cnn-classifier-toolkit 0.1.0__tar.gz

cnn_classifier_toolkit-0.1.0/.gitignore

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+.DS_Store
+.venv/
+__pycache__/
+*.py[cod]
+*.egg-info/
+.pytest_cache/
+.mypy_cache/
+.ruff_cache/
+.hypothesis/
+.coverage
+.coverage.*
+htmlcov/
+dist/
+build/
+site/
+/runs/
+/data/
+.worktrees/
+.claude/worktrees/

cnn_classifier_toolkit-0.1.0/LICENSE

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cnn_classifier_toolkit-0.1.0/PKG-INFO

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+Metadata-Version: 2.5
+Name: cnn-classifier-toolkit
+Version: 0.1.0
+Summary: A config-driven, reproducible PyTorch toolkit for CNN image classification.
+Project-URL: Homepage, https://github.com/pengzhao-ai/cnn-classifier
+Project-URL: Documentation, https://pengzhao-ai.github.io/cnn-classifier/
+Project-URL: Repository, https://github.com/pengzhao-ai/cnn-classifier
+Project-URL: Changelog, https://github.com/pengzhao-ai/cnn-classifier/blob/main/CHANGELOG.md
+Project-URL: Issues, https://github.com/pengzhao-ai/cnn-classifier/issues
+Author: Peng Zhao
+License-Expression: Apache-2.0
+License-File: LICENSE
+Keywords: classification,cnn,deep-learning,experiment-tracking,image-classification,pytorch,reproducible-research,toolkit
+Classifier: Development Status :: 3 - Alpha
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Classifier: Typing :: Typed
+Requires-Python: <3.14,>=3.11
+Requires-Dist: jinja2>=3.1
+Requires-Dist: matplotlib>=3.8
+Requires-Dist: numpy>=2.0
+Requires-Dist: pillow>=10.0
+Requires-Dist: pydantic>=2.6
+Requires-Dist: pyyaml>=6.0
+Requires-Dist: rich>=13.0
+Requires-Dist: tifffile>=2024.1
+Requires-Dist: torch<3,>=2.15
+Requires-Dist: torchvision<1,>=0.29
+Requires-Dist: typer>=0.12
+Provides-Extra: all
+Requires-Dist: hypothesis>=6.98; extra == 'all'
+Requires-Dist: mkdocs-material>=9.5; extra == 'all'
+Requires-Dist: mkdocstrings[python]>=0.24; extra == 'all'
+Requires-Dist: mypy>=1.11; extra == 'all'
+Requires-Dist: pandas>=2.2; extra == 'all'
+Requires-Dist: pre-commit>=3.7; extra == 'all'
+Requires-Dist: pytest-cov>=5.0; extra == 'all'
+Requires-Dist: pytest>=8.0; extra == 'all'
+Requires-Dist: ruff>=0.6; extra == 'all'
+Requires-Dist: scikit-learn>=1.4; extra == 'all'
+Requires-Dist: tensorboard>=2.16; extra == 'all'
+Requires-Dist: torchinfo>=1.8; extra == 'all'
+Requires-Dist: types-pyyaml>=6.0; extra == 'all'
+Provides-Extra: dev
+Requires-Dist: hypothesis>=6.98; extra == 'dev'
+Requires-Dist: mypy>=1.11; extra == 'dev'
+Requires-Dist: pandas>=2.2; extra == 'dev'
+Requires-Dist: pre-commit>=3.7; extra == 'dev'
+Requires-Dist: pytest-cov>=5.0; extra == 'dev'
+Requires-Dist: pytest>=8.0; extra == 'dev'
+Requires-Dist: ruff>=0.6; extra == 'dev'
+Requires-Dist: types-pyyaml>=6.0; extra == 'dev'
+Provides-Extra: docs
+Requires-Dist: mkdocs-material>=9.5; extra == 'docs'
+Requires-Dist: mkdocstrings[python]>=0.24; extra == 'docs'
+Provides-Extra: tracking
+Requires-Dist: tensorboard>=2.16; extra == 'tracking'
+Provides-Extra: viz
+Requires-Dist: scikit-learn>=1.4; extra == 'viz'
+Requires-Dist: torchinfo>=1.8; extra == 'viz'
+Description-Content-Type: text/markdown
+
+# CNN Classifier Toolkit
+
+[![Python 3.11–3.13](https://img.shields.io/badge/python-3.11--3.13-blue)](https://www.python.org/)
+[![License: Apache-2.0](https://img.shields.io/badge/license-Apache--2.0-green)](LICENSE)
+[![Docs](https://img.shields.io/badge/docs-pengzhao--ai.github.io%2Fcnn--classifier-indigo)](https://pengzhao-ai.github.io/cnn-classifier/)
+
+A config-driven, reproducible PyTorch toolkit for CNN image classification.
+
+The toolkit turns a new image/label dataset into a trained, evaluated, and
+reported classifier through a typed YAML configuration. The same library powers
+the command line, so a quick smoke test and a full experiment use one pipeline.
+
+It is published on PyPI as `cnn-classifier-toolkit`; the import package remains
+`cnn_classifier` and the CLI remains `cnncls`.
+
+## Results at a glance
+
+| Experiment | Result | Budget |
+|---|---:|---|
+| CIFAR-10 scratch baseline | **92.25% test**, 92.78% best validation | 50 epochs, 22.3 min MPS |
+| ResNet-18 fine-tune, 32×32 | **94.98% test** | 30 epochs, 19.5 min MPS |
+| ResNet-18 scratch, 32×32 | 90.88% test | 30 epochs, 19.6 min MPS |
+| ResNet-18 linear probe | 62.66% test | 30 epochs, 8.4 min MPS |
+| Four core ablations | BN on +19.4 pp; cosine +8.5 pp; residual off +0.7 pp; augmentation off +3.1 pp | 8 epochs, 10k train subset |
+| Optical degradation classifier | 85.71% test | 20 epochs, 7.5 s MPS |
+| Bring-your-own-data quickstart | contract verified | 2 epochs, under a minute |
+
+![CIFAR-10 training history](https://raw.githubusercontent.com/pengzhao-ai/cnn-classifier/main/docs/images/cifar10_training_history.png)
+
+Reference: 92.42% validation / 92.61% test on MPS, seed 42. The reproduced test
+result is within 0.4 percentage points and clears the ≥90% gate. See the
+[CIFAR-10 case study](https://pengzhao-ai.github.io/cnn-classifier/case_studies/cifar10/)
+for the environment and caveats.
+
+## What is in the core
+
+| Area | What you get |
+|---|---|
+| Data | torchvision, ImageFolder, CSV manifest, NumPy, and synthetic adapters; 8-bit and 16-bit image I/O; group-safe splits; leakage and duplicate inspection |
+| Models | configurable simple CNN, configurable residual CNN, torchvision backbone wrapper, 32×32 stem adaptation, freezing, differential parameter groups |
+| Training | callbacks, early stopping, checkpoint/resume, AMP, gradient clipping and accumulation, MixUp/CutMix, EMA, warmup/cosine/step/plateau schedules |
+| Evaluation | top-k, per-class metrics, confusion matrices, NLL, calibration (ECE/MCE/Brier), bootstrap intervals, TTA, latency, error analysis |
+| Diagnostics | one-batch overfit, shape tracing, gradient reports, determinism checks |
+| Artifacts | resolved config, environment and git metadata, data fingerprints, metrics, checkpoints, predictions, figures, model contract |
+| Reports | self-contained HTML and Markdown, inline figures, no CDN or network dependency |
+| Devices | automatic CUDA, Apple MPS, or CPU selection |
+
+## Install
+
+### From PyPI
+
+```bash
+pip install cnn-classifier-toolkit
+cnncls doctor
+```
+
+### From a checkout
+
+```bash
+make sync
+source .venv/bin/activate
+cnncls doctor
+```
+
+`make sync` installs the package non-editable so the `cnncls` entry point works
+reliably on macOS, where an editable `.pth` can be hidden after PyTorch loads.
+Run `make sync` again after changing library code. Without activating the
+environment, use `uv run --no-sync cnncls ...`.
+
+## Quickstart
+
+Train a tiny deterministic smoke model with no downloads:
+
+```bash
+cnncls train -c configs/tests/synthetic.yaml --set training.epochs=1
+```
+
+The command creates a run directory under `runs/` containing the resolved
+configuration, data fingerprints, model contract, checkpoints, test
+predictions, figures, `report.html`, and `report.md`.
+
+Inspect the pipeline before training:
+
+```bash
+cnncls inspect-data -c configs/tests/synthetic.yaml
+cnncls debug -c configs/tests/synthetic.yaml --overfit-batch --steps 20
+cnncls train -c configs/tests/synthetic.yaml --dry-run
+```
+
+Evaluate, predict, and rebuild reports from artifacts:
+
+```bash
+cnncls evaluate --checkpoint runs/<run>/checkpoints/best.pt --split test
+cnncls predict --checkpoint runs/<run>/checkpoints/best.pt --input image.png
+cnncls report --run runs/<run>
+cnncls compare runs/<run-a> runs/<run-b> --out results/comparison
+```
+
+## Demos
+
+| Demo | What it shows | Entry point |
+|---|---|---|
+| CIFAR-10 scratch | reference residual CNN and the full training path | `python demos/cifar10/scripts/run_scratch.py` |
+| Transfer benchmark | scratch vs linear probe vs fine-tune at 32×32 | `python demos/cifar10/scripts/run_transfer.py` |
+| Ablations | four controlled pairs on a reduced CIFAR split | `python demos/ablations/run_ablations.py` |
+| Optical degradation | manifest data, group-safe splits, confusion analysis | `python demos/optics_degradation/scripts/run_optics.py` |
+| Bring your own data | raw-to-intake contract and custom adapters | `python demos/bring_your_own_data/scripts/run_quickstart.py` |
+
+The bring-your-own-data quickstart uses a committed 16-bit fixture and finishes
+in a few seconds.
+
+## Command line
+
+| Command | Purpose |
+|---|---|
+| `cnncls init DIR` | Scaffold a config, README, and data layout |
+| `cnncls doctor` | Versions, device selection, optional dependencies |
+| `cnncls inspect-data -c CONFIG` | Class balance, duplicates, corruption, leakage, model contract |
+| `cnncls debug -c CONFIG` | One-batch overfit, shape trace, gradients, determinism |
+| `cnncls train -c CONFIG` | Train, evaluate, write figures and the report |
+| `cnncls evaluate --checkpoint PATH` | Evaluate on `test` or `val`, write predictions and metrics |
+| `cnncls predict --checkpoint PATH --input PATH` | Image, folder, or manifest inference |
+| `cnncls report --run DIR` | Rebuild HTML and Markdown from artifacts |
+| `cnncls compare RUN... --out DIR` | Fair comparison with test-fingerprint enforcement |
+
+`train --dry-run` builds the dataset and model, runs one forward/backward pass,
+prints the contract and parameter counts, and exits without writing a run.
+
+## Documentation
+
+The full site is published at
+[https://pengzhao-ai.github.io/cnn-classifier/](https://pengzhao-ai.github.io/cnn-classifier/):
+
+- [Quickstart](https://pengzhao-ai.github.io/cnn-classifier/quickstart/)
+- [How it works](https://pengzhao-ai.github.io/cnn-classifier/how_it_works/)
+- [Models & architectures](https://pengzhao-ai.github.io/cnn-classifier/models/)
+- [Configuration](https://pengzhao-ai.github.io/cnn-classifier/configuration/)
+- [Techniques](https://pengzhao-ai.github.io/cnn-classifier/techniques/augmentation/)
+- [CIFAR-10 demo](https://pengzhao-ai.github.io/cnn-classifier/case_studies/cifar10/)
+- [Bring your own data](https://pengzhao-ai.github.io/cnn-classifier/bring_your_own_data/)
+- [CLI](https://pengzhao-ai.github.io/cnn-classifier/cli/)
+- [API](https://pengzhao-ai.github.io/cnn-classifier/api/)
+
+## Project layout
+
+```text
+src/cnn_classifier/
+├── config/       typed YAML schema, defaults chain, CLI overrides
+├── core/         devices, seeding, hashing, shared contracts
+├── data/         adapters, image I/O, splits, transforms, inspection
+├── models/       CNN builders, torchvision wrapper, transfer utilities
+├── training/     trainer, callbacks, checkpoints, optimizer, schedules, AMP
+├── evaluation/   metrics, calibration, bootstrap, latency, comparison
+├── diagnostics/  overfit, tracing, gradients, determinism
+├── viz/          publication-style figures and HTML/Markdown reports
+├── runs/         run directories and artifact writers
+└── cli.py        `cnncls` command line
+```
+
+## Development
+
+```bash
+make test        # library tests
+make coverage    # core coverage gate
+make lint        # ruff
+make typecheck   # mypy
+make docs        # this site
+make build       # wheel and sdist
+make gate        # all of the above
+```
+
+Contributor notes are in [`CONTRIBUTING.md`](CONTRIBUTING.md).
+
+## License
+
+Apache-2.0. See [`LICENSE`](LICENSE).
+
+## Citation
+
+If you use this toolkit, cite it using [`CITATION.cff`](CITATION.cff).

cnn_classifier_toolkit-0.1.0/README.md

@@ -0,0 +1,180 @@
+# CNN Classifier Toolkit
+
+[![Python 3.11–3.13](https://img.shields.io/badge/python-3.11--3.13-blue)](https://www.python.org/)
+[![License: Apache-2.0](https://img.shields.io/badge/license-Apache--2.0-green)](LICENSE)
+[![Docs](https://img.shields.io/badge/docs-pengzhao--ai.github.io%2Fcnn--classifier-indigo)](https://pengzhao-ai.github.io/cnn-classifier/)
+
+A config-driven, reproducible PyTorch toolkit for CNN image classification.
+
+The toolkit turns a new image/label dataset into a trained, evaluated, and
+reported classifier through a typed YAML configuration. The same library powers
+the command line, so a quick smoke test and a full experiment use one pipeline.
+
+It is published on PyPI as `cnn-classifier-toolkit`; the import package remains
+`cnn_classifier` and the CLI remains `cnncls`.
+
+## Results at a glance
+
+| Experiment | Result | Budget |
+|---|---:|---|
+| CIFAR-10 scratch baseline | **92.25% test**, 92.78% best validation | 50 epochs, 22.3 min MPS |
+| ResNet-18 fine-tune, 32×32 | **94.98% test** | 30 epochs, 19.5 min MPS |
+| ResNet-18 scratch, 32×32 | 90.88% test | 30 epochs, 19.6 min MPS |
+| ResNet-18 linear probe | 62.66% test | 30 epochs, 8.4 min MPS |
+| Four core ablations | BN on +19.4 pp; cosine +8.5 pp; residual off +0.7 pp; augmentation off +3.1 pp | 8 epochs, 10k train subset |
+| Optical degradation classifier | 85.71% test | 20 epochs, 7.5 s MPS |
+| Bring-your-own-data quickstart | contract verified | 2 epochs, under a minute |
+
+![CIFAR-10 training history](https://raw.githubusercontent.com/pengzhao-ai/cnn-classifier/main/docs/images/cifar10_training_history.png)
+
+Reference: 92.42% validation / 92.61% test on MPS, seed 42. The reproduced test
+result is within 0.4 percentage points and clears the ≥90% gate. See the
+[CIFAR-10 case study](https://pengzhao-ai.github.io/cnn-classifier/case_studies/cifar10/)
+for the environment and caveats.
+
+## What is in the core
+
+| Area | What you get |
+|---|---|
+| Data | torchvision, ImageFolder, CSV manifest, NumPy, and synthetic adapters; 8-bit and 16-bit image I/O; group-safe splits; leakage and duplicate inspection |
+| Models | configurable simple CNN, configurable residual CNN, torchvision backbone wrapper, 32×32 stem adaptation, freezing, differential parameter groups |
+| Training | callbacks, early stopping, checkpoint/resume, AMP, gradient clipping and accumulation, MixUp/CutMix, EMA, warmup/cosine/step/plateau schedules |
+| Evaluation | top-k, per-class metrics, confusion matrices, NLL, calibration (ECE/MCE/Brier), bootstrap intervals, TTA, latency, error analysis |
+| Diagnostics | one-batch overfit, shape tracing, gradient reports, determinism checks |
+| Artifacts | resolved config, environment and git metadata, data fingerprints, metrics, checkpoints, predictions, figures, model contract |
+| Reports | self-contained HTML and Markdown, inline figures, no CDN or network dependency |
+| Devices | automatic CUDA, Apple MPS, or CPU selection |
+
+## Install
+
+### From PyPI
+
+```bash
+pip install cnn-classifier-toolkit
+cnncls doctor
+```
+
+### From a checkout
+
+```bash
+make sync
+source .venv/bin/activate
+cnncls doctor
+```
+
+`make sync` installs the package non-editable so the `cnncls` entry point works
+reliably on macOS, where an editable `.pth` can be hidden after PyTorch loads.
+Run `make sync` again after changing library code. Without activating the
+environment, use `uv run --no-sync cnncls ...`.
+
+## Quickstart
+
+Train a tiny deterministic smoke model with no downloads:
+
+```bash
+cnncls train -c configs/tests/synthetic.yaml --set training.epochs=1
+```
+
+The command creates a run directory under `runs/` containing the resolved
+configuration, data fingerprints, model contract, checkpoints, test
+predictions, figures, `report.html`, and `report.md`.
+
+Inspect the pipeline before training:
+
+```bash
+cnncls inspect-data -c configs/tests/synthetic.yaml
+cnncls debug -c configs/tests/synthetic.yaml --overfit-batch --steps 20
+cnncls train -c configs/tests/synthetic.yaml --dry-run
+```
+
+Evaluate, predict, and rebuild reports from artifacts:
+
+```bash
+cnncls evaluate --checkpoint runs/<run>/checkpoints/best.pt --split test
+cnncls predict --checkpoint runs/<run>/checkpoints/best.pt --input image.png
+cnncls report --run runs/<run>
+cnncls compare runs/<run-a> runs/<run-b> --out results/comparison
+```
+
+## Demos
+
+| Demo | What it shows | Entry point |
+|---|---|---|
+| CIFAR-10 scratch | reference residual CNN and the full training path | `python demos/cifar10/scripts/run_scratch.py` |
+| Transfer benchmark | scratch vs linear probe vs fine-tune at 32×32 | `python demos/cifar10/scripts/run_transfer.py` |
+| Ablations | four controlled pairs on a reduced CIFAR split | `python demos/ablations/run_ablations.py` |
+| Optical degradation | manifest data, group-safe splits, confusion analysis | `python demos/optics_degradation/scripts/run_optics.py` |
+| Bring your own data | raw-to-intake contract and custom adapters | `python demos/bring_your_own_data/scripts/run_quickstart.py` |
+
+The bring-your-own-data quickstart uses a committed 16-bit fixture and finishes
+in a few seconds.
+
+## Command line
+
+| Command | Purpose |
+|---|---|
+| `cnncls init DIR` | Scaffold a config, README, and data layout |
+| `cnncls doctor` | Versions, device selection, optional dependencies |
+| `cnncls inspect-data -c CONFIG` | Class balance, duplicates, corruption, leakage, model contract |
+| `cnncls debug -c CONFIG` | One-batch overfit, shape trace, gradients, determinism |
+| `cnncls train -c CONFIG` | Train, evaluate, write figures and the report |
+| `cnncls evaluate --checkpoint PATH` | Evaluate on `test` or `val`, write predictions and metrics |
+| `cnncls predict --checkpoint PATH --input PATH` | Image, folder, or manifest inference |
+| `cnncls report --run DIR` | Rebuild HTML and Markdown from artifacts |
+| `cnncls compare RUN... --out DIR` | Fair comparison with test-fingerprint enforcement |
+
+`train --dry-run` builds the dataset and model, runs one forward/backward pass,
+prints the contract and parameter counts, and exits without writing a run.
+
+## Documentation
+
+The full site is published at
+[https://pengzhao-ai.github.io/cnn-classifier/](https://pengzhao-ai.github.io/cnn-classifier/):
+
+- [Quickstart](https://pengzhao-ai.github.io/cnn-classifier/quickstart/)
+- [How it works](https://pengzhao-ai.github.io/cnn-classifier/how_it_works/)
+- [Models & architectures](https://pengzhao-ai.github.io/cnn-classifier/models/)
+- [Configuration](https://pengzhao-ai.github.io/cnn-classifier/configuration/)
+- [Techniques](https://pengzhao-ai.github.io/cnn-classifier/techniques/augmentation/)
+- [CIFAR-10 demo](https://pengzhao-ai.github.io/cnn-classifier/case_studies/cifar10/)
+- [Bring your own data](https://pengzhao-ai.github.io/cnn-classifier/bring_your_own_data/)
+- [CLI](https://pengzhao-ai.github.io/cnn-classifier/cli/)
+- [API](https://pengzhao-ai.github.io/cnn-classifier/api/)
+
+## Project layout
+
+```text
+src/cnn_classifier/
+├── config/       typed YAML schema, defaults chain, CLI overrides
+├── core/         devices, seeding, hashing, shared contracts
+├── data/         adapters, image I/O, splits, transforms, inspection
+├── models/       CNN builders, torchvision wrapper, transfer utilities
+├── training/     trainer, callbacks, checkpoints, optimizer, schedules, AMP
+├── evaluation/   metrics, calibration, bootstrap, latency, comparison
+├── diagnostics/  overfit, tracing, gradients, determinism
+├── viz/          publication-style figures and HTML/Markdown reports
+├── runs/         run directories and artifact writers
+└── cli.py        `cnncls` command line
+```
+
+## Development
+
+```bash
+make test        # library tests
+make coverage    # core coverage gate
+make lint        # ruff
+make typecheck   # mypy
+make docs        # this site
+make build       # wheel and sdist
+make gate        # all of the above
+```
+
+Contributor notes are in [`CONTRIBUTING.md`](CONTRIBUTING.md).
+
+## License
+
+Apache-2.0. See [`LICENSE`](LICENSE).
+
+## Citation
+
+If you use this toolkit, cite it using [`CITATION.cff`](CITATION.cff).