nezaret 0.1.0__tar.gz

nezaret-0.1.0/CHANGELOG.md

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+# Changelog
+
+## 0.1.0: first release
+
+**`nezaret lint`, for MONAI Bundle configs.** Reads `train.json`,
+`inference.json` and their YAML equivalents as data, resolves `@` references,
+`%` macros (including `%other.json#…`) and `$@a + @b` concatenation without
+evaluating anything, and checks every transform pipeline it finds against
+eleven rules. Each rule names a way a pipeline produces a wrong result
+**without raising an error**.
+
+| Rule | Severity |
+|---|---|
+| `NZ101` label-interpolation | error |
+| `NZ102` label-intensity | error (warning for min-max scaling) |
+| `NZ103` geometry-split | error (warning when a key is never moved at all) |
+| `NZ104` unknown-target | error |
+| `NZ105` discrete-interpolation | error |
+| `NZ106` saved-not-inverted | warning |
+| `NZ107` label-guided-eval | error |
+| `NZ108` random-in-eval | warning |
+| `NZ109` train-eval-mismatch | warning |
+| `NZ110` missing-channel-first | info |
+| `NZ111` no-determinism | info |
+
+**`lint_compose()`, for pipelines built in Python.** Reads the attributes of a
+live `monai.transforms.Compose` (including `OneOf`, `SomeOf`, `RandomOrder` and
+nested `Compose`) into the same model, so the same rules apply.
+
+**What it knows about MONAI was read from MONAI 1.6.1**: the default `mode` of
+every resampling transform, `Invertd`'s `nearest_interp=True`, the intensity
+defaults compared between training and evaluation, and the 2446 names MONAI's
+`ComponentLocator` resolves. The live test suite re-checks all of it against
+the installed MONAI.
+
+**Tested against MONAI's model zoo.** All 37 bundles, 157 config files and 174
+pipelines: 6 errors and 7 warnings, every error read against the bundle source.
+Seven false positives found during development became clean tests (listed in
+TESTING.md). The six true errors, in four bundles, are in the README.
+
+Zero runtime dependencies. PyYAML for YAML bundles and MONAI for
+`lint_compose()` are optional extras.

nezaret-0.1.0/INSTALL.md

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+# Installing nezaret
+
+## Just the tool
+
+```bash
+pip install nezaret
+```
+
+That is everything for JSON bundle configs. nezaret has **zero runtime
+dependencies** and works on Python 3.10 or newer. It needs no account, no
+server, no GPU, and makes no network call.
+
+Verify:
+
+```bash
+python -c "import nezaret; print(nezaret.__version__)"
+nezaret doctor
+```
+
+---
+
+## The optional extras
+
+| Extra | Pulls | Needed for |
+|---|---|---|
+| `nezaret[yaml]` | PyYAML | bundles written in YAML (`train.yaml`). Without it those files are skipped with a note, never silently |
+| `nezaret[monai]` | MONAI ≥ 1.4, and through it **PyTorch** | `nezaret.lint_compose()` on live pipeline objects, and the live test suite |
+| `nezaret[all]` | both | |
+| `nezaret[dev]` | pytest, PyYAML | running the tests |
+
+```bash
+pip install "nezaret[yaml]"     # most people want this one
+```
+
+**Linting a bundle never needs MONAI.** Bundle configs are read as data, so a
+laptop with no CUDA and no torch checks them as well as a GPU server does. Only
+`lint_compose()` needs MONAI, because it reads attributes off transform objects
+that must already exist in your process.
+
+PyTorch is a large download (several hundred MB, more with CUDA). If you only
+want MONAI for `lint_compose()` on a CPU machine, the CPU wheel is much smaller:
+
+```bash
+pip install torch --index-url https://download.pytorch.org/whl/cpu
+pip install "nezaret[monai]"
+```
+
+### Which MONAI
+
+nezaret's rules were written against **MONAI 1.6.1**, and the list of names
+MONAI can resolve (for `NZ104`) was read from that release. Other MONAI
+versions should work with `lint_compose()` as long as the transform classes
+keep their attribute names, but only 1.6.1 has been tested. `nezaret doctor`
+says when your MONAI differs from 1.6.1; the live tests then say whether
+anything nezaret assumes has changed:
+
+```bash
+pytest tests/test_live_monai.py -v
+```
+
+---
+
+## Offline or behind a slow connection
+
+Because the core has no dependencies, the wheel is the whole install (about
+40 KB). On any machine with access to PyPI:
+
+```bash
+pip download nezaret --no-deps -d wheels/
+pip download pyyaml --no-deps -d wheels/      # optional, for YAML bundles
+```
+
+Copy `wheels/` across and:
+
+```bash
+pip install --no-index --find-links wheels/ nezaret pyyaml
+```
+
+---
+
+## From source
+
+```bash
+git clone https://github.com/aslansd/nezaret
+cd nezaret
+pip install -e ".[dev]"
+pytest -q
+```
+
+See [TESTING.md](TESTING.md) for what a green run looks like in each
+environment.

nezaret-0.1.0/LICENSE

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nezaret-0.1.0/MANIFEST.in

@@ -0,0 +1,12 @@
+include LICENSE
+include README.md
+include INSTALL.md
+include TESTING.md
+include PUBLISHING.md
+include TROUBLESHOOTING.md
+include ROADMAP.md
+include CHANGELOG.md
+include src/nezaret/data/*.json
+recursive-include examples *.py *.json
+recursive-include tests *.py
+recursive-include tools *.py

nezaret-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: nezaret
+Version: 0.1.0
+Summary: Find MONAI pipeline faults that do not raise errors: misaligned labels, interpolated class maps, evaluation that peeks at the ground truth.
+Author: Aslan Satary Dizaji
+License-Expression: Apache-2.0
+Project-URL: Homepage, https://github.com/aslansd/nezaret
+Project-URL: Repository, https://github.com/aslansd/nezaret
+Project-URL: Issues, https://github.com/aslansd/nezaret/issues
+Keywords: MONAI,medical-imaging,segmentation,linter,validation,reproducibility
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Intended Audience :: Healthcare Industry
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Classifier: Topic :: Scientific/Engineering :: Image Processing
+Classifier: Topic :: Software Development :: Quality Assurance
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Provides-Extra: yaml
+Requires-Dist: pyyaml>=6; extra == "yaml"
+Provides-Extra: monai
+Requires-Dist: monai>=1.4; extra == "monai"
+Provides-Extra: dev
+Requires-Dist: pytest>=8; extra == "dev"
+Requires-Dist: pyyaml>=6; extra == "dev"
+Provides-Extra: all
+Requires-Dist: pyyaml>=6; extra == "all"
+Requires-Dist: monai>=1.4; extra == "all"
+Dynamic: license-file
+
+# nezaret
+
+**نظارت**: *oversight, supervision, inspection.* The same word in Persian
+(*nezārat*), Turkish (*nezaret*) and Azerbaijani (*nəzarət*).
+
+Find faults in [MONAI](https://monai.io) pipelines that **do not raise
+errors**: a label map resampled with bilinear interpolation, a rotation applied
+to the image but not its label, a validation crop chosen from the ground truth,
+an inference pipeline that preprocesses differently from training.
+
+Each of these trains, evaluates and reports a number. The number is wrong, and
+nothing in the run says so.
+
+**No dependencies. Runs offline. Reads configs as data; never imports torch, never
+runs a transform.**
+
+```bash
+pip install nezaret
+nezaret lint path/to/bundle
+```
+
+Python 3.10+. Apache 2.0. Rules are checked against MONAI 1.6.1.
+
+[PyPI](https://pypi.org/project/nezaret/) · [INSTALL](INSTALL.md) ·
+[TESTING](TESTING.md) · [PUBLISHING](PUBLISHING.md) ·
+[TROUBLESHOOTING](TROUBLESHOOTING.md) · [ROADMAP](ROADMAP.md) ·
+[CHANGELOG](CHANGELOG.md)
+
+---
+
+## The thirty-second version
+
+```text
+$ nezaret lint examples/faulty_bundle
+configs/inference.json
+  E NZ104 unknown-target           preprocessing#transforms#1
+      'AddChanneld' is not a MONAI 1.6.1 component. It was removed or renamed in MONAI; use EnsureChannelFirstd with channel_dim="no_channel".
+  W NZ106 saved-not-inverted       postprocessing#transforms#2
+      SaveImaged writes 'pred' without Invertd, but the preprocessing at inference.json:preprocessing changes the grid (Orientationd, Spacingd).
+  W NZ109 train-eval-mismatch      preprocessing
+      compared with train.json:train#preprocessing: NormalizeIntensityd only in training; Orientationd.axcodes: train 'RAS' vs eval 'LPS'
+
+configs/train.json
+  E NZ101 label-interpolation      train#deterministic_transforms#3
+      Spacingd resamples label key 'label' with mode 'bilinear' (MONAI's default); label maps need 'nearest'.
+  E NZ102 label-intensity          train#random_transforms#2
+      RandGaussianNoised changes voxel values of label key(s) 'label'.
+  E NZ103 geometry-split           train#random_transforms#1
+      RandRotated transforms 'image' but not 'label', which were loaded together and stop being aligned here.
+  E NZ107 label-guided-eval        validate#preprocessing#transforms#4
+      CropForegroundd in an evaluation pipeline takes its region from ground-truth key 'label' (source_key).
+  W NZ109 train-eval-mismatch      validate#preprocessing
+      compared with train.json:train#preprocessing: NormalizeIntensityd only in training
+  I NZ111 no-determinism           train#preprocessing
+      random transforms in training and no set_determinism or seed in this file or the config it overrides.
+
+2 file(s), 4 pipeline(s): 5 error(s), 3 warning(s), 1 info
+```
+
+Every location is a MONAI Bundle `#`-path, so `train#deterministic_transforms#3`
+is the fourth entry of that list. A finding on a transform reached through
+`$@train#deterministic_transforms + @train#random_transforms` points at the list
+the transform is written in, not at the expression.
+
+---
+
+## What it checks
+
+| Rule | Severity | Catches |
+|---|---|---|
+| `NZ101` label-interpolation | error | a label key resampled with a non-nearest mode, **including MONAI's defaults** (`Spacingd`, `RandAffined`: bilinear; `Resized`, `Zoomd`, `RandZoomd`: area) |
+| `NZ102` label-intensity | error | intensity transforms (noise, scaling, normalisation, contrast) on a label key; min-max scaling is a warning, since 0/255 → 0/1 masks are a real idiom |
+| `NZ103` geometry-split | error | a spatial transform (orientation, spacing, crop, pad, flip, rotate, zoom) applied to some of the arrays loaded together but not the others |
+| `NZ104` unknown-target | error | a `_target_` MONAI cannot resolve, with the replacement for removed ones (`AddChanneld`, `AsChannelFirstd`, `IgniteMetric`…) |
+| `NZ105` discrete-interpolation | error | `Invertd(nearest_interp=false)` after `AsDiscreted`, which interpolates class indices |
+| `NZ106` saved-not-inverted | warning | predictions saved on the resampled grid, without `Invertd` or `resample=true` |
+| `NZ107` label-guided-eval | error | validation or inference that crops by the ground truth (`CropForegroundd(source_key=label)`, label-guided random crops) |
+| `NZ108` random-in-eval | warning | a random transform in validation or inference |
+| `NZ109` train-eval-mismatch | warning | orientation, spacing, size or intensity scaling that differs between training and evaluation, **across files of the same bundle** |
+| `NZ110` missing-channel-first | info | a spatial transform before any channel-first step |
+| `NZ111` no-determinism | info | random training transforms and no seed anywhere |
+
+`nezaret rules` lists them; `nezaret explain NZ107` says why one matters and
+how to fix it.
+
+The defaults nezaret relies on were read from `inspect.signature` of MONAI
+1.6.1, not from documentation, and `tests/test_live_monai.py` re-checks them
+against whatever MONAI is installed.
+
+---
+
+## What it found in MONAI's own model zoo
+
+Linting all 37 bundles of [Project-MONAI/model-zoo](https://github.com/Project-MONAI/model-zoo)
+(commit `feb2e8c`, 20 October 2026; 157 config files, 174 pipelines) gives
+**6 errors, 7 warnings and 5 info**. Every error, and every warning below, was read
+against the bundle source by hand:
+
+| Bundle | Rule | What the config does |
+|---|---|---|
+| `prostate_mri_anatomy` train | NZ101 ×3 | `RandAffined`, `Rand3DElasticd` and `RandZoomd` on `["image", "label"]` with no `mode`, so the label is resampled bilinearly (twice) and by area averaging |
+| `prostate_mri_anatomy` inference | NZ105 | `AsDiscreted(argmax)`, then `Invertd(nearest_interp=false)` on the class map |
+| `renalStructures_CECT_segmentation` train | NZ101 | `RandZoomd` on the label with the default `area` mode |
+| `renalStructures_CECT_segmentation` inference | NZ109 | training loads with `as_closest_canonical=true` (RAS); inference reorients to `LPS` |
+| `wholeBrainSeg_Large_UNEST_segmentation` train | NZ109 | `NormalizeIntensityd` sits in `random_transforms`; validation copies only the deterministic list, so the checkpoint is selected on unnormalised inputs while training and inference normalise |
+| `mednist_reg` train | NZ104 | `IgniteMetric`, renamed `IgniteMetricHandler` |
+
+The reference bundles (`spleen_ct_segmentation`, `swin_unetr_btcv_segmentation`)
+come back clean. `tests/test_model_zoo.py` turns this table into a regression
+test.
+
+The remaining warnings are judgement calls nezaret cannot settle from the
+config alone: e.g. `lung_nodule_ct_detection` resamples only at inference
+because its README resamples the training data offline, which the message
+says.
+
+---
+
+## Commands
+
+```bash
+nezaret lint PATH...                 # a config file, a bundle, or a folder of bundles
+nezaret lint PATH --format markdown  # or json; -o report.md to write a file
+nezaret lint PATH --fail-on warning  # exit 1 on warnings too (default: errors only)
+nezaret lint PATH --ignore NZ108,no-determinism
+nezaret lint PATH --label-keys seg,organs
+nezaret rules
+nezaret explain NZ103
+nezaret doctor
+```
+
+Exit codes: `0` clean, `1` a finding at or above `--fail-on`, `2` nothing
+could be checked. That makes it a CI step as it stands:
+
+```yaml
+- run: pip install "nezaret[yaml]"
+- run: nezaret lint configs/ --fail-on error
+```
+
+A directory with a `configs/` folder is one bundle; a directory holding
+configs is one bundle; anything else is searched for `configs/` folders.
+Cross-file rules only compare files within one bundle.
+
+---
+
+## From Python
+
+```python
+import nezaret
+
+report = nezaret.lint("my_bundle/")          # Report
+report.ok                                     # no errors
+report.findings                               # [Finding(rule, severity, file, location, message, ...)]
+report.to_json(); report.to_markdown()
+
+nezaret.lint_config(config_dict, name="train.json")
+```
+
+For pipelines built in Python rather than in a config (needs MONAI installed):
+
+```python
+report = nezaret.lint_compose(train_transforms, role="train")
+report = nezaret.lint_compose(val_transforms, role="eval")
+report = nezaret.lint_compose(post_transforms, role="post", preprocessing=val_transforms)
+```
+
+nezaret reads the transform objects' attributes; it does not call them, load
+data or need a GPU. `role` has to be given because an object does not say what
+it is used for. See `examples/lint_compose_example.py`.
+
+---
+
+## How it decides what is a label
+
+In this order:
+
+1. `--label-keys` / `label_keys=`, if given, and nothing else.
+2. Key names such as `label`, `seg`, `mask`, `gt`, `annotation`, `target`
+   (also `label_inst`, `seg_1`, `lbl`…).
+3. A per-key `mode` list that mixes `nearest` with something else: the author
+   saying which keys are label maps.
+4. The `label_key` of a label-guided crop.
+
+A single `mode: "nearest"` for every key is *not* evidence: some bundles
+resample their images that way.
+
+## What it does not do
+
+- **It does not evaluate `$` expressions.** `@` references, `%` macros
+  (including `%other.json#…`) and `$@a + @b` concatenation are resolved
+  statically; any other expression is treated as unknown and the rules that
+  would need it are skipped, never guessed. A pipeline built entirely by an
+  expression is not checked.
+- **It does not read your data list or your images.** It cannot know that
+  your data list supplies four files per key (which is why `NZ110` is info) or
+  that two cases come from the same patient. That is `nezaret data`, planned
+  for 0.2.0 (see the [ROADMAP](ROADMAP.md)).
+- **It does not judge custom transforms.** After a `scripts.*` step that may
+  add, merge or drop keys, the key-tracking rules stop rather than guess.
+
+---
+
+## Licence
+
+Apache 2.0. See [LICENSE](LICENSE).