Merge branch 'breaking-improvments' of https://github.com/HopkinsIDD/…

…flepiMoP into breaking-improvments

.github/workflows/ci.yml

@@ -30,7 +30,7 @@ jobs:
         run: |
           source /var/python/3.10/virtualenv/bin/activate
           python -m pip install --upgrade pip
-          python -m pip install flepimop/gempyor_pkg/
+          python -m pip install "flepimop/gempyor_pkg[test]"
         shell: bash
       - name: Install local R packages
         run: Rscript build/local_install.R

flepimop/gempyor_pkg/setup.cfg

@@ -31,10 +31,17 @@ install_requires =
     pyarrow
     sympy
     dask
-    pytest
     scipy
     graphviz
 
+# see https://stackoverflow.com/questions/58826164/dependencies-requirements-for-setting-up-testing-and-installing-a-python-lib
+# installed for pip install -e ".[test]"
+[options.extras_require]  
+test =
+    pytest
+    mock
+
+
 [options.entry_points]
 console_scripts =
     gempyor-outcomes = gempyor.simulate_outcome:simulate

flepimop/gempyor_pkg/src/gempyor/compartments.py

@@ -283,7 +283,7 @@ def fromFile(self, compartments_file, transitions_file):
 
         return
 
-    def get_comp_idx(self, comp_dict: dict) -> int:
+    def get_comp_idx(self, comp_dict: dict, error_info: str = "no information") -> int:
         """
         return the index of a compartiment given a filter. The filter has to isolate a compartiment,
         but it ignore columns that don't exist:
@@ -294,7 +294,7 @@ def get_comp_idx(self, comp_dict: dict) -> int:
         comp_idx = self.compartments[mask].index.values
         if len(comp_idx) != 1:
             raise ValueError(
-                f"The provided dictionary does not allow to isolate a compartment: {comp_dict} isolate {self.compartments[mask]} from options {self.compartments}"
+                f"The provided dictionary does not allow to isolate a compartment: {comp_dict} isolate {self.compartments[mask]} from options {self.compartments}. The get_comp_idx function was called by'{error_info}'." 
             )
         return comp_idx[0]
 
@@ -476,7 +476,7 @@ def parse_parameter_strings_to_numpy_arrays_v2(self, parameters, parameter_names
                 f = sp.sympify(formula, locals=symbolic_parameters_namespace)
                 parsed_formulas.append(f)
             except Exception as e:
-                print(f"Cannot parse formula: '{formula}' from paramters {parameter_names}")
+                print(f"Cannot parse formula: '{formula}' from parameters {parameter_names}")
                 raise (e)  # Print the error message for debugging
 
         # the list order needs to be right.

flepimop/gempyor_pkg/src/gempyor/seeding_ic.py

@@ -50,8 +50,8 @@ def _DataFrame2NumbaDict(df, amounts, setup) -> nb.typed.Dict:
                 )
                 source_dict = {grp_name: row[f"source_{grp_name}"] for grp_name in cmp_grp_names}
                 destination_dict = {grp_name: row[f"destination_{grp_name}"] for grp_name in cmp_grp_names}
-                seeding_dict["seeding_sources"][idx] = setup.compartments.get_comp_idx(source_dict)
-                seeding_dict["seeding_destinations"][idx] = setup.compartments.get_comp_idx(destination_dict)
+                seeding_dict["seeding_sources"][idx] = setup.compartments.get_comp_idx(source_dict, error_info = f"(seeding source at idx={idx}, row_index={row_index}, row=>>{row}<<)")
+                seeding_dict["seeding_destinations"][idx] = setup.compartments.get_comp_idx(destination_dict, error_info = f"(seeding destination at idx={idx}, row_index={row_index}, row=>>{row}<<)")
                 seeding_dict["seeding_subpops"][idx] = setup.subpop_struct.subpop_names.index(row["subpop"])
                 seeding_amounts[idx] = amounts[idx]
                 #id_seed+=1
@@ -326,14 +326,7 @@ def draw_seeding(self, sim_id: int, setup) -> nb.typed.Dict:
         return _DataFrame2NumbaDict(df=seeding, amounts=amounts, setup=setup)
 
     def load_seeding(self, sim_id: int, setup) -> nb.typed.Dict:
-        method = "NoSeeding"
-
-        if self.seeding_config is not None and "method" in self.seeding_config.keys():
-            method = self.seeding_config["method"].as_str()
-        if method not in ["FolderDraw", "SetInitialConditions", "InitialConditionsFolderDraw", "NoSeeding", "FromFile"]:
-            raise NotImplementedError(
-                f"Seeding method in inference run must be FolderDraw, SetInitialConditions, FromFile or InitialConditionsFolderDraw [got: {method}]"
-            )
+        """ only difference with draw seeding is that the sim_id is now sim_id2load"""
         return self.draw_seeding(sim_id=sim_id, setup=setup)
 
     def load_ic(self, sim_id: int, setup) -> nb.typed.Dict: