Easy Install and MISC Fix

.github/tests/test-DataIO/DataIOTest.py

@@ -24,7 +24,7 @@ def yt_inline_ProjectionPlot( fields ):
     # Do yt operation
     prjz = yt.ProjectionPlot(ds, 'z', fields)
 
-    # Include this line, otherwise yt will save one copy in each rank.
+    # Save figure only on root process
     if yt.is_root():
         prjz.save()
 
@@ -37,13 +37,6 @@ def yt_inline_ProfilePlot():
 
 def yt_inline_ParticlePlot():
     ds = yt_libyt.libytDataset()
-
-    ## ParticleProjectionPlot
-    #==========================
-    # par = yt.ParticleProjectionPlot(ds, "z")
-
-    ## ParticlePlot
-    #==========================
     par = yt.ParticlePlot(ds, "particle_position_x", "particle_position_y", "Level", center = 'c')
 
     if yt.is_root():

.github/workflows/cmake-build-test.yml

@@ -1,4 +1,4 @@
-# Test if it can run on multiplatform and both in serial (gcc) and parallel (openmpi)
+# Test if libyt can build with different options, download dependencies, and install and link correctly.
 
 name: CMake Build Test
 
@@ -24,80 +24,74 @@ jobs:
         platform:
           - os: ubuntu-latest
             mpi: 'openmpi'
-          - os: macos-latest
+            check_shared_lib: ldd lib/libyt.so
+          - os: macos-12
             mpi: 'mpich'
+            check_shared_lib: otool -l lib/libyt.dylib
         python-version: ['3.7', '3.8', '3.9', '3.10', '3.11', '3.12']
 
     steps:
       - name: Checkout libyt repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: CMake Version
         run: cmake --version
 
       - name: Setup Python ${{ matrix.python-version }} environment
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
           architecture: 'x64'
           cache: 'pip'
       - run: |
           python -m pip install --upgrade pip
-          pip install -r ${{ github.workspace }}/.github/tools/requirements.txt
+          pip install numpy
 
       - name: Setup MPI environment
         uses: mpi4py/setup-mpi@v1
         with:
           mpi: ${{ matrix.platform.mpi }}
 
-      - name: Install yt, mpi4py, and yt_libyt
-        run: |
-          pip install mpi4py yt
-          pip install yt-libyt
-
       - name: Update GitHub Environment Variables
         run: |
-          echo "LIBYT_PARALLEL_INSTALL_PATH=${{ github.workspace }}/libyt_parallel" >> $GITHUB_ENV
-          echo "LIBYT_SERIAL_INSTALL_PATH=${{ github.workspace }}/libyt_serial" >> $GITHUB_ENV
+          echo "LIBYT_TEST_INSTALL_FOLDER=${{ github.workspace }}/libyt_installation" >> $GITHUB_ENV
 
-      - name: Build libyt -- Parallel (MPI)
+      - name: Test Option -DSERIAL_MODE=ON
         run: | 
           cd ${{ github.workspace }}
           rm -rf build
-          cmake -B build -S .
+          cmake -B build -S . -DSERIAL_MODE=ON
           cmake --build build
-          cmake --install build --prefix "${{ env.LIBYT_PARALLEL_INSTALL_PATH }}"
+          cmake --install build --prefix "${{ env.LIBYT_TEST_INSTALL_FOLDER }}/libyt-serial-on"
+          cd "${{ env.LIBYT_TEST_INSTALL_FOLDER }}/libyt-serial-on"
+          ${{ matrix.platform.check_shared_lib }}
 
-      - name: Build libyt -- Serial (GCC)
+      - name: Test Option -DINTERACTIVE_MODE=ON
         run: | 
           cd ${{ github.workspace }}
-          rm -rf build-serial
-          cmake -B build-serial -S . -DSERIAL_MODE=ON
-          cmake --build build-serial
-          cmake --install build-serial --prefix "${{ env.LIBYT_SERIAL_INSTALL_PATH }}"
-
-      - name: Prepare Test
-        run: |
-          cd ${{ github.workspace }}/example
-          cp ${{ github.workspace }}/.github/tests/test-DataIO/DataIOTest.py .
-
-      - name: Generate Density Data for Testing
-        run: |
-          cd ${{ github.workspace }}/example
-          cp ${{ github.workspace }}/.github/tools/generate_density_data.cpp .
-          g++ -o generate_density_data generate_density_data.cpp
-          ./generate_density_data
+          rm -rf build
+          cmake -B build -S . -DINTERACTIVE_MODE=ON
+          cmake --build build
+          cmake --install build --prefix "${{ env.LIBYT_TEST_INSTALL_FOLDER }}/libyt-interactive-on"
+          cd "${{ env.LIBYT_TEST_INSTALL_FOLDER }}/libyt-interactive-on"
+          ${{ matrix.platform.check_shared_lib }}
 
-      - name: Test Run and DataIO Test - example - Serial
+      - name: Test Option -DJUPYTER_KERNEL=ON
         run: |
-          cd ${{ github.workspace }}/example
-          make clean
-          make OPTIONS=-DSERIAL_MODE LIBYT_PATH="${{ env.LIBYT_SERIAL_INSTALL_PATH }}"
-          ./example DataIOTest.py
+          cd ${{ github.workspace }}
+          rm -rf build
+          cmake -B build -S . -DJUPYTER_KERNEL=ON
+          cmake --build build
+          cmake --install build --prefix "${{ env.LIBYT_TEST_INSTALL_FOLDER }}/libyt-jupyter-on"
+          cd "${{ env.LIBYT_TEST_INSTALL_FOLDER }}/libyt-jupyter-on"
+          ${{ matrix.platform.check_shared_lib }}
 
-      - name: Test Run and DataIO Test - example - Parallel (MPI 3)
+      - name: Test Option -DSUPPORT_TIMER=ON
         run: |
-          cd ${{ github.workspace }}/example
-          make clean
-          make LIBYT_PATH="${{ env.LIBYT_PARALLEL_INSTALL_PATH }}"
-          OMPI_MCA_osc=sm,pt2pt mpirun -np 3 ./example DataIOTest.py
+          cd ${{ github.workspace }}
+          rm -rf build
+          cmake -B build -S . -DSUPPORT_TIMER=ON
+          cmake --build build
+          cmake --install build --prefix "${{ env.LIBYT_TEST_INSTALL_FOLDER }}/libyt-timer-on"
+          cd "${{ env.LIBYT_TEST_INSTALL_FOLDER }}/libyt-timer-on"
+          ${{ matrix.platform.check_shared_lib }}

.github/workflows/example-test-run.yml

@@ -0,0 +1,102 @@
+# Test if example can run on multiplatform and both in serial (gcc) and parallel (openmpi)
+
+name: Example Test Run
+
+on:
+  push:
+    branches: [ main ]
+    paths-ignore:
+      - 'doc/**'
+      - '**.md'
+  pull_request:
+    branches: [ main ]
+    paths-ignore:
+      - 'doc/**'
+      - '**.md'
+  workflow_dispatch:
+
+jobs:
+  example-test-run:
+    runs-on: ${{ matrix.platform.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        platform:
+          - os: ubuntu-latest
+            mpi: 'openmpi'
+          - os: macos-12
+            mpi: 'mpich'
+        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11', '3.12']
+
+    steps:
+      - name: Checkout libyt repo
+        uses: actions/checkout@v4
+
+      - name: CMake Version
+        run: cmake --version
+
+      - name: Setup Python ${{ matrix.python-version }} environment
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          architecture: 'x64'
+          cache: 'pip'
+      - run: |
+          python -m pip install --upgrade pip
+          pip install -r ${{ github.workspace }}/.github/tools/requirements.txt
+
+      - name: Setup MPI environment
+        uses: mpi4py/setup-mpi@v1
+        with:
+          mpi: ${{ matrix.platform.mpi }}
+
+      - name: Install yt, mpi4py, and yt_libyt
+        run: |
+          pip install mpi4py yt yt_libyt
+
+      - name: Update GitHub Environment Variables
+        run: |
+          echo "LIBYT_PARALLEL_INSTALL_PATH=${{ github.workspace }}/libyt_parallel" >> $GITHUB_ENV
+          echo "LIBYT_SERIAL_INSTALL_PATH=${{ github.workspace }}/libyt_serial" >> $GITHUB_ENV
+
+      - name: Build libyt -- Parallel (MPI)
+        run: | 
+          cd ${{ github.workspace }}
+          rm -rf build
+          cmake -B build -S . -DINTERACTIVE_MODE=ON -DJUPYTER_KERNEL=ON
+          cmake --build build
+          cmake --install build --prefix "${{ env.LIBYT_PARALLEL_INSTALL_PATH }}"
+
+      - name: Build libyt -- Serial (GCC)
+        run: | 
+          cd ${{ github.workspace }}
+          rm -rf build-serial
+          cmake -B build-serial -S . -DSERIAL_MODE=ON -DINTERACTIVE_MODE=ON -DJUPYTER_KERNEL=ON
+          cmake --build build-serial
+          cmake --install build-serial --prefix "${{ env.LIBYT_SERIAL_INSTALL_PATH }}"
+
+      - name: Prepare Test
+        run: |
+          cd ${{ github.workspace }}/example/amr-example
+          cp ${{ github.workspace }}/.github/tests/test-DataIO/DataIOTest.py .
+
+      - name: Generate Density Data for Testing
+        run: |
+          cd ${{ github.workspace }}/example/amr-example
+          cp ${{ github.workspace }}/.github/tools/generate_density_data.cpp .
+          g++ -o generate_density_data generate_density_data.cpp
+          ./generate_density_data
+
+      - name: Test Run and DataIO Test - example - Serial
+        run: |
+          cd ${{ github.workspace }}/example/amr-example
+          make clean
+          make OPTIONS=-DSERIAL_MODE LIBYT_PATH="${{ env.LIBYT_SERIAL_INSTALL_PATH }}"
+          ./example DataIOTest.py
+
+      - name: Test Run and DataIO Test - example - Parallel (MPI Size 3)
+        run: |
+          cd ${{ github.workspace }}/example/amr-example
+          make clean
+          make LIBYT_PATH="${{ env.LIBYT_PARALLEL_INSTALL_PATH }}"
+          OMPI_MCA_osc=sm,pt2pt mpirun -np 3 ./example DataIOTest.py

.gitignore

@@ -2,4 +2,11 @@
 *.pyc
 libyt.so
 libyt.so.*
-doc/_site
+doc/_site
+doc/_build/
+vendor/cppzmq/
+vendor/nlohmann_json/
+vendor/xeus/
+vendor/xeus-zmq/
+vendor/xtl/
+vendor/libzmq/

CMakeLists.txt

@@ -10,9 +10,14 @@ option(JUPYTER_KERNEL    "Use Jupyter notebook interface"
 option(SUPPORT_TIMER     "Support time profiling"                                                             OFF)
 
 ## set paths ##
+# It is recommended that we always provide PYTHON_PATH and MPI_PATH.
+# libyt will also try to find the package if the paths weren't provided.
 set(PYTHON_PATH    "" CACHE PATH "Path to Python installation prefix (Always)")
 set(MPI_PATH       "" CACHE PATH "Path to MPI installation prefix (-DSERIAL_MODE=OFF)")
 set(READLINE_PATH  "" CACHE PATH "Path to Readline installation prefix (-DINTERACTIVE_MODE=ON)")
+
+## set paths (optional) ##
+# libyt will get the dependencies if it cannot find one when needed.
 set(nlohmann_json_DIR "" CACHE PATH "Path to nlohmann_jsonConfig.cmake (-DJUPYTER_KERNEL=ON)")
 set(cppzmq_DIR        "" CACHE PATH "Path to cppzmqConfig.cmake (-DJUPYTER_KERNEL=ON)")
 set(xtl_DIR           "" CACHE PATH "Path to xtlConfig.cmake (-DJUPYTER_KERNEL=ON)")
@@ -26,35 +31,19 @@ set(CMAKE_CXX_STANDARD 14)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 
 ## build static/shared library ##
-option(BUILD_SHARED_LIBS "Building using shared libraries"    ON )
+option(BUILD_SHARED_LIBS "Building using shared libraries"                                                    ON )
 
 ## find dependencies ##
+set(Python_ROOT_DIR ${PYTHON_PATH})
+find_package(Python 3.7 COMPONENTS Development NumPy REQUIRED)
+
 if (NOT SERIAL_MODE)
     set(MPI_HOME ${MPI_PATH})
     find_package(MPI REQUIRED)
 endif ()
 
-if (JUPYTER_KERNEL)
-    find_package(xeus-zmq 1.0 REQUIRED)
-endif ()
-
-set(Python_ROOT_DIR ${PYTHON_PATH})
-find_package(Python COMPONENTS Development NumPy REQUIRED)
-
-## config files ##
-if (JUPYTER_KERNEL)
-    set(LIBYT_KERNELSPEC_RELATIVE_PATH "share/jupyter/kernels/libyt_kernel")
-    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${LIBYT_KERNELSPEC_RELATIVE_PATH}/kernel.json
-                   ./${LIBYT_KERNELSPEC_RELATIVE_PATH}/kernel.json COPYONLY)
-endif ()
-
 ## sub directory ##
+add_subdirectory(vendor)                    # for vendoring
 add_subdirectory(src)                       # for library
-#add_subdirectory(example)                   # for example exe
-
-###### INSTALLATION RULE ###############################################################################################
-if (JUPYTER_KERNEL)
-    include(GNUInstallDirs)
-    install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${LIBYT_KERNELSPEC_RELATIVE_PATH}/kernel.json
-            DESTINATION "${LIBYT_KERNELSPEC_RELATIVE_PATH}")
-endif ()
+add_subdirectory(share)                     # for share
+add_subdirectory(example)                   # for example exe

README.md

@@ -1,5 +1,6 @@
 # libyt
-[![CMake Build Test](https://github.com/yt-project/libyt/actions/workflows/cmake-build-test.yml/badge.svg)](https://github.com/yt-project/libyt/actions/workflows/cmake-build-test.yml)
+[![CMake Build Test](https://github.com/yt-project/libyt/actions/workflows/cmake-build-test.yml/badge.svg?branch=main)](https://github.com/yt-project/libyt/actions/workflows/cmake-build-test.yml)
+[![Example Test Run](https://github.com/yt-project/libyt/actions/workflows/example-test-run.yml/badge.svg?branch=main)](https://github.com/yt-project/libyt/actions/workflows/example-test-run.yml)
 [![Documentation Status](https://readthedocs.org/projects/libyt/badge/?version=latest)](https://libyt.readthedocs.io/en/latest/?badge=latest)
 
 `libyt` is an open source C library for simulation, that allows researchers to analyze and visualize data using [`yt`](https://yt-project.org/) or other Python packages in parallel during simulation runtime. In this way, we can skip the step of writing data to local disk before doing analysis using Python. This greatly reduce the disk usage, and increase the temporal resolution.