Remove Simulate profile (to move to Vivarium profiling) (#669)

* remove simulate profile

* add changelog

* remove unused

* Update CHANGELOG.rst

Author: patricktnast

CHANGELOG.rst

@@ -1,3 +1,7 @@
+**3.6.0 - 10/27/25**
+
+  - Move simulate profile command to vivarium_profiling package
+  
 **3.5.6 - 10/23/25**
 
   - Split Interfaces and their respective Managers into different modules

docs/source/tutorials/running_a_simulation/cli.rst

@@ -6,7 +6,7 @@ Running from the Command Line
 
 To run from the command line, we'll use the
 :mod:`simulate <vivarium.interface.cli>` command. This command is actually a
-group containing three sub-commands: ``run``, ``test``, and ``profile``. We will
+group containing two sub-commands: ``run`` and ``test``. We will
 focus on ``run`` here.
 
 The basic use of ``simulate run`` requires no more than a

src/vivarium/interface/cli.py

@@ -17,9 +17,6 @@
     *   - | **test**
         - | Runs an example simulation that comes packaged with ``vivarium``.
           | Useful as an installation test.
-    *   - | **profile**
-        - | Produces a profile of a simulation using the python
-          | :mod:`cProfile` module
 
 For more information, see the :ref:`tutorial <cli_tutorial>` on running
 simulations from the command line.
@@ -30,10 +27,7 @@
 
 """
 
-import cProfile
 import os
-import pstats
-from datetime import datetime as dt
 from pathlib import Path
 from time import time
 
@@ -173,71 +167,3 @@ def test() -> None:
 
     click.echo()
     click.secho("Installation test successful!", fg="green")
-
-
-@simulate.command()
-@click.argument(
-    "model_specification",
-    type=click.Path(exists=True, dir_okay=False, resolve_path=True),
-)
-@click.option(
-    "--results_directory",
-    "-o",
-    type=click.Path(resolve_path=True),
-    default=Path("~/vivarium_results/").expanduser(),
-    show_default=True,
-    help=(
-        "The directory to write results to. A folder will be created "
-        "in this directory with the same name as the configuration file."
-    ),
-)
-@click.option(
-    "--skip_writing",
-    is_flag=True,
-    help=(
-        "Skip writing the simulation results to the output directory; the time spent "
-        "normally writing simulation results to disk will not be included in the profiling "
-        "statistics."
-    ),
-)
-@click.option(
-    "--skip_processing",
-    is_flag=True,
-    help=(
-        "Skip processing the resulting binary file to a human-readable .txt file "
-        "sorted by cumulative runtime; the resulting .stats file can still be read "
-        "and processed later using the pstats module."
-    ),
-)
-def profile(
-    model_specification: Path,
-    results_directory: Path,
-    skip_writing: bool,
-    skip_processing: bool,
-) -> None:
-    """Run a simulation based on the provided MODEL_SPECIFICATION and profile the run."""
-    model_specification = Path(model_specification)
-    results_directory = Path(results_directory)
-    results_root = results_directory / f"{dt.now().strftime('%Y_%m_%d_%H_%M_%S')}"
-    configure_logging_to_file(output_directory=results_root)
-
-    if skip_writing:
-        configuration_override = {}
-    else:
-        output_data_root = results_root / "results"
-        output_data_root.mkdir(parents=True, exist_ok=False)
-        configuration_override = {
-            "output_data": {"results_directory": str(output_data_root)},
-        }
-
-    out_stats_file = results_root / f"{model_specification.name}".replace("yaml", "stats")
-    sim = SimulationContext(model_specification, configuration=configuration_override)
-    command = f"sim.run_simulation()"
-    cProfile.runctx(command, globals=globals(), locals=locals(), filename=str(out_stats_file))
-
-    if not skip_processing:
-        out_txt_file = Path(str(out_stats_file) + ".txt")
-        with out_txt_file.open("w") as f:
-            p = pstats.Stats(str(out_stats_file), stream=f)
-            p.sort_stats("cumulative")
-            p.print_stats()