Remove gempyor.seeding Dependence On gempyor.model_info.ModelInfo

flepimop/gempyor_pkg/docs/integration_benchmark.ipynb

@@ -410,7 +410,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": null,
    "id": "07bfd952-5c42-4704-81cc-5de0c917c0ab",
    "metadata": {
     "execution": {
@@ -450,7 +450,7 @@
     "\n",
     "with Timer(\"onerun_SEIR.seeding\"):\n",
     "    initial_conditions = s.initial_conditions.get_from_config(sim_id, modinf=s)\n",
-    "    seeding_data, seeding_amounts = s.seeding.get_from_config(sim_id, modinf=s)\n",
+    "    seeding_data, seeding_amounts = s.get_seeding_data(sim_id)\n",
     "\n",
     "mobility_subpop_indices = s.mobility.indices\n",
     "mobility_data_indices = s.mobility.indptr\n",

flepimop/gempyor_pkg/docs/integration_doc.ipynb

@@ -70,7 +70,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "id": "96230106-73e3-4681-b562-6a7269513375",
    "metadata": {
     "execution": {
@@ -109,7 +109,7 @@
     "\n",
     "\n",
     "initial_conditions = gempyor_inference.s.initial_conditions.get_from_config(sim_id2write, modinf=gempyor_inference.s)\n",
-    "seeding_data, seeding_amounts = gempyor_inference.s.seeding.get_from_config(sim_id2write, modinf=gempyor_inference.s)\n",
+    "seeding_data, seeding_amounts = gempyor_inference.s.get_seeding_data(sim_id2write)\n",
     "\n",
     "\n",
     "p_draw = gempyor_inference.s.parameters.parameters_quick_draw(\n",

flepimop/gempyor_pkg/docs/interface.ipynb

@@ -169,7 +169,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 15,
+   "execution_count": null,
    "id": "63618148-81db-4fe0-9395-7f21878c1372",
    "metadata": {
     "execution": {
@@ -254,20 +254,15 @@
     "\n",
     "### Run every time:\n",
     "with Timer(\"onerun_SEIR.seeding\"):\n",
+    "    seeding_data, seeding_amounts = gempyor_inference.s.get_seeding_data(sim_id2load if load_ID else sim_id2write)\n",
     "    if load_ID:\n",
     "        initial_conditions = gempyor_inference.s.initial_conditions.get_from_file(\n",
     "            sim_id2load, modinf=gempyor_inference.s\n",
     "        )\n",
-    "        seeding_data, seeding_amounts = gempyor_inference.s.seeding.get_from_file(\n",
-    "            sim_id2load, modinf=gempyor_inference.s\n",
-    "        )\n",
     "    else:\n",
     "        initial_conditions = gempyor_inference.s.initial_conditions.get_from_config(\n",
     "            sim_id2write, modinf=gempyor_inference.s\n",
     "        )\n",
-    "        seeding_data, seeding_amounts = gempyor_inference.s.seeding.get_from_config(\n",
-    "            sim_id2write, modinf=gempyor_inference.s\n",
-    "        )\n",
     "\n",
     "with Timer(\"SEIR.parameters\"):\n",
     "    # Draw or load parameters\n",

flepimop/gempyor_pkg/src/gempyor/dev/dev_seir.py

@@ -35,7 +35,7 @@
     out_prefix=prefix,
 )
 
-seeding_data = modinf.seeding.get_from_config(sim_id=100, modinf=modinf)
+seeding_data = modinf.get_seeding_data(100)
 initial_conditions = modinf.initial_conditions.get_from_config(sim_id=100, modinf=modinf)
 
 mobility_subpop_indices = modinf.mobility.indices

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.seeding.get_from_config(sim_id=0, modinf=modinf)
+    seeding_data, seeding_amounts = modinf.get_seeding_data(0)
 
     # reduce them
     parameters = modinf.parameters.parameters_reduce(p_draw, npi_seir)
@@ -672,20 +672,17 @@ def one_simulation(
                 self.lastsim_parsed_parameters = parsed_parameters
 
             with Timer("onerun_SEIR.seeding"):
+                seeding_data, seeding_amounts = self.modinf.get_seeding_data(
+                    sim_id2load if load_ID else sim_id2write
+                )
                 if load_ID:
                     initial_conditions = self.modinf.initial_conditions.get_from_file(
                         sim_id2load, modinf=self.modinf
                     )
-                    seeding_data, seeding_amounts = self.modinf.seeding.get_from_file(
-                        sim_id2load, modinf=self.modinf
-                    )
                 else:
                     initial_conditions = self.modinf.initial_conditions.get_from_config(
                         sim_id2write, modinf=self.modinf
                     )
-                    seeding_data, seeding_amounts = self.modinf.seeding.get_from_config(
-                        sim_id2write, modinf=self.modinf
-                    )
                 self.lastsim_seeding_data = seeding_data
                 self.lastsim_seeding_amounts = seeding_amounts
                 self.lastsim_initial_conditions = initial_conditions

flepimop/gempyor_pkg/src/gempyor/model_info.py

@@ -1,5 +1,14 @@
+import datetime
+import logging
+import os
+import pathlib
+
+import confuse
+import numba as nb
+import numpy as np
+import numpy.typing as npt
 import pandas as pd
-import datetime, os, logging, pathlib, confuse
+
 from . import (
     seeding,
     subpopulation_structure,
@@ -296,30 +305,15 @@ def get_output_filename(self, ftype: str, sim_id: int, extension_override: str =
     def get_filename(
         self, ftype: str, sim_id: int, input: bool, extension_override: str = ""
     ):
-        """return a CSP formated filename."""
-
-        if extension_override:  # empty strings are Falsy
-            extension = extension_override
-        else:  # Constructed like this because in some test, extension is not defined
-            extension = self.extension
-
-        if input:
-            run_id = self.in_run_id
-            prefix = self.in_prefix
-        else:
-            run_id = self.out_run_id
-            prefix = self.out_prefix
-
-        fn = self.path_prefix / file_paths.create_file_name(
-            run_id=run_id,
-            prefix=prefix,
-            index=sim_id + self.first_sim_index - 1,
+        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,
+            extension=extension_override if extension_override else self.extension,
             inference_filepath_suffix=self.inference_filepath_suffix,
             inference_filename_prefix=self.inference_filename_prefix,
-            ftype=ftype,
-            extension=extension,
         )
-        return fn
 
     def get_setup_name(self):
         return self.setup_name
@@ -359,3 +353,33 @@ def write_simID(
             df=df,
         )
         return fname
+
+    def get_seeding_data(self, sim_id: int) -> tuple[nb.typed.Dict, npt.NDArray[np.number]]:
+        """
+        Pull the seeding data for the info represented by this model info instance.
+
+        Args:
+            sim_id: The simulation ID to pull seeding data for.
+
+        Returns:
+            A tuple containing the seeding data dictionary and the seeding data array.
+
+        See Also:
+            `gempyor.seeding.Seeding.get_from_config`
+        """
+        return self.seeding.get_from_config(
+            self.compartments,
+            self.subpop_struct,
+            self.n_days,
+            self.ti,
+            self.tf,
+            (
+                None
+                if self.seeding_config is None
+                else self.get_input_filename(
+                    ftype=self.seeding_config["seeding_file_type"].get(),
+                    sim_id=sim_id,
+                    extension_override="csv",
+                )
+            ),
+        )