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Entrypoints and Examples

Use the installed console script, not python -m, when you want the canonical runtime surface.

This page gives the shortest supported command paths. It should help someone reach a known-good route quickly, without having to rebuild the whole repository just to discover the right entrypoint.

Start With Intent, Not With Commands

Most confusion in this repository comes from choosing a workflow that is wider than the real question. Start with intent first:

  • verify when the question is "is this checkout healthy"
  • refresh when the question is "did the tracked evidence change"
  • publish when the question is "what public output does the repository now say"
  • inspect species-level animal work when the question is narrower than a full public rebuild

Verification Entry Points

make install
artifacts/root/check-venv/bin/bijux-pollenomics --version
make lock-check
make lint
make test
make test-generated-artifacts
make test-all
make docs

Use make test-generated-artifacts when the question is specifically about the governed docs, reports, and other generated-publication contracts. Use make test-all when you want the full local gate instead of the faster default test slice.

Collection And Publication Examples

artifacts/root/check-venv/bin/bijux-pollenomics collect-data all --version v66 --output-root data
artifacts/root/check-venv/bin/bijux-pollenomics publish-reports --aadr-root data/aadr --version v66 --context-root data --output-root docs/report

These are the shortest canonical routes for rebuilding tracked source material and tracked public report outputs.

Narrow aDNA Surfaces

artifacts/root/check-venv/bin/bijux-pollenomics adna-archive-projects
artifacts/root/check-venv/bin/bijux-pollenomics adna-domestication-coverage
artifacts/root/check-venv/bin/bijux-pollenomics adna-species
artifacts/root/check-venv/bin/bijux-pollenomics adna-species-review --species ovis_aries

Atlas And Country Surfaces

artifacts/root/check-venv/bin/bijux-pollenomics report-country Sweden --aadr-root data/aadr --version v66 --context-root data --output-root docs/report
artifacts/root/check-venv/bin/bijux-pollenomics report-multi-country-map Sweden Norway Finland Denmark --aadr-root data/aadr --version v66 --context-root data --output-root docs/report

Which Route To Choose

  • choose the verification route if you need confidence without rewriting tracked repository state
  • choose collect-data if the goal is source refresh or normalization review
  • choose publish-reports if the goal is public report and atlas output review
  • choose the narrower aDNA commands if the question is species, archive, or review specific

When To Stop

  • stop after verification commands if the goal is only repository health
  • stop after collect-data if the goal is data refresh review
  • stop after publish-reports if the goal is publication-surface review

That stop rule matters. Many problems in this repository come from running a much broader workflow than the question actually requires.