sunset the usage of seeding_ic

HopkinsIDD · Mar 28, 2024 · 7710987 · 7710987
1 parent 281407b
commit 7710987
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Showing 4 changed files with 12 additions and 12 deletions.
diff --git a/flepimop/gempyor_pkg/src/gempyor/dev/dev_seir.py b/flepimop/gempyor_pkg/src/gempyor/dev/dev_seir.py
@@ -35,8 +35,8 @@
     out_prefix=prefix,
 )
 
-seeding_data = modinf.seedingAndIC.draw_seeding(sim_id=100, setup=modinf)
-initial_conditions = modinf.seedingAndIC.draw_ic(sim_id=100, setup=modinf)
+seeding_data = modinf.seeding.get_from_config(sim_id=100, setup=modinf)
+initial_conditions = modinf.initial_conditions.get_from_config(sim_id=100, setup=modinf)
 
 mobility_subpop_indices = modinf.mobility.indices
 mobility_data_indices = modinf.mobility.indptr

diff --git a/flepimop/gempyor_pkg/src/gempyor/model_info.py b/flepimop/gempyor_pkg/src/gempyor/model_info.py
@@ -1,6 +1,6 @@
 import pandas as pd
 import datetime, os, logging, pathlib
-from . import seeding_ic, subpopulation_structure, parameters, compartments, file_paths
+from . import seeding, subpopulation_structure, parameters, compartments, file_paths, initial_conditions
 from .utils import read_df, write_df
 
 logger = logging.getLogger(__name__)
@@ -115,8 +115,8 @@ def __init__(
                 tf=self.tf,
                 subpop_names=self.subpop_struct.subpop_names,
             )
-            self.seeding = seeding_ic.SeedingFactory(config = self.seeding_config)
-            self.initial_conditions = seeding_ic.InitialConditionsFactory(config = self.initial_conditions_config)
+            self.seeding = seeding.SeedingFactory(config = self.seeding_config)
+            self.initial_conditions = initial_conditions.InitialConditionsFactory(config = self.initial_conditions_config)
             # really ugly references to the config globally here.
             if config["compartments"].exists() and self.seir_config is not None:
                 self.compartments = compartments.Compartments(

diff --git a/flepimop/gempyor_pkg/tests/seir/test_ic.py b/flepimop/gempyor_pkg/tests/seir/test_ic.py
@@ -1,6 +1,6 @@
 import os
 import pytest
-from gempyor import seeding_ic, model_info
+from gempyor import seeding, model_info, initial_conditions
 from gempyor.utils import config
 
 DATA_DIR = os.path.dirname(__file__) + "/data"
@@ -21,7 +21,7 @@ def test_IC_success(self):
             outcome_modifiers_scenario=None,
             write_csv=False,
         )
-        sic = seeding_ic.InitialConditionsFactory(config=s.initial_conditions_config)
+        sic = initial_conditions.InitialConditionsFactory(config=s.initial_conditions_config)
         assert sic.initial_conditions_config == s.initial_conditions_config
 
     def test_IC_allow_missing_node_compartments_success(self):
@@ -40,7 +40,7 @@ def test_IC_allow_missing_node_compartments_success(self):
 
         s.initial_conditions_config["allow_missing_nodes"] = True
         s.initial_conditions_config["allow_missing_compartments"] = True
-        sic = seeding_ic.InitialConditionsFactory(config=s.initial_conditions_config)
+        sic = initial_conditions.InitialConditionsFactory(config=s.initial_conditions_config)
         assert sic.initial_conditions_config == s.initial_conditions_config
 
         initial_conditions = sic.get_from_config(sim_id=100, setup=s)
@@ -61,6 +61,6 @@ def test_IC_IC_notImplemented_fail(self):
                 write_csv=False,
             )
             s.initial_conditions_config["method"] = "unknown"
-            sic = seeding_ic.InitialConditionsFactory(config=s.initial_conditions_config)
+            sic = initial_conditions.InitialConditionsFactory(config=s.initial_conditions_config)
 
             sic.get_from_config(sim_id=100, setup=s)
diff --git a/flepimop/gempyor_pkg/tests/seir/test_seeding.py b/flepimop/gempyor_pkg/tests/seir/test_seeding.py
@@ -1,5 +1,5 @@
 import os
-from gempyor import seeding_ic, model_info
+from gempyor import seeding, model_info
 from gempyor.utils import config
 
 DATA_DIR = os.path.dirname(__file__) + "/data"
@@ -20,7 +20,7 @@ def test_Seeding_success(self):
             outcome_modifiers_scenario=None,
             write_csv=False,
         )
-        sic = seeding_ic.SeedingFactory(config=s.seeding_config)
+        sic = seeding.SeedingFactory(config=s.seeding_config)
         assert sic.seeding_config == s.seeding_config
 
     def test_Seeding_draw_success(self):
@@ -36,7 +36,7 @@ def test_Seeding_draw_success(self):
             outcome_modifiers_scenario=None,
             write_csv=False,
         )
-        sic = seeding_ic.SeedingFactory(config=s.seeding_config)
+        sic = seeding.SeedingFactory(config=s.seeding_config)
         s.seeding_config["method"] = "NoSeeding"
 
         seeding = sic.get_from_config(sim_id=100, setup=s)