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Cargo, connect, firmware, help: move to darkbio-wire v0.18.0 and serv… …e apps by digest (#47) Moves `ark` to darkbio-wire v0.18.0 for ArkOS v0.14.0, where apps can use other apps, and bumps the version to v0.6.0. `ark run FILE` hashes the file and names its module by digest when it creates the task. It serves the bytes as the Ark asks for them, streaming from the file, then starts the owner's approval. Loading has no overall time limit, and `--timeout` never shortens it. `ark` serves only the file it was given, so an app that uses other apps runs from Ark Hub for now, and `ark` refuses the Ark's requests for any other digest. The help calls the second pass the processing pass, and lists the `[outputs]` and `[apps.NAME]` tables. The firmware floor rises to 0.14.0, and the develop cutoff to the v0.14.0 boot image, stamped 2026-10-29 09:43:35 UTC. The tests cover module request validation, a dependency refusal, loading and approval outlasting inactivity, a disconnect while loading, and failures reading the file. --------- Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com> Co-authored-by: Astra <noreply@openai.com>
Cargo, connect, firmware, help: move to darkbio-wire v0.18.0 and serv… …e apps by digest (#47) Moves `ark` to darkbio-wire v0.18.0 for ArkOS v0.14.0, where apps can use other apps, and bumps the version to v0.6.0. `ark run FILE` hashes the file and names its module by digest when it creates the task. It serves the bytes as the Ark asks for them, streaming from the file, then starts the owner's approval. Loading has no overall time limit, and `--timeout` never shortens it. `ark` serves only the file it was given, so an app that uses other apps runs from Ark Hub for now, and `ark` refuses the Ark's requests for any other digest. The help calls the second pass the processing pass, and lists the `[outputs]` and `[apps.NAME]` tables. The firmware floor rises to 0.14.0, and the develop cutoff to the v0.14.0 boot image, stamped 2026-10-29 09:43:35 UTC. The tests cover module request validation, a dependency refusal, loading and approval outlasting inactivity, a disconnect while loading, and failures reading the file. --------- Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com> Co-authored-by: Astra <noreply@openai.com>
Cargo, http: update dependencies for the audit advisories, move to ur… …eq v3.5.0 (#46) Moves `ark` to darkbio-crypto 0.20.1, darkbio-trust 0.7.1 and darkbio-wire 0.17.1, refreshes `Cargo.lock` to the latest releases compatible with Rust 1.95, and moves ureq to 3.5.0. This clears the three advisories the nightly audit reports. - rustls-webpki moves from 0.103.15 to 0.103.16 (RUSTSEC-2026-0382) and webpki-roots from 1.0.9 to 1.0.11 (RUSTSEC-2026-0381). The private keys of distrusted emSign intermediates are public, and the bundled roots still accepted paths through them, so anyone on the network path could impersonate an endpoint `ark` reaches over TLS. - ctutils moves from 0.4.2 to 0.4.6 (RUSTSEC-2026-0385). Nothing in the tree calls the affected helpers. ureq 3.5 added optional per-read and per-write caps to `NextTimeout` in its unversioned transport module. `Idle::bound` in `src/http.rs` now carries them through when it clips the deadline. `ark` sets neither cap, so its timeouts behave as before. --------- Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com> Co-authored-by: Astra <noreply@openai.com>
firmware: raise the firmware floor and develop cutoff to the v0.13.1 … …release (#44) Raises `ark`'s firmware floor to 0.13.1 and its develop cutoff to the v0.13.1 release, whose boot image an Ark reports as 1792446096 (2026-10-19 21:41:36 UTC). The gate tests take the stamps of the v0.13.0 release, the last develop build before v0.13.1, and the release itself. The old cutoff's comment read 10:23:16, the time the build logged the stamp, while 1792403986 itself is 09:59:46 UTC. The new comment gives the stamp's own time. Co-authored-by: Astra <noreply@openai.com> Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
firmware: raise the firmware floor and develop cutoff to the v0.13.1 … …release (#44) Raises `ark`'s firmware floor to 0.13.1 and its develop cutoff to the v0.13.1 release, whose boot image an Ark reports as 1792446096 (2026-10-19 21:41:36 UTC). The gate tests take the stamps of the v0.13.0 release, the last develop build before v0.13.1, and the release itself. The old cutoff's comment read 10:23:16, the time the build logged the stamp, while 1792403986 itself is 09:59:46 UTC. The new comment gives the stamp's own time. Co-authored-by: Astra <noreply@openai.com> Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
Cargo, data, firmware, help: add the structural and copy number varia… …nt slots (#43) Moves `ark` to darkbio-wire 0.17.0 and the six dataset slots of ArkOS v0.13.0, which adds Structural Variants and Copy Number Variants beside Small Variants. - `ark data` names all six slots: `reference-genome`, `gene-annotations`, `small-variants`, `variant-catalog`, `structural-variants` and `copy-number-variants`. `snp-indel-calls` is gone. - An upload or fetch into a slot whose required slot is empty fails with `dependency-missing`, exit 5, before the owner is asked. - `ark data fetch --sample NAME` fills a public 1000 Genomes person's three personal slots in order, each with its own pin check and approval, and refuses before any download while a personal slot holds data. - `ark` requires firmware v0.13.0, and a develop build published from that release on. The help topics describe the new slots. Not run against a live Ark yet. --------- Co-authored-by: Astra <noreply@openai.com> Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
data, help: list the public samples and fetch one into the personal s… …lot (#42) Lets anyone try an Ark on real data without their own genome. It is the cli half of dashboard #33, which merged on 14 October. - `ark data samples` lists the 1000 Genomes Project's 3,202 people, with variant calls from Illumina's DRAGEN 4.4.7. With no population it lists the 26 populations. A population code lists its people, `--sex` narrows them and `--all` lists everyone. The list is built into ark, so the command needs no Ark. - Each sample keeps a fixed name, an adjective and a given name that matches the person's sex, such as `affable-hazel` for HG03730. Any two adjectives, and any two given names, differ by at least two edits, so one mistyped letter fails instead of reaching another person. Commands take the name or the sample ID. - `ark data fetch snp-indel-calls --sample NAME` fills the empty personal slot with a sample. ark downloads the whole file, 390 to 550 MiB, and checks its size and SHA-256 against values built into ark. Only then does the upload ask the owner on their phone. A failed upload is not retried, since that would ask the owner again, but the cache keeps the download. - Under `--no-cache` a sample waits in a temporary file, which the OS removes even when a signal ends ark. - The version moves to the v0.5.0 release cycle, since this adds commands. - rustls moves to 0.23.46 for RUSTSEC-2026-0346 to 0349, published on 14 October, which fail the audit on main as well. **Known gap:** the personal slot keeps its `snp-indel-calls` name here. The rename to `small-variants` comes with wire 0.17.0 in a later PR. --------- Co-authored-by: Astra <noreply@openai.com> Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
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