vivarium-profiling 0.4.0__tar.gz

vivarium_profiling-0.4.0/.github/CODEOWNERS

@@ -0,0 +1,2 @@
+# default owners
+* @albrja @hussain-jafari @patricktnast @rmudambi @stevebachmeier

vivarium_profiling-0.4.0/.github/pull_request_template.md

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+## Title: Summary, imperative, start upper case, don't end with a period
+<!-- Ideally, <=50 chars. 50 chars is here..: -->
+
+### Description
+<!-- For use in commit message, wrap at 72 chars. 72 chars is here: -->
+- *Category*: <!-- one of bugfix, data artifact, implementation, observers,
+                   post-processing, refactor, revert, test, release, other/misc -->
+- *JIRA issue*: https://jira.ihme.washington.edu/browse/MIC-XYZ
+- *Research reference*: <!--Link to research documentation for code -->
+
+### Changes and notes
+<!-- 
+Change description – why, what, anything unexplained by the above.
+Include guidance to reviewers if changes are complex.
+--> 
+
+### Verification and Testing
+<!--
+Details on how code was verified. Consider: plots, images, (small) csv files.
+-->
+

vivarium_profiling-0.4.0/.github/workflows/update_readme.yml

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+# -----------------------------------------------------------------------------
+#   - invoked on push to any branch
+# -----------------------------------------------------------------------------
+name: update README
+on: push
+
+jobs:
+  update-readme:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v2
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.11
+      - name: Update README
+        run: |
+          pip install packaging
+          python update_readme.py
+      - name: Commit and push changes
+        run: |
+          git config --local user.email "action@github.com"
+          git config --local user.name "github-actions"
+          git diff --quiet && git diff --staged --quiet || (
+            git add README.rst
+            git commit -am "update README with supported Python versions"
+            git pull --rebase origin ${{ github.ref_name }}
+            git push origin ${{ github.ref_name }}
+          )
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

vivarium_profiling-0.4.0/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# Pycharm project settings
+.idea/
+
+# Version file
+src/*/_version.py
+
+# Copilot instructions
+.github/copilot_instructions.md
+.github/prompts/
+
+# VS Code settings
+.vscode/

vivarium_profiling-0.4.0/CHANGELOG.rst

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+**0.4.0 - 05/11/26**
+
+BREAKING CHANGE: Initial release from vivarium-suite monorepo. The import path is 
+now ``vivarium.profiling`` (was ``vivarium_profiling``). The ``vivarium-compat``
+shim redirects the old path with a ``DeprecationWarning``; update imports before
+that shim is removed.
+
+**0.3.6 - 05/05/26**
+
+Archive notice: this package is archived and no longer maintained. Please use the 
+vivarium-suite monorepo for future development. Refer to the README for more details.
+
+**0.3.5 - 04/21/26**
+
+- Update for VPH v5
+
+**0.3.4 - 04/16/26**
+
+- Tighten vivarium_build_utils pin
+
+**0.3.3 - 04/15/26**
+
+- Update vivarium_build_utils pin
+
+**0.3.2 - 03/25/26**
+
+- Remove upstream_repos from Jenkinsfile
+
+**0.3.1 - 01/27/2026**
+
+- Adjust the parameters for run_benchmark command
+- Update makefile
+
+**0.3.0 - 01/22/2026**
+
+- Convert data ETL to click commands
+- add configurable function call patterns
+- add notebook support
+
+**0.2.0 - 01/02/2026**
+
+- Add MultiComponentParser with Causes, Risks, RiskEffects
+
+**0.1.0 - 10/24/2025**
+
+- Convert bash script to python
+- add profiling CLI with scalene backend
+
+**0.0.1 - 10/20/2025**
+
+- Initial release

vivarium_profiling-0.4.0/CODEOWNERS

@@ -0,0 +1,2 @@
+# default owners
+* @albrja @hussain-jafari @patricktnast @rmudambi @stevebachmeier

vivarium_profiling-0.4.0/Jenkinsfile

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+/* This Jenkinsfile simply loads the `reusable_pipeline` pipeline from the
+vivariu_build_utils repository (https://github.com/ihmeuw/vivarium_build_utils).
+
+vivarium_build_utils is loaded as a Jenkins shared library 
+(https://www.jenkins.io/doc/book/pipeline/shared-libraries/).
+Jenkins shared library convention dictates that importable modules must be stored
+in the 'vars' folder.
+
+Jenkins shared libraries can be configured in the Jenkins UI:
+* Manage Jenkins
+  * Configure System
+    * Global Pipeline Libraries section
+      * Library subsection
+        * Name: The Name for the lib
+        * Version: The branch you want to use. Throws an error
+                   for nonexistent branches.
+        * Project Repository: Url to the shared lib
+        * Credentials: SSH key to access the repo
+
+Note that updating the shared repo will take affect on the next pipeline invocation.
+*/ 
+
+// Load the get_vbu_version function from vivarium_build_utils/bootstrap/
+// (the directory to load from is defined in the Jenkins shared library configuration)
+@Library("get_vbu_version@main") _
+
+// Load the full vivarium_build_utils library at the expected version
+library("vivarium_build_utils@${get_vbu_version()}")
+
+reusable_pipeline(
+    scheduled_branches: ['main'],
+    skip_doc_build: true,
+    run_mypy: false,
+    env_reqs: 'ci_jenkins',
+)

vivarium_profiling-0.4.0/LICENSE

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+BSD 3-Clause License
+
+Copyright 2022 Institute for Health Metrics and Evaluation
+All rights reserved
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

vivarium_profiling-0.4.0/Makefile

@@ -0,0 +1,116 @@
+# Check if we're running in Jenkins
+ifdef JENKINS_URL
+# 	Files are already in workspace from shared library
+	MAKE_INCLUDES := .
+else
+# 	For local dev, use the installed vivarium_build_utils package if it exists
+# 	First, check if we can import vivarium_build_utils and assign 'yes' or 'no'.
+# 	We do this by importing the package in python and redirecting stderr to the null device.
+# 	If the import is successful (&&), it will print 'yes', otherwise (||) it will print 'no'.
+	VIVARIUM_BUILD_UTILS_AVAILABLE := $(shell python -c "import vivarium_build_utils" 2>/dev/null && echo "yes" || echo "no")
+# 	If vivarium_build_utils is available, get the makefiles path or else set it to empty
+	ifeq ($(VIVARIUM_BUILD_UTILS_AVAILABLE),yes)
+		MAKE_INCLUDES := $(shell python -c "from vivarium_build_utils.resources import get_makefiles_path; print(get_makefiles_path())")
+	else
+		MAKE_INCLUDES :=
+	endif
+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
+include $(MAKE_INCLUDES)/test.mk
+else # empty
+# Use this help message (since the vivarium_build_utils version is not available)
+help:
+	@echo
+	@echo "For Make's standard help, run 'make --help'."
+	@echo
+	@echo "Most of our Makefile targets are provided by the vivarium_build_utils"
+	@echo "package. To access them, you need to create a development environment first."
+	@echo
+	@echo "make build-env"
+	@echo
+	@echo "USAGE:"
+	@echo "  make build-env [type=<environment type>] [name=<environment name>] [py=<python version>] [include_timestamp=<yes|no>] [lfs=<yes|no>]"
+	@echo
+	@echo "ARGUMENTS:"
+	@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>'"
+	@echo "  2. Run 'make help' again to see all newly available targets"
+	@echo
+endif
+
+build-env: # Create a new environment with installed packages
+#	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 $(name) pip install vivarium_build_utils
+#	Install packages based on type
+	@if [ "$(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 "Don't forget to activate it with: 'conda activate $(name)'"
+	@echo

vivarium_profiling-0.4.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: vivarium-profiling
+Version: 0.4.0
+Summary: Profiling and benchmarking tools for Vivarium simulations.
+Author-email: The vivarium developers <vivarium.dev@gmail.com>
+License: BSD 3-Clause
+Requires-Python: >=3.10
+Description-Content-Type: text/x-rst
+License-File: LICENSE
+Requires-Dist: vivarium-compat>=0.1.2
+Requires-Dist: vivarium_dependencies[click,loguru,numpy,pandas,scipy,tables]
+Requires-Dist: vivarium_build_utils<4.0.0,>=3.0.2
+Requires-Dist: gbd_mapping>=4.1.6
+Requires-Dist: vivarium>=4.1.2
+Requires-Dist: vivarium_public_health>=5.0.0
+Requires-Dist: jinja2
+Requires-Dist: pyyaml
+Requires-Dist: memory_profiler
+Requires-Dist: matplotlib
+Requires-Dist: seaborn
+Requires-Dist: scalene
+Requires-Dist: nbformat>=5.0
+Provides-Extra: test
+Requires-Dist: vivarium_dependencies[pytest]; extra == "test"
+Provides-Extra: cluster
+Requires-Dist: vivarium_cluster_tools>=2.1.17; extra == "cluster"
+Provides-Extra: data
+Requires-Dist: vivarium_inputs>=5.2.6; extra == "data"
+Requires-Dist: vivarium-profiling[cluster]; extra == "data"
+Provides-Extra: interactive
+Requires-Dist: vivarium_dependencies[interactive]; extra == "interactive"
+Provides-Extra: dev
+Requires-Dist: vivarium-profiling[cluster,interactive,test]; extra == "dev"
+Requires-Dist: vivarium_dependencies[lint]; extra == "dev"
+Provides-Extra: ci-github
+Requires-Dist: vivarium-profiling[test]; extra == "ci-github"
+Requires-Dist: vivarium_dependencies[lint]; extra == "ci-github"
+Provides-Extra: ci-jenkins
+Requires-Dist: vivarium-profiling[ci_github,cluster]; extra == "ci-jenkins"
+Dynamic: license-file
+
+==================
+vivarium.profiling
+==================
+
+Profiling and benchmarking tools for Vivarium simulations.
+
+.. contents::
+   :depth: 1
+
+Installation
+------------
+
+``vivarium-profiling`` is published on PyPI as part of the vivarium-suite monorepo:
+
+.. code-block:: bash
+
+   pip install vivarium-profiling
+
+For local development against the monorepo source, see the monorepo README at
+https://github.com/ihmeuw/vivarium-suite.
+
+Supported Python versions: 3.10, 3.11
+
+**HDF5 backing storage.** Vivarium uses the Hierarchical Data Format (HDF) for its
+data artifacts, and the libraries pip needs to read these files may not be present
+on your system. If you encounter HDF5-related errors, install the system tooling
+into your conda env:
+
+.. code-block:: bash
+
+   conda install hdf5
+
+**git-lfs and data artifacts.** When cloning the monorepo, large data artifacts
+are stored via ``git-lfs``. A clone that completes very quickly likely fetched
+only the checksum files rather than the artifacts themselves, and your simulations
+will fail. If you suspect this happened, pull the data explicitly:
+
+.. code-block:: bash
+
+   git-lfs pull
+
+Source layout
+-------------
+
+The package lives at ``src/vivarium/profiling/`` and provides these subpackages:
+
+- ``components`` - custom Vivarium components used by the profiling models
+- ``constants`` - project-level constants and metadata
+- ``data`` - artifact builder helpers
+- ``model_specifications`` - model spec YAMLs (e.g. ``model_spec_scaling.yaml``)
+- ``plugins`` - the ``MultiComponentParser`` plugin
+- ``templates`` - Jupyter notebook templates for analysis
+- ``tools`` - the CLI entry points (``profile_sim``, ``run_benchmark``, ``summarize``,
+  ``make_artifacts``)
+
+
+Profiling and Benchmarking
+---------------------------
+
+This repository provides tools for profiling and benchmarking Vivarium simulations
+to analyze their performance characteristics. See the tutorials at
+https://vivarium.readthedocs.io/en/latest/tutorials/running_a_simulation/index.html
+and https://vivarium.readthedocs.io/en/latest/tutorials/exploration.html for general instructions
+on running simulations with Vivarium.
+
+Configuring Scaling Simulations
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+This repository includes a custom ``MultiComponentParser`` plugin that allows you to
+easily create scaling simulations by defining multiple instances of diseases and risks
+using a simplified YAML syntax.
+
+To use the parser, add it to your model specification::
+
+    plugins:
+        required:
+            component_configuration_parser:
+                controller: "vivarium.profiling.plugins.parser.MultiComponentParser"
+
+Then use the ``causes`` and ``risks`` multi-config blocks:
+
+**Causes Configuration**
+
+Define multiple disease instances with automatic numbering::
+
+    components:
+        causes:
+            lower_respiratory_infections:
+                number: 4          # Creates 4 disease instances
+                duration: 28       # Disease duration in days
+                observers: True    # Auto-create DiseaseObserver components
+
+This creates components named ``lower_respiratory_infections_1``,
+``lower_respiratory_infections_2``, etc., each with its own observer if enabled.
+
+**Risks Configuration**
+
+Define multiple risk instances and their effects on causes::
+
+    components:
+        risks:
+            high_systolic_blood_pressure:
+                number: 2
+                observers: False    # Set False for continuous risks
+                affected_causes:
+                    lower_respiratory_infections:
+                        effect_type: nonloglinear
+                        measure: incidence_rate
+                        number: 2   # Affects first 2 LRI instances
+
+            unsafe_water_source:
+                number: 2
+                observers: True     # Set True for categorical risks
+                affected_causes:
+                    lower_respiratory_infections:
+                        effect_type: loglinear
+                        number: 2
+
+See ``model_specifications/model_spec_scaling.yaml`` for a complete working example
+of a scaling simulation configuration.
+
+
+Running Benchmark Simulations
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+The ``profile_sim`` command profiles runtime and memory usage for a single simulation of a vivarium model
+given a model specification file. The underlying simulation model can
+be any vivarium-based model, including the aforementioned scaling simulations as well as models in a 
+separate repository. This will generate, in addition to the standard simulation outputs, profiling data 
+depending on the profiler backend provided. By default, runtime profiling is performed with ``cProfile``, but 
+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 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
+to help identify performance bottlenecks.
+
+The command creates a timestamped directory containing:
+
+- ``benchmark_results.csv``: Raw profiling data for each run
+- ``summary.csv``: Aggregated statistics (automatically generated)
+- ``performance_analysis.png``: Performance charts (automatically generated)
+- Additional analysis plots for runtime phases and bottlenecks
+
+
+Analyzing Benchmark Results
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+The ``summarize`` command processes benchmark results and creates visualizations.
+This runs automatically after ``run_benchmark``, but can also be run manually
+for custom analysis after the fact.
+
+By default, this creates the following files in the specified output directory:
+
+- ``summary.csv``: Aggregated statistics with mean, median, std, min, max
+  for all metrics, plus percent differences from baseline
+- ``performance_analysis.png``: Runtime and memory usage comparison charts
+- ``runtime_analysis_*.png``: Individual phase runtime charts (setup, run, etc.)
+- ``bottleneck_fraction_*.png``: Bottleneck fraction scaling analysis
+
+You can also generate an interactive Jupyter notebook including the same default plots
+and summary dataframe with a ``--nb`` flag, in which case the command also creates an
+``analysis.ipynb`` file in the output directory.
+
+
+Customizing Result Extraction
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+By default, the benchmarking tools extract standard profiling metrics:
+
+- Simulation phases: setup, initialize_simulants, run, finalize, report
+- Common bottlenecks: gather_results, pipeline calls, population views
+- Memory usage and total runtime
+
+You can customize which metrics to extract by creating an extraction config YAML file.
+See ``extraction_config_example.yaml`` for a complete annotated example.
+
+**Basic Pattern Structure**::
+
+    patterns:
+      - name: my_function          # Logical name for the metric
+        filename: my_module.py     # Source file containing the function
+        function_name: my_function # Function name to match
+        extract_cumtime: true      # Extract cumulative time (default: true)
+        extract_percall: false     # Extract time per call (default: false)
+        extract_ncalls: false      # Extract number of calls (default: false)
+
+In turn, this yaml can be passed to the ``run_benchmark`` and ``summarize`` commands
+using the ``--extraction_config`` flag. ``summarize`` will automatically create runtime
+analysis plots for the specified functions.