feat: Load Atmospheric CAF files from single file input, include SR Proxy reading, and add functionality for FC/PC event selection

.github/workflows/CDImage.yml

@@ -32,7 +32,7 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v6
+        uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10
 
       - name: Log in to GitHub Container Registry
         run: echo "${{ secrets.GITHUB_TOKEN }}" | docker login ghcr.io -u ${{ github.actor }} --password-stdin
@@ -62,7 +62,7 @@ jobs:
           fi
 
       - name: Delete old images
-        uses: actions/delete-package-versions@v5
+        uses: actions/delete-package-versions@e5bc658cc4c965c472efe991f8beea3981499c55
         with:
           package-name: 'mach3'
           package-type: 'container'

.github/workflows/CIBuild.yml

@@ -28,7 +28,7 @@ jobs:
     name: Build CI ${{ matrix.os }}
 
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10
 
       - name: Log in to GitHub Container Registry
         run: echo "${{ secrets.GITHUB_TOKEN }}" | docker login ghcr.io -u ${{ github.actor }} --password-stdin

.github/workflows/CIValidations.yml

@@ -33,7 +33,7 @@ jobs:
     name: Run Test ${{matrix.name}}
     steps:
       # Checkout the repository code
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10
       - name: Log in to GitHub Container Registry
         run: echo "${{ secrets.GITHUB_TOKEN }}" | docker login ghcr.io -u ${{ github.actor }} --password-stdin
 
@@ -49,7 +49,7 @@ jobs:
 
       # Run event rates
       - name: Run Event Rates
-        uses: addnab/docker-run-action@v3
+        uses: addnab/docker-run-action@4f65fabd2431ebc8d299f8e5a018d79a769ae185
         with:
           image: ghcr.io/dune/mach3:alma9_ci
           shell: bash

.github/workflows/Doxygen.yml

@@ -1,56 +1,19 @@
 ---
-# This is a basic workflow make doxygen documentation
-# every time develop is updated
-name: Doxygen
+name: Doxygen GitHub Pages Deploy Action
 
-# Controls when the workflow will run
 on:
-  # Triggers the workflow on push or pull request events but only for the develop branch
   push:
-    branches: [develop]
-
-  # Allows you to run this workflow manually from the Actions tab
+    branches:
+      - develop
   workflow_dispatch:
 
-# A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:
-  # This workflow contains a single job called "Doxygen"
-
-  Doxygen:
-    # The type of runner that the job will run on
+  deploy:
     runs-on: ubuntu-latest
-
-    permissions:
-      contents: write
-      id-token: write
-
-    # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
-      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
-      - uses: actions/checkout@v6
-
-      # Updates the package list to ensure you get the latest version of packages
-      - run: sudo apt-get update
-
-      # Installs texlive for LaTeX support in Doxygen documentation
-      - run: sudo apt-get install -y texlive
-
-      # Installs libjs-mathjax for rendering mathematical notation in Doxygen documentation
-      - run: sudo apt-get install -y libjs-mathjax
-
-      # Install perl for bibtex
-      - run: sudo apt-get install -y perl
-
-      # Runs a single command using the runners shell
-      - name: Doxygen Action
-        uses: mattnotmitt/doxygen-action@v1.12.0
-        with:
-          doxyfile-path: './Docs/Doxyfile'
-          working-directory: .
-
-      # Deploys the generated documentation to GitHub Pages
-      - name: Deploy
-        uses: peaceiris/actions-gh-pages@v4
+      - uses: DenverCoder1/doxygen-github-pages-action@a30f9538f8ef1305aeceb563018f452c7a62d200
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
-          publish_dir: ./Docs/html
+          branch: gh-pages
+          folder: doc/html
+          config_file: Doxyfile

.github/workflows/Greetings.yml

@@ -10,7 +10,7 @@ jobs:
       issues: write
       pull-requests: write
     steps:
-    - uses: actions/first-interaction@v3
+    - uses: actions/first-interaction@1c4688942c71f71d4f5502a26ea67c331730fa4d
       with:
         repo_token: ${{ secrets.GITHUB_TOKEN }}
         issue_message: "This is your first issue, thank you for contributing to MaCh3 DUNE!"

.github/workflows/Linter.yml

@@ -13,13 +13,13 @@ jobs:
 
     steps:
       - name: Checkout code
-        uses: actions/checkout@v6
+        uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10
         with:
           fetch-depth: 0
 
       - name: Run Super Linter
-        uses: github/super-linter@v7
-        continue-on-error: true
+        uses: github/super-linter@b807e99ddd37e444d189cfd2c2ca1274d8ae8ef1
+        continue-on-error: false
         env:
           LINTER_RULES_PATH: .github/linters
           VALIDATE_MARKDOWN: true  # Enable Markdown linting

.github/workflows/PRTitleChecker.yml

@@ -16,7 +16,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
 
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10
 
       - uses: thehanimo/pr-title-checker@v1.4.3
         with:

CMakeLists.txt

@@ -60,7 +60,7 @@ endif()
 
 #=================== DUNEAnaObj
 if(NOT DEFINED DUNE_ANAOBJ_BRANCH)
-  set(DUNE_ANAOBJ_BRANCH v03_06_00)
+  set(DUNE_ANAOBJ_BRANCH v03_14_00)
   set(DUNE_ANAOBJ_BRANCH ${DUNE_ANAOBJ_BRANCH} CACHE STRING "Specify which duneanaobj branch to use")
 endif()
 
@@ -124,8 +124,8 @@ endif()
 ##################################  MaCh3  ######################################
 #If MaCh3 was sourced find it, otherwise use CPM
 SET(MaCh3_FOUND FALSE)
-find_package(MaCh3 2.5.0 EXACT QUIET)
-set(MaCh3_CORE_BRANCH v2.5.0 CACHE STRING "Specify the MaCh3 core branch to use")
+find_package(MaCh3 2.5.1 EXACT QUIET)
+set(MaCh3_CORE_BRANCH v2.5.1 CACHE STRING "Specify the MaCh3 core branch to use")
 message(STATUS "Using MaCh3_CORE_BRANCH: ${MaCh3_CORE_BRANCH}")
 
 if(NOT MaCh3_FOUND)
@@ -239,6 +239,13 @@ endif()
 
 ################################# Build MaCh3 ##################################
 add_library(MaCh3DUNECompilerOptions INTERFACE)
+
+if(MaCh3_DUNE_USE_SRProxy)
+  target_compile_definitions(MaCh3DUNECompilerOptions INTERFACE MaCh3_DUNE_USE_SRProxy=1)
+else()
+  target_compile_definitions(MaCh3DUNECompilerOptions INTERFACE MaCh3_DUNE_USE_SRProxy=0)
+endif()
+
 set_target_properties(MaCh3DUNECompilerOptions PROPERTIES EXPORT_NAME CompilerOptions)
 
 target_include_directories(MaCh3DUNECompilerOptions

Configs/EventRates_Atmospherics.yaml

@@ -103,62 +103,9 @@ ProcessMCMC:
   CalcBipolarPlot: false
   CalcParameterEvolution: false
 
-  #=============================================================================
+#=============================================================================
 
-"Projections": [
-  {
-    "Name": "RecoNuEnergy",
-    "VarString": "RecoNeutrinoEnergy",
-    "VarBins": [0.0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.2, 1.4],
-    "KinematicCuts": [
-      {
-        "Range": [0.1, 0.8],
-        "Name": "TrueNuEnergy",
-        "VarString": "TrueNeutrinoEnergy"
-      },
-      {
-        "Range": [0.4, 1.0],
-        "Name": "TrueCosZ",
-        "VarString": "TrueCosineZ"
-      }
-    ],
-    "CategoryCuts": [
-      {
-        "Name": "OscillationChannel_Single",
-        "VarString": "OscChannel",
-        "Breakdown": [[0.0], [1.0], [2.0], [3.0], [4.0], [5.0], [6.0], [7.0], [8.0], [9.0], [10.0], [11.0]],
-        "Names": ["nue_x_nue", "nue_x_numu", "nue_x_nutau", "numu_x_nue",
-                  "numu_x_numu", "numu_x_nutau", "nuebar_x_nuebar",
-                  "nuebar_x_numubar", "nuebar_x_nutaubar", "numubar_x_nuebar",
-                  "numubar_x_numubar", "numubar_x_nutaubar"],
-      },
-      {
-        "Name": "OscillationChannel_Group",
-        "VarString": "OscChannel",
-        "Breakdown": [[0.0, 1.0, 2.0, 3.0, 4.0, 5.0], [6.0, 7.0, 8.0, 9.0, 10.0, 11.0]],
-        "Names": ["Nu", "Nubar"],
-      },
-      {
-        "Name": "Mode_Single",
-        "VarString": "Mode",
-        "Breakdown": [[0.0], [1.0], [2.0], [3.0], [4.0], [5.0], [6.0], [7.0], [8.0],
-                      [9.0], [10.0], [11.0], [12.0], [13.0], [14.0], [15.0], [16.0],
-                      [17.0], [18.0], [19.0], [20.0], [21.0], [22.0], [23.0],
-                      [24.0], [25.0], [26.0]],
-      },
-      {
-        "Name": "Mode_Group",
-        "VarString": "Mode",
-        "Breakdown": [[0.0], [2.0], [3.0], [9.0], [15.0], [16.0], [1.0, 4.0, 5.0, 6.0, 7.0, 8.0, 10.0, 11.0, 12.0, 13.0], [14.0, 17.0, 18.0, 19.0, 20.0, 21.0, 22.0, 23.0, 24.0, 25.0, 26.0]],
-        "Names": ["CCQE", "CCDIS", "CCRES", "CCMEC", "NCDIS", "NCRES", "CCOth", "NCOth"],
-      }
-    ],
-  },
-
-  {
-    "Name": "TrueNuEnergy",
-    "VarString": "TrueNeutrinoEnergy",
-    "VarBins": [0.0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.2, 1.4, 1.6, 1.8, 2.0,
-                2.2, 2.4, 2.6, 2.8, 3.0, 3.5, 4.0, 4.5, 5.0, 6.0, 7.0, 8.0, 9.0, 10.0],
-  }
-]
+Projections:
+  - Name: "MinDistToWall"
+    VarStrings: ["MinDistToWall"]
+    VarBins: [[0.0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.2, 1.4]]

Configs/Samples/AtmosphericParameterBinning.yaml

@@ -1,3 +1,4 @@
-Atm:
-    TrueNeutrinoEnergy: [0.0, 0.5, 1.0, 1.5, 2.0, 2.5, 3.0, 3.5, 4.0, 4.5, 5.0, 5.5, 6.0, 6.5, 7.0, 7.5, 8.0, 8.5, 9.0, 9.5]
-    TrueCosineZ: [-1, -0.8, -0.6, -0.4, -0.2, 0, 0.2, 0.4, 0.6, 0.8, 1]
+---
+TrueNeutrinoEnergy: [0.0, 0.5, 1.0, 1.5, 2.0, 2.5, 3.0, 3.5, 4.0, 4.5, 5.0, 5.5, 6.0, 6.5, 7.0, 7.5, 8.0, 8.5, 9.0, 9.5]
+TrueCosineZ: [-1, -0.8, -0.6, -0.4, -0.2, 0, 0.2, 0.4, 0.6, 0.8, 1]
+MinDistToWall: [-100, -50, -20, -10, -5, -4, -3, -2, -1, 0, 1, 2, 3, 4, 5, 10, 20, 30, 40, 50, 100, 150, 200, 300, 400, 500, 1000, 2000, 3000, 5000, 10000, 100000, 1000000000]

Configs/Samples/BeamParameterBinning.yaml

@@ -1,3 +1,4 @@
+---
 FHC_numu:
     IsFHC: [-0.5, 0.5, 1.5]
     RecoNeutrinoEnergy: [0., 0.5, 1., 1.25, 1.5, 1.75, 2., 2.25, 2.5, 2.75, 3., 3.25, 3.5, 3.75, 4., 5., 6., 10.]