+++ /dev/null
-:orphan:
-
-GROMACS
-=======
-
-Description
------------
-
-**GROMACS** is a full-featured suite of programs to perform molecular dynamics
-simulations - in other words, to simulate the behavior of systems with hundreds
-to millions of particles, using Newtonian equations of motion.
-It is primarily used for research on proteins, lipids, and polymers, but can be
-applied to a wide variety of chemical and biological research questions.
-
-Synopsis
---------
-
-The following commands make up the GROMACS suite. Please refer to their
-individual man pages for further details.
-
-.. include:: bytopic.rst
-
-Additional documentation
-------------------------
-
-Consult the manual at <http://www.gromacs.org> for an introduction to molecular
-dynamics in general and GROMACS in particular, as well as an overview of the
-individual programs.
-
-References
-----------
-
-The development of GROMACS is mainly funded by academic research grants.
-To help us fund development, the authors humbly ask that you cite the GROMACS papers:
-
-H.J.C. Berendsen, D. van der Spoel and R. van Drunen. **GROMACS: A message-passing
-parallel molecular dynamics implementation**. Comp. Phys. Comm. *91*, 43-56 (1995)
-
-Erik Lindahl, Berk Hess and David van der Spoel. **GROMACS 3.0: A package for
-molecular simulation and trajectory analysis**. J. Mol. Mod. *7*, 306-317 (2001)
-
-B. Hess, C. Kutzner, D. van der Spoel, and E. Lindahl. **GROMACS 4: Algorithms for
-Highly Efficient, Load-Balanced, and Scalable Molecular Simulation**.
-J. Chem. Theory Comput. *4*, 3, 435-447 (2008),
-<http://dx.doi.org/10.1021/ct700301q>
-
-Authors
--------
-
-Current developers:
-
-David van der Spoel <spoel@gromacs.org>
-Berk Hess <hess@gromacs.org>
-Erik Lindahl <lindahl@gromacs.org>
-
-A full list of present and former contributors
-is available at <http://www.gromacs.org>
-
-This manual page is largely based on the GROMACS online reference, and the text
-was prepared originally by Nicholas Breen <nbreen@ofb.net>.
-
-Bugs
-----
-
-GROMACS has no major known bugs, but be warned that it stresses your CPU more
-than most software. Systems with slightly flaky hardware may prove unreliable
-while running heavy-duty simulations. If at all possible, please try to
-reproduce bugs on another machine before reporting them.
#include "gromacs/onlinehelp/helpwritercontext.h"
#include "gromacs/options/basicoptions.h"
#include "gromacs/options/options.h"
+#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/baseversion.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/file.h"
const CommandLineModuleMap &modules,
const CommandLineModuleGroupList &groups);
- void exportHelp(HelpExportInterface *exporter) const;
+ void exportHelp(HelpExportInterface *exporter);
boost::scoped_ptr<RootHelpTopic> rootTopic_;
const ProgramContextInterface &programContext_;
struct RootHelpText
{
- static const char name[];
static const char title[];
static const char *const text[];
};
-// The first two are not used.
-const char RootHelpText::name[] = "";
-const char RootHelpText::title[] = "";
-const char *const RootHelpText::text[] = { "" };
+// These are used for the gmx.1 man page.
+// TODO: Do not hardcode them here, but pass them from the outside to make this
+// code more generic.
+const char RootHelpText::title[] = "molecular dynamics simulation suite";
+const char *const RootHelpText::text[] = {
+ "|Gromacs| is a full-featured suite of programs to perform molecular",
+ "dynamics simulations, i.e., to simulate the behavior of systems with",
+ "hundreds to millions of particles using Newtonian equations of motion.",
+ "It is primarily used for research on proteins, lipids, and polymers, but",
+ "can be applied to a wide variety of chemical and biological research",
+ "questions.",
+};
/*! \brief
* Help topic that forms the root of the help tree for the help subcommand.
*
* \ingroup module_commandline
*/
-class RootHelpTopic : public CompositeHelpTopic<RootHelpText>
+class RootHelpTopic : public AbstractCompositeHelpTopic
{
public:
/*! \brief
{
}
+ virtual const char *name() const { return helpModule_.binaryName_.c_str(); }
+ virtual const char *title() const { return title_.c_str(); }
+
//! Adds a top-level topic and optionally marks it as exported.
void addTopic(HelpTopicPointer topic, bool bExported)
{
addSubTopic(move(topic));
}
//! Exports all the top-level topics with the given exporter.
- void exportHelp(HelpExportInterface *exporter) const;
+ void exportHelp(HelpExportInterface *exporter);
virtual void writeHelp(const HelpWriterContext &context) const;
private:
+ // unused because of the writeHelp() override
+ virtual std::string helpText() const { return ""; }
+
const CommandLineHelpModuleImpl &helpModule_;
+ std::string title_;
std::vector<std::string> exportedTopics_;
GMX_DISALLOW_COPY_AND_ASSIGN(RootHelpTopic);
};
-void RootHelpTopic::exportHelp(HelpExportInterface *exporter) const
+void RootHelpTopic::exportHelp(HelpExportInterface *exporter)
{
std::vector<std::string>::const_iterator topicName;
for (topicName = exportedTopics_.begin();
GMX_RELEASE_ASSERT(topic != NULL, "Exported help topic no longer found");
exporter->exportTopic(*topic);
}
+ // For now, the title is only set for the export to make it not appear in
+ // console output, which makes things consistent for 'gmx help' and
+ // 'gmx help <command>'.
+ title_ = RootHelpText::title;
+ exporter->exportTopic(*this);
}
void RootHelpTopic::writeHelp(const HelpWriterContext &context) const
{
- if (context.outputFormat() != eHelpOutputFormat_Console)
- {
- // TODO: Implement once the situation with Redmine issue #969 is more
- // clear.
- GMX_THROW(NotImplementedError(
- "Root help is not implemented for this output format"));
- }
{
- CommandLineCommonOptionsHolder optionsHolder;
- CommandLineHelpContext cmdlineContext(*helpModule_.context_);
- cmdlineContext.setModuleDisplayName(helpModule_.binaryName_);
+ CommandLineCommonOptionsHolder optionsHolder;
+ boost::scoped_ptr<CommandLineHelpContext> cmdlineContext;
+ if (helpModule_.context_ != NULL)
+ {
+ cmdlineContext.reset(new CommandLineHelpContext(*helpModule_.context_));
+ }
+ else
+ {
+ cmdlineContext.reset(new CommandLineHelpContext(context));
+ }
+ cmdlineContext->setModuleDisplayName(helpModule_.binaryName_);
optionsHolder.initOptions();
+ Options &options = *optionsHolder.options();
+ options.setDescription(RootHelpText::text);
// TODO: Add <command> [<args>] into the synopsis.
- CommandLineHelpWriter(*optionsHolder.options())
- .writeHelp(cmdlineContext);
+ CommandLineHelpWriter(options)
+ .setShowDescriptions(context.outputFormat() != eHelpOutputFormat_Console)
+ .writeHelp(*cmdlineContext);
+ }
+ if (context.outputFormat() == eHelpOutputFormat_Console)
+ {
+ // TODO: Consider printing a list of "core" commands. Would require someone
+ // to determine such a set...
+ writeSubTopicList(context,
+ "Additional help is available on the following topics:");
+ // TODO: Make these respect the binary name passed in, to make tests work better.
+ context.writeTextBlock("To access the help, use '[PROGRAM] help <topic>'.");
+ context.writeTextBlock("For help on a command, use '[PROGRAM] help <command>'.");
+ }
+ else
+ {
+ context.writeTitle(formatString("%s commands", helpModule_.binaryName_.c_str()));
+ context.writeTextBlock(
+ "The following commands are available. Please refer to their "
+ "individual man pages or [TT][PROGRAM] help <command>[tt] "
+ "for further details.");
+ context.writeTextBlock("");
+ context.writeTextBlock(".. include:: /man/bytopic.rst");
}
- // TODO: Consider printing a list of "core" commands. Would require someone
- // to determine such a set...
- writeSubTopicList(context,
- "Additional help is available on the following topics:");
- // TODO: Make these respect the binary name passed in, to make tests work better.
- context.writeTextBlock("To access the help, use '[PROGRAM] help <topic>'.");
- context.writeTextBlock("For help on a command, use '[PROGRAM] help <command>'.");
}
/********************************************************************
private:
FileOutputRedirectorInterface *outputRedirector_;
+ const std::string &binaryName_;
HelpLinks links_;
boost::scoped_ptr<File> indexFile_;
boost::scoped_ptr<File> manPagesFile_;
HelpExportReStructuredText::HelpExportReStructuredText(
const CommandLineHelpModuleImpl &helpModule)
: outputRedirector_(helpModule.outputRedirector_),
+ binaryName_(helpModule.binaryName_),
links_(eHelpOutputFormat_Rst)
{
File linksFile("links.dat", "r");
// This would make Sphinx reruns much faster.
File file(outputRedirector_->openFileForWriting("programs/" + tag + ".rst"));
file.writeLine(formatString(".. _%s:", displayName.c_str()));
- if (0 == displayName.compare("gmx mdrun"))
+ if (0 == displayName.compare(binaryName_ + " mdrun"))
{
// Make an extra link target for the convenience of
// MPI-specific documentation
file.writeLine(" See also");
file.writeLine(" --------");
file.writeLine();
- file.writeLine(" :manpage:`gromacs(7)`");
+ file.writeLine(formatString(" :manpage:`%s(1)`", binaryName_.c_str()));
file.writeLine();
file.writeLine(" More information about |Gromacs| is available at <http://www.gromacs.org/>.");
file.close();
{
indexFile_->close();
indexFile_.reset();
- manPagesFile_->writeLine(" ('man/gromacs.7', 'gromacs', 'molecular dynamics simulation suite', '', 7)");
+ // TODO: Generalize.
+ manPagesFile_->writeLine(
+ formatString(" ('programs/%s', '%s', '%s', '', 1)",
+ binaryName_.c_str(), binaryName_.c_str(),
+ RootHelpText::title));
manPagesFile_->writeLine("]");
manPagesFile_->close();
manPagesFile_.reset();
indexFile_->writeLine(title);
indexFile_->writeLine(std::string(std::strlen(title), '-'));
manPagesFile_->writeLine(title);
- manPagesFile_->writeLine(std::string(std::strlen(title), '+'));
+ manPagesFile_->writeLine(std::string(std::strlen(title), '^'));
ModuleGroupContents::const_iterator module;
for (module = modules.begin(); module != modules.end(); ++module)
indexFile_->writeLine(formatString("| :doc:`%s <%s>` - %s",
displayName.c_str(), tag.c_str(),
module->second));
- manPagesFile_->writeLine(formatString("| ``%s`` - %s",
- displayName.c_str(),
+ manPagesFile_->writeLine(formatString(":manpage:`%s(1)`\n %s",
+ tag.c_str(),
module->second));
}
indexFile_->writeLine();
const std::string path("programs/" + std::string(topic.name()) + ".rst");
File file(outputRedirector_->openFileForWriting(path));
HelpWriterContext context(&file, eHelpOutputFormat_Rst, &links_);
+ if (topic.name() == binaryName_)
+ {
+ context.writeTextBlock(":orphan:");
+ context.writeTextBlock("");
+ }
HelpManager manager(topic, context);
manager.writeCurrentTopic();
}
{
}
-void CommandLineHelpModuleImpl::exportHelp(HelpExportInterface *exporter) const
+void CommandLineHelpModuleImpl::exportHelp(HelpExportInterface *exporter)
{
// TODO: Would be nicer to have the file names supplied by the build system
// and/or export a list of files from here.
return 0;
}
- File &outputFile = impl_->outputRedirector_->standardOutput();
- HelpLinks links(eHelpOutputFormat_Console);
+ File &outputFile = impl_->outputRedirector_->standardOutput();
+ HelpLinks links(eHelpOutputFormat_Console);
initProgramLinks(&links, *impl_);
- boost::scoped_ptr<CommandLineHelpContext> context(
- new CommandLineHelpContext(&outputFile,
- eHelpOutputFormat_Console, &links));
- context->setShowHidden(impl_->bHidden_);
+ CommandLineHelpContext context(&outputFile, eHelpOutputFormat_Console, &links);
+ context.setShowHidden(impl_->bHidden_);
if (impl_->moduleOverride_ != NULL)
{
- context->setModuleDisplayName(impl_->programContext_.displayName());
- impl_->moduleOverride_->writeHelp(*context);
+ context.setModuleDisplayName(impl_->programContext_.displayName());
+ impl_->moduleOverride_->writeHelp(context);
return 0;
}
- impl_->context_ = context.get();
+ impl_->context_ = &context;
- HelpManager helpManager(*impl_->rootTopic_, context->writerContext());
+ HelpManager helpManager(*impl_->rootTopic_, context.writerContext());
try
{
for (int i = 1; i < argc; ++i)
('programs/test-help', 'test-help', "Print help information", '', 1),
('programs/test-module', 'test-module', "First module", '', 1),
('programs/test-other', 'test-other', "Second module", '', 1),
- ('man/gromacs.7', 'gromacs', 'molecular dynamics simulation suite', '', 7)
+ ('programs/test', 'test', 'molecular dynamics simulation suite', '', 1)
]
]]></String>
<String Name="programs/test-help.rst"><![CDATA[
See also
--------
- :manpage:`gromacs(7)`
+ :manpage:`test(1)`
More information about |Gromacs| is available at <http://www.gromacs.org/>.
]]></String>
See also
--------
- :manpage:`gromacs(7)`
+ :manpage:`test(1)`
More information about |Gromacs| is available at <http://www.gromacs.org/>.
]]></String>
See also
--------
- :manpage:`gromacs(7)`
+ :manpage:`test(1)`
More information about |Gromacs| is available at <http://www.gromacs.org/>.
]]></String>
]]></String>
<String Name="man/bytopic.rst"><![CDATA[
Group 1
-+++++++
-| ``test module`` - First module
+^^^^^^^
+:manpage:`test-module(1)`
+ First module
Group 2
-+++++++
-| ``test other`` - Second module
+^^^^^^^
+:manpage:`test-other(1)`
+ Second module
]]></String>
<String Name="programs/topic1.rst"><![CDATA[
Another topic
=============
Help text
+]]></String>
+ <String Name="programs/test.rst"><![CDATA[
+:orphan:
+
+molecular dynamics simulation suite
+===================================
+Synopsis
+--------
+::
+
+ test [-[no]h] [-[no]quiet] [-[no]version] [-[no]copyright] [-nice <int>]
+ [-[no]backup]
+
+Description
+-----------
+|Gromacs| is a full-featured suite of programs to perform molecular
+dynamics simulations, i.e., to simulate the behavior of systems with
+hundreds to millions of particles using Newtonian equations of motion.
+It is primarily used for research on proteins, lipids, and polymers, but
+can be applied to a wide variety of chemical and biological research
+questions.
+
+Options
+-------
+Other options:
+
+``-[no]h`` (no)
+ Print help and quit
+``-[no]quiet`` (no)
+ Do not print common startup info or quotes
+``-[no]version`` (no)
+ Print extended version information and quit
+``-[no]copyright`` (yes)
+ Print copyright information on startup
+``-nice`` <int> (19)
+ Set the nicelevel (default depends on command)
+``-[no]backup`` (yes)
+ Write backups if output files exist
+
+test commands
+-------------
+The following commands are available. Please refer to their individual man pages or ``commandline-test help <command>`` for further details.
+
+.. include:: /man/bytopic.rst
]]></String>
</ReferenceData>
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff