inline T Math::pow(T x) {
return (pow(x) * x);
}
template <> inline UInt Math::pow<0, UInt>(__attribute__((unused)) UInt x) {
return (1);
}
template <> inline Real Math::pow<0, Real>(__attribute__((unused)) Real x) {
return (1.);
}
/* -------------------------------------------------------------------------- */
template
Real Math::NewtonRaphson::solve(const Functor & funct, Real x_0) {
Real x = x_0;
Real f_x = funct.f(x);
UInt iter = 0;
while (std::abs(f_x) > this->tolerance && iter < this->max_iteration) {
x -= f_x / funct.f_prime(x);
f_x = funct.f(x);
iter++;
}
AKANTU_DEBUG_ASSERT(iter < this->max_iteration,
"Newton Raphson ("
<< funct.name << ") solve did not converge in "
<< this->max_iteration << " iterations (tolerance: "
<< this->tolerance << ")");
return x;
}
diff --git a/src/io/parser/cppargparse/cppargparse.cc b/src/io/parser/cppargparse/cppargparse.cc
index fb83e174f..70c2d9a08 100644
--- a/src/io/parser/cppargparse/cppargparse.cc
+++ b/src/io/parser/cppargparse/cppargparse.cc
@@ -1,526 +1,528 @@
/**
* @file cppargparse.cc
*
* @author Nicolas Richart
*
* @date creation: Thu Apr 03 2014
* @date last modification: Wed Nov 11 2015
*
* @brief implementation of the ArgumentParser
*
* @section LICENSE
*
* Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see .
*
*/
/* -------------------------------------------------------------------------- */
#include "cppargparse.hh"
#include
#include
#include
#include
#include
#include
#include
#include
#include
#include
#include
#include
namespace cppargparse {
/* -------------------------------------------------------------------------- */
static inline std::string to_upper(const std::string & str) {
std::string lstr = str;
std::transform(lstr.begin(), lstr.end(), lstr.begin(),
(int (*)(int))std::toupper);
return lstr;
}
/* -------------------------------------------------------------------------- */
/* ArgumentParser */
/* -------------------------------------------------------------------------- */
ArgumentParser::ArgumentParser() : external_exit(NULL), prank(0), psize(1) {
this->addArgument("-h;--help", "show this help message and exit", 0, _boolean,
false, true);
}
/* -------------------------------------------------------------------------- */
ArgumentParser::~ArgumentParser() {
for (_Arguments::iterator it = arguments.begin(); it != arguments.end();
++it) {
delete it->second;
}
}
/* -------------------------------------------------------------------------- */
void ArgumentParser::setParallelContext(int prank, int psize) {
this->prank = prank;
this->psize = psize;
}
/* -------------------------------------------------------------------------- */
void ArgumentParser::_exit(const std::string & msg, int status) {
if (prank == 0) {
if (msg != "") {
std::cerr << msg << std::endl;
std::cerr << std::endl;
}
this->print_help(std::cerr);
}
if (external_exit)
(*external_exit)(status);
else {
exit(status);
}
}
/* -------------------------------------------------------------------------- */
const ArgumentParser::Argument & ArgumentParser::
operator[](const std::string & name) const {
Arguments::const_iterator it = success_parsed.find(name);
if (it != success_parsed.end()) {
return *(it->second);
} else {
throw std::range_error("No argument named \'" + name +
"\' was found in the parsed argument," +
" make sur to specify it \'required\'" +
" or to give it a default value");
}
}
/* -------------------------------------------------------------------------- */
bool ArgumentParser::has(const std::string & name) const {
return (success_parsed.find(name) != success_parsed.end());
}
/* -------------------------------------------------------------------------- */
void ArgumentParser::addArgument(const std::string & name_or_flag,
const std::string & help, int nargs,
ArgumentType type) {
_addArgument(name_or_flag, help, nargs, type);
}
/* -------------------------------------------------------------------------- */
ArgumentParser::_Argument &
ArgumentParser::_addArgument(const std::string & name, const std::string & help,
int nargs, ArgumentType type) {
- _Argument * arg = NULL;
+ _Argument * arg = nullptr;
switch (type) {
case _string: {
arg = new ArgumentStorage();
break;
}
case _float: {
arg = new ArgumentStorage();
break;
}
case _integer: {
arg = new ArgumentStorage();
break;
}
case _boolean: {
arg = new ArgumentStorage();
break;
}
}
arg->help = help;
arg->nargs = nargs;
arg->type = type;
std::stringstream sstr(name);
std::string item;
std::vector tmp_keys;
while (std::getline(sstr, item, ';')) {
tmp_keys.push_back(item);
}
int long_key = -1;
int short_key = -1;
bool problem = (tmp_keys.size() > 2) || (name == "");
for (std::vector::iterator it = tmp_keys.begin();
it != tmp_keys.end(); ++it) {
if (it->find("--") == 0) {
problem |= (long_key != -1);
long_key = it - tmp_keys.begin();
} else if (it->find("-") == 0) {
problem |= (long_key != -1);
short_key = it - tmp_keys.begin();
}
}
problem |= ((tmp_keys.size() == 2) && (long_key == -1 || short_key == -1));
if (problem) {
+ delete arg;
throw std::invalid_argument("Synthax of name or flags is not correct. "
"Possible synthax are \'-f\', \'-f;--foo\', "
"\'--foo\', \'bar\'");
}
if (long_key != -1) {
arg->name = tmp_keys[long_key];
arg->name.erase(0, 2);
} else if (short_key != -1) {
arg->name = tmp_keys[short_key];
arg->name.erase(0, 1);
} else {
arg->name = tmp_keys[0];
pos_args.push_back(arg);
arg->required = (nargs != _one_if_possible);
arg->is_positional = true;
}
arguments[arg->name] = arg;
if (!arg->is_positional) {
if (short_key != -1) {
std::string key = tmp_keys[short_key];
key_args[key] = arg;
arg->keys.push_back(key);
}
if (long_key != -1) {
std::string key = tmp_keys[long_key];
key_args[key] = arg;
arg->keys.push_back(key);
}
}
return *arg;
}
#if not HAVE_STRDUP
static char * strdup(const char * str) {
size_t len = strlen(str);
char *x = (char *)malloc(len+1); /* 1 for the null terminator */
if(!x) return NULL; /* malloc could not allocate memory */
memcpy(x,str,len+1); /* copy the string into the new buffer */
return x;
}
#endif
/* -------------------------------------------------------------------------- */
void ArgumentParser::parse(int & argc, char **& argv, int flags,
bool parse_help) {
bool stop_in_not_parsed = flags & _stop_on_not_parsed;
bool remove_parsed = flags & _remove_parsed;
std::vector argvs;
for (int i = 0; i < argc; ++i) {
argvs.push_back(std::string(argv[i]));
}
unsigned int current_position = 0;
if (this->program_name == "" && argc > 0) {
std::string prog = argvs[current_position];
const char * c_prog = prog.c_str();
char * c_prog_tmp = strdup(c_prog);
std::string base_prog(basename(c_prog_tmp));
this->program_name = base_prog;
std::free(c_prog_tmp);
}
std::queue<_Argument *> positional_queue;
for (PositionalArgument::iterator it = pos_args.begin(); it != pos_args.end();
++it)
positional_queue.push(*it);
std::vector argvs_to_remove;
++current_position; // consume argv[0]
while (current_position < argvs.size()) {
std::string arg = argvs[current_position];
++current_position;
ArgumentKeyMap::iterator key_it = key_args.find(arg);
bool is_positional = false;
_Argument * argument_ptr = NULL;
if (key_it == key_args.end()) {
if (positional_queue.empty()) {
if (stop_in_not_parsed)
this->_exit("Argument " + arg + " not recognized", EXIT_FAILURE);
continue;
} else {
argument_ptr = positional_queue.front();
is_positional = true;
--current_position;
}
} else {
argument_ptr = key_it->second;
}
if (remove_parsed && !is_positional && argument_ptr->name != "help") {
argvs_to_remove.push_back(current_position - 1);
}
_Argument & argument = *argument_ptr;
unsigned int min_nb_val = 0, max_nb_val = 0;
switch (argument.nargs) {
case _one_if_possible:
max_nb_val = 1;
break; // "?"
case _at_least_one:
min_nb_val = 1; // "+"
+ [[gnu::fallthrough]];
case _any:
max_nb_val = argc - current_position;
break; // "*"
default:
min_nb_val = max_nb_val = argument.nargs; // "N"
}
std::vector values;
unsigned int arg_consumed = 0;
if (max_nb_val <= (argc - current_position)) {
for (; arg_consumed < max_nb_val; ++arg_consumed) {
std::string v = argvs[current_position];
++current_position;
bool is_key = key_args.find(v) != key_args.end();
bool is_good_type = checkType(argument.type, v);
if (!is_key && is_good_type) {
values.push_back(v);
if (remove_parsed)
argvs_to_remove.push_back(current_position - 1);
} else {
// unconsume not parsed argument for optional
- if (!is_positional || (is_positional && is_key))
+ if (!is_positional || is_key)
--current_position;
break;
}
}
}
if (arg_consumed < min_nb_val) {
if (!is_positional) {
this->_exit("Not enought values for the argument " + argument.name +
" where provided",
EXIT_FAILURE);
} else {
if (stop_in_not_parsed)
this->_exit("Argument " + arg + " not recognized", EXIT_FAILURE);
}
} else {
if (is_positional)
positional_queue.pop();
if (!argument.parsed) {
success_parsed[argument.name] = &argument;
argument.parsed = true;
if ((argument.nargs == _one_if_possible || argument.nargs == 0) &&
arg_consumed == 0) {
if (argument.has_const)
argument.setToConst();
else if (argument.has_default)
argument.setToDefault();
} else {
argument.setValues(values);
}
} else {
this->_exit("Argument " + argument.name +
" already present in the list of argument",
EXIT_FAILURE);
}
}
}
for (_Arguments::iterator ait = arguments.begin(); ait != arguments.end();
++ait) {
_Argument & argument = *(ait->second);
if (!argument.parsed) {
if (argument.has_default) {
argument.setToDefault();
success_parsed[argument.name] = &argument;
}
if (argument.required) {
this->_exit("Argument " + argument.name + " required but not given!",
EXIT_FAILURE);
}
}
}
// removing the parsed argument if remove_parsed is true
if (argvs_to_remove.size()) {
std::vector::const_iterator next_to_remove = argvs_to_remove.begin();
for (int i = 0, c = 0; i < argc; ++i) {
if (next_to_remove == argvs_to_remove.end() || i != *next_to_remove) {
argv[c] = argv[i];
++c;
} else {
if (next_to_remove != argvs_to_remove.end())
++next_to_remove;
}
}
argc -= argvs_to_remove.size();
}
this->argc = &argc;
this->argv = &argv;
if (this->arguments["help"]->parsed && parse_help) {
this->_exit();
}
}
/* -------------------------------------------------------------------------- */
bool ArgumentParser::checkType(ArgumentType type,
const std::string & value) const {
std::stringstream sstr(value);
switch (type) {
case _string: {
std::string s;
sstr >> s;
break;
}
case _float: {
double d;
sstr >> d;
break;
}
case _integer: {
int i;
sstr >> i;
break;
}
case _boolean: {
bool b;
sstr >> b;
break;
}
}
return (sstr.fail() == false);
}
/* -------------------------------------------------------------------------- */
void ArgumentParser::printself(std::ostream & stream) const {
for (Arguments::const_iterator it = success_parsed.begin();
it != success_parsed.end(); ++it) {
const Argument & argument = *(it->second);
argument.printself(stream);
stream << std::endl;
}
}
/* -------------------------------------------------------------------------- */
void ArgumentParser::print_usage(std::ostream & stream) const {
stream << "Usage: " << this->program_name;
- std::stringstream sstr_opt;
// print shorten usage
for (_Arguments::const_iterator it = arguments.begin(); it != arguments.end();
++it) {
const _Argument & argument = *(it->second);
if (!argument.is_positional) {
if (!argument.required)
stream << " [";
stream << argument.keys[0];
this->print_usage_nargs(stream, argument);
if (!argument.required)
stream << "]";
}
}
for (PositionalArgument::const_iterator it = pos_args.begin();
it != pos_args.end(); ++it) {
const _Argument & argument = **it;
this->print_usage_nargs(stream, argument);
}
stream << std::endl;
}
/* -------------------------------------------------------------------------- */
void ArgumentParser::print_usage_nargs(std::ostream & stream,
const _Argument & argument) const {
std::string u_name = to_upper(argument.name);
switch (argument.nargs) {
case _one_if_possible:
stream << " [" << u_name << "]";
break;
case _at_least_one:
stream << " " << u_name;
+ [[gnu::fallthrough]];
case _any:
stream << " [" << u_name << " ...]";
break;
default:
for (int i = 0; i < argument.nargs; ++i) {
stream << " " << u_name;
}
}
}
void ArgumentParser::print_help(std::ostream & stream) const {
this->print_usage(stream);
if (!pos_args.empty()) {
stream << std::endl;
stream << "positional arguments:" << std::endl;
for (PositionalArgument::const_iterator it = pos_args.begin();
it != pos_args.end(); ++it) {
const _Argument & argument = **it;
this->print_help_argument(stream, argument);
}
}
if (!key_args.empty()) {
stream << std::endl;
stream << "optional arguments:" << std::endl;
for (_Arguments::const_iterator it = arguments.begin();
it != arguments.end(); ++it) {
const _Argument & argument = *(it->second);
if (!argument.is_positional) {
this->print_help_argument(stream, argument);
}
}
}
}
void ArgumentParser::print_help_argument(std::ostream & stream,
const _Argument & argument) const {
std::string key("");
if (argument.is_positional)
key = argument.name;
else {
std::stringstream sstr;
for (unsigned int i = 0; i < argument.keys.size(); ++i) {
if (i != 0)
sstr << ", ";
sstr << argument.keys[i];
this->print_usage_nargs(sstr, argument);
}
key = sstr.str();
}
stream << " " << std::left << std::setw(15) << key << " " << argument.help;
argument.printDefault(stream);
stream << std::endl;
}
}