wip: Adding all configuration options as arguments #988
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- Renames `toposats.run_topostats` > `topostats.run_modules` as its more descriptive of what the submodule is doing. - Moves generic command line options to be arguments of the parser. - Adds arguments to each sub-parser for all module options. - Adds tests to check that each argument is correctly returned. - Updated and made a few names consistent. This is still a Work In Progress but it shouldn't break anything (tests have all passed locally). Whether to merge this depends perhaps on the desire to tag and make a release and whether there is anything else pending that is considered essential to be in that release (e.g. documentation). If so then _don't_ merge this.
ns-rse
requested review from
MaxGamill-Sheffield,
SylviaWhittle and
llwiggins
Tests using [`pytest-regtest-2.3.2`](https://pypi.org/project/pytest-regtest/#history) are [failing on OSX](https://github.com/AFM-SPM/TopoStats/actions/runs/11780199328/job/32810287345?pr=988) pegging version to `pytest-regtest==2.3.1` to see if this resolves the issue.
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Merge conflict resolved and a temporary fix to get around a problem with |
SylviaWhittle
approved these changes
Nov 12, 2024
Co-authored-by: Sylvia Whittle <[email protected]>
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toposats.run_topostats>topostats.run_modulesas its more descriptive of what the submodule is doing.This is still a Work In Progress but it shouldn't break anything (tests have all passed locally).
Whether to merge this depends perhaps on the desire to tag and make a release and whether there is anything else pending that is considered essential to be in that release (e.g. documentation). If so then don't merge this.