Inference does not undersand init conditions that are not init files

[jcblemai]

Blocker for #118

• If there is an initial condition section in config, then inference assume there will be init files
• it is not the case, depending on the method for initial condition. Sometime it's just a file in data

(the same apply to seeding, but we can wait for #90 to fix that, this initial condition causes an immediate bug that block submission)

[shauntruelove]

i can deal with this. good catch

[saraloo]

I think this is working - just checking the model outputs.

Something is trying to create directories repeatedly though

[1] "Running 5 simulations"
Joining with `by = join_by(date, subpop)`
[1] "Running WITH inference"
[1] "Chimeric reset is TRUE"
 [1] "config"                      "run_id"
 [3] "seir_modifiers_scenarios"    "outcome_modifiers_scenarios"
 [5] "jobs"                        "iterations_per_slot"
 [7] "this_slot"                   "this_block"
 [9] "stoch_traj_flag"             "ground_truth_start"
[11] "ground_truth_end"            "flepi_path"
[13] "python"                      "rpath"
[15] "is-resume"                   "is-interactive"
[17] "reset_chimeric_on_accept"    "memory_profiling"
[19] "memory_profiling_iters"      "subpop_len"
[21] "help"
[1] "Running seir modifier scenario: inference"
[1] "Running outcome modifier scenario: fake"
[1] "gempyor_inference_runner created successfully."
Warning in dir.create(dirname(rc), recursive = TRUE) :
  'model_output/USA_inference_fake/SMH_Flu_2023_R1_medVax_H3_simple_noimm/seed/global/intermediate' already exists
Warning in dir.create(dirname(rc), recursive = TRUE) :
  'model_output/USA_inference_fake/SMH_Flu_2023_R1_medVax_H3_simple_noimm/init/global/intermediate' already exists
Warning in dir.create(dirname(rc), recursive = TRUE) :
  'model_output/USA_inference_fake/SMH_Flu_2023_R1_medVax_H3_simple_noimm/llik/global/intermediate' already exists
Warning in dir.create(dirname(rc), recursive = TRUE) :
  'model_output/USA_inference_fake/SMH_Flu_2023_R1_medVax_H3_simple_noimm/seed/chimeric/intermediate' already exists
Warning in dir.create(dirname(rc), recursive = TRUE) :
  'model_output/USA_inference_fake/SMH_Flu_2023_R1_medVax_H3_simple_noimm/init/chimeric/intermediate' already exists
Warning in dir.create(dirname(rc), recursive = TRUE) :
  'model_output/USA_inference_fake/SMH_Flu_2023_R1_medVax_H3_simple_noimm/seir/chimeric/intermediate' already exists
Warning in dir.create(dirname(rc), recursive = TRUE) :
  'model_output/USA_inference_fake/SMH_Flu_2023_R1_medVax_H3_simple_noimm/snpi/chimeric/intermediate' already exists
Warning in dir.create(dirname(rc), recursive = TRUE) :
  'model_output/USA_inference_fake/SMH_Flu_2023_R1_medVax_H3_simple_noimm/hnpi/chimeric/intermediate' already exists
Warning in dir.create(dirname(rc), recursive = TRUE) :
  'model_output/USA_inference_fake/SMH_Flu_2023_R1_medVax_H3_simple_noimm/spar/chimeric/intermediate' already exists
Warning in dir.create(dirname(rc), recursive = TRUE) :
  'model_output/USA_inference_fake/SMH_Flu_2023_R1_medVax_H3_simple_noimm/hosp/chimeric/intermediate' already exists
Warning in dir.create(dirname(rc), recursive = TRUE) :
  'model_output/USA_inference_fake/SMH_Flu_2023_R1_medVax_H3_simple_noimm/hpar/chimeric/intermediate' already exists
Warning in dir.create(dirname(rc), recursive = TRUE) :
  'model_output/USA_inference_fake/SMH_Flu_2023_R1_medVax_H3_simple_noimm/llik/chimeric/intermediate' already exists

[jcblemai]

@shauntruelove this is fixed right ?