Fixes examples and bugfixes solver and default preprocessing module

[bch0w]

This PR fixes examples in the devel branch after some API changes had broken them, which includes updates and bugfixes to the Solver and Preprocessing modules. Currently all 3 examples are now working and generally matching previous results. Most importantly, fixes some critical bugs that were introduced to the Default preprocessing module in #181

Change Log

Examples

• Updates parameter names to match updates that originally broke examples in #181

Preprocessing

• Adds developer 'serial' mode for Default preprocessing for better debugging

Bugfixes

• Critical: Default trim function was swapping obs and syn waveforms leading to incorrect misfit and adjoint sources
• Critical: Removes previous update to traveltime misfit function which did not allow negative misfit, causing incorrect adjoint sources, while retaining requirement for positive-only misfit values
• Fixes Default preprocessing waveform plotting (better scaling)
• Adds iteration and step count to file IDs of waveform figures so that subsequent plotting does not overwrite figures
• Fixes default preprocess inability to grab future results during preprocessing

Solver

• Fixes updates to SPECFEM2D parameter file that was not allowing velocity model to be changed
• Solver was not properly copying over initial model files due to uninstantiated path (order of operations error)
• Feature generate_data now saves synthetic observations to disk (path_data) and then copies over to scratch directory

General Updates

• Aesthetic fix to allow new lines after text borders on standardized messages, previously inputs were placed on the same line as the border
• Fixes workflow crashing when line search fails due to not being evaluate the NoneType that is passed around for model

[bch0w]

Hi @mnagaso, the latest devel branch should have some working examples for you to look at. Please let me know if you run into any other issues or have any questions! Thanks again for bringing this up!

[mnagaso]

Hello @bch0w,

Thank you very much for your immediate update for the examples! This PR is very helpful for me to understand the structure of the library and your recent updates! I am briefly trying to use seisflows. So I will be very happy if I will be able to make any futher feedbacks.

I very much like the abstruction of the code structure for using all the 3 varieties of Specfem with one library.

[bch0w]

No problem! I appreciate your feedback so far, it'll be very useful to have your continued input on the code. And you can thank @rmodrak for the structure, the modular design he implemented has been really nice to work with as the package grows in complexity.