factoring out click interface for optimize_network

pyproject.toml

@@ -28,6 +28,7 @@ matplotlib = "^3.6.0"
 quantities = "^0.13.0"
 pydantic = "^2.3.0"
 neuron = "^8.2.3"
+distgfs = {version = "^1.1.0", optional = true}
 
 
 [tool.poetry.dev-dependencies]
@@ -88,6 +89,7 @@ check-config = "scripts.tools.check_config:main"
 cut-slice = "scripts.tools.cut_slice:main"
 sample-cells = "scripts.tools.sample_cells:main"
 reposition-trees = "scripts.tools.reposition_trees:main"
+optimize-network = "scripts.optimization.optimize_network:main_cli"
 
 
 [build-system]

src/miv_simulator/optimize_network.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 """
-Dentate Gyrus model optimization script for optimization with dmosopt
+Network model optimization script for optimization with dmosopt
 """
 
 import os, sys, logging, datetime, gc
@@ -133,56 +133,7 @@ def init_controller(subworld_size, use_coreneuron):
         h.pc.psolve(0.05)
 
 
-@click.command(
-    context_settings=dict(
-        ignore_unknown_options=True,
-        allow_extra_args=True,
-    )
-)
-@click.option(
-    "--config-path",
-    required=True,
-    type=str,
-    help="optimization configuration file name",
-)
-@click.option(
-    "--target-features-path",
-    required=False,
-    type=click.Path(),
-    help="path to neuroh5 file containing target rate maps used for rate optimization",
-)
-@click.option(
-    "--target-features-namespace",
-    type=str,
-    required=False,
-    default="Input Spikes",
-    help="namespace containing target rate maps used for rate optimization",
-)
-@click.option(
-    "--optimize-file-dir",
-    type=click.Path(exists=True, file_okay=False, dir_okay=True),
-    default="results",
-)
-@click.option(
-    "--optimize-file-name",
-    type=click.Path(exists=False, file_okay=True, dir_okay=False),
-)
-@click.option("--nprocs-per-worker", type=int, default=1)
-@click.option("--n-epochs", type=int, default=1)
-@click.option("--n-initial", type=int, default=30)
-@click.option("--initial-maxiter", type=int, default=50)
-@click.option("--initial-method", type=str, default="glp")
-@click.option("--optimizer-method", type=str, default="nsga2")
-@click.option("--population-size", type=int, default=100)
-@click.option("--num-generations", type=int, default=200)
-@click.option("--resample-fraction", type=float)
-@click.option("--mutation-rate", type=float)
-@click.option("--collective-mode", type=str, default="gather")
-@click.option("--spawn-startup-wait", type=int, default=3)
-@click.option("--spawn-workers", is_flag=True)
-@click.option("--get-best", is_flag=True)
-@click.option("--verbose", "-v", is_flag=True)
-def main(
+def optimize_network(
     config_path,
     target_features_path,
     target_features_namespace,
@@ -541,17 +492,3 @@ def compute_objectives(local_features, operational_config, opt_targets):
     )
 
     return {0: result}
-
-
-if __name__ == "__main__":
-    main(
-        args=sys.argv[
-            (
-                list_find(
-                    lambda x: os.path.basename(x) == os.path.basename(__file__),
-                    sys.argv,
-                )
-                + 1
-            ) :
-        ]
-    )

src/scripts/optimization/optimize_network.py

@@ -0,0 +1,100 @@
+import os
+import sys
+import click
+from miv_simulator import utils
+from miv_simulator.optimize_network import optimize_network
+
+
+@click.command(
+    context_settings=dict(
+        ignore_unknown_options=True,
+        allow_extra_args=True,
+    )
+)
+@click.option(
+    "--config-path",
+    required=True,
+    type=str,
+    help="optimization configuration file name",
+)
+@click.option(
+    "--target-features-path",
+    required=False,
+    type=click.Path(),
+    help="path to neuroh5 file containing target rate maps used for rate optimization",
+)
+@click.option(
+    "--target-features-namespace",
+    type=str,
+    required=False,
+    default="Input Spikes",
+    help="namespace containing target rate maps used for rate optimization",
+)
+@click.option(
+    "--optimize-file-dir",
+    type=click.Path(exists=True, file_okay=False, dir_okay=True),
+    default="results",
+)
+@click.option(
+    "--optimize-file-name",
+    type=click.Path(exists=False, file_okay=True, dir_okay=False),
+)
+@click.option("--nprocs-per-worker", type=int, default=1)
+@click.option("--n-epochs", type=int, default=1)
+@click.option("--n-initial", type=int, default=30)
+@click.option("--initial-maxiter", type=int, default=50)
+@click.option("--initial-method", type=str, default="glp")
+@click.option("--optimizer-method", type=str, default="nsga2")
+@click.option("--population-size", type=int, default=100)
+@click.option("--num-generations", type=int, default=200)
+@click.option("--resample-fraction", type=float)
+@click.option("--mutation-rate", type=float)
+@click.option("--collective-mode", type=str, default="gather")
+@click.option("--spawn-startup-wait", type=int, default=3)
+@click.option("--spawn-workers", is_flag=True)
+@click.option("--get-best", is_flag=True)
+@click.option("--verbose", "-v", is_flag=True)
+def main_cli(
+    config_path,
+    target_features_path,
+    target_features_namespace,
+    optimize_file_dir,
+    optimize_file_name,
+    nprocs_per_worker,
+    n_epochs,
+    n_initial,
+    initial_maxiter,
+    initial_method,
+    optimizer_method,
+    population_size,
+    num_generations,
+    resample_fraction,
+    mutation_rate,
+    collective_mode,
+    spawn_startup_wait,
+    spawn_workers,
+    get_best,
+    verbose,
+):
+    optimize_network(
+        config_path,
+        target_features_path,
+        target_features_namespace,
+        optimize_file_dir,
+        optimize_file_name,
+        nprocs_per_worker,
+        n_epochs,
+        n_initial,
+        initial_maxiter,
+        initial_method,
+        optimizer_method,
+        population_size,
+        num_generations,
+        resample_fraction,
+        mutation_rate,
+        collective_mode,
+        spawn_startup_wait,
+        spawn_workers,
+        get_best,
+        verbose,
+    )