yaml output in ulnes_model_fit.py

[rpoleski]

Adding output in YAML format was on my task list for quite some time. The obvious advantage is that such output can then be easily read using python scripts. I see your approach is to add print(..., file=self._yaml_results_file) in many places. This makes some functions quite long, so it would be good to make them shorter. The disadvantage is that the code structure is less clear - there are many if self._yaml_results: statements in different places of the code. The alternative would be to add to a dict everything that should go to the output file and print it at the end using something like:

with open(self._output_yaml_file, "w") as output:
    yaml.dump(self._yaml_info, output, default_flow_style=False)

Here we get less control over how exactly the file looks like. I'm not yet sure which approach is better. Note that current changes do not work if fitting is done using MultiNest instead of EMCEE. Any opinions?

[rpoleski]

I would change option name: "results" -> "yaml output" (i.e., more specific). Current approach allows sending the yaml output to standard output, which for me doesn't make much sense. Current version is OK and only some minor changes will be needed. I should work on it soon.

[rpoleski]

Ok, I've better understood this code. I've realized that flush=True was there similarly to self._print_model_file. I've brought it back. To be done:

• [x] make format fully compliant with yaml standard; current output would be loaded as, e.g., 'u_0': '0.52807 +0.03417 -0.02608' and we would like a list or a dict instead of a string that has 3 floats,
• [x] test MultiNest output,
• [x] "Best model" section should have 3 keys: chi2, parameters, and fluxes,
• [x] decide if we want to allow yaml-format output to sys.stdout - @mjmroz what do you think?
• [ ] update version number and accept PR.

[rpoleski]

Tasks left + new ones:

• [x] YAML output for MN with multimode,
• [x] shorten: _parse_results_MultiNest_multimodal(),
• [x] shorten: _parse_other_output_parameters(),
• [x] MAYBE shorten: _print_yaml_best_model(),
• [x] test all possible EMCEE/MNsinglemode/MNmultimode combinations once more,
• [x] update version number
• [x] accept PR