Fixing DPI settings

[ns-rse]

Closes #807

Current process is...

1. topostats/entry_point.create_parser : get arguments from commandline via the process_parser subparser (includes DPI)
2. topostats/run_topostats.run_topostats() : loads the dictionary and updates it with any values from arg, will update savefig_dpi with --savefig-dpi value.
3. Validate the updated configuration.
4. Load the default topostats/plotting_dictionary.yaml to the main config["plotting"]["plot_dict"]". This adds in all the image specific settings such as title and importantly DPI values for each image.
5. Validate the config["plotting"] configuration.
6. Update the plotting configuration with via utils.update_plotting_config(). This adds all the options not defined in the plotting_dictionary with those from topostats/default_config.yaml.

This was wrong because we have plotting_config["plot_dict"][image] = {**options, **main_config} and so the options from **main_config override those from **options as you can not have dictionaries with duplicate keys.

This has been fixed by...

1. Updating the values from plot_dictionary with any that exist in the default_config.yaml under the plotting section. Importantly this means that if any are None they do not update, logic that already existed in update_config().
2. Then adding to each image within plot_dictionary any values from the plotting section of default_config.yaml that do not already exist.

This avoids replacing the defaults from plot_dictionary with None values from the plotting section of default_config.yaml.

Tests included which check equality of dictionaries and that LOGGER.info() is included when changes are made to the DPI.

Other Changes

• LOGGER.info() to LOGGER.debug() in topostats.io.dict_to_hdf5 as I don't think printing the keys is that informative.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 84.77%. Comparing base (de3ac4b) to head (ccfbe23).
Report is 63 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #808      +/-   ##
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+ Coverage   84.73%   84.77%   +0.04%     
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  Files          21       21              
  Lines        3196     3205       +9     
==========================================
+ Hits         2708     2717       +9     
  Misses        488      488              

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[MaxGamill-Sheffield]

Looks good, and tests well!

I've just added a commit to change the "Options: .." bit in the config file so it no longer talks about "figure".

P.S. thanks for changing the .topostats logger setting too, it was driving me up the wall hahaha