feature(config|run_modules): make default_config flexible#1301
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Whilst developing entry points for [AFMSlicer](https://github.com/AFM-SPM/AFMSlicer) I found that the current implementation of the `config.reconcile_config_args()` function was too restrictive. Try and use it in another package and it will load the `default_config.yaml` from TopoStats. This pull-request changes the functionality and adds the parameter `default_config` to the `config.reconcile_config.args()`. This is loaded via `get_data(package=topostats.__package__, resource="default_config.yaml")` prior to calling `reconcile_config_args()` (and so AFMSlicer will use `get_data(package=afmslicer.__package__, resource="default_config.yaml")`). All pre-commit and unit/regression tests pass.
Ensures `TopoStats.config` attribute is `deepcopy()` of the configuration passed into the `LoadScans` class.
SylviaWhittle
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Feb 18, 2026
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I haven't tested this locally, but this reads correct, and I assume you've tested it for what you're using it for.
This is a good improvement to interoperability as per FAIR4RS too. :)
(I also just like modularity and elegance of this kind of addition)
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Thanks @SylviaWhittle, yes works with AFMSlicer and I can now load the correct configuration. Working out how to build on and extend functionality is interesting, there are a few other places (such as creating configuration files) where I've already made things more flexible (I broke that in doing so before getting it right!). It's well worth it though. |
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Weird the test fail under Python 3.10 on M$-Win again, I'll re-run once but if it fails will merge. |
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Whilst developing entry points for AFMSlicer I found that the current
implementation of the
config.reconcile_config_args()function was too restrictive. Try and use it in another packageand it will load the
default_config.yamlfrom TopoStats.This pull-request changes the functionality and adds the parameter
default_configto theconfig.reconcile_config.args(). This is loaded viaget_data(package=topostats.__package__, resource="default_config.yaml")prior to callingreconcile_config_args()(and so AFMSlicer will useget_data(package=afmslicer.__package__, resource="default_config.yaml")).All pre-commit and unit/regression tests pass.
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