Merge pull request #34 from thermotools/prep_merge

New functionality
thermotools · Nov 8, 2024 · 529cc57 · 529cc57
2 parents f03d317 + d088835
commit 529cc57
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diff --git a/release_bodyFile.md → .github/release_bodyFile.md b/release_bodyFile.md → .github/release_bodyFile.md
diff --git a/.github/workflows/cibuildwheel.yml b/.github/workflows/cibuildwheel.yml
@@ -7,9 +7,13 @@ jobs:
     name: Build wheels on ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
     strategy:
+      fail-fast: false
       matrix:
-        os: [windows-latest, macOS-latest] 
-
+        os: [windows-latest, macOS-latest, ubuntu-latest] 
+    env:
+      THERMOPACK_DIR: thermopack-${{ matrix.os }}
+      THERMOPACK_DIR_WINDOWS: "D:/a/KineticGas/KineticGas/thermopack-windows-latest/thermopack-windows-latest"
+      THERMOPACK_URL: https://github.com/vegardjervell/thermopack/releases/download/Latest-beta
     steps:
       - uses: actions/checkout@v4
       - name: checkout submodules
@@ -18,20 +22,38 @@ jobs:
       # Used to host cibuildwheel
       - uses: actions/setup-python@v4
 
-      - name: Install cibuildwheel and other dependencies
-        run: python -m pip install cibuildwheel==2.17.0 build wheel setuptools
+      - name: Fetch Thermopack
+        if: matrix.os != 'windows-latest'
+        run: |
+            curl -L -o thermopack.zip ${{ env.THERMOPACK_URL }}/thermopack-${{ matrix.os }}.zip
+            unzip thermopack.zip
+            export THERMOPACK_DIR=${PWD}/${{ env.THERMOPACK_DIR }}/
+            curl -L -o thermopack_whl.zip ${{ env.THERMOPACK_URL }}/wheel-v2-${{ matrix.os }}.zip
+            unzip thermopack_whl.zip
+            pip install wheel-v2-${{ matrix.os }}/*
 
-      - name: Build sdist
-        run: pipx run build --sdist --outdir wheelhouse
-        if: runner.os == 'Windows'
+      - name: Fetch Thermopack (Windows)
+        if: matrix.os == 'windows-latest'
+        shell: pwsh
+        run: |
+          Invoke-WebRequest -Uri "${{ env.THERMOPACK_URL }}/thermopack-${{ matrix.os }}.zip" -OutFile "thermopack.zip"
+          Expand-Archive -Path "thermopack.zip" -DestinationPath "${{ env.THERMOPACK_DIR }}"
+          $THERMOPACK_DIR = "${PWD}/${{ env.THERMOPACK_DIR }}/${{ env.THERMOPACK_DIR }}"
+          [System.Environment]::SetEnvironmentVariable("THERMOPACK_DIR", $THERMOPACK_DIR)
+          "$THERMOPACK_DIR=$THERMOPACK_DIR" | Out-File -FilePath $env:GITHUB_ENV -Append
+          Invoke-WebRequest -Uri "${{ env.THERMOPACK_URL }}/wheel-v2-${{ matrix.os }}.zip" -OutFile "thermopack_whl.zip"
+          Expand-Archive -Path "thermopack_whl.zip" -DestinationPath "wheel-v2-${{ matrix.os }}"
+          cd wheel-v2-${{ matrix.os }}
+          pip install (Get-ChildItem wheel-v2-windows-latest\*.whl).FullName
 
       - name: Build wheels
         uses: pypa/[email protected] # run: python -m cibuildwheel --output-dir wheelhouse
         env:
           CIBW_ARCHS: auto64
           CIBW_ARCHS_MACOS: "universal2"
-          CIBW_ENVIRONMENT_MACOS: MACOSX_DEPLOYMENT_TARGET=11.0
-          CIBW_ENVIRONMENT_LINUX: CXXFLAGS='-fconcepts'
+          CIBW_ENVIRONMENT_MACOS: MACOSX_DEPLOYMENT_TARGET=11.0 THERMOPACK_DIR=${PWD}/${{ env.THERMOPACK_DIR }}
+          CIBW_ENVIRONMENT_LINUX: CXXFLAGS='-fconcepts' THERMOPACK_DIR=${PWD}/${{ env.THERMOPACK_DIR }}
+          CIBW_ENVIRONMENT_WINDOWS: THERMOPACK_DIR=${{ env.THERMOPACK_DIR_WINDOWS}}
           CIBW_BUILD_VERBOSITY_WINDOWS: 2
           CIBW_SKIP: "*pypy* *pp* *cp36* *cp37* *musl*"
         with:
@@ -56,7 +78,7 @@ jobs:
          pattern: wheels-*
 
   release_wheels: # Create or update the release tagged Latest-beta, and upload wheels to that release.
-    if: ${{ github.event.pull_request.merged }}
+    # if: github.ref == 'refs/heads/main' && github.event_name == 'push'
     needs: build_wheels
     runs-on: ubuntu-latest
     permissions:
@@ -91,7 +113,7 @@ jobs:
         tag: Latest-beta
         commit: main
         makeLatest: true
-        bodyFile: "release_bodyFile.md"
+        bodyFile: ".github/release_bodyFile.md"
         artifacts: "wheels-*.zip"
 
 
diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml
@@ -0,0 +1,85 @@
+name: Run Tests
+on: push
+
+jobs:
+    test:
+        name: Test on ${{ matrix.os }}
+        runs-on: ${{ matrix.os }}
+        strategy:
+            fail-fast: false
+            matrix:
+                os: [macOS-latest, macOS-12, ubuntu-latest, windows-latest]
+        env:
+          THERMOPACK_DIR: thermopack-${{ matrix.os }}
+          THERMOPACK_URL: https://github.com/vegardjervell/thermopack/releases/download/Latest-beta
+        steps:
+            - uses: actions/checkout@v4
+            - name: checkout submodules
+              run: git submodule update --init --recursive
+
+            # Used to host cibuildwheel
+            - uses: actions/setup-python@v4
+
+            - name: Install thermopack
+              if: matrix.os != 'windows-latest'
+              run: |
+                curl -L -o thermopack.zip ${{ env.THERMOPACK_URL }}/thermopack-${{ matrix.os }}.zip
+                unzip thermopack.zip
+                export THERMOPACK_DIR=${PWD}/thermopack-${{ matrix.os }}/
+                curl -L -o thermopack_whl.zip ${{ env.THERMOPACK_URL }}/wheel-v2-${{ matrix.os }}.zip
+                unzip thermopack_whl.zip
+                pip install wheel-v2-${{ matrix.os }}/*
+            
+            - name: Build KineticGas
+              if: matrix.os != 'windows-latest'
+              run: |
+                echo "THERMOPACK_DIR (GH_ENV) : ${{ env.THERMOPACK_DIR }} / (ENV) ${THERMOPACK_DIR}"
+                export THERMOPACK_DIR=${PWD}/${{ env.THERMOPACK_DIR }}
+                ls -R ${THERMOPACK_DIR}
+                mkdir build
+                cd build
+                cmake ..
+                make -j4 install
+
+            - name: Install thermopack Windows
+              if: matrix.os == 'windows-latest'
+              shell: pwsh
+              run: |
+                Invoke-WebRequest -Uri "${{ env.THERMOPACK_URL }}/wheel-v2-${{ matrix.os }}.zip" -OutFile "thermopack_whl.zip"
+                Expand-Archive -Path "thermopack_whl.zip" -DestinationPath "wheel-v2-${{ matrix.os }}"
+                cd wheel-v2-${{ matrix.os }}
+                pip install (Get-ChildItem wheel-v2-windows-latest\*.whl).FullName
+
+            - name: Build KineticGas Windows
+              if: matrix.os == 'windows-latest'
+              shell: pwsh
+              run: |
+                Invoke-WebRequest -Uri "${{ env.THERMOPACK_URL }}/thermopack-${{ matrix.os }}.zip" -OutFile "thermopack.zip"
+                Expand-Archive -Path "thermopack.zip" -DestinationPath "${{ env.THERMOPACK_DIR }}"
+                $THERMOPACK_DIR = "$PWD\${{ env.THERMOPACK_DIR }}\thermopack-${{ matrix.os }}"
+                [System.Environment]::SetEnvironmentVariable("THERMOPACK_DIR", $THERMOPACK_DIR)
+                ls -R ${THERMOPACK_DIR}
+                mkdir build
+                cd build
+                cmake ..
+                cmake --build . --config=Release --target install
+            
+            - name: Build KineticGas Windows
+              if: matrix.os == 'windows-latest'
+              shell: pwsh
+              run: |
+                pip install .
+                $THERMOPACK_DIR = "$PWD/${{ env.THERMOPACK_DIR }}"
+                mkdir build
+                cd build
+                cmake ..
+                cmake --build . --config=Release --target install
+
+            - name: Inspect libpykingas
+              if: matrix.os != 'ubuntu-latest' && matrix.os != 'windows-latest'
+              run: otool -L pykingas/libpykingas.*
+
+            - name: Run pytests
+              run: |
+                pip install .[test]
+                pytest tests/
diff --git a/.gitignore b/.gitignore
@@ -9,8 +9,10 @@ venv/
 venv*/
 pypi_release/wheelhouse/*.whl
 *__pycache__/
+pypi_release/dist/
 
 build/
+pykingas/fluids/
 pykingas.egg-info/
 venv*
 rebuild.sh
@@ -19,4 +21,5 @@ rebuild.sh
 *.mplstyle
 sandbox/*
 sandbox/archive/*
-*.so
+*.so
+*.dylib
diff --git a/.gitmodules b/.gitmodules
@@ -1,3 +1,15 @@
 [submodule "cpp/external/pybind11"]
 	path = cpp/external/pybind11
 	url = https://github.com/pybind/pybind11.git
+[submodule "cpp/external/json"]
+	path = cpp/external/json
+	url = https://github.com/nlohmann/json.git
+[submodule "cpp/external/eigen"]
+	path = cpp/external/eigen
+	url = https://gitlab.com/libeigen/eigen.git
+[submodule "cpp/external/autodiff"]
+	path = cpp/external/autodiff
+	url = https://github.com/autodiff/autodiff.git
+[submodule "cpp/external/thermopack"]
+	path = cpp/external/thermopack
+	url = https://github.com/thermotools/thermopack.git
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -2,25 +2,110 @@ cmake_minimum_required(VERSION 3.16)
 cmake_policy(VERSION 3.12)
 project(KineticGas LANGUAGES C CXX)
 
+string(ASCII 27 Esc)
+set(ColorDefault "${Esc}[0m")
+set(ColorBlue "${Esc}[34m")
+set(ColorYellow "${Esc}[93m")
+set(ColorRed "${Esc}[31m")
+set(ColorDefault "${Esc}[0m")
+
+option(build "Recompile KineticGas?" ON) # If set to off, assumes that KineticGas is installed and does nothing. Useful in combination with pip
+if(NOT build)
+  message(STATUS "Assuming KineticGas is already built and installed. Exiting ...")
+  message(STATUS "${ColorBlue}To disable this behaviour, clear the CMakeCache and re-run cmake.${ColorDefault}")
+  return()
+endif()
+
+if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
+    message(STATUS "No build type specified, defaulting to Release")
+    set(CMAKE_BUILD_TYPE "Release" CACHE STRING "Build type" FORCE)
+endif()
+
 SET(CMAKE_CXX_STANDARD 17)
 
 # Find the module development requirements (requires FindPython from 3.17 or scikit-build-core's built-in backport)
 set(Python_FIND_VIRTUALENV ONLY)
 
 if(NOT MSVC)
-  set(CMAKE_CXX_FLAGS "-Wall -Wextra -Wno-unknown-pragmas -Wno-unused-parameter -Wno-sign-compare -pthread")
+  set(CMAKE_CXX_FLAGS "-Wfatal-errors -Wall -Wextra -Wno-unknown-pragmas -Wno-unused-parameter -Wno-sign-compare -pthread")
   set(CMAKE_CXX_FLAGS_RELEASE "-O3 -Wno-unused-parameter")
   set(CMAKE_CXX_FLAGS_DEBUG "-g -O0 -DDEBUG -Wno-unused-parameter -Wno-unused-const-variable")
 endif(NOT MSVC)
 
-file(GLOB SOURCES ${CMAKE_CURRENT_SOURCE_DIR}/cpp/*.cpp)
+list(APPEND CMAKE_PREFIX_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cpp/external)
+
+set(JSON_INCLUDE ${CMAKE_CURRENT_SOURCE_DIR}/cpp/external/json/include/)
+set(EIGEN_INCLUDE ${CMAKE_CURRENT_SOURCE_DIR}/cpp/external/eigen/)
+set(AUTODIFF_INCLUDE ${CMAKE_CURRENT_SOURCE_DIR}/cpp/external/autodiff)
+set(PYBIND11_ROOT ${CMAKE_CURRENT_SOURCE_DIR}/cpp/external/pybind11)
+
+set(SRC_DIR ${CMAKE_CURRENT_SOURCE_DIR}/cpp)
+file(GLOB COMMON_SRC ${SRC_DIR}/*.cpp)
+list(REMOVE_ITEM COMMON_SRC ${SRC_DIR}/bindings.cpp ${SRC_DIR}/run_kineticgas.cpp)
+list(APPEND COMMON_SRC ${SRC_DIR}/Integration/Integration.cpp)
+
+if (DEFINED ENV{THERMOPACK_DIR})
+  set(THERMOPACK_DIR $ENV{THERMOPACK_DIR})
+  message(STATUS "Searching for thermopack in THERMOPACK_DIR: $ENV{THERMOPACK_DIR}")
+else()
+  message(STATUS "THERMOPACK_DIR is not defined!")
+  set(THERMOPACK_DIR ${CMAKE_CURRENT_SOURCE_DIR}/cpp/external/thermopack)
+  message(STATUS "Setting THERMOPACK_DIR: ${THERMOPACK_DIR}")
+endif()
+
+find_package(THERMOPACK REQUIRED)
+if(NOT THERMOPACK_INSTALLED)
+  message(STATUS "${ColorRed}ThermoPack was found, but is not installed. If you have installed ThermoPack, 
+set the environment variable 'THERMOPACK_DIR=</path/to/thermopack>' to help cmake find your installation.${ColorDefault}")
+  message(STATUS "${ColorBlue}Target 'thermopack' created from the files found at ${THERMOPACK_ROOT}.${ColorDefault}")
+  message(STATUS "${ColorBlue}Try Running `make install` to build and install thermopack, before re-running `cmake .. && make install` to build KineticGas.${ColorDefault}")
+  add_subdirectory(${THERMOPACK_ROOT}) # We need to build thermopack, because it has not been installed.
+  return() # Hoping that thermopack target has been created by thermopack, exiting ...
+endif()
+
+if(NOT DEFINED(FLUID_DIR))
+  set(FLUID_DIR "../fluids" CACHE STRING "Default search path for fluid files")
+endif()
+message(STATUS "Default search path for fluid files (relative to dynamic library): ${FLUID_DIR}")
+
+option(purecpp "Build pure cpp lib" OFF)
+if (purecpp)
+  message(STATUS "${ColorBlue}Generating C++ library targets. Run `cmake [-Dpurecpp=OFF] ..` to skip this target (you will need to clear the CMakeCache first).${ColorDefault}")
+  set(libTARGET kineticgas)
+  add_library(${libTARGET} SHARED ${COMMON_SRC})
+  target_include_directories(${libTARGET} PUBLIC ${JSON_INCLUDE} ${EIGEN_INCLUDE} ${AUTODIFF_INCLUDE})
+  target_compile_definitions(${libTARGET} PUBLIC "-DFLUID_DIR=${FLUID_DIR}")
+  target_link_libraries(${libTARGET} thermopack)
+  install(TARGETS ${libTARGET} DESTINATION ${CMAKE_CURRENT_SOURCE_DIR}/lib)
+
+  set(runTARGET run_kineticgas)
+  add_executable(${runTARGET} ${SRC_DIR}/run_kineticgas.cpp)
+  target_link_libraries(${runTARGET} ${libTARGET})
+else()
+  message(STATUS "${ColorYellow}Not generating C++ library targets. Run `cmake -Dpurecpp=ON ..` to generate these targets (you will need to clear the CMakeCache first).${ColorDefault}")
+endif()
+
+option(pylib "Build library for pykingas" ON)
+if (pylib)
+  message(STATUS "${ColorBlue}Generating libpykingas target. Run `cmake -Dpylib=OFF ..` to skip this target (you will need to clear the CMakeCache first).${ColorDefault}")
+  set(pyTARGET libpykingas)
+  set(pykingas_path ${CMAKE_CURRENT_SOURCE_DIR}/pykingas)
+  add_subdirectory(${PYBIND11_ROOT})
+  pybind11_add_module(${pyTARGET} ${COMMON_SRC} ${SRC_DIR}/bindings.cpp)
+
+  if(NOT MSVC)
+    set_target_properties(${pyTARGET} PROPERTIES 
+                          INSTALL_RPATH ${THERMOPACK_ROOT}/installed
+                          INSTALL_RPATH_USE_LINK_PATH TRUE)
+  endif()
 
-project(pykingas)
-set(TARGET libpykingas)
+  set(pyFLUID_DIR "./fluids" CACHE STRING "Default search path for fluid files (pykingas)")
+  message(STATUS "pykingas search path for fluids (relative to pykingas directory): ${pyFLUID_DIR}")
 
-# Add a library using FindPython's tooling (pybind11 also provides a helper like this)
-add_subdirectory("${CMAKE_CURRENT_SOURCE_DIR}/cpp/external/pybind11")
-pybind11_add_module(${TARGET} ${SOURCES} "${CMAKE_CURRENT_SOURCE_DIR}/cpp/Integration/Integration.cpp")
+  target_include_directories(${pyTARGET} PUBLIC ${JSON_INCLUDE} ${EIGEN_INCLUDE} ${AUTODIFF_INCLUDE})
+  target_link_libraries(${pyTARGET} PRIVATE thermopack)
+  target_compile_definitions(${pyTARGET} PUBLIC "-DPYLIB -DFLUID_DIR=${pyFLUID_DIR}")
 
-# The install directory is the output (wheel) directory
-install(TARGETS ${TARGET} DESTINATION ${CMAKE_CURRENT_SOURCE_DIR}/pykingas)
+  install(TARGETS ${pyTARGET} DESTINATION ${pykingas_path})
+  file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/fluids DESTINATION ${pykingas_path})
+endif()
diff --git a/README.md b/README.md
@@ -488,7 +488,12 @@ The `frame_of_reference` kwarg works as normal when setting `use_independent=Fal
 
 A standalone C++ library, that does not depend upon the Python wrapper, is currently under development. See branches under `pure_cpp/` for the most up to date information on that.
 
-# Advanced usage
+---
+layout: default
+version: 
+title: Advanced usage
+permalink: /vcurrent/advanced.html
+---
 
 ## Modifying and adding fluids
 
@@ -542,7 +547,7 @@ Functionality making it simple to implement new potentials is at the core of `Ki
 
 ### Implementing the C++ side
 
-All classes that inherit from `KineticGas` must implement the methods `omega`, which returns the collision integrals, the method `model_rdf`, which returns the radial distribution function at contact, and the method `get_contact_diameters`, which returns the collision diameters. 
+All classes that inherit from `KineticGas` must implement the methods `omega`, which returns the collision integrals, the method `model_rdf`, which returns the radial distribution function at contact, and the method `get_collision_diameters`, which returns the collision diameters. 
 
 Out of these, the `omega` method is implemented in the  `Spherical` class which instead requires that inheritting classes implement the methods `potential`, `potential_derivative_r` and `potential_dblderivative_rr`, corresponding to the pair potential, and its first and second derivative wrt. distance. 
 
@@ -551,13 +556,13 @@ The options for implementing a new potential are then
  * Inherit `KineticGas`
    * Implement `omega` (The collision integrals)
    * Implement `model_rdf` (The radial distribution function at contact)
-   * Implement `get_contact_diameters` (The collision diameters)
+   * Implement `get_collision_diameters` (The collision diameters)
  * Inherit `Spherical`
    * Implement `potential` (The pair-potential)
    * Implement `potential_derivative_r` (Derivative of the pair-potential)
    * Implement `potential_dblderivative_rr` (Second derivative of the pair-potential)
    * Implement `model_rdf` (The radial distribution function at contact)
-   * Implement `get_contact_diameters` (The collision diameters)
+   * Implement `get_collision_diameters` (The collision diameters)
 
 ### Implementing the Python side
 
@@ -574,7 +579,12 @@ class MyNewPotential(py_KineticGas)
         self.eos = <Some ThermoPack EoS>(comps)
 ```
 
-# Structure
+---
+layout: default
+version: 
+title: Structure
+permalink: /vcurrent/structure.html
+---
 
 See the [structure docs](https://github.com/thermotools/KineticGas/blob/main/docs/structure/structure.pdf) for more information.
 
@@ -626,7 +636,12 @@ Stuff is illustrated here as well:
 
 `docs/` : Documentation
 
-# Fluid identifiers
+---
+layout: default
+version: 
+title: Fluid identifiers
+permalink: /vcurrent/fluid_identifiers.html
+---
 
 *Note* : Many of these fluid parameters have been pulled directly from the [ThermoPack](https://github.com/thermotools/thermopack) fluid database for SAFT-VR Mie parameters. In the cases where SAFT-VR Mie uses segment numbers $>1$ to describe the fluids, the parameter sets cannot be expected to be suitable for use with RET-Mie.