feat: Unified binary (CLI)

[Charlotte-Knight]

User Interface

This PR introduces a single binary through which to run MaCh3 executables. In other words, it introduces a unified CLI.

For example, one can run mach3 --help and get:

Usage:  [--help] [--version] {diag,penterm,process,tutorial}

Optional arguments:
  -h, --help     shows help message and exits
  -v, --version  prints version information and exits

Subcommands:
  diag
  penterm
  process       Main exectable responsible for different types of MCMC processing like drawing posteriors, triangle plots etc.

and then run ProcessMCMC with:

mach3 process config.yaml chain.root

So far, the following executables have been implemented:

• DiagMCMC
• ProcessMCMC
• GetPenaltyTerm

And the functionality exists for experiments to add their own executables via plugins. An example of this is included in MaCh3Tutorial via this PR: mach3-software/MaCh3Tutorial#252. There, you can run the MCMCTutorial executable like:

mach3 tutorial TutorialConfigs/FitterConfig.yaml --MCMCSteps 100000

The previous name for the commands can still be used like:

ProcessMCMC config.yaml chain.root

and the user will be presented with a deprecation warning like:

[2026-06-01 14:04:37.661] [warning] [ProcessMCMC.cpp:5] Deprecation Warning: Use of the standalone executable will be deprecated in future releases.
[2026-06-01 14:04:37.661] [warning] [ProcessMCMC.cpp:6]                    : you can use 'mach3 process' as a direct replacement instead.

Feedback

We're open to suggestions about the naming of the commands, e.g. whether mach3 process makes sense or maybe mach3 processmcmc etc. And anything other comments are welcome of course.

Future Plans

Assuming that this PR is merged, we imagine that this executable will start to gain traction with some users, and hopefully, we can gather feedback. In time, we can implement that feedback and eventually implement the rest of the executables and remove the old interface.

Implementation

TODO: Comments about implementation for the other devs. For example, all of the executables going under the CLI/API directory.

Subcommand map

Old Executable Name	CLI Subcommand
ProcessMCMC	process
DiagMCMC	diag
GetPenaltyTerm	penterm

---

• I have read and followed the contributing guidelines.

[KSkwarczynski]

I have plenty of comments, although majority are nitpicky and style.

My main comment is lack of documentation or short explanation why X was done like this etc.

Doesn't have to be encyplopedia.

[KSkwarczynski]

Is std::cerr etc used here because it is part of CLI not actual executable?

[KSkwarczynski]

Can we hide this under MaCh3_Safe_Include_Start ?

MaCh3/Manager/Core.h

Lines 122 to 125 in d491feb

	/// @brief KS: Avoiding warning checking for headers
	/// @details Many external files don't strictly adhere to rigorous C++ standards.
	/// Inline functions in such headers may cause errors when compiled with strict MaCh3 compiler flags.
	/// @warning Use this for any external header file to avoid warnings.

[alexanderrichards]

I don't understand this comment, can you ellaborate?

[KSkwarczynski]

So mach3 is compiled with very rigorous set compilation flags (Werror, Wall etc.)
Sometimes header files have actual implementation and they "external" headers are being compiled with MaCh3 flags.

Which causes compilation errors.

By doing

_MaCh3_Safe_Include_Start_ //{
#include "argparse/argparse.hpp"
_MaCh3_Safe_Include_End_ //}

we says compiler to ignore some warnigns/errors for a given header.
Which allows to avoid having annoing errors.

[KSkwarczynski]

I also think this need to be updated

MaCh3/cmake/Templates/Doxyfile.in

Lines 858 to 872 in d491feb

	INPUT = . \
	Doc/MaCh3Web/mainpage.md \
	Doc/MaCh3Web/Definitions.dox \
	Doc/mach3logo.png \
	Manager \
	Splines \
	Samples \
	NuDock \
	Fitters \
	Diagnostics \
	Plotting \
	Plotting/plottingUtils \
	Parameters \
	python \
	Doc/User-Guide/

[KSkwarczynski]

There are some merge conflicts.

Is it possible to use
///
instead of

/**
 *
 */

for a doxygen to be consistent with rest of code base?