software-liability-definitions

The canonical antibody chemical-liability taxonomy, published as one Platforma software package. One definitional source for every block that scans, scores, or repairs liabilities. Definitions only — never a scan. SDK docs: docs.platforma.bio.

Published as @platforma-open/milaboratories.software-liability-definitions, entrypoint main.

How a block consumes it

defsSw := assets.importSoftware("@platforma-open/milaboratories.software-liability-definitions:main")
// ... exec.builder().software(defsSw) ... then read the JSON it writes

Runs under @platforma-open/milaboratories.runenv-python-3:3.12.10, the base Python runenv. The emitter is standard library only — src/requirements.txt lists nothing.

One extra exec per run buys one definitional source. That is the price of the python one-source-root rule: a python artifact takes exactly one root, and each block is its own git repo, so no shared source tree exists.

Consumers

| Block | State | |---|---| | antibody-variant-designer | new — will read this package from the start; not wired yet | | antibody-sequence-liabilities | to migrate — replace liabilities-calc-script/src/definitions.py | | 3D-Structure-Based-Liabilities | to migrate — replace the literal in software/liabilities-script/motifs.py |

No block imports the package yet. Migrating both shipped blocks is what discharges the parity check their copies currently owe each other.

Development

pnpm install
pnpm run build                      # pl-pkg build
uv run --group dev pytest -q        # pins the emitted shape and the transcribed values

The suite needs no backend.

Local dev

pnpm run build writes descriptors that point at this working copy. From the consuming block root, pnpm run build:dev then produces a .sw.json with local.path into this source — no docker build, no upload. That works against a local backend only.

Remote dev

A K8s Platforma cannot read a developer's filesystem, so the software must arrive as a docker image. From the consuming block root:

pnpm run build:dev-remote

It builds a linux/amd64 image per entrypoint, pushes it to the dev ECR public.ecr.aws/u5p1x5q2/pl-containers, and rewrites the .sw.json docker.tag fields. K8s nodes pull anonymously — nothing to configure cluster-side. On a 403 or an expired token:

aws sso login && aws ecr-public get-login-password --region us-east-1 \
  | docker login --username AWS --password-stdin public.ecr.aws

Releasing

1. pnpm changeset — every change to the taxonomy needs a version bump. CI does not re-upload an existing version, so without a bump the registry keeps serving the old artifact under the same version string.
2. Merge to main; CI publishes.

Verify the upload:

curl -sI "https://bin.pl-open.science/software/platforma-open/milaboratories.software-liability-definitions/main/<version>.tgz" | head -2

200 = published, 404 = not yet.

License

MIT — see LICENSE.