Migrate to header-only yaml (#143)

* Add FKYAML

* Port configreader

* Remove yaml-cpp dependency

* Remove yaml-cpp from CI

* Revert Makefile change

Author: fsimonis

.github/workflows/request-deb-package.yaml

@@ -54,7 +54,7 @@ jobs:
           apt update
           apt -y upgrade
           apt -y install git build-essential lsb-release cmake libeigen3-dev libxml2-dev libboost-all-dev python3-dev python3-numpy petsc-dev sed
-          apt -y install libarpack2-dev libspooles-dev libyaml-cpp-dev
+          apt -y install libarpack2-dev libspooles-dev
       - name: Install preCICE
         uses: precice/setup-precice-action@main
         with:

.github/workflows/ubuntu_build.yml

@@ -39,7 +39,7 @@ jobs:
       with:
         ref: ${{ github.ref }}
     - name: install dependencies
-      run: sudo apt install libarpack2-dev libspooles-dev libyaml-cpp-dev -y
+      run: sudo apt install libarpack2-dev libspooles-dev -y
     - name: Download CalculiX
       run: wget http://www.dhondt.de/ccx_2.20.src.tar.bz2
     - name: Unpack Calculix

.pre-commit-config.yaml

@@ -5,6 +5,7 @@ repos:
   hooks:
   - id: clang-format
     files: "^adapter"
+    exclude: "^adapter/fkYAML.hpp"
 # Official repo for default hooks
 - repo: https://github.com/pre-commit/pre-commit-hooks
   rev: 'v4.3.0'

Makefile

@@ -5,7 +5,7 @@
 CCX_VERSION			= 2.20
 CCX             = $(HOME)/CalculiX/ccx_$(CCX_VERSION)/src
 
-### Change these if you built SPOOLES, ARPACK, or yaml-cpp from source ###
+### Change these if you built SPOOLES, or ARPACK from source ###
 # SPOOLES include flags (e.g. -I$(HOME)/SPOOLES.2.2 )
 SPOOLES_INCLUDE   = -I/usr/include/spooles/
 # SPOOLES library flags (e.g. $(HOME)/SPOOLES.2.2/spooles.a)
@@ -15,11 +15,6 @@ SPOOLES_LIBS      = -lspooles
 ARPACK_INCLUDE    =
 # ARPACK library flags (e.g. $(HOME)/ARPACK/libarpack_INTEL.a)
 ARPACK_LIBS       = -larpack -llapack -lblas
-#
-# yaml-cpp include flags (e.g. -I$(HOME)/yaml-cpp/include)
-YAML_INCLUDE      = -I/usr/include/
-# yaml-cpp library flags (e.g. -L$(HOME)/yaml-cpp/build -lyaml-cpp)
-YAML_LIBS         = -lyaml-cpp
 
 # Get the CFLAGS and LIBS from pkg-config (preCICE version >= 1.4.0).
 # If pkg-config cannot find the libprecice.pc meta-file, you may need to set the
@@ -37,22 +32,20 @@ INCLUDES = \
 	-I$(CCX) \
 	$(SPOOLES_INCLUDE) \
 	$(PKGCONF_CFLAGS) \
-	$(ARPACK_INCLUDE) \
-	$(YAML_INCLUDE)
+	$(ARPACK_INCLUDE)
 
 LIBS = \
 	$(SPOOLES_LIBS) \
 	$(PKGCONF_LIBS) \
 	-lstdc++ \
-	$(YAML_LIBS) \
 	$(ARPACK_LIBS) \
 	-lpthread -lm -lc
 
 # Compilers and flags
 #CFLAGS = -g -Wall -std=c++11 -O0 -fopenmp $(INCLUDES) -DARCH="Linux" -DSPOOLES -DARPACK -DMATRIXSTORAGE
 #FFLAGS = -g -Wall -O0 -fopenmp $(INCLUDES)
 
-CFLAGS = -Wall -O3 -fopenmp $(INCLUDES) -DARCH="Linux" -DSPOOLES -DARPACK -DMATRIXSTORAGE -DUSE_MT
+CFLAGS = -Wall -O3 -fopenmp $(INCLUDES) -DARCH="Linux" -DSPOOLES -DARPACK -DMATRIXSTORAGE -DUSE_MT -Wno-implicit-function-declaration
 
 # OS-specific options
 UNAME_S := $(shell uname -s)
@@ -62,7 +55,7 @@ else
 	CC = mpicc
 endif
 
-FFLAGS = -Wall -O3 -fopenmp $(INCLUDES) ${ADDITIONAL_FFLAGS}
+FFLAGS = -Wall -O3 -fopenmp $(INCLUDES) ${ADDITIONAL_FFLAGS} -Wno-implicit-function-declaration
 # Note for GCC 10 or newer: add -fallow-argument-mismatch in the above flags
 FC = mpifort
 # FC = mpif90

Makefile_i8_PaStiX

@@ -4,7 +4,7 @@
 # Path to original CalculiX source (e.g. $(HOME)/ccx_2.20/src )
 CCX             = $(HOME)/CalculiX/ccx_2.20/src
 
-### Change these if you built SPOOLES, ARPACK, or yaml-cpp from source ###
+### Change these if you built SPOOLES, or ARPACK from source ###
 # SPOOLES include flags (e.g. -I$(HOME)/SPOOLES.2.2 )
 SPOOLES_INCLUDE   = -I/usr/include/spooles/
 # SPOOLES library flags (e.g. $(HOME)/SPOOLES.2.2/spooles.a)
@@ -15,11 +15,6 @@ ARPACK_INCLUDE    =
 # ARPACK library flags (e.g. $(HOME)/ARPACK/libarpack_INTEL.a)
 ARPACK_LIBS       = $(HOME)/ARPACK/libarpack_INTEL.a 
 #ARPACK_LIBS       = -larpack -llapack -lblas
-#
-# yaml-cpp include flags (e.g. -I$(HOME)/yaml-cpp/include)
-YAML_INCLUDE      = -I/usr/include/
-# yaml-cpp library flags (e.g. -L$(HOME)/yaml-cpp/build -lyaml-cpp)
-YAML_LIBS         = -lyaml-cpp
 
 # Get the CFLAGS and LIBS from pkg-config (preCICE version >= 1.4.0).
 # If pkg-config cannot find the libprecice.pc meta-file, you may need to set the
@@ -49,14 +44,12 @@ INCLUDES = \
 	$(SPOOLES_INCLUDE) \
 	$(PKGCONF_CFLAGS) \
 	$(ARPACK_INCLUDE) \
-	$(YAML_INCLUDE) \
 	$(PASTIX_INCLUDE)
 
 LIBS = \
 	$(SPOOLES_LIBS) \
 	$(PKGCONF_LIBS) \
 	-lstdc++ \
-	$(YAML_LIBS) \
 	$(ARPACK_LIBS) \
 	-lpthread -lm -lc \
 	$(PASTIX_LIBS) \
@@ -102,7 +95,7 @@ $(OBJDIR)/%.o : %.f
 $(OBJDIR)/%.o : adapter/%.c
 	$(CC) $(CFLAGS) -c $< -o $@
 $(OBJDIR)/%.o : adapter/%.cpp
-	g++ -std=c++11 $(YAML_INCLUDE) -c $< -o $@ $(LIBS)
+	g++ -std=c++11 -c $< -o $@ $(LIBS)
 	#$(CC) $(CFLAGS) $(INCLUDES) -c $< -o $@ $(LIBS)
 
 # Source files in the $(CCX) folder

adapter/ConfigReader.cpp

@@ -12,16 +12,22 @@
 #include <cassert>
 #include <cstdlib>
 #include <cstring>
-#include <iostream>
+#include <fstream>
 #include <iterator>
 #include "ConfigReader.h"
-#include "yaml-cpp/yaml.h"
+#include "fkYAML.hpp"
+
+fkyaml::node load_yaml(char const *configFilename)
+{
+  std::ifstream ifs(configFilename);
+  return fkyaml::node::deserialize(ifs);
+}
 
 void ConfigReader_Read(char const *configFilename, char const *participantName, AdapterConfig *adapterConfig)
 {
-  YAML::Node config = YAML::LoadFile(configFilename);
+  auto config = load_yaml(configFilename);
 
-  adapterConfig->preciceConfigFilename = strdup(config["precice-config-file"].as<std::string>().c_str());
+  adapterConfig->preciceConfigFilename = strdup(config["precice-config-file"].get_value<std::string>().c_str());
 
   int numInterfaces            = config["participants"][participantName]["interfaces"].size();
   adapterConfig->numInterfaces = numInterfaces;
@@ -33,61 +39,61 @@ void ConfigReader_Read(char const *configFilename, char const *participantName,
     new (currentInterfacePointer) InterfaceConfig();
     InterfaceConfig &interface = *currentInterfacePointer;
 
-    if (config["participants"][participantName]["interfaces"][i]["nodes-mesh"]) {
-      interface.nodesMeshName = strdup(config["participants"][participantName]["interfaces"][i]["nodes-mesh"].as<std::string>().c_str());
+    if (config["participants"][participantName]["interfaces"][i].contains("nodes-mesh")) {
+      interface.nodesMeshName = strdup(config["participants"][participantName]["interfaces"][i]["nodes-mesh"].get_value<std::string>().c_str());
       interface.map           = 0;
-    } else if (config["participants"][participantName]["interfaces"][i]["nodes-mesh-with-connectivity"]) {
-      interface.nodesMeshName = strdup(config["participants"][participantName]["interfaces"][i]["nodes-mesh-with-connectivity"].as<std::string>().c_str());
+    } else if (config["participants"][participantName]["interfaces"][i].contains("nodes-mesh-with-connectivity")) {
+      interface.nodesMeshName = strdup(config["participants"][participantName]["interfaces"][i]["nodes-mesh-with-connectivity"].get_value<std::string>().c_str());
       interface.map           = 1;
     } else {
       interface.nodesMeshName = NULL;
     }
 
-    if (config["participants"][participantName]["interfaces"][i]["faces-mesh"]) {
-      interface.facesMeshName = strdup(config["participants"][participantName]["interfaces"][i]["faces-mesh"].as<std::string>().c_str());
+    if (config["participants"][participantName]["interfaces"][i].contains("faces-mesh")) {
+      interface.facesMeshName = strdup(config["participants"][participantName]["interfaces"][i]["faces-mesh"].get_value<std::string>().c_str());
     } else {
       interface.facesMeshName = NULL;
     }
 
-    if (config["participants"][participantName]["interfaces"][i]["mesh"]) {
-      interface.facesMeshName = strdup(config["participants"][participantName]["interfaces"][i]["mesh"].as<std::string>().c_str());
+    if (config["participants"][participantName]["interfaces"][i].contains("mesh")) {
+      interface.facesMeshName = strdup(config["participants"][participantName]["interfaces"][i]["mesh"].get_value<std::string>().c_str());
     }
 
-    std::string patchName = config["participants"][participantName]["interfaces"][i]["patch"].as<std::string>();
+    std::string patchName = config["participants"][participantName]["interfaces"][i]["patch"].get_value<std::string>();
     std::transform(patchName.begin(), patchName.end(), patchName.begin(), toupper);
     interface.patchName = strdup(patchName.c_str());
 
     interface.numWriteData = config["participants"][participantName]["interfaces"][i]["write-data"].size();
     interface.numReadData  = config["participants"][participantName]["interfaces"][i]["read-data"].size();
 
-    if (config["participants"][participantName]["interfaces"][i]["write-data"]) {
+    if (config["participants"][participantName]["interfaces"][i].contains("write-data")) {
       if (interface.numWriteData == 0) {
         // write-data is a string
         interface.numWriteData      = 1;
         interface.writeDataNames    = (char **) malloc(sizeof(char *) * interface.numWriteData);
-        interface.writeDataNames[0] = strdup(config["participants"][participantName]["interfaces"][i]["write-data"].as<std::string>().c_str());
+        interface.writeDataNames[0] = strdup(config["participants"][participantName]["interfaces"][i]["write-data"].get_value<std::string>().c_str());
       } else {
         // write-data is an array
         interface.writeDataNames = (char **) malloc(sizeof(char *) * interface.numWriteData);
 
         for (int j = 0; j < interface.numWriteData; j++) {
-          interface.writeDataNames[j] = strdup(config["participants"][participantName]["interfaces"][i]["write-data"][j].as<std::string>().c_str());
+          interface.writeDataNames[j] = strdup(config["participants"][participantName]["interfaces"][i]["write-data"][j].get_value<std::string>().c_str());
         }
       }
     }
 
-    if (config["participants"][participantName]["interfaces"][i]["read-data"]) {
+    if (config["participants"][participantName]["interfaces"][i].contains("read-data")) {
       if (interface.numReadData == 0) {
         // read-data is a string
         interface.numReadData      = 1;
         interface.readDataNames    = (char **) malloc(sizeof(char *) * interface.numReadData);
-        interface.readDataNames[0] = strdup(config["participants"][participantName]["interfaces"][i]["read-data"].as<std::string>().c_str());
+        interface.readDataNames[0] = strdup(config["participants"][participantName]["interfaces"][i]["read-data"].get_value<std::string>().c_str());
       } else {
         // read-data is an array
         interface.readDataNames = (char **) malloc(sizeof(char *) * interface.numReadData);
 
         for (int j = 0; j < interface.numReadData; j++) {
-          interface.readDataNames[j] = strdup(config["participants"][participantName]["interfaces"][i]["read-data"][j].as<std::string>().c_str());
+          interface.readDataNames[j] = strdup(config["participants"][participantName]["interfaces"][i]["read-data"][j].get_value<std::string>().c_str());
         }
       }
     }