feat(nmr-cli): add nmr-correlation as a new command - #140
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vcnainala merged 6 commits intoSep 21, 2026
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I will review this PR as soon as I can. Thanks |
… add real yargs defaults/aliases
… reference equality
hamed-musallam
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September 10, 2026 07:53
hamed-musallam
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All the comments have been addressed by @MuhammadAbeerAkmal . Could you please review and approve it, @vcnainala? Thank you! |
vcnainala
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* feat: add include/exclude file filters to parse-spectra (#138) * feat(nmr-cli): update NMRium core packages to v2.6.0 * chore(nmr-cli): update dependencies * feat(nmr-cli): add include/exclude file filters to parse-spectra * feat(API): add include/exclude file filters to spectra parse endpoints * feat(nmr-cli): update NMRium core packages to v2.7.0 * refactor: parallelize parse spectra pipeline across concurrent worker/browser lanes (#141) Replace the single-threaded, one-browser-per-spectrum flow with a fixed number of concurrent lanes, each owning a persistent worker thread (CPU processing/detection) and, when snapshots are enabled, a persistent browser page: - run-pipeline.ts / run-concurrency.ts: drive parse -> process -> detect -> snapshot across N lanes instead of one spectrum at a time. - spectrum-worker.ts / worker-entry.ts: offload processing, detection, and serialization to worker threads so CPU work no longer blocks the main thread. - browser-manager.ts: reuse one browser/context per lane across every spectrum it handles, instead of relaunching per spectrum. - prase-spectra.ts: delegate to the new pipeline; stream output via outputResult instead of buffering the full result in memory. * Revert "refactor: parallelize parse spectra pipeline across concurrent worker…" (#142) This reverts commit 1c39986. * feat(nmr-cli): add nmr-correlation as a new command (#140) * feat: expose nmr-correlation package as a new nmr-cli command * Address review: support local directory input, filter for FT spectra, add real yargs defaults/aliases * Address round 2 review: explicit if/else branching, clarify spectrum filter rationale * Address review: filter correlation spectra by ranges/zones instead of reference equality * Address review: extract readSpectra and filterSpectra helper functions * chore: upgrade actions and dependencies in workflow files to latest versions * fix: update miniconda3 version and improve nodejs installation proces… (#145) * fix: update miniconda3 version and improve nodejs installation process in Dockerfile * fix: use conda-forge as the only conda channel --------- Co-authored-by: hamed musallam <hamed.musallam@gmail.com> * fix: correct GitHub contributors badge link and minor text adjustments in README --------- Co-authored-by: hamed-musallam <35760236+hamed-musallam@users.noreply.github.com> Co-authored-by: abeer.dev <56149548+MuhammadAbeerAkmal@users.noreply.github.com> Co-authored-by: hamed musallam <hamed.musallam@gmail.com>
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Problem:
No CLI command currently exposes
nmr-correlation's functionality, requested in #66, build correlation data from NMR spectra given a spectra ZIP URL and molecular formula.What changed:
nmr-cli, following the same pattern aspeaks-to-nmrium: fetches spectra from a URL, processes them, and callsnmr-correlation'sbuildCorrelationData(...).H: 0.02, C: 0.25) confirmed by @vcnainalaprase-spectra.ts(extracted a sharedbuildWebSourcehelper to avoid duplicating URL-parsing logic) instead of rewriting it.buildCorrelationDataunchecked.Known limitation:
While testing, I found a pre-existing, unrelated bug #139 that currently makes every spectrum fail a step of the shared processing pipeline, meaning real cross-spectrum correlation links couldn't be verified end-to-end with public test data. The formula-only fallback path (when no spectra process successfully) is fully verified and correct; the "compares/links real signals" path is implemented per
nmr-correlation's documented API but untested pending a fix for #139.