Merge pull request #103 from SotaYoshida/dev

Dev
SotaYoshida · Oct 31, 2023 · 6e137b7 · 6e137b7
2 parents adc22d7 + 11e4487
commit 6e137b7
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diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -2,13 +2,12 @@ name: CI
 on:
   push:
     branches:
-      - main
+      - dev
       - develop
     tags: '*'
-  pull_request:
+    exclude: "log_sample_script.txt"
+
 concurrency:
-  # Skip intermediate builds: always.
-  # Cancel intermediate builds: only if it is a pull request build.
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }}
 jobs:
@@ -18,30 +17,81 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        version:
-          - '1.7'
-          - 'nightly'
-        os:
-          - ubuntu-latest
-        arch:
-          - x64
+        include:
+          - {version: '1.9',   os: ubuntu-latest,  payload: serial}
+          - {version: '1.9',   os: macOS-latest,   payload: serial}
+          - {version: '1.9',   os: windows-latest, payload: serial}
     steps:
       - uses: actions/checkout@v2
       - uses: julia-actions/setup-julia@v1
         with:
           version: ${{ matrix.version }}
-          arch: ${{ matrix.arch }}
+          arch: x64
       - uses: julia-actions/cache@v1
       - uses: julia-actions/julia-buildpkg@v1
       - uses: julia-actions/julia-runtest@v1
+        env:
+          JULIA_NUM_THREADS: 2
+        if: ${{ matrix.payload == 'serial' }}
+        continue-on-error: ${{ matrix.version == 'nightly' }}
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - {version: '1.9',   os: 'ubuntu-latest',  payload: mpi}
+        mpi: [ 'openmpi' ]
+    name: mpi test
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.version }}
+          arch: x64
+      - uses: julia-actions/cache@v1
+      - uses: julia-actions/julia-buildpkg@v1
+      - name: "Run mpi tests"
+        run: |
+          export JULIA_PROJECT=@.
+          export JULIA_MPIEXEC=mpiexecjl
+          export JULIA_NUM_THREADS=1
+          julia --project -e 'ENV["JULIA_MPI_BINARY"]=""; using Pkg; Pkg.add("MPI"); Pkg.build("MPI"; verbose=true); using MPI; MPI.install_mpiexecjl()'
+          julia --project=@. -e "using InteractiveUtils; versioninfo(verbose=true)"
+          julia --project=@. -e "using Pkg; Pkg.instantiate(); Pkg.build()"
+          export PATH=$PATH:/home/runner/.julia/bin
+          mpiexecjl -n 4 julia --depwarn=yes --project=@. ./test/mpirun_test.jl	  
+  build2:    
+    runs-on: 'ubuntu-latest'
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - {version: '1.9',   os: 'ubuntu-latest'}
+    name: Run sample_script.jl
+    steps:     
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.version }}
+          arch: x64
+      - uses: julia-actions/cache@v1
+      - uses: julia-actions/julia-buildpkg@v1 
+      - run: | 
+          git_hash=$(git rev-parse --short "$GITHUB_SHA")          
+          julia --project="@." -t 4 ./example/sample_script.jl > ./example/log_sample_script.txt
+      - name: commit changed logfile
+        uses: stefanzweifel/[email protected]
+        with:
+          commit_message: Update log_sample_script.txt  
   docs:
     name: Documentation
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
       - uses: julia-actions/setup-julia@v1
         with:
-          version: '1'
+          version: '1.9'
       - uses: julia-actions/julia-buildpkg@v1
       - uses: julia-actions/julia-docdeploy@v1
         env:
@@ -53,3 +103,6 @@ jobs:
             using NuclearToolkit
             DocMeta.setdocmeta!(NuclearToolkit, :DocTestSetup, :(using NuclearToolkit); recursive=true)
             doctest(NuclearToolkit)'
+
+
+
diff --git a/.github/workflows/CI_pullrequest.yml b/.github/workflows/CI_pullrequest.yml
@@ -0,0 +1,116 @@
+name: CI_PR
+on:
+  pull_request:
+    branches:
+      - main
+      - develop
+    tags: '*'
+    exclude: "log_sample_script.txt"
+concurrency:
+  # Skip intermediate builds: always.
+  # Cancel intermediate builds: only if it is a pull request build.
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }}
+jobs:
+  test:
+    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - {version: '1.9',   os: ubuntu-latest,  payload: serial}
+          - {version: '1.9',   os: macOS-latest,   payload: serial}
+          - {version: '1.9',   os: windows-latest, payload: serial}
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.version }}
+          arch: x64
+      - uses: julia-actions/cache@v1
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-runtest@v1
+        env:
+          JULIA_NUM_THREADS: 2
+        if: ${{ matrix.payload == 'serial' }}
+        continue-on-error: ${{ matrix.version == 'nightly' }}
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - {version: '1.9',   os: ubuntu-latest,  payload: mpi}
+        mpi: [ 'openmpi' ]
+    name: mpi test
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.version }}
+          arch: x64
+      - uses: julia-actions/cache@v1
+      - uses: julia-actions/julia-buildpkg@v1
+      - name: "Run mpi tests"
+        run: |
+          export JULIA_PROJECT=@.
+          export JULIA_MPIEXEC=mpiexecjl
+          export JULIA_NUM_THREADS=1
+          julia --project -e 'ENV["JULIA_MPI_BINARY"]=""; using Pkg; Pkg.add("MPI"); Pkg.build("MPI"; verbose=true); using MPI; MPI.install_mpiexecjl()'
+          julia --project=@. -e "using InteractiveUtils; versioninfo(verbose=true)"
+          julia --project=@. -e "using Pkg; Pkg.instantiate(); Pkg.build()"
+          export PATH=$PATH:/home/runner/.julia/bin
+          mpiexecjl -n 4 julia --depwarn=yes --project=@. ./test/mpirun_test.jl	  
+
+  # build2:    
+  #   runs-on: ubuntu-latest
+  #   strategy:
+  #     fail-fast: false
+  #     matrix:
+  #       include:
+  #         - {version: '1.8',   os: ubuntu-latest}
+  #   name: Run sample_script.jl
+  #   steps:     
+  #     - uses: actions/checkout@v2
+  #       with:
+  #         fetch-depth: 0 
+  #     - uses: julia-actions/setup-julia@v1
+  #       with:
+  #         version: ${{ matrix.version }}
+  #         arch: x64
+  #     - uses: julia-actions/cache@v1
+  #     - uses: julia-actions/julia-buildpkg@v1 
+  #     - run: | 
+  #         git_hash=$(git rev-parse --short "$GITHUB_SHA")
+  #         echo git_hash $git_hash     
+  #         echo running on branch ${GITHUB_REF##*/}    
+  #         echo git_hash:[$git_hash]  > ./example/log_sample_script.txt
+  #         julia --project="@." -t 4 ./example/sample_script.jl >> ./example/log_sample_script.txt
+  #         git add example/log_sample_script.txt
+      # - name: commit changed logfile
+      #   uses: stefanzweifel/[email protected]
+      #   with:
+      #     commit_message: Update log_sample_script.txt  
+  docs:
+    name: Documentation
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: '1.9'
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-docdeploy@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}
+      - run: |
+          julia --project=docs -e '
+            using Documenter: DocMeta, doctest
+            using NuclearToolkit
+            DocMeta.setdocmeta!(NuclearToolkit, :DocTestSetup, :(using NuclearToolkit); recursive=true)
+            doctest(NuclearToolkit)'
+
+
+
diff --git a/.github/workflows/draft-pdf.yml b/.github/workflows/draft-pdf.yml
@@ -0,0 +1,26 @@
+on:
+  push:
+    paths:
+      - "paper/*"
+
+jobs:
+  paper:
+    runs-on: ubuntu-latest
+    name: Paper Draft
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+      - name: Build draft PDF
+        uses: openjournals/openjournals-draft-action@master
+        with:
+          journal: joss
+          # This should be the path to the paper within your repo.
+          paper-path: paper/paper.md
+      - name: Upload
+        uses: actions/upload-artifact@v1
+        with:
+          name: paper
+          # This is the output path where Pandoc will write the compiled
+          # PDF. Note, this should be the same directory as the input
+          # paper.md
+          path: paper/paper.pdf
diff --git a/.gitignore b/.gitignore
@@ -27,3 +27,6 @@ docs/.DS_Store
 *.snt.bin
 /snts
 /flowOmega
+logfile.dat
+*/logfile.dat
+