mrnavax 0.14.0__tar.gz

mrnavax-0.14.0/.github/workflows/docs.yml

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+name: docs
+
+on:
+  push:
+    branches: [main]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+concurrency:
+  group: pages
+  cancel-in-progress: true
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e ".[docs]"
+
+      - name: Build
+        run: mkdocs build --strict
+
+      - uses: actions/upload-pages-artifact@v3
+        with:
+          path: site
+
+  deploy:
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    steps:
+      - id: deployment
+        uses: actions/deploy-pages@v4

mrnavax-0.14.0/.github/workflows/publish.yml

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+name: publish
+
+# Publish Python distribution to PyPI via Trusted Publishing (OIDC).
+# Triggered ONLY by tag pushes (e.g. `git tag v0.13.1 && git push --tags`).
+#
+# Setup (one-time, requires PyPI admin):
+#   1. Go to https://pypi.org/manage/account/publishing/
+#   2. Register a new pending trusted publisher:
+#        - Owner:       rollroyces
+#        - Repository:  mrnavax
+#        - Workflow:    publish.yml   <-- THIS file
+#        - Environment: pypi
+#   3. Create the matching GitHub Environment in repo Settings → Environments:
+#        - "pypi" — require manual approval before deploy (recommended)
+#
+# Then future workflow:
+#   git tag vX.Y.Z && git push --tags
+#   # → builds dist → uploads to PyPI automatically (after approval).
+
+on:
+  push:
+    tags:
+      - 'v*'
+
+# Cancel any in-flight publish run when a new tag is pushed.
+concurrency:
+  group: publish
+  cancel-in-progress: false  # never cancel a partially-completed PyPI upload
+
+# Required for OIDC token (Trusted Publishing).
+permissions:
+  contents: read
+  id-token: write
+
+jobs:
+  build:
+    name: Build distribution
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          persist-credentials: false
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install build
+        run: python -m pip install --upgrade pip build
+
+      - name: Build sdist + wheel
+        run: python -m build --sdist --wheel
+
+      - name: Verify built artifacts
+        run: |
+          ls -lh dist/
+          # Sanity-check that the wheel version matches the git tag.
+          WHL_VER=$(python -c "import tomllib; print(tomllib.load(open('pyproject.toml','rb'))['project']['version'])")
+          TAG_VER=${GITHUB_REF_NAME#v}
+          echo "pyproject version: $WHL_VER"
+          echo "git tag version:   $TAG_VER"
+          if [ "$WHL_VER" != "$TAG_VER" ]; then
+            echo "::error::pyproject.toml version ($WHL_VER) does not match git tag ($TAG_VER)"
+            exit 1
+          fi
+
+      - name: Upload artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+          if-no-files-found: error
+
+  publish-to-pypi:
+    name: Publish to PyPI
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      # Manual approval gate is configured under repo Settings → Environments → pypi
+      name: pypi
+      url: https://pypi.org/project/mrnavax/
+
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+

mrnavax-0.14.0/.github/workflows/smoke.yml

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+name: smoke
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  smoke:
+    name: python ${{ matrix.python-version }}
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.11", "3.12", "3.13", "3.14"]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: CLI help (sanity)
+        run: |
+          python -m mrnavax.cli --help
+          for tool in codon neoantigen trial lnp scrna; do
+            python -m mrnavax.cli $tool --help
+          done
+
+      - name: Codon analyze
+        run: |
+          python -m mrnavax.cli codon \
+            --sequence mrnavax/examples/cas9.fasta \
+            --out /tmp/cas9_analysis.json
+          test -s /tmp/cas9_analysis.json
+          python -c "import json; d=json.load(open('/tmp/cas9_analysis.json')); assert d['n_codons']>0; assert 0<=d['cai']<=1; print('codon OK:', d['cai'])"
+
+      - name: Codon optimize
+        run: |
+          python -m mrnavax.cli codon \
+            --sequence mrnavax/examples/cas9.fasta --optimize \
+            --out /tmp/cas9_optimized.json
+          python -c "import json; d=json.load(open('/tmp/cas9_optimized.json')); assert d['after']['cai']>d['before']['cai']; print('optimize OK:', d['before']['cai'],'->',d['after']['cai'])"
+
+      - name: Neoantigen screen (mock)
+        run: |
+          python -m mrnavax.cli neoantigen \
+            --variants mrnavax/examples/tp53_variants.csv \
+            --hla HLA-A*02:01 --backend mock \
+            --out /tmp/tp53_screen.json
+          python -c "import json; d=json.load(open('/tmp/tp53_screen.json')); assert len(d['candidates'])>=5; print('neoantigen OK:', len(d['candidates']),'calls')"
+
+      - name: Trial match (mock)
+        run: |
+          python -m mrnavax.cli trial \
+            --patient mrnavax/examples/patient_summary.txt \
+            --trials mrnavax/examples/trials.jsonl --top-k 5 \
+            --backend mock \
+            --out /tmp/trial_match.json
+          python -c "import json; d=json.load(open('/tmp/trial_match.json')); assert len(d['ranked'])>=1; print('trial OK:', d['ranked'][0]['nct_id'])"
+
+      - name: LNP advise
+        run: |
+          for target in liver lung tumor; do
+            python -m mrnavax.cli lnp --target $target --cargo mRNA \
+              --intent "cancer vaccine" --out /tmp/lnp_$target.json
+          done
+          python -c "import json; d=json.load(open('/tmp/lnp_lung.json')); assert d['shortlist']; print('lnp OK:', len(d['shortlist']),'candidates')"
+
+      - name: scRNA pipeline
+        run: |
+          python -m mrnavax.cli scrna \
+            --expression mrnavax/examples/cells.csv \
+            --variants mrnavax/examples/variants_coding.csv \
+            --proteins mrnavax/examples/proteins.fasta \
+            --tumor-markers TP53,KRAS,BRAF \
+            --out /tmp/scrna.json
+          python -c "import json; d=json.load(open('/tmp/scrna.json')); assert d['n_cells']>0; assert d['n_candidate_peptides']>0; assert 'tumor_cluster' in d; print('scrna OK:', d['n_candidate_peptides'],'peptides from cluster', d['tumor_cluster'])"
+
+      - name: Backend integrity check (network-free)
+        env:
+          MRNA_AI_FORCE_MOCK: "1"
+          MRNA_AI_SKIP_MEDCPT_CHECK: "1"
+        run: |
+          python -m mrnavax.backends --check-all
+          # Also install-validate each optional extra's import path (without invoking models).
+          python -c "
+          # Stdlib-only core must work
+          from mrnavax import codon_optimizer, neoantigen_screener, trial_matcher, lnp_advisor, sc_rna_pipeline, llm, backends
+          print('core imports: OK')
+
+          # Optional: confirm mhcflurry is callable as a function even when not installed
+          from mrnavax.neoantigen_screener import _mhcflurry_available
+          print('mhcflurry_available():', _mhcflurry_available())
+          "

mrnavax-0.14.0/.gitignore

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+__pycache__/
+*.pyc
+.venv*/
+dist/
+build/
+site/
+.eggs/
+*.egg-info/
+outputs/*.json
+outputs/*.csv
+outputs/*.txt
+.env
+
+# macOS Finder metadata
+.DS_Store