v1.0.0

[YeChen-IDM]

• [x] bump version from 0.0.1 to 1.0.0
• [x] Update requirements.txt: emodpy-malaria~=2.0
• [x] Update run_sim.py to be more testable
• [x] add regression tests for comparing inputs generated by run_sim.py( config, campaign, demographics and custom report files)
• [x] Update code to work with latest Emodpy-Malaria
• [x] Update snakemake workflow to support both local Eradication and Eradication from Emod-Malaria.
• [x] Update readme.md
• [x] add ggplot images and pdf report

[YeChen-IDM]

Tests failed with:

File "/opt/hostedtoolcache/Python/3.9.13/x64/lib/python3.9/site-packages/simulations/helpers.py", line 14, in <module>
    from emodpy_malaria.interventions.inputeir import InputEIR
ImportError: cannot import name 'InputEIR' from 'emodpy_malaria.interventions.inputeir' (/opt/hostedtoolcache/Python/3.9.13/x64/lib/python3.9/site-packages/emodpy_malaria/interventions/inputeir.py)

"InputEIR" is no longer in emodpy_malaria: Need to update our code to work with latest Emodpy-Malaria

[YeChen-IDM]

The R plotting script failed with the following error:

<error/vctrs_error_subscript_oob>
Error in `chr_as_locations()`:
! Can't subset columns that don't exist.
x Column `benchmark` doesn't exist.
---
Backtrace:
  1. base::source("C:/Github/Malaria/Update/malaria-model_validation/create_plots/run_generate_validation_comparisons_site.R")
  5. global generate_infectiousness_outputs(...)
       at malaria-model_validation/create_plots/run_generate_validation_comparisons_site.R:65:0
  6. global plot_infectiousness_ref_sim_comparison(combined_df)
       at malaria-model_validation/create_plots/helpers_coordinate_each_relationship.R:222:2
  8. tidyr:::pivot_longer.data.frame(...)
  9. tidyr::build_longer_spec(...)
 10. tidyselect::eval_select(enquo(cols), data[unique(names(data))])
 11. tidyselect:::eval_select_impl(...)
 20. tidyselect:::vars_select_eval(...)
 21. tidyselect:::walk_data_tree(expr, data_mask, context_mask, error_call)
 22. tidyselect:::eval_c(expr, data_mask, context_mask)
 23. tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
 24. tidyselect:::walk_data_tree(new, data_mask, context_mask)
 25. tidyselect:::as_indices_sel_impl(...)
 26. tidyselect:::as_indices_impl(x, vars, call = call, strict = strict)
 27. tidyselect:::chr_as_locations(x, vars, call = call)
Run `rlang::last_trace()` to see the full context.

[YeChen-IDM]

Some of the benchmark data is filtered out since the parasite density bins are not the same and caused the error I posted earlier.

Warning messages:
1: In sort(unique(sim_df_agg2$densitybin)) == sort(unique(bench_df_agg2$densitybin)) :
  longer object length is not a multiple of shorter object length
2: In prepare_infect_df(coord_csv, simulation_output_filepath, base_reference_filepath,  :
  New and benchmark simulation parasite density bins are not the same for site:laye_2007. Removing benchmark sims.
3: In sort(unique(sim_df_agg2$densitybin)) == sort(unique(bench_df_agg2$densitybin)) :
  longer object length is not a multiple of shorter object length
4: In prepare_infect_df(coord_csv, simulation_output_filepath, base_reference_filepath,  :
  New and benchmark simulation parasite density bins are not the same for site:dapelogo_2007. Removing benchmark sims.

[YeChen-IDM]

Here is some result with the latest Emod( benchmark data is from the previous Eradication that we used):