Test validation augmentation

.git-blame-ignore-revs

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+# Revisions to skip in `git blame`.
+#
+# Enable locally with:
+#   git config blame.ignoreRevsFile .git-blame-ignore-revs
+#
+# GitHub picks this file up automatically.
+
+# style: apply ruff autofix and formatter (#34)
+4c78918e1be261ca2373f1fbfb302654c7803a03

.github/CODEOWNERS

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+# Owners are requested for review automatically on every pull request.
+# Combined with a branch protection rule requiring one approval, this is the
+# "requiring code-review" half of issue #34.
+#
+# See https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-code-owners
+
+*                       @Hendrik-code @NathanMolinier
+
+# Changing the CI, packaging or linting setup affects every contributor.
+/.github/               @Hendrik-code
+/pyproject.toml         @Hendrik-code
+/.pre-commit-config.yaml @Hendrik-code

.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug report
+about: Something does not work as expected
+title: ''
+labels: bug
+assignees: ''
+---
+
+**Describe the bug**
+A clear and concise description of what goes wrong.
+
+**To reproduce**
+Steps to reproduce the behaviour, ideally with the exact command:
+
+```bash
+# e.g. AUGLAB_PARAMS_GPU_JSON=/abs/path/params.json nnUNetv2_train 100 3d_fullres 0 -tr nnUNetTrainerDAExtGPU
+```
+
+**Config JSON**
+If the problem involves augmentation parameters, paste the relevant part of your
+transform params JSON (or attach the file).
+
+```json
+
+```
+
+**Expected behaviour**
+What you expected to happen instead.
+
+**Error output**
+The full traceback, not just the last line.
+
+```
+
+```
+
+**Environment**
+- AugLab version or commit:
+- Python version:
+- PyTorch version and CUDA build:
+- nnU-Net version (if applicable):
+- OS:
+
+**Additional context**
+Anything else that might matter — dataset, image orientation, patch size.

.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: Feature request
+about: Suggest a new augmentation, option, or improvement
+title: ''
+labels: enhancement
+assignees: ''
+---
+
+**What problem does this solve?**
+A clear description of the limitation you are hitting.
+
+**Proposed solution**
+What you would like AugLab to do.
+
+**If this is a new augmentation**
+- What does it simulate (acquisition artefact, contrast change, anatomy change)?
+- Reference or paper, if there is one:
+- Should it run on GPU, CPU, or both?
+- What parameters should the config JSON expose?
+
+**Alternatives considered**
+Other approaches you thought about.
+
+**Additional context**
+Screenshots, example images, or links.

.github/ISSUE_TEMPLATE/question.md

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+---
+name: Question
+about: Ask about usage, configuration, or results
+title: ''
+labels: question
+assignees: ''
+---
+
+**Your question**
+What you are trying to do and where you are stuck.
+
+**What you have tried**
+Commands, config JSONs, or documentation you already looked at.
+
+**Environment (if relevant)**
+- AugLab version or commit:
+- Python / PyTorch version:

.github/pull_request_template.md

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+## What does this change?
+
+<!-- A short description. If it fixes an issue, write "Fixes #123" so GitHub links them. -->
+
+## Why?
+
+<!-- The motivation. What was broken or missing? -->
+
+## How was it tested?
+
+<!-- Delete what does not apply. -->
+
+- [ ] `pytest` passes locally
+- [ ] `pre-commit run --all-files` passes
+- [ ] Added or updated tests covering the change
+- [ ] Ran a training / augmentation job end to end
+
+## Anything reviewers should look at closely?
+
+<!-- Tricky bits, trade-offs, or decisions you were unsure about. -->
+
+## Checklist
+
+- [ ] Augmentation behaviour is unchanged, or the change is intentional and described above
+- [ ] New transforms are reachable from a config JSON
+- [ ] `project.version` in `pyproject.toml` bumped, if this should be released

.github/workflows/lint.yml

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+name: lint
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+permissions:
+  contents: read
+
+concurrency:
+  group: lint-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  # Runs the pre-commit hooks rather than a bare `ruff check`, so the hooks
+  # contributors run locally and the ones CI enforces cannot drift apart.
+  #
+  # Deliberately does NOT auto-commit fixes back to the branch: that breaks on
+  # pull requests from forks and rewrites contributors' branches under them.
+  # A red check plus `pre-commit run --all-files` locally is the fix.
+  pre-commit:
+    name: pre-commit
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - uses: pre-commit/action@v3.0.1

.github/workflows/publish.yml

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+name: publish to PyPI
+
+on:
+  release:
+    types: [created]
+  workflow_dispatch:
+    inputs:
+      repository:
+        description: Which index to upload to
+        required: true
+        default: testpypi
+        type: choice
+        options: [testpypi, pypi]
+
+permissions:
+  contents: read
+
+jobs:
+  publish:
+    name: build and upload
+    runs-on: ubuntu-latest
+    # Requires the PYPI_API_TOKEN (and, for dry runs, TEST_PYPI_API_TOKEN)
+    # repository secret. Until that is set by an admin this job cannot upload.
+    environment: pypi
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          # poetry-dynamic-versioning derives the version from the git tag;
+          # a shallow clone has no tags and would build as 0.0.0.
+          fetch-depth: 0
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install build tooling
+        run: |
+          python -m pip install --upgrade pip
+          pip install build twine
+
+      - name: Build sdist and wheel
+        run: python -m build
+
+      - name: Check the built version came from the release tag
+        # poetry-dynamic-versioning derives the version from the tag, so the two cannot
+        # disagree the way a hand-maintained project.version could. What can
+        # still go wrong is the tag not matching [tool.poetry-dynamic-versioning].pattern,
+        # or the checkout arriving without tags -- both of which silently yield
+        # the 0.0.0 fallback or a .dev version. Catch that before uploading.
+        if: github.event_name == 'release'
+        run: |
+          python - <<'PY'
+          import glob, os, pathlib, re, sys
+
+          from packaging.version import InvalidVersion, Version
+
+          tag = os.environ["RELEASE_TAG"]
+          # Same prefixes as [tool.poetry-dynamic-versioning].pattern.
+          expected = re.sub(r"^(?:[rvV]|release[-_])", "", tag)
+          built = {pathlib.Path(p).name.split("-")[1] for p in glob.glob("dist/*.whl")}
+
+          print(f"tag={tag!r} expected={expected!r} built={sorted(built)}")
+
+          # Compare parsed versions, not strings: a tag like v2.0.0-beta1 is
+          # legitimately normalised to 2.0.0b1 in the artifact name.
+          try:
+              if {Version(b) for b in built} != {Version(expected)}:
+                  raise InvalidVersion
+          except InvalidVersion:
+              sys.exit(
+                  f"built version {sorted(built)} does not match release tag '{tag}'. "
+                  "Either the tag does not match [tool.poetry-dynamic-versioning].pattern in "
+                  "pyproject.toml, or the checkout has no tags (needs fetch-depth: 0)."
+              )
+          PY
+        env:
+          RELEASE_TAG: ${{ github.event.release.tag_name }}
+
+      - name: Refuse to publish a fallback version
+        run: |
+          python - <<'PY'
+          import glob, pathlib, sys
+
+          built = {pathlib.Path(p).name.split("-")[1] for p in glob.glob("dist/*.whl")}
+          if "0.0.0" in built:
+              sys.exit(
+                  "refusing to publish 0.0.0 -- poetry-dynamic-versioning found no git tag, so the "
+                  "version is the fallback rather than a real release"
+              )
+          print(f"version looks real: {sorted(built)}")
+          PY
+
+      - name: Check distribution metadata
+        run: twine check dist/*
+
+      - name: Verify the wheel ships the package data
+        run: |
+          python - <<'PY'
+          import glob, sys, zipfile
+
+          names = zipfile.ZipFile(glob.glob("dist/*.whl")[0]).namelist()
+          if "auglab/configs/transform_params_gpu.json" not in names:
+              sys.exit("refusing to publish: wheel has no config JSONs")
+          if len([n for n in names if n.endswith(".py")]) < 20:
+              sys.exit("refusing to publish: wheel is missing modules")
+          print("wheel contents look complete")
+          PY
+
+      - name: Upload to TestPyPI
+        if: github.event_name == 'workflow_dispatch' && inputs.repository == 'testpypi'
+        env:
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.TEST_PYPI_API_TOKEN }}
+          TWINE_REPOSITORY: testpypi
+        run: twine upload dist/*
+
+      - name: Upload to PyPI
+        if: github.event_name == 'release' || (github.event_name == 'workflow_dispatch' && inputs.repository == 'pypi')
+        env:
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}
+        # Uploads the sdist as well as the wheel; auglab currently has no sdist
+        # on PyPI, which blocks anyone who needs to build from source.
+        run: twine upload dist/*