Nymph2 2/develop

.dockerignore

@@ -0,0 +1,31 @@
+#general:
+*.swp
+*.o
+*.so
+*.a
+*.dylib
+
+#mac
+.DS_Store
+
+#from Eclipse
+.project
+.cproject
+
+#from cmake
+CMakeCache.txt
+CMakeFiles/
+Makefile
+build*/
+cbuild*/
+cmake_install.cmake
+*Dict.h
+*Dict.cxx
+Documentation/ReferenceGuide/Doxyfile
+Source/Main/ExtractEvents
+Source/Main/SimpleElectronHunt
+Source/Applications/Main/SimpleElectronHunt
+install_manifest.txt
+
+# from emacs
+*~

.github/workflows/build.yaml

@@ -0,0 +1,257 @@
+name: Build and Test Nymph
+
+on:
+  pull_request:
+  push:
+    branches: [main, develop]
+    tags: ['*']
+
+env:
+  Nymph_BUILD_NYMPH_EXE: ON
+  Nymph_ENABLE_EXECUTABLES: ON
+  Nymph_ENABLE_PYTHON: OFF
+  Nymph_ENABLE_TESTING: ON
+  Nymph_SINGLETHREADED: OFF
+  Nymph_BUILD_TYPE: Debug
+  Nymph_TAG: test
+  NARG: 2
+
+jobs:
+
+  docker_build:
+    name: Build and Test in Docker
+
+    runs-on: ubuntu-latest
+
+    steps:
+
+      - name: Checkout the repo 
+        uses: actions/checkout@v4
+        with:
+          submodules: recursive
+
+      - name: Build
+        id: build
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          push: false
+          load: true
+          build-args: |
+            img_repo=${{ env.BASE_IMAGE_REPO }}
+            img_tag=${{ env.BASE_IMAGE_TAG }}
+            build_type=${{ env.Nymph_BUILD_TYPE }}
+            build_tests_exe=${{ env.Nymph_ENABLE_TESTING }}
+            nymph_tag=${{ env.Nymph_TAG }}
+            narg=${{ env.NARG }}
+          platforms: linux/amd64
+          tags: ${{ env.Nymph_TAG }}
+
+      - name: Unit Tests
+        run: |
+          docker run --rm ${{ env.Nymph_TAG }} bash -c "/usr/local/p8/nymph/${{ env.Nymph_TAG }}/bin/RunTests"
+
+
+  build_cpp:
+    name: Build and Test Cpp
+
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macOS-latest]
+        python-version: [3]
+
+    steps:
+
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          submodules: recursive
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Mac Dependencies
+        if: startsWith(matrix.os, 'macos')  # Mac only
+        run: |
+          brew install \
+            boost \
+            rapidjson \
+            yaml-cpp
+          sudo mkdir -p /usr/local/include && \
+            sudo chown -R $(whoami) /usr/local/include
+          sudo mkdir -p /usr/local/lib && \
+            sudo chown -R $(whoami) /usr/local/lib
+          sudo mkdir -p /usr/local/bin && \
+            sudo chown -R $(whoami) /usr/local/bin
+          sudo mkdir -p /usr/local/share && \
+            sudo chown -R $(whoami) /usr/local/share
+          git clone https://github.com/pybind/pybind11.git
+          cd pybind11
+          git checkout v3.0.0
+          mkdir build
+          cd build
+          cmake -DPYBIND11_TEST=FALSE ..
+          make -j${{ env.NARG }} install
+
+      - name: Linux Dependencies
+        if: startsWith(matrix.os, 'ubuntu')  # Linux only
+        run: |
+          sudo apt-get update
+          sudo apt-get install -yq \
+            libboost-all-dev \
+            libyaml-cpp-dev \
+            rapidjson-dev
+          git clone https://github.com/pybind/pybind11.git
+          cd pybind11
+          git checkout v3.0.0
+          mkdir build
+          cd build
+          sudo cmake -DPYBIND11_TEST=FALSE ..
+          sudo make -j${{ env.NARG }} install
+          cd ../..
+          pip install "pybind11[global]"
+
+      - name: Configure CMake
+        run: |
+          mkdir -p build
+          cd build
+          cmake -DCMAKE_BUILD_TYPE=${Nymph_BUILD_TYPE} \
+            -DNymph_BUILD_NYMPH_EXE=${Nymph_BUILD_NYMPH_EXE} \
+            -DNymph_ENABLE_EXECUTABLES=${Nymph_ENABLE_EXECUTABLES} \
+            -DNymph_ENABLE_PYTHON=${Nymph_ENABLE_PYTHON} \
+            -DNymph_ENABLE_TESTING=${Nymph_ENABLE_TESTING} \
+            -DNymph_SINGLETHREADED=${Nymph_SINGLETHREADED} \
+            ..
+
+      - name: CMake Build
+        run: |
+          cd build
+          make -j${{ env.NARG }} install
+
+      - name: Run tests
+        run: |
+          cd build
+          Testing/RunTests
+
+      - name: Build CppRepo Example
+        env:
+          Nymph_ENABLE_TESTING: OFF
+          Nymph_TAG: nymph2_2/cppexample
+        run: |
+          cd Examples/CppRepo
+          ./BUILD_ME.sh
+
+  build_python:
+    name: Build and Test Python
+
+    runs-on: ${{ matrix.os }}
+
+    env:
+      Nymph_ENABLE_PYTHON: ON
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macOS-latest]
+        python-version: [3]
+
+    steps:
+
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          submodules: recursive
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Mac Dependencies
+        if: startsWith(matrix.os, 'macos')  # Mac only
+        run: |
+          brew install \
+            boost \
+            rapidjson \
+            yaml-cpp
+          sudo mkdir -p /usr/local/include && \
+            sudo chown -R $(whoami) /usr/local/include
+          sudo mkdir -p /usr/local/lib && \
+            sudo chown -R $(whoami) /usr/local/lib
+          sudo mkdir -p /usr/local/bin && \
+            sudo chown -R $(whoami) /usr/local/bin
+          sudo mkdir -p /usr/local/share && \
+            sudo chown -R $(whoami) /usr/local/share
+          git clone https://github.com/pybind/pybind11.git
+          cd pybind11
+          git checkout v3.0.0
+          mkdir build
+          cd build
+          cmake -DPYBIND11_TEST=FALSE ..
+          make -j${{ env.NARG }} install
+
+      - name: Linux Dependencies
+        if: startsWith(matrix.os, 'ubuntu')  # Linux only
+        run: |
+          sudo apt-get update
+          sudo apt-get install -yq \
+            libboost-all-dev \
+            libyaml-cpp-dev \
+            rapidjson-dev
+          git clone https://github.com/pybind/pybind11.git
+          cd pybind11
+          git checkout v3.0.0
+          mkdir build
+          cd build
+          sudo cmake -DPYBIND11_TEST=FALSE ..
+          sudo make -j${{ env.NARG }} install
+
+      - name: Build Nymph/Cpp
+        run: |
+          mkdir -p build
+          cd build
+          cmake -DCMAKE_BUILD_TYPE=${Nymph_BUILD_TYPE} \
+            -DNymph_BUILD_NYMPH_EXE=${Nymph_BUILD_NYMPH_EXE} \
+            -DNymph_ENABLE_EXECUTABLES=${Nymph_ENABLE_EXECUTABLES} \
+            -DNymph_ENABLE_PYTHON=${Nymph_ENABLE_PYTHON} \
+            -DNymph_ENABLE_TESTING=${Nymph_ENABLE_TESTING} \
+            -DNymph_SINGLETHREADED=${Nymph_SINGLETHREADED} \
+            -DPBUILDER_PY_INSTALL_IN_SITELIB=TRUE \
+            ..
+          make -j${{ env.NARG }} install
+
+      - name: Install Nymph/Python
+        run: |
+          env
+          pip -v install -e .
+
+      - name: Run Tests
+        run: |
+          cd Testing/Python/Bindings
+          python -m unittest discover -v
+
+# eventually include these tests
+#          cd ../nymph
+#          python -m unittest discover -v
+
+      - name: Build PyRepo Example
+        env:
+          Nymph_ENABLE_TESTING: OFF
+          Nymph_ENABLE_PYTHON: ON
+          Nymph_TAG: nymph2_2/cppexample
+        run: |
+          cd Examples/PyRepo
+          ./BUILD_ME.sh
+          hello-world
+
+
+# For debugging
+      - name: Setup tmate session
+        if: ${{ ! success() }}
+        uses: mxschmitt/action-tmate@v3
+

.gitignore

@@ -1,31 +1,49 @@
-#general:
-*.swp
+# from emacs
+*~
+
+# Compiled Object files
+*.slo
+*.lo
 *.o
+*.obj
+
+# Precompiled Headers
+*.gch
+*.pch
+
+# Compiled Dynamic libraries
 *.so
-*.a
 *.dylib
+*.dll
 
-#mac
-.DS_Store
+# Fortran module files
+*.mod
+*.smod
 
-#from Eclipse
+# Compiled Static libraries
+*.lai
+*.la
+*.a
+*.lib
+
+# Executables
+*.exe
+*.out
+*.app
+
+# Eclipse
 .project
 .cproject
+.settings/
 
-#from cmake
-CMakeCache.txt
-CMakeFiles/
-Makefile
+# VSCode
+.vscode/
+
+# Build directories
 build*/
-cbuild*/
-cmake_install.cmake
-*Dict.h
-*Dict.cxx
-Documentation/ReferenceGuide/Doxyfile
-Source/Main/ExtractEvents
-Source/Main/SimpleElectronHunt
-Source/Applications/Main/SimpleElectronHunt
-install_manifest.txt
 
-# from emacs
-*~
+# Python Package
+dist*/
+Python/*.egg-info
+Examples/PyRepo/*.egg-info
+__pycache__

.gitmodules

@@ -1,3 +1,6 @@
 [submodule "Scarab"]
 	path = Scarab
 	url = https://github.com/project8/scarab
+[submodule "External/cereal"]
+	path = External/cereal
+	url = https://github.com/USCiLab/cereal.git

AUTHORS

@@ -4,8 +4,10 @@ Authors and Copyright Holders for Nymph
 Individuals
 -----------
 Noah S. Oblath [1]
+Benjamin H. LaRoque [2]
 
 
 Institutions
 ------------
 1. Pacific Northwest National Laboratory, Richland, WA
+2. University of California, Santa Barbara, CA