Several methods adopted recently came from other crystallographic packages - the screw-absence test
from POINTLESS, MINPK and the profile-fit reweighting from XDS/Otwinowski, the CC1/2 cutoff and merge
outlier rejection from DIALS, the per-frame indexing gate from CrystFEL - and nothing in the
repository said where such a debt is recorded. The licence side was already worked out (licences beside
the vendored code, verbatim texts in licenses/ collected by COLLECT.sh, a row in THIRD_PARTY_NOTICES.md,
all installed under share/doc/jfjoch); the credit side was ad hoc.
Write the rule into CLAUDE.md. It states the distinction that matters: vendoring or linking someone's
CODE creates a LICENCE obligation, discharged in licenses/ and THIRD_PARTY_NOTICES.md; reimplementing
an algorithm from a PAPER creates none of that but creates an obligation of academic CREDIT, discharged
in docs/ACKNOWLEDGEMENT.md and in a comment at the algorithm. Neither substitutes for the other, and
taking both source and paper incurs both. It also fixes the citation form (authors, title, year,
journal, volume, pages, verified DOI), and says in-source credit goes at the algorithm, not the file
header, in the one-line style the code already uses.
Then bring the repository into compliance for the works concerned: docs/ACKNOWLEDGEMENT.md gains a
section acknowledging XDS, DIALS, POINTLESS/CCP4, MOSFLM, CrystFEL, GEMMI, the Kabsch/Otwinowski
profile fit, the Diederichs & Karplus statistics and the IUCr nomenclature reports, each with a DOI
checked against Crossref; docs/CPU_DATA_ANALYSIS.md's reference list gains the ones it was missing;
and four algorithms gain a line naming their source where no adjacent comment carried one.
No licence change. licenses/ and THIRD_PARTY_NOTICES.md are untouched.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
leonarski_fandClaude Opus 5
43627e22dc