SPARCED new organization #33
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Recompile SPARCED_legacy with the original Jupyter Notebook under the name SPARCED_legacy (ensures compatibility with version 2.0.0) Run a default simulation of SPARCED_legacy on the original Jupyter Notebook with perturbations as specified in the default.txt file
Run SPARCED_legacy model using the 2.0.0 pipeline under the same conditions as with the 1.3.0 control Results showed no difference at all between both, but the 1.3.0 version doesn't save time by default, which is useful for plotting.
Recompile SPARCED_standard with the original legacy SPARCED input data files (v1.3.0) using the 2.0.0 pipeline Run a default simulation of SPARCED_standard using the 2.0.0 pipeline with perturbations as specified in the default.txt file Those control results are strictly identical to those for SPARCED_legacy
This pipeline was tested on the SPARCED_standard model for a) no incubation specified at all b) an incubation defined to 0 hours and c) an incubation set to 24 hours.
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This is the SPARCED's new organization.
Although some further work could be done (add scripts for incubation, improve file handling, tidy up run SPARCED scripts etc. - there could always be more work), this version recapitulates in a new organization the current SPARCED's model on the main branch.
Both Arnab and Jonah got it working on their own machines, so it's reproducible.
After merging my branch, we could launch the Read The Docs to get beautiful documentation online, under the form of a website 😄