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Merge branch 'develop' of https://github.com/paboyle/Grid into develop

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paboyle
2018-04-17 10:57:18 +01:00
parent ddcaa6ad29 c8d4d184ee
commit f7f043d8cf
8 changed files with 1948 additions and 1597 deletions
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19
lib/parallelIO/IldgIO.h
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@@ -248,7 +248,6 @@ class GridLimeReader : public BinaryIO {
template<class serialisable_object>
void readLimeObject(serialisable_object &object,std::string object_name,std::string record_name)
{
std::string xmlstring;
// should this be a do while; can we miss a first record??
while ( limeReaderNextRecord(LimeR) == LIME_SUCCESS ) {
@@ -262,7 +261,8 @@ class GridLimeReader : public BinaryIO {
limeReaderReadData((void *)&xmlc[0], &nbytes, LimeR);
// std::cout << GridLogMessage<< " readLimeObject matches XML " << &xmlc[0] <<std::endl;
XmlReader RD(&xmlc[0],"");
std::string xmlstring(&xmlc[0]);
XmlReader RD(xmlstring, true, "");
read(RD,object_name,object);
return;
}
@@ -698,9 +698,11 @@ class IldgReader : public GridLimeReader {
//////////////////////////////////
// ILDG format record
std::string xmlstring(&xmlc[0]);
if ( !strncmp(limeReaderType(LimeR), ILDG_FORMAT,strlen(ILDG_FORMAT)) ) {
XmlReader RD(&xmlc[0],"");
XmlReader RD(xmlstring, true, "");
read(RD,"ildgFormat",ildgFormat_);
if ( ildgFormat_.precision == 64 ) format = std::string("IEEE64BIG");
@@ -715,13 +717,13 @@ class IldgReader : public GridLimeReader {
}
if ( !strncmp(limeReaderType(LimeR), ILDG_DATA_LFN,strlen(ILDG_DATA_LFN)) ) {
FieldMetaData_.ildg_lfn = std::string(&xmlc[0]);
FieldMetaData_.ildg_lfn = xmlstring;
found_ildgLFN = 1;
}
if ( !strncmp(limeReaderType(LimeR), GRID_FORMAT,strlen(ILDG_FORMAT)) ) {
XmlReader RD(&xmlc[0],"");
XmlReader RD(xmlstring, true, "");
read(RD,"FieldMetaData",FieldMetaData_);
format = FieldMetaData_.floating_point;
@@ -735,18 +737,17 @@ class IldgReader : public GridLimeReader {
}
if ( !strncmp(limeReaderType(LimeR), SCIDAC_RECORD_XML,strlen(SCIDAC_RECORD_XML)) ) {
std::string xmls(&xmlc[0]);
// is it a USQCD info field
if ( xmls.find(std::string("usqcdInfo")) != std::string::npos ) {
if ( xmlstring.find(std::string("usqcdInfo")) != std::string::npos ) {
// std::cout << GridLogMessage<<"...found a usqcdInfo field"<<std::endl;
XmlReader RD(&xmlc[0],"");
XmlReader RD(xmlstring, true, "");
read(RD,"usqcdInfo",usqcdInfo_);
found_usqcdInfo = 1;
}
}
if ( !strncmp(limeReaderType(LimeR), SCIDAC_CHECKSUM,strlen(SCIDAC_CHECKSUM)) ) {
XmlReader RD(&xmlc[0],"");
XmlReader RD(xmlstring, true, "");
read(RD,"scidacChecksum",scidacChecksum_);
found_scidacChecksum = 1;
}

44
lib/pugixml/README.md
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@@ -1,44 +0,0 @@
pugixml [![Build Status](https://travis-ci.org/zeux/pugixml.svg?branch=master)](https://travis-ci.org/zeux/pugixml) [![Build status](https://ci.appveyor.com/api/projects/status/9hdks1doqvq8pwe7/branch/master?svg=true)](https://ci.appveyor.com/project/zeux/pugixml)
=======
pugixml is a C++ XML processing library, which consists of a DOM-like interface with rich traversal/modification
capabilities, an extremely fast XML parser which constructs the DOM tree from an XML file/buffer, and an XPath 1.0
implementation for complex data-driven tree queries. Full Unicode support is also available, with Unicode interface
variants and conversions between different Unicode encodings (which happen automatically during parsing/saving).
pugixml is used by a lot of projects, both open-source and proprietary, for performance and easy-to-use interface.
## Documentation
Documentation for the current release of pugixml is available on-line as two separate documents:
* [Quick-start guide](http://pugixml.org/docs/quickstart.html), that aims to provide enough information to start using the library;
* [Complete reference manual](http://pugixml.org/docs/manual.html), that describes all features of the library in detail.
You’re advised to start with the quick-start guide; however, many important library features are either not described in it at all or only mentioned briefly; if you require more information you should read the complete manual.
## License
This library is available to anybody free of charge, under the terms of MIT License:
Copyright (c) 2006-2015 Arseny Kapoulkine
Permission is hereby granted, free of charge, to any person
obtaining a copy of this software and associated documentation
files (the "Software"), to deal in the Software without
restriction, including without limitation the rights to use,
copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the
Software is furnished to do so, subject to the following
conditions:
The above copyright notice and this permission notice shall be
included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
OTHER DEALINGS IN THE SOFTWARE.

9
lib/pugixml/pugiconfig.hpp
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@@ -1,7 +1,7 @@
/**
* pugixml parser - version 1.6
* pugixml parser - version 1.9
* --------------------------------------------------------
* Copyright (C) 2006-2015, by Arseny Kapoulkine (arseny.kapoulkine@gmail.com)
* Copyright (C) 2006-2018, by Arseny Kapoulkine (arseny.kapoulkine@gmail.com)
* Report bugs and download new versions at http://pugixml.org/
*
* This library is distributed under the MIT License. See notice at the end
@@ -17,6 +17,9 @@
// Uncomment this to enable wchar_t mode
// #define PUGIXML_WCHAR_MODE
// Uncomment this to enable compact mode
// #define PUGIXML_COMPACT
// Uncomment this to disable XPath
// #define PUGIXML_NO_XPATH
@@ -46,7 +49,7 @@
#endif
/**
* Copyright (c) 2006-2015 Arseny Kapoulkine
* Copyright (c) 2006-2018 Arseny Kapoulkine
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation

2279
lib/pugixml/pugixml.cc
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File diff suppressed because it is too large Load Diff

107
lib/pugixml/pugixml.h
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@@ -1,7 +1,7 @@
/**
* pugixml parser - version 1.6
* pugixml parser - version 1.9
* --------------------------------------------------------
* Copyright (C) 2006-2015, by Arseny Kapoulkine (arseny.kapoulkine@gmail.com)
* Copyright (C) 2006-2018, by Arseny Kapoulkine (arseny.kapoulkine@gmail.com)
* Report bugs and download new versions at http://pugixml.org/
*
* This library is distributed under the MIT License. See notice at the end
@@ -13,7 +13,7 @@
#ifndef PUGIXML_VERSION
// Define version macro; evaluates to major * 100 + minor so that it's safe to use in less-than comparisons
# define PUGIXML_VERSION 160
# define PUGIXML_VERSION 190
#endif
// Include user configuration file (this can define various configuration macros)
@@ -72,6 +72,44 @@
# endif
#endif
// If the platform is known to have move semantics support, compile move ctor/operator implementation
#ifndef PUGIXML_HAS_MOVE
# if __cplusplus >= 201103
# define PUGIXML_HAS_MOVE
# elif defined(_MSC_VER) && _MSC_VER >= 1600
# define PUGIXML_HAS_MOVE
# endif
#endif
// If C++ is 2011 or higher, add 'noexcept' specifiers
#ifndef PUGIXML_NOEXCEPT
# if __cplusplus >= 201103
# define PUGIXML_NOEXCEPT noexcept
# elif defined(_MSC_VER) && _MSC_VER >= 1900
# define PUGIXML_NOEXCEPT noexcept
# else
# define PUGIXML_NOEXCEPT
# endif
#endif
// Some functions can not be noexcept in compact mode
#ifdef PUGIXML_COMPACT
# define PUGIXML_NOEXCEPT_IF_NOT_COMPACT
#else
# define PUGIXML_NOEXCEPT_IF_NOT_COMPACT PUGIXML_NOEXCEPT
#endif
// If C++ is 2011 or higher, add 'override' qualifiers
#ifndef PUGIXML_OVERRIDE
# if __cplusplus >= 201103
# define PUGIXML_OVERRIDE override
# elif defined(_MSC_VER) && _MSC_VER >= 1700
# define PUGIXML_OVERRIDE override
# else
# define PUGIXML_OVERRIDE
# endif
#endif
// Character interface macros
#ifdef PUGIXML_WCHAR_MODE
# define PUGIXML_TEXT(t) L ## t
@@ -158,6 +196,11 @@ namespace pugi
// is a valid document. This flag is off by default.
const unsigned int parse_fragment = 0x1000;
// This flag determines if plain character data is be stored in the parent element's value. This significantly changes the structure of
// the document; this flag is only recommended for parsing documents with many PCDATA nodes in memory-constrained environments.
// This flag is off by default.
const unsigned int parse_embed_pcdata = 0x2000;
// The default parsing mode.
// Elements, PCDATA and CDATA sections are added to the DOM tree, character/reference entities are expanded,
// End-of-Line characters are normalized, attribute values are normalized using CDATA normalization rules.
@@ -206,6 +249,9 @@ namespace pugi
// Write every attribute on a new line with appropriate indentation. This flag is off by default.
const unsigned int format_indent_attributes = 0x40;
// Don't output empty element tags, instead writing an explicit start and end tag even if there are no children. This flag is off by default.
const unsigned int format_no_empty_element_tags = 0x80;
// The default set of formatting flags.
// Nodes are indented depending on their depth in DOM tree, a default declaration is output if document has none.
const unsigned int format_default = format_indent;
@@ -268,7 +314,7 @@ namespace pugi
// Construct writer from a FILE* object; void* is used to avoid header dependencies on stdio
xml_writer_file(void* file);
virtual void write(const void* data, size_t size);
virtual void write(const void* data, size_t size) PUGIXML_OVERRIDE;
private:
void* file;
@@ -283,7 +329,7 @@ namespace pugi
xml_writer_stream(std::basic_ostream<char, std::char_traits<char> >& stream);
xml_writer_stream(std::basic_ostream<wchar_t, std::char_traits<wchar_t> >& stream);
virtual void write(const void* data, size_t size);
virtual void write(const void* data, size_t size) PUGIXML_OVERRIDE;
private:
std::basic_ostream<char, std::char_traits<char> >* narrow_stream;
@@ -354,6 +400,8 @@ namespace pugi
// Set attribute value with type conversion (numbers are converted to strings, boolean is converted to "true"/"false")
bool set_value(int rhs);
bool set_value(unsigned int rhs);
bool set_value(long rhs);
bool set_value(unsigned long rhs);
bool set_value(double rhs);
bool set_value(float rhs);
bool set_value(bool rhs);
@@ -367,6 +415,8 @@ namespace pugi
xml_attribute& operator=(const char_t* rhs);
xml_attribute& operator=(int rhs);
xml_attribute& operator=(unsigned int rhs);
xml_attribute& operator=(long rhs);
xml_attribute& operator=(unsigned long rhs);
xml_attribute& operator=(double rhs);
xml_attribute& operator=(float rhs);
xml_attribute& operator=(bool rhs);
@@ -601,8 +651,8 @@ namespace pugi
xpath_node_set select_nodes(const xpath_query& query) const;
// (deprecated: use select_node instead) Select single node by evaluating XPath query.
xpath_node select_single_node(const char_t* query, xpath_variable_set* variables = 0) const;
xpath_node select_single_node(const xpath_query& query) const;
PUGIXML_DEPRECATED xpath_node select_single_node(const char_t* query, xpath_variable_set* variables = 0) const;
PUGIXML_DEPRECATED xpath_node select_single_node(const xpath_query& query) const;
#endif
@@ -701,6 +751,8 @@ namespace pugi
// Set text with type conversion (numbers are converted to strings, boolean is converted to "true"/"false")
bool set(int rhs);
bool set(unsigned int rhs);
bool set(long rhs);
bool set(unsigned long rhs);
bool set(double rhs);
bool set(float rhs);
bool set(bool rhs);
@@ -714,6 +766,8 @@ namespace pugi
xml_text& operator=(const char_t* rhs);
xml_text& operator=(int rhs);
xml_text& operator=(unsigned int rhs);
xml_text& operator=(long rhs);
xml_text& operator=(unsigned long rhs);
xml_text& operator=(double rhs);
xml_text& operator=(float rhs);
xml_text& operator=(bool rhs);
@@ -945,10 +999,11 @@ namespace pugi
// Non-copyable semantics
xml_document(const xml_document&);
const xml_document& operator=(const xml_document&);
xml_document& operator=(const xml_document&);
void create();
void destroy();
void _create();
void _destroy();
void _move(xml_document& rhs) PUGIXML_NOEXCEPT_IF_NOT_COMPACT;
public:
// Default constructor, makes empty document
@@ -957,6 +1012,12 @@ namespace pugi
// Destructor, invalidates all node/attribute handles to this document
~xml_document();
#ifdef PUGIXML_HAS_MOVE
// Move semantics support
xml_document(xml_document&& rhs) PUGIXML_NOEXCEPT_IF_NOT_COMPACT;
xml_document& operator=(xml_document&& rhs) PUGIXML_NOEXCEPT_IF_NOT_COMPACT;
#endif
// Removes all nodes, leaving the empty document
void reset();
@@ -970,7 +1031,7 @@ namespace pugi
#endif
// (deprecated: use load_string instead) Load document from zero-terminated string. No encoding conversions are applied.
xml_parse_result load(const char_t* contents, unsigned int options = parse_default);
PUGIXML_DEPRECATED xml_parse_result load(const char_t* contents, unsigned int options = parse_default);
// Load document from zero-terminated string. No encoding conversions are applied.
xml_parse_result load_string(const char_t* contents, unsigned int options = parse_default);
@@ -1095,10 +1156,10 @@ namespace pugi
xpath_variable_set(const xpath_variable_set& rhs);
xpath_variable_set& operator=(const xpath_variable_set& rhs);
#if __cplusplus >= 201103
#ifdef PUGIXML_HAS_MOVE
// Move semantics support
xpath_variable_set(xpath_variable_set&& rhs);
xpath_variable_set& operator=(xpath_variable_set&& rhs);
xpath_variable_set(xpath_variable_set&& rhs) PUGIXML_NOEXCEPT;
xpath_variable_set& operator=(xpath_variable_set&& rhs) PUGIXML_NOEXCEPT;
#endif
// Add a new variable or get the existing one, if the types match
@@ -1139,10 +1200,10 @@ namespace pugi
// Destructor
~xpath_query();
#if __cplusplus >= 201103
#ifdef PUGIXML_HAS_MOVE
// Move semantics support
xpath_query(xpath_query&& rhs);
xpath_query& operator=(xpath_query&& rhs);
xpath_query(xpath_query&& rhs) PUGIXML_NOEXCEPT;
xpath_query& operator=(xpath_query&& rhs) PUGIXML_NOEXCEPT;
#endif
// Get query expression return type
@@ -1201,7 +1262,7 @@ namespace pugi
explicit xpath_exception(const xpath_parse_result& result);
// Get error message
virtual const char* what() const throw();
virtual const char* what() const throw() PUGIXML_OVERRIDE;
// Get parse result
const xpath_parse_result& result() const;
@@ -1280,10 +1341,10 @@ namespace pugi
xpath_node_set(const xpath_node_set& ns);
xpath_node_set& operator=(const xpath_node_set& ns);
#if __cplusplus >= 201103
#ifdef PUGIXML_HAS_MOVE
// Move semantics support
xpath_node_set(xpath_node_set&& rhs);
xpath_node_set& operator=(xpath_node_set&& rhs);
xpath_node_set(xpath_node_set&& rhs) PUGIXML_NOEXCEPT;
xpath_node_set& operator=(xpath_node_set&& rhs) PUGIXML_NOEXCEPT;
#endif
// Get collection type
@@ -1317,7 +1378,7 @@ namespace pugi
xpath_node* _end;
void _assign(const_iterator begin, const_iterator end, type_t type);
void _move(xpath_node_set& rhs);
void _move(xpath_node_set& rhs) PUGIXML_NOEXCEPT;
};
#endif
@@ -1375,7 +1436,7 @@ namespace std
#endif
/**
* Copyright (c) 2006-2015 Arseny Kapoulkine
* Copyright (c) 2006-2018 Arseny Kapoulkine
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation

6
lib/pugixml/readme.txt
View File

@@ -1,6 +1,6 @@
pugixml 1.6 - an XML processing library
pugixml 1.9 - an XML processing library
Copyright (C) 2006-2015, by Arseny Kapoulkine (arseny.kapoulkine@gmail.com)
Copyright (C) 2006-2018, by Arseny Kapoulkine (arseny.kapoulkine@gmail.com)
Report bugs and download new versions at http://pugixml.org/
This is the distribution of pugixml, which is a C++ XML processing library,
@@ -28,7 +28,7 @@ The distribution contains the following folders:
This library is distributed under the MIT License:
Copyright (c) 2006-2015 Arseny Kapoulkine
Copyright (c) 2006-2018 Arseny Kapoulkine
Permission is hereby granted, free of charge, to any person
obtaining a copy of this software and associated documentation

63
lib/serialisation/XmlIO.cc
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@@ -31,6 +31,17 @@ Author: paboyle <paboyle@ph.ed.ac.uk>
using namespace Grid;
using namespace std;
void Grid::xmlCheckParse(const pugi::xml_parse_result &result, const std::string name)
{
if (!result)
{
std::cerr << "XML parsing error for " << name << std::endl;
std::cerr << "XML error description: " << result.description() << std::endl;
std::cerr << "XML error offset : " << result.offset << std::endl;
abort();
}
}
// Writer implementation ///////////////////////////////////////////////////////
XmlWriter::XmlWriter(const string &fileName, string toplev) : fileName_(fileName)
{
@@ -54,6 +65,19 @@ void XmlWriter::push(const string &s)
node_ = node_.append_child(s.c_str());
}
void XmlWriter::pushXmlString(const std::string &s)
{
pugi::xml_document doc;
auto result = doc.load_buffer(s.c_str(), s.size());
xmlCheckParse(result, "fragment\n'" + s +"'");
for (pugi::xml_node child = doc.first_child(); child; child = child.next_sibling())
{
node_ = node_.append_copy(child);
}
pop();
}
void XmlWriter::pop(void)
{
node_ = node_.parent();
@@ -65,31 +89,23 @@ std::string XmlWriter::XmlString(void)
return oss.str();
}
XmlReader::XmlReader(const char *xmlstring,string toplev) : fileName_("")
{
pugi::xml_parse_result result;
result = doc_.load_string(xmlstring);
if ( !result ) {
cerr << "XML error description (from char *): " << result.description() << "\nXML\n"<< xmlstring << "\n";
cerr << "XML error offset (from char *) " << result.offset << "\nXML\n"<< xmlstring <<"\n";
abort();
}
if ( toplev == std::string("") ) {
node_ = doc_;
} else {
node_ = doc_.child(toplev.c_str());
}
}
// Reader implementation ///////////////////////////////////////////////////////
XmlReader::XmlReader(const string &fileName,string toplev) : fileName_(fileName)
XmlReader::XmlReader(const std::string &s, const bool isBuffer,
std::string toplev)
{
pugi::xml_parse_result result;
result = doc_.load_file(fileName_.c_str());
if ( !result ) {
cerr << "XML error description: " << result.description() <<" "<< fileName_ <<"\n";
cerr << "XML error offset : " << result.offset <<" "<< fileName_ <<"\n";
abort();
if (isBuffer)
{
fileName_ = "<string>";
result = doc_.load_string(s.c_str());
xmlCheckParse(result, "string\n'" + s + "'");
}
else
{
fileName_ = s;
result = doc_.load_file(s.c_str());
xmlCheckParse(result, "file '" + fileName_ + "'");
}
if ( toplev == std::string("") ) {
node_ = doc_;
@@ -98,7 +114,7 @@ XmlReader::XmlReader(const string &fileName,string toplev) : fileName_(fileName)
}
}
bool XmlReader::push(const string &s)
bool XmlReader::push(const std::string &s)
{
if (node_.child(s.c_str()))
{
@@ -129,7 +145,6 @@ bool XmlReader::nextElement(const std::string &s)
{
return false;
}
}
template <>

8
lib/serialisation/XmlIO.h
View File

@@ -43,6 +43,7 @@ Author: paboyle <paboyle@ph.ed.ac.uk>
namespace Grid
{
void xmlCheckParse(const pugi::xml_parse_result &result, const std::string name);
class XmlWriter: public Writer<XmlWriter>
{
@@ -50,6 +51,7 @@ namespace Grid
XmlWriter(const std::string &fileName, std::string toplev = std::string("grid") );
virtual ~XmlWriter(void);
void push(const std::string &s);
void pushXmlString(const std::string &s);
void pop(void);
template <typename U>
void writeDefault(const std::string &s, const U &x);
@@ -65,8 +67,8 @@ namespace Grid
class XmlReader: public Reader<XmlReader>
{
public:
XmlReader(const char *xmlstring,std::string toplev = std::string("grid") );
XmlReader(const std::string &fileName,std::string toplev = std::string("grid") );
XmlReader(const std::string &fileName, const bool isBuffer = false,
std::string toplev = std::string("grid") );
virtual ~XmlReader(void) = default;
bool push(const std::string &s);
void pop(void);
@@ -75,6 +77,8 @@ namespace Grid
void readDefault(const std::string &s, U &output);
template <typename U>
void readDefault(const std::string &s, std::vector<U> &output);
private:
void checkParse(const pugi::xml_parse_result &result, const std::string name);
private:
pugi::xml_document doc_;
pugi::xml_node node_;