Fix merge conflict with develop

.github/CONTRIBUTING.md

@@ -15,18 +15,16 @@ void Foo(){}
 try
 ```cpp
 /// @brief I like comments
+/// @details anything longer than ~80 should go in a details
 void Foo(){}
 ```
-After making release or tag please
-```bash
-cd Doc
-doxygen Doxyfile
-```
-to produce both html and latex file. To produce book like pdf file:
-```bash
-cd latex
-pdflatex refman.tex
+You can
+```cpp
+/// @param blarb this is parameter needed for function
+/// @return returning some fancy number
+int Fool(int blarb){}
 ```
+Doxygen documentation will be updated after each commit to develop.
 
 ## Logger
 MaCh3 is using spdlog logger see [here](https://github.com/gabime/spdlog/tree/master). And wraps it around MaCh3 names [here](https://github.com/mach3-software/MaCh3/blob/develop/manager/MaCh3Logger.h)
@@ -63,7 +61,7 @@ bool AsimovFit = false;
 
 if(config[AsimovFit])
 {
-  AsimovFit = config[AsimovFit].as<bool>;
+  AsimovFit = config[AsimovFit].as<bool>();
 }
 ```
 This can be replaced with:
@@ -75,17 +73,18 @@ bool AsimovFit = GetFromManager<bool>(config[AsimovFit], false);
 Some fits require a lot of RAM. The easiest and fastest solution to reduce RAM
 is to use `float` instead of `double`.
 
-MaCh3 has a custom type defined as `_float_`, which is usually a `double`
+MaCh3 has a custom type defined as `M3::float_t`, which is usually a `double`
 unless the `_LOW_MEMORY_STRUCTS_` directive is defined at the compilation
-level. When defined, `_float_` will be an actual `float`.
+level. When defined, `M3::float_t` will be an actual `float`.
 
-By using `_float_`, one can flexibly change between these types. During
+By using `M3::float_t`, one can flexibly change between these types. During
 development, it is advised to use these data types unless specific data
 types are necessary due to desired precision, code safety, etc.
 
 ## Error handling
 MaCh3 uses custom error handling implemented [here](https://github.com/mach3-software/MaCh3/blob/develop/manager/MaCh3Exception.h)
-Instead of throw
+
+Never ever ever bare throw. Always throw an exception, preferably one that subclasses one defined by the standard library in `<stdexcept>`.
 ```cpp
 throw;
 ```
@@ -98,7 +97,66 @@ or
 ```cpp
 throw MaCh3Exception(__FILE__ , __LINE__ );
 ```
-This way we can ensure error messages are unified and user always get hints where in the code problem occurred. If current MaCh3Exception is not sufficient consider implementing new or expanding current exceptions in MaCh3Exception.h.
+This way we can ensure error messages are unified and user always get hints where in the code problem occurred. If current `MaCh3Exception` is not sufficient consider implementing new or expanding current exceptions in MaCh3Exception.h.
+
+## Compiler warning levels getting you down?
+
+If you are trying to compile some new development and it is failing because of some innocuous warning that has been elevated to an error by the compiler flags, please don't just turn off the flags. A much better approach is to disable the diagnostic locally. This makes it easier to keep most of the code stringently checked, while giving you, the developer, the ability to stay in flow.
+It also allows for later 'fixing' of these warnings, if they need to be fixed, to be done systematically by greping for the relevant directives.
+
+The way to turn off diagnostics is, as below:
+
+```c++
+#pragma GCC diagnostic ignored "-Wfloat-conversion"
+```
+
+N.B. that clang also understands these directives, so don't panic that they have `GCC` in them.
+
+This will disable that diagnostic for the rest of the compilation unit (usually a .cc file). Note that this means if you include these in headerfiles, they will disable diagnostics more widely, please try and disable the diagnostics over as little code as possible.
+
+If a specific error is really getting you down and its showing up everywhere, the serious option is to disable it repo-wide by modifying the `MaCh3Warnings` interface target, defined in the top-level project [CMakeLists.txt](../CMakeLists.txt) like so:
+
+```cmake
+target_compile_options(MaCh3Warnings INTERFACE
+    # ...
+    -Wno-conversion
+    # ...
+)
+```
+
+Please attempt more localised options before reaching for this, but sometimes this represents the best way to proceed with development without 'fixing' innocuous warnings.
+
+The really serious option is to configure with: `-DMaCh3_WERROR_ENABLED=OFF`, which will disable the `-Werror` flag.
+
+### An example
+
+We got this compiler error:
+
+```shell
+/root/software/MaCh3/MaCh3_splitpr/splines/splineFDBase.cpp: In member function ‘virtual void splineFDBase::CalcSplineWeights()’:
+/root/software/MaCh3/MaCh3_splitpr/splines/splineFDBase.cpp:349:35: error: useless cast to type ‘double’ [-Werror=useless-cast]
+  349 |     weightvec_Monolith[iSpline] = double(weight);
+      |                                   ^~~~~~~~~~~~~~
+cc1plus: all warnings being treated as errors
+```
+
+for this code:
+
+```c++
+    weightvec_Monolith[iSpline] = double(weight);
+```
+
+The compiler is right, that this is a useless cast, but `weight` can sometimes be a float, in which case we would get a conversion warning/error, so it seems like a no-win situation. We can 'save' the current diagnostics with `#pragma GCC diagnostic push`, disable the relevant one as above, and then revert to the saved set of diagnostics with `#pragma GCC diagnostic pop`.
+Putting it all together might look like:
+
+```c++
+#pragma GCC diagnostic push
+#pragma GCC diagnostic ignored "-Wuseless-cast"
+    weightvec_Monolith[iSpline] = double(weight);
+#pragma GCC diagnostic pop
+```
+
+This allows us to disable the diagnostic just for the relevant line.
 
 ## Formatting
 To ensure a unified style in MaCh3 software you can use a clang-format file which has instructions about formatting code.

.github/workflows/CDImage.yml

@@ -1,3 +1,4 @@
+---
 # Update MaCh3 container image registry with newest updates
 name: Image CD
 
@@ -24,6 +25,10 @@ jobs:
             file: Doc/MaCh3DockerFiles/Alma9/Dockerfile
             tag_latest: alma9latest
             installoptions: -j4
+          - os: rocky9cuda
+            file: Doc/MaCh3DockerFiles/Rocky9/Dockerfile
+            tag_latest: rocky9cudalatest
+            installoptions: -j4
 #          - os: ubuntu22.04
 #            file: Doc/MaCh3DockerFiles/Ubuntu22.04/Dockerfile
 #            tag_latest: ubuntu22.04latest
@@ -36,40 +41,40 @@ jobs:
     name: Image CD ${{ matrix.os }}
 
     steps:
-    - name: Checkout repository
-      uses: actions/checkout@v4
+      - name: Checkout repository
+        uses: actions/checkout@v4
 
-    - name: Log in to GitHub Container Registry
-      run: echo "${{ secrets.GITHUB_TOKEN }}" | docker login ghcr.io -u ${{ github.actor }} --password-stdin
+      - name: Log in to GitHub Container Registry
+        run: echo "${{ secrets.GITHUB_TOKEN }}" | docker login ghcr.io -u ${{ github.actor }} --password-stdin
 
-    - name: Build Docker image
-      run: |
-        if [ "${{ github.ref_type }}" == 'tag' ]; then
-          docker build . \
-            --file ${{ matrix.file }} \
-            --tag ghcr.io/${{ github.repository_owner }}/mach3:${{ matrix.os }}${{ github.ref_name }} \
-            --build-arg MACH3_VERSION=${{ github.ref_name }} \
-            --build-arg INSTALL_OPTIONS="${{ matrix.installoptions }}"
-        else
-          docker build . \
-            --file ${{ matrix.file }} \
-            --tag ghcr.io/${{ github.repository_owner }}/mach3:${{ matrix.tag_latest }} \
-            --build-arg MACH3_VERSION=develop \
-            --build-arg INSTALL_OPTIONS="${{ matrix.installoptions }}"
-        fi
+      - name: Build Docker image
+        run: |
+          if [ "${{ github.ref_type }}" == "tag" ]; then
+            docker build . \
+              --file "${{ matrix.file }}" \
+              --tag "ghcr.io/${{ github.repository_owner }}/mach3:${{ matrix.os }}${{ github.ref_name }}" \
+              --build-arg MACH3_VERSION="${{ github.ref_name }}" \
+              --build-arg INSTALL_OPTIONS="${{ matrix.installoptions }}"
+          else
+            docker build . \
+              --file "${{ matrix.file }}" \
+              --tag "ghcr.io/${{ github.repository_owner }}/mach3:${{ matrix.tag_latest }}" \
+              --build-arg MACH3_VERSION="develop" \
+              --build-arg INSTALL_OPTIONS="${{ matrix.installoptions }}"
+          fi
 
-    - name: Push Docker image
-      run: |
-        if [ "${{ github.ref_type }}" == 'tag' ]; then
-          docker push ghcr.io/${{ github.repository_owner }}/mach3:${{ matrix.os }}${{ github.ref_name }}
-        else
-          docker push ghcr.io/${{ github.repository_owner }}/mach3:${{ matrix.tag_latest }}
-        fi
+      - name: Push Docker image
+        run: |
+          if [ "${{ github.ref_type }}" == "tag" ]; then
+            docker push "ghcr.io/${{ github.repository_owner }}/mach3:${{ matrix.os }}${{ github.ref_name }}"
+          else
+            docker push "ghcr.io/${{ github.repository_owner }}/mach3:${{ matrix.tag_latest }}"
+          fi
 
-    - name: Delete old images
-      uses: actions/delete-package-versions@v5
-      with:
-        package-name: 'mach3'
-        package-type: 'container'
-        min-versions-to-keep: 5
-        delete-only-untagged-versions: 'true'
+      - name: Delete old images
+        uses: actions/delete-package-versions@v5
+        with:
+          package-name: 'mach3'
+          package-type: 'container'
+          min-versions-to-keep: 5
+          delete-only-untagged-versions: 'true'

.github/workflows/CIBuild.yml

@@ -30,6 +30,10 @@ jobs:
             file: Doc/MaCh3DockerFiles/Fedora32/Dockerfile
             tag: fedora32latest
             cmakeoptions: -DMaCh3_PYTHON_ENABLED=ON -DMaCh3_LOW_MEMORY_STRUCTS_ENABLED=ON
+          - os: Rocky9 CUDA
+            file: Doc/MaCh3DockerFiles/Rocky9/Dockerfile
+            tag: rocky9latest
+            cmakeoptions: -DMaCh3_PYTHON_ENABLED=ON
 
     name: Build CI ${{ matrix.os }}
 

.github/workflows/CIPythonValidations.yml

@@ -0,0 +1,43 @@
+# Performs unit and integration testing
+
+name: Validations Python CI 
+
+# The events that trigger the workflow
+on:
+  pull_request:
+    branches: [ develop ]
+
+permissions:
+  contents: read
+  packages: write
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    container:
+      image: ghcr.io/mach3-software/mach3:alma9latest
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Get MaCh3 Validations
+      run: |
+        cd /opt/
+        git clone https://github.com/mach3-software/MaCh3Tutorial.git MaCh3Validations
+
+    - name: Install pytest
+      working-directory: /opt/MaCh3Validations
+      run: |
+        mkdir python-test-modules
+        pip install -r ./CIValidations/PythonTests/requirements.txt -t python-test-modules/
+
+    - name: Validations
+      working-directory: /opt/MaCh3Validations
+      run: |
+        source /opt/root/v6-26-10/bin/thisroot.sh
+        export PYTHONPATH=$PYTHONPATH:$PWD/python-test-modules/
+        export MACH3=$PWD
+        
+        python3 -m pytest --config Inputs/ManagerTest.yaml CIValidations/PythonTests
+        

.github/workflows/CIValidations.yml

@@ -21,10 +21,10 @@ jobs:
       fail-fast: false  # Prevents cancellation of remaining jobs if one fails
       matrix:
         include:
-          - name: Spline Validations
+          - name: Reweight Validations
             test_1: ./CIValidations/SplineValidations
             test_2: ./CIValidations/SamplePDFValidations
-            test_3: empty
+            test_3: ./CIValidations/NuOscillatorInterfaceValidations
             test_4: empty
             test_5: empty
             test_6: empty
@@ -33,7 +33,7 @@ jobs:
           - name: Covariance Validations
             test_1: ./CIValidations/CovarianceValidations
             test_2: ./CIValidations/MaCh3ModeValidations
-            test_3: empty
+            test_3: ./CIValidations/UnitTests/manager_tests
             test_4: empty
             test_5: empty
             test_6: empty
@@ -75,7 +75,7 @@ jobs:
         cd MaCh3Validations
         mkdir build
         cd build
-        cmake ../ -DMaCh3_Branch=${{ github.head_ref }}
+        cmake ../ -DMaCh3_Branch=${{ github.head_ref }} -DMaCh3Tutorial_UNITTESTS_ENABLED=TRUE
 
     - name: Build MaCh3 Validations
       run: |

.github/workflows/Doxygen.yml

@@ -48,19 +48,20 @@ jobs:
       - run: sudo apt-get install -y perl
 
       # Runs a single command using the runners shell
-      - name: Doxygen Action
-        uses: mattnotmitt/[email protected]
+      - uses: DenverCoder1/[email protected]
         with:
-          doxyfile-path: './Doxyfile'
-          working-directory: ./Doc
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          folder: Doc/html
+          branch: gh-pages
+          config_file: Doc/Doxyfile
 
       - name: Upload Doxygen Artifact
         uses: actions/upload-artifact@v4
         with:
           retention-days: 1
           name: DoxygenHTML
           path: Doc/html
-          
+
   Sphinx:
     # The type of runner that the job will run on
     runs-on: ubuntu-latest
@@ -120,7 +121,7 @@ jobs:
           name: DocumentationHTML
           path: to-upload
 
-          
+
   Deploy:
     runs-on: ubuntu-latest
     needs: [Doxygen, Sphinx]