tests.yml

name: CI

on:
  push:
    branches:
      - main
      - master
  pull_request:

permissions:
  contents: read

jobs:
  quality:
    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        python-version: ["3.10", "3.11", "3.12"]

    steps:
      - name: Checkout repository
        uses: actions/checkout@v4

      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v5
        with:
          python-version: ${{ matrix.python-version }}
          cache: pip

      - name: Install dependencies
        run: |
          python -m pip install --upgrade pip
          python -m pip install -e ".[dev,pepsickle]"

      - name: Run lint checks
        run: ./lint.sh

      - name: Build distribution artifacts
        run: python -m build --sdist --wheel --no-isolation

      - name: Run public pytest subset
        run: |
          pytest -ra \
            tests/test_binding_prediction.py \
            tests/test_binding_prediction_collection.py \
            tests/test_cli_parsing_helpers.py \
            tests/test_cli_registry.py \
            tests/test_class2_allele_formats.py \
            tests/test_cli_filters.py \
            tests/test_mhc_formats.py \
            tests/test_netchop_parse.py \
            tests/test_process_helpers.py \
            tests/test_pred.py \
            tests/test_annotate_table.py \
            tests/test_prime.py \
            tests/test_mixmhc2pred2.py \
            tests/test_deeptap.py \
            tests/test_calis.py \
            tests/test_eramer.py \
            tests/test_wrapper_base.py \
            tests/test_deepimmuno.py \
            tests/test_tlimmuno2.py \
            tests/test_processing_predictor.py \
            tests/test_pepsickle.py \
            tests/test_bigmhc.py \
            tests/test_unparseable_alleles.py \
            tests/test_nettcr.py \
            tests/test_tulip.py \
            tests/test_random.py

  integration-netmhc:
    if: github.repository == 'openvax/mhctools'
    runs-on: ubuntu-22.04
    env:
      # Deterministic, cacheable location for MHCflurry model weights, shared
      # by the fetch step and the test run.
      MHCFLURRY_DATA_DIR: ${{ github.workspace }}/mhcflurry-data
    steps:
      - name: Checkout repository
        uses: actions/checkout@v4

      - name: Set up Python 3.12
        uses: actions/setup-python@v5
        with:
          python-version: "3.12"
          cache: pip

      - name: Checkout private netmhc-bundle repo
        uses: actions/checkout@v4
        with:
          repository: openvax/netmhc-bundle
          ref: v1.0.0
          token: ${{ secrets.NETMHC_BUNDLE_ACCESS_TOKEN }}
          path: netmhc-bundle

      - name: Install netmhc-bundle dependencies
        run: |
          sudo apt-get update
          sudo apt-get install -y tcsh gawk python2

      - name: Install dependencies
        run: |
          python -m pip install --upgrade pip
          python -m pip install -e ".[dev]"
          python -m pip install 'setuptools<81'

      - name: Resolve MHCflurry version for the cache key
        id: mhcflurry
        run: |
          echo "version=$(python -c 'import mhcflurry; print(mhcflurry.__version__)')" >> "$GITHUB_OUTPUT"

      - name: Cache MHCflurry model weights
        uses: actions/cache@v4
        with:
          path: ${{ github.workspace }}/mhcflurry-data
          key: mhcflurry-${{ runner.os }}-${{ steps.mhcflurry.outputs.version }}

      - name: Install MHCflurry data
        run: |
          # On a cache hit this is a no-op; on a miss, retry so a transient
          # download failure (e.g. the HTTP 504 that flaked a prior run)
          # doesn't fail the whole job.
          for attempt in 1 2 3; do
            if mhcflurry-downloads fetch; then exit 0; fi
            echo "mhcflurry-downloads fetch failed (attempt ${attempt}/3); retrying in 15s" >&2
            sleep 15
          done
          echo "mhcflurry-downloads fetch failed after 3 attempts" >&2
          exit 1

      - name: Configure netMHC tool paths
        env:
          NETMHC_BUNDLE_HOME: ${{ github.workspace }}/netmhc-bundle
        run: |
          # Wrapper scripts have hardcoded /tools/src paths; symlink so they resolve
          sudo mkdir -p /tools
          sudo ln -s "$NETMHC_BUNDLE_HOME" /tools/src

      - name: Run full test suite
        env:
          NETMHC_BUNDLE_HOME: ${{ github.workspace }}/netmhc-bundle
          NETMHC_BUNDLE_TMPDIR: ${{ github.workspace }}/netmhc-bundle-tmp
        run: |
          mkdir -p "$NETMHC_BUNDLE_TMPDIR"
          export PATH="$PATH:$NETMHC_BUNDLE_HOME/bin"
          ./test.sh

  integration-tulip:
    # Exercises the TULIP wrapper end-to-end: mhctools runs in one interpreter
    # and shells out to an ISOLATED sidecar env (torch + transformers==4.32.1)
    # holding a public TULIP-TCR checkout. TULIP is GPLv3; we clone (not vendor)
    # it here, same as running any user-provided external tool.
    runs-on: ubuntu-22.04
    env:
      # Cacheable uv wheel cache (torch/transformers are large downloads).
      UV_CACHE_DIR: ${{ github.workspace }}/.uv-cache
    steps:
      - name: Checkout repository
        uses: actions/checkout@v4

      # Python 3.11 so transformers==4.32.1's tokenizers install from a
      # prebuilt wheel (no cp312 wheel exists; a Rust build would be needed).
      - name: Set up Python 3.11
        uses: actions/setup-python@v5
        with:
          python-version: "3.11"
          cache: pip

      - name: Install mhctools
        run: |
          python -m pip install --upgrade pip
          python -m pip install -e ".[dev]"

      # Cache the uv wheel downloads (torch, transformers==4.32.1, ...). Keyed
      # on the setup script, which pins the dependency set, so a change there
      # busts the cache.
      - name: Cache uv sidecar downloads
        uses: actions/cache@v4
        with:
          path: ${{ github.workspace }}/.uv-cache
          key: uv-${{ runner.os }}-py311-${{ hashFiles('scripts/setup_tulip_env.sh') }}

      # Cache the public TULIP-TCR checkout (~100 MB with weights + data). The
      # setup script skips cloning when predict.py is already present. Bump the
      # -v1 suffix to force a fresh clone.
      - name: Cache TULIP-TCR checkout
        uses: actions/cache@v4
        with:
          path: ${{ github.workspace }}/TULIP-TCR
          key: tulip-tcr-${{ runner.os }}-v1

      - name: Build isolated TULIP sidecar env + clone TULIP-TCR
        env:
          # This job's `python` is already 3.11; use it for the sidecar env.
          TULIP_SETUP_PYTHON: python
        run: |
          python -m pip install uv
          scripts/setup_tulip_env.sh "${{ github.workspace }}/tulip-env" \
            "${{ github.workspace }}/TULIP-TCR"

      - name: Run TULIP wrapper tests (incl. end-to-end)
        env:
          TULIP_HOME: ${{ github.workspace }}/TULIP-TCR
          TULIP_PYTHON: ${{ github.workspace }}/tulip-env/bin/python
        run: |
          python -m pytest tests/test_tulip.py -ra