dual_threshold_optimization 2.0.1

Dual Threshold Optimization compares two ranked lists of features (e.g. genes) to determine the rank threshold for each list that minimizes the hypergeometric p-value of the overlap of features. It then calculates a permutation based empirical p-value and an FDR. Details can be found [in this paper](https://doi.org/10.1101/gr.259655.119)
Documentation 
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name: Rust Release

on:
  push:
    branches:
      - main
  
env:
  GH_TOKEN: ${{ github.token }}

jobs:
  build:
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        os: [ubuntu-latest, macos-latest, windows-latest]
        feature: ["default", mpi]

    steps:
      # Step 1: Checkout the code
      - name: Checkout
        uses: actions/checkout@v3

      # Step 2: Install OpenMPI (for mpi feature only)
      - name: Install OpenMPI
        if: matrix.feature == 'mpi' && runner.os == 'Linux'
        run: |
          sudo apt-get update \
          && sudo apt-get install -y libopenmpi-dev openmpi-bin

      # Step 3: Cache Rust dependencies
      - name: Cache Rust dependencies
        uses: actions/cache@v3
        with:
          path: target
          key: ${{ runner.OS }}-${{ matrix.feature }}-build-${{ hashFiles('**/Cargo.lock') }}
          restore-keys: |
            ${{ runner.OS }}-${{ matrix.feature }}-build-

      # Step 4: Install Rust toolchain
      - name: Install Rust toolchain
        uses: actions-rs/toolchain@v1
        with:
          toolchain: beta
          default: true
          override: true
          target: ${{ matrix.os == 'macos-latest' && 'x86_64-apple-darwin' || matrix.os == 'windows-latest' && 'x86_64-pc-windows-msvc' || '' }}

      # Step 5: Build the binary with features
      - name: Build
        shell: bash
        run: |
          if [ "${{ matrix.feature }}" == "mpi" ] && [ "${{ matrix.os }}" != "ubuntu-latest" ]; then
            echo "Skipping mpi build for non-Linux systems"
            exit 0
          fi
          cargo build --release ${{ matrix.feature == 'mpi' && '--features mpi' || '' }}
          mv target/release/dual_threshold_optimization \
            target/release/dual_threshold_optimization-${{ matrix.os }}-${{ matrix.feature }}${{ runner.os == 'Windows' && '.exe' || '' }}

      # Step 6: Upload artifact
      - name: Upload artifact
        uses: actions/upload-artifact@v3
        if: success()
        with:
          name: dual_threshold_optimization-${{ matrix.os }}-${{ matrix.feature }}
          path: target/release/dual_threshold_optimization-${{ matrix.os }}-${{ matrix.feature }}${{ runner.os == 'Windows' && '.exe' || '' }}

  release:
    runs-on: ubuntu-latest
    needs: [build]

    steps:
      # Step 1: Checkout the code
      - name: Checkout
        uses: actions/checkout@v3

      # Step 2: Extract version from Cargo.toml
      - name: Get version from Cargo.toml
        id: version
        run: |
          VERSION=$(grep '^version =' Cargo.toml | head -n 1 | cut -d '"' -f 2)
          echo "VERSION=$VERSION"
          echo "version=$VERSION" >> $GITHUB_ENV

      # Step 3: Create a release
      - name: Create GitHub release
        uses: actions/create-release@v1
        env:
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
        with:
          tag_name: "v${{ env.version }}"
          release_name: "${{ env.version }}"
          draft: false
          prerelease: false

      # Step 4: Download artifacts from build jobs
      - name: Download artifacts
        uses: actions/download-artifact@v3
        with:
          path: binaries

      # Step 5: Upload binaries to the release
      - name: Upload binaries to release
        run: |
          for file in binaries/*/*; do
            if [ -f "$file" ]; then
              echo "Uploading $file"
              gh release upload "v${{ env.version }}" "$file" --clobber
            fi
          done