Removing/data path

batch/inference_job_launcher.py

@@ -431,7 +431,9 @@ def autodetect_params(config, data_path, *, num_jobs=None, sims_per_job=None, nu
             print(f"Setting number of blocks to {num_blocks} [via num_blocks (-k) argument]")
             print(f"Setting sims per job to {sims_per_job} [via {iterations_per_slot} iterations_per_slot in config]")
         else:
-            geodata_fname = pathlib.Path(data_path, config["data_path"]) / config["subpop_setup"]["geodata"]
+            if config["data_path"]:
+                raise ValueError("The config has a data_path section. This is no longer supported.")
+            geodata_fname = pathlib.Path(data_path) / config["subpop_setup"]["geodata"]
             with open(geodata_fname) as geodata_fp:
                 num_subpops = sum(1 for line in geodata_fp)
 

flepimop/gempyor_pkg/docs/integration_benchmark.ipynb

@@ -122,7 +122,7 @@
     "config.set_file(config_path)\n",
     "\n",
     "spatial_config = config[\"subpop_setup\"]\n",
-    "spatial_base_path = pathlib.Path(\"../../COVID19_USA/\" + config[\"data_path\"].get())\n",
+    "spatial_base_path = pathlib.Path(\"../../COVID19_USA/\")\n",
     "seir_modifiers_scenario = seir_modifiers_scenario\n",
     "outcome_modifiers_scenario = outcome_modifiers_scenario\n",
     "stoch_traj_flag = stoch_traj_flag  # Truthy: stochastic simulation, Falsy: determnistic mean of the binomial draws\n",

flepimop/gempyor_pkg/src/gempyor/model_info.py

@@ -77,8 +77,9 @@ def __init__(
 
         # 3. What about subpopulations
         spatial_config = config["subpop_setup"]
-        spatial_base_path = config["data_path"].get()
-        spatial_base_path = pathlib.Path(spatial_path_prefix + spatial_base_path)
+        if config["data_path"].exists():
+            raise ValueError("The config has a data_path section. This is no longer supported.")
+        spatial_base_path = pathlib.Path(spatial_path_prefix)
 
         self.subpop_struct = subpopulation_structure.SubpopulationStructure(
             setup_name=config["setup_name"].get(),

flepimop/gempyor_pkg/tests/interface/data/config.yml

@@ -2,7 +2,6 @@ name: minimal for interface
 setup_name: minimal4interface
 start_date: 2020-01-31
 end_date: 2020-05-31
-data_path: data
 nslots: 1
 
 

flepimop/gempyor_pkg/tests/interface/data/config_min_test.yml

@@ -2,7 +2,6 @@ name: minimal for interface
 setup_name: minimal4interface
 start_date: 2020-01-31
 end_date: 2020-05-31
-data_path: data
 nslots: 1
 
 

flepimop/gempyor_pkg/tests/interface/data/config_minimal.yaml

@@ -2,7 +2,6 @@ name: minimal
 setup_name: minimal
 start_date: 2020-01-31
 end_date: 2020-05-31
-data_path: data
 nslots: 15
 
 

flepimop/gempyor_pkg/tests/interface/data/config_test.yml

@@ -2,7 +2,6 @@ name: minimal_test
 setup_name: minimal_test_setup
 start_date: 2020-01-31
 end_date: 2020-05-31
-data_path: data
 nslots: 5
 
 

flepimop/gempyor_pkg/tests/npi/config_test_spatial_group_npi.yml

@@ -1,7 +1,6 @@
 name: USA
 setup_name: FCH
 smh_round: R12
-data_path: data
 start_date: 2020-01-01
 end_date: 2022-09-03
 end_date_groundtruth: 2022-03-05

flepimop/gempyor_pkg/tests/npi/data/config_minimal.yaml

@@ -2,7 +2,6 @@ name: minimal
 setup_name: minimal
 start_date: 2020-01-31
 end_date: 2020-05-31
-data_path: data
 nslots: 15
 
 

flepimop/gempyor_pkg/tests/npi/data/config_test.yml

@@ -2,7 +2,6 @@ name: minimal_test
 setup_name: minimal_test_setup
 start_date: 2020-01-31
 end_date: 2020-05-31
-data_path: data
 nslots: 5