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CLI --help without torch; difference-map phases, DELFWT and extrapolations - #93
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import torchref no longer imports torch: the top-level re-exports and the subpackages load on first access through a module __getattr__. Every CLI module defers its torch-dependent imports until after parse_args, and the choice lists --help shows come from torchref.cli._choices, a torch-free mirror pinned to its sources by a test. --help drops from ~4 s to ~0.1 s. torchref.difference-map: - refuses --all-columns without -lm, and a non-default --ded-weight unless -lm --all-columns writes the model-phased columns it weights - requires -o to name a .mtz file, checked before any data is read - writes <name>_summary.json beside the MTZ (inputs, dataset scaling, R-factors, q-weight and shrinkage diagnostics), as difference-refine does - sizes the model FFT grid from the data's d_min when --dmin is not given - names itself, not difference-refine, in the MTZ history Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_014aviwqFcZpxP3HWNy1ZruY
…ctory
- The difference map (DELFWT/PHDELWT, dF, weights, KSCALE, Fc_dark) takes its
phases from a scale fit of the dark model alone, in difference-map and
difference-refine, so it no longer changes when a light model is given
- DELFWT = dF times the --ded-weight weight, so Coot opens the difference map
- The phase-aware and scalar extrapolations are written by default beside
the shrunk one; --all-columns now gates only the model-phased difference
and intensity columns
- FC/PHIC/PHIC_diff are renamed Fc_light/PHFc_light/PHdFc, matching Fc_dark
- difference-map takes -o as a directory (difference_map.mtz, summary.json)
and both difference CLIs gain --dmax; difference-refine sizes the model
grid from the data without --dmin
- -lm/--fraction sit in an "optional" help group
- Column builders return {label: (values, MTZ type)}; the torch-free choice
mirror and lazy torchref exports are compacted, and the new tests dropped
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_014aviwqFcZpxP3HWNy1ZruY
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The argparse converter imported difference_power for its bounds check, so a bad value paid torch start-up before the usage error. The bounds now come from the torch-free mirror; DifferencePowerConfig still validates at run time. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_014aviwqFcZpxP3HWNy1ZruY
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Summary
--helpwithout importing torchimport torchrefno longer imports torch: the top-level re-exports and subpackages load on first access via a module__getattr__.TORCHREF_DTYPE_*/TORCHREF_DEVICEare read on that first access.parse_args; the choice lists shown in--helpcome fromtorchref/cli/_choices.py, a torch-free mirror of the source tables.--helpdrops from ~4 s to ~0.1 s.torchref.difference-map/torchref.difference-refineDELFWT/PHDELWT,dF, weights,KSCALE,Fc_dark) takes its phases from a scale fit of the dark model alone, so it no longer changes when a light model is given. The joint fit is used only for the light-model, extrapolation and two-moment layers.DELFWT=dF× the--ded-weightweight, so Coot opens the difference map directly.2FEXT_PHASED-Fc/PHFEXT_PHASED) and classic scalar (2FEXT_SCALAR-Fc/PHFEXT_SCALAR) extrapolations are written by default beside the shrunkFWT/PHWT.--all-columnsnow gates only the model-phased difference and intensity columns. The single-weightFEXT_*-Fccolumns are dropped.FC/PHIC/PHIC_diff→Fc_light/PHFc_light/PHdFc, consistent withFc_dark/Fo_light.-ois an output directory (difference_map.mtz,summary.jsonwith inputs, scaling, R-factors and weight/shrinkage fits);-lm/--fractionsit in an "optional" help group; incompatible-lm/--fraction/--all-columnscombinations are refused up front.--dmax; without--dminthe models' FFT grid follows the data's resolution instead of a fixed 1.0 Å.{label: (values, MTZ type)}, removing the duplicated type tables; the extrapolation constructions are one loop.Net diff is −72 lines.
Breaking for scripts
-ois now a directory.FC,PHIC,PHIC_diff,FEXT_PHASED-Fc,FEXT_SCALAR-Fcare renamed or removed.Testing
tests/unit(full suite passed on the first commit; CLI, import-smoke and DED-weight unit tests re-run on the final head: 324 passed).tests/integration/test_cli_ded_weights.pyandtest_cli_two_moment_mtz.pywith--run-slow(16 passed), updated for the new labels,DELFWTand the-odirectory.-lmagree to within run-to-run noise;--helpof every console script leaves torch unimported.Generated by Claude Code