fix merge conflicts

.github/CODEOWNERS

@@ -13,3 +13,5 @@ CMakeLists.txt     @sbryngelson @henryleberre
 .vscode/           @sbryngelson @henryleberre
 .github/workflows/ @sbryngelson @henryleberre
 
+# Spencer H. Bryngelson & Ben Wilfong
+.typos.toml        @sbryngelson @wilfonba

.github/codecov.yml

@@ -0,0 +1,10 @@
+coverage:
+  status:
+    project:
+      default:
+        target: 1%
+        threshold: 1%
+    patch:
+      default:
+        target: 1%
+        threshold: 1%

.github/file-filter.yml

@@ -7,7 +7,7 @@ fortran_src: &fortran_src
 
 python_src: &python_src
   - '**/*.py'
-  - 'toolchain/requirements.txt'
+  - 'toolchain/pyproject.toml'
 
 cmakelist: &cmakelist
   - 'CMakeLists.txt'
@@ -22,12 +22,16 @@ scripts: &scripts
   - 'toolchain/bootstrap/**'
 
 yml: &yml
-  - '**/*.yml'
+  - '.github/workflows/phoenix/**'
+  - '.github/workflows/frontier/**'
+  - '.github/workflows/bench.yml'
+  - '.github/workflows/test.yml'
+  - '.github/workflows/formatting.yml'
 
 checkall: &checkall
   - *fortran_src
   - *python_src
   - *cmakelist
   - *tests
   - *scripts
-  - *yml
+  - *yml

.github/workflows/bench.yml

@@ -20,7 +20,8 @@ jobs:
 
   self:
     name: Georgia Tech | Phoenix (NVHPC)
-    if: github.repository == 'MFlowCode/MFC'
+    if: github.repository == 'MFlowCode/MFC' && needs.file-changes.outputs.checkall == 'true'
+    needs: file-changes
     strategy:
       matrix:
         device: ['cpu', 'gpu']
@@ -33,12 +34,12 @@ jobs:
       ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION: true
     steps:
       - name: Clone - PR
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           path: pr
 
       - name: Clone - Master
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           repository: MFlowCode/MFC
           ref: master
@@ -56,7 +57,7 @@ jobs:
           (cd pr && ./mfc.sh bench_diff ../master/bench-${{ matrix.device }}.yaml ../pr/bench-${{ matrix.device }}.yaml)
 
       - name: Archive Logs
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         if:   always()
         with:
           name: logs-${{ matrix.device }}

.github/workflows/cleanliness.yml

@@ -3,103 +3,125 @@ name: Cleanliness
 on: [push, pull_request, workflow_dispatch]
 
 jobs:
-    cleanliness:
-        name: Code Cleanliness Test
-        runs-on: "ubuntu-latest"
-        env:
-            pr_everything: 0
-            master_everything: 0
-        steps:
-            - name: Clone - PR
-              uses: actions/checkout@v3
-              with:
-                path: pr
-            - name: Clone - Master
-              uses: actions/checkout@v3
-              with:
-                repository: MFlowCode/MFC
-                ref: master
-                path: master
-
-            - name: Setup Ubuntu
-              run: |
-                sudo apt update -y
-                sudo apt install -y tar wget make cmake gcc g++ python3 python3-dev "openmpi-*" libopenmpi-dev
-            
-            - name: Build
-              run: |
-                (cd pr && /bin/bash mfc.sh build -j $(nproc) --debug 2> ../pr.txt) 
-                (cd master && /bin/bash mfc.sh build -j $(nproc) --debug 2> ../master.txt)
-                sed -i '/\/pr\//d' pr.txt
-                sed -i '/\/master\//d' master.txt
-            
-            - name: Unused Variables Diff
-              run: |
-                grep -F 'Wunused-variable' master.txt > mUnused.txt
-                grep -F 'Wunused-variable' pr.txt > prUnused.txt
-                diff prUnused.txt mUnused.txt || true
-            
-            - name: Unused Dummy Arguments Diff
-              run: |
-                grep -F 'Wunused-dummy-argument' pr.txt > prDummy.txt
-                grep -F 'Wunused-dummy-argument' master.txt > mDummy.txt
-                diff prDummy.txt mDummy.txt || true
-
-            - name: Unused Value Diff
-              run: |
-                grep -F 'Wunused-value' pr.txt > prUnused_val.txt
-                grep -F 'Wunused-value' master.txt > mUnused_val.txt
-                diff prUnused_val.txt mUnused_val.txt || true
-
-            - name: Maybe Uninitialized Variables Diff
-              run: |
-                grep -F 'Wmaybe-uninitialized' pr.txt > prMaybe.txt
-                grep -F 'Wmaybe-uninitialized' master.txt > mMaybe.txt
-                diff prMaybe.txt mMaybe.txt || true
-
-
-            - name: Everything Diff
-              run: |
-                grep '\-W' pr.txt > pr_every.txt 
-                grep '\-W' master.txt > m_every.txt
-                diff pr_every.txt m_every.txt || true
-
-            - name: List of Warnings
-              run: |
-                cat pr_every.txt
-                
-
-            - name: Summary
-              run: |  
-                pr_variable=$(grep -c -F 'Wunused-variable' pr.txt)
-                pr_argument=$(grep -c -F 'Wunused-dummy-argument' pr.txt)
-                pr_value=$(grep -c -F 'Wunused-value' pr.txt)
-                pr_uninit=$(grep -c -F 'Wmaybe-uninitialized' pr.txt)
-                pr_everything=$(grep -c '\-W' pr.txt)
-
-                master_variable=$(grep -c -F 'Wunused-variable' master.txt)
-                master_argument=$(grep -c -F 'Wunused-dummy-argument' master.txt)
-                master_value=$(grep -c -F 'Wunused-value' master.txt)
-                master_uninit=$(grep -c -F 'Wmaybe-uninitialized' master.txt)
-                master_everything=$(grep -c '\-W' master.txt  )    
-
-                echo "pr_everything=$pr_everything" >> $GITHUB_ENV
-                echo "master_everything=$master_everything" >> $GITHUB_ENV
-
-                echo "Difference is how many warnings were added or removed from master to PR."
-                echo "Negative numbers are better since you are removing warnings." 
-                echo " "
-                echo "Unused Variable Count: $pr_variable, Difference: $((pr_variable - master_variable))"
-                echo "Unused Dummy Argument: $pr_argument, Difference: $((pr_argument - master_argument))"
-                echo "Unused Value: $pr_value, Difference: $((pr_value - master_value))"
-                echo "Maybe Uninitialized: $pr_uninit, Difference: $((pr_uninit - master_uninit))"
-                echo "Everything: $pr_everything, Difference: $((pr_everything - master_everything))"
-            
-
-            - name: Check Differences
-              if: env.pr_everything > env.master_everything 
-              run: |
-                echo "Difference between warning count in PR is greater than in master."
-                exit 1
+  file-changes:
+    name: Detect File Changes
+    runs-on: 'ubuntu-latest'
+    outputs: 
+      checkall: ${{ steps.changes.outputs.checkall }}
+    steps:
+      - name: Clone
+        uses: actions/checkout@v4
+
+      - name: Detect Changes
+        uses: dorny/paths-filter@v3
+        id: changes
+        with: 
+          filters: ".github/file-filter.yml"
+
+  cleanliness:
+      name: Code Cleanliness Check
+      if: needs.file-changes.outputs.checkall == 'true'
+      needs: file-changes
+      runs-on: "ubuntu-latest"
+      env:
+          pr_everything: 0
+          master_everything: 0
+      steps:
+          - name: Clone - PR
+            uses: actions/checkout@v4
+            with:
+              path: pr
+          - name: Clone - Master
+            uses: actions/checkout@v4
+            with:
+              repository: MFlowCode/MFC
+              ref: master
+              path: master
+
+          - name: Setup Ubuntu
+            run: |
+              sudo apt update -y
+              sudo apt install -y tar wget make cmake gcc g++ python3 python3-dev "openmpi-*" libopenmpi-dev
+          
+          - name: Build
+            run: |
+              (cd pr && /bin/bash mfc.sh build -j $(nproc) --debug 2> ../pr.txt) 
+              (cd master && /bin/bash mfc.sh build -j $(nproc) --debug 2> ../master.txt)
+              sed -i '/\/pr\//d' pr.txt
+              sed -i '/\/master\//d' master.txt
+          
+          - name: Unused Variables Diff
+            continue-on-error: true
+            run: |
+              grep -F 'Wunused-variable' master.txt > mUnused.txt
+              grep -F 'Wunused-variable' pr.txt > prUnused.txt
+              diff prUnused.txt mUnused.txt
+          
+          - name: Unused Dummy Arguments Diff
+            continue-on-error: true
+            run: |
+              grep -F 'Wunused-dummy-argument' pr.txt > prDummy.txt 
+              grep -F 'Wunused-dummy-argument' master.txt > mDummy.txt
+              diff prDummy.txt mDummy.txt
+
+          - name: Unused Value Diff
+            continue-on-error: true
+            run: |
+              grep -F 'Wunused-value' pr.txt > prUnused_val.txt
+              grep -F 'Wunused-value' master.txt > mUnused_val.txt
+              diff prUnused_val.txt mUnused_val.txt
+
+          - name: Maybe Uninitialized Variables Diff
+            continue-on-error: true
+            run: |
+              grep -F 'Wmaybe-uninitialized' pr.txt > prMaybe.txt
+              grep -F 'Wmaybe-uninitialized' master.txt > mMaybe.txt
+              diff prMaybe.txt mMaybe.txt
+
+
+          - name: Everything Diff
+            continue-on-error: true
+            run: |
+              grep '\-W' pr.txt > pr_every.txt
+              grep '\-W' master.txt > m_every.txt
+              diff pr_every.txt m_every.txt
+
+          - name: List of Warnings
+            run: |
+              cat pr_every.txt
+              
+
+          - name: Summary
+            continue-on-error: true
+            run: |  
+              pr_variable=$(grep -c -F 'Wunused-variable' pr.txt)
+              pr_argument=$(grep -c -F 'Wunused-dummy-argument' pr.txt)
+              pr_value=$(grep -c -F 'Wunused-value' pr.txt)
+              pr_uninit=$(grep -c -F 'Wmaybe-uninitialized' pr.txt)
+              pr_everything=$(grep -c '\-W' pr.txt)
+
+              master_variable=$(grep -c -F 'Wunused-variable' master.txt)
+              master_argument=$(grep -c -F 'Wunused-dummy-argument' master.txt)
+              master_value=$(grep -c -F 'Wunused-value' master.txt)
+              master_uninit=$(grep -c -F 'Wmaybe-uninitialized' master.txt)
+              master_everything=$(grep -c '\-W' master.txt  )    
+
+              echo "pr_everything=$pr_everything" >> $GITHUB_ENV
+              echo "master_everything=$master_everything" >> $GITHUB_ENV
+
+              echo "Difference is how many warnings were added or removed from master to PR."
+              echo "Negative numbers are better since you are removing warnings." 
+              echo " "
+              echo "Unused Variable Count: $pr_variable, Difference: $((pr_variable - master_variable))"
+              echo "Unused Dummy Argument: $pr_argument, Difference: $((pr_argument - master_argument))"
+              echo "Unused Value: $pr_value, Difference: $((pr_value - master_value))"
+              echo "Maybe Uninitialized: $pr_uninit, Difference: $((pr_uninit - master_uninit))"
+              echo "Everything: $pr_everything, Difference: $((pr_everything - master_everything))"
+          
+
+          - name: Check Differences
+            if: env.pr_everything > env.master_everything 
+            run: |
+              echo "Difference between warning count in PR is greater than in master."
 
 

.github/workflows/coverage.yml

@@ -31,8 +31,7 @@ jobs:
         run: |
             sudo apt update -y
             sudo apt install -y tar wget make cmake gcc g++ python3 python3-dev "openmpi-*" libopenmpi-dev
-            
-      
+
       - name: Build
         run: /bin/bash mfc.sh build -j $(nproc) --gcov
 
@@ -42,7 +41,6 @@ jobs:
       - name: Upload coverage reports to Codecov
         uses: codecov/codecov-action@v4
         with:
-          token: ${{ secrets.CODECOV_TOKEN }}
           fail_ci_if_error: false
           verbose: true
         env:

.github/workflows/docs.yml

@@ -1,16 +1,17 @@
 name: Documentation
 
-on: [push, pull_request, workflow_dispatch]
+on:
+  schedule:
+    - cron: '0 0 * * *'  # This runs every day at midnight UTC
+  workflow_dispatch:
+  push:
+  pull_request:
 
 jobs:
   docs:
     name:    Build & Publish
     runs-on: ubuntu-latest
 
-    concurrency:
-      group: docs-publish
-      cancel-in-progress: true
-
     steps:
     - uses: actions/checkout@v4
 
@@ -47,7 +48,7 @@ jobs:
         echo "excluded-count = ${{ steps.sitemap.outputs.excluded-count }}"
 
     - name: Publish Documentation
-      if:   github.repository == 'MFlowCode/MFC' && github.ref == 'refs/heads/master' && github.event_name == 'push'
+      if:   github.repository == 'MFlowCode/MFC' && github.ref == 'refs/heads/master' && ( github.event_name == 'cron' || github.event_name == 'workflow_dispatch' )
       run:  |
         set +e
         git ls-remote "${{ secrets.DOC_PUSH_URL }}" -q

.github/workflows/count.yml → .github/workflows/line-count.yml

@@ -3,8 +3,25 @@ name: Check Line Counts
 on: [push, pull_request, workflow_dispatch]
 
 jobs:
+  file-changes:
+    name: Detect File Changes
+    runs-on: 'ubuntu-latest'
+    outputs: 
+      checkall: ${{ steps.changes.outputs.checkall }}
+    steps:
+      - name: Clone
+        uses: actions/checkout@v4
+
+      - name: Detect Changes
+        uses: dorny/paths-filter@v3
+        id: changes
+        with: 
+          filters: ".github/file-filter.yml"
+
   sz:
     name: Core MFC Line Difference
+    if: needs.file-changes.outputs.checkall == 'true'
+    needs: file-changes
     permissions:
       contents: read
       pull-requests: write

.github/workflows/phoenix/bench.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-n_ranks=4
+n_ranks=12
 
 if [ "$job_device" == "gpu" ]; then
     n_ranks=$(nvidia-smi -L | wc -l)        # number of GPUs on node
@@ -9,7 +9,7 @@ if [ "$job_device" == "gpu" ]; then
 fi
 
 if ["$job_device" == "gpu"]; then
-    ./mfc.sh bench --mem 8 -j $(nproc) -o "$job_slug.yaml" -- -c phoenix $device_opts -n $n_ranks
+    ./mfc.sh bench --mem 12 -j $(nproc) -o "$job_slug.yaml" -- -c phoenix $device_opts -n $n_ranks
 else
     ./mfc.sh bench --mem 1 -j $(nproc) -o "$job_slug.yaml" -- -c phoenix $device_opts -n $n_ranks
-fi
+fi