Call positional args with names

* Per @pearsonca, @jcblemai suggestions call positional arguements with names. * Restyle call to `get_seeding_data` in `gempyor.seir.onerun_SEIR`.
HopkinsIDD · Jan 8, 2025 · 085beca · 085beca
1 parent 692865f
commit 085beca
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Showing 6 changed files with 30 additions and 29 deletions.
diff --git a/flepimop/gempyor_pkg/src/gempyor/dev/dev_seir.py b/flepimop/gempyor_pkg/src/gempyor/dev/dev_seir.py
@@ -35,7 +35,7 @@
     out_prefix=prefix,
 )
 
-seeding_data = modinf.get_seeding_data(100)
+seeding_data = modinf.get_seeding_data(sim_id=100)
 initial_conditions = modinf.initial_conditions.get_from_config(sim_id=100, modinf=modinf)
 
 mobility_subpop_indices = modinf.mobility.indices

diff --git a/flepimop/gempyor_pkg/src/gempyor/inference.py b/flepimop/gempyor_pkg/src/gempyor/inference.py
@@ -164,7 +164,7 @@ def get_static_arguments(modinf: model_info.ModelInfo):
     )
 
     initial_conditions = modinf.initial_conditions.get_from_config(sim_id=0, modinf=modinf)
-    seeding_data, seeding_amounts = modinf.get_seeding_data(0)
+    seeding_data, seeding_amounts = modinf.get_seeding_data(sim_id=0)
 
     # reduce them
     parameters = modinf.parameters.parameters_reduce(p_draw, npi_seir)
@@ -673,7 +673,7 @@ def one_simulation(
 
             with Timer("onerun_SEIR.seeding"):
                 seeding_data, seeding_amounts = self.modinf.get_seeding_data(
-                    sim_id2load if load_ID else sim_id2write
+                    sim_id=sim_id2load if load_ID else sim_id2write
                 )
                 if load_ID:
                     initial_conditions = self.modinf.initial_conditions.get_from_file(

diff --git a/flepimop/gempyor_pkg/src/gempyor/model_info.py b/flepimop/gempyor_pkg/src/gempyor/model_info.py
@@ -306,10 +306,10 @@ def get_filename(
         self, ftype: str, sim_id: int, input: bool, extension_override: str = ""
     ):
         return self.path_prefix / file_paths.create_file_name(
-            self.in_run_id if input else self.out_run_id,
-            self.in_prefix if input else self.out_prefix,
-            sim_id + self.first_sim_index - 1,
-            ftype,
+            run_id=self.in_run_id if input else self.out_run_id,
+            prefix=self.in_prefix if input else self.out_prefix,
+            index=sim_id + self.first_sim_index - 1,
+            ftype=ftype,
             extension=extension_override if extension_override else self.extension,
             inference_filepath_suffix=self.inference_filepath_suffix,
             inference_filename_prefix=self.inference_filename_prefix,
@@ -368,12 +368,12 @@ def get_seeding_data(self, sim_id: int) -> tuple[nb.typed.Dict, npt.NDArray[np.n
             `gempyor.seeding.Seeding.get_from_config`
         """
         return self.seeding.get_from_config(
-            self.compartments,
-            self.subpop_struct,
-            self.n_days,
-            self.ti,
-            self.tf,
-            (
+            compartments=self.compartments,
+            subpop_struct=self.subpop_struct,
+            n_days=self.n_days,
+            ti=self.ti,
+            tf=self.tf,
+            input_filename=(
                 None
                 if self.seeding_config is None
                 else self.get_input_filename(

diff --git a/flepimop/gempyor_pkg/src/gempyor/seir.py b/flepimop/gempyor_pkg/src/gempyor/seir.py
@@ -277,12 +277,13 @@ def onerun_SEIR(
             initial_conditions = modinf.initial_conditions.get_from_file(
                 sim_id2load, modinf=modinf
             )
-            seeding_data, seeding_amounts = modinf.get_seeding_data(sim_id2load)
         else:
             initial_conditions = modinf.initial_conditions.get_from_config(
                 sim_id2write, modinf=modinf
             )
-            seeding_data, seeding_amounts = modinf.get_seeding_data(sim_id2write)
+        seeding_data, seeding_amounts = modinf.get_seeding_data(
+            sim_id=sim_id2load if load_ID else sim_id2write
+        )
 
     with Timer("onerun_SEIR.parameters"):
         # Draw or load parameters

diff --git a/flepimop/gempyor_pkg/tests/seir/test_seeding.py b/flepimop/gempyor_pkg/tests/seir/test_seeding.py
@@ -40,12 +40,12 @@ def test_Seeding_draw_success(self):
         s.seeding_config["method"] = "NoSeeding"
 
         seeding_result = sic.get_from_config(
-            s.compartments,
-            s.subpop_struct,
-            s.n_days,
-            s.ti,
-            s.tf,
-            s.get_input_filename(
+            compartments=s.compartments,
+            subpop_struct=s.subpop_struct,
+            n_days=s.n_days,
+            ti=s.ti,
+            tf=s.tf,
+            input_filename=s.get_input_filename(
                 ftype=s.seeding_config["seeding_file_type"].get(),
                 sim_id=0,
                 extension_override="csv",

diff --git a/flepimop/gempyor_pkg/tests/seir/test_seir.py b/flepimop/gempyor_pkg/tests/seir/test_seir.py
@@ -73,7 +73,7 @@ def test_constant_population_legacy_integration():
     )
     integration_method = "legacy"
 
-    seeding_data, seeding_amounts = modinf.get_seeding_data(100)
+    seeding_data, seeding_amounts = modinf.get_seeding_data(sim_id=100)
     initial_conditions = modinf.initial_conditions.get_from_config(
         sim_id=100, modinf=modinf
     )
@@ -152,7 +152,7 @@ def test_constant_population_rk4jit_integration_fail():
         )
         modinf.seir_config["integration"]["method"] = "rk4.jit"
 
-        seeding_data, seeding_amounts = modinf.get_seeding_data(100)
+        seeding_data, seeding_amounts = modinf.get_seeding_data(sim_id=100)
         initial_conditions = modinf.initial_conditions.get_from_config(
             sim_id=100, modinf=modinf
         )
@@ -229,7 +229,7 @@ def test_constant_population_rk4jit_integration():
     # s.integration_method = "rk4.jit"
     assert modinf.seir_config["integration"]["method"].get() == "rk4"
 
-    seeding_data, seeding_amounts = modinf.get_seeding_data(100)
+    seeding_data, seeding_amounts = modinf.get_seeding_data(sim_id=100)
     initial_conditions = modinf.initial_conditions.get_from_config(
         sim_id=100, modinf=modinf
     )
@@ -304,7 +304,7 @@ def test_steps_SEIR_nb_simple_spread_with_txt_matrices():
         out_prefix=prefix,
     )
 
-    seeding_data, seeding_amounts = modinf.get_seeding_data(100)
+    seeding_data, seeding_amounts = modinf.get_seeding_data(sim_id=100)
     initial_conditions = modinf.initial_conditions.get_from_config(
         sim_id=100, modinf=modinf
     )
@@ -413,7 +413,7 @@ def test_steps_SEIR_nb_simple_spread_with_csv_matrices():
         out_prefix=prefix,
     )
 
-    seeding_data, seeding_amounts = modinf.get_seeding_data(100)
+    seeding_data, seeding_amounts = modinf.get_seeding_data(sim_id=100)
     initial_conditions = modinf.initial_conditions.get_from_config(
         sim_id=100, modinf=modinf
     )
@@ -490,7 +490,7 @@ def test_steps_SEIR_no_spread():
         out_prefix=prefix,
     )
 
-    seeding_data, seeding_amounts = modinf.get_seeding_data(100)
+    seeding_data, seeding_amounts = modinf.get_seeding_data(sim_id=100)
     initial_conditions = modinf.initial_conditions.get_from_config(
         sim_id=100, modinf=modinf
     )
@@ -767,7 +767,7 @@ def test_parallel_compartments_with_vacc():
         out_prefix=prefix,
     )
 
-    seeding_data, seeding_amounts = modinf.get_seeding_data(100)
+    seeding_data, seeding_amounts = modinf.get_seeding_data(sim_id=100)
     initial_conditions = modinf.initial_conditions.get_from_config(
         sim_id=100, modinf=modinf
     )
@@ -861,7 +861,7 @@ def test_parallel_compartments_no_vacc():
         out_prefix=prefix,
     )
 
-    seeding_data, seeding_amounts = modinf.get_seeding_data(100)
+    seeding_data, seeding_amounts = modinf.get_seeding_data(sim_id=100)
     initial_conditions = modinf.initial_conditions.get_from_config(
         sim_id=100, modinf=modinf
     )