From 7509341e43311c757d67c8c672ad1e40b858bfe0 Mon Sep 17 00:00:00 2001
From: John Vincent Cauilan <64677361+johvincau@users.noreply.github.com>
Date: Sat, 6 Jul 2024 12:05:29 -0500
Subject: [PATCH 01/43] Add basic Python dependency caching

---
 .github/workflows/ci.yml | 22 +++++++++++++++++-----
 1 file changed, 17 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 9293e319b42..a3818374dc7 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -65,10 +65,10 @@ jobs:
             python-version: "3.10"
             omp: n
             mpi: y
-    name: "Python ${{ matrix.python-version }} (omp=${{ matrix.omp }},
-      mpi=${{ matrix.mpi }}, dagmc=${{ matrix.dagmc }}, ncrystal=${{ matrix.ncrystal }},
-      libmesh=${{ matrix.libmesh }}, event=${{ matrix.event }}
-      vectfit=${{ matrix.vectfit }})"
+    name: "Python ${{ matrix.python-version }} (omp=${{ matrix.omp }}, 
+      mpi=${{ matrix.mpi }}, dagmc=${{ matrix.dagmc }}, 
+      ncrystal=${{ matrix.ncrystal }},libmesh=${{ matrix.libmesh }}, 
+      event=${{ matrix.event }}, vectfit=${{ matrix.vectfit }})"
 
     env:
       MPI: ${{ matrix.mpi }}
@@ -94,6 +94,18 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
+      - name: Restore Python cache
+        uses: actions/cache@v4
+        with:
+          path: ${{ env.pythonLocation }}
+          key:  python-cache-(python=${{ matrix.python-version }} (omp=${{ matrix.omp }}
+            mpi=${{ matrix.mpi }} dagmc=${{ matrix.dagmc }} ncrystal=${{ matrix.ncrystal }}
+            libmesh=${{ matrix.libmesh }} event=${{ matrix.event }}
+            vectfit=${{ matrix.vectfit }})
+          # How to handle when each individual dependency changes?
+          # Should each dependency have its own individual cache?
+          # Or should they all be bundled together?
+
       - name: Environment Variables
         run: |
           echo "DAGMC_ROOT=$HOME/DAGMC"
@@ -143,7 +155,7 @@ jobs:
         shell: bash
         run: $GITHUB_WORKSPACE/tools/ci/gha-before-script.sh
 
-      - name: test
+      - name: test ## possibly refactor to make more 
         shell: bash
         run: |
           CTEST_OUTPUT_ON_FAILURE=1 make test -C $GITHUB_WORKSPACE/build/

From 1524cf74bbfb83f5ec8545db68a784ebf0ea1ef3 Mon Sep 17 00:00:00 2001
From: John Vincent Cauilan <64677361+johvincau@users.noreply.github.com>
Date: Tue, 16 Jul 2024 13:46:44 -0500
Subject: [PATCH 02/43] Test NJOY install script refactor for specific install
 location

---
 .github/workflows/ci.yml     |  9 +++++++--
 tools/ci/gha-install-njoy.sh | 13 ++++++++++---
 2 files changed, 17 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index a3818374dc7..17ed2424a4a 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -104,7 +104,6 @@ jobs:
             vectfit=${{ matrix.vectfit }})
           # How to handle when each individual dependency changes?
           # Should each dependency have its own individual cache?
-          # Or should they all be bundled together?
 
       - name: Environment Variables
         run: |
@@ -137,6 +136,12 @@ jobs:
         if: ${{ matrix.vectfit == 'y' }}
         run: sudo apt install -y libblas-dev liblapack-dev
 
+      #- name: Install NJOY2016
+      #  uses: actions/cache@v4
+      #  with:
+      #    path: "$HOME/NJOY2016"
+      #    key: NJOY2016-
+
       - name: install
         shell: bash
         run: |
@@ -155,7 +160,7 @@ jobs:
         shell: bash
         run: $GITHUB_WORKSPACE/tools/ci/gha-before-script.sh
 
-      - name: test ## possibly refactor to make more 
+      - name: test
         shell: bash
         run: |
           CTEST_OUTPUT_ON_FAILURE=1 make test -C $GITHUB_WORKSPACE/build/
diff --git a/tools/ci/gha-install-njoy.sh b/tools/ci/gha-install-njoy.sh
index 8255ffea836..b045b7610dd 100755
--- a/tools/ci/gha-install-njoy.sh
+++ b/tools/ci/gha-install-njoy.sh
@@ -1,7 +1,14 @@
 #!/bin/bash
 set -ex
+
+# NJOY variables
+NJOY_BRANCH='main'
+NJOY_REPO='https://github.com/njoy/NJOY2016'
+NJOY_INSTALL_DIR=$HOME/NJOY2016/
+
 cd $HOME
-git clone https://github.com/njoy/NJOY2016
-cd NJOY2016
+git clone -b $NJOY_BRANCH $NJOY_REPO
+cd $NJOY_INSTALL_DIR
 mkdir build && cd build
-cmake -Dstatic=on .. && make 2>/dev/null && sudo make install
+cmake -Dstatic=on -DCMAKE_INSTALL_PREFIX=$NJOY_INSTALL_DIR .. 
+make 2>/dev/null && sudo make install
\ No newline at end of file

From 1bc85729dba3387132f9b0d2c1b14bbfcf499c07 Mon Sep 17 00:00:00 2001
From: John Vincent Cauilan <64677361+johvincau@users.noreply.github.com>
Date: Tue, 23 Jul 2024 15:53:37 -0500
Subject: [PATCH 03/43] Temporarily turn off testing suite

---
 .github/workflows/ci.yml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 17ed2424a4a..e6235a313f0 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -160,11 +160,11 @@ jobs:
         shell: bash
         run: $GITHUB_WORKSPACE/tools/ci/gha-before-script.sh
 
-      - name: test
-        shell: bash
-        run: |
-          CTEST_OUTPUT_ON_FAILURE=1 make test -C $GITHUB_WORKSPACE/build/
-          $GITHUB_WORKSPACE/tools/ci/gha-script.sh
+      #- name: test
+      #  shell: bash
+      #  run: |
+      #    CTEST_OUTPUT_ON_FAILURE=1 make test -C $GITHUB_WORKSPACE/build/
+      #    $GITHUB_WORKSPACE/tools/ci/gha-script.sh
 
       - name: after_success
         shell: bash

From ac060420c42921fee19aaabcc73ecde575cfefb6 Mon Sep 17 00:00:00 2001
From: John Vincent Cauilan <64677361+johvincau@users.noreply.github.com>
Date: Wed, 24 Jul 2024 11:49:54 -0500
Subject: [PATCH 04/43] Refactor mcpl install script

---
 tools/ci/gha-install-mcpl.sh | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/tools/ci/gha-install-mcpl.sh b/tools/ci/gha-install-mcpl.sh
index 9b8609398a0..df0eb376725 100755
--- a/tools/ci/gha-install-mcpl.sh
+++ b/tools/ci/gha-install-mcpl.sh
@@ -1,7 +1,13 @@
 #!/bin/bash
 set -ex
+
+MCPL_BRANCH='main'
+MCPL_REPO='https://github.com/mctools/mcpl'
+MCPL_INSTALL_DIR=$HOME/mcpl/
+
 cd $HOME
-git clone https://github.com/mctools/mcpl
-cd mcpl
+git clone -b $MCPL_BRANCH $MCPL_REPO
+cd $MCPL_INSTALL_DIR
 mkdir build && cd build
-cmake .. && make 2>/dev/null && sudo make install
+cmake .. -DCMAKE_INSTALL_PREFIX=$MCPL_INSTALL_DIR
+make 2>/dev/null && sudo make install
\ No newline at end of file

From d7c1bdc475594de88e3daadd2ef7a7dab8080ad3 Mon Sep 17 00:00:00 2001
From: John Vincent Cauilan <64677361+johvincau@users.noreply.github.com>
Date: Wed, 24 Jul 2024 11:50:27 -0500
Subject: [PATCH 05/43] Add commit hashing and dependency caching for testing

---
 .github/workflows/ci.yml | 34 +++++++++++++++++++++++++---------
 tools/ci/gha-caches.sh   | 28 ++++++++++++++++++++++++++++
 tools/ci/gha-install.sh  |  8 ++++++--
 3 files changed, 59 insertions(+), 11 deletions(-)
 create mode 100755 tools/ci/gha-caches.sh

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index e6235a313f0..1330dd526d5 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -102,8 +102,6 @@ jobs:
             mpi=${{ matrix.mpi }} dagmc=${{ matrix.dagmc }} ncrystal=${{ matrix.ncrystal }}
             libmesh=${{ matrix.libmesh }} event=${{ matrix.event }}
             vectfit=${{ matrix.vectfit }})
-          # How to handle when each individual dependency changes?
-          # Should each dependency have its own individual cache?
 
       - name: Environment Variables
         run: |
@@ -136,11 +134,29 @@ jobs:
         if: ${{ matrix.vectfit == 'y' }}
         run: sudo apt install -y libblas-dev liblapack-dev
 
-      #- name: Install NJOY2016
-      #  uses: actions/cache@v4
-      #  with:
-      #    path: "$HOME/NJOY2016"
-      #    key: NJOY2016-
+      - name: Grab hashes of required dependencies (just NJOY, DAGMC, and MCPL for now)
+        run: |
+          $GITHUB_WORKSPACE/tools/ci/gha-caches.sh
+          
+      - name: Restore NJOY2016 from cache
+        uses: actions/cache@v4
+        with:
+          path: ~/NJOY2016/
+          key: NJOY2016-${{ env.NJOY_HASH}}
+
+      - name: Restore DAGMC from cache
+        if: ${{ matrix.dagmc == 'y' }}
+        uses: actions/cache@v4
+        with:
+          path: |
+            ~/NJOY2016/
+          key: DAGMC-${{ env.DAGMC_HASH}}/MOAB-${{ env.MOAB_HASH }}
+      
+      - name: Restore MCPL
+        uses: actions/cache@v4
+        with:
+          path: ~/MCPL/
+          key: MCPL-${{ env.MCPL_HASH }}  
 
       - name: install
         shell: bash
@@ -148,13 +164,13 @@ jobs:
           echo "$HOME/NJOY2016/build" >> $GITHUB_PATH
           $GITHUB_WORKSPACE/tools/ci/gha-install.sh
 
-      - name: cache-xs
+      - name: Restore endf-b-vii.1 cache
         uses: actions/cache@v4
         with:
           path: |
             ~/nndc_hdf5
             ~/endf-b-vii.1
-          key: ${{ runner.os }}-build-xs-cache
+          key: endf-b-vii.1-cache
 
       - name: before
         shell: bash
diff --git a/tools/ci/gha-caches.sh b/tools/ci/gha-caches.sh
new file mode 100755
index 00000000000..8f6faefda75
--- /dev/null
+++ b/tools/ci/gha-caches.sh
@@ -0,0 +1,28 @@
+#!/bin/bash
+set -ex
+
+echo "NJOY_HASH=$(git ls-remote https://github.com/njoy/NJOY2016.git | cut -f 1 | head -c 15)" >> $GITHUB_ENV
+
+if [[ $DAGMC = 'y' ]]; then
+    echo "MOAB_HASH=$(git ls-remote https://bitbucket.org/fathomteam/moab.git | cut -f 1 | head -c 15)" >> $GITHUB_ENV
+    echo "DAGMC_HASH=$(git ls-remote https://github.com/svalinn/dagmc.git | cut -f 1 | head -c 15)" >> $GITHUB_ENV
+fi
+
+# Check for NCrystal cache if needed
+#if [[ $NCRYSTAL = 'y' ]]; then
+#    ./tools/ci/gha-install-ncrystal.sh
+#fi
+
+# Install vectfit for WMP generation if needed
+#if [[ $VECTFIT = 'y' ]]; then
+#    ./tools/ci/gha-install-vectfit.sh
+#fi
+
+# Check for libmesh cache if needed
+#if [[ $LIBMESH = 'y' ]]; then
+#    ./tools/ci/gha-install-libmesh.sh
+#fi
+
+echo "MCPL_HASH=$(git ls-remote https://github.com/mctools/mcpl.git | cut -f 1 | head -c 15)" >> $GITHUB_ENV
+
+# may be able to use this to control the directories to be cached.
\ No newline at end of file
diff --git a/tools/ci/gha-install.sh b/tools/ci/gha-install.sh
index 87952fda9cb..1ad2356addd 100755
--- a/tools/ci/gha-install.sh
+++ b/tools/ci/gha-install.sh
@@ -7,7 +7,9 @@ pip install --upgrade pytest
 pip install --upgrade numpy
 
 # Install NJOY 2016
-./tools/ci/gha-install-njoy.sh
+if [[ ! -d "$HOME/NJOY2016" ]]; then
+    ./tools/ci/gha-install-njoy.sh
+fi
 
 # Install DAGMC if needed
 if [[ $DAGMC = 'y' ]]; then
@@ -30,7 +32,9 @@ if [[ $LIBMESH = 'y' ]]; then
 fi
 
 # Install MCPL
-./tools/ci/gha-install-mcpl.sh
+if [[ ! -d "$HOME/MCPL" ]]; then
+    ./tools/ci/gha-install-mcpl.sh
+fi
 
 # For MPI configurations, make sure mpi4py and h5py are built against the
 # correct version of MPI

From d168428e5cc2d19802f8b27947dd0dba0e16dad3 Mon Sep 17 00:00:00 2001
From: John Vincent Cauilan <64677361+johvincau@users.noreply.github.com>
Date: Wed, 24 Jul 2024 13:16:46 -0500
Subject: [PATCH 06/43] Adjust MCPL branch

---
 .github/workflows/ci.yml     | 4 ++--
 tools/ci/gha-install-mcpl.sh | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 1330dd526d5..6d727967521 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -138,13 +138,13 @@ jobs:
         run: |
           $GITHUB_WORKSPACE/tools/ci/gha-caches.sh
           
-      - name: Restore NJOY2016 from cache
+      - name: Restore NJOY2016
         uses: actions/cache@v4
         with:
           path: ~/NJOY2016/
           key: NJOY2016-${{ env.NJOY_HASH}}
 
-      - name: Restore DAGMC from cache
+      - name: Restore DAGMC
         if: ${{ matrix.dagmc == 'y' }}
         uses: actions/cache@v4
         with:
diff --git a/tools/ci/gha-install-mcpl.sh b/tools/ci/gha-install-mcpl.sh
index df0eb376725..63f9cebf458 100755
--- a/tools/ci/gha-install-mcpl.sh
+++ b/tools/ci/gha-install-mcpl.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 set -ex
 
-MCPL_BRANCH='main'
+MCPL_BRANCH='master'
 MCPL_REPO='https://github.com/mctools/mcpl'
 MCPL_INSTALL_DIR=$HOME/mcpl/
 
@@ -9,5 +9,5 @@ cd $HOME
 git clone -b $MCPL_BRANCH $MCPL_REPO
 cd $MCPL_INSTALL_DIR
 mkdir build && cd build
-cmake .. -DCMAKE_INSTALL_PREFIX=$MCPL_INSTALL_DIR
+cmake -DCMAKE_INSTALL_PREFIX=$MCPL_INSTALL_DIR ..
 make 2>/dev/null && sudo make install
\ No newline at end of file

From b572a0e5d06cfb84e8f930bef3cec77f85fb1792 Mon Sep 17 00:00:00 2001
From: John Vincent Cauilan <64677361+johvincau@users.noreply.github.com>
Date: Wed, 24 Jul 2024 13:35:28 -0500
Subject: [PATCH 07/43] Add MCPL build to path

---
 .github/workflows/ci.yml      | 29 ++++++++++++++++-------------
 tools/ci/gha-caches.sh        |  9 +++++----
 tools/ci/gha-install-dagmc.sh |  4 ++--
 tools/ci/gha-install-mcpl.sh  |  9 +++++----
 tools/ci/gha-install-njoy.sh  |  4 ++--
 tools/ci/gha-install.sh       | 21 ++++++++++++++++++++-
 6 files changed, 50 insertions(+), 26 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 6d727967521..770092ef834 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -134,29 +134,32 @@ jobs:
         if: ${{ matrix.vectfit == 'y' }}
         run: sudo apt install -y libblas-dev liblapack-dev
 
-      - name: Grab hashes of required dependencies (just NJOY, DAGMC, and MCPL for now)
+      - name: Grab hashes of required dependencies (just NJOY, and MCPL for now)
         run: |
           $GITHUB_WORKSPACE/tools/ci/gha-caches.sh
           
       - name: Restore NJOY2016
         uses: actions/cache@v4
         with:
-          path: ~/NJOY2016/
-          key: NJOY2016-${{ env.NJOY_HASH}}
+          path: ~/NJOY2016
+          key: NJOY2016-${{ env.NJOY_HASH }} 
+          restore-keys: NJOY2016-
 
       - name: Restore DAGMC
         if: ${{ matrix.dagmc == 'y' }}
         uses: actions/cache@v4
         with:
           path: |
-            ~/NJOY2016/
-          key: DAGMC-${{ env.DAGMC_HASH}}/MOAB-${{ env.MOAB_HASH }}
+            ~/DAGMC
+            ~/MOAB
+          key: DAGMC-${{ env.DAGMC_HASH }}/MOAB-${{ env.MOAB_HASH }}
       
-      - name: Restore MCPL
+      - name: Restore mcpl
         uses: actions/cache@v4
         with:
-          path: ~/MCPL/
-          key: MCPL-${{ env.MCPL_HASH }}  
+          path: ~/mcpl
+          key: mcpl-${{ env.MCPL_HASH }} 
+          restore-keys: mcpl-
 
       - name: install
         shell: bash
@@ -176,11 +179,11 @@ jobs:
         shell: bash
         run: $GITHUB_WORKSPACE/tools/ci/gha-before-script.sh
 
-      #- name: test
-      #  shell: bash
-      #  run: |
-      #    CTEST_OUTPUT_ON_FAILURE=1 make test -C $GITHUB_WORKSPACE/build/
-      #    $GITHUB_WORKSPACE/tools/ci/gha-script.sh
+      - name: test
+        shell: bash
+        run: |
+          CTEST_OUTPUT_ON_FAILURE=1 make test -C $GITHUB_WORKSPACE/build/
+          $GITHUB_WORKSPACE/tools/ci/gha-script.sh
 
       - name: after_success
         shell: bash
diff --git a/tools/ci/gha-caches.sh b/tools/ci/gha-caches.sh
index 8f6faefda75..2dcbc4dc646 100755
--- a/tools/ci/gha-caches.sh
+++ b/tools/ci/gha-caches.sh
@@ -3,10 +3,11 @@ set -ex
 
 echo "NJOY_HASH=$(git ls-remote https://github.com/njoy/NJOY2016.git | cut -f 1 | head -c 15)" >> $GITHUB_ENV
 
-if [[ $DAGMC = 'y' ]]; then
-    echo "MOAB_HASH=$(git ls-remote https://bitbucket.org/fathomteam/moab.git | cut -f 1 | head -c 15)" >> $GITHUB_ENV
-    echo "DAGMC_HASH=$(git ls-remote https://github.com/svalinn/dagmc.git | cut -f 1 | head -c 15)" >> $GITHUB_ENV
-fi
+
+#if [[ $DAGMC = 'y' ]]; then
+#    echo "MOAB_HASH=$(git ls-remote https://bitbucket.org/fathomteam/moab.git | cut -f 1 | head -c 15)" >> $GITHUB_ENV
+#    echo "DAGMC_HASH=$(git ls-remote https://github.com/svalinn/dagmc.git | cut -f 1 | head -c 15)" >> $GITHUB_ENV
+#fi
 
 # Check for NCrystal cache if needed
 #if [[ $NCRYSTAL = 'y' ]]; then
diff --git a/tools/ci/gha-install-dagmc.sh b/tools/ci/gha-install-dagmc.sh
index 82759c9bcce..fb41503854e 100755
--- a/tools/ci/gha-install-dagmc.sh
+++ b/tools/ci/gha-install-dagmc.sh
@@ -21,7 +21,7 @@ git clone -b $MOAB_BRANCH $MOAB_REPO
 mkdir build && cd build
 cmake ../moab -DENABLE_HDF5=ON -DENABLE_NETCDF=ON -DBUILD_SHARED_LIBS=ON -DCMAKE_INSTALL_PREFIX=$MOAB_INSTALL_DIR -DENABLE_BLASLAPACK=OFF
 make -j && make -j install
-rm -rf $HOME/MOAB/moab $HOME/MOAB/build
+#rm -rf $HOME/MOAB/moab $HOME/MOAB/build
 
 # DAGMC Install
 cd $HOME
@@ -30,6 +30,6 @@ git clone -b $DAGMC_BRANCH $DAGMC_REPO
 mkdir build && cd build
 cmake ../dagmc -DBUILD_TALLY=ON -DCMAKE_INSTALL_PREFIX=$DAGMC_INSTALL_DIR -DBUILD_STATIC_LIBS=OFF -DMOAB_DIR=$MOAB_INSTALL_DIR
 make -j install
-rm -rf $HOME/DAGMC/dagmc $HOME/DAGMC/build
+#rm -rf $HOME/DAGMC/dagmc $HOME/DAGMC/build
 
 cd $CURRENT_DIR
diff --git a/tools/ci/gha-install-mcpl.sh b/tools/ci/gha-install-mcpl.sh
index 63f9cebf458..179221829a0 100755
--- a/tools/ci/gha-install-mcpl.sh
+++ b/tools/ci/gha-install-mcpl.sh
@@ -1,13 +1,14 @@
 #!/bin/bash
 set -ex
 
+# MCPL variables
 MCPL_BRANCH='master'
 MCPL_REPO='https://github.com/mctools/mcpl'
-MCPL_INSTALL_DIR=$HOME/mcpl/
+#MCPL_INSTALL_DIR=$HOME/mcpl/
 
 cd $HOME
-git clone -b $MCPL_BRANCH $MCPL_REPO
-cd $MCPL_INSTALL_DIR
+git clone $MCPL_REPO
+cd mcpl
 mkdir build && cd build
-cmake -DCMAKE_INSTALL_PREFIX=$MCPL_INSTALL_DIR ..
+cmake .. # -DCMAKE_INSTALL_PREFIX=$MCPL_INSTALL_DIR
 make 2>/dev/null && sudo make install
\ No newline at end of file
diff --git a/tools/ci/gha-install-njoy.sh b/tools/ci/gha-install-njoy.sh
index b045b7610dd..5b63afdcf6f 100755
--- a/tools/ci/gha-install-njoy.sh
+++ b/tools/ci/gha-install-njoy.sh
@@ -8,7 +8,7 @@ NJOY_INSTALL_DIR=$HOME/NJOY2016/
 
 cd $HOME
 git clone -b $NJOY_BRANCH $NJOY_REPO
-cd $NJOY_INSTALL_DIR
+cd NJOY2016
 mkdir build && cd build
-cmake -Dstatic=on -DCMAKE_INSTALL_PREFIX=$NJOY_INSTALL_DIR .. 
+cmake -Dstatic=on .. #-DCMAKE_INSTALL_PREFIX=$NJOY_INSTALL_DIR
 make 2>/dev/null && sudo make install
\ No newline at end of file
diff --git a/tools/ci/gha-install.sh b/tools/ci/gha-install.sh
index 1ad2356addd..cd3a51b7a49 100755
--- a/tools/ci/gha-install.sh
+++ b/tools/ci/gha-install.sh
@@ -9,11 +9,16 @@ pip install --upgrade numpy
 # Install NJOY 2016
 if [[ ! -d "$HOME/NJOY2016" ]]; then
     ./tools/ci/gha-install-njoy.sh
+else
+    cd $HOME/NJOY2016/build && cmake -Dstatic=on .. &&
+    make 2>/dev/null && sudo make install
 fi
 
 # Install DAGMC if needed
 if [[ $DAGMC = 'y' ]]; then
+    #if [[ ! -d "$HOME/DAGMC" | ! -d "$HOME/MOAB"]]; then
     ./tools/ci/gha-install-dagmc.sh
+    #else
 fi
 
 # Install NCrystal if needed
@@ -32,10 +37,14 @@ if [[ $LIBMESH = 'y' ]]; then
 fi
 
 # Install MCPL
-if [[ ! -d "$HOME/MCPL" ]]; then
+if [[ ! -d "$HOME/mcpl" ]]; then
     ./tools/ci/gha-install-mcpl.sh
+else
+    cd $HOME/mcpl/build && cmake  .. && 
+    make 2>/dev/null && sudo make install
 fi
 
+
 # For MPI configurations, make sure mpi4py and h5py are built against the
 # correct version of MPI
 if [[ $MPI == 'y' ]]; then
@@ -52,4 +61,14 @@ fi
 python tools/ci/gha-install.py
 
 # Install Python API in editable mode
+<<<<<<< HEAD
 pip install -e .[test,vtk,ci]
+=======
+pip install -e .[test,vtk]
+
+# For coverage testing of the C++ source files
+pip install cpp-coveralls
+
+# For coverage testing of the Python source files
+pip install coveralls
+>>>>>>> 9198dde0e (Fix gha-install issue)

From d2dec2da1326a963be60ffa51a43e69bb4389921 Mon Sep 17 00:00:00 2001
From: John Vincent Cauilan <64677361+johvincau@users.noreply.github.com>
Date: Fri, 26 Jul 2024 13:24:25 -0500
Subject: [PATCH 08/43] Return to github workspace after reinstalling makes

---
 .github/workflows/ci.yml     | 10 +++++-----
 tools/ci/gha-install-mcpl.sh |  5 ++---
 tools/ci/gha-install-njoy.sh |  7 +++----
 tools/ci/gha-install.sh      |  8 ++++----
 4 files changed, 14 insertions(+), 16 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 770092ef834..c0879ab9436 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -179,11 +179,11 @@ jobs:
         shell: bash
         run: $GITHUB_WORKSPACE/tools/ci/gha-before-script.sh
 
-      - name: test
-        shell: bash
-        run: |
-          CTEST_OUTPUT_ON_FAILURE=1 make test -C $GITHUB_WORKSPACE/build/
-          $GITHUB_WORKSPACE/tools/ci/gha-script.sh
+      #- name: test
+      #  shell: bash
+      #  run: |
+      #    CTEST_OUTPUT_ON_FAILURE=1 make test -C $GITHUB_WORKSPACE/build/
+      #    $GITHUB_WORKSPACE/tools/ci/gha-script.sh
 
       - name: after_success
         shell: bash
diff --git a/tools/ci/gha-install-mcpl.sh b/tools/ci/gha-install-mcpl.sh
index 179221829a0..ead3344f5a0 100755
--- a/tools/ci/gha-install-mcpl.sh
+++ b/tools/ci/gha-install-mcpl.sh
@@ -2,13 +2,12 @@
 set -ex
 
 # MCPL variables
-MCPL_BRANCH='master'
 MCPL_REPO='https://github.com/mctools/mcpl'
-#MCPL_INSTALL_DIR=$HOME/mcpl/
+MCPL_INSTALL_DIR=$HOME/mcpl/build
 
 cd $HOME
 git clone $MCPL_REPO
 cd mcpl
 mkdir build && cd build
-cmake .. # -DCMAKE_INSTALL_PREFIX=$MCPL_INSTALL_DIR
+cmake .. #-DCMAKE_INSTALL_PREFIX=$MCPL_INSTALL_DIR &&
 make 2>/dev/null && sudo make install
\ No newline at end of file
diff --git a/tools/ci/gha-install-njoy.sh b/tools/ci/gha-install-njoy.sh
index 5b63afdcf6f..1fde1650f6e 100755
--- a/tools/ci/gha-install-njoy.sh
+++ b/tools/ci/gha-install-njoy.sh
@@ -2,13 +2,12 @@
 set -ex
 
 # NJOY variables
-NJOY_BRANCH='main'
 NJOY_REPO='https://github.com/njoy/NJOY2016'
-NJOY_INSTALL_DIR=$HOME/NJOY2016/
+NJOY_INSTALL_DIR=$HOME/NJOY2016
 
 cd $HOME
-git clone -b $NJOY_BRANCH $NJOY_REPO
+git clone $NJOY_REPO
 cd NJOY2016
 mkdir build && cd build
-cmake -Dstatic=on .. #-DCMAKE_INSTALL_PREFIX=$NJOY_INSTALL_DIR
+cmake -Dstatic=on .. #-DCMAKE_INSTALL_PREFIX=$NJOY_INSTALL_DIR &&
 make 2>/dev/null && sudo make install
\ No newline at end of file
diff --git a/tools/ci/gha-install.sh b/tools/ci/gha-install.sh
index cd3a51b7a49..4ac246cbff5 100755
--- a/tools/ci/gha-install.sh
+++ b/tools/ci/gha-install.sh
@@ -10,8 +10,8 @@ pip install --upgrade numpy
 if [[ ! -d "$HOME/NJOY2016" ]]; then
     ./tools/ci/gha-install-njoy.sh
 else
-    cd $HOME/NJOY2016/build && cmake -Dstatic=on .. &&
-    make 2>/dev/null && sudo make install
+    cd $HOME/NJOY2016/build && sudo make install
+    cd $GITHUB_WORKSPACE
 fi
 
 # Install DAGMC if needed
@@ -40,8 +40,8 @@ fi
 if [[ ! -d "$HOME/mcpl" ]]; then
     ./tools/ci/gha-install-mcpl.sh
 else
-    cd $HOME/mcpl/build && cmake  .. && 
-    make 2>/dev/null && sudo make install
+    cd $HOME/mcpl/build && sudo make install
+    cd $GITHUB_WORKSPACE
 fi
 
 

From dd2f4fbab6e11b7a0afae33279a974219a2d9bee Mon Sep 17 00:00:00 2001
From: John Vincent Cauilan <64677361+johvincau@users.noreply.github.com>
Date: Fri, 26 Jul 2024 13:46:46 -0500
Subject: [PATCH 09/43] Re-add support for DAGMC caching

---
 tools/ci/gha-caches.sh  |  9 ++++-----
 tools/ci/gha-install.sh | 11 ++++++++---
 2 files changed, 12 insertions(+), 8 deletions(-)

diff --git a/tools/ci/gha-caches.sh b/tools/ci/gha-caches.sh
index 2dcbc4dc646..8f6faefda75 100755
--- a/tools/ci/gha-caches.sh
+++ b/tools/ci/gha-caches.sh
@@ -3,11 +3,10 @@ set -ex
 
 echo "NJOY_HASH=$(git ls-remote https://github.com/njoy/NJOY2016.git | cut -f 1 | head -c 15)" >> $GITHUB_ENV
 
-
-#if [[ $DAGMC = 'y' ]]; then
-#    echo "MOAB_HASH=$(git ls-remote https://bitbucket.org/fathomteam/moab.git | cut -f 1 | head -c 15)" >> $GITHUB_ENV
-#    echo "DAGMC_HASH=$(git ls-remote https://github.com/svalinn/dagmc.git | cut -f 1 | head -c 15)" >> $GITHUB_ENV
-#fi
+if [[ $DAGMC = 'y' ]]; then
+    echo "MOAB_HASH=$(git ls-remote https://bitbucket.org/fathomteam/moab.git | cut -f 1 | head -c 15)" >> $GITHUB_ENV
+    echo "DAGMC_HASH=$(git ls-remote https://github.com/svalinn/dagmc.git | cut -f 1 | head -c 15)" >> $GITHUB_ENV
+fi
 
 # Check for NCrystal cache if needed
 #if [[ $NCRYSTAL = 'y' ]]; then
diff --git a/tools/ci/gha-install.sh b/tools/ci/gha-install.sh
index 4ac246cbff5..aa8b9a26374 100755
--- a/tools/ci/gha-install.sh
+++ b/tools/ci/gha-install.sh
@@ -16,9 +16,14 @@ fi
 
 # Install DAGMC if needed
 if [[ $DAGMC = 'y' ]]; then
-    #if [[ ! -d "$HOME/DAGMC" | ! -d "$HOME/MOAB"]]; then
-    ./tools/ci/gha-install-dagmc.sh
-    #else
+    if [ ! -d "$HOME/DAGMC" ] || [ ! -d "$HOME/MOAB" ]
+    then
+        ./tools/ci/gha-install-dagmc.sh
+    else
+        cd $HOME/DAGMC/build && make -j install
+        cd $HOME/MOAB/build && make -j install
+        cd $GITHUB_WORKSPACE
+    fi
 fi
 
 # Install NCrystal if needed

From 9a170cdcd62c846c1cdb410457980da94309194a Mon Sep 17 00:00:00 2001
From: John Vincent Cauilan <64677361+johvincau@users.noreply.github.com>
Date: Fri, 26 Jul 2024 15:13:14 -0500
Subject: [PATCH 10/43] Reenable testing and fix DAGMC hashing

---
 .github/workflows/ci.yml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index c0879ab9436..770092ef834 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -179,11 +179,11 @@ jobs:
         shell: bash
         run: $GITHUB_WORKSPACE/tools/ci/gha-before-script.sh
 
-      #- name: test
-      #  shell: bash
-      #  run: |
-      #    CTEST_OUTPUT_ON_FAILURE=1 make test -C $GITHUB_WORKSPACE/build/
-      #    $GITHUB_WORKSPACE/tools/ci/gha-script.sh
+      - name: test
+        shell: bash
+        run: |
+          CTEST_OUTPUT_ON_FAILURE=1 make test -C $GITHUB_WORKSPACE/build/
+          $GITHUB_WORKSPACE/tools/ci/gha-script.sh
 
       - name: after_success
         shell: bash

From 67a4740c0da812635a3b102335a9d441b5e7ec52 Mon Sep 17 00:00:00 2001
From: John Vincent Cauilan <64677361+johvincau@users.noreply.github.com>
Date: Mon, 29 Jul 2024 10:57:27 -0500
Subject: [PATCH 11/43] Add cache support for ncrystal and temporarily take out
 testing

---
 .github/workflows/ci.yml | 24 +++++++++++++++++-------
 tools/ci/gha-caches.sh   | 20 +++++++++++++-------
 tools/ci/gha-install.sh  |  9 ++++++++-
 3 files changed, 38 insertions(+), 15 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 770092ef834..f184b91d280 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -134,7 +134,7 @@ jobs:
         if: ${{ matrix.vectfit == 'y' }}
         run: sudo apt install -y libblas-dev liblapack-dev
 
-      - name: Grab hashes of required dependencies (just NJOY, and MCPL for now)
+      - name: Hash remote required dependencies
         run: |
           $GITHUB_WORKSPACE/tools/ci/gha-caches.sh
           
@@ -153,7 +153,17 @@ jobs:
             ~/DAGMC
             ~/MOAB
           key: DAGMC-${{ env.DAGMC_HASH }}/MOAB-${{ env.MOAB_HASH }}
-      
+
+      - name: Restore NCrystal
+        if: ${{ matrix.ncrystal == 'y' }}
+        uses: actions/cache@v4
+        with:
+          path: 
+            ~/ncrystal_bld
+            ~/ncrystal_inst
+          key: NCrystal-${{ env.NC_HASH }} 
+          restore-keys: NCrystal-
+
       - name: Restore mcpl
         uses: actions/cache@v4
         with:
@@ -179,11 +189,11 @@ jobs:
         shell: bash
         run: $GITHUB_WORKSPACE/tools/ci/gha-before-script.sh
 
-      - name: test
-        shell: bash
-        run: |
-          CTEST_OUTPUT_ON_FAILURE=1 make test -C $GITHUB_WORKSPACE/build/
-          $GITHUB_WORKSPACE/tools/ci/gha-script.sh
+      #- name: test
+      #  shell: bash
+      #  run: |
+      #    CTEST_OUTPUT_ON_FAILURE=1 make test -C $GITHUB_WORKSPACE/build/
+      #    $GITHUB_WORKSPACE/tools/ci/gha-script.sh
 
       - name: after_success
         shell: bash
diff --git a/tools/ci/gha-caches.sh b/tools/ci/gha-caches.sh
index 8f6faefda75..377e6800e53 100755
--- a/tools/ci/gha-caches.sh
+++ b/tools/ci/gha-caches.sh
@@ -1,17 +1,22 @@
 #!/bin/bash
 set -ex
 
-echo "NJOY_HASH=$(git ls-remote https://github.com/njoy/NJOY2016.git | cut -f 1 | head -c 15)" >> $GITHUB_ENV
+echo "NJOY_HASH=$(git ls-remote https://github.com/njoy/NJOY2016.git | cut -f 1 |\
+    head -c 15)" >> $GITHUB_ENV
 
 if [[ $DAGMC = 'y' ]]; then
-    echo "MOAB_HASH=$(git ls-remote https://bitbucket.org/fathomteam/moab.git | cut -f 1 | head -c 15)" >> $GITHUB_ENV
-    echo "DAGMC_HASH=$(git ls-remote https://github.com/svalinn/dagmc.git | cut -f 1 | head -c 15)" >> $GITHUB_ENV
+    echo "MOAB_HASH=$(git ls-remote https://bitbucket.org/fathomteam/moab.git |\
+    cut -f 1 | head -c 15)" >> $GITHUB_ENV
+
+    echo "DAGMC_HASH=$(git ls-remote https://github.com/svalinn/dagmc.git |\
+     cut -f 1 | head -c 15)" >> $GITHUB_ENV
 fi
 
 # Check for NCrystal cache if needed
-#if [[ $NCRYSTAL = 'y' ]]; then
-#    ./tools/ci/gha-install-ncrystal.sh
-#fi
+if [[ $NCRYSTAL = 'y' ]]; then
+    echo "NC_HASH=$(git ls-remote https://github.com/mctools/ncrystal \
+    --branch develop | cut -f 1 | head -c 15)" >> $GITHUB_ENV
+fi
 
 # Install vectfit for WMP generation if needed
 #if [[ $VECTFIT = 'y' ]]; then
@@ -23,6 +28,7 @@ fi
 #    ./tools/ci/gha-install-libmesh.sh
 #fi
 
-echo "MCPL_HASH=$(git ls-remote https://github.com/mctools/mcpl.git | cut -f 1 | head -c 15)" >> $GITHUB_ENV
+echo "MCPL_HASH=$(git ls-remote https://github.com/mctools/mcpl.git | cut -f 1 |\
+    head -c 15)" >> $GITHUB_ENV
 
 # may be able to use this to control the directories to be cached.
\ No newline at end of file
diff --git a/tools/ci/gha-install.sh b/tools/ci/gha-install.sh
index aa8b9a26374..08fe12eb0ff 100755
--- a/tools/ci/gha-install.sh
+++ b/tools/ci/gha-install.sh
@@ -28,7 +28,14 @@ fi
 
 # Install NCrystal if needed
 if [[ $NCRYSTAL = 'y' ]]; then
-    ./tools/ci/gha-install-ncrystal.sh
+    if [ ! -d "$HOME/ncrystal_bld" ]
+    then
+        ./tools/ci/gha-install-ncrystal.sh
+    else
+        cd $HOME/ncrystal_bld && make -j install
+        eval $( "$HOME/ncrystal_inst/bin/ncrystal-config" --setup )
+        cd $GITHUB_WORKSPACE
+    fi
 fi
 
 # Install vectfit for WMP generation if needed

From afd514473be63fdf1e58b3339b0a963d26669ddf Mon Sep 17 00:00:00 2001
From: John Vincent Cauilan <64677361+johvincau@users.noreply.github.com>
Date: Mon, 29 Jul 2024 11:55:07 -0500
Subject: [PATCH 12/43] Re-add testing and minor tweaks for ncrystal

---
 .github/workflows/ci.yml         | 14 +++++++-------
 tools/ci/gha-install-ncrystal.sh |  1 -
 tools/ci/gha-install.sh          |  4 ++--
 3 files changed, 9 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index f184b91d280..cb8f25a9bd2 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -134,7 +134,7 @@ jobs:
         if: ${{ matrix.vectfit == 'y' }}
         run: sudo apt install -y libblas-dev liblapack-dev
 
-      - name: Hash remote required dependencies
+      - name: Hash dependencies to check caches
         run: |
           $GITHUB_WORKSPACE/tools/ci/gha-caches.sh
           
@@ -158,7 +158,7 @@ jobs:
         if: ${{ matrix.ncrystal == 'y' }}
         uses: actions/cache@v4
         with:
-          path: 
+          path: |
             ~/ncrystal_bld
             ~/ncrystal_inst
           key: NCrystal-${{ env.NC_HASH }} 
@@ -189,11 +189,11 @@ jobs:
         shell: bash
         run: $GITHUB_WORKSPACE/tools/ci/gha-before-script.sh
 
-      #- name: test
-      #  shell: bash
-      #  run: |
-      #    CTEST_OUTPUT_ON_FAILURE=1 make test -C $GITHUB_WORKSPACE/build/
-      #    $GITHUB_WORKSPACE/tools/ci/gha-script.sh
+      - name: test
+        shell: bash
+        run: |
+          CTEST_OUTPUT_ON_FAILURE=1 make test -C $GITHUB_WORKSPACE/build/
+          $GITHUB_WORKSPACE/tools/ci/gha-script.sh
 
       - name: after_success
         shell: bash
diff --git a/tools/ci/gha-install-ncrystal.sh b/tools/ci/gha-install-ncrystal.sh
index 16f77e13e2b..f352e700612 100755
--- a/tools/ci/gha-install-ncrystal.sh
+++ b/tools/ci/gha-install-ncrystal.sh
@@ -34,7 +34,6 @@ make install
 #      yet. If it appears in the future, we should add it here.
 
 # Output the configuration to the log
-
 "${INST_DIR}/bin/ncrystal-config" --setup
 
 # Change environmental variables
diff --git a/tools/ci/gha-install.sh b/tools/ci/gha-install.sh
index 08fe12eb0ff..fac1aaa5ebf 100755
--- a/tools/ci/gha-install.sh
+++ b/tools/ci/gha-install.sh
@@ -32,14 +32,14 @@ if [[ $NCRYSTAL = 'y' ]]; then
     then
         ./tools/ci/gha-install-ncrystal.sh
     else
-        cd $HOME/ncrystal_bld && make -j install
+        cd $HOME/ncrystal_bld && make install
         eval $( "$HOME/ncrystal_inst/bin/ncrystal-config" --setup )
         cd $GITHUB_WORKSPACE
     fi
 fi
 
 # Install vectfit for WMP generation if needed
-if [[ $VECTFIT = 'y' ]]; then
+if [[ $VECTFIT = 'y' ]]; then 
     ./tools/ci/gha-install-vectfit.sh
 fi
 

From 8349c8af7440a6f7f787e629d69eb904effed31e Mon Sep 17 00:00:00 2001
From: John Vincent Cauilan <64677361+johvincau@users.noreply.github.com>
Date: Tue, 30 Jul 2024 12:00:40 -0500
Subject: [PATCH 13/43] Add cache support for libmesh

---
 .github/workflows/ci.yml        | 29 ++++++++++++++++++++---------
 tools/ci/gha-caches.sh          | 17 ++++++++---------
 tools/ci/gha-install-libmesh.sh |  5 +++--
 tools/ci/gha-install-mcpl.sh    |  2 +-
 tools/ci/gha-install-njoy.sh    |  2 +-
 tools/ci/gha-install.sh         | 12 ++++++++++--
 6 files changed, 43 insertions(+), 24 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index cb8f25a9bd2..907d4690dee 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -65,10 +65,7 @@ jobs:
             python-version: "3.10"
             omp: n
             mpi: y
-    name: "Python ${{ matrix.python-version }} (omp=${{ matrix.omp }}, 
-      mpi=${{ matrix.mpi }}, dagmc=${{ matrix.dagmc }}, 
-      ncrystal=${{ matrix.ncrystal }},libmesh=${{ matrix.libmesh }}, 
-      event=${{ matrix.event }}, vectfit=${{ matrix.vectfit }})"
+    
 
     env:
       MPI: ${{ matrix.mpi }}
@@ -86,6 +83,15 @@ jobs:
       # FI_EFA_FORK_SAFE=1 in more recent versions.
       RDMAV_FORK_SAFE: 1
 
+    name: "Py ${{ matrix.python-version }} 
+      (omp=${{ matrix.omp }}, 
+      mpi=${{ matrix.mpi }}, 
+      dagmc=${{ matrix.dagmc }}, 
+      ncrystal=${{ matrix.ncrystal }},
+      libmesh=${{ matrix.libmesh }}, 
+      event=${{ matrix.event }}, 
+      vectfit=${{ matrix.vectfit }})"
+
     steps:
       - uses: actions/checkout@v4
 
@@ -98,7 +104,7 @@ jobs:
         uses: actions/cache@v4
         with:
           path: ${{ env.pythonLocation }}
-          key:  python-cache-(python=${{ matrix.python-version }} (omp=${{ matrix.omp }}
+          key:  py-(python=${{ matrix.python-version }} (omp=${{ matrix.omp }}
             mpi=${{ matrix.mpi }} dagmc=${{ matrix.dagmc }} ncrystal=${{ matrix.ncrystal }}
             libmesh=${{ matrix.libmesh }} event=${{ matrix.event }}
             vectfit=${{ matrix.vectfit }})
@@ -143,7 +149,6 @@ jobs:
         with:
           path: ~/NJOY2016
           key: NJOY2016-${{ env.NJOY_HASH }} 
-          restore-keys: NJOY2016-
 
       - name: Restore DAGMC
         if: ${{ matrix.dagmc == 'y' }}
@@ -159,22 +164,28 @@ jobs:
         uses: actions/cache@v4
         with:
           path: |
+            ~/ncrystal_src
             ~/ncrystal_bld
             ~/ncrystal_inst
           key: NCrystal-${{ env.NC_HASH }} 
-          restore-keys: NCrystal-
 
+      - name: Restore libmesh
+        if: ${{ matrix.libmesh == 'y' }} 
+        uses: actions/cache@v4
+        with:
+          path: |
+            ~/LIBMESH
+          key: libmesh-mpi-${{matrix.mpi}}-${{ env.NC_HASH }} 
+  
       - name: Restore mcpl
         uses: actions/cache@v4
         with:
           path: ~/mcpl
           key: mcpl-${{ env.MCPL_HASH }} 
-          restore-keys: mcpl-
 
       - name: install
         shell: bash
         run: |
-          echo "$HOME/NJOY2016/build" >> $GITHUB_PATH
           $GITHUB_WORKSPACE/tools/ci/gha-install.sh
 
       - name: Restore endf-b-vii.1 cache
diff --git a/tools/ci/gha-caches.sh b/tools/ci/gha-caches.sh
index 377e6800e53..e0b374e0a3f 100755
--- a/tools/ci/gha-caches.sh
+++ b/tools/ci/gha-caches.sh
@@ -5,8 +5,8 @@ echo "NJOY_HASH=$(git ls-remote https://github.com/njoy/NJOY2016.git | cut -f 1
     head -c 15)" >> $GITHUB_ENV
 
 if [[ $DAGMC = 'y' ]]; then
-    echo "MOAB_HASH=$(git ls-remote https://bitbucket.org/fathomteam/moab.git |\
-    cut -f 1 | head -c 15)" >> $GITHUB_ENV
+    echo "MOAB_HASH=$(git ls-remote https://bitbucket.org/fathomteam/moab.git \
+    --branch Version5.1.0 | cut -f 1 | head -c 15)" >> $GITHUB_ENV
 
     echo "DAGMC_HASH=$(git ls-remote https://github.com/svalinn/dagmc.git |\
      cut -f 1 | head -c 15)" >> $GITHUB_ENV
@@ -24,11 +24,10 @@ fi
 #fi
 
 # Check for libmesh cache if needed
-#if [[ $LIBMESH = 'y' ]]; then
-#    ./tools/ci/gha-install-libmesh.sh
-#fi
-
-echo "MCPL_HASH=$(git ls-remote https://github.com/mctools/mcpl.git | cut -f 1 |\
-    head -c 15)" >> $GITHUB_ENV
+if [[ $LIBMESH = 'y' ]]; then
+    echo "NC_HASH=$(git ls-remote https://github.com/libmesh/libmesh \
+    --branch v1.7.1 | cut -f 1 | head -c 15)" >> $GITHUB_ENV
+fi
 
-# may be able to use this to control the directories to be cached.
\ No newline at end of file
+echo "MCPL_HASH=$(git ls-remote https://github.com/mctools/mcpl.git |\
+    cut -f 1 | head -c 15)" >> $GITHUB_ENV
diff --git a/tools/ci/gha-install-libmesh.sh b/tools/ci/gha-install-libmesh.sh
index cb808ae5b3b..6771e69d5a6 100755
--- a/tools/ci/gha-install-libmesh.sh
+++ b/tools/ci/gha-install-libmesh.sh
@@ -13,10 +13,11 @@ if [[ $MPI == 'y' ]]; then
     ../libmesh/configure --prefix=$HOME/LIBMESH CXX=mpicxx CC=mpicc FC=mpifort F77=mpif77 \
         --enable-exodus --disable-netcdf-4 --disable-eigen --disable-lapack
 else
-    ../libmesh/configure --prefix=$HOME/LIBMESH --enable-exodus --disable-netcdf-4 --disable-eigen --disable-lapack --disable-mpi
+    ../libmesh/configure --prefix=$HOME/LIBMESH --enable-exodus --disable-netcdf-4 \
+    --disable-eigen --disable-lapack --disable-mpi
 fi
 make -j4 install
 export LIBMESH_PC=$HOME/LIBMESH/lib/pkgconfig/
-rm -rf $HOME/LIBMESH/build
+#rm -rf $HOME/LIBMESH/build
 
 popd
diff --git a/tools/ci/gha-install-mcpl.sh b/tools/ci/gha-install-mcpl.sh
index ead3344f5a0..7cbb58acd69 100755
--- a/tools/ci/gha-install-mcpl.sh
+++ b/tools/ci/gha-install-mcpl.sh
@@ -9,5 +9,5 @@ cd $HOME
 git clone $MCPL_REPO
 cd mcpl
 mkdir build && cd build
-cmake .. #-DCMAKE_INSTALL_PREFIX=$MCPL_INSTALL_DIR &&
+cmake .. -DCMAKE_INSTALL_PREFIX=$MCPL_INSTALL_DIR &&
 make 2>/dev/null && sudo make install
\ No newline at end of file
diff --git a/tools/ci/gha-install-njoy.sh b/tools/ci/gha-install-njoy.sh
index 1fde1650f6e..01a19da249d 100755
--- a/tools/ci/gha-install-njoy.sh
+++ b/tools/ci/gha-install-njoy.sh
@@ -9,5 +9,5 @@ cd $HOME
 git clone $NJOY_REPO
 cd NJOY2016
 mkdir build && cd build
-cmake -Dstatic=on .. #-DCMAKE_INSTALL_PREFIX=$NJOY_INSTALL_DIR &&
+cmake -Dstatic=on .. -DCMAKE_INSTALL_PREFIX=$NJOY_INSTALL_DIR &&
 make 2>/dev/null && sudo make install
\ No newline at end of file
diff --git a/tools/ci/gha-install.sh b/tools/ci/gha-install.sh
index fac1aaa5ebf..57320bf5a9a 100755
--- a/tools/ci/gha-install.sh
+++ b/tools/ci/gha-install.sh
@@ -13,6 +13,7 @@ else
     cd $HOME/NJOY2016/build && sudo make install
     cd $GITHUB_WORKSPACE
 fi
+echo "$HOME/NJOY2016/build" >> $GITHUB_PATH
 
 # Install DAGMC if needed
 if [[ $DAGMC = 'y' ]]; then
@@ -32,7 +33,7 @@ if [[ $NCRYSTAL = 'y' ]]; then
     then
         ./tools/ci/gha-install-ncrystal.sh
     else
-        cd $HOME/ncrystal_bld && make install
+        cd $HOME/ncrystal_bld
         eval $( "$HOME/ncrystal_inst/bin/ncrystal-config" --setup )
         cd $GITHUB_WORKSPACE
     fi
@@ -45,7 +46,14 @@ fi
 
 # Install libMesh if needed
 if [[ $LIBMESH = 'y' ]]; then
-    ./tools/ci/gha-install-libmesh.sh
+    if [ ! -d "$HOME/LIBMESH" ]
+    then
+        ./tools/ci/gha-install-libmesh.sh
+    else
+        cd $HOME/LIBMESH/build && make -j4 install
+        export LIBMESH_PC=$HOME/LIBMESH/lib/pkgconfig/
+        cd $GITHUB_WORKSPACE
+    fi
 fi
 
 # Install MCPL

From 41e8f3dba6813232a9d5da27e4b7c764c4c02141 Mon Sep 17 00:00:00 2001
From: John Vincent Cauilan <64677361+johvincau@users.noreply.github.com>
Date: Tue, 30 Jul 2024 13:36:27 -0500
Subject: [PATCH 14/43] Test removal of make install

---
 .github/workflows/ci.yml |  6 +++---
 tools/ci/gha-install.sh  | 10 +++++-----
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 907d4690dee..74c71b0e26e 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -104,9 +104,9 @@ jobs:
         uses: actions/cache@v4
         with:
           path: ${{ env.pythonLocation }}
-          key:  py-(python=${{ matrix.python-version }} (omp=${{ matrix.omp }}
-            mpi=${{ matrix.mpi }} dagmc=${{ matrix.dagmc }} ncrystal=${{ matrix.ncrystal }}
-            libmesh=${{ matrix.libmesh }} event=${{ matrix.event }}
+          key:  py-${{ matrix.python-version }}-(omp=${{ matrix.omp }}-
+            mpi=${{ matrix.mpi }}-dagmc=${{ matrix.dagmc }}-ncrystal=${{ matrix.ncrystal }}-
+            libmesh=${{ matrix.libmesh }}-event=${{ matrix.event }}-
             vectfit=${{ matrix.vectfit }})
 
       - name: Environment Variables
diff --git a/tools/ci/gha-install.sh b/tools/ci/gha-install.sh
index 57320bf5a9a..cb7d7e00113 100755
--- a/tools/ci/gha-install.sh
+++ b/tools/ci/gha-install.sh
@@ -10,7 +10,7 @@ pip install --upgrade numpy
 if [[ ! -d "$HOME/NJOY2016" ]]; then
     ./tools/ci/gha-install-njoy.sh
 else
-    cd $HOME/NJOY2016/build && sudo make install
+    #cd $HOME/NJOY2016/build && sudo make install
     cd $GITHUB_WORKSPACE
 fi
 echo "$HOME/NJOY2016/build" >> $GITHUB_PATH
@@ -21,8 +21,8 @@ if [[ $DAGMC = 'y' ]]; then
     then
         ./tools/ci/gha-install-dagmc.sh
     else
-        cd $HOME/DAGMC/build && make -j install
-        cd $HOME/MOAB/build && make -j install
+        #cd $HOME/DAGMC/build && make -j install
+        #cd $HOME/MOAB/build && make -j install
         cd $GITHUB_WORKSPACE
     fi
 fi
@@ -50,7 +50,7 @@ if [[ $LIBMESH = 'y' ]]; then
     then
         ./tools/ci/gha-install-libmesh.sh
     else
-        cd $HOME/LIBMESH/build && make -j4 install
+        #cd $HOME/LIBMESH/build && make -j4 install
         export LIBMESH_PC=$HOME/LIBMESH/lib/pkgconfig/
         cd $GITHUB_WORKSPACE
     fi
@@ -60,7 +60,7 @@ fi
 if [[ ! -d "$HOME/mcpl" ]]; then
     ./tools/ci/gha-install-mcpl.sh
 else
-    cd $HOME/mcpl/build && sudo make install
+    #cd $HOME/mcpl/build && sudo make install
     cd $GITHUB_WORKSPACE
 fi
 

From b38e1fa4f811afbc54f143ed4dd56856c4eec0c8 Mon Sep 17 00:00:00 2001
From: John Vincent Cauilan <64677361+johvincau@users.noreply.github.com>
Date: Tue, 30 Jul 2024 13:44:50 -0500
Subject: [PATCH 15/43] Fix mcpl install dir and remove testing again

---
 .github/workflows/ci.yml     | 16 ++++++++--------
 tools/ci/gha-install-mcpl.sh |  2 +-
 2 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 74c71b0e26e..41e703c872d 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -104,9 +104,9 @@ jobs:
         uses: actions/cache@v4
         with:
           path: ${{ env.pythonLocation }}
-          key:  py-${{ matrix.python-version }}-(omp=${{ matrix.omp }}-
-            mpi=${{ matrix.mpi }}-dagmc=${{ matrix.dagmc }}-ncrystal=${{ matrix.ncrystal }}-
-            libmesh=${{ matrix.libmesh }}-event=${{ matrix.event }}-
+          key:  py-${{ matrix.python-version }}-(omp=${{ matrix.omp }} 
+            mpi=${{ matrix.mpi }} dagmc=${{ matrix.dagmc }} ncrystal=${{ matrix.ncrystal }} 
+            libmesh=${{ matrix.libmesh }} event=${{ matrix.event }} 
             vectfit=${{ matrix.vectfit }})
 
       - name: Environment Variables
@@ -200,11 +200,11 @@ jobs:
         shell: bash
         run: $GITHUB_WORKSPACE/tools/ci/gha-before-script.sh
 
-      - name: test
-        shell: bash
-        run: |
-          CTEST_OUTPUT_ON_FAILURE=1 make test -C $GITHUB_WORKSPACE/build/
-          $GITHUB_WORKSPACE/tools/ci/gha-script.sh
+      #- name: test
+      #  shell: bash
+      #  run: |
+      #    CTEST_OUTPUT_ON_FAILURE=1 make test -C $GITHUB_WORKSPACE/build/
+      #    $GITHUB_WORKSPACE/tools/ci/gha-script.sh
 
       - name: after_success
         shell: bash
diff --git a/tools/ci/gha-install-mcpl.sh b/tools/ci/gha-install-mcpl.sh
index 7cbb58acd69..7de970810c7 100755
--- a/tools/ci/gha-install-mcpl.sh
+++ b/tools/ci/gha-install-mcpl.sh
@@ -3,7 +3,7 @@ set -ex
 
 # MCPL variables
 MCPL_REPO='https://github.com/mctools/mcpl'
-MCPL_INSTALL_DIR=$HOME/mcpl/build
+MCPL_INSTALL_DIR=$HOME/mcpl/
 
 cd $HOME
 git clone $MCPL_REPO

From 8dc462c29ada46ad9de4eb94e49c140014a07e0f Mon Sep 17 00:00:00 2001
From: John Vincent Cauilan <64677361+johvincau@users.noreply.github.com>
Date: Tue, 30 Jul 2024 13:53:26 -0500
Subject: [PATCH 16/43] Add mcpl prefix path to gha-install.py

---
 .github/workflows/ci.yml     | 10 +++++-----
 tools/ci/gha-install-mcpl.sh |  2 +-
 tools/ci/gha-install.py      |  2 ++
 3 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 41e703c872d..5bfdf2d9ed3 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -200,11 +200,11 @@ jobs:
         shell: bash
         run: $GITHUB_WORKSPACE/tools/ci/gha-before-script.sh
 
-      #- name: test
-      #  shell: bash
-      #  run: |
-      #    CTEST_OUTPUT_ON_FAILURE=1 make test -C $GITHUB_WORKSPACE/build/
-      #    $GITHUB_WORKSPACE/tools/ci/gha-script.sh
+      - name: test
+        shell: bash
+        run: |
+          CTEST_OUTPUT_ON_FAILURE=1 make test -C $GITHUB_WORKSPACE/build/
+          $GITHUB_WORKSPACE/tools/ci/gha-script.sh
 
       - name: after_success
         shell: bash
diff --git a/tools/ci/gha-install-mcpl.sh b/tools/ci/gha-install-mcpl.sh
index 7de970810c7..4af01d61c47 100755
--- a/tools/ci/gha-install-mcpl.sh
+++ b/tools/ci/gha-install-mcpl.sh
@@ -3,7 +3,7 @@ set -ex
 
 # MCPL variables
 MCPL_REPO='https://github.com/mctools/mcpl'
-MCPL_INSTALL_DIR=$HOME/mcpl/
+MCPL_INSTALL_DIR=$HOME/mcpl
 
 cd $HOME
 git clone $MCPL_REPO
diff --git a/tools/ci/gha-install.py b/tools/ci/gha-install.py
index f046e863470..7d49f46616b 100644
--- a/tools/ci/gha-install.py
+++ b/tools/ci/gha-install.py
@@ -11,6 +11,8 @@ def install(omp=False, mpi=False, phdf5=False, dagmc=False, libmesh=False, ncrys
 
     # Build in debug mode by default with support for MCPL
     cmake_cmd = ['cmake', '-DCMAKE_BUILD_TYPE=Debug', '-DOPENMC_USE_MCPL=on']
+    mcpl_cmake_path = os.environ.get('HOME') + '/mcpl/lib/cmake/MCPL'
+    cmake_cmd.append(f'-DMCPL_DIR={mcpl_cmake_path}')
 
     # Turn off OpenMP if specified
     if not omp:

From 8877edbec0e857fb78b54b9927394c1b0ea20c1b Mon Sep 17 00:00:00 2001
From: John Vincent Cauilan <64677361+johvincau@users.noreply.github.com>
Date: Wed, 31 Jul 2024 12:09:56 -0500
Subject: [PATCH 17/43] Cache vectfit and temporarily remove testing

---
 .github/workflows/ci.yml | 21 +++++++++++++++++++++
 tools/ci/gha-caches.sh   | 15 ++++++++-------
 tools/ci/gha-install.sh  | 13 +++++--------
 3 files changed, 34 insertions(+), 15 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 5bfdf2d9ed3..52f1ba16c3f 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -169,6 +169,18 @@ jobs:
             ~/ncrystal_inst
           key: NCrystal-${{ env.NC_HASH }} 
 
+      - name: Restore vectfit
+        if: ${{ matrix.vectfit == 'y' }} 
+        uses: actions/cache@v4
+        with:
+          path: |
+            ~/pybind11
+            ~/xtl
+            ~/xtensor-python
+            ~/xtensor-blas
+            ~/vectfit
+          key: vectfit-${{ env.VF_HASH }}/pybind-${{ env.PYBIND_HASH }}
+
       - name: Restore libmesh
         if: ${{ matrix.libmesh == 'y' }} 
         uses: actions/cache@v4
@@ -176,12 +188,21 @@ jobs:
           path: |
             ~/LIBMESH
           key: libmesh-mpi-${{matrix.mpi}}-${{ env.NC_HASH }} 
+<<<<<<< HEAD
   
       - name: Restore mcpl
         uses: actions/cache@v4
         with:
           path: ~/mcpl
           key: mcpl-${{ env.MCPL_HASH }} 
+=======
+
+      #- name: Restore mcpl
+      #  uses: actions/cache@v4
+      #  with:
+      #    path: ~/mcpl
+      #    key: mcpl-${{ env.MCPL_HASH }} 
+>>>>>>> 322d1d221 (Cache vectfit and temporarily remove testing)
 
       - name: install
         shell: bash
diff --git a/tools/ci/gha-caches.sh b/tools/ci/gha-caches.sh
index e0b374e0a3f..4ea8624c765 100755
--- a/tools/ci/gha-caches.sh
+++ b/tools/ci/gha-caches.sh
@@ -9,21 +9,22 @@ if [[ $DAGMC = 'y' ]]; then
     --branch Version5.1.0 | cut -f 1 | head -c 15)" >> $GITHUB_ENV
 
     echo "DAGMC_HASH=$(git ls-remote https://github.com/svalinn/dagmc.git |\
-     cut -f 1 | head -c 15)" >> $GITHUB_ENV
+    cut -f 1 | head -c 15)" >> $GITHUB_ENV
 fi
 
-# Check for NCrystal cache if needed
 if [[ $NCRYSTAL = 'y' ]]; then
     echo "NC_HASH=$(git ls-remote https://github.com/mctools/ncrystal \
     --branch develop | cut -f 1 | head -c 15)" >> $GITHUB_ENV
 fi
 
-# Install vectfit for WMP generation if needed
-#if [[ $VECTFIT = 'y' ]]; then
-#    ./tools/ci/gha-install-vectfit.sh
-#fi
+if [[ $VECTFIT = 'y' ]]; then
+    echo "PYBIND_HASH=$(git ls-remote https://github.com/pybind/pybind11 \
+    --branch master | cut -f 1 | head -c 15)" >> $GITHUB_ENV
+
+    echo "VF_HASH=$(git ls-remote https://github.com/liangjg/vectfit.git |\
+    cut -f 1 | head -c 15)" >> $GITHUB_ENV
+fi
 
-# Check for libmesh cache if needed
 if [[ $LIBMESH = 'y' ]]; then
     echo "NC_HASH=$(git ls-remote https://github.com/libmesh/libmesh \
     --branch v1.7.1 | cut -f 1 | head -c 15)" >> $GITHUB_ENV
diff --git a/tools/ci/gha-install.sh b/tools/ci/gha-install.sh
index cb7d7e00113..4ffd90e268a 100755
--- a/tools/ci/gha-install.sh
+++ b/tools/ci/gha-install.sh
@@ -46,22 +46,19 @@ fi
 
 # Install libMesh if needed
 if [[ $LIBMESH = 'y' ]]; then
-    if [ ! -d "$HOME/LIBMESH" ]
+    if [ ! -d "$HOME/vectfit" ]
     then
-        ./tools/ci/gha-install-libmesh.sh
+        ./tools/ci/gha-install-vectfit.sh
     else
-        #cd $HOME/LIBMESH/build && make -j4 install
-        export LIBMESH_PC=$HOME/LIBMESH/lib/pkgconfig/
-        cd $GITHUB_WORKSPACE
+        pip install $HOME/pybind11
+        pip install wheel
+        pip install --no-build-isolation ./vectfit
     fi
 fi
 
 # Install MCPL
 if [[ ! -d "$HOME/mcpl" ]]; then
     ./tools/ci/gha-install-mcpl.sh
-else
-    #cd $HOME/mcpl/build && sudo make install
-    cd $GITHUB_WORKSPACE
 fi
 
 

From 83d41deb108b735013fd83881b457dd261b79760 Mon Sep 17 00:00:00 2001
From: John Vincent Cauilan <64677361+johvincau@users.noreply.github.com>
Date: Wed, 31 Jul 2024 16:23:31 -0500
Subject: [PATCH 18/43] Handle case for successful vectfit restore

---
 tools/ci/gha-install.sh | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/tools/ci/gha-install.sh b/tools/ci/gha-install.sh
index 4ffd90e268a..4cf8e2e8d05 100755
--- a/tools/ci/gha-install.sh
+++ b/tools/ci/gha-install.sh
@@ -41,7 +41,10 @@ fi
 
 # Install vectfit for WMP generation if needed
 if [[ $VECTFIT = 'y' ]]; then 
-    ./tools/ci/gha-install-vectfit.sh
+    if [ ! -d "$HOME/vectfit" ]
+    then
+        ./tools/ci/gha-install-vectfit.sh
+    fi
 fi
 
 # Install libMesh if needed

From 57b6388c6d0507e2aa90fda73a82915d12eb0f1c Mon Sep 17 00:00:00 2001
From: John Vincent Cauilan <64677361+johvincau@users.noreply.github.com>
Date: Thu, 1 Aug 2024 15:11:14 -0500
Subject: [PATCH 19/43] Try renaming scheme for job matrix

---
 .github/workflows/ci.yml | 202 +++++++++++++++++++++++++++++----------
 1 file changed, 151 insertions(+), 51 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 52f1ba16c3f..2cdc0cca4a7 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -21,51 +21,157 @@ env:
   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
 jobs:
+  job-setup:
+    runs-on: ubuntu-latest
+    outputs:
+      matrix: ${{ steps.set-matrix.outputs.matrix }}
+    steps:
+      - uses: actions/checkout@v4
+      - name: set job matrix for main
+        id: jobs
+        shell: bash
+        run: |
+          echo "matrix={
+          \"include\": 
+          {
+          \"job-name\": \"Py3.10\",
+          \"python-version\": \"3.10\",
+          \"omp\": \"n\",
+          \"mpi\": \"n\",
+          \"dagmc\": \"n\",
+          \"ncrystal\": \"n\",
+          \"libmesh\": \"n\",
+          \"event\": \"n\",
+          \"vectfit\": \"n\"
+          },
+          {
+          \"job-name\": \"Py3.10 omp\",
+          \"python-version\": \"3.10\",
+          \"omp\": \"y\",
+          \"mpi\": \"n\",
+          \"dagmc\": \"n\",
+          \"ncrystal\": \"n\",
+          \"libmesh\": \"n\",
+          \"event\": \"n\",
+          \"vectfit\": \"n\"
+          },
+          {
+          \"job-name\": \"Py3.10 mpi\",
+          \"python-version\": \"3.10\",
+          \"omp\": \"n\",
+          \"mpi\": \"y\",
+          \"dagmc\": \"n\",
+          \"ncrystal\": \"n\",
+          \"libmesh\": \"n\",
+          \"event\": \"n\",
+          \"vectfit\": \"n\"
+          },
+          {
+          \"job-name\": \"Py3.10 omp mpi\",
+          \"python-version\": \"3.10\",
+          \"omp\": \"y\",
+          \"mpi\": \"y\",
+          \"dagmc\": \"n\",
+          \"ncrystal\": \"n\",
+          \"libmesh\": \"n\",
+          \"event\": \"n\",
+          \"vectfit\": \"n\"
+          },
+          {
+          \"job-name\": \"Py3.11\",
+          \"python-version\": \"3.11\",
+          \"omp\": \"n\",
+          \"mpi\": \"n\",
+          \"dagmc\": \"n\",
+          \"ncrystal\": \"n\",
+          \"libmesh\": \"n\",
+          \"event\": \"n\",
+          \"vectfit\": \"n\"
+          },
+          {
+          \"job-name\": \"Py3.12\",
+          \"python-version\": \"3.12\",
+          \"omp\": \"n\",
+          \"mpi\": \"n\",
+          \"dagmc\": \"n\",
+          \"ncrystal\": \"n\",
+          \"libmesh\": \"n\",
+          \"event\": \"n\",
+          \"vectfit\": \"n\"
+          },
+          {
+          \"job-name\": \"Py3.10 omp mpi dagmc\",
+          \"python-version\": \"3.10\",
+          \"omp\": \"y\",
+          \"mpi\": \"y\",
+          \"dagmc\": \"y\",
+          \"ncrystal\": \"n\",
+          \"libmesh\": \"n\",
+          \"event\": \"n\",
+          \"vectfit\": \"n\"
+          },
+          {
+          \"job-name\": \"Py3.10 ncrystal\",
+          \"python-version\": \"3.10\",
+          \"omp\": \"n\",
+          \"mpi\": \"n\",
+          \"dagmc\": \"n\",
+          \"ncrystal\": \"y\",
+          \"libmesh\": \"n\",
+          \"event\": \"n\",
+          \"vectfit\": \"n\"
+          },
+          {
+          \"job-name\": \"Py3.10 omp mpi libmesh\",
+          \"python-version\": \"3.10\",
+          \"omp\": \"y\",
+          \"mpi\": \"y\",
+          \"dagmc\": \"n\",
+          \"ncrystal\": \"n\",
+          \"libmesh\": \"y\",
+          \"event\": \"n\",
+          \"vectfit\": \"n\"
+          },
+          {
+          \"job-name\": \"Py3.10 omp libmesh\",
+          \"python-version\": \"3.10\",
+          \"omp\": \"y\",
+          \"mpi\": \"n\",
+          \"dagmc\": \"n\",
+          \"ncrystal\": \"n\",
+          \"libmesh\": \"y\",
+          \"event\": \"n\",
+          \"vectfit\": \"n\"
+          },
+          {
+          \"job-name\": \"Py3.10 omp event\",
+          \"python-version\": \"3.10\",
+          \"omp\": \"y\",
+          \"mpi\": \"n\",
+          \"dagmc\": \"n\",
+          \"ncrystal\": \"n\",
+          \"libmesh\": \"n\",
+          \"event\": \"y\",
+          \"vectfit\": \"n\"
+          },
+          {
+          \"job-name\": \"Py3.10 mpi vectfit\",
+          \"python-version\": \"3.10\",
+          \"omp\": \"n\",
+          \"mpi\": \"y\",
+          \"dagmc\": \"n\",
+          \"ncrystal\": \"n\",
+          \"libmesh\": \"n\",
+          \"event\": \"n\",
+          \"vectfit\": \"y\"
+          }}" >> $GITHUB_OUTPUT
+
   main:
     runs-on: ubuntu-22.04
     strategy:
-      matrix:
-        python-version: ["3.10"]
-        mpi: [n, y]
-        omp: [n, y]
-        dagmc: [n]
-        ncrystal: [n]
-        libmesh: [n]
-        event: [n]
-        vectfit: [n]
-
-        include:
-          - python-version: "3.11"
-            omp: n
-            mpi: n
-          - python-version: "3.12"
-            omp: n
-            mpi: n
-          - dagmc: y
-            python-version: "3.10"
-            mpi: y
-            omp: y
-          - ncrystal: y
-            python-version: "3.10"
-            mpi: n
-            omp: n
-          - libmesh: y
-            python-version: "3.10"
-            mpi: y
-            omp: y
-          - libmesh: y
-            python-version: "3.10"
-            mpi: n
-            omp: y
-          - event: y
-            python-version: "3.10"
-            omp: y
-            mpi: n
-          - vectfit: y
-            python-version: "3.10"
-            omp: n
-            mpi: y
-    
+      matrix: ${{fromJson(needs.setup.outputs.matrix)}}
+
+    name: "${{ matrix.job-name }}"
 
     env:
       MPI: ${{ matrix.mpi }}
@@ -83,15 +189,6 @@ jobs:
       # FI_EFA_FORK_SAFE=1 in more recent versions.
       RDMAV_FORK_SAFE: 1
 
-    name: "Py ${{ matrix.python-version }} 
-      (omp=${{ matrix.omp }}, 
-      mpi=${{ matrix.mpi }}, 
-      dagmc=${{ matrix.dagmc }}, 
-      ncrystal=${{ matrix.ncrystal }},
-      libmesh=${{ matrix.libmesh }}, 
-      event=${{ matrix.event }}, 
-      vectfit=${{ matrix.vectfit }})"
-
     steps:
       - uses: actions/checkout@v4
 
@@ -197,6 +294,7 @@ jobs:
           key: mcpl-${{ env.MCPL_HASH }} 
 =======
 
+<<<<<<< HEAD
       #- name: Restore mcpl
       #  uses: actions/cache@v4
       #  with:
@@ -204,6 +302,8 @@ jobs:
       #    key: mcpl-${{ env.MCPL_HASH }} 
 >>>>>>> 322d1d221 (Cache vectfit and temporarily remove testing)
 
+=======
+>>>>>>> f991cf9bb (Try renaming scheme for job matrix)
       - name: install
         shell: bash
         run: |

From 62c31aa9ac74a2d9c270c5a7e5bdb6978cdfa9dd Mon Sep 17 00:00:00 2001
From: John Vincent Cauilan <64677361+johvincau@users.noreply.github.com>
Date: Mon, 5 Aug 2024 15:30:07 -0500
Subject: [PATCH 20/43] Extract job matrix from json

---
 .github/workflows/ci.yml | 147 +--------------------------------------
 tools/ci/matrix.json     | 136 ++++++++++++++++++++++++++++++++++++
 2 files changed, 137 insertions(+), 146 deletions(-)
 create mode 100644 tools/ci/matrix.json

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 2cdc0cca4a7..40096cfce21 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -21,155 +21,10 @@ env:
   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
 jobs:
-  job-setup:
-    runs-on: ubuntu-latest
-    outputs:
-      matrix: ${{ steps.set-matrix.outputs.matrix }}
-    steps:
-      - uses: actions/checkout@v4
-      - name: set job matrix for main
-        id: jobs
-        shell: bash
-        run: |
-          echo "matrix={
-          \"include\": 
-          {
-          \"job-name\": \"Py3.10\",
-          \"python-version\": \"3.10\",
-          \"omp\": \"n\",
-          \"mpi\": \"n\",
-          \"dagmc\": \"n\",
-          \"ncrystal\": \"n\",
-          \"libmesh\": \"n\",
-          \"event\": \"n\",
-          \"vectfit\": \"n\"
-          },
-          {
-          \"job-name\": \"Py3.10 omp\",
-          \"python-version\": \"3.10\",
-          \"omp\": \"y\",
-          \"mpi\": \"n\",
-          \"dagmc\": \"n\",
-          \"ncrystal\": \"n\",
-          \"libmesh\": \"n\",
-          \"event\": \"n\",
-          \"vectfit\": \"n\"
-          },
-          {
-          \"job-name\": \"Py3.10 mpi\",
-          \"python-version\": \"3.10\",
-          \"omp\": \"n\",
-          \"mpi\": \"y\",
-          \"dagmc\": \"n\",
-          \"ncrystal\": \"n\",
-          \"libmesh\": \"n\",
-          \"event\": \"n\",
-          \"vectfit\": \"n\"
-          },
-          {
-          \"job-name\": \"Py3.10 omp mpi\",
-          \"python-version\": \"3.10\",
-          \"omp\": \"y\",
-          \"mpi\": \"y\",
-          \"dagmc\": \"n\",
-          \"ncrystal\": \"n\",
-          \"libmesh\": \"n\",
-          \"event\": \"n\",
-          \"vectfit\": \"n\"
-          },
-          {
-          \"job-name\": \"Py3.11\",
-          \"python-version\": \"3.11\",
-          \"omp\": \"n\",
-          \"mpi\": \"n\",
-          \"dagmc\": \"n\",
-          \"ncrystal\": \"n\",
-          \"libmesh\": \"n\",
-          \"event\": \"n\",
-          \"vectfit\": \"n\"
-          },
-          {
-          \"job-name\": \"Py3.12\",
-          \"python-version\": \"3.12\",
-          \"omp\": \"n\",
-          \"mpi\": \"n\",
-          \"dagmc\": \"n\",
-          \"ncrystal\": \"n\",
-          \"libmesh\": \"n\",
-          \"event\": \"n\",
-          \"vectfit\": \"n\"
-          },
-          {
-          \"job-name\": \"Py3.10 omp mpi dagmc\",
-          \"python-version\": \"3.10\",
-          \"omp\": \"y\",
-          \"mpi\": \"y\",
-          \"dagmc\": \"y\",
-          \"ncrystal\": \"n\",
-          \"libmesh\": \"n\",
-          \"event\": \"n\",
-          \"vectfit\": \"n\"
-          },
-          {
-          \"job-name\": \"Py3.10 ncrystal\",
-          \"python-version\": \"3.10\",
-          \"omp\": \"n\",
-          \"mpi\": \"n\",
-          \"dagmc\": \"n\",
-          \"ncrystal\": \"y\",
-          \"libmesh\": \"n\",
-          \"event\": \"n\",
-          \"vectfit\": \"n\"
-          },
-          {
-          \"job-name\": \"Py3.10 omp mpi libmesh\",
-          \"python-version\": \"3.10\",
-          \"omp\": \"y\",
-          \"mpi\": \"y\",
-          \"dagmc\": \"n\",
-          \"ncrystal\": \"n\",
-          \"libmesh\": \"y\",
-          \"event\": \"n\",
-          \"vectfit\": \"n\"
-          },
-          {
-          \"job-name\": \"Py3.10 omp libmesh\",
-          \"python-version\": \"3.10\",
-          \"omp\": \"y\",
-          \"mpi\": \"n\",
-          \"dagmc\": \"n\",
-          \"ncrystal\": \"n\",
-          \"libmesh\": \"y\",
-          \"event\": \"n\",
-          \"vectfit\": \"n\"
-          },
-          {
-          \"job-name\": \"Py3.10 omp event\",
-          \"python-version\": \"3.10\",
-          \"omp\": \"y\",
-          \"mpi\": \"n\",
-          \"dagmc\": \"n\",
-          \"ncrystal\": \"n\",
-          \"libmesh\": \"n\",
-          \"event\": \"y\",
-          \"vectfit\": \"n\"
-          },
-          {
-          \"job-name\": \"Py3.10 mpi vectfit\",
-          \"python-version\": \"3.10\",
-          \"omp\": \"n\",
-          \"mpi\": \"y\",
-          \"dagmc\": \"n\",
-          \"ncrystal\": \"n\",
-          \"libmesh\": \"n\",
-          \"event\": \"n\",
-          \"vectfit\": \"y\"
-          }}" >> $GITHUB_OUTPUT
-
   main:
     runs-on: ubuntu-22.04
     strategy:
-      matrix: ${{fromJson(needs.setup.outputs.matrix)}}
+      matrix: ${{ fromJson("$GITHUB_WORKSPACE/tools/ci/matrix.json") }}
 
     name: "${{ matrix.job-name }}"
 
diff --git a/tools/ci/matrix.json b/tools/ci/matrix.json
new file mode 100644
index 00000000000..3ddca93baf5
--- /dev/null
+++ b/tools/ci/matrix.json
@@ -0,0 +1,136 @@
+{
+    "include": [
+        {
+        "job-name": "Py3.10",
+        "python-version": "3.10",
+        "omp": "n",
+        "mpi": "n",
+        "dagmc": "n",
+        "ncrystal": "n",
+        "libmesh": "n",
+        "event": "n",
+        "vectfit": "n"
+        },
+        {
+        "job-name": "Py3.10 omp",
+        "python-version": "3.10",
+        "omp": "y",
+        "mpi": "n",
+        "dagmc": "n",
+        "ncrystal": "n",
+        "libmesh": "n",
+        "event": "n",
+        "vectfit": "n"
+        },
+        {
+        "job-name": "Py3.10 mpi",
+        "python-version": "3.10",
+        "omp": "n",
+        "mpi": "y",
+        "dagmc": "n",
+        "ncrystal": "n",
+        "libmesh": "n",
+        "event": "n",
+        "vectfit": "n"
+        },
+        {
+        "job-name": "Py3.10 omp mpi",
+        "python-version": "3.10",
+        "omp": "y",
+        "mpi": "y",
+        "dagmc": "n",
+        "ncrystal": "n",
+        "libmesh": "n",
+        "event": "n",
+        "vectfit": "n"
+        },
+        {
+        "job-name": "Py3.11",
+        "python-version": "3.11",
+        "omp": "n",
+        "mpi": "n",
+        "dagmc": "n",
+        "ncrystal": "n",
+        "libmesh": "n",
+        "event": "n",
+        "vectfit": "n"
+        },
+        {
+        "job-name": "Py3.12",
+        "python-version": "3.12",
+        "omp": "n",
+        "mpi": "n",
+        "dagmc": "n",
+        "ncrystal": "n",
+        "libmesh": "n",
+        "event": "n",
+        "vectfit": "n"
+        },
+        {
+        "job-name": "Py3.10 omp mpi dagmc",
+        "python-version": "3.10",
+        "omp": "y",
+        "mpi": "y",
+        "dagmc": "y",
+        "ncrystal": "n",
+        "libmesh": "n",
+        "event": "n",
+        "vectfit": "n"
+        },
+        {
+        "job-name": "Py3.10 ncrystal",
+        "python-version": "3.10",
+        "omp": "n",
+        "mpi": "n",
+        "dagmc": "n",
+        "ncrystal": "y",
+        "libmesh": "n",
+        "event": "n",
+        "vectfit": "n"
+        },
+        {
+        "job-name": "Py3.10 omp mpi libmesh",
+        "python-version": "3.10",
+        "omp": "y",
+        "mpi": "y",
+        "dagmc": "n",
+        "ncrystal": "n",
+        "libmesh": "y",
+        "event": "n",
+        "vectfit": "n"
+        },
+        {
+        "job-name": "Py3.10 omp libmesh",
+        "python-version": "3.10",
+        "omp": "y",
+        "mpi": "n",
+        "dagmc": "n",
+        "ncrystal": "n",
+        "libmesh": "y",
+        "event": "n",
+        "vectfit": "n"
+        },
+        {
+        "job-name": "Py3.10 omp event",
+        "python-version": "3.10",
+        "omp": "y",
+        "mpi": "n",
+        "dagmc": "n",
+        "ncrystal": "n",
+        "libmesh": "n",
+        "event": "y",
+        "vectfit": "n"
+        },
+        {
+        "job-name": "Py3.10 mpi vectfit",
+        "python-version": "3.10",
+        "omp": "n",
+        "mpi": "y",
+        "dagmc": "n",
+        "ncrystal": "n",
+        "libmesh": "n",
+        "event": "n",
+        "vectfit": "y"
+        }
+    ]
+}
\ No newline at end of file

From 1e7de1e8ebc9fc7643ca523acca2cd1b5a7d7ad0 Mon Sep 17 00:00:00 2001
From: John Vincent Cauilan <64677361+johvincau@users.noreply.github.com>
Date: Mon, 5 Aug 2024 15:45:31 -0500
Subject: [PATCH 21/43] Add in setup-job and try JSON input/output scheme

---
 .github/workflows/ci.yml | 18 +++++++++++++++++-
 tools/ci/matrix.json     |  3 ++-
 2 files changed, 19 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 40096cfce21..d528633ee7a 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -21,10 +21,26 @@ env:
   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
 jobs:
+  setup: 
+    runs-on: ubuntu-22.04
+    outputs:
+      matrix: ${{ steps.read-json.outputs.matrix }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Read JSON
+        id: read-json
+        shell: bash
+        run: |
+            echo "matrix<<EOF" >> $GITHUB_OUTPUT
+            cat $GITHUB_WORKSPACE/tools/ci/matrix.json >> $GITHUB_OUTPUT
+
   main:
     runs-on: ubuntu-22.04
+    needs: setup
     strategy:
-      matrix: ${{ fromJson("$GITHUB_WORKSPACE/tools/ci/matrix.json") }}
+      matrix: "${{ fromJSON( needs.setup.outputs.matrix ) }}"
 
     name: "${{ matrix.job-name }}"
 
diff --git a/tools/ci/matrix.json b/tools/ci/matrix.json
index 3ddca93baf5..3383552bea9 100644
--- a/tools/ci/matrix.json
+++ b/tools/ci/matrix.json
@@ -133,4 +133,5 @@
         "vectfit": "y"
         }
     ]
-}
\ No newline at end of file
+}
+EOF
\ No newline at end of file

From faa48835d5a83d9b15f451349388f7c6fcf22dbf Mon Sep 17 00:00:00 2001
From: John Vincent Cauilan <64677361+johvincau@users.noreply.github.com>
Date: Mon, 5 Aug 2024 18:50:24 -0500
Subject: [PATCH 22/43] Clean up comments and prepare for PR

---
 .github/workflows/ci.yml        | 20 +-------------------
 tools/ci/gha-caches.sh          |  3 ---
 tools/ci/gha-install-dagmc.sh   |  4 ++--
 tools/ci/gha-install-libmesh.sh |  2 +-
 tools/ci/gha-install-mcpl.sh    |  1 -
 tools/ci/gha-install.sh         |  7 -------
 6 files changed, 4 insertions(+), 33 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index d528633ee7a..60af96efa65 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -156,25 +156,7 @@ jobs:
           path: |
             ~/LIBMESH
           key: libmesh-mpi-${{matrix.mpi}}-${{ env.NC_HASH }} 
-<<<<<<< HEAD
-  
-      - name: Restore mcpl
-        uses: actions/cache@v4
-        with:
-          path: ~/mcpl
-          key: mcpl-${{ env.MCPL_HASH }} 
-=======
-
-<<<<<<< HEAD
-      #- name: Restore mcpl
-      #  uses: actions/cache@v4
-      #  with:
-      #    path: ~/mcpl
-      #    key: mcpl-${{ env.MCPL_HASH }} 
->>>>>>> 322d1d221 (Cache vectfit and temporarily remove testing)
-
-=======
->>>>>>> f991cf9bb (Try renaming scheme for job matrix)
+
       - name: install
         shell: bash
         run: |
diff --git a/tools/ci/gha-caches.sh b/tools/ci/gha-caches.sh
index 4ea8624c765..83ac2943922 100755
--- a/tools/ci/gha-caches.sh
+++ b/tools/ci/gha-caches.sh
@@ -29,6 +29,3 @@ if [[ $LIBMESH = 'y' ]]; then
     echo "NC_HASH=$(git ls-remote https://github.com/libmesh/libmesh \
     --branch v1.7.1 | cut -f 1 | head -c 15)" >> $GITHUB_ENV
 fi
-
-echo "MCPL_HASH=$(git ls-remote https://github.com/mctools/mcpl.git |\
-    cut -f 1 | head -c 15)" >> $GITHUB_ENV
diff --git a/tools/ci/gha-install-dagmc.sh b/tools/ci/gha-install-dagmc.sh
index fb41503854e..82759c9bcce 100755
--- a/tools/ci/gha-install-dagmc.sh
+++ b/tools/ci/gha-install-dagmc.sh
@@ -21,7 +21,7 @@ git clone -b $MOAB_BRANCH $MOAB_REPO
 mkdir build && cd build
 cmake ../moab -DENABLE_HDF5=ON -DENABLE_NETCDF=ON -DBUILD_SHARED_LIBS=ON -DCMAKE_INSTALL_PREFIX=$MOAB_INSTALL_DIR -DENABLE_BLASLAPACK=OFF
 make -j && make -j install
-#rm -rf $HOME/MOAB/moab $HOME/MOAB/build
+rm -rf $HOME/MOAB/moab $HOME/MOAB/build
 
 # DAGMC Install
 cd $HOME
@@ -30,6 +30,6 @@ git clone -b $DAGMC_BRANCH $DAGMC_REPO
 mkdir build && cd build
 cmake ../dagmc -DBUILD_TALLY=ON -DCMAKE_INSTALL_PREFIX=$DAGMC_INSTALL_DIR -DBUILD_STATIC_LIBS=OFF -DMOAB_DIR=$MOAB_INSTALL_DIR
 make -j install
-#rm -rf $HOME/DAGMC/dagmc $HOME/DAGMC/build
+rm -rf $HOME/DAGMC/dagmc $HOME/DAGMC/build
 
 cd $CURRENT_DIR
diff --git a/tools/ci/gha-install-libmesh.sh b/tools/ci/gha-install-libmesh.sh
index 6771e69d5a6..dd1c1b37f96 100755
--- a/tools/ci/gha-install-libmesh.sh
+++ b/tools/ci/gha-install-libmesh.sh
@@ -18,6 +18,6 @@ else
 fi
 make -j4 install
 export LIBMESH_PC=$HOME/LIBMESH/lib/pkgconfig/
-#rm -rf $HOME/LIBMESH/build
+rm -rf $HOME/LIBMESH/build
 
 popd
diff --git a/tools/ci/gha-install-mcpl.sh b/tools/ci/gha-install-mcpl.sh
index 4af01d61c47..7915378aab5 100755
--- a/tools/ci/gha-install-mcpl.sh
+++ b/tools/ci/gha-install-mcpl.sh
@@ -3,7 +3,6 @@ set -ex
 
 # MCPL variables
 MCPL_REPO='https://github.com/mctools/mcpl'
-MCPL_INSTALL_DIR=$HOME/mcpl
 
 cd $HOME
 git clone $MCPL_REPO
diff --git a/tools/ci/gha-install.sh b/tools/ci/gha-install.sh
index 4cf8e2e8d05..081d68bd653 100755
--- a/tools/ci/gha-install.sh
+++ b/tools/ci/gha-install.sh
@@ -9,9 +9,6 @@ pip install --upgrade numpy
 # Install NJOY 2016
 if [[ ! -d "$HOME/NJOY2016" ]]; then
     ./tools/ci/gha-install-njoy.sh
-else
-    #cd $HOME/NJOY2016/build && sudo make install
-    cd $GITHUB_WORKSPACE
 fi
 echo "$HOME/NJOY2016/build" >> $GITHUB_PATH
 
@@ -20,10 +17,6 @@ if [[ $DAGMC = 'y' ]]; then
     if [ ! -d "$HOME/DAGMC" ] || [ ! -d "$HOME/MOAB" ]
     then
         ./tools/ci/gha-install-dagmc.sh
-    else
-        #cd $HOME/DAGMC/build && make -j install
-        #cd $HOME/MOAB/build && make -j install
-        cd $GITHUB_WORKSPACE
     fi
 fi
 

From f43fed5b09ef7c22660afe3b0335a271c61fdf08 Mon Sep 17 00:00:00 2001
From: John Vincent Cauilan <64677361+johvincau@users.noreply.github.com>
Date: Tue, 6 Aug 2024 12:24:42 -0500
Subject: [PATCH 23/43] Minor tweaks and clean up trash

---
 tools/ci/gha-install.sh | 14 ++------------
 tools/ci/matrix.json    | 24 ++++++++++++------------
 2 files changed, 14 insertions(+), 24 deletions(-)

diff --git a/tools/ci/gha-install.sh b/tools/ci/gha-install.sh
index 081d68bd653..960f15c655c 100755
--- a/tools/ci/gha-install.sh
+++ b/tools/ci/gha-install.sh
@@ -42,9 +42,9 @@ fi
 
 # Install libMesh if needed
 if [[ $LIBMESH = 'y' ]]; then
-    if [ ! -d "$HOME/vectfit" ]
+    if [ ! -d "$HOME/libmesh" ]
     then
-        ./tools/ci/gha-install-vectfit.sh
+        ./tools/ci/gha-install-libmesh.sh
     else
         pip install $HOME/pybind11
         pip install wheel
@@ -74,14 +74,4 @@ fi
 python tools/ci/gha-install.py
 
 # Install Python API in editable mode
-<<<<<<< HEAD
 pip install -e .[test,vtk,ci]
-=======
-pip install -e .[test,vtk]
-
-# For coverage testing of the C++ source files
-pip install cpp-coveralls
-
-# For coverage testing of the Python source files
-pip install coveralls
->>>>>>> 9198dde0e (Fix gha-install issue)
diff --git a/tools/ci/matrix.json b/tools/ci/matrix.json
index 3383552bea9..72d236fbd7e 100644
--- a/tools/ci/matrix.json
+++ b/tools/ci/matrix.json
@@ -1,7 +1,7 @@
 {
     "include": [
         {
-        "job-name": "Py3.10",
+        "job-name": "Python 3.10",
         "python-version": "3.10",
         "omp": "n",
         "mpi": "n",
@@ -12,7 +12,7 @@
         "vectfit": "n"
         },
         {
-        "job-name": "Py3.10 omp",
+        "job-name": "Python 3.10 [omp]",
         "python-version": "3.10",
         "omp": "y",
         "mpi": "n",
@@ -23,7 +23,7 @@
         "vectfit": "n"
         },
         {
-        "job-name": "Py3.10 mpi",
+        "job-name": "Python 3.10 [mpi]",
         "python-version": "3.10",
         "omp": "n",
         "mpi": "y",
@@ -34,7 +34,7 @@
         "vectfit": "n"
         },
         {
-        "job-name": "Py3.10 omp mpi",
+        "job-name": "Python 3.10 [omp,mpi]",
         "python-version": "3.10",
         "omp": "y",
         "mpi": "y",
@@ -45,7 +45,7 @@
         "vectfit": "n"
         },
         {
-        "job-name": "Py3.11",
+        "job-name": "Python 3.11",
         "python-version": "3.11",
         "omp": "n",
         "mpi": "n",
@@ -56,7 +56,7 @@
         "vectfit": "n"
         },
         {
-        "job-name": "Py3.12",
+        "job-name": "Python 3.12",
         "python-version": "3.12",
         "omp": "n",
         "mpi": "n",
@@ -67,7 +67,7 @@
         "vectfit": "n"
         },
         {
-        "job-name": "Py3.10 omp mpi dagmc",
+        "job-name": "Python 3.10 [omp,mpi,dagmc]",
         "python-version": "3.10",
         "omp": "y",
         "mpi": "y",
@@ -78,7 +78,7 @@
         "vectfit": "n"
         },
         {
-        "job-name": "Py3.10 ncrystal",
+        "job-name": "Python 3.10 [ncrystal]",
         "python-version": "3.10",
         "omp": "n",
         "mpi": "n",
@@ -89,7 +89,7 @@
         "vectfit": "n"
         },
         {
-        "job-name": "Py3.10 omp mpi libmesh",
+        "job-name": "Python 3.10 [omp,mpi,libmesh]",
         "python-version": "3.10",
         "omp": "y",
         "mpi": "y",
@@ -100,7 +100,7 @@
         "vectfit": "n"
         },
         {
-        "job-name": "Py3.10 omp libmesh",
+        "job-name": "Python 3.10 [omp,libmesh]",
         "python-version": "3.10",
         "omp": "y",
         "mpi": "n",
@@ -111,7 +111,7 @@
         "vectfit": "n"
         },
         {
-        "job-name": "Py3.10 omp event",
+        "job-name": "Python 3.10 [omp,event]",
         "python-version": "3.10",
         "omp": "y",
         "mpi": "n",
@@ -122,7 +122,7 @@
         "vectfit": "n"
         },
         {
-        "job-name": "Py3.10 mpi vectfit",
+        "job-name": "Python 3.10 [mpi,vectfit]",
         "python-version": "3.10",
         "omp": "n",
         "mpi": "y",

From a5b5a75029dbfae6a0168f310e964e1ca9783244 Mon Sep 17 00:00:00 2001
From: John Vincent Cauilan <64677361+johvincau@users.noreply.github.com>
Date: Wed, 14 Aug 2024 09:11:16 -0500
Subject: [PATCH 24/43] Remove mcpl build dir flag

---
 tools/ci/gha-install-mcpl.sh | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/tools/ci/gha-install-mcpl.sh b/tools/ci/gha-install-mcpl.sh
index 7915378aab5..3713d40e065 100755
--- a/tools/ci/gha-install-mcpl.sh
+++ b/tools/ci/gha-install-mcpl.sh
@@ -8,5 +8,4 @@ cd $HOME
 git clone $MCPL_REPO
 cd mcpl
 mkdir build && cd build
-cmake .. -DCMAKE_INSTALL_PREFIX=$MCPL_INSTALL_DIR &&
-make 2>/dev/null && sudo make install
\ No newline at end of file
+cmake .. && make 2>/dev/null && sudo make install
\ No newline at end of file

From 2264f3eeae51fa37979e12fc93fe78609ea17c16 Mon Sep 17 00:00:00 2001
From: John Vincent Cauilan <64677361+johvincau@users.noreply.github.com>
Date: Wed, 14 Aug 2024 09:54:10 -0500
Subject: [PATCH 25/43] Remove nonfunctional mcpl_cmake_path and -DMCPL_DIR
 cmake flags

---
 tools/ci/gha-install.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/tools/ci/gha-install.py b/tools/ci/gha-install.py
index 7d49f46616b..f046e863470 100644
--- a/tools/ci/gha-install.py
+++ b/tools/ci/gha-install.py
@@ -11,8 +11,6 @@ def install(omp=False, mpi=False, phdf5=False, dagmc=False, libmesh=False, ncrys
 
     # Build in debug mode by default with support for MCPL
     cmake_cmd = ['cmake', '-DCMAKE_BUILD_TYPE=Debug', '-DOPENMC_USE_MCPL=on']
-    mcpl_cmake_path = os.environ.get('HOME') + '/mcpl/lib/cmake/MCPL'
-    cmake_cmd.append(f'-DMCPL_DIR={mcpl_cmake_path}')
 
     # Turn off OpenMP if specified
     if not omp:

From cd4d97747067d7eda9ed210b4a2a06a20e86d372 Mon Sep 17 00:00:00 2001
From: John Vincent Cauilan <64677361+johvincau@users.noreply.github.com>
Date: Wed, 14 Aug 2024 10:11:55 -0500
Subject: [PATCH 26/43] Fix libmesh/vectfit install commands in gha-install.sh

---
 tools/ci/gha-install.sh | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/tools/ci/gha-install.sh b/tools/ci/gha-install.sh
index 960f15c655c..45ac2a2015a 100755
--- a/tools/ci/gha-install.sh
+++ b/tools/ci/gha-install.sh
@@ -37,6 +37,10 @@ if [[ $VECTFIT = 'y' ]]; then
     if [ ! -d "$HOME/vectfit" ]
     then
         ./tools/ci/gha-install-vectfit.sh
+    else
+        pip install $HOME/pybind11
+        pip install wheel
+        pip install --no-build-isolation ./vectfit
     fi
 fi
 
@@ -45,10 +49,6 @@ if [[ $LIBMESH = 'y' ]]; then
     if [ ! -d "$HOME/libmesh" ]
     then
         ./tools/ci/gha-install-libmesh.sh
-    else
-        pip install $HOME/pybind11
-        pip install wheel
-        pip install --no-build-isolation ./vectfit
     fi
 fi
 

From 36d0dedd07a898bd71fe2f9b1f810176cf017528 Mon Sep 17 00:00:00 2001
From: John Vincent Cauilan <64677361+johvincau@users.noreply.github.com>
Date: Wed, 14 Aug 2024 10:20:25 -0500
Subject: [PATCH 27/43] Improve gha-caches.sh hash commands

---
 tools/ci/gha-caches.sh | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/tools/ci/gha-caches.sh b/tools/ci/gha-caches.sh
index 83ac2943922..71edbc3fbbb 100755
--- a/tools/ci/gha-caches.sh
+++ b/tools/ci/gha-caches.sh
@@ -1,31 +1,31 @@
 #!/bin/bash
 set -ex
 
-echo "NJOY_HASH=$(git ls-remote https://github.com/njoy/NJOY2016.git | cut -f 1 |\
+echo "NJOY_HASH=$(git ls-remote https://github.com/njoy/NJOY2016.git HEAD |\
     head -c 15)" >> $GITHUB_ENV
 
 if [[ $DAGMC = 'y' ]]; then
     echo "MOAB_HASH=$(git ls-remote https://bitbucket.org/fathomteam/moab.git \
-    --branch Version5.1.0 | cut -f 1 | head -c 15)" >> $GITHUB_ENV
+    --branch Version5.1.0 HEAD | head -c 15)" >> $GITHUB_ENV
 
-    echo "DAGMC_HASH=$(git ls-remote https://github.com/svalinn/dagmc.git |\
-    cut -f 1 | head -c 15)" >> $GITHUB_ENV
+    echo "DAGMC_HASH=$(git ls-remote https://github.com/svalinn/dagmc.git HEAD |\
+    head -c 15)" >> $GITHUB_ENV
 fi
 
 if [[ $NCRYSTAL = 'y' ]]; then
     echo "NC_HASH=$(git ls-remote https://github.com/mctools/ncrystal \
-    --branch develop | cut -f 1 | head -c 15)" >> $GITHUB_ENV
+    --branch develop HEAD | head -c 15)" >> $GITHUB_ENV
 fi
 
 if [[ $VECTFIT = 'y' ]]; then
     echo "PYBIND_HASH=$(git ls-remote https://github.com/pybind/pybind11 \
-    --branch master | cut -f 1 | head -c 15)" >> $GITHUB_ENV
+    --branch master HEAD | head -c 15)" >> $GITHUB_ENV
 
-    echo "VF_HASH=$(git ls-remote https://github.com/liangjg/vectfit.git |\
-    cut -f 1 | head -c 15)" >> $GITHUB_ENV
+    echo "VF_HASH=$(git ls-remote https://github.com/liangjg/vectfit.git HEAD |\
+    head -c 15)" >> $GITHUB_ENV
 fi
 
 if [[ $LIBMESH = 'y' ]]; then
     echo "NC_HASH=$(git ls-remote https://github.com/libmesh/libmesh \
-    --branch v1.7.1 | cut -f 1 | head -c 15)" >> $GITHUB_ENV
+    --branch v1.7.1 HEAD | head -c 15)" >> $GITHUB_ENV
 fi

From f1076433c59b769c12442fda3b688021a1c3fac6 Mon Sep 17 00:00:00 2001
From: John Vincent Cauilan <64677361+johvincau@users.noreply.github.com>
Date: Wed, 14 Aug 2024 10:27:21 -0500
Subject: [PATCH 28/43] Clarify GHA 'setup' step name

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 60af96efa65..cb5dda90906 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -29,7 +29,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - name: Read JSON
+      - name: Send JSON matrix contents to job output
         id: read-json
         shell: bash
         run: |

From 048feeb9e1eed9d5ddf4afcd54a973a35e7e05be Mon Sep 17 00:00:00 2001
From: John Vincent Cauilan <64677361+johvincau@users.noreply.github.com>
Date: Wed, 14 Aug 2024 10:58:39 -0500
Subject: [PATCH 29/43] Remove build dirs after NJOY and vectfit installs

---
 tools/ci/gha-install-njoy.sh    | 3 ++-
 tools/ci/gha-install-vectfit.sh | 5 +++++
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/tools/ci/gha-install-njoy.sh b/tools/ci/gha-install-njoy.sh
index 01a19da249d..5ab20db25b0 100755
--- a/tools/ci/gha-install-njoy.sh
+++ b/tools/ci/gha-install-njoy.sh
@@ -10,4 +10,5 @@ git clone $NJOY_REPO
 cd NJOY2016
 mkdir build && cd build
 cmake -Dstatic=on .. -DCMAKE_INSTALL_PREFIX=$NJOY_INSTALL_DIR &&
-make 2>/dev/null && sudo make install
\ No newline at end of file
+make 2>/dev/null && sudo make install
+rm -rf $HOME/NJOY2016/build
\ No newline at end of file
diff --git a/tools/ci/gha-install-vectfit.sh b/tools/ci/gha-install-vectfit.sh
index bd38e1ea8cd..c4a3ffc97ad 100755
--- a/tools/ci/gha-install-vectfit.sh
+++ b/tools/ci/gha-install-vectfit.sh
@@ -20,22 +20,27 @@ cd $HOME
 git clone -b $PYBIND_BRANCH $PYBIND_REPO
 cd pybind11 && mkdir build && cd build && cmake .. && sudo make install
 pip install $HOME/pybind11
+rm -rf build
 
 cd $HOME
 git clone -b $XTL_BRANCH $XTL_REPO
 cd xtl && mkdir build && cd build && cmake .. && sudo make install
+rm -rf build
 
 cd $HOME
 git clone -b $XTENSOR_BRANCH $XTENSOR_REPO
 cd xtensor && mkdir build && cd build && cmake .. && sudo make install
+rm -rf build
 
 cd $HOME
 git clone -b $XTENSOR_PYTHON_BRANCH $XTENSOR_PYTHON_REPO
 cd xtensor-python && mkdir build && cd build && cmake .. && sudo make install
+rm -rf build
 
 cd $HOME
 git clone -b $XTENSOR_BLAS_BRANCH $XTENSOR_BLAS_REPO
 cd xtensor-blas && mkdir build && cd build && cmake .. && sudo make install
+rm -rf build
 
 # Install wheel (remove when vectfit supports installation with build isolation)
 pip install wheel

From 652c57c532f9db76ab90063c7e67d0be8657f46a Mon Sep 17 00:00:00 2001
From: John Vincent Cauilan <64677361+johvincau@users.noreply.github.com>
Date: Wed, 14 Aug 2024 13:19:07 -0500
Subject: [PATCH 30/43] Try removing NJOY2016 tests dir after install

---
 tools/ci/gha-install-njoy.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/ci/gha-install-njoy.sh b/tools/ci/gha-install-njoy.sh
index 5ab20db25b0..586e1025f37 100755
--- a/tools/ci/gha-install-njoy.sh
+++ b/tools/ci/gha-install-njoy.sh
@@ -11,4 +11,4 @@ cd NJOY2016
 mkdir build && cd build
 cmake -Dstatic=on .. -DCMAKE_INSTALL_PREFIX=$NJOY_INSTALL_DIR &&
 make 2>/dev/null && sudo make install
-rm -rf $HOME/NJOY2016/build
\ No newline at end of file
+rm -rf $HOME/NJOY2016/build $HOME/NJOY2016/tests
\ No newline at end of file

From 6e9b9416be6edf20fe49c5825227b6ef6ad17399 Mon Sep 17 00:00:00 2001
From: John Vincent Cauilan <64677361+johvincau@users.noreply.github.com>
Date: Wed, 14 Aug 2024 14:34:42 -0500
Subject: [PATCH 31/43] Fix vectfit in gha-install.sh

---
 tools/ci/gha-install.sh | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/tools/ci/gha-install.sh b/tools/ci/gha-install.sh
index 45ac2a2015a..2b03cda8fa0 100755
--- a/tools/ci/gha-install.sh
+++ b/tools/ci/gha-install.sh
@@ -38,9 +38,11 @@ if [[ $VECTFIT = 'y' ]]; then
     then
         ./tools/ci/gha-install-vectfit.sh
     else
+        cd $HOME
         pip install $HOME/pybind11
         pip install wheel
         pip install --no-build-isolation ./vectfit
+        cd $GITHUB_WORKSPACE
     fi
 fi
 

From a35fa53590413b0caf8f1472f63f5dd174c6a256 Mon Sep 17 00:00:00 2001
From: John Vincent Cauilan <64677361+johvincau@users.noreply.github.com>
Date: Wed, 14 Aug 2024 15:55:49 -0500
Subject: [PATCH 32/43] Re-add NJOY2016 tests dir

---
 tools/ci/gha-install-njoy.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/ci/gha-install-njoy.sh b/tools/ci/gha-install-njoy.sh
index 586e1025f37..5ab20db25b0 100755
--- a/tools/ci/gha-install-njoy.sh
+++ b/tools/ci/gha-install-njoy.sh
@@ -11,4 +11,4 @@ cd NJOY2016
 mkdir build && cd build
 cmake -Dstatic=on .. -DCMAKE_INSTALL_PREFIX=$NJOY_INSTALL_DIR &&
 make 2>/dev/null && sudo make install
-rm -rf $HOME/NJOY2016/build $HOME/NJOY2016/tests
\ No newline at end of file
+rm -rf $HOME/NJOY2016/build
\ No newline at end of file

From dd7896694fab0c5f5c7c7882c775c94ca3dfbcac Mon Sep 17 00:00:00 2001
From: John Vincent Cauilan <64677361+johvincau@users.noreply.github.com>
Date: Thu, 15 Aug 2024 11:22:33 -0500
Subject: [PATCH 33/43] Revert vectfit changes in gha-install.sh

---
 tools/ci/gha-install.sh | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/tools/ci/gha-install.sh b/tools/ci/gha-install.sh
index 2b03cda8fa0..5e94b162c1a 100755
--- a/tools/ci/gha-install.sh
+++ b/tools/ci/gha-install.sh
@@ -37,12 +37,6 @@ if [[ $VECTFIT = 'y' ]]; then
     if [ ! -d "$HOME/vectfit" ]
     then
         ./tools/ci/gha-install-vectfit.sh
-    else
-        cd $HOME
-        pip install $HOME/pybind11
-        pip install wheel
-        pip install --no-build-isolation ./vectfit
-        cd $GITHUB_WORKSPACE
     fi
 fi
 

From b6391690867cd58c3bde03b12edac30db753a875 Mon Sep 17 00:00:00 2001
From: John Vincent Cauilan <64677361+johvincau@users.noreply.github.com>
Date: Thu, 15 Aug 2024 14:03:53 -0500
Subject: [PATCH 34/43] Revert all changes to NJOY and vectfit caches to fix
 install issues

---
 tools/ci/gha-install-njoy.sh    | 3 +--
 tools/ci/gha-install-vectfit.sh | 7 +------
 2 files changed, 2 insertions(+), 8 deletions(-)

diff --git a/tools/ci/gha-install-njoy.sh b/tools/ci/gha-install-njoy.sh
index 5ab20db25b0..01a19da249d 100755
--- a/tools/ci/gha-install-njoy.sh
+++ b/tools/ci/gha-install-njoy.sh
@@ -10,5 +10,4 @@ git clone $NJOY_REPO
 cd NJOY2016
 mkdir build && cd build
 cmake -Dstatic=on .. -DCMAKE_INSTALL_PREFIX=$NJOY_INSTALL_DIR &&
-make 2>/dev/null && sudo make install
-rm -rf $HOME/NJOY2016/build
\ No newline at end of file
+make 2>/dev/null && sudo make install
\ No newline at end of file
diff --git a/tools/ci/gha-install-vectfit.sh b/tools/ci/gha-install-vectfit.sh
index c4a3ffc97ad..2ead59fc229 100755
--- a/tools/ci/gha-install-vectfit.sh
+++ b/tools/ci/gha-install-vectfit.sh
@@ -20,27 +20,22 @@ cd $HOME
 git clone -b $PYBIND_BRANCH $PYBIND_REPO
 cd pybind11 && mkdir build && cd build && cmake .. && sudo make install
 pip install $HOME/pybind11
-rm -rf build
 
 cd $HOME
 git clone -b $XTL_BRANCH $XTL_REPO
 cd xtl && mkdir build && cd build && cmake .. && sudo make install
-rm -rf build
 
 cd $HOME
 git clone -b $XTENSOR_BRANCH $XTENSOR_REPO
 cd xtensor && mkdir build && cd build && cmake .. && sudo make install
-rm -rf build
 
 cd $HOME
 git clone -b $XTENSOR_PYTHON_BRANCH $XTENSOR_PYTHON_REPO
 cd xtensor-python && mkdir build && cd build && cmake .. && sudo make install
-rm -rf build
 
 cd $HOME
 git clone -b $XTENSOR_BLAS_BRANCH $XTENSOR_BLAS_REPO
 cd xtensor-blas && mkdir build && cd build && cmake .. && sudo make install
-rm -rf build
 
 # Install wheel (remove when vectfit supports installation with build isolation)
 pip install wheel
@@ -48,4 +43,4 @@ pip install wheel
 # Install vectfit
 cd $HOME
 git clone https://github.com/liangjg/vectfit.git
-pip install --no-build-isolation ./vectfit
+pip install --no-build-isolation ./vectfit
\ No newline at end of file

From 1897a46b2da82b134d9d55923b2f9ae3ac5d30ff Mon Sep 17 00:00:00 2001
From: John Vincent Cauilan <64677361+johvincau@users.noreply.github.com>
Date: Thu, 15 Aug 2024 17:33:29 -0500
Subject: [PATCH 35/43] Re-try removal of njoy-specific testing suite

---
 tools/ci/gha-install-njoy.sh | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/tools/ci/gha-install-njoy.sh b/tools/ci/gha-install-njoy.sh
index 01a19da249d..21db928b07b 100755
--- a/tools/ci/gha-install-njoy.sh
+++ b/tools/ci/gha-install-njoy.sh
@@ -10,4 +10,5 @@ git clone $NJOY_REPO
 cd NJOY2016
 mkdir build && cd build
 cmake -Dstatic=on .. -DCMAKE_INSTALL_PREFIX=$NJOY_INSTALL_DIR &&
-make 2>/dev/null && sudo make install
\ No newline at end of file
+make 2>/dev/null && sudo make install
+rm -rf $HOME/NJOY2016/tests
\ No newline at end of file

From 6a1d1c04473002ae7d1a9d18d518384068aa856b Mon Sep 17 00:00:00 2001
From: John Vincent Cauilan <64677361+johvincau@users.noreply.github.com>
Date: Fri, 16 Aug 2024 12:32:26 -0500
Subject: [PATCH 36/43] Remove njoy build directory after successful build to
 trim cache

---
 tools/ci/gha-install-njoy.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/ci/gha-install-njoy.sh b/tools/ci/gha-install-njoy.sh
index 21db928b07b..eeec8138759 100755
--- a/tools/ci/gha-install-njoy.sh
+++ b/tools/ci/gha-install-njoy.sh
@@ -11,4 +11,4 @@ cd NJOY2016
 mkdir build && cd build
 cmake -Dstatic=on .. -DCMAKE_INSTALL_PREFIX=$NJOY_INSTALL_DIR &&
 make 2>/dev/null && sudo make install
-rm -rf $HOME/NJOY2016/tests
\ No newline at end of file
+rm -rf $HOME/NJOY2016/tests $HOME/NJOY2016/build
\ No newline at end of file

From 6ef06d3b861dd51e86225d2c862911d797f24074 Mon Sep 17 00:00:00 2001
From: John Vincent Cauilan <64677361+johvincau@users.noreply.github.com>
Date: Fri, 16 Aug 2024 13:08:50 -0500
Subject: [PATCH 37/43] Retain NJOY build directory for cache

---
 tools/ci/gha-install-njoy.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/ci/gha-install-njoy.sh b/tools/ci/gha-install-njoy.sh
index eeec8138759..21db928b07b 100755
--- a/tools/ci/gha-install-njoy.sh
+++ b/tools/ci/gha-install-njoy.sh
@@ -11,4 +11,4 @@ cd NJOY2016
 mkdir build && cd build
 cmake -Dstatic=on .. -DCMAKE_INSTALL_PREFIX=$NJOY_INSTALL_DIR &&
 make 2>/dev/null && sudo make install
-rm -rf $HOME/NJOY2016/tests $HOME/NJOY2016/build
\ No newline at end of file
+rm -rf $HOME/NJOY2016/tests
\ No newline at end of file

From d7714cee5bb928b6c05dee35d58f99a8d1d780a6 Mon Sep 17 00:00:00 2001
From: John Vincent Cauilan <64677361+johvincau@users.noreply.github.com>
Date: Mon, 26 Aug 2024 11:52:46 -0500
Subject: [PATCH 38/43] Properly add NJOY dir to path and remove build dir

---
 tools/ci/gha-install-njoy.sh | 3 ++-
 tools/ci/gha-install.sh      | 2 +-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/tools/ci/gha-install-njoy.sh b/tools/ci/gha-install-njoy.sh
index 21db928b07b..9f2775add77 100755
--- a/tools/ci/gha-install-njoy.sh
+++ b/tools/ci/gha-install-njoy.sh
@@ -11,4 +11,5 @@ cd NJOY2016
 mkdir build && cd build
 cmake -Dstatic=on .. -DCMAKE_INSTALL_PREFIX=$NJOY_INSTALL_DIR &&
 make 2>/dev/null && sudo make install
-rm -rf $HOME/NJOY2016/tests
\ No newline at end of file
+rm -rf $HOME/NJOY2016/tests
+rm -rf $HOME/NJOY2016/build
\ No newline at end of file
diff --git a/tools/ci/gha-install.sh b/tools/ci/gha-install.sh
index 5e94b162c1a..4ac67d6ece9 100755
--- a/tools/ci/gha-install.sh
+++ b/tools/ci/gha-install.sh
@@ -10,7 +10,7 @@ pip install --upgrade numpy
 if [[ ! -d "$HOME/NJOY2016" ]]; then
     ./tools/ci/gha-install-njoy.sh
 fi
-echo "$HOME/NJOY2016/build" >> $GITHUB_PATH
+echo "$HOME/NJOY2016" >> $GITHUB_PATH
 
 # Install DAGMC if needed
 if [[ $DAGMC = 'y' ]]; then

From 53e9353faac8ddf6d68e9880dc9620acabea7063 Mon Sep 17 00:00:00 2001
From: John Vincent Cauilan <64677361+johvincau@users.noreply.github.com>
Date: Mon, 26 Aug 2024 12:06:13 -0500
Subject: [PATCH 39/43] Remove Python-version-dependency caches

---
 .github/workflows/ci.yml | 9 ---------
 1 file changed, 9 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index cb5dda90906..c65bdca413b 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -68,15 +68,6 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
-      - name: Restore Python cache
-        uses: actions/cache@v4
-        with:
-          path: ${{ env.pythonLocation }}
-          key:  py-${{ matrix.python-version }}-(omp=${{ matrix.omp }} 
-            mpi=${{ matrix.mpi }} dagmc=${{ matrix.dagmc }} ncrystal=${{ matrix.ncrystal }} 
-            libmesh=${{ matrix.libmesh }} event=${{ matrix.event }} 
-            vectfit=${{ matrix.vectfit }})
-
       - name: Environment Variables
         run: |
           echo "DAGMC_ROOT=$HOME/DAGMC"

From f7f32bf18da1b88f7fb06160181ef944b961d01b Mon Sep 17 00:00:00 2001
From: Paul Romano <paul.k.romano@gmail.com>
Date: Tue, 27 Aug 2024 17:05:01 -0500
Subject: [PATCH 40/43] NJOY2016/bin should be on PATH

---
 tools/ci/gha-install.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tools/ci/gha-install.sh b/tools/ci/gha-install.sh
index 4ac67d6ece9..132c66bd95b 100755
--- a/tools/ci/gha-install.sh
+++ b/tools/ci/gha-install.sh
@@ -10,7 +10,7 @@ pip install --upgrade numpy
 if [[ ! -d "$HOME/NJOY2016" ]]; then
     ./tools/ci/gha-install-njoy.sh
 fi
-echo "$HOME/NJOY2016" >> $GITHUB_PATH
+echo "$HOME/NJOY2016/bin" >> $GITHUB_PATH
 
 # Install DAGMC if needed
 if [[ $DAGMC = 'y' ]]; then
@@ -33,7 +33,7 @@ if [[ $NCRYSTAL = 'y' ]]; then
 fi
 
 # Install vectfit for WMP generation if needed
-if [[ $VECTFIT = 'y' ]]; then 
+if [[ $VECTFIT = 'y' ]]; then
     if [ ! -d "$HOME/vectfit" ]
     then
         ./tools/ci/gha-install-vectfit.sh

From fceb651f255bb6afcdf04a6c08101f9a60836788 Mon Sep 17 00:00:00 2001
From: John Vincent Cauilan <64677361+johvincau@users.noreply.github.com>
Date: Thu, 2 Jan 2025 21:11:59 -0600
Subject: [PATCH 41/43] Trim NJOY cache

---
 .github/workflows/ci.yml | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index c65bdca413b..74291ce86da 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -106,7 +106,11 @@ jobs:
       - name: Restore NJOY2016
         uses: actions/cache@v4
         with:
-          path: ~/NJOY2016
+          path: |
+            ~/NJOY2016/metaconfigure
+            ~/NJOY2016/src
+            ~/NJOY2016/build/njoy
+            ~/NJOY2016/build/libnjoy.so
           key: NJOY2016-${{ env.NJOY_HASH }} 
 
       - name: Restore DAGMC

From dac7cb0cda82340976e23195b9cd49cc821f5aca Mon Sep 17 00:00:00 2001
From: John Vincent Cauilan <64677361+johvincau@users.noreply.github.com>
Date: Thu, 2 Jan 2025 21:12:53 -0600
Subject: [PATCH 42/43] Enforce 180 minutes for total CI suite

---
 .github/workflows/ci.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 74291ce86da..7ca4efe31d4 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -38,6 +38,7 @@ jobs:
 
   main:
     runs-on: ubuntu-22.04
+    timeout-minutes: 180
     needs: setup
     strategy:
       matrix: "${{ fromJSON( needs.setup.outputs.matrix ) }}"

From b4ec8641708fa81e9a7047ef2953795328681a42 Mon Sep 17 00:00:00 2001
From: John Vincent Cauilan <64677361+johvincau@users.noreply.github.com>
Date: Mon, 13 Jan 2025 20:06:57 -0600
Subject: [PATCH 43/43] Update matrix.json to have base Python version 3.11

---
 tools/ci/matrix.json | 48 ++++++++++++++++++++++----------------------
 1 file changed, 24 insertions(+), 24 deletions(-)

diff --git a/tools/ci/matrix.json b/tools/ci/matrix.json
index 72d236fbd7e..3e50ecf2eee 100644
--- a/tools/ci/matrix.json
+++ b/tools/ci/matrix.json
@@ -1,8 +1,8 @@
 {
     "include": [
         {
-        "job-name": "Python 3.10",
-        "python-version": "3.10",
+        "job-name": "Python 3.11",
+        "python-version": "3.11",
         "omp": "n",
         "mpi": "n",
         "dagmc": "n",
@@ -12,8 +12,8 @@
         "vectfit": "n"
         },
         {
-        "job-name": "Python 3.10 [omp]",
-        "python-version": "3.10",
+        "job-name": "Python 3.11 [omp]",
+        "python-version": "3.11",
         "omp": "y",
         "mpi": "n",
         "dagmc": "n",
@@ -23,8 +23,8 @@
         "vectfit": "n"
         },
         {
-        "job-name": "Python 3.10 [mpi]",
-        "python-version": "3.10",
+        "job-name": "Python 3.11 [mpi]",
+        "python-version": "3.11",
         "omp": "n",
         "mpi": "y",
         "dagmc": "n",
@@ -34,8 +34,8 @@
         "vectfit": "n"
         },
         {
-        "job-name": "Python 3.10 [omp,mpi]",
-        "python-version": "3.10",
+        "job-name": "Python 3.11 [omp,mpi]",
+        "python-version": "3.11",
         "omp": "y",
         "mpi": "y",
         "dagmc": "n",
@@ -45,8 +45,8 @@
         "vectfit": "n"
         },
         {
-        "job-name": "Python 3.11",
-        "python-version": "3.11",
+        "job-name": "Python 3.12",
+        "python-version": "3.12",
         "omp": "n",
         "mpi": "n",
         "dagmc": "n",
@@ -56,8 +56,8 @@
         "vectfit": "n"
         },
         {
-        "job-name": "Python 3.12",
-        "python-version": "3.12",
+        "job-name": "Python 3.13",
+        "python-version": "3.13",
         "omp": "n",
         "mpi": "n",
         "dagmc": "n",
@@ -67,8 +67,8 @@
         "vectfit": "n"
         },
         {
-        "job-name": "Python 3.10 [omp,mpi,dagmc]",
-        "python-version": "3.10",
+        "job-name": "Python 3.11 [omp,mpi,dagmc]",
+        "python-version": "3.11",
         "omp": "y",
         "mpi": "y",
         "dagmc": "y",
@@ -78,8 +78,8 @@
         "vectfit": "n"
         },
         {
-        "job-name": "Python 3.10 [ncrystal]",
-        "python-version": "3.10",
+        "job-name": "Python 3.11 [ncrystal]",
+        "python-version": "3.11",
         "omp": "n",
         "mpi": "n",
         "dagmc": "n",
@@ -89,8 +89,8 @@
         "vectfit": "n"
         },
         {
-        "job-name": "Python 3.10 [omp,mpi,libmesh]",
-        "python-version": "3.10",
+        "job-name": "Python 3.11 [omp,mpi,libmesh]",
+        "python-version": "3.11",
         "omp": "y",
         "mpi": "y",
         "dagmc": "n",
@@ -100,8 +100,8 @@
         "vectfit": "n"
         },
         {
-        "job-name": "Python 3.10 [omp,libmesh]",
-        "python-version": "3.10",
+        "job-name": "Python 3.11 [omp,libmesh]",
+        "python-version": "3.11",
         "omp": "y",
         "mpi": "n",
         "dagmc": "n",
@@ -111,8 +111,8 @@
         "vectfit": "n"
         },
         {
-        "job-name": "Python 3.10 [omp,event]",
-        "python-version": "3.10",
+        "job-name": "Python 3.11 [omp,event]",
+        "python-version": "3.11",
         "omp": "y",
         "mpi": "n",
         "dagmc": "n",
@@ -122,8 +122,8 @@
         "vectfit": "n"
         },
         {
-        "job-name": "Python 3.10 [mpi,vectfit]",
-        "python-version": "3.10",
+        "job-name": "Python 3.11 [mpi,vectfit]",
+        "python-version": "3.11",
         "omp": "n",
         "mpi": "y",
         "dagmc": "n",