chemsift (cloud CLI)

The chemsift CLI lets scientists submit and manage jobs on AWS.

Install from PyPI:

pip install chemsift

Commands

• chemsift login: Authenticate and store credentials
• chemsift register <input-dir>: Upload a registry_input/ and start a registration job
• chemsift map <register-job-id>: Run the mapped pipeline against a completed register job
• chemsift query <register-job-id> --molecules <csv> --yaml <yml>: Submit a query job
• chemsift supervised <register-job-id> --yaml <yml> [--state <csv>]: Submit one round of active-learning screening
• chemsift status <job-id>: Check status of a job
• chemsift download <job-id> <output-dir>: Download results of a completed job
• chemsift list: List all job IDs for the current user

Supervised workflow

# Round 0 — no state file yet
chemsift supervised <register-job-id> --yaml supervised.yml

# Wait for completion, download state CSV, fill 'label' column (0=inactive, 1=active)
chemsift status <job-id>
chemsift download <job-id> .

# Subsequent rounds — pass labelled state CSV
chemsift supervised <register-job-id> --yaml supervised.yml --state state.csv

Development

This project uses Poetry for dependency management and packaging.

Setup

cd cli
poetry install
poetry run chemsift --help

Releasing a new version to PyPI

Publishing is fully automated — CI builds and uploads the package to PyPI when a cli-v* tag is pushed. The tag version must match pyproject.toml exactly or CI will fail the verification step.

Step 1 — bump the version in pyproject.toml:

cd cli
poetry version patch   # or: minor, major, or an explicit version e.g. 1.2.0

Step 2 — commit and merge to main:

git add cli/pyproject.toml
git commit -m "chore: bump chemsift CLI to $(cd cli && poetry version -s)"
# open a PR, get it merged into main

Step 3 — tag the merge commit and push the tag:

git checkout main
git pull
git tag cli-v$(cd cli && poetry version -s)   # e.g. cli-v1.2.0
git push --tags

Pushing the tag triggers the publish-cli.yml workflow, which:

1. Verifies the tag matches the version in pyproject.toml
2. Builds the sdist and wheel
3. Publishes to PyPI via OIDC Trusted Publishing (no API token needed)