Edits to make test_outcome_scenario pass

* 'compartments' and 'seir' sections are now required in the config for
  inferece.
* Added logic to `get_static_arguments` to allow it to work without an
  'seir_modifiers' section in the config.

flepimop/gempyor_pkg/src/gempyor/inference.py

@@ -144,8 +144,10 @@ def get_static_arguments(modinf: model_info.ModelInfo):
     ) = modinf.compartments.get_transition_array()
 
     outcomes_parameters = outcomes.read_parameters_from_config(modinf)
-    npi_seir = seir.build_npi_SEIR(
-        modinf=modinf, load_ID=False, sim_id2load=None, config=config
+    npi_seir = (
+        seir.build_npi_SEIR(modinf=modinf, load_ID=False, sim_id2load=None, config=config)
+        if modinf.npi_config_seir is not None
+        else None
     )
     if modinf.npi_config_outcomes:
         npi_outcomes = outcomes.build_outcome_modifiers(
@@ -211,7 +213,7 @@ def get_static_arguments(modinf: model_info.ModelInfo):
             ),  # TODO add more information
         )
 
-    snpi_df_ref = npi_seir.getReductionDF()
+    snpi_df_ref = npi_seir.getReductionDF() if npi_seir is not None else pd.DataFrame()
 
     outcomes_df, hpar_df = outcomes.compute_all_multioutcomes(
         modinf=modinf,

flepimop/gempyor_pkg/src/gempyor/model_info.py

@@ -120,6 +120,7 @@ def __init__(
 
         # 4. the SEIR structure
         self.seir_config = None
+        self.seir_modifiers_library = None
         if config["seir"].exists():
             self.seir_config = config["seir"]
             self.parameters_config = config["seir"]["parameters"]

flepimop/gempyor_pkg/tests/outcomes/config.yml

@@ -7,6 +7,36 @@ nslots: 1
 subpop_setup:
   geodata: data/geodata.csv
 
+compartments:
+  infection_stage: ["S", "E", "I", "R"]
+
+seir:
+  integration:
+    method: rk4
+    dt: 1
+  parameters:
+    sigma:
+      value: 1 / 4
+    gamma:
+      value: 1 / 5
+    Ro:
+      value: 2.5
+  transitions:
+    - source: ["S"]
+      destination: ["E"]
+      rate: ["Ro * gamma"]
+      proportional_to: [["S"],["I"]]
+      proportion_exponent: ["1","1"]
+    - source: ["E"]
+      destination: ["I"]
+      rate: ["sigma"]
+      proportional_to: ["E"]
+      proportion_exponent: ["1"]
+    - source: ["I"]
+      destination: ["R"]
+      rate: ["gamma"]
+      proportional_to: ["I"]
+      proportion_exponent: ["1"]
 
 outcomes:
   method: delayframe

flepimop/gempyor_pkg/tests/outcomes/test_outcomes0.py

@@ -18,8 +18,6 @@
 import pyarrow as pa
 from gempyor import file_paths, model_info, outcomes
 
-config_filepath_prefix = ""  #'tests/outcomes/'
-
 ### To generate files for this test, see notebook Test Outcomes  playbook.ipynb in COVID19_Maryland
 
 geoid = ["15005", "15007", "15009", "15001", "15003"]
@@ -29,10 +27,10 @@
 os.chdir(os.path.dirname(__file__))
 
 
-def test_outcome_scenario():
-    os.chdir(os.path.dirname(__file__))  ## this is redundant but necessary. Why ?
+def test_outcome_scenario(monkeypatch: pytest.MonkeyPatch) -> None:
+    monkeypatch.chdir(os.path.dirname(__file__))
     inference_simulator = gempyor.GempyorInference(
-        config_filepath=f"{config_filepath_prefix}config.yml",
+        config_filepath=f"config.yml",
         run_id=1,
         prefix="",
         first_sim_index=1,