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docs: add CLI reference and extractor docs for nexuslims extract#101

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jat255 merged 3 commits intomainfrom
docs/extract-cli-reference
Apr 1, 2026
Merged

docs: add CLI reference and extractor docs for nexuslims extract#101
jat255 merged 3 commits intomainfrom
docs/extract-cli-reference

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@jat255 jat255 commented Apr 1, 2026

Summary

  • Adds a full nexuslims extract section to docs/user_guide/cli_reference.md with usage, all options, exit codes, and examples
  • Adds a new Command-Line Extraction section to docs/user_guide/extractors.md cross-linked from the CLI reference
  • Corrects misleading help text in nexusLIMS/cli/extract.py: the default preview and --write JSON output go alongside the input file, not into NX_DATA_PATH, unless the file is under NX_INSTRUMENT_DATA_PATH
  • Updates the top-level help output and shell completion example to include extract
  • Adds towncrier doc fragment docs/changes/96.doc.md

Test plan

  • Build docs locally with ./scripts/build_docs.sh --skip-tui-demos and confirm no warnings
  • Verify nexuslims extract --help output matches the updated help strings
  • Spot-check that nexuslims extract <file> writes preview alongside the file as expected

jat255 added a commit that referenced this pull request Apr 1, 2026
jat255 added 2 commits March 31, 2026 22:39
Documents the `nexuslims extract` command in cli_reference.md and
extractors.md, and corrects the help text in extract.py to accurately
describe where output files are written (alongside the input file, not
the NexusLIMS data directory, unless the file is under
NX_INSTRUMENT_DATA_PATH).
@jat255 jat255 force-pushed the docs/extract-cli-reference branch from 86c6359 to 32c76d0 Compare April 1, 2026 04:39
@jat255 jat255 merged commit 312cf16 into main Apr 1, 2026
0 of 17 checks passed
@jat255 jat255 deleted the docs/extract-cli-reference branch April 1, 2026 04:44
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