Cloudy big fix

[stephenmwilkins]

This is mostly concerned with updating the cloudy grid generation functionality.

• more comments/descriptions
• updated handling of abundances
• updated (some) parameter files
• updated synthesizer grid creation and fixed bug
• added cloudy functionality (requires the correct synthesizer branch)
• removed the Apollo specific pipeline for use in a separate repo

I have not:

• Updated all the parameter files for the different variants [waiting for feedback]
• I have not implemented grid_io functionality because these codes create HDF5 files in a different way and I do not believe it's a good use of effort at the moment.

Issue Type

• [x] Bug
• [x] Document
• [x] Enhancement

Checklist

• [x] I have read the [CONTRIBUTING.md]()
• [x] I have added docstrings to all methods
• [x] I have added sufficient comments to all lines
• [x] I have made corresponding changes to the documentation
• [x] My changes generate no pep8 errors
• [] I have added tests that prove my fix is effective or that my feature works
• [x] New and existing unit tests pass locally with my changes

[sophie-newman]

What is c23.01-sps-c17.03.yaml ? Confused about it being both c23.01 and c17.03

[stephenmwilkins]

What is c23.01-sps-c17.03.yaml ? Confused about it being both c23.01 and c17.03

Understandable confusion, this is going to be for testing. When we implement c23.01 there are going to be different default choices from c17.03. This parameter file is meant for running c23.01 but using the default choices in c17.03. I couldn't think of a better name!

[sophie-newman]

What is c23.01-sps-c17.03.yaml ? Confused about it being both c23.01 and c17.03

Understandable confusion, this is going to be for testing. When we implement c23.01 there are going to be different default choices from c17.03. This parameter file is meant for running c23.01 but using the default choices in c17.03. I couldn't think of a better name!

Ah I see. I did create a c23.01 param file though using the c17.03 params assuming they would be updated in time

[stephenmwilkins]

FYI this now works correctly insofar as it can be used to generate cloudy input grid and then a synthesizer reprocessed grid.

[sophie-newman]

I will run these changes through my codes tomorrow when I have more time to check them before merging anything