command line tools builds

[pavlis]

Our current setup does not seem to have a mechanism to build any kind of command line tools that can be run from the unix shell from the command line. At present, I think we have two that are not installed in a way the users can use them. The ones I'm aware of are found in python/mspasspy/db/script. They are command line tool called dbverify and dbclean.

In the cxx tree we have the functionality of a "make install' that creates 3 directories under MSPASS_HOME (or it might be MSPASSHOME) called: data, include, and lib. I think we need:

1. To add a "bin" directory to the install tree
2. We need a mechanism to install python command line tools like dbclean and dbverify to that bin directory.

That is a suggestion, but the details about where this is installed and how are less important. What we need is a standard place to put command line tools that users would execute from the command line. Since our container runs a unix os that is sensible and we could set up the container to have that directory in the path some a shell run from a notebook would immecdiately see those tools.

This could be useful in a number of contexts:

1. I can see uses for some simple command line tools that simplify certain standard operations like pretty printing of certain standard reports.
2. I can see a reason for the evolution of adopting certain common C or Fortran programs for data prep. Maybe less for the framework itself, but we should have a place for user's to put special stuff they need for their special applications using some legacy code.

This came up because I encountered this issue when converting my plane wave migration code - an example legacy code. I have a set of command line tools I use for data preparation that need a home and right now I don't know how to handle it short of a manual copy of the python scripts to some special directory.

[pavlis]

postscript to the previous. I have a specific example script I want to generalize to put into mspass that has emerged as a need for handling the pwmig conversion. The tool I have in mind is a generic tool to convert a table stored in a text file (csv or text file in fixed formats ala Antelope's Datascope) and store the results in a MongoDB collection. I don't think the tool needs to be designed by committee, but I think you will likely agree when I'm done it will have some utility. It needs to be a command line tool but in python, so resolving the topic of this discussion will be important.

[wangyinz]

The bin directory is already there. If you go to our mspass container, you can see that the two scripts (dbclean and dbverify) are in the correct directory:

# which mspass-dbclean
/usr/local/bin/mspass-dbclean
# ls /usr/local/bin/mspass*
/usr/local/bin/mspass-dbclean  /usr/local/bin/mspass-dbverify

Note that the setup will put them under the /usr/local/bin if we do a system install, and it should be under the ~/.local/ directory for the user install. I believe this is also the common behavior of Python packages. All you need to do is to create the script and then point to them in the setup.py script here:

mspass/setup.py

Lines 66 to 71 in 35c5e77

	ENTRY_POINTS = {
	'console_scripts': [
	'mspass-dbclean = mspasspy.db.script.dbclean:main',
	'mspass-dbverify = mspasspy.db.script.dbverify:main',
	],
	}

To put a C binary into the same bin directory using the setup.py script is a bit tricky. I guess we could do something similar to what we setup for the ccore module here:

mspass/setup.py

Lines 41 to 43 in 35c5e77

	extdir = os.path.abspath(os.path.dirname(self.get_ext_fullpath(ext.name)))
	cmake_args = ['-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=' + extdir,
	'-DPYTHON_EXECUTABLE=' + sys.executable]

All we need to do is set the CMAKE_RUNTIME_OUTPUT_DIRECTORY variable properly, but I am not exactly sure how at the moment. The other question is whether we have an absolute need to have binaries written in C for the main mspass package. It seems to me that this is better to be avoided.