Merge emcee_batch Into dev
#404
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…unciton that just run a simulation
…into emcee_batch
…into emcee_batch
|
Didn't run automatically since I had this marked as draft, but manually ran them and GH actions do pass:
With commit 05b760b. |
TimothyWillard
requested review from
emprzy,
pearsonca,
saraloo,
twallema,
MacdonaldJoshuaCaleb and
fang19911030
anjalika-nande
approved these changes
Dec 2, 2024
pearsonca
requested changes
Dec 2, 2024
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what's going on with this file? not whole sale deleted, but definitely substantially reduced.
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This file was heavily modified in ce59add. It's written by the examples/simple_usa_statelevel/inference_benchmark.ipynb notebook. Although, I'm having difficultly running it locally since it relies on files outside of the flepiMoP repository (probably on @jcblemai laptop) and dependencies not installed by flepiMoP. I've created an issue to follow up on this: #410.
Original issue was addressed by adding the needed file with `--force` and `model_output` related gitignores for the inference tests can be removed.
Utilize confuse more by relying on it's `as_str_seq` getter for pulling a sequence of strings in a yaml file as a list of strings in python per an @pearsonca suggestion.
Added a unit test to test run the `flepimop modifiers config-plot` command and check that it produces the expected output files of plots.
pearsonca
approved these changes
Dec 3, 2024
Move the call to `get_static_arguments` under the 'emcee' inference branch. This avoids calling `outcomes.read_parameters_from_config` twice. That function has a side effect of editing the outcome modifiers config. See #373 (comment) for details.
Closed
Init `static_sim_arguments` attribute with `None` and then manually extract the unique strings from the compartments transition array in the `flepimop modifiers config-plot` CLI tool when interacting with non-EMCEE inference configs.
emprzy
approved these changes
Dec 4, 2024
This was referenced Dec 4, 2024
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Describe your changes.
This pull request makes the changes required to shape the
emcee_batchbranch into an appropriate format fordev.Does this pull request make any user interface changes? If so please describe.
The user interface changes are:
GempyorInference. Likely not a major change for users as any users doing inference are usually specifying compartments and transitions, but is a change for unit testing.Those are reflected in updates to the documentation in the "Inference with EMCEE" GitBook documentation page.
What does your pull request address? Tag relevant issues.
This pull request addresses GH-403.