Merge branch 'breaking-improvments' of https://github.com/HopkinsIDD/…

…flepiMoP into breaking-improvments

batch/inference_job_launcher.py

@@ -396,7 +396,7 @@ def launch_batch(
     outcome_modifiers_scenarios = None
     if config["seir_modifiers"]["scenarios"].exists():
         seir_modifiers_scenarios = config["seir_modifiers"]["scenarios"]
-    if config["outcome_modifiers"]["scenarios"]:
+    if config["outcome_modifiers"]["scenarios"].exists():
         outcome_modifiers_scenarios = config["outcome_modifiers"]["scenarios"]
 
     handler.launch(job_name, config_file, seir_modifiers_scenarios, outcome_modifiers_scenarios)

flepimop/R_packages/flepicommon/R/file_paths.R

@@ -49,9 +49,9 @@ create_prefix <- function(..., prefix='',sep='-',trailing_separator=""){
 
 ## Function for creating file names from their components
 ##' @export
-create_file_name <- function(run_id, prefix, suffix, index, type, extension='parquet', create_directory = TRUE){
-  rc <- sprintf("model_output/%s/%s/%s/%09d.%s.%s.%s", prefix, type, suffix, index, run_id, type, extension)
-  if(create_directory){
+create_file_name <- function(run_id, prefix, filepath_suffix, filename_prefix, index, type, extension='parquet', create_directory = TRUE){
+  rc <- sprintf("model_output/%s/%s/%s/%s/%s%09d.%s.%s.%s", prefix,run_id, type, filepath_suffix, filename_prefix, index, run_id, type, extension)
+  if(create_directory){ # Add filename prefix here.
     if(!dir.exists(dirname(rc))){
       dir.create(dirname(rc), recursive = TRUE)
     }

flepimop/R_packages/inference/tests/testthat/test-perform_MCMC_step_copies.R

@@ -20,15 +20,15 @@ test_that("MCMC step copies (global) are correctly performed when we are not at
     dir.create("MCMC_step_copy_test")
     setwd("MCMC_step_copy_test")
     ##get file names
-    seed_src <- flepicommon::create_file_name(run_id,global_local_prefix,current_index,'seed','csv')
-    init_src <- flepicommon::create_file_name(run_id,global_local_prefix,current_index,'init','parquet')
-    seir_src <- flepicommon::create_file_name(run_id,global_local_prefix,current_index,'seir','parquet')
-    hosp_src <- flepicommon::create_file_name(run_id,global_local_prefix,current_index,'hosp','parquet')
-    llik_src <- flepicommon::create_file_name(run_id,global_local_prefix,current_index,'llik','parquet')
-    snpi_src <- flepicommon::create_file_name(run_id,global_local_prefix,current_index,'snpi','parquet')
-    spar_src <- flepicommon::create_file_name(run_id,global_local_prefix,current_index,'spar','parquet')
-    hnpi_src <- flepicommon::create_file_name(run_id,global_local_prefix,current_index,'hnpi','parquet')
-    hpar_src <- flepicommon::create_file_name(run_id,global_local_prefix,current_index,'hpar','parquet')
+    seed_src <- flepicommon::create_file_name(run_id=run_id, prefix=global_local_prefix,current_index,'seed','csv')
+    init_src <- flepicommon::create_file_name(run_id=run_id, prefix=global_local_prefix,current_index,'init','parquet')
+    seir_src <- flepicommon::create_file_name(run_id=run_id, prefix=global_local_prefix,current_index,'seir','parquet')
+    hosp_src <- flepicommon::create_file_name(run_id=run_id, prefix=global_local_prefix,current_index,'hosp','parquet')
+    llik_src <- flepicommon::create_file_name(run_id=run_id, prefix=global_local_prefix,current_index,'llik','parquet')
+    snpi_src <- flepicommon::create_file_name(run_id=run_id, prefix=global_local_prefix,current_index,'snpi','parquet')
+    spar_src <- flepicommon::create_file_name(run_id=run_id, prefix=global_local_prefix,current_index,'spar','parquet')
+    hnpi_src <- flepicommon::create_file_name(run_id=run_id, prefix=global_local_prefix,current_index,'hnpi','parquet')
+    hpar_src <- flepicommon::create_file_name(run_id=run_id, prefix=global_local_prefix,current_index,'hpar','parquet')
 
 
 
@@ -44,7 +44,7 @@ test_that("MCMC step copies (global) are correctly performed when we are not at
     arrow::write_parquet(data.frame(file="hpar"), hpar_src)
 
     ##print(hosp_src)
-    ##print(flepicommon::create_file_name(run_id,gf_prefix,slot,'hosp','parquet'))
+    ##print(flepicommon::create_file_name(run_id=run_id, prefix=gf_prefix,slot,'hosp','parquet'))
 
     res <- perform_MCMC_step_copies_global(current_index,
                                     slot,
@@ -82,15 +82,15 @@ test_that("MCMC step copies (global) are correctly performed when we are at the
     dir.create("MCMC_step_copy_test")
     setwd("MCMC_step_copy_test")
     ##get file names
-    seed_src <- flepicommon::create_file_name(run_id,global_block_prefix,block-1,'seed','csv')
-    init_src <- flepicommon::create_file_name(run_id,global_block_prefix,block-1,'init','parquet')
-    seir_src <- flepicommon::create_file_name(run_id,global_block_prefix,block-1,'seir','parquet')
-    hosp_src <- flepicommon::create_file_name(run_id,global_block_prefix,block-1,'hosp','parquet')
-    llik_src <- flepicommon::create_file_name(run_id,global_block_prefix,block-1,'llik','parquet')
-    snpi_src <- flepicommon::create_file_name(run_id,global_block_prefix,block-1,'snpi','parquet')
-    spar_src <- flepicommon::create_file_name(run_id,global_block_prefix,block-1,'spar','parquet')
-    hnpi_src <- flepicommon::create_file_name(run_id,global_block_prefix,block-1,'hnpi','parquet')
-    hpar_src <- flepicommon::create_file_name(run_id,global_block_prefix,block-1,'hpar','parquet')
+    seed_src <- flepicommon::create_file_name(run_id=run_id, prefix=global_block_prefix,block-1,'seed','csv')
+    init_src <- flepicommon::create_file_name(run_id=run_id, prefix=global_block_prefix,block-1,'init','parquet')
+    seir_src <- flepicommon::create_file_name(run_id=run_id, prefix=global_block_prefix,block-1,'seir','parquet')
+    hosp_src <- flepicommon::create_file_name(run_id=run_id, prefix=global_block_prefix,block-1,'hosp','parquet')
+    llik_src <- flepicommon::create_file_name(run_id=run_id, prefix=global_block_prefix,block-1,'llik','parquet')
+    snpi_src <- flepicommon::create_file_name(run_id=run_id, prefix=global_block_prefix,block-1,'snpi','parquet')
+    spar_src <- flepicommon::create_file_name(run_id=run_id, prefix=global_block_prefix,block-1,'spar','parquet')
+    hnpi_src <- flepicommon::create_file_name(run_id=run_id, prefix=global_block_prefix,block-1,'hnpi','parquet')
+    hpar_src <- flepicommon::create_file_name(run_id=run_id, prefix=global_block_prefix,block-1,'hpar','parquet')
 
     ##create the copy from  files
     readr::write_csv(data.frame(file="seed"), seed_src)
@@ -104,7 +104,7 @@ test_that("MCMC step copies (global) are correctly performed when we are at the
     arrow::write_parquet(data.frame(file="hpar"), hpar_src)
 
     print(hosp_src)
-    print(flepicommon::create_file_name(run_id,global_block_prefix,block,'hosp','parquet'))
+    print(flepicommon::create_file_name(run_id=run_id, prefix=global_block_prefix,block,'hosp','parquet'))
 
     res <- perform_MCMC_step_copies_global(current_index,
                                     slot,
@@ -142,14 +142,14 @@ test_that("MCMC step copies (chimeric) are correctly performed when we are not a
     dir.create("MCMC_step_copy_test")
     setwd("MCMC_step_copy_test")
     ##get file names
-    seed_src <- flepicommon::create_file_name(run_id,chimeric_local_prefix,current_index,'seed','csv')
-    seir_src <- flepicommon::create_file_name(run_id,chimeric_local_prefix,current_index,'seir','parquet')
-    hosp_src <- flepicommon::create_file_name(run_id,chimeric_local_prefix,current_index,'hosp','parquet')
-    llik_src <- flepicommon::create_file_name(run_id,chimeric_local_prefix,current_index,'llik','parquet')
-    snpi_src <- flepicommon::create_file_name(run_id,chimeric_local_prefix,current_index,'snpi','parquet')
-    spar_src <- flepicommon::create_file_name(run_id,chimeric_local_prefix,current_index,'spar','parquet')
-    hnpi_src <- flepicommon::create_file_name(run_id,chimeric_local_prefix,current_index,'hnpi','parquet')
-    hpar_src <- flepicommon::create_file_name(run_id,chimeric_local_prefix,current_index,'hpar','parquet')
+    seed_src <- flepicommon::create_file_name(run_id=run_id, prefix=chimeric_local_prefix,current_index,'seed','csv')
+    seir_src <- flepicommon::create_file_name(run_id=run_id, prefix=chimeric_local_prefix,current_index,'seir','parquet')
+    hosp_src <- flepicommon::create_file_name(run_id=run_id, prefix=chimeric_local_prefix,current_index,'hosp','parquet')
+    llik_src <- flepicommon::create_file_name(run_id=run_id, prefix=chimeric_local_prefix,current_index,'llik','parquet')
+    snpi_src <- flepicommon::create_file_name(run_id=run_id, prefix=chimeric_local_prefix,current_index,'snpi','parquet')
+    spar_src <- flepicommon::create_file_name(run_id=run_id, prefix=chimeric_local_prefix,current_index,'spar','parquet')
+    hnpi_src <- flepicommon::create_file_name(run_id=run_id, prefix=chimeric_local_prefix,current_index,'hnpi','parquet')
+    hpar_src <- flepicommon::create_file_name(run_id=run_id, prefix=chimeric_local_prefix,current_index,'hpar','parquet')
 
 
 
@@ -164,7 +164,7 @@ test_that("MCMC step copies (chimeric) are correctly performed when we are not a
     arrow::write_parquet(data.frame(file="hpar"), hpar_src)
 
     ##print(hosp_src)
-    ##print(flepicommon::create_file_name(run_id,cf_prefix,slot,'hosp','parquet'))
+    ##print(flepicommon::create_file_name(run_id=run_id, prefix=cf_prefix,slot,'hosp','parquet'))
 
     res <- perform_MCMC_step_copies_chimeric(current_index,
                                            slot,
@@ -203,14 +203,14 @@ test_that("MCMC step copies (chimeric) are correctly performed when we are at th
     dir.create("MCMC_step_copy_test")
     setwd("MCMC_step_copy_test")
     ##get file names
-    seed_src <- flepicommon::create_file_name(run_id,chimeric_block_prefix,block-1,'seed','csv')
-    seir_src <- flepicommon::create_file_name(run_id,chimeric_block_prefix,block-1,'seir','parquet')
-    hosp_src <- flepicommon::create_file_name(run_id,chimeric_block_prefix,block-1,'hosp','parquet')
-    llik_src <- flepicommon::create_file_name(run_id,chimeric_block_prefix,block-1,'llik','parquet')
-    snpi_src <- flepicommon::create_file_name(run_id,chimeric_block_prefix,block-1,'snpi','parquet')
-    spar_src <- flepicommon::create_file_name(run_id,chimeric_block_prefix,block-1,'spar','parquet')
-    hnpi_src <- flepicommon::create_file_name(run_id,chimeric_block_prefix,block-1,'hnpi','parquet')
-    hpar_src <- flepicommon::create_file_name(run_id,chimeric_block_prefix,block-1,'hpar','parquet')
+    seed_src <- flepicommon::create_file_name(run_id=run_id, prefix=chimeric_block_prefix,block-1,'seed','csv')
+    seir_src <- flepicommon::create_file_name(run_id=run_id, prefix=chimeric_block_prefix,block-1,'seir','parquet')
+    hosp_src <- flepicommon::create_file_name(run_id=run_id, prefix=chimeric_block_prefix,block-1,'hosp','parquet')
+    llik_src <- flepicommon::create_file_name(run_id=run_id, prefix=chimeric_block_prefix,block-1,'llik','parquet')
+    snpi_src <- flepicommon::create_file_name(run_id=run_id, prefix=chimeric_block_prefix,block-1,'snpi','parquet')
+    spar_src <- flepicommon::create_file_name(run_id=run_id, prefix=chimeric_block_prefix,block-1,'spar','parquet')
+    hnpi_src <- flepicommon::create_file_name(run_id=run_id, prefix=chimeric_block_prefix,block-1,'hnpi','parquet')
+    hpar_src <- flepicommon::create_file_name(run_id=run_id, prefix=chimeric_block_prefix,block-1,'hpar','parquet')
 
 
 
@@ -225,7 +225,7 @@ test_that("MCMC step copies (chimeric) are correctly performed when we are at th
     arrow::write_parquet(data.frame(file="hpar"), hpar_src)
 
     print(hosp_src)
-    print(flepicommon::create_file_name(run_id,chimeric_block_prefix,block,'hosp','parquet'))
+    print(flepicommon::create_file_name(run_id=run_id, prefix=chimeric_block_prefix,block,'hosp','parquet'))
 
     res <- perform_MCMC_step_copies_chimeric(current_index,
                                            slot,

flepimop/gempyor_pkg/src/gempyor/file_paths.py

@@ -13,10 +13,8 @@ def create_file_name_without_extension(run_id, prefix, index, ftype, inference_f
     if create_directory:
         os.makedirs(create_dir_name(run_id, prefix, ftype, inference_filepath_suffix, inference_filename_prefix), exist_ok=True)
     filename = pathlib.Path("model_output", prefix, ftype, inference_filepath_suffix,
-                            f"{inference_filename_prefix}.{index:>09}.{run_id}.{ftype}") 
-    print(f" making {filename}")
+                            f"{inference_filename_prefix}{index:>09}.{run_id}.{ftype}") 
     # old:  "model_output/%s/%s%09d.%s.%s" % (ftype, prefix, index, run_id, ftype)
-
     return filename
 
 def run_id():

flepimop/gempyor_pkg/src/gempyor/interface.py

@@ -43,7 +43,7 @@ def __init__(
         self,
         config_path,
         run_id="test_run_id",
-        prefix="test_prefix",
+        prefix=None,
         first_sim_index=1,
         seir_modifiers_scenario=None,
         outcome_modifiers_scenario=None,
@@ -97,7 +97,7 @@ def __init__(
         print(
             f"""  gempyor >> Running ***{'STOCHASTIC' if stoch_traj_flag else 'DETERMINISTIC'}*** simulation;\n"""
             f"""  gempyor >> ModelInfo {self.modinf.setup_name}; index: {self.modinf.first_sim_index}; run_id: {in_run_id},\n"""
-            f"""  gempyor >> prefix: {in_prefix};"""  # ti: {s.ti}; tf: {s.tf};
+            f"""  gempyor >> prefix: {self.modinf.in_prefix};"""  # ti: {s.ti}; tf: {s.tf};
         )
 
         self.already_built = False  # whether we have already build the costly objects that need just one build

flepimop/gempyor_pkg/src/gempyor/seeding_ic.py

@@ -267,7 +267,7 @@ def draw_seeding(self, sim_id: int, setup) -> nb.typed.Dict:
         elif method == "FolderDraw":
             seeding = pd.read_csv(
                 setup.get_input_filename(
-                    ftype=setup.seeding_config["seeding_file_type"],
+                    ftype=setup.seeding_config["seeding_file_type"].get(),
                     sim_id=sim_id,
                     extension_override="csv",
                 ),

flepimop/gempyor_pkg/src/gempyor/simulate.py

@@ -304,7 +304,7 @@ def simulate(
         outcome_modifiers_scenarios = None
         if config["outcomes"].exists() and config["outcome_modifiers"].exists():
             if config["outcome_modifiers"]["scenarios"].exists():
-                outcome_modifiers_scenarios = config["outcomes"]["scenarios"].as_str_seq()
+                outcome_modifiers_scenarios = config["outcome_modifiers"]["scenarios"].as_str_seq()
 
     outcome_modifiers_scenarios = as_list(outcome_modifiers_scenarios)
     seir_modifiers_scenarios = as_list(seir_modifiers_scenarios)