radiologist-core 0.1.0__tar.gz

radiologist_core-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2026 @CedrickArmel
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

radiologist_core-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: radiologist-core
+Version: 0.1.0
+Summary: Modeling library for the radiologist pipeline
+Keywords: chest-xray,medical-imaging,machine-learning,pytorch
+Author: Cédrick-Armel YEBOUET
+License-Expression: MIT
+License-File: LICENSE
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
+Requires-Dist: pillow>=12.2.0
+Requires-Dist: radiologist-etl>=0.1.0
+Requires-Dist: radiologist-registry>=0.1.0
+Requires-Dist: radiologist-utils>=0.1.0
+Requires-Dist: torch>=2.12.0
+Requires-Dist: torchvision>=0.27.0
+Requires-Dist: webdataset>=1.0.0
+Requires-Dist: lightning>=2.6.0
+Requires-Dist: torchmetrics>=1.9.0
+Requires-Dist: hydra-core>=1.3.0
+Requires-Dist: omegaconf>=2.3.0
+Requires-Dist: fsspec>=2026.4.0
+Requires-Dist: captum>=0.9.0 ; extra == 'all'
+Requires-Dist: gcsfs>=2026.4.0 ; extra == 'all'
+Requires-Dist: onnx>=1.21.0 ; extra == 'all'
+Requires-Dist: onnxruntime~=1.23.2 ; extra == 'all'
+Requires-Dist: onnxscript>=0.7.0 ; extra == 'all'
+Requires-Dist: wandb>=0.27.0 ; extra == 'all'
+Requires-Dist: gcsfs>=2026.4.0 ; extra == 'gcs'
+Requires-Dist: onnx>=1.21.0 ; extra == 'onnx-export'
+Requires-Dist: onnxruntime~=1.23.2 ; extra == 'onnx-export'
+Requires-Dist: onnxscript>=0.7.0 ; extra == 'onnx-export'
+Requires-Dist: wandb>=0.27.0 ; extra == 'wandb'
+Requires-Dist: captum>=0.9.0 ; extra == 'xai'
+Requires-Python: >=3.10
+Project-URL: Homepage, https://github.com/CedrickArmel/radiologist
+Project-URL: Repository, https://github.com/CedrickArmel/radiologist
+Project-URL: Documentation, https://cedrickarmel.github.io/radiologist/
+Project-URL: Issues, https://github.com/CedrickArmel/radiologist/issues
+Provides-Extra: all
+Provides-Extra: gcs
+Provides-Extra: onnx-export
+Provides-Extra: wandb
+Provides-Extra: xai
+Description-Content-Type: text/markdown
+
+# radiologist-core
+
+[![ci](https://github.com/CedrickArmel/radiologist/actions/workflows/ci.yml/badge.svg)](https://github.com/CedrickArmel/radiologist/actions/workflows/ci.yml)
+[![codecov](https://codecov.io/gh/CedrickArmel/radiologist/branch/main/graph/badge.svg)](https://codecov.io/gh/CedrickArmel/radiologist)
+[![PyPI](https://img.shields.io/pypi/v/radiologist-core)](https://pypi.org/project/radiologist-core/)
+![tested on](https://img.shields.io/badge/tested%20on-ubuntu--latest%20%7C%20python%203.10-blue)
+
+The ML engine. Provides the Lightning training loop, streaming data module, focal loss, GradCAM attribution, and W&B model registry integration for chest X-ray classification.
+
+## Business context
+
+Once clean, labelled WebDataset shards exist (produced by `radiologist-etl`), this package trains a classifier capable of distinguishing:
+
+- **Healthy** lung (no finding)
+- **Viral** pneumonia / COVID (infectious infiltrates)
+- **Opacity** (other lung opacities)
+
+The trained model is exported as two ONNX artefacts — one for deterministic inference with visual explanations (GradCAM), one for uncertainty-aware inference (MC-Dropout) — and linked to a W&B Model Registry collection for downstream consumption by an inference or serving layer.
+
+## Key capabilities
+
+| Capability | What it enables |
+|---|---|
+| Class-balanced streaming | Trains on imbalanced clinical data without manual oversampling scripts |
+| Prior-calibrated bias init | Logit outputs are calibrated to class prevalence from the first step |
+| Focal Loss | Focuses learning on hard, misclassified examples rather than easy majority samples |
+| GradCAM attribution | Produces heatmaps showing which lung region drove the prediction |
+| MC-Dropout ONNX export | Enables uncertainty estimation at inference time (multiple stochastic passes) |
+| HPO-friendly best-metric tracking | Optuna / W&B Sweeps receive the best epoch score, not the last |
+
+## Package layout
+
+```
+radiologist-core/src/radiologist/core/
+├── train.py            # Hydra entry point and train() function
+├── module.py           # LModule (LightningModule)
+├── losses.py           # FocalLoss
+├── data/
+│   ├── datamodule.py   # WebDatasetDataModule
+│   └── shards.py       # shard discovery helpers
+├── callbacks/
+│   ├── attribution.py  # GradCAM + Integrated Gradients
+│   ├── best_metric.py  # best-epoch metric tracking
+│   └── wandb_summary.py
+├── registry/
+│   └── export.py       # export_onnx (checkpoint → deterministic + MC-Dropout ONNX)
+└── configs/            # Hydra config tree
+```
+
+## Training a model
+
+### Prerequisites
+
+- Shards on GCS (or local) produced by `radiologist-etl`
+- W&B API key in the environment (`WANDB_API_KEY`)
+
+### Quick start
+
+```bash
+cd radiologist-core
+uv run --active python -m radiologist.core.train
+```
+
+The defaults load from `src/radiologist/core/configs/train.yaml`. Override on the command line:
+
+```bash
+uv run --active python -m radiologist.core.train \
+    trainer.max_epochs=30 \
+    datamodule.shard_root=gs://my-bucket/shards/ \
+    datamodule.split_manifest_uri=gs://my-bucket/manifests/manifest-abc123.jsonl \
+    seed=42
+```
+
+### Evaluation only
+
+```bash
+uv run --active python -m radiologist.core.train \
+    --config-name eval \
+    ckpt_path=/path/to/checkpoint.ckpt
+```
+
+## Core components
+
+### `LModule`
+
+A backbone-agnostic `LightningModule`. Pass any `nn.Module` as `net`.
+
+```python
+from radiologist.core import LModule
+from torchvision.models import resnet50
+
+module = LModule(
+    net=resnet50(num_classes=3),
+    loss=FocalLoss(gamma=2, alpha=1),
+    metric=MulticlassFBetaScore(num_classes=3, beta=1.0, average="macro"),
+    optimizer=partial(AdamW, lr=1e-3, weight_decay=1e-2),
+    scheduler=partial(sequential_scheduler, ...),
+    trainable_layers=None,   # None = full re-init; list of dot-paths = fine-tune
+    priors=None,             # overridden from datamodule at setup time
+)
+```
+
+On `setup('fit')`, `LModule` does one of two things depending on `trainable_layers`:
+
+- **`None`** — reinitialise all weights (Kaiming normal on Conv, Xavier on Linear). Use when training from scratch.
+- **`["layer4", "fc"]`** — freeze all parameters, then selectively unfreeze by dot-path. Use when fine-tuning a pretrained backbone.
+
+In both cases, if class priors are available (from the datamodule), the final `nn.Linear` bias is initialised to `−log(priors)`, giving calibrated starting logits.
+
+### `WebDatasetDataModule`
+
+Streams images from WebDataset tar shards. Handles class-balanced sampling automatically.
+
+```python
+from radiologist.core import WebDatasetDataModule
+
+dm = WebDatasetDataModule(
+    shard_root="gs://bucket/shards/",
+    split_manifest_uri="gs://bucket/manifests/manifest-abc123.jsonl",
+    label_map={"normal": "healthy", "pneumonia": "viral", "COVID": "viral"},
+    batch_size=32,
+)
+```
+
+The `label_map` collapses raw ETL folder names (e.g. `normal`, `COVID`) into model class names (e.g. `healthy`, `viral`). This decouples the dataset's folder structure from the model's output space.
+
+Training dataloader: one `wds.WebDataset` pipeline per class with `resampled=True` (infinite streaming), combined via `wds.RandomMix` weighted by inverse class frequency, then unbatch → shuffle → rebatch for global shuffling within an epoch. Validation and test dataloaders are flat sequential pipelines with no resampling.
+
+### `FocalLoss`
+
+```python
+from radiologist.core import FocalLoss
+
+loss = FocalLoss(gamma=2.0, alpha=1.0, use_softmax=True, reduction="mean")
+```
+
+Applies softmax to logits, computes `alpha * (1 − pt)^gamma * −log(pt)`. Supports optional one-hot conversion and `mean | sum | none` reductions.
+
+### Callbacks
+
+#### `AttributionCallback`
+
+Computes Layer GradCAM and Integrated Gradients every `every_n_val_epochs` validation epochs and on all test batches. Saves normalised PNGs to `{log_dir}/attributions/` and logs them to W&B. Skipped gracefully when `captum` is not installed.
+
+```yaml
+# configs/callbacks/default.yaml
+attribution:
+  _target_: radiologist.core.callbacks.AttributionCallback
+  target_layer: layer4.1.conv2
+  every_n_val_epochs: 5
+  n_test_batches: 4
+  n_samples_per_batch: 4
+```
+
+#### `BestMetricCallback`
+
+Writes `best_{monitor}` to `trainer.callback_metrics` after every validation epoch. When training finishes, HPO frameworks (Optuna, W&B Sweeps) read the best epoch score rather than the last.
+
+#### `WandbDefineSummaryCallback`
+
+Calls `wandb.run.define_metric` at fit start so the W&B run summary panel highlights the best validation score automatically.
+
+## Exporting and promoting a trained model
+
+`radiologist.core.registry.export_onnx` turns a Lightning checkpoint into two local ONNX files — it has no W&B interaction:
+
+```python
+from radiologist.core.registry import export_onnx
+
+result = export_onnx(
+    ckpt_path="/path/to/checkpoint.ckpt",
+    run_id="wandb-run-id",
+    input_shape=(1, 1, 224, 224),
+    classes=["healthy", "viral", "opacity"],
+    cam_target_layer="layer4.1.conv2",
+    out_dir="/tmp/onnx-export",
+)
+```
+
+This produces:
+
+1. **Deterministic** — `_CamWrapper` forward hook returns `(logits, activation)`. Useful for inference with visual explanation.
+2. **MC-Dropout** — `nn.Dropout` layers left in training mode (`TrainingMode.PRESERVE`, no constant folding). Run multiple forward passes and aggregate for uncertainty estimation.
+
+Uploading the exported ONNX files as W&B artifacts and linking them into a registry collection is handled by `radiologist-registry` (`WandbRegistry.log_model_artifacts()` then `WandbRegistry.promote()`, or the `radiologist-registry push` / `promote` CLI). See [`radiologist-registry/README.md`](../radiologist-registry/README.md) for the full flow.
+
+## Configuration reference
+
+The Hydra config tree lives at `src/radiologist/core/configs/`. Key files:
+
+| File | Purpose |
+|---|---|
+| `train.yaml` | Root config; wires all sub-configs |
+| `eval.yaml` | Evaluation-only mode (`train: false`, `ckpt_path: ???`) |
+| `trainer.yaml` | Lightning Trainer (precision, gradient clipping, deterministic) |
+| `datamodule/default.yaml` | Shard URIs, label map, transforms, normalisation |
+| `module/resnet50.yaml` | ResNet-50 backbone, `num_classes` interpolated from datamodule |
+| `module/loss/focal_loss.yaml` | γ=2, α=1, softmax, mean |
+| `module/optimizer/adamw.yaml` | AdamW, lr=1e-3, weight_decay=1e-2 |
+| `module/scheduler/sequential.yaml` | Linear warmup 500 steps → cosine annealing 10 000 steps |
+| `module/metric/fbeta_score.yaml` | Macro F1 (`MulticlassFBetaScore`, β=1) |
+| `callbacks/default.yaml` | BestMetric, WandbSummary, Attribution, ModelCheckpoint, LRMonitor |
+
+## Optional extras
+
+Install the `onnx-export` extra for ONNX export and W&B registry features:
+
+```bash
+uv add --active "radiologist-core[onnx-export]"
+```
+
+Adds: `onnx`, `onnxruntime`, `onnxscript`.
+
+## Dependencies
+
+Core: `radiologist-utils`, `torch`, `torchvision`, `lightning`, `webdataset`, `torchmetrics`, `wandb`, `hydra-core`.
+
+Optional (`onnx-export`): `onnx`, `onnxruntime`, `onnxscript`.
+
+Optional (`attribution`): `captum`.

radiologist_core-0.1.0/README.md

@@ -0,0 +1,220 @@
+# radiologist-core
+
+[![ci](https://github.com/CedrickArmel/radiologist/actions/workflows/ci.yml/badge.svg)](https://github.com/CedrickArmel/radiologist/actions/workflows/ci.yml)
+[![codecov](https://codecov.io/gh/CedrickArmel/radiologist/branch/main/graph/badge.svg)](https://codecov.io/gh/CedrickArmel/radiologist)
+[![PyPI](https://img.shields.io/pypi/v/radiologist-core)](https://pypi.org/project/radiologist-core/)
+![tested on](https://img.shields.io/badge/tested%20on-ubuntu--latest%20%7C%20python%203.10-blue)
+
+The ML engine. Provides the Lightning training loop, streaming data module, focal loss, GradCAM attribution, and W&B model registry integration for chest X-ray classification.
+
+## Business context
+
+Once clean, labelled WebDataset shards exist (produced by `radiologist-etl`), this package trains a classifier capable of distinguishing:
+
+- **Healthy** lung (no finding)
+- **Viral** pneumonia / COVID (infectious infiltrates)
+- **Opacity** (other lung opacities)
+
+The trained model is exported as two ONNX artefacts — one for deterministic inference with visual explanations (GradCAM), one for uncertainty-aware inference (MC-Dropout) — and linked to a W&B Model Registry collection for downstream consumption by an inference or serving layer.
+
+## Key capabilities
+
+| Capability | What it enables |
+|---|---|
+| Class-balanced streaming | Trains on imbalanced clinical data without manual oversampling scripts |
+| Prior-calibrated bias init | Logit outputs are calibrated to class prevalence from the first step |
+| Focal Loss | Focuses learning on hard, misclassified examples rather than easy majority samples |
+| GradCAM attribution | Produces heatmaps showing which lung region drove the prediction |
+| MC-Dropout ONNX export | Enables uncertainty estimation at inference time (multiple stochastic passes) |
+| HPO-friendly best-metric tracking | Optuna / W&B Sweeps receive the best epoch score, not the last |
+
+## Package layout
+
+```
+radiologist-core/src/radiologist/core/
+├── train.py            # Hydra entry point and train() function
+├── module.py           # LModule (LightningModule)
+├── losses.py           # FocalLoss
+├── data/
+│   ├── datamodule.py   # WebDatasetDataModule
+│   └── shards.py       # shard discovery helpers
+├── callbacks/
+│   ├── attribution.py  # GradCAM + Integrated Gradients
+│   ├── best_metric.py  # best-epoch metric tracking
+│   └── wandb_summary.py
+├── registry/
+│   └── export.py       # export_onnx (checkpoint → deterministic + MC-Dropout ONNX)
+└── configs/            # Hydra config tree
+```
+
+## Training a model
+
+### Prerequisites
+
+- Shards on GCS (or local) produced by `radiologist-etl`
+- W&B API key in the environment (`WANDB_API_KEY`)
+
+### Quick start
+
+```bash
+cd radiologist-core
+uv run --active python -m radiologist.core.train
+```
+
+The defaults load from `src/radiologist/core/configs/train.yaml`. Override on the command line:
+
+```bash
+uv run --active python -m radiologist.core.train \
+    trainer.max_epochs=30 \
+    datamodule.shard_root=gs://my-bucket/shards/ \
+    datamodule.split_manifest_uri=gs://my-bucket/manifests/manifest-abc123.jsonl \
+    seed=42
+```
+
+### Evaluation only
+
+```bash
+uv run --active python -m radiologist.core.train \
+    --config-name eval \
+    ckpt_path=/path/to/checkpoint.ckpt
+```
+
+## Core components
+
+### `LModule`
+
+A backbone-agnostic `LightningModule`. Pass any `nn.Module` as `net`.
+
+```python
+from radiologist.core import LModule
+from torchvision.models import resnet50
+
+module = LModule(
+    net=resnet50(num_classes=3),
+    loss=FocalLoss(gamma=2, alpha=1),
+    metric=MulticlassFBetaScore(num_classes=3, beta=1.0, average="macro"),
+    optimizer=partial(AdamW, lr=1e-3, weight_decay=1e-2),
+    scheduler=partial(sequential_scheduler, ...),
+    trainable_layers=None,   # None = full re-init; list of dot-paths = fine-tune
+    priors=None,             # overridden from datamodule at setup time
+)
+```
+
+On `setup('fit')`, `LModule` does one of two things depending on `trainable_layers`:
+
+- **`None`** — reinitialise all weights (Kaiming normal on Conv, Xavier on Linear). Use when training from scratch.
+- **`["layer4", "fc"]`** — freeze all parameters, then selectively unfreeze by dot-path. Use when fine-tuning a pretrained backbone.
+
+In both cases, if class priors are available (from the datamodule), the final `nn.Linear` bias is initialised to `−log(priors)`, giving calibrated starting logits.
+
+### `WebDatasetDataModule`
+
+Streams images from WebDataset tar shards. Handles class-balanced sampling automatically.
+
+```python
+from radiologist.core import WebDatasetDataModule
+
+dm = WebDatasetDataModule(
+    shard_root="gs://bucket/shards/",
+    split_manifest_uri="gs://bucket/manifests/manifest-abc123.jsonl",
+    label_map={"normal": "healthy", "pneumonia": "viral", "COVID": "viral"},
+    batch_size=32,
+)
+```
+
+The `label_map` collapses raw ETL folder names (e.g. `normal`, `COVID`) into model class names (e.g. `healthy`, `viral`). This decouples the dataset's folder structure from the model's output space.
+
+Training dataloader: one `wds.WebDataset` pipeline per class with `resampled=True` (infinite streaming), combined via `wds.RandomMix` weighted by inverse class frequency, then unbatch → shuffle → rebatch for global shuffling within an epoch. Validation and test dataloaders are flat sequential pipelines with no resampling.
+
+### `FocalLoss`
+
+```python
+from radiologist.core import FocalLoss
+
+loss = FocalLoss(gamma=2.0, alpha=1.0, use_softmax=True, reduction="mean")
+```
+
+Applies softmax to logits, computes `alpha * (1 − pt)^gamma * −log(pt)`. Supports optional one-hot conversion and `mean | sum | none` reductions.
+
+### Callbacks
+
+#### `AttributionCallback`
+
+Computes Layer GradCAM and Integrated Gradients every `every_n_val_epochs` validation epochs and on all test batches. Saves normalised PNGs to `{log_dir}/attributions/` and logs them to W&B. Skipped gracefully when `captum` is not installed.
+
+```yaml
+# configs/callbacks/default.yaml
+attribution:
+  _target_: radiologist.core.callbacks.AttributionCallback
+  target_layer: layer4.1.conv2
+  every_n_val_epochs: 5
+  n_test_batches: 4
+  n_samples_per_batch: 4
+```
+
+#### `BestMetricCallback`
+
+Writes `best_{monitor}` to `trainer.callback_metrics` after every validation epoch. When training finishes, HPO frameworks (Optuna, W&B Sweeps) read the best epoch score rather than the last.
+
+#### `WandbDefineSummaryCallback`
+
+Calls `wandb.run.define_metric` at fit start so the W&B run summary panel highlights the best validation score automatically.
+
+## Exporting and promoting a trained model
+
+`radiologist.core.registry.export_onnx` turns a Lightning checkpoint into two local ONNX files — it has no W&B interaction:
+
+```python
+from radiologist.core.registry import export_onnx
+
+result = export_onnx(
+    ckpt_path="/path/to/checkpoint.ckpt",
+    run_id="wandb-run-id",
+    input_shape=(1, 1, 224, 224),
+    classes=["healthy", "viral", "opacity"],
+    cam_target_layer="layer4.1.conv2",
+    out_dir="/tmp/onnx-export",
+)
+```
+
+This produces:
+
+1. **Deterministic** — `_CamWrapper` forward hook returns `(logits, activation)`. Useful for inference with visual explanation.
+2. **MC-Dropout** — `nn.Dropout` layers left in training mode (`TrainingMode.PRESERVE`, no constant folding). Run multiple forward passes and aggregate for uncertainty estimation.
+
+Uploading the exported ONNX files as W&B artifacts and linking them into a registry collection is handled by `radiologist-registry` (`WandbRegistry.log_model_artifacts()` then `WandbRegistry.promote()`, or the `radiologist-registry push` / `promote` CLI). See [`radiologist-registry/README.md`](../radiologist-registry/README.md) for the full flow.
+
+## Configuration reference
+
+The Hydra config tree lives at `src/radiologist/core/configs/`. Key files:
+
+| File | Purpose |
+|---|---|
+| `train.yaml` | Root config; wires all sub-configs |
+| `eval.yaml` | Evaluation-only mode (`train: false`, `ckpt_path: ???`) |
+| `trainer.yaml` | Lightning Trainer (precision, gradient clipping, deterministic) |
+| `datamodule/default.yaml` | Shard URIs, label map, transforms, normalisation |
+| `module/resnet50.yaml` | ResNet-50 backbone, `num_classes` interpolated from datamodule |
+| `module/loss/focal_loss.yaml` | γ=2, α=1, softmax, mean |
+| `module/optimizer/adamw.yaml` | AdamW, lr=1e-3, weight_decay=1e-2 |
+| `module/scheduler/sequential.yaml` | Linear warmup 500 steps → cosine annealing 10 000 steps |
+| `module/metric/fbeta_score.yaml` | Macro F1 (`MulticlassFBetaScore`, β=1) |
+| `callbacks/default.yaml` | BestMetric, WandbSummary, Attribution, ModelCheckpoint, LRMonitor |
+
+## Optional extras
+
+Install the `onnx-export` extra for ONNX export and W&B registry features:
+
+```bash
+uv add --active "radiologist-core[onnx-export]"
+```
+
+Adds: `onnx`, `onnxruntime`, `onnxscript`.
+
+## Dependencies
+
+Core: `radiologist-utils`, `torch`, `torchvision`, `lightning`, `webdataset`, `torchmetrics`, `wandb`, `hydra-core`.
+
+Optional (`onnx-export`): `onnx`, `onnxruntime`, `onnxscript`.
+
+Optional (`attribution`): `captum`.

radiologist_core-0.1.0/pyproject.toml

@@ -0,0 +1,90 @@
+[build-system]
+build-backend = "uv_build"
+requires = ["uv_build>=0.9.28,<0.10.0"]
+
+[project]
+dependencies = [
+    "Pillow>=12.2.0",
+    "radiologist-etl>=0.1.0",
+    "radiologist-registry>=0.1.0",
+    "radiologist-utils>=0.1.0",
+    "torch>=2.12.0",
+    "torchvision>=0.27.0",
+    "webdataset>=1.0.0",
+    "lightning>=2.6.0",
+    "torchmetrics>=1.9.0",
+    "hydra-core>=1.3.0",
+    "omegaconf>=2.3.0",
+    "fsspec>=2026.4.0",
+]
+name = "radiologist-core"
+version = "0.1.0"
+description = "Modeling library for the radiologist pipeline"
+readme = "README.md"
+license = "MIT"
+license-files = ["LICENSE"]
+keywords = [
+    "chest-xray",
+    "medical-imaging",
+    "machine-learning",
+    "pytorch",
+]
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Science/Research",
+    "Programming Language :: Python :: 3.10",
+    "Topic :: Scientific/Engineering :: Artificial Intelligence",
+]
+requires-python = ">=3.10"
+
+[[project.authors]]
+name = "Cédrick-Armel YEBOUET"
+
+[project.scripts]
+radiologist-core = "radiologist.core.train:main"
+
+[project.optional-dependencies]
+all = [
+    "captum>=0.9.0",
+    "gcsfs>=2026.4.0",
+    "onnx>=1.21.0",
+    "onnxruntime~=1.23.2",
+    "onnxscript>=0.7.0",
+    "wandb>=0.27.0",
+]
+gcs = ["gcsfs>=2026.4.0"]
+onnx-export = [
+    "onnx>=1.21.0",
+    "onnxruntime~=1.23.2",
+    "onnxscript>=0.7.0",
+]
+wandb = ["wandb>=0.27.0"]
+xai = ["captum>=0.9.0"]
+
+[project.urls]
+Homepage = "https://github.com/CedrickArmel/radiologist"
+Repository = "https://github.com/CedrickArmel/radiologist"
+Documentation = "https://cedrickarmel.github.io/radiologist/"
+Issues = "https://github.com/CedrickArmel/radiologist/issues"
+
+[tool.commitizen]
+name = "cz_conventional_commits"
+version_provider = "uv"
+version_scheme = "pep440"
+tag_format = "${version}-radiologist-core"
+ignored_tag_formats = ["${version}-radiologist-*"]
+update_changelog_on_bump = true
+bump_message = "bump: radiologist-core $current_version → $new_version"
+
+[tool.uv.build-backend]
+namespace = true
+module-name = "radiologist.core"
+
+[tool.uv.sources.radiologist-etl]
+workspace = true
+
+[tool.uv.sources.radiologist-registry]
+workspace = true
+
+[tool.uv.sources.radiologist-utils]
+workspace = true

radiologist_core-0.1.0/pyproject.toml.orig

@@ -0,0 +1,79 @@
+[build-system]
+build-backend = "uv_build"
+requires = ["uv_build>=0.9.28,<0.10.0"]
+
+[project]
+dependencies = [
+    "Pillow>=12.2.0",
+    "radiologist-etl>=0.1.0",
+    "radiologist-registry>=0.1.0",
+    "radiologist-utils>=0.1.0",
+    "torch>=2.12.0",
+    "torchvision>=0.27.0",
+    "webdataset>=1.0.0",
+    "lightning>=2.6.0",
+    "torchmetrics>=1.9.0",
+    "hydra-core>=1.3.0",
+    "omegaconf>=2.3.0",
+    "fsspec>=2026.4.0",
+]
+name = "radiologist-core"
+version = "0.1.0"
+description = "Modeling library for the radiologist pipeline"
+readme = "README.md"
+license = "MIT"
+license-files = ["LICENSE"]
+authors = [{ name = "Cédrick-Armel YEBOUET" }]
+keywords = ["chest-xray", "medical-imaging", "machine-learning", "pytorch"]
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Science/Research",
+    "Programming Language :: Python :: 3.10",
+    "Topic :: Scientific/Engineering :: Artificial Intelligence",
+]
+requires-python = ">=3.10"
+
+[project.scripts]
+radiologist-core = "radiologist.core.train:main"
+
+[project.optional-dependencies]
+all = [
+    "captum>=0.9.0",
+    "gcsfs>=2026.4.0",
+    "onnx>=1.21.0",
+    "onnxruntime~=1.23.2",
+    "onnxscript>=0.7.0",
+    "wandb>=0.27.0",
+]
+gcs = ["gcsfs>=2026.4.0"]
+onnx-export = [
+    "onnx>=1.21.0",
+    "onnxruntime~=1.23.2",
+    "onnxscript>=0.7.0",
+]
+wandb = ["wandb>=0.27.0"]
+xai = ["captum>=0.9.0"]
+
+[project.urls]
+Homepage = "https://github.com/CedrickArmel/radiologist"
+Repository = "https://github.com/CedrickArmel/radiologist"
+Documentation = "https://cedrickarmel.github.io/radiologist/"
+Issues = "https://github.com/CedrickArmel/radiologist/issues"
+
+[tool.commitizen]
+name = "cz_conventional_commits"
+version_provider = "uv"
+version_scheme = "pep440"
+tag_format = "${version}-radiologist-core"
+ignored_tag_formats = ["${version}-radiologist-*"]
+update_changelog_on_bump = true
+bump_message = "bump: radiologist-core $current_version → $new_version"
+
+[tool.uv.build-backend]
+namespace = true
+module-name = "radiologist.core"
+
+[tool.uv.sources]
+radiologist-etl = { workspace = true }
+radiologist-registry = { workspace = true }
+radiologist-utils = { workspace = true }