make-commands

name

make-commands

description

Reference for the shared `make` targets used across vivarium repositories, centralized in `vivarium/build_utils/resources/makefiles/`. Use this when the task involves making a new conda environment, formatting code, running development checks, or type hinting. Use whenever the user asks what a `make <target>` does in a vivarium repo, mentions running `make` in this ecosystem, or whenever another skill or instruction says "run `make X`" and you need to know exactly what it does, its arguments, env vars, and side effects.

Vivarium make commands

How the system works

Every vivarium repo's top-level Makefile is a thin shim. In a local dev shell it imports two shared makefiles from the installed vivarium.build_utils package:

include $(MAKE_INCLUDES)/base.mk
include $(MAKE_INCLUDES)/test.mk

Both files live at vivarium/build_utils/resources/makefiles/. That means the same set of make targets is available in essentially every vivarium library. When you see make <target> in a vivarium context, look here.

The only target that lives in the downstream Makefile itself is build-env, because it has to bootstrap vivarium_build_utils into a fresh conda env before the shared base.mk can be loaded. Under Jenkins ($JENKINS_URL set), the makefiles are pulled from the workspace instead of from an installed package.

PACKAGE_NAME is automatically set to the current directory's basename, so the targets reorient themselves correctly per-repo.

Quickly figuring out which target the user wants

make (no args) prints a generated list of every defined target with its inline # description. make help prints a curated, grouped help message.

Things to know that surprise people

• lint doesn't fix anything. It checks. To actually format, run format.
• make with no args runs list, not help. .DEFAULT_GOAL := list is set in base.mk.
• make install re-runs setup-slack every time. Idempotent, but expect to see Slack bot config output.
• test-* targets read RUNSLOW/RUNWEEKLY as make variables, not pytest CLI flags. make test-all --runslow will not work; make test-all RUNSLOW=true will.
• Under Jenkins, MAKE_INCLUDES := . — Jenkins copies base.mk/test.mk into the workspace ahead of time. In local dev, they're loaded from the installed vivarium.build_utils Python package via get_makefiles_path().
• make help and make --help are different. The latter is the built-in GNU Make help, which just lists global options and variables. The former is a custom target that prints a curated message about the available targets in this ecosystem.

When the user asks "what does make X do?"

1. Run make help and look for the target in the output. The inline descriptions are usually enough to answer the question, but if not, you can also:
2. Check the local Makefile in the user's CWD — downstream repos sometimes add repo-specific targets on top of the shared base.
3. Read vivarium/build_utils/resources/makefiles/base.mk and test.mk directly — those are the source of truth and may have changed since this skill was written.