Merge emcee_batch Into dev
#404
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…unciton that just run a simulation
…into emcee_batch
…into emcee_batch
Merged in the remaining components of `gempyor` and resolved corresponding conflicts.
Added a runtime error to `get_static_arguements` if `modinf` compartments attribute is `None` and a corresponding test. Also rearranged the logic in `ModelInfo.__init__` to always initialize a `compartments` attribute, even if it's `None`.
* 'compartments' and 'seir' sections are now required in the config for inferece. * Added logic to `get_static_arguments` to allow it to work without an 'seir_modifiers' section in the config.
Updated test in `test_outcomes.py` to pass by adding the required 'compartments' and 'seir' sections to the config for inference.
Added required 'compartments' and 'seir' sections for inference to the 'config_npi.yml'.
Updated the 'config_npi_custom_pnames.yml' config to add the required 'compartments' and 'seir' sections for inference.
TimothyWillard
added
gempyor
* Had to move seeding file to meet expected directory structure. * Initialize `ModelInfo.npi_config_outcomes` with `None` always. * Early exit for `read_parameters_from_config` if `ModelInfo.outcomes_config` is `None`.
Had to manually add seeding files to the `model_output/` directory to make them work.
Add a 'transitions' section to the 'seir' config section to let the `test_spatial_groups` NPIs test pass.
Added a bug fix to `compute_all_multioutcomes` to look for if a sourced outcome exists and has not been processed yet and if so skip that outcome for now and re-add it to the end of the outcomes to process. Required for the `test_outcomes_pcomp` and `test_outcomes_pcomp_read_write` tests to pass. Also minor edits to `config_mc_selection.yml` to add the required 'compartments'/'seir' sections.
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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
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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.