Seisflows

- Hotfix for updated SPECFEM2D parameter file 197

A collection of bugfixes and feature improvement (big thanks to evcano for major PR 168)

- Improved code organization for readability
- Allow acoustic domain and pressure seismograms in SPECFEM2D (164)
- Improved workflow feature `export_residuals` (168)
- Allow workflow toggling of SPECFEM parameter `SAVE_FORWARD_ARRAYS`
- System support for HPC Wisteria (U. Tokyo) (176)
- Makes the location of the `submit` and `run` scripts a System Class
variable which can be overwritten.
- Adds `system.Fujitsu` as a generalized System class for HPCs using the
Fujitsu workload manager
- Adds `system.Wisteria` for System interactions with HPC Wisteria
- Custom run and submit scripts for Wisteria hardcoded to RSCGRP RC58, not
generalized at the moment

Bugfixes
- Broken symlinks for Cluster runscript locations when SeisFlows is
installed via Pip (162), added Manifest.in file to fix this.
- Max workers in concurrent jobs was set with the wrong variable (160), replaced iwth correct variable
- Bracketing line search allows non-passing models to pass line search under certain criteria, fixed.
- Solver directory intialization was too general when searching for
source files (169), leading to an incorrect number of source files being detected, process now only looks for sources files that start with source prefix (e.g., CMTSOLUTION, FORCESOLUTION)
- Residuals files were sometimes written incorrectly (168) which lead to broken file reading. Residuals files are now written out at a more granular level to avoid multiple processes trying to write to one file
- Residuals files were appended to by all processes during line search, leading to incorrect misfit values (168); fixed by above bugfix.
- Updated trial model was not exposed to line search after step count > 1 (168), fixed
- Incorrect step lengths defined when resuming workflow (168), fixed
- Exported synthetic traces were overwritten each iteration (168). They are now tagged by iteration + step count to avoid overwriting
- output_optim.txt was not writing the correct misfit values for each
iteration, fixed

155
- Synthetics and observations can have a different format
- New parameters `obs_data_format` and `syn_data_format` replace old parameter
`data_format`
- Observations can have SAC format
- Added <unit_output> variable to default preprocessing module
- Added hard check: the observed and synthetic data format must be correct
- Added hard check: synthetic and observations files must match
- Added function to check that all required adjoint sources exist
- Critical Bugfix: Adjoint traces were incorrectly written as synthetics and not
as calculated adjoint sources.

158
- Removes GitHub links in dependencies in favor of PyPi packages
- Fixes broken Pyatoa import statements
- Pyadjoint misfit functions are now listed properly in the Pyaflowa docstring-

- Updates and simplifies install procedure using 'environment.yml' and
'pyproject.toml' files.
- Docs: Adds contributor's guide message to main docs page