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HopkinsIDD · Nov 13, 2024 · dd9c00f · dd9c00f
1 parent 7ba97ce
commit dd9c00f
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Showing 8 changed files with 28 additions and 15 deletions.
diff --git a/flepimop/gempyor_pkg/src/gempyor/NPI/MultiPeriodModifier.py b/flepimop/gempyor_pkg/src/gempyor/NPI/MultiPeriodModifier.py
@@ -6,6 +6,7 @@
 from . import helpers
 from .base import NPIBase
 
+
 class MultiPeriodModifier(NPIBase):
     def __init__(
         self,

diff --git a/flepimop/gempyor_pkg/src/gempyor/NPI/SinglePeriodModifier.py b/flepimop/gempyor_pkg/src/gempyor/NPI/SinglePeriodModifier.py
@@ -6,6 +6,7 @@
 from . import helpers
 from .base import NPIBase
 
+
 class SinglePeriodModifier(NPIBase):
     def __init__(
         self,

diff --git a/flepimop/gempyor_pkg/src/gempyor/NPI/StackedModifier.py b/flepimop/gempyor_pkg/src/gempyor/NPI/StackedModifier.py
@@ -63,7 +63,8 @@ def __init__(
 
             sub_npi = NPIBase.execute(
                 npi_config=scenario_npi_config,
-                modinf_ti=modinf_ti, modinf_tf=modinf_tf,
+                modinf_ti=modinf_ti,
+                modinf_tf=modinf_tf,
                 modifiers_library=modifiers_library,
                 subpops=subpops,
                 loaded_df=loaded_df,

diff --git a/flepimop/gempyor_pkg/src/gempyor/NPI/base.py b/flepimop/gempyor_pkg/src/gempyor/NPI/base.py
@@ -1,6 +1,7 @@
 import abc
 import datetime
 
+
 class NPIBase(abc.ABC):
     __plugins__ = {}
 

diff --git a/flepimop/gempyor_pkg/src/gempyor/dev/dev_seir.py b/flepimop/gempyor_pkg/src/gempyor/dev/dev_seir.py
@@ -44,7 +44,8 @@
 
 npi = NPI.NPIBase.execute(
     npi_config=modinf.npi_config_seir,
-    modinf_ti=modinf.ti, modinf_tf=modinf.tf,
+    modinf_ti=modinf.ti,
+    modinf_tf=modinf.tf,
     modifiers_library=modinf.seir_modifiers_library,
     subpops=modinf.subpop_struct.subpop_names,
     pnames_overlap_operation_sum=modinf.parameters.stacked_modifier_method["sum"],

diff --git a/flepimop/gempyor_pkg/src/gempyor/outcomes.py b/flepimop/gempyor_pkg/src/gempyor/outcomes.py
@@ -75,7 +75,8 @@ def build_outcome_modifiers(
 
         npi = NPI.NPIBase.execute(
             npi_config=modinf.npi_config_outcomes,
-            modinf_ti=modinf.ti, modinf_tf=modinf.tf,
+            modinf_ti=modinf.ti,
+            modinf_tf=modinf.tf,
             modifiers_library=modinf.outcome_modifiers_library,
             subpops=modinf.subpop_struct.subpop_names,
             loaded_df=loaded_df,

diff --git a/flepimop/gempyor_pkg/src/gempyor/seir.py b/flepimop/gempyor_pkg/src/gempyor/seir.py
@@ -237,13 +237,12 @@ def build_npi_SEIR(
 
         npi = NPI.NPIBase.execute(
             npi_config=modinf.npi_config_seir,
-            modinf_ti=modinf.ti, modinf_tf=modinf.tf,
+            modinf_ti=modinf.ti,
+            modinf_tf=modinf.tf,
             modifiers_library=modinf.seir_modifiers_library,
             subpops=modinf.subpop_struct.subpop_names,
             loaded_df=loaded_df,
-            pnames_overlap_operation_sum=modinf.parameters.stacked_modifier_method[
-                "sum"
-            ],
+            pnames_overlap_operation_sum=modinf.parameters.stacked_modifier_method["sum"],
             pnames_overlap_operation_reductionprod=modinf.parameters.stacked_modifier_method[
                 "reduction_product"
             ],

diff --git a/flepimop/gempyor_pkg/tests/seir/test_seir.py b/flepimop/gempyor_pkg/tests/seir/test_seir.py
@@ -80,7 +80,8 @@ def test_constant_population_legacy_integration():
 
     npi = NPI.NPIBase.execute(
         npi_config=modinf.npi_config_seir,
-        modinf_ti=modinf.ti, modinf_tf=modinf.tf,
+        modinf_ti=modinf.ti,
+        modinf_tf=modinf.tf,
         modifiers_library=modinf.seir_modifiers_library,
         subpops=modinf.subpop_struct.subpop_names,
         pnames_overlap_operation_sum=modinf.parameters.stacked_modifier_method["sum"],
@@ -157,7 +158,8 @@ def test_constant_population_rk4jit_integration_fail():
 
         npi = NPI.NPIBase.execute(
             npi_config=modinf.npi_config_seir,
-            modinf_ti=modinf.ti, modinf_tf=modinf.tf,
+            modinf_ti=modinf.ti,
+            modinf_tf=modinf.tf,
             modifiers_library=modinf.seir_modifiers_library,
             subpops=modinf.subpop_struct.subpop_names,
             pnames_overlap_operation_sum=modinf.parameters.stacked_modifier_method["sum"],
@@ -233,7 +235,8 @@ def test_constant_population_rk4jit_integration():
 
     npi = NPI.NPIBase.execute(
         npi_config=modinf.npi_config_seir,
-        modinf_ti=modinf.ti, modinf_tf=modinf.tf,
+        modinf_ti=modinf.ti,
+        modinf_tf=modinf.tf,
         modifiers_library=modinf.seir_modifiers_library,
         subpops=modinf.subpop_struct.subpop_names,
         pnames_overlap_operation_sum=modinf.parameters.stacked_modifier_method["sum"],
@@ -307,7 +310,8 @@ def test_steps_SEIR_nb_simple_spread_with_txt_matrices():
 
     npi = NPI.NPIBase.execute(
         npi_config=modinf.npi_config_seir,
-        modinf_ti=modinf.ti, modinf_tf=modinf.tf,
+        modinf_ti=modinf.ti,
+        modinf_tf=modinf.tf,
         modifiers_library=modinf.seir_modifiers_library,
         subpops=modinf.subpop_struct.subpop_names,
         pnames_overlap_operation_sum=modinf.parameters.stacked_modifier_method["sum"],
@@ -415,7 +419,8 @@ def test_steps_SEIR_nb_simple_spread_with_csv_matrices():
 
     npi = NPI.NPIBase.execute(
         npi_config=modinf.npi_config_seir,
-        modinf_ti=modinf.ti, modinf_tf=modinf.tf,
+        modinf_ti=modinf.ti,
+        modinf_tf=modinf.tf,
         modifiers_library=modinf.seir_modifiers_library,
         subpops=modinf.subpop_struct.subpop_names,
         pnames_overlap_operation_sum=modinf.parameters.stacked_modifier_method["sum"],
@@ -493,7 +498,8 @@ def test_steps_SEIR_no_spread():
 
     npi = NPI.NPIBase.execute(
         npi_config=modinf.npi_config_seir,
-        modinf_ti=modinf.ti, modinf_tf=modinf.tf,
+        modinf_ti=modinf.ti,
+        modinf_tf=modinf.tf,
         modifiers_library=modinf.seir_modifiers_library,
         subpops=modinf.subpop_struct.subpop_names,
         pnames_overlap_operation_sum=modinf.parameters.stacked_modifier_method["sum"],
@@ -767,7 +773,8 @@ def test_parallel_compartments_with_vacc():
 
     npi = NPI.NPIBase.execute(
         npi_config=modinf.npi_config_seir,
-        modinf_ti=modinf.ti, modinf_tf=modinf.tf,
+        modinf_ti=modinf.ti,
+        modinf_tf=modinf.tf,
         modifiers_library=modinf.seir_modifiers_library,
         subpops=modinf.subpop_struct.subpop_names,
         pnames_overlap_operation_sum=modinf.parameters.stacked_modifier_method["sum"],
@@ -860,7 +867,8 @@ def test_parallel_compartments_no_vacc():
 
     npi = NPI.NPIBase.execute(
         npi_config=modinf.npi_config_seir,
-        modinf_ti=modinf.ti, modinf_tf=modinf.tf,
+        modinf_ti=modinf.ti,
+        modinf_tf=modinf.tf,
         modifiers_library=modinf.seir_modifiers_library,
         subpops=modinf.subpop_struct.subpop_names,
         pnames_overlap_operation_sum=modinf.parameters.stacked_modifier_method["sum"],