Prepare CLEAR Nature publication release

.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+  pull_request:
+
+permissions:
+  contents: read
+
+jobs:
+  test:
+    name: Test (Python ${{ matrix.python-version }})
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]
+
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: pip
+      - name: Install package and test dependencies
+        run: python -m pip install --upgrade pip && python -m pip install -e ".[test]"
+      - name: Run unit tests
+        run: python -m pytest
+
+  package:
+    name: Validate distributions
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+          cache: pip
+      - name: Install build tools
+        run: python -m pip install --upgrade pip build twine
+      - name: Build source and wheel distributions
+        run: python -m build
+      - name: Inspect wheel contents
+        shell: python
+        run: |
+          import glob
+          import zipfile
+
+          wheel, = glob.glob("dist/*.whl")
+          with zipfile.ZipFile(wheel) as archive:
+              names = set(archive.namelist())
+          required = {
+              "clear/__init__.py",
+              "clear/hub.py",
+              "clear/concepts.py",
+              "clear/bpe_simple_vocab_16e6.txt.gz",
+          }
+          missing = required.difference(names)
+          if missing:
+              raise SystemExit(f"wheel is missing required files: {sorted(missing)}")
+      - name: Validate distribution metadata
+        run: python -m twine check dist/*

CITATION.cff

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+cff-version: 1.2.0
+message: "If you use CLEAR, please cite the Nature Biomedical Engineering article."
+title: "CLEAR: Concept-Level Embeddings for Auditable Radiology"
+type: software
+authors:
+  - family-names: Han
+    given-names: Tianyu
+    orcid: "https://orcid.org/0000-0002-8636-6462"
+  - family-names: Wu
+    given-names: Riga
+  - family-names: Tian
+    given-names: Yu
+  - family-names: Khader
+    given-names: Firas
+  - family-names: Adams
+    given-names: Lisa C.
+    orcid: "https://orcid.org/0000-0001-5836-4542"
+  - family-names: Bressem
+    given-names: Keno K.
+    orcid: "https://orcid.org/0000-0001-9249-8624"
+  - family-names: Davatzikos
+    given-names: Christos
+    orcid: "https://orcid.org/0000-0002-1025-8561"
+  - family-names: Kather
+    given-names: Jakob Nikolas
+  - family-names: Shen
+    given-names: Li
+    orcid: "https://orcid.org/0000-0002-5443-0503"
+  - family-names: Mankoff
+    given-names: David A.
+  - family-names: Barbosa
+    given-names: Eduardo Mortani
+    name-suffix: Jr.
+  - family-names: Truhn
+    given-names: Daniel
+    orcid: "https://orcid.org/0000-0002-9605-0728"
+repository-code: "https://github.com/peterhan91/CLEAR"
+url: "https://github.com/peterhan91/CLEAR"
+license: Apache-2.0
+version: 0.1.0
+preferred-citation:
+  type: article
+  authors:
+    - family-names: Han
+      given-names: Tianyu
+    - family-names: Wu
+      given-names: Riga
+    - family-names: Tian
+      given-names: Yu
+    - family-names: Khader
+      given-names: Firas
+    - family-names: Adams
+      given-names: Lisa C.
+    - family-names: Bressem
+      given-names: Keno K.
+    - family-names: Davatzikos
+      given-names: Christos
+    - family-names: Kather
+      given-names: Jakob Nikolas
+    - family-names: Shen
+      given-names: Li
+    - family-names: Mankoff
+      given-names: David A.
+    - family-names: Barbosa
+      given-names: Eduardo Mortani
+      name-suffix: Jr.
+    - family-names: Truhn
+      given-names: Daniel
+  title: "CLEAR: an auditable foundation model for radiology grounded in clinical concepts"
+  journal: Nature Biomedical Engineering
+  year: 2026
+  doi: "10.1038/s41551-026-01741-4"
+  url: "https://doi.org/10.1038/s41551-026-01741-4"