synthrad-sct 0.1.0__tar.gz

synthrad_sct-0.1.0/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
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synthrad_sct-0.1.0/PKG-INFO

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+Metadata-Version: 2.5
+Name: synthrad-sct
+Version: 0.1.0
+Summary: One-command installer for the COMP3888 P40 abdomen MRI-to-sCT models
+Project-URL: Source, https://github.sydney.edu.au/fyan0582/COMP3888_W11_04_P40/tree/main/installer
+Project-URL: Weights, https://github.sydney.edu.au/dmat0262/synthrad-sct-weights
+Author: COMP3888 W11-04 P40
+Keywords: installer,medical-imaging,mri,synthetic-ct,synthrad
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Requires-Python: >=3.9
+Requires-Dist: pyyaml>=6
+Requires-Dist: questionary>=2
+Requires-Dist: rich>=13
+Description-Content-Type: text/markdown
+
+# synthrad-sct installer
+
+One command that sets up the abdomen MRI-to-sCT models from this repository:
+it clones the code, builds a Python 3.11 environment, downloads the trained
+weights, checks them, and runs a smoke test. No retraining.
+
+## For the client
+
+You need [uv](https://docs.astral.sh/uv/getting-started/installation/),
+git and the [GitHub CLI](https://cli.github.com), plus read access to this
+repository and [dmat0262/synthrad-sct-weights](https://github.sydney.edu.au/dmat0262/synthrad-sct-weights)
+on `github.sydney.edu.au` (on campus or VPN). You do not need to clone anything.
+
+Log in once, so that uv, git and the installer reuse the same login and never ask for a token:
+
+```bash
+gh auth login --hostname github.sydney.edu.au
+uvx synthrad-sct init
+```
+
+The installer asks a few questions:
+
+1. **GitHub token**, only if you skipped `gh auth login`. Make one at
+   <https://github.sydney.edu.au/settings/tokens/new?scopes=repo>, or set
+   `SYNTHRAD_GITHUB_TOKEN`.
+2. **Where to clone.** Skipped if you run it inside an existing clone.
+3. **Which models.** B6 and B2 are pre-selected.
+4. **CPU or CUDA.** Detected automatically. On macOS it is always CPU.
+5. **Web previewer.** Optionally installs the Gradio demo, which supports B2 or B3.
+
+Then it:
+
+- creates `.venv` with Python 3.11, which uv downloads if needed;
+- installs PyTorch 2.5.1 and the pinned NumPy/SimpleITK/SciPy versions the
+  weights were trained with;
+- downloads each `epoch_0400.pt` and checks its SHA-256 against the hash
+  recorded with the test results;
+- puts each file where the inference code already looks:
+  `<experiment>/checkpoints_AB_400epochs/<run>/epoch_0400.pt`;
+- writes `ct_free_inference/configs/inference.local.yaml`;
+- runs `ct_free_inference/smoke_models.py` on the downloaded weights.
+
+If a download is interrupted, run the command again. It resumes and skips
+anything already downloaded and checked.
+
+| Model | What it is | Test MAE (HU) | Evidence |
+| --- | --- | ---: | --- |
+| B6 | 2.5D U-Net + PatchGAN, 5 slices, GAN weight 0.01 | 108.80 | MRI-only pipeline |
+| B2 | 2.5D U-Net + PatchGAN, 5 slices, 256 crop | 113.03 | historical paired workflow |
+| B0 | 2D U-Net + PatchGAN, centre slice | 114.20 | historical paired workflow |
+| B3 | 2.5D U-Net + PatchGAN, 5 slices, 512 crop | 118.00 | historical paired workflow |
+
+See [AB_EXPERIMENTS_README.md](https://github.sydney.edu.au/fyan0582/COMP3888_W11_04_P40/blob/main/AB_EXPERIMENTS_README.md) for what the
+evidence columns mean.
+
+### Other commands
+
+```bash
+synthrad-sct list                           # models, scores, which are installed
+synthrad-sct doctor                         # check git/uv/token/GPU/.venv/weights
+synthrad-sct download --models B3 B0        # add weights to an existing setup
+synthrad-sct init -y --models B6 --device cpu --no-previewer   # no prompts
+```
+
+Prefix each with `uvx`, or install once with `uv tool install synthrad-sct`.
+Without PyPI, the same CLI runs straight from Git:
+`uvx --from "git+https://github.sydney.edu.au/fyan0582/COMP3888_W11_04_P40.git#subdirectory=installer" synthrad-sct init`.
+
+## For the team: publishing the weights
+
+The weights are files on the `weights-v1` release of
+[dmat0262/synthrad-sct-weights](https://github.sydney.edu.au/dmat0262/synthrad-sct-weights),
+kept apart from this course repository so they outlive it. They are never
+committed to Git: GitHub rejects files over 100 MB. You need the [GitHub CLI](https://cli.github.com) logged in
+with `gh auth login --hostname github.sydney.edu.au`.
+
+```bash
+cd installer
+uv run synthrad-sct publish --dry-run B0=/path/B0/epoch_0400.pt B2=/path/B2/epoch_0400.pt \
+  B3=/path/B3/epoch_0400.pt B6=/path/B6/epoch_0400.pt
+# then the same command without --dry-run
+```
+
+`publish` first writes the weights repository's `README.md` (a model card)
+and `SHA256SUMS` from the pinned table, then creates the release if needed and
+uploads the files. It refuses any file whose SHA-256 differs from the checkpoint the
+reported results came from. Hashes are pinned in
+`src/synthrad_sct/models.py`, and the tests check them against `results/` and
+`metadata/`. If a model is retrained, update the recorded results and the
+pinned hash together, and publish under a new tag.
+
+## Releasing to PyPI
+
+Bump `version` in `pyproject.toml` and `__init__.py`, then:
+
+```bash
+cd installer
+rm -rf dist && uv build
+UV_PUBLISH_TOKEN=pypi-… uv publish
+```
+
+If the package is ever removed from PyPI, switch the commands in this README and
+`weights_repo.INSTALL` back to the Git form first.
+
+## Tests
+
+```bash
+cd installer
+uv run --with numpy --with SimpleITK python -m unittest discover -s tests -v
+```

synthrad_sct-0.1.0/README.md

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+# synthrad-sct installer
+
+One command that sets up the abdomen MRI-to-sCT models from this repository:
+it clones the code, builds a Python 3.11 environment, downloads the trained
+weights, checks them, and runs a smoke test. No retraining.
+
+## For the client
+
+You need [uv](https://docs.astral.sh/uv/getting-started/installation/),
+git and the [GitHub CLI](https://cli.github.com), plus read access to this
+repository and [dmat0262/synthrad-sct-weights](https://github.sydney.edu.au/dmat0262/synthrad-sct-weights)
+on `github.sydney.edu.au` (on campus or VPN). You do not need to clone anything.
+
+Log in once, so that uv, git and the installer reuse the same login and never ask for a token:
+
+```bash
+gh auth login --hostname github.sydney.edu.au
+uvx synthrad-sct init
+```
+
+The installer asks a few questions:
+
+1. **GitHub token**, only if you skipped `gh auth login`. Make one at
+   <https://github.sydney.edu.au/settings/tokens/new?scopes=repo>, or set
+   `SYNTHRAD_GITHUB_TOKEN`.
+2. **Where to clone.** Skipped if you run it inside an existing clone.
+3. **Which models.** B6 and B2 are pre-selected.
+4. **CPU or CUDA.** Detected automatically. On macOS it is always CPU.
+5. **Web previewer.** Optionally installs the Gradio demo, which supports B2 or B3.
+
+Then it:
+
+- creates `.venv` with Python 3.11, which uv downloads if needed;
+- installs PyTorch 2.5.1 and the pinned NumPy/SimpleITK/SciPy versions the
+  weights were trained with;
+- downloads each `epoch_0400.pt` and checks its SHA-256 against the hash
+  recorded with the test results;
+- puts each file where the inference code already looks:
+  `<experiment>/checkpoints_AB_400epochs/<run>/epoch_0400.pt`;
+- writes `ct_free_inference/configs/inference.local.yaml`;
+- runs `ct_free_inference/smoke_models.py` on the downloaded weights.
+
+If a download is interrupted, run the command again. It resumes and skips
+anything already downloaded and checked.
+
+| Model | What it is | Test MAE (HU) | Evidence |
+| --- | --- | ---: | --- |
+| B6 | 2.5D U-Net + PatchGAN, 5 slices, GAN weight 0.01 | 108.80 | MRI-only pipeline |
+| B2 | 2.5D U-Net + PatchGAN, 5 slices, 256 crop | 113.03 | historical paired workflow |
+| B0 | 2D U-Net + PatchGAN, centre slice | 114.20 | historical paired workflow |
+| B3 | 2.5D U-Net + PatchGAN, 5 slices, 512 crop | 118.00 | historical paired workflow |
+
+See [AB_EXPERIMENTS_README.md](https://github.sydney.edu.au/fyan0582/COMP3888_W11_04_P40/blob/main/AB_EXPERIMENTS_README.md) for what the
+evidence columns mean.
+
+### Other commands
+
+```bash
+synthrad-sct list                           # models, scores, which are installed
+synthrad-sct doctor                         # check git/uv/token/GPU/.venv/weights
+synthrad-sct download --models B3 B0        # add weights to an existing setup
+synthrad-sct init -y --models B6 --device cpu --no-previewer   # no prompts
+```
+
+Prefix each with `uvx`, or install once with `uv tool install synthrad-sct`.
+Without PyPI, the same CLI runs straight from Git:
+`uvx --from "git+https://github.sydney.edu.au/fyan0582/COMP3888_W11_04_P40.git#subdirectory=installer" synthrad-sct init`.
+
+## For the team: publishing the weights
+
+The weights are files on the `weights-v1` release of
+[dmat0262/synthrad-sct-weights](https://github.sydney.edu.au/dmat0262/synthrad-sct-weights),
+kept apart from this course repository so they outlive it. They are never
+committed to Git: GitHub rejects files over 100 MB. You need the [GitHub CLI](https://cli.github.com) logged in
+with `gh auth login --hostname github.sydney.edu.au`.
+
+```bash
+cd installer
+uv run synthrad-sct publish --dry-run B0=/path/B0/epoch_0400.pt B2=/path/B2/epoch_0400.pt \
+  B3=/path/B3/epoch_0400.pt B6=/path/B6/epoch_0400.pt
+# then the same command without --dry-run
+```
+
+`publish` first writes the weights repository's `README.md` (a model card)
+and `SHA256SUMS` from the pinned table, then creates the release if needed and
+uploads the files. It refuses any file whose SHA-256 differs from the checkpoint the
+reported results came from. Hashes are pinned in
+`src/synthrad_sct/models.py`, and the tests check them against `results/` and
+`metadata/`. If a model is retrained, update the recorded results and the
+pinned hash together, and publish under a new tag.
+
+## Releasing to PyPI
+
+Bump `version` in `pyproject.toml` and `__init__.py`, then:
+
+```bash
+cd installer
+rm -rf dist && uv build
+UV_PUBLISH_TOKEN=pypi-… uv publish
+```
+
+If the package is ever removed from PyPI, switch the commands in this README and
+`weights_repo.INSTALL` back to the Git form first.
+
+## Tests
+
+```bash
+cd installer
+uv run --with numpy --with SimpleITK python -m unittest discover -s tests -v
+```

synthrad_sct-0.1.0/pyproject.toml

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+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[project]
+name = "synthrad-sct"
+version = "0.1.0"
+description = "One-command installer for the COMP3888 P40 abdomen MRI-to-sCT models"
+readme = "README.md"
+requires-python = ">=3.9"
+dependencies = ["rich>=13", "questionary>=2", "PyYAML>=6"]
+authors = [{ name = "COMP3888 W11-04 P40" }]
+keywords = ["synthrad", "mri", "synthetic-ct", "medical-imaging", "installer"]
+classifiers = [
+    "Environment :: Console",
+    "Intended Audience :: Science/Research",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3",
+    "Topic :: Scientific/Engineering :: Medical Science Apps.",
+]
+
+[project.urls]
+Source = "https://github.sydney.edu.au/fyan0582/COMP3888_W11_04_P40/tree/main/installer"
+Weights = "https://github.sydney.edu.au/dmat0262/synthrad-sct-weights"
+
+[project.scripts]
+synthrad-sct = "synthrad_sct.cli:main"
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/synthrad_sct"]

synthrad_sct-0.1.0/src/synthrad_sct/__init__.py

@@ -0,0 +1 @@
+__version__ = "0.1.0"

synthrad_sct-0.1.0/src/synthrad_sct/__main__.py

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+import sys
+from .cli import main
+
+sys.exit(main())