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MetaPathways 4.0.1: reliable nested Pathway Tools builds - #18
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Prepare 4.0.0 publication with documented dependency policy
Documentation build overview
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RyloByte
marked this pull request as ready for review
October 10, 2026 14:58
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Nested Pathway Tools builds previously stalled on FUSE or failed during inherited mounts and APT user switching. The 4.0.1 release container bundles an unlicensed Ubuntu dependency rootfs; build_pt selects it automatically and strips inherited binds only for the inner build. Conda installations retain the host-Apptainer recipe. No licensed installer, software, MetaCyc data or patches are published.
Adds bounded vendor HTTP retries, base package provenance, isolated test configuration and an optional --unsquash test route. Updates version, installation docs and changelog.
Validation: 174 local tests (the localhost test passed separately outside the socket-restricted sandbox), 23 release tests, strict Sphinx build, nested licensed build/startup/BLAST validation, and complete nested tiny-sample PGDB inference/export/archive. Vendor HTTP 503 required checksum-verified official patches from the existing private SIF for licensed integration. Actual 4.0.1 package/container CI is pending; publication remains disabled until it passes.