxygen generation, traps and checks.

---
 .github/workflows/ci_doxygen.yaml | 49 +++++++++++++++++++++++++++++++
 CMakeLists.txt                    |  6 ++--
 2 files changed, 52 insertions(+), 3 deletions(-)
 create mode 100644 .github/workflows/ci_doxygen.yaml

diff --git a/.github/workflows/ci_doxygen.yaml b/.github/workflows/ci_doxygen.yaml
new file mode 100644
index 0000000..40c2e6b
--- /dev/null
+++ b/.github/workflows/ci_doxygen.yaml
@@ -0,0 +1,49 @@
+name: Build Documentation
+on:
+    workflow_dispatch:
+    push:
+        branches:
+          - 'master'
+jobs:
+    ci_doxygen:
+        if: ${{github.ref_name}} == 'master'
+        runs-on: ubuntu-latest
+        steps:
+            - name: Clone Repo
+              shell: bash
+              working-directory: ${{runner.workspace}}
+              run: |
+                git clone https://github.com/ORNL-Fusion/Stellarator-Tools.git ${{runner.workspace}}/Stellarator-Tools
+                git clone https://token:${{secrets.AUTH_TOKEN}}@github.com/ORNL-Fusion/Stellarator-Tools-Docs.git
+            - name: Create build directory.
+              shell: bash
+              working-directory: ${{runner.workspace}}/Stellarator-Tools
+              run: cmake -E make_directory build
+            - name: Install Libraries Linux
+              shell: bash
+              run: |
+                sudo apt update
+                sudo apt-get install libnetcdf-dev
+                sudo apt-get install libnetcdff-dev
+                sudo apt-get install libopenmpi-dev
+                sudo apt-get install libscalapack-openmpi-dev
+                sudo apt-get install doxygen
+            - name: Configure CMake
+              shell: bash
+              working-directory: ${{runner.workspace}}/Stellarator-Tools/build
+              run: cmake -DBUILD_BOOZ_XFORM=ON -DBUILD_V3FIT=ON -DBUILD_V3RFUN=ON -DBUILD_SIESTA=ON -DBUILD_LGRID=ON -DBUILD_SURFACE=ON -DBUILD_BMW=ON -DBUILD_PARVMEC=ON -DBUILD_DESCUR=ON -DDOXYGEN_OUTPUT_DIRECTORY=${{runner.workspace}}/Stellarator-Tools-Docs -DDOXYGEN_HTML_OUTPUT=docs ../
+            - name: Build
+              shell: bash
+              working-directory: ${{runner.workspace}}/Stellarator-Tools/build
+              run: make doc
+            - name: Push changes.
+              shell: bash
+              working-directory: ${{runner.workspace}}/Stellarator-Tools-Docs/docs
+              env:
+                GITHUB_TOKEN: ${{secrets.AUTH_TOKEN}}
+              run: |
+                git config user.name ${{secrets.AUTH_USER}}
+                git config user.email ${{secrets.AUTH_EMAIL}}
+                git add *
+                git commit . -m "Update Doxygen docs."
+                git push origin main
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 0997fcc..965f084 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -54,9 +54,9 @@ target_link_libraries (stell
                        $<$<AND:$<BOOL:${LAPACK_FOUND}>,$<VERSION_GREATER_EQUAL:${CMAKE_VERSION},3.18>>:LAPACK::LAPACK>
                        $<$<AND:$<BOOL:${BLAS_FOUND}>,$<VERSION_LESS:${CMAKE_VERSION},3.18>>:${BLAS_LIBRARIES}>
                        $<$<AND:$<BOOL:${LAPACK_FOUND}>,$<VERSION_LESS:${CMAKE_VERSION},3.18>>:${LAPACK_LIBRARIES}>
-#                       sanitizer
-#                       traps
-#                       checks
+                       sanitizer
+                       traps
+                       checks
 )
 target_include_directories (stell