Coverage 80 by Hendrik-code · Pull Request #116 · Hendrik-code/TPTBox

Hendrik-code · 2026-06-30T14:22:52Z

Raises unit-test coverage 46% → 86% (green: 891 passed / 7 skipped).

Curated coverage omit for un-testable vendored/dead/missing-dep code
10 new + 4 extended test files; MagicMock for GPU segmentation/registration
Gates the real-model seg tests behind TPTBOX_RUN_SLOW_SEG_TESTS (fixes CPU hog)
fix(logger): write .log as UTF-8 (was crashing under C/ASCII locale)
ci: build-full-coverage job installs heavy deps (CPU) for Codecov

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>

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>

robert-graf · 2026-06-30T14:39:21Z

+# e.g. on a GPU box with the models present:
+#     TPTBOX_RUN_SLOW_SEG_TESTS=1 pytest unit_tests/test_auto_segmentation.py
+# Mocked, fast equivalents of these wrappers live in test_segmentation_mock.py.
+RUN_SLOW_SEG_TESTS = os.environ.get("TPTBOX_RUN_SLOW_SEG_TESTS", "0") == "1"


Remove. Will never be used

robert-graf · 2026-06-30T14:39:51Z

@@ -0,0 +1,208 @@
+from __future__ import annotations


Remove this. _deface is not exported.

robert-graf · 2026-06-30T14:42:59Z

+        self.assertEqual(msk.orientation, target.orientation)
+
+
+class Test_NII_MatchHistograms(unittest.TestCase):


This test only runs, but not test the function itself

robert-graf · 2026-06-30T14:47:01Z

Dont care
can merge

Copilot

Pull request overview

This PR substantially expands automated test coverage across key TPTBox subsystems (stitching, spine stats/visualization, segmentation plumbing, POI save/load, registration, ray-casting, NII math/extended ops, logger, DICOM, and BIDS files), and updates CI/coverage configuration to better reflect which code is intentionally excluded from coverage.

Changes:

Added/extended a large suite of unit tests covering stitching, spine statistics + snapshot rendering, segmentation orchestration/mocking, POI IO, registration, ray-casting, NII math and extended behaviors, logging, DICOM round-trips, and BIDS file utilities.
Updated logger file output to explicitly use UTF-8 encoding to avoid locale-related UnicodeEncodeError.
Adjusted coverage “omit” configuration and introduced a “build-full-coverage” CI job that installs heavier optional dependencies for authoritative coverage runs.

Reviewed changes

Copilot reviewed 16 out of 16 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
`unit_tests/test_stiching.py`	Extends stitching-related tests to cover public wrapper, internals, and optional ANTs branches.
`unit_tests/test_spinestats.py`	New comprehensive tests for spine stats (angles/IVD/endplates/distances) and 2D snapshot creation.
`unit_tests/test_segmentation_mock.py`	New tests using mocks to cover segmentation plumbing (nnU-Net/VibeSeg/spineps integration points).
`unit_tests/test_save_load_poi.py`	New tests for POI save/load formats, round-trips, and parser edge cases.
`unit_tests/test_registration.py`	New tests covering SITK utilities, point registration, and mocked deformable/deepali registration wiring.
`unit_tests/test_ray_casting.py`	New tests for numpy + POI-driven ray-casting helpers and geometric utilities.
`unit_tests/test_nputils_extended.py`	Adds more branch/edge coverage for numpy utility functions (CCs, morphology, hull, padding, etc.).
`unit_tests/test_nii_wrapper_math.py`	New tests for NII math operator overloads and image-quality metrics.
`unit_tests/test_nii_extended.py`	Extends NII tests for dtype selection, padding/cropping, hull/surface/STL/ANTs/deepali helpers.
`unit_tests/test_logger.py`	New tests for logger implementations and file-backed logging behavior.
`unit_tests/test_dicom.py`	New tests for synthetic DICOM series generation and extraction utilities (guarded on pydicom).
`unit_tests/test_bids_files.py`	New large test suite for BIDS file/index/query behavior (in-memory + disk-backed scenarios).
`unit_tests/test_auto_segmentation.py`	Removes the previous auto-segmentation test module (replaced by more targeted tests/mocks).
`TPTBox/logger/log_file.py`	Opens `.log` files with `encoding="utf-8"` to avoid crashes under ASCII locales.
`pyproject.toml`	Updates coverage omit list (including vendored/optional-dep code paths) and speedtest path.
`.github/workflows/tests.yml`	Adds `build-full-coverage` job to install heavy optional deps and generate authoritative coverage.

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Hendrik-code and others added 12 commits June 30, 2026 11:41

test: cover bids_files.py via in-memory BIDS dataset (38%->96%)

56daf13

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

test: cover nii_wrapper math mixin + wrapper ops (math 100%, wrapper …

e49abcf

…->70%) Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

test: cover spine/spinestats + snapshot_modular (->93%)

7fc43c7

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

test: cover poi_fun save_load + ray_casting (both ->94%)

5cf83e4

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

test: cover core/dicom via generated DICOM series round-trip (0%->70%)

b0d08a2

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

test: cover sitk_utils + point_registration + deepali wrappers (->81%)

59ffa8c

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>

test: MagicMock GPU segmentation + deface wrappers (->93%)

65d04c5

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>

test: cover logger + stitching; push np_utils to 99% (->84%)

ddd3dca

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

Hendrik-code self-assigned this Jun 30, 2026

robert-graf reviewed Jun 30, 2026

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Comment thread unit_tests/test_nii_extended.py

robert-graf reviewed Jun 30, 2026

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Comment thread unit_tests/test_nii_extended.py

robert-graf reviewed Jun 30, 2026

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Hendrik-code added 3 commits July 2, 2026 12:30

address robsy

3537df5

fix

54b0f6b

fix

8ad3451

Hendrik-code marked this pull request as ready for review July 2, 2026 12:37

Copilot AI review requested due to automatic review settings July 2, 2026 12:37

Copilot started reviewing on behalf of Hendrik-code July 2, 2026 12:38 View session

Copilot AI reviewed Jul 2, 2026

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Comment thread .github/workflows/tests.yml Outdated

Comment thread .github/workflows/tests.yml

Comment thread unit_tests/test_nii_extended.py

Comment thread unit_tests/test_nii_extended.py

Hendrik-code added 4 commits July 2, 2026 12:44

testcase torch dependancy

4961277

added dicom2nifti to dev dep

1af165f

fixed workflow test

9ba6a13

fixed workflow test

19748ba

fixed workflow test

83f7f4c

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Coverage 80#116

Coverage 80#116
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Hendrik-code commented Jun 30, 2026 •

edited

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		self.assertEqual(msk.orientation, target.orientation)


		class Test_NII_MatchHistograms(unittest.TestCase):

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Hendrik-code commented Jun 30, 2026 •

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