added kymograph to post_processing

Author: mrodrig6

.github/file-filter.yml

@@ -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']
@@ -46,8 +47,8 @@ jobs:
 
       - name: Bench (Master v. PR)
         run: |
-          (cd pr     && bash .github/workflows/phoenix/submit.sh .github/workflows/phoenix/bench.sh ${{ matrix.device }}) &
-          (cd master && bash .github/workflows/phoenix/submit.sh .github/workflows/phoenix/bench.sh ${{ matrix.device }}) &
+          (cd pr     && bash .github/workflows/phoenix/submit-bench.sh .github/workflows/phoenix/bench.sh ${{ matrix.device }}) &
+          (cd master && bash .github/workflows/phoenix/submit-bench.sh .github/workflows/phoenix/bench.sh ${{ matrix.device }}) &
           wait %1 && wait %2
 
       - name: Generate & Post Comment

.github/workflows/docs.yml

@@ -47,8 +47,14 @@ jobs:
         echo "url-count = ${{ steps.sitemap.outputs.url-count }}"
         echo "excluded-count = ${{ steps.sitemap.outputs.excluded-count }}"
 
+    - name: Linkcheck - Lychee
+      uses: lycheeverse/lychee-action@v2
+      with:
+        args: -c .lychee.toml build/install/docs/mfc/
+        fail: false
+
     - name: Publish Documentation
-      if:   github.repository == 'MFlowCode/MFC' && github.ref == 'refs/heads/master' && github.event_name == 'cron'
+      if:   github.repository == 'MFlowCode/MFC' && github.ref == 'refs/heads/master' &&  (github.event_name == 'schedule' || github.event_name == 'workflow_dispatch' )
       run:  |
         set +e
         git ls-remote "${{ secrets.DOC_PUSH_URL }}" -q

.github/workflows/formatting.yml

@@ -10,6 +10,9 @@ jobs:
     steps:
     - uses: actions/checkout@v4
 
+    - name: MFC Python setup
+      run: ./mfc.sh init
+
     - name: Check formatting
       run: |
         ./mfc.sh format -j $(nproc)

.github/workflows/frontier/build.sh

@@ -1,4 +1,4 @@
 #!/bin/bash
 
 . ./mfc.sh load -c f -m g
-./mfc.sh build -j 8 --gpu
+./mfc.sh test --dry-run -j 8 --gpu

.github/workflows/frontier/submit.sh

@@ -21,9 +21,9 @@ sbatch <<EOT
 #SBATCH -A CFD154                  # charge account
 #SBATCH -N 1                       # Number of nodes required
 #SBATCH -n 8                       # Number of cores required
-#SBATCH -t 02:00:00                # Duration of the job (Ex: 15 mins)
-#SBATCH -q debug                   # QOS Name
+#SBATCH -t 01:00:00                # Duration of the job (Ex: 15 mins)
 #SBATCH -o$job_slug.out            # Combined output and error messages file
+#SBATCH -q debug                   # Use debug QOS - only one job per user allowed in queue!
 #SBATCH -W                         # Do not exit until the submitted job terminates.
 
 set -e

.github/workflows/line-count.yml

@@ -1,4 +1,4 @@
-name: Check Line Counts
+name: Lines of Code
 
 on: [push, pull_request, workflow_dispatch]
 
@@ -49,5 +49,6 @@ jobs:
           cd $BASE
           export MFC_PR=$PR
           pwd
+          ./mfc.sh init &> tmp.txt
           ./mfc.sh count_diff
 

.github/workflows/links.yml

@@ -0,0 +1,40 @@
+name: Lint Source
+
+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"
+
+  lint-source:
+    name: Lint Source
+    runs-on: 'ubuntu-latest'
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Install Fortitude
+      run: pip install fortitude-lint ansi2txt
+
+    - name: Lint the source code
+      run:  fortitude check --file-extensions=f90,fpp,fypp --ignore=E001,S001,S101,M011,F001,S041,T001,S101 ./src/** || true
+
+    - name: Ensure kind is specified
+      run:  fortitude check --file-extensions=f90,fpp,fypp --select=P001 ./src/**
+
+    - name: No double precision intrinsics
+      run: |
+        ! grep -iR 'double_precision\|dsqrt\|dexp\|dlog\|dble\|dabs\|double\ precision\|real(8)\|real(4)\|dprod\|dmin\|dmax\|dfloat\|dreal\|dcos\|dsin\|dtan\|dsign\|dtanh\|dsinh\|dcosh\|d0' --exclude-dir=syscheck --exclude="*nvtx*" --exclude="*precision_select*" ./src/*
+

.github/workflows/lint-source.yml

@@ -1,14 +1,17 @@
-name: Lint
+name: Lint Toolchain
 
 on: [push, pull_request, workflow_dispatch]
 
 jobs:
-  docs:
+  lint-toolchain:
     name:    Lint Toolchain
     runs-on: ubuntu-latest
 
     steps:
     - uses: actions/checkout@v4
 
+    - name: MFC Python setup
+      run: ./mfc.sh init
+
     - name: Lint the toolchain
       run: ./mfc.sh lint