Issue 395 - Adds support for reading the sources as a yaml-node

[lsawade]

Description

The current framework of defining the source-file makes it difficult to read the specfem_config.yaml. This dislodges the current setup of reading databases and sources together. By creating a setup.sources entity and setup.get_sources which returns a YAML::Node.

If the source-file is defined setup.sources will be populated with a YAML::Node that is loaded from source-file. If source-dict is defined setup.sources is populated directly with the source-dict YAML::Node.

This allows for defining the sources in Python as part of the runtime_config dictionary.

See here for a very barebone implementation of a simulation in Python with bathymetry: Example

For now I'm not adding documentation because I do not think we want the CPP user to use the code like this.

Also, a general overhaul of the setup structure may be necessary. To not break anything setup.get_databases() still returns a tuple, but source_database is an empty string of the database_configuration was instantiated with using source-dict.

Issue Number

Closes #395

Checklist

Please make sure to check developer documentation on specfem docs.

• I ran the code through pre-commit to check style
• My code passes all the integration tests
• I have added sufficient unittests to test my changes
• I have added/updated documentation for the changes I am proposing
• I have updated CMakeLists to ensure my code builds
• My code builds across all platforms