Lobster AI 1.2.2

This page lists the changes in Lobster AI 1.2.2 and its known limitations.

Installation

uv pip install "lobster-ai[full]==1.2.2"

PyPI

Non-interactive Omics-OS Cloud setup

Lobster AI 1.2.2 adds non-interactive flags for selecting the local omics-os gateway provider, so agents, CI pipelines and scripts can configure local Python inference through an Omics-OS Cloud account without a third-party provider key:

export OMICS_OS_API_KEY="..."             # from app.omics-os.com/account
lobster init --non-interactive --use-omics-os --skip-extras --skip-ssl-test
lobster status                             # shows configuration, not account proof
lobster agents list                        # inspect installed task agents

• --use-omics-os resolves OMICS_OS_API_KEY, then the active saved Python profile, then (workspace mode) CWD .env and global credentials.env. --global skips the CWD file.
• --omics-os-key <key> takes precedence but can expose the key in process arguments; prefer the environment variable.
• Do not combine Cloud setup with another provider's flags — the other explicit provider takes priority.

Saved, not checked

Init's success message means saved, not checked. It persists configuration but does not verify account access, key validity or inference. In lobster status, Account Access: Not checked (configuration only) is configuration display, not authentication proof. Stop on an unexpected provider, missing task agents or setup errors; "already configured" means no rewrite, not a new key rotation or an authentication check.

lobster config-test --json invokes a paid LLM test, may contact NCBI and writes a workspace probe. Run it only with explicit permission. Require exit 0 and JSON valid: true; for a Cloud setup also require checks.llm_provider.provider: "omics-os".

Credential file permissions

Init's secret .env and global credentials.env writers create files at 0600 and tighten existing rewrites to 0600 before truncating or writing data. A no-force init finding an owned regular POSIX secret file may also tighten it to 0600 without changing credential bytes; if that fails, init warns with a manual chmod 600 command and the original exit status is unchanged. A restrictive umask is defense in depth, not the only protection. Runtime credential loading does not repair legacy file modes, and POSIX mode protection is not a Windows ACL guarantee. Keep credential files and backups private and out of version control.

LOBSTER_CLOUD_KEY remains a legacy supplement: the cloud-processing service it connected to is no longer offered. If it is set, lobster chat and lobster query try to connect at startup and then continue in local mode, so leave it unset. It does not select the omics-os gateway.

Managed Omics-OS Cloud sessions

The npm CLI @omicsos/lobster (0.4.2) is a separate route for managed server-side sessions where agents run in Omics-OS Cloud, not locally. Sign in with lobster cloud login --device. Multi-agent Cloud analyses are under investigation; not all local-engine workflows are available in a managed Cloud session yet. Signing in with npm does not install or configure the local Python engine — for local Python inference with a Cloud account, use the lobster-ai package and the --use-omics-os init flags above.

Known limitations

Omics-OS Cloud sign-in

• The Python package's lobster cloud login does not start a supported browser flow in this release. For a managed Cloud session, use the npm CLI @omicsos/lobster and lobster cloud login --device. For local Python inference with a Cloud account, use lobster init --non-interactive --use-omics-os.

Data import

• The GEO download does not yet pick the expression matrix of series that ship only a gene-by-cell text file, for example GSE109564. Workaround: read the downloaded file yourself with pandas (pd.read_csv(path, sep="\t", index_col=0), which gives genes × cells), build an AnnData with cells as observations, write it with write_h5ad, and load the .h5ad file in Lobster.
• Some compressed GEO text matrices are refused when a few row labels are not recognized as gene names (such as HGNC:12345, Y_RNA or Metazoa_SRP), even if the other labels are. Setting transpose explicitly does not change this.
• If saving a required GEO import fails (for example, disk full), that queue entry cannot be retried in the same session, and a partial file may remain in the workspace. Remove the partial file from the workspace and start a new session.

Differential expression results

• DE results with "/" in a comparison group label can become unavailable through their saved result pointer after an H5AD save and reload. Use group labels without "/" before running DE; renaming a dataset or export file afterwards does not repair results that already exist.

Notebook export

• After you resume a saved session, a pipeline exported with /pipeline export can contain some steps twice, so the exported notebook may repeat filtering or normalization. Check the notebook before you run it again.

Bulk differential expression

• The direct bulk DE tool (run_bulk_de_direct) applies an out-group expression filter by default, which is designed for marker genes. On typical bulk data it can remove most genes; if it removes all of them, the tool refuses and says so. For bulk designs, use run_de_with_formula.

Custom code

• Custom code (execute_custom_code) runs locally with your own user permissions. Enable it only for agents you trust with your workspace.
• The value your code returns as its result may be at most 16 MiB. If it is larger, Lobster reports that the result could not be read and saves no figure from that run. For large outputs, write them to a file in your workspace or store them as a dataset, and return a short summary instead.

Figures

• Creating the same HTML view twice at the same moment can leave a duplicate view.
• If Lobster cannot remove an old figure revision's file from disk, the file stays in place and keeps using disk space.
• Local figure deletion is not yet available as a CLI command or agent tool.
• The classic terminal plot dashboard does not list figures saved by custom code; the native figure listing does.