seisflows refactor and overhaul (v2.1.0) #139
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…dding arguments and not just *args
…t makes more sense to have it be a solver function
…t module capabilities
…ge. all future development will just take place in seisflows directory to avoid confusion removed 'edit' command from CLI tool
…voids confusion about having incomplete 'base' modules which aren't useful on their own
…n. no api changes, just more concise source code and functions residing in more logical locations. Also replaced the Dict object defined in config with a simpler dictionary replacement
…ep things simpler cleaning up docstrings and code formatting around
Refactors the code for better source code readability. Does not change public api of the codebase.
…ntiated. reworked init statement to avoid this
…ters for a freshly created parameter file
…rameters, these can just be read from the SPECFEM Par_file which is assumed to be correct. Also removed the checks related to these and adjusted the way misfit is calculated so that it doesnt explicitely need to be passed this information combined some of the solver parameters which were redundant optimization rosenbrock test running but not working as intended
…s definitions, which avoids some funky late type conversions in config defined a seisflows Base object which dictates the structure that all seisflows modules must have. This is intended to replace the individual Base objects defined in each of the sub-modules old Base modules (preprocess, postprocess) will now be named Default to better signify their role in the workflow (Base felt too abstract) removed Solver plugins. they weren't being used Removed error tools as they seemed overly abstract and were only used in one location. Replaced ParameterError with ValueError in the one instance of it Postprocess.default is now redefined with the new Base class definition, which no longer calls sys modules at the top of the script, removes the required property and defines required in __init__, inherits some properties from Base and explicitely defines super() where functions are being inherited.
…iables housing strings for seisflows_parameters and seisflows_paths
… 1) not explicitely importing opther modules with sys modules during import, but are doing this at run time with the self.par attribute required paths and parameters are defined in __init__ and the required() attribute is now removed. We explicitely call inherited functions, even if they are just calling the underlying functions. This will make it easier for new users to track down where functions are coming from. Child classes which define new methods will make these methods private (leading underscore) so as to not confuse them with inherited or overwritten methods of the base class also going back to the old method of explicitely stating things (e.g., naming 'scratch' instead of hiding it behind PATH.SCRATCH). This leads to repeated strings, but makes it easier to follow structure
…only a specfem dependent base class, and to remove confusion from core base class
…n', whereas before it was 'installation'
…to flag '--with_mpi' when running example, removed example 4 since we can just run example 3 with MPI which is the same thing
…proc parameters to allow running with mpi directly
feature singularity workflow to deal with Chinook incompatible operating system
…Docker image on Chinook. Removes a lot of the automation of SeisFlows but this first go is for making sure this approach will work for running SeisFlows on Chinook through Singularity
…es, whereas before their logs were sent to the ether removed check function from singularity because the checks were not working from inside the container workstation now always checks mpiexec, even if nproc == 1
…quicker identification
…y to avoid any confusion and broken symlinks when running out of a container
plot_2d_image adds NaN values to the top edge of the model before interpolation to the regular grid. In order to, fix the representation issue with complex topographies.
Plot 2D improvement for models with complex topographies
starting work on optimization of command line tool and package imports for speeduprelated to #138
…ts own tool for faster imports SeisFlows command line tool moved heavier imports into functions to speed up call times for other functions that don't need it fixed import statements and all tests pass
…em time to catch up also fixed bug where job number had new lines in it removed specfem3d chinook version, not needed anymore
migration has a new exit condition if no misfit kernels are created from the combine/smooth operation
…e slurm submission system causing errors
bch0w
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Major package overhaul constituting PRs from #124 to #137. Please see relevant issues and PR's for changes made, but bullet point of the changes involved in devel since PR #124
Relevant PRs: #124 #125 #126 #127 #128 #129 #130 #131 #132 #133 #134 #135 #137
Relevant Issues: #123 #12 #138