MCP write tools in the background; legume-mcp 0.3; version 0.10.1

Cargo.toml

@@ -9,7 +9,7 @@ edition = "2021"
 readme = "README.md"
 # Own version (decoupled from workspace.version): data-beans evolves its CLI /
 # QC API independently of the shared utility crates.
-version = "0.10.0"
+version = "0.10.1"
 rust-version = "1.91"
 # Ship only the sources, README and license: nothing else in the working tree
 # (data stores, saved name lists, scratch files) can end up on crates.io.
@@ -97,7 +97,7 @@ ratatui = { version = "0.30", default-features = false, features = ["crossterm"]
 # Detachable sessions for the views; no pictures, so no graphics.
 legume-tui = { version = "0.3.2", optional = true, default-features = false, features = ["clap", "logs"] }
 # Its `tui` view (`data-beans mcp watch`) comes on with data-beans' `tui`.
-legume-mcp = { version = "0.1", optional = true }
+legume-mcp = { version = "0.3", optional = true }
 legume-plot = { version = "0.3.2", optional = true }
 base64 = { version = "0.22", optional = true }
 
@@ -106,5 +106,5 @@ base64 = { version = "0.22", optional = true }
 # tests/detach_session.rs.
 legume-tui = { version = "0.3.2", default-features = false, features = ["testing"] }
 # tests/mcp_server.rs follows a server through the watch pane.
-legume-mcp = { version = "0.1", features = ["tui"] }
+legume-mcp = { version = "0.3", features = ["tui"] }
 ratatui = { version = "0.30", default-features = false, features = ["crossterm"] }

README.md

@@ -101,11 +101,13 @@ Look before you derive:
 
 Quality control: qc runs the cell QC senna and pinto apply (a near-empty floor, then robust MAD bands on detected genes, total counts and the mito fraction). Call it without `out` first: it reports each metric's median, the band and how many cells fall outside, and writes nothing. Adjust n_mads or the caps until the drops are what the data warrant, then call it with `out` to write the kept cells as a new backend. plot shows the same settings as a figure (histograms with the band edges, counts against genes by verdict), so look at it before and after tuning.
 
-Derive new backends with import (mtx, zarr triplets, fragments, h5ad, 10x; say in `source` where the input came from), subset, subsample, split, convert and merge. Each writes to `out`, which must not exist yet: no tool replaces a file. Leave `out` out and the output goes in today's results folder, named after its input and the tool. Outputs are .zarr.zip archives unless `out` ends in .zarr (a directory) or .h5. Paths are resolved against the server's working directory; results give the paths written.
+Derive new backends with import (mtx, zarr triplets, fragments, h5ad, 10x; say in `source` where the input came from), subset, subsample, split, convert and merge. Each writes to `out`, which must not exist yet: no tool replaces a file. Leave `out` out and the output goes in today's results folder, named after its input and the tool. Outputs are .zarr.zip archives unless `out` ends in .zarr (a directory) or .h5. Paths are resolved against the server's working directory; results give the paths written. On a big store, pass `background` to these (and to qc with `out`): the call returns a job at once, with the paths it will write.
 
 A person may be watching (`data-beans mcp watch`): a "Note from the user" in a result is theirs to you; take it into account. A call they stopped fails with "stopped by the user": do not run it again unasked.
 ```
 
+After these, [legume-mcp](https://crates.io/crates/legume-mcp) adds its own notes: where the records go (below), and how to follow a background job.
+
 ### Tools
 
 | Tool | What it does | Writes |
@@ -124,6 +126,9 @@ A person may be watching (`data-beans mcp watch`): a "Note from the user" in a r
 | `convert` | zarr ↔ h5, `.zarr` ↔ `.zarr.zip` | a backend |
 | `merge` | backends side by side, batch-labelled; `common_rows` keeps the rows all share | a backend and its `.batch.gz` |
 | `notebook` | the agent's plan, observations and conclusions (from legume-mcp) | the day's `notebook.md` |
+| `job_status`, `job_wait`, `job_cancel` | follow or stop a step started with `background` (from legume-mcp) | |
+
+Every tool that writes a backend (`qc` with `out`, `import`, `subset`, `subsample`, `split`, `convert`, `merge`) takes `background`: it returns at once with the `job` and the paths it will write (`written`, and merge's `batches`, qc's `report`). Wait for `job_wait` to say `done` before using them: a `.zarr` or `.h5` is there, half written, while the job runs. What the command printed (qc's medians and bands, say) is the job's `output`. Until the job ends, its outputs are no other call's to write.
 
 No tool replaces a file: an output that is an input, or anything named after the output beside it, is refused, and `squeeze`, which rewrites its input, is not offered.