Parallel multi-lens code review across maintainability, DRY, design, tests, documentation, and functional correctness.
Trace a simulation regression across vivarium repositories to identify the behavioral change causing it.
Use when: analyzing diffs between branches across one or more repos, summarizing code changes relevant to a regression, identifying which component changes could affect simulation outcomes.
Test a single hypothesis about the cause of a simulation regression by comparing old and new code.
Use when: reviewing code for design and data structure choices, algorithmic efficiency, whether the right abstractions are used, representation trade-offs, API surface design.
Use when: reviewing code for documentation quality, including docstrings, comments, README/changelog updates, and public API documentation accuracy.
Use when: reviewing code for DRY violations, duplicated logic, repeated patterns, opportunities to extract helpers or shared utilities, near-identical code blocks.
Use when the user asks about vivarium-suite CI — build status, Jenkins console logs, job structure, GitHub Actions runs, etc. Covers the GH Actions / Jenkins setup, the per-package Multibranch Pipeline layout, URL-to-jobFullName translation for the Jenkins MCP, and parallel matrix log interleaving.
Use when the user is performing post-install configuration for components shipped by this plugin — work that the plugin install itself doesn't perform.
Uses power tools
Uses Bash, Write, or Edit tools
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Monorepo for the Vivarium simulation framework and ecosystem libraries.
| Directory | PyPI name | Import path |
|---|---|---|
libs/core/ | vivarium-core | import vivarium.core |
libs/public-health/ | vivarium-public-health | import vivarium.public_health |
libs/config-tree/ | vivarium-config-tree | import vivarium.config_tree |
libs/cluster-tools/ | vivarium-cluster-tools | import vivarium.cluster_tools |
libs/testing-utils/ | vivarium-testing-utils | import vivarium.testing_utils |
libs/helpers/ | vivarium-helpers | import vivarium.helpers |
libs/gbd-mapping/ | vivarium-gbd-mapping | import vivarium.gbd_mapping |
libs/risk-distributions/ | vivarium-risk-distributions | import vivarium.risk_distributions |
libs/profiling/ | vivarium-profiling | import vivarium.profiling |
libs/build-utils/ | vivarium-build-utils | import vivarium.build_utils |
libs/dependencies/ | vivarium-dependencies | (meta-package) |
libs/compat/ | vivarium-compat | (import compatibility shim — temporary) |
Developer tooling that is not a Python package and is not published to PyPI lives under tools/.
These are not built or released by the monorepo's CI/release workflows.
| Directory | Purpose |
|---|---|
tools/ai-tools/ | Claude Code plugin: custom agent workflows for vivarium development (code review, regression debugging) |
Each package has its own development environment. From the package directory:
cd libs/core
make build-env name=vivarium-dev
conda activate vivarium-dev
To install a package into an already-active environment:
pip install -e "libs/core[dev]"
# or with uv:
uv pip install -e "libs/core[dev]"
CI uses uv as the package manager.
.github/workflows/ci.yml) — runs only for affected packagesJenkinsfileReleases are triggered automatically when a CHANGELOG.rst is updated on main. A release can
also be triggered manually via workflow_dispatch on .github/workflows/release.yml (useful for
recovery or retries). See that file for details.
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