Change run_benchmark arguments (#15)

* remove old model specs

* Adjust how model specs are passed in

* Update CHANGELOG for version 0.3.1

* update makefile to modern version (#16)

---------

Co-authored-by: Steve Bachmeier <23350991+stevebachmeier@users.noreply.github.com>

Author: patricktnast

CHANGELOG.rst

@@ -1,3 +1,8 @@
+**v0.3.1 - 01/27/2026**
+
+ - Adjust the parameters for run_benchmark command
+ - Update makefile
+
 **v0.3.0 - 01/22/2026**
 
  - Convert data ETL to click commands

Makefile

@@ -19,6 +19,9 @@ endif
 # Set the package name as the last part of this file's parent directory path
 PACKAGE_NAME = $(notdir $(CURDIR))
 
+# Helper function for validating enum arguments
+validate_arg = $(if $(filter-out $(2),$(1)),$(error Error: '$(3)' must be one of: $(2), got '$(1)'))
+
 ifneq ($(MAKE_INCLUDES),) # not empty
 # Include makefiles from vivarium_build_utils
 include $(MAKE_INCLUDES)/base.mk
@@ -35,15 +38,19 @@ help:
 	@echo "make build-env"
 	@echo
 	@echo "USAGE:"
-	@echo "  make build-env name=<environment_name> [py=<python_version>]"
+	@echo "  make build-env [type=<environment type>] [name=<environment name>] [py=<python version>] [include_timestamp=<yes|no>] [lfs=<yes|no>]"
 	@echo
 	@echo "ARGUMENTS:"
-	@echo "  name  [required]  Name of the conda environment to create"
-	@echo "  py    [optional]  Python version (defaults to latest supported)"
-	@echo
-	@echo "EXAMPLE:"
-	@echo "  make build-env name=vivarium_dev"
-	@echo "  make build-env name=vivarium_dev py=3.9"
+	@echo "  type [optional]"
+	@echo "      Type of conda environment. Either 'simulation' (default) or 'artifact'"
+	@echo "  name [optional]"
+	@echo "      Name of the conda environment to create (defaults to <PACKAGE_NAME>_<TYPE>)"
+	@echo "  include_timestamp [optional]"
+	@echo "      Whether to append a timestamp to the environment name. Either 'yes' or 'no' (default)"
+	@echo "  lfs [optional]"
+	@echo "      Whether to install git-lfs in the environment. Either 'yes' or 'no' (default)"
+	@echo "  py [optional]"
+	@echo "      Python version (defaults to latest supported)"
 	@echo
 	@echo "After creating the environment:"
 	@echo "  1. Activate it: 'conda activate <environment_name>'"
@@ -52,18 +59,58 @@ help:
 endif
 
 build-env: # Create a new environment with installed packages
-ifndef name
-	@echo "Error: name is required and must be passed in as a keyword argument."
-	@echo "Usage: make build-env name=<ENV_NAME> py=<PYTHON_VERSION>"
-	@exit 1
-endif
-#	Check if py is set, otherwise use the latest supported version
+#	Validate arguments - exit if unsupported arguments are passed
+	@allowed="type name lfs py include_timestamp"; \
+	for arg in $(filter-out build-env,$(MAKECMDGOALS)) $(MAKEFLAGS); do \
+		case $$arg in \
+			*=*) \
+				arg_name=$${arg%%=*}; \
+				if ! echo " $$allowed " | grep -q " $$arg_name "; then \
+					allowed_list=$$(echo $$allowed | sed 's/ /, /g'); \
+					echo "Error: Invalid argument '$$arg_name'. Allowed arguments are: $$allowed_list" >&2; \
+					exit 1; \
+				fi \
+				;; \
+		esac; \
+	done
+	
+#   Handle arguments and set defaults
+#   type
+	@$(eval type ?= simulation)
+	@$(call validate_arg,$(type),simulation artifact,type)
+#	name
+	@$(eval name ?= $(PACKAGE_NAME)_$(type))
+#	timestamp
+	@$(eval include_timestamp ?= no)
+	@$(call validate_arg,$(include_timestamp),yes no,include_timestamp)
+	@$(if $(filter yes,$(include_timestamp)),$(eval override name := $(name)_$(shell date +%Y%m%d_%H%M%S)),)
+#	lfs
+	@$(eval lfs ?= no)
+	@$(call validate_arg,$(lfs),yes no,lfs)
+#	python version
 	@$(eval py ?= $(shell python -c "import json; versions = json.load(open('python_versions.json')); print(max(versions, key=lambda x: tuple(map(int, x.split('.')))))"))
+	
 	conda create -n $(name) python=$(py) --yes
 # 	Bootstrap vivarium_build_utils into the new environment
 	conda run -n $(name) pip install vivarium_build_utils
-	conda run -n $(name) make install
+#	Install packages based on type
+	@if [ "$(type)" = "simulation" ]; then \
+		conda run -n $(name) make install ENV_REQS=dev; \
+		conda install -n $(name) redis -c anaconda -y; \
+	elif [ "$(type)" = "artifact" ]; then \
+		conda run -n $(name) make install ENV_REQS=data; \
+	fi
+	@if [ "$(lfs)" = "yes" ]; then \
+		conda run -n $(name) conda install -c conda-forge git-lfs --yes; \
+		conda run -n $(name) git lfs install; \
+	fi
+
+	@echo
+	@echo "Finished building environment"
+	@echo "  name: $(name)"
+	@echo "  type: $(type)"
+	@echo "  git-lfs installed: $(lfs)"
+	@echo "  python version: $(py)"
 	@echo
-	@echo "Environment built ($(name))"
 	@echo "Don't forget to activate it with: 'conda activate $(name)'"
 	@echo

README.rst

@@ -178,7 +178,7 @@ depending on the profiler backend provided. By default, runtime profiling is per
 you can also use ``scalene`` for more detailed call stack analysis.
 
 The ``run_benchmark`` command runs multiple iterations of one or more model specification, in order to compare
-the results. It requires at least one baseline model (specified as ``model_spec_baseline.yaml``) for comparison,
+the results. It requires at least one baseline model for comparison,
 and any other number of 'experiment' models to benchmark against the baseline, which can be passed via glob patterns.
 You can separately configure the sample size of runs for the baseline and experiment models. The command aggregates
 the profiling results and generates summary statistics and visualizations for a default set of important function calls