Configurable group ids region names

[mgeplf]

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[codecov-commenter]

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[mgeplf]

@lecriste; this is ready to try - please pass the config with the updates for the steps that require changes, and let me know if it it works

[lecriste]

I tested the four steps requiring the config and I confirm I got the expected result.

[lecriste]

The main Readme should be updated with the new --group-ids-config-path argument for the four CLIs,

[mgeplf]

The main Readme should be updated with the new --group-ids-config-path argument for the four CLIs

Since it's not a required argument, I think it's ok to allow people to discover it themselves if they need the additional configurability.

[lecriste]

The main Readme should be updated with the new --group-ids-config-path argument for the four CLIs

Since it's not a required argument, I think it's ok to allow people to discover it themselves if they need the additional configurability.

How can one discover it?

[mgeplf]

How can one discover it?

Using the --help that's provided with all the commands and subcommands:

atlas-densities cell-densities glia-cell-densities --help

[lecriste]

How can one discover it?

Using the --help that's provided with all the commands and subcommands:

atlas-densities cell-densities glia-cell-densities --help

I find it quite hidden.
Also, it is a required argument for the functions, it's just the click option that provides a default value.

[mgeplf]

I find it quite hidden.

It's a tradeoff between having a readme that is quite large and comprehensive vs. something that can be run and tested for people to see what is available - if they need more functionality, they should read the --help options, IMO.

Also, it is a required argument for the functions, it's just the click option that provides a default value.

The README is documenting the CLI, so the fact that it's required for the function isn't really an issue, I would say.

[lecriste]

I would mention the new config CLIs argument in the main ReadMe.