[us-commits] [ehb54/ultrascan3] fdf1cc: perceiver: retain the cctbx copyright notice on th...

[emre brookes]

  Branch: refs/heads/ehb54-issue-980
  Home:   https://github.com/ehb54/ultrascan3
  Commit: fdf1cc9946950fca9623060adbea5314345c8d09
      https://github.com/ehb54/ultrascan3/commit/fdf1cc9946950fca9623060adbea5314345c8d09
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-08-17 (Mon, 17 Aug 2026)

  Changed paths:
    A us_somo/develop/perceiver/data/ref/cctbx_LICENSE.txt
    M us_somo/develop/perceiver/data/ref/it1992.cpp

  Log Message:
  -----------
  perceiver: retain the cctbx copyright notice on the vendored it1992.cpp

data/ref/it1992.cpp is a verbatim copy of cctbx's transcription of International
Tables Vol. C Table 6.1.1.4, carrying none of its copyright or license.  The
cctbx license is BSD-style and its condition (1) requires source redistributions
to retain the copyright notice, the conditions and the disclaimer.

Add the notice and vendor the full license text alongside as cctbx_LICENSE.txt.
The file is not compiled -- gen_saxs_entries.py parses it to generate
somo.saxs_atoms entries -- but it is redistributed in source form, which is
exactly what condition (1) covers.

Reported-by: aaron-auc


  Commit: 6e2db3a595a525b590459c977fd97680bb22e7dc
      https://github.com/ehb54/ultrascan3/commit/6e2db3a595a525b590459c977fd97680bb22e7dc
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-08-17 (Mon, 17 Aug 2026)

  Changed paths:
    M us_somo/develop/perceiver/tests/regression.cpp

  Log Message:
  -----------
  perceiver: fail the regression test when it scores nothing

The regression target scores against demo PDB structures that are NOT committed
to the repository.  read_pdb() returns an empty list for a missing file, so it
scored 0 atoms, every percentage divided by zero and printed 0.000%, and it
exited 0 -- reporting 'genuine perception errors remaining: 0 (0.000%)' having
looked at nothing.  Confirmed by running it from a clean checkout: it passed,
with 0 atoms scored, on all eight demo structures.

A test that reports success because it examined nothing is worse than no test.
Name any input that yielded no atoms, and exit 2 when nothing was scored at all,
saying that the demo structures are absent.

The structures themselves are a separate call: committing them (or a fixture
subset) is a data decision -- size and provenance -- not a code fix.

Reported-by: aaron-auc


  Commit: a93e298c34721d73ee0f58b2d46848473d030e77
      https://github.com/ehb54/ultrascan3/commit/a93e298c34721d73ee0f58b2d46848473d030e77
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-08-17 (Mon, 17 Aug 2026)

  Changed paths:
    A us_somo/develop/perceiver/data/ref/cctbx_LICENSE.txt
    M us_somo/develop/perceiver/data/ref/it1992.cpp
    M us_somo/develop/perceiver/tests/regression.cpp

  Log Message:
  -----------
  Merge pull request #519 from ehb54/ehb54-issue-1009-perceiver-review-fixes

perceiver: cctbx notice, and stop the regression test passing on no data


Compare: https://github.com/ehb54/ultrascan3/compare/fa2ad021f3ad...a93e298c3472

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