v0.4.3 (#62)

* GEMS-221: Fixed build spdlog in header-only mode or as lib for thermofun project * GEMS-221: Set spdlog in header-only mode for thermofun project, checked build&install * Restore fixed * Fixed local install python code * GEMS-217: Fixed memory leaks which were definitely lost t in ThermoFun project. * Fixed python install for win64 * Fixed version in install dependent * Fixed * v0.4.3 * removed setuptools and version of chemicalfun --------- Co-authored-by: svetad <sv.dmytr@gmail.com> Co-authored-by: G. Dan Miron <dan.miron@psi.com> Co-authored-by: Allan Leal <allanmulin@gmail.com>
thermohub · Mar 2, 2023 · c47e45c · c47e45c
1 parent 0fc47c0
commit c47e45c
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Showing 9 changed files with 86 additions and 85 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -1,15 +1,15 @@
 # Require a certain version of cmake
 cmake_minimum_required(VERSION 3.9)
 
+# Set the name of the project
+project(ThermoFun VERSION 0.4.3 LANGUAGES CXX)
+
 # Set the cmake module path of the project
 set(CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake/modules")
 
 # Use ccache to speed up repeated compilations
 include(CCache)
 
-# Set the name of the project
-project(ThermoFun VERSION 0.4.2 LANGUAGES CXX)
-
 # Define variables with the GNU standard installation directories
 include(GNUInstallDirs)
 
@@ -43,6 +43,13 @@ else()
     set(CMAKE_POSITION_INDEPENDENT_CODE ON)
 endif()
 
+# Used into conda only
+if(DEFINED ENV{CONDA_PREFIX})
+   option(USE_SPDLOG_PRECOMPILED "Use spdlog in compiled version" ON)
+else()
+   option(USE_SPDLOG_PRECOMPILED "Use spdlog in compiled version" OFF)
+endif()
+
 # Set the default build type to Release
 if(NOT CMAKE_BUILD_TYPE)
     # The build type selection for the project

diff --git a/ThermoFun/CMakeLists.txt b/ThermoFun/CMakeLists.txt
@@ -1,3 +1,4 @@
+
 # Recursively collect all header files from the current directory
 file(GLOB_RECURSE HEADER_FILES RELATIVE ${CMAKE_CURRENT_SOURCE_DIR} *.hpp *.h)
 
@@ -24,8 +25,6 @@ add_library(ThermoFun::ThermoFun ALIAS ThermoFun)
 # Link ThermoFun against all required dependencies
 target_link_libraries(ThermoFun
     PUBLIC ChemicalFun::ChemicalFun
- #   PUBLIC spdlog::spdlog
-    PRIVATE nlohmann_json::nlohmann_json
 )
 
 # Specify the include directories of the library target

diff --git a/ThermoFun/Common/Exception.cpp b/ThermoFun/Common/Exception.cpp
@@ -19,6 +19,8 @@ void update_loggers( bool use_cout, const std::string& logfile_name, size_t log_
 {
     auto thermofun_logger = spdlog::get("thermofun");
     auto chemicalfun_logger = spdlog::get("chemicalfun");
+    if(!thermofun_logger || !chemicalfun_logger)
+        return;
 
     // change level
     spdlog::level::level_enum log_lev = spdlog::level::info;
@@ -49,6 +51,8 @@ void clear_loggers( const std::string& logfile_name)
 {
     auto thermofun_logger = spdlog::get("thermofun");
     auto chemicalfun_logger = spdlog::get("chemicalfun");
+    if(!thermofun_logger || !chemicalfun_logger)
+        return;
 
     thermofun_logger->sinks().clear();
     chemicalfun_logger->sinks().clear();

diff --git a/ThermoFun/ThermoEngine.cpp b/ThermoFun/ThermoEngine.cpp
@@ -87,11 +87,18 @@ struct ThermoEngine::Impl
 
     Impl()
     {
+        set_fn() ;
     }
 
     Impl(const Database &database)
         : database(database)
     {
+        set_fn();
+    }
+
+    void set_fn()
+    {
+
         thermo_properties_substance_fn = [=](double T, double P_, double &P, std::string symbol) {
             auto x = P_;
             return thermoPropertiesSubstance(T, P, symbol);
@@ -748,8 +755,10 @@ struct ThermoEngine::Impl
 };
 
 ThermoEngine::ThermoEngine(const std::string filename)
-    : pimpl(new Impl(*(new const Database(filename))))
+    : pimpl()
 {
+    Database db(filename);
+    pimpl.reset(new Impl(db));
 }
 
 ThermoEngine::ThermoEngine(const Database &database)

diff --git a/cmake/modules/ThermoFunFindDeps.cmake b/cmake/modules/ThermoFunFindDeps.cmake
@@ -9,22 +9,22 @@ if(TFUN_BUILD_PYTHON)
     endif()
 endif()
 
-find_package(nlohmann_json REQUIRED)
-if(NOT nlohmann_json_FOUND)
-    message(FATAL_ERROR "nlohmann_json library not found")
-endif()
+#find_package(nlohmann_json REQUIRED)
+#if(NOT nlohmann_json_FOUND)
+#    message(FATAL_ERROR "nlohmann_json library not found")
+#endif()
 
 find_package(ChemicalFun REQUIRED)
 if(NOT ChemicalFun_FOUND)
     message(FATAL_ERROR "ChemicalFun library not found")
 endif()
 
-find_package(spdlog REQUIRED)
-if(NOT spdlog_FOUND)
-    message(FATAL_ERROR "spdlog not found")
+if(USE_SPDLOG_PRECOMPILED)
+   if(NOT TARGET spdlog::spdlog)
+       find_package(spdlog CONFIG REQUIRED)
+       if(NOT spdlog_FOUND)
+           message(FATAL_ERROR "spdlog not found")
+       endif()
+   endif()
 endif()
 
-find_package(fmt REQUIRED)
-if(NOT fmt_FOUND)
-    message(FATAL_ERROR "fmt not found")
-endif()
diff --git a/environment.devenv.yml b/environment.devenv.yml
@@ -6,7 +6,6 @@ channels:
   - conda-forge
 
 dependencies:
-  - setuptools=59.7.0
   - pip
   - gxx_linux-64  # [linux]
   - cmake
@@ -16,9 +15,7 @@ dependencies:
   - clangxx_osx-64  # [osx]
   - pybind11
   - nlohmann_json
- # - spdlog=1.11.0
- # - fmt=9.1.0
-  - chemicalfun=0.1.6
+  - chemicalfun
   - python={{ python_version }}
   - pytest
   - vs2019_win-64  # [win]

diff --git a/install-dependencies.sh b/install-dependencies.sh
@@ -1,50 +1,49 @@
 #!/bin/bash
-# Installing dependencies needed to build ThermoFun on (k)ubuntu linux 16.04 or 18.04
+# Installing dependencies needed to build ThermoFun on (k)ubuntu linux 20.04
 
 EXTN=so
 
-#sudo rm -f /usr/local/include/nlohmann/json.hpp
-#sudo rm -rf /usr/local/include/eigen3/Eigen
+#sudo rm -rf /usr/local/include/nlohmann
+#sudo rm -rf /usr/local/include/eigen3/Eigen/Eigen
 #sudo rm -rf /usr/local/include/pybind11
 #sudo rm -rf /usr/local/include/spdlog
-#sudo rm -rf /usr/local/include/fmt
 #sudo rm -f /usr/local/lib/libChemicalFun.$EXTN
 
 workfolder=${PWD}
 BRANCH_TFUN=master
 BUILD_TYPE=Release
 
-# nlohmann/json
+# nlohmann/json library v. 3.6.1 or up
+# if not installed in /usr/local/include/nlohmann)
 test -f /usr/local/include/nlohmann/json.hpp || {
 
-	# Building json library
+	# Getting nlohmann/json library
 	mkdir -p ~/code && \
-                cd ~/code && \
+		cd ~/code && \
 		git clone https://github.com/nlohmann/json.git && \
 		cd json && \
 		mkdir -p build && \
 		cd build && \
-		cmake .. -DJSON_BuildTests=OFF && \
-		make && \
+		cmake .. -DCMAKE_BUILD_TYPE=Release -DJSON_BuildTests=OFF -DJSON_MultipleHeaders=ON && \
 		sudo make install
 
 	# Removing generated build files
 	cd ~ && \
 		 rm -rf ~/code
 }
 
-# spdlog 
-# if no spdlog installed in /usr/local/lib/ (/usr/local/include/spdlog)
-test -d /usr/local/include/spdlog || {
+# Eigen3 math library (added for building and installing xGEMS)
+# if not installed in /usr/local/include/eigen3)
+test -d /usr/local/include/eigen3/Eigen || {
 
-        # Building thermofun library
+        # Building eigen library
         mkdir -p ~/code && \
                 cd ~/code && \
-                git clone https://github.com/gabime/spdlog -b v1.11.0  && \
-                cd spdlog && \
+                git clone https://gitlab.com/libeigen/eigen.git -b 3.4.0 && \
+                cd eigen && \
                 mkdir -p build && \
                 cd build && \
-                cmake .. -DCMAKE_BUILD_TYPE=Release -DSPDLOG_BUILD_TESTS=OFF -DCMAKE_INSTALL_LIBDIR=lib -DSPDLOG_BUILD_SHARED=ON -DSPDLOG_FMT_EXTERNAL=ON \
+                cmake .. \
                 make && \
                 sudo make install
 
@@ -53,20 +52,16 @@ test -d /usr/local/include/spdlog || {
                  rm -rf ~/code
 }
 
-# fmt 
-# if no spdlog installed in /usr/local/lib/ (/usr/local/include/fmt)
-test -d /usr/local/include/fmt || {
+# spdlog 
+# if no spdlog installed in /usr/local/include/spdlog (copy only headers)
+test -d /usr/local/include/spdlog || {
 
-        # Building thermofun library
+        # Building spdlog library
         mkdir -p ~/code && \
                 cd ~/code && \
-                git clone hhttps://github.com/fmtlib/fmt.git -b v9.1.0  && \
-                cd fmt && \
-                mkdir -p build && \
-                cd build && \
-                cmake .. \
-                make && \
-                sudo make install
+                git clone https://github.com/gabime/spdlog -b v1.11.0  && \
+                cd spdlog/include && \
+                sudo cp -r spdlog /usr/local/include
 
         # Removing generated build files
         cd ~ && \
@@ -77,40 +72,19 @@ test -d /usr/local/include/fmt || {
 test -d /usr/local/include/pybind11 || {
 
         # Building pybind11 library
-        mkdir -p ~/code && \
-                cd ~/code && \
-                git clone https://github.com/pybind/pybind11.git && \
-                cd pybind11 && \
-                mkdir -p build && \
-                cd build && \
-                cmake .. -DPYBIND11_TEST=OFF && \
-                make && \
-                sudo make install
-
-        # Removing generated build files
-        cd ~ && \
-                 rm -rf ~/code
-}
-
-# Eigen
-# Eigen3 math library (added for building and installing xGEMS)
-# if not installed in /usr/local/include/eigen3)
-test -d /usr/local/include/eigen3/Eigen || {
-
-        # Building eigen library
-        mkdir -p ~/code && \
-                cd ~/code && \
-                git clone https://gitlab.com/libeigen/eigen.git -b 3.4.0 && \
-                cd eigen && \
-                mkdir -p build && \
-                cd build && \
-                cmake .. \
-                make && \
-                sudo make install
+	mkdir -p ~/code && \
+		cd ~/code && \
+		git clone https://github.com/pybind/pybind11.git && \
+		cd pybind11 && \
+		mkdir -p build && \
+		cd build && \
+		cmake .. -DPYBIND11_TEST=OFF && \
+		make && \
+		sudo make install
 
-        # Removing generated build files
-        cd ~ && \
-                 rm -rf ~/code
+	# Removing generated build files
+	cd ~ && \
+		 rm -rf ~/code
 }
 
 
@@ -126,7 +100,7 @@ test -f /usr/local/lib/libChemicalFun.$EXTN || {
                 cd chemicalfun && \
                 mkdir -p build && \
                 cd build && \
-                        cmake .. -DCMAKE_CXX_FLAGS=-fPIC -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DTFUN_BUILD_PYTHON=OFF && \
+                        cmake .. -DCMAKE_CXX_FLAGS=-fPIC -DCMAKE_BUILD_TYPE=$BUILD_TYPE  && \
         make -j $threads && \
                 sudo make install
 

diff --git a/python/pyThermoFun/CMakeLists.txt b/python/pyThermoFun/CMakeLists.txt
@@ -9,4 +9,4 @@ include_directories(${PROJECT_SOURCE_DIR}/python)
 pybind11_add_module(PyThermoFun ${SOURCE_FILES} NO_EXTRAS) # NO_EXTRAS used to decrease linking time, but causes larger module file size
 
 # Link PyThermoFun against ThermoFun library
-target_link_libraries(PyThermoFun LINK_PRIVATE ThermoFun::ThermoFun)
+target_link_libraries(PyThermoFun PUBLIC ThermoFun::ThermoFun)
diff --git a/python/thermofun/CMakeLists.txt b/python/thermofun/CMakeLists.txt
@@ -11,11 +11,22 @@ set(SETUP_PY ${CMAKE_CURRENT_BINARY_DIR}/setup.py)
 # Configure the setup.py script with the provided CMake variables
 configure_file(${SETUP_PY_IN} ${SETUP_PY})
 
+# https://www.scivision.dev/cmake-install-python-package/
+# https://pip.pypa.io/en/stable/topics/local-project-installs/#editable-installs
+# detect virtualenv and set Pip args accordingly
+if(DEFINED ENV{VIRTUAL_ENV} OR DEFINED ENV{CONDA_PREFIX})
+  set(_PIP_ARG)
+else()
+  set(_PIP_ARG "--user")
+endif()
+#message(STATUS "_PIP_ARG: ${_PIP_ARG}")
+
 # Create a custom target to build thermofun python package during build stage
 add_custom_target(thermofun ALL
     COMMAND ${CMAKE_COMMAND} -E copy $<TARGET_FILE:PyThermoFun> 
         ${CMAKE_CURRENT_BINARY_DIR}/$<TARGET_FILE_NAME:PyThermoFun>
-    COMMAND ${PYTHON_EXECUTABLE} ${SETUP_PY} --quiet install --prefix=${CMAKE_BINARY_DIR}
+    #COMMAND ${PYTHON_EXECUTABLE} -m pip install ${_PIP_ARG} -e ${CMAKE_CURRENT_BINARY_DIR}
+    COMMAND ${PYTHON_EXECUTABLE} -m pip install --prefix ${CMAKE_BINARY_DIR} --ignore-installed .
     WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
 
 # Set dependencies of thermofun target
@@ -43,7 +54,7 @@ install(CODE
     endif()
 
     execute_process(
-        COMMAND ${PYTHON_EXECUTABLE} ${SETUP_PY} install --prefix=\${THERMOFUN_PYTHON_INSTALL_PREFIX_NATIVE}
+        COMMAND ${PYTHON_EXECUTABLE} -m pip install --prefix \${THERMOFUN_PYTHON_INSTALL_PREFIX_NATIVE} ${CMAKE_CURRENT_BINARY_DIR}
         WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
 "
 )