937 update CI actions

.github/actions/build-py/action.yml

@@ -30,8 +30,16 @@ runs:
           cp dist/*.whl wheelhouse
         fi
         cp -r wheelhouse ..
-    - name: Upload Python Wheels
+    - name: Upload Python Wheels Simulation # See Issue #939
       uses: actions/upload-artifact@v3
+      if: inputs.package == 'simulation'
+      with:
+        name: python-wheels-${{ inputs.package }}
+        path: pycode/wheelhouse
+    - name: Upload Python Wheels
+      uses: actions/upload-artifact@v4
+      if: inputs.package != 'simulation'
       with:
         name: python-wheels-${{ inputs.package }}
         path: pycode/wheelhouse
+

.github/actions/linux-benchmark/action.yml

@@ -14,7 +14,7 @@ runs:
         sudo apt-get -qq -y install libhdf5-10* wget gnupg lcov
         sudo apt-get -qq update
     - name: Download built test directory
-      uses: actions/download-artifact@v3
+      uses: actions/download-artifact@v4
       with:
         name: ${{ inputs.build-artifact }}
         path: cpp
@@ -30,7 +30,7 @@ runs:
         sudo chmod a+x abm_benchmark
         ./abm_benchmark  --benchmark_out="abm_benchmark.json" --benchmark_repetitions=10
     - name: Upload benchmark result
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       with:
         name: abm-benchmark-report
         path: cpp/build/bin/abm_benchmark.json

.github/actions/linux-build/action.yml

@@ -97,7 +97,7 @@ runs:
         cd cpp
         tar -czf build.tar.gz build
     - name: Upload built directory
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       with:
         #artifacts in one pipeline must have a different name, so options must add a suffix to the artifact name if different values are used in the same pipeline
         name: build-cpp-linux-${{ inputs.compiler }}-${{ inputs.version }}-${{ inputs.config }}${{ inputs.optional-dependencies == 'OFF' && '-nodep' || ''}}${{ inputs.openmp == 'ON' && '-omp' || ''}}

.github/actions/linux-run_examples/action.yml

@@ -14,7 +14,7 @@ runs:
         sudo apt-get -qq -y install libhdf5-10* wget gnupg lcov
         sudo apt-get -qq update
     - name: Download examples directory
-      uses: actions/download-artifact@v3
+      uses: actions/download-artifact@v4
       with:
         name: ${{ inputs.build-artifact }}
         path: cpp

.github/actions/linux-test/action.yml

@@ -1,17 +1,25 @@
 name: "Linux Test"
 description: "Run the C++ unit tests on linux."
 inputs:
-  build-artifact:
-    description: "Name of the build artifact that contains the unit test binary."
+  artifact-pattern:
+    description: "Name of the build artifact that contains the unit test binary, and coverage artifacts that will be uploaded."
     required: true
   coverage:
     description: "Create coverage report (ON or OFF)"
     required: false
     default: "OFF"
+  optional-deps:
+    description: "Optional dependencies of unit test binary (ON or OFF, default ON). If OFF, adds `-nodep` to the artifact name."
+    required: false
+    default: "ON"
   num-repeat:
     description: "Repeat tests, e.g. to catch random failures like race conditions."
     required: false
     default: "1"
+  openmp: 
+    description: "Enabled Multithreading with OpenMP (ON or OFF, default OFF). If ON, adds `-omp` to the name of the artifact."
+    required: false
+    default: "OFF"
 runs:
   using: "composite"
   steps:
@@ -22,9 +30,9 @@ runs:
         sudo apt-get -qq -y install libhdf5-10* wget gnupg lcov
         sudo apt-get -qq update
     - name: Download built test directory
-      uses: actions/download-artifact@v3
+      uses: actions/download-artifact@v4
       with:
-        name: ${{ inputs.build-artifact }}
+        name: build-cpp-linux-${{ inputs.artifact-pattern }}${{ inputs.optional-deps == 'OFF' && '-nodep' || ''}}${{ inputs.openmp == 'ON' && '-omp' || ''}}
         path: cpp
     - name: extract build archive
       shell: bash
@@ -48,16 +56,16 @@ runs:
           cmake --build . --target coverage/fast
         fi
     - name: Upload test report
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       with:
-        name: test-cpp-linux-report
+        name: test-cpp-linux-report-${{ inputs.artifact-pattern }}${{ inputs.optional-deps == 'OFF' && '-nodep' || ''}}${{ inputs.openmp == 'ON' && '-omp' || ''}}
         path: cpp/build/bin/report.xml
         if-no-files-found: error
         retention-days: 1
     - name: Upload coverage reports
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       with:
-        name: test-cpp-coverage-reports
+        name: test-cpp-coverage-reports-${{ inputs.artifact-pattern }}${{ inputs.optional-deps == 'OFF' && '-nodep' || ''}}${{ inputs.openmp == 'ON' && '-omp' || ''}}
         path: |
           cpp/build/coverage.info
           cpp/build/coverage

.github/actions/test-docs/action.yml

@@ -14,7 +14,7 @@ runs:
         cd docs
         doxygen
     - name: Upload Documentation
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       with:
         name: documentation
         path: docs/html

.github/actions/test-py/action.yml

@@ -25,25 +25,32 @@ runs:
           sudo apt-get -qq -y install python3-pip gnupg
         fi
         python -m pip install --upgrade pip
-    - name: Download Python Wheels
+    - name: Download Python Wheels Simulation
       uses: actions/download-artifact@v3
+      if: inputs.package == 'simulation' #WORKAROUND! See Issue #939
+      with:
+        name: python-wheels-${{ inputs.package }}
+        path: pycode/wheelhouse
+    - name: Download Python Wheels
+      uses: actions/download-artifact@v4
+      if: inputs.package != 'simulation'
       with:
         name: python-wheels-${{ inputs.package }}
         path: pycode/wheelhouse
     - name: Download additional Python Wheels for plot package
-      uses: actions/download-artifact@v3
+      uses: actions/download-artifact@v4
       if:  inputs.package == 'plot'
       with:
         name: python-wheels-epidata
         path: pycode/wheelhouse
     - name: Download Python Wheels for surrogatemodel
-      uses: actions/download-artifact@v3
+      uses: actions/download-artifact@v3 #WORKAROUND! Upgrade to v4 asap. See Issue #939
       if:  inputs.package == 'surrogatemodel'
       with:
         name: python-wheels-simulation
         path: pycode/wheelhouse
     - name: Set up Python ${{ inputs.version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ inputs.version }}
     - name: Install Python Wheels
@@ -80,11 +87,11 @@ runs:
           gethospitalizationdata --help
         fi
     - name: Upload coverage reports
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       with:
-        name: test-py-coverage-reports-${{ inputs.package }}
+        name: test-py-coverage-reports-${{ inputs.package }}-${{ inputs.version }}
         path: |
-          pycode/memilio-${{ inputs.package }}/**/coverage_python.xml
+          pycode/memilio-${{ inputs.package }}/**/coverage_python_${{ inputs.version }}.xml
           coverage_python
         retention-days: 7
         if-no-files-found: ${{ inputs.coverage == 'ON' && 'error' || 'ignore' }}

.github/actions/test-pylint/action.yml

@@ -14,7 +14,7 @@ runs:
         sudo apt-get -qq -y install python3-pip gnupg
         python -m pip install --upgrade pip
     - name: Download Python Wheels
-      uses: actions/download-artifact@v3
+      uses: actions/download-artifact@v4
       with:
         name: python-wheels-${{ inputs.package }}
     - name: Install Python Wheels
@@ -31,7 +31,7 @@ runs:
         python setup.py pylint
         pylint-json2html -f jsonextended -o build_pylint/pylint.html < build_pylint/pylint_extended.json
     - name: Upload Pylint Report
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       with:
         name: pylint-report-${{ inputs.package }}
         path: pycode/memilio-${{ inputs.package }}/build_pylint/pylint.html

.github/actions/windows-build/action.yml

@@ -51,7 +51,7 @@ runs:
         cmake -G "Ninja" -DCMAKE_BUILD_TYPE=${{ inputs.config }} -DMEMILIO_USE_BUNDLED_JSONCPP=${{ inputs.optional-dependencies }} -DHDF5_USE_STATIC_LIBRARIES=ON -DHDF5_DIR="${{github.workspace}}/hdf5/share/cmake/hdf5" ..
         cmake --build . -- -j 4
     - name: Upload built binary files
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       with:
         #artifacts in one pipeline must have a different name, so options must add a suffix to the artifact name if different values are used in the same pipeline
         name: build-cpp-windows-msvc-${{ inputs.version }}-${{ inputs.config }}${{ inputs.optional-dependencies == 'OFF' && '-nodep' || ''}}

.github/actions/windows-run_examples/action.yml

@@ -8,7 +8,7 @@ runs:
   using: "composite"
   steps:
     - name: Download built example directory
-      uses: actions/download-artifact@v3
+      uses: actions/download-artifact@v4
       with:
         name: ${{ inputs.build-artifact }}
         path: cpp/build-win/bin

.github/actions/windows-test/action.yml

@@ -1,26 +1,30 @@
 name: "Windows Test"
 description: "Run the C++ unit tests on Windows"
 inputs:
-  build-artifact:
-    description: "Name of the build artifact that contains the unit test binary."
+  artifact-pattern:
+    description: "Name of the build artifact that contains the unit test binary, will also be used for upload artifacts."
     required: true
+  optional-deps:
+    description: "Optional dependencies of unit test binary (ON or OFF, default ON). If OFF, adds `-nodep` to the artifact name."
+    required: false
+    default: "ON"
 runs:
   using: "composite"
   steps:
     - name: Download built test directory
-      uses: actions/download-artifact@v3
+      uses: actions/download-artifact@v4
       with:
-        name: ${{ inputs.build-artifact }}
+        name: build-cpp-windows-${{ inputs.artifact-pattern }}${{ inputs.optional-deps == 'OFF' && '-nodep' || ''}}
         path: cpp/build-win/bin
     - name: Run unit tests
       shell: pwsh
       run: |
         cd cpp/build-win/bin
         .\memilio-test.exe --gtest_output="xml:report.xml"
     - name: Upload report
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       with:
-        name: test-cpp-win-report
+        name: test-cpp-win-report-${{ inputs.artifact-pattern }}${{ inputs.optional-deps == 'OFF' && '-nodep' || ''}}
         path: |
           cpp/build-win/bin/report.xml
         retention-days: 1

.github/workflows/epidata_main.yml

@@ -22,40 +22,42 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
-    - uses: actions/setup-python@v4
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: 3.11
-    - uses: pre-commit/action@v3.0.0
+    - uses: pre-commit/action@v3.0.1
 
   build-py-epidata:
     runs-on: ubuntu-latest
-    container:
-      image: quay.io/pypa/manylinux2014_x86_64
+    container: quay.io/pypa/manylinux_2_28_x86_64
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: ./.github/actions/build-py
         with:
           package: epidata
 
   build-py-plot:
     if: github.event.pull_request.draft == false
     runs-on: ubuntu-latest
-    container:
-      image: quay.io/pypa/manylinux2014_x86_64
+    container: quay.io/pypa/manylinux_2_28_x86_64
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: ./.github/actions/build-py
         with:
           package: plot
 
   test-py-epidata:
     needs: build-py-epidata
+    strategy:
+      matrix: 
+        version: ["3.8", "3.11"]
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: ./.github/actions/test-py
         with: 
+          version: ${{ matrix.version }}
           package: epidata
           coverage: ON
 
@@ -67,17 +69,31 @@ jobs:
         version: ["3.8", "3.11"]
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: ./.github/actions/test-py
         with: 
+          version: ${{ matrix.version }}
           package: plot
           coverage: ON 
 
+  merge-artifacts:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        packages: [epidata, plot]
+    needs: [test-py-plot, test-py-epidata]
+    steps:
+      - name: merge epidata reports
+        uses: actions/upload-artifact/merge@v4
+        with:
+          name: test-py-coverage-reports-${{ matrix.packages }}
+          pattern: test-py-coverage-reports-${{ matrix.packages }}-*
+
   test-pylint-epidata:
     needs: build-py-epidata
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: ./.github/actions/test-pylint
         with:
           package: epidata
@@ -86,7 +102,7 @@ jobs:
     needs: build-py-plot
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: ./.github/actions/test-pylint
         with:
           package: plot
@@ -96,19 +112,19 @@ jobs:
     runs-on: ubuntu-latest
     continue-on-error: true
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Install dependencies
         run: |
           sudo apt-get -qq update
           sudo apt-get -qq -y install python3-pip gnupg
           python -m pip install --upgrade pip
       - name: Download Python Wheels
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
           name: python-wheels-epidata
           path: pycode/wheelhouse
       - name: Set up Python 3.11
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.11
       - name: Install Python Wheels
@@ -126,7 +142,7 @@ jobs:
           getvaccinationdata -o data_dl --no-progress-indicators
           gethospitalizationdata -o data_dl --no-progress-indicators
       - name: Upload Data
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: data
           path: |