update seeding- and initial_conditions- related tests

HopkinsIDD · Apr 12, 2024 · 1d07afc · 1d07afc
1 parent 7710987
commit 1d07afc
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Showing 7 changed files with 9 additions and 747 deletions.
diff --git a/flepimop/gempyor_pkg/src/gempyor/initial_conditions.py b/flepimop/gempyor_pkg/src/gempyor/initial_conditions.py
@@ -5,7 +5,7 @@
 from numba.typed import Dict
 import confuse
 import logging
-from simulation_component import SimulationComponent
+from .simulation_component import SimulationComponent
 from . import utils
 from .utils import read_df
 

diff --git a/flepimop/gempyor_pkg/src/gempyor/seeding.py b/flepimop/gempyor_pkg/src/gempyor/seeding.py
@@ -4,7 +4,7 @@
 import pandas as pd
 import confuse
 import logging
-from simulation_component import SimulationComponent
+from .simulation_component import SimulationComponent
 from . import utils
 import numba as nb
 

diff --git a/flepimop/gempyor_pkg/src/gempyor/seeding_ic.py b/flepimop/gempyor_pkg/src/gempyor/seeding_ic.py
diff --git a/flepimop/gempyor_pkg/src/gempyor/simulation_component.py b/flepimop/gempyor_pkg/src/gempyor/simulation_component.py
@@ -1,3 +1,7 @@
+import confuse
+import numpy as np
+
+
 class SimulationComponent:
     def __init__(self, config: confuse.ConfigView):
         raise NotImplementedError("This method should be overridden in subclasses.")

diff --git a/flepimop/gempyor_pkg/tests/seir/test_ic.py b/flepimop/gempyor_pkg/tests/seir/test_ic.py
@@ -41,10 +41,8 @@ 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 = initial_conditions.InitialConditionsFactory(config=s.initial_conditions_config)
-        assert sic.initial_conditions_config == s.initial_conditions_config
+        sic.get_from_config(sim_id=100, setup=s)
 
-        initial_conditions = sic.get_from_config(sim_id=100, setup=s)
-        print(initial_conditions)
 
     def test_IC_IC_notImplemented_fail(self):
         with pytest.raises(NotImplementedError, match=r".*unknown.*initial.*conditions.*"):

diff --git a/flepimop/gempyor_pkg/tests/seir/test_seeding.py b/flepimop/gempyor_pkg/tests/seir/test_seeding.py
@@ -39,5 +39,5 @@ def test_Seeding_draw_success(self):
         sic = seeding.SeedingFactory(config=s.seeding_config)
         s.seeding_config["method"] = "NoSeeding"
 
-        seeding = sic.get_from_config(sim_id=100, setup=s)
-        print(seeding)
+        seeding_result = sic.get_from_config(sim_id=100, setup=s)
+        print(seeding_result)
diff --git a/flepimop/gempyor_pkg/tests/seir/test_seeding_ic.py b/flepimop/gempyor_pkg/tests/seir/test_seeding_ic.py