hypex-tool-setup
Skill0 starsChanged 13 days agoApache-2.0View on GitHub
Activate and verify the PkDE-provisioned Hypex tools before running a hypothesis-exploration workflow.
1 other project uses a version of this, 1 of them edited.
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- GoogleCloudPlatform/LifeSciencesedited, first seen Oct 13, 2026
Other versions1 project uses a version of this.
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The file
Files
Hypex Tool Setup in PkDE
The PkDE bootstrapper provisions hypex, elo, and prox from the source
vendored in applications/PkDE/tools/vendor/hypex. Literature access is part
of the pkde CLI; there is no separate lit executable in PkDE.
Activate
Source the generated environment file, not the venv activation script:
source "${PKDE_ROOT:-.}/bin/env.sh"This activates the PkDE venv, adds tools/bin to PATH, sets
PKDE_TOOLS_HOME, and selects the provisioned environment stamp.
Verify
pkde doctor --json
hypex --help
elo --help
prox --helppkde doctor must report binary hypex, binary elo, binary prox, and
hypothesis strategy: hypex as ok. A missing or non-runnable command is a
capability failure. Report it to the supervisor; do not build tools ad hoc in
a worker container or install packages into the shared venv.
Tool Inventory
| Tool | Provisioning | Purpose |
pkde | PkDE Python package | Literature, citations, Hypex ingest/analyze, and PkDE artifacts |
hypex | Vendored Go source | Hypothesis datastore lifecycle and schema validation |
elo | Vendored Go source | Tournament pairings, ratings, and standings |
prox | Vendored Python source | Similarity, clustering, and near-duplicate detection |
The bootstrapper is the only owner of provisioning. Repair a missing tool by
re-running applications/PkDE/tools/install.sh; --binaries-only is suitable
when the full Python environment, including prox dependencies, already exists.
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