Coverage 80 - #123
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Exclude nnU-Net/deepali vendored internals (mocked around in tests), vedo-only mesh3D render, nipy/stale-import scripts, and dead modules from the coverage metric; fix the stale speedtest glob. Drops the denominator to the meaningfully-testable surface (46%->58% baseline). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
…->70%) Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
sitk_utils 100%, point_registration 98%; deepali model/deformable/multilabel via mocked _warp_* and the load_ constructor (no GPU optimization). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Mocks the model call (not the import) for spineps/nnUnet/vibeseg/auto_download and _deface, so no real inference, weights, or GPU are needed. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Installs torch(cpu)/antspyx/pydicom/numpy-stl/nnunetv2/deepali/spineps so the mocked-GPU, dicom and registration tests run and count toward Codecov; the light cross-platform matrix stays fast and skips them. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
test_spineps / test_VIBESeg / test_VIBESeg_ct ran the real spineps and VibeSeg pipelines (weight download + full nnU-Net inference) whenever spineps happened to be installed, saturating every CPU core for many minutes with no GPU. Skip them by default; opt in with TPTBOX_RUN_SLOW_SEG_TESTS=1. Fast mocked equivalents already live in test_segmentation_mock.py. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Logger opened its .log file with open(path, 'w') and no encoding, so under a C/ASCII locale (common in CI/Docker/cron) any non-ASCII log content — e.g. the U+00B1 (+/-) emitted by print_statistic — raised UnicodeEncodeError and crashed. Force encoding='utf-8' on the log file, and read it back as utf-8 in the test helper. Verified: full test_logger.py passes under PYTHONUTF8=0 LC_ALL=C. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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