Refactoring2 mergo to base master - #3

master and modernise are two independent modernisations of the same 2021 code,
not successive versions of one. modernise branched in 2021 and was developed in
June 2026; refactoring2, merged into master as #3, was developed separately and
landed in May. Neither contains the other. This makes modernise the basis, on
the evidence below.

  test suite                     74 passed        348 passed, 1 skipped
  popen.maxPopen(tres > 0)       AttributeError   works
  popen.EC50(tres > 0)           AttributeError   works
  stdout noise from one call     558 KB           none
  packaging                      fixed in #4      already correct
  declared dependencies          also Deprecated  numpy, scipy - and it
                                 and tabulate     imports no others
  documentation                  35-file Sphinx   11 Markdown files
                                 tree

The missed-events failures are the substantive point. refactoring2 moved
functions into classes but left module-level callers reaching for qml.GXY,
qml.eGs, qml.phiHJC and qml.dARSdS, none of which exist at module level any
more, so every resolution-corrected Popen calculation on master raises. The
class QMatrix also carries two live debug prints and computes five matrix
inversions eagerly on construction. A 74-test suite did not catch any of it.

Mechanics: this is a merge with modernise's tree taken wholesale, not a
force-push. Both histories are preserved and refactoring2 remains reachable
through the second parent.

Two things are carried over from master rather than taken from modernise:

  * .gitignore, which modernise had deleted
  * the eight tracked scalcs/__pycache__/*.pyc files are dropped again, as in #6

hjclib.py does not survive into this tree. It is the most finished part of
refactoring2 - HJCMatrix, AsymptoticPDF, ExactPDFCalculator, DerivativeCalculator
in 1488 lines - and it is the model to work from when the class API is redone on
top of this base, with 348 tests underneath it to catch the kind of half-migration
that broke master. It is kept on the branch classapi/refactoring2.

Verified on the merged tree: 348 passed, 1 skipped; maxPopen and EC50 at
tres = 30 us return 0.95345 and 2.3561e-06 with no stray output; and the
Colquhoun & Lape (2012) reproduction notebook runs against it unchanged, all
twelve published values within 0.129 %, ALL CHECKS PASSED.

The v0.5.1 and v0.5.1-cl2012 tags are unaffected: they are immutable and point
at cf0df11, and the corrigendum notebook is pinned to the tag.

Co-Authored-By: Claude Opus 5 <[email protected]>