Make llvm not default for Rust

.github/workflows/julia-release.yml

@@ -97,8 +97,38 @@ jobs:
       - name: Set up Rust
         run: rustup show
 
-      - name: Setup LLVM 14.0.6
-        uses: ./.github/actions/setup-llvm
+      - name: Install LLVM 14.0.6 using pecos-llvm (Unix)
+        if: runner.os != 'Windows'
+        run: |
+          echo "Installing LLVM using pecos-llvm-utils..."
+          cargo run -p pecos-llvm-utils --bin pecos-llvm --release -- install
+
+          echo "Setting LLVM environment variables..."
+          export PECOS_LLVM=$(cargo run -p pecos-llvm-utils --bin pecos-llvm --release -- find 2>/dev/null)
+          export LLVM_SYS_140_PREFIX="$PECOS_LLVM"
+
+          echo "PECOS_LLVM=$PECOS_LLVM" >> $GITHUB_ENV
+          echo "LLVM_SYS_140_PREFIX=$LLVM_SYS_140_PREFIX" >> $GITHUB_ENV
+
+          echo "Verifying LLVM installation..."
+          cargo run -p pecos-llvm-utils --bin pecos-llvm --release -- check
+
+      - name: Install LLVM 14.0.6 using pecos-llvm (Windows)
+        if: runner.os == 'Windows'
+        shell: pwsh
+        run: |
+          Write-Host "Installing LLVM using pecos-llvm-utils..."
+          cargo run -p pecos-llvm-utils --bin pecos-llvm --release -- install
+
+          Write-Host "Setting LLVM environment variables..."
+          $env:PECOS_LLVM = (cargo run -p pecos-llvm-utils --bin pecos-llvm --release -- find 2>$null)
+          $env:LLVM_SYS_140_PREFIX = $env:PECOS_LLVM
+
+          "PECOS_LLVM=$env:PECOS_LLVM" | Out-File -FilePath $env:GITHUB_ENV -Encoding utf8 -Append
+          "LLVM_SYS_140_PREFIX=$env:LLVM_SYS_140_PREFIX" | Out-File -FilePath $env:GITHUB_ENV -Encoding utf8 -Append
+
+          Write-Host "Verifying LLVM installation..."
+          cargo run -p pecos-llvm-utils --bin pecos-llvm --release -- check
 
       - name: Install Rust target
         run: |

.github/workflows/julia-test.yml

@@ -57,8 +57,38 @@ jobs:
     - name: Set up Rust
       run: rustup show
 
-    - name: Setup LLVM 14.0.6
-      uses: ./.github/actions/setup-llvm
+    - name: Install LLVM 14.0.6 using pecos-llvm (Unix)
+      if: runner.os != 'Windows'
+      run: |
+        echo "Installing LLVM using pecos-llvm-utils..."
+        cargo run -p pecos-llvm-utils --bin pecos-llvm --release -- install
+
+        echo "Setting LLVM environment variables..."
+        export PECOS_LLVM=$(cargo run -p pecos-llvm-utils --bin pecos-llvm --release -- find 2>/dev/null)
+        export LLVM_SYS_140_PREFIX="$PECOS_LLVM"
+
+        echo "PECOS_LLVM=$PECOS_LLVM" >> $GITHUB_ENV
+        echo "LLVM_SYS_140_PREFIX=$LLVM_SYS_140_PREFIX" >> $GITHUB_ENV
+
+        echo "Verifying LLVM installation..."
+        cargo run -p pecos-llvm-utils --bin pecos-llvm --release -- check
+
+    - name: Install LLVM 14.0.6 using pecos-llvm (Windows)
+      if: runner.os == 'Windows'
+      shell: pwsh
+      run: |
+        Write-Host "Installing LLVM using pecos-llvm-utils..."
+        cargo run -p pecos-llvm-utils --bin pecos-llvm --release -- install
+
+        Write-Host "Setting LLVM environment variables..."
+        $env:PECOS_LLVM = (cargo run -p pecos-llvm-utils --bin pecos-llvm --release -- find 2>$null)
+        $env:LLVM_SYS_140_PREFIX = $env:PECOS_LLVM
+
+        "PECOS_LLVM=$env:PECOS_LLVM" | Out-File -FilePath $env:GITHUB_ENV -Encoding utf8 -Append
+        "LLVM_SYS_140_PREFIX=$env:LLVM_SYS_140_PREFIX" | Out-File -FilePath $env:GITHUB_ENV -Encoding utf8 -Append
+
+        Write-Host "Verifying LLVM installation..."
+        cargo run -p pecos-llvm-utils --bin pecos-llvm --release -- check
 
     - name: Cache Rust
       uses: Swatinem/rust-cache@v2

.github/workflows/python-test.yml

@@ -57,8 +57,38 @@ jobs:
       with:
         workspaces: python/pecos-rslib
 
-    - name: Setup LLVM 14.0.6
-      uses: ./.github/actions/setup-llvm
+    - name: Install LLVM 14.0.6 using pecos-llvm (Unix)
+      if: runner.os != 'Windows'
+      run: |
+        echo "Installing LLVM using pecos-llvm-utils..."
+        cargo run -p pecos-llvm-utils --bin pecos-llvm --release -- install
+
+        echo "Setting LLVM environment variables..."
+        export PECOS_LLVM=$(cargo run -p pecos-llvm-utils --bin pecos-llvm --release -- find 2>/dev/null)
+        export LLVM_SYS_140_PREFIX="$PECOS_LLVM"
+
+        echo "PECOS_LLVM=$PECOS_LLVM" >> $GITHUB_ENV
+        echo "LLVM_SYS_140_PREFIX=$LLVM_SYS_140_PREFIX" >> $GITHUB_ENV
+
+        echo "Verifying LLVM installation..."
+        cargo run -p pecos-llvm-utils --bin pecos-llvm --release -- check
+
+    - name: Install LLVM 14.0.6 using pecos-llvm (Windows)
+      if: runner.os == 'Windows'
+      shell: pwsh
+      run: |
+        Write-Host "Installing LLVM using pecos-llvm-utils..."
+        cargo run -p pecos-llvm-utils --bin pecos-llvm --release -- install
+
+        Write-Host "Setting LLVM environment variables..."
+        $env:PECOS_LLVM = (cargo run -p pecos-llvm-utils --bin pecos-llvm --release -- find 2>$null)
+        $env:LLVM_SYS_140_PREFIX = $env:PECOS_LLVM
+
+        "PECOS_LLVM=$env:PECOS_LLVM" | Out-File -FilePath $env:GITHUB_ENV -Encoding utf8 -Append
+        "LLVM_SYS_140_PREFIX=$env:LLVM_SYS_140_PREFIX" | Out-File -FilePath $env:GITHUB_ENV -Encoding utf8 -Append
+
+        Write-Host "Verifying LLVM installation..."
+        cargo run -p pecos-llvm-utils --bin pecos-llvm --release -- check
 
     - name: Build and test PECOS (Windows)
       if: runner.os == 'Windows'
@@ -86,6 +116,9 @@ jobs:
         # Also ensure LLVM bin is in PATH
         $llvmBinDir = Join-Path -Path $env:LLVM_SYS_140_PREFIX -ChildPath "bin"
         if (Test-Path $llvmBinDir) {
+          # Update PATH for current session (so pytest can find llvm-as)
+          $env:PATH = "$llvmBinDir;$env:PATH"
+          # Update PATH for future steps
           "$llvmBinDir" | Out-File -FilePath $env:GITHUB_PATH -Encoding utf8 -Append
           Write-Host "Added LLVM bin to PATH: $llvmBinDir"
         }
@@ -227,7 +260,7 @@ jobs:
             if [ -f "$lib" ]; then
               libname=$(basename "$lib")
               if otool -L "$lib" 2>/dev/null | grep -q "libunwind"; then
-                echo "  ⚠️  $libname HAS libunwind reference:"
+                echo "  [WARNING] $libname HAS libunwind reference:"
                 otool -L "$lib" | grep libunwind
               fi
             fi
@@ -293,10 +326,10 @@ jobs:
 
               exit 1
             else
-              echo "✅ SUCCESS: No @rpath/libunwind reference found!"
+              echo "[OK] No @rpath/libunwind reference found"
             fi
           else
-            echo "⚠️  WARNING: Could not find extension module to check"
+            echo "[WARNING] Could not find extension module to check"
           fi
         fi
 

.github/workflows/rust-test.yml

@@ -49,8 +49,20 @@ jobs:
         with:
           save-if: ${{ github.ref_name == 'master' || github.ref_name == 'development' || github.ref_name == 'dev' }}
 
-      - name: Setup LLVM 14.0.6
-        uses: ./.github/actions/setup-llvm
+      - name: Install LLVM 14.0.6 using pecos-llvm
+        run: |
+          echo "Installing LLVM using pecos-llvm-utils..."
+          cargo run -p pecos-llvm-utils --bin pecos-llvm --release -- install
+
+          echo "Setting LLVM environment variables..."
+          export PECOS_LLVM=$(cargo run -p pecos-llvm-utils --bin pecos-llvm --release -- find 2>/dev/null)
+          export LLVM_SYS_140_PREFIX="$PECOS_LLVM"
+
+          echo "PECOS_LLVM=$PECOS_LLVM" >> $GITHUB_ENV
+          echo "LLVM_SYS_140_PREFIX=$LLVM_SYS_140_PREFIX" >> $GITHUB_ENV
+
+          echo "Verifying LLVM installation..."
+          cargo run -p pecos-llvm-utils --bin pecos-llvm --release -- check
 
       - name: Install rustfmt
         run: rustup component add rustfmt
@@ -62,7 +74,13 @@ jobs:
         run: rustup component add clippy
 
       - name: Run clippy
-        run: cargo clippy --workspace --all-targets -- -D warnings
+        run: |
+          echo "Running clippy with all features (including LLVM)..."
+          cargo clippy --workspace --exclude pecos --exclude pecos-quest --all-targets --all-features -- -D warnings
+          echo "Running clippy on pecos with all non-GPU features..."
+          cargo clippy -p pecos --all-targets --features "llvm,selene,qasm,phir,all-simulators" -- -D warnings
+          echo "Running clippy on pecos-quest with CPU features only..."
+          cargo clippy -p pecos-quest --all-targets --features "cpu" -- -D warnings
 
   rust-lint-no-llvm:
     runs-on: ubuntu-latest
@@ -179,8 +197,38 @@ jobs:
         with:
           save-if: ${{ github.ref_name == 'master' || github.ref_name == 'development' || github.ref_name == 'dev' }}
 
-      - name: Setup LLVM 14.0.6
-        uses: ./.github/actions/setup-llvm
+      - name: Install LLVM 14.0.6 using pecos-llvm (Unix)
+        if: matrix.os != 'windows-latest'
+        run: |
+          echo "Installing LLVM using pecos-llvm-utils..."
+          cargo run -p pecos-llvm-utils --bin pecos-llvm --release -- install
+
+          echo "Setting LLVM environment variables..."
+          export PECOS_LLVM=$(cargo run -p pecos-llvm-utils --bin pecos-llvm --release -- find 2>/dev/null)
+          export LLVM_SYS_140_PREFIX="$PECOS_LLVM"
+
+          echo "PECOS_LLVM=$PECOS_LLVM" >> $GITHUB_ENV
+          echo "LLVM_SYS_140_PREFIX=$LLVM_SYS_140_PREFIX" >> $GITHUB_ENV
+
+          echo "Verifying LLVM installation..."
+          cargo run -p pecos-llvm-utils --bin pecos-llvm --release -- check
+
+      - name: Install LLVM 14.0.6 using pecos-llvm (Windows)
+        if: matrix.os == 'windows-latest'
+        shell: pwsh
+        run: |
+          Write-Host "Installing LLVM using pecos-llvm-utils..."
+          cargo run -p pecos-llvm-utils --bin pecos-llvm --release -- install
+
+          Write-Host "Setting LLVM environment variables..."
+          $env:PECOS_LLVM = (cargo run -p pecos-llvm-utils --bin pecos-llvm --release -- find 2>$null)
+          $env:LLVM_SYS_140_PREFIX = $env:PECOS_LLVM
+
+          "PECOS_LLVM=$env:PECOS_LLVM" | Out-File -FilePath $env:GITHUB_ENV -Encoding utf8 -Append
+          "LLVM_SYS_140_PREFIX=$env:LLVM_SYS_140_PREFIX" | Out-File -FilePath $env:GITHUB_ENV -Encoding utf8 -Append
+
+          Write-Host "Verifying LLVM installation..."
+          cargo run -p pecos-llvm-utils --bin pecos-llvm --release -- check
 
       - name: Set up Visual Studio environment on Windows
         if: matrix.os == 'windows-latest'
@@ -203,11 +251,16 @@ jobs:
 
           echo "RUSTFLAGS: $RUSTFLAGS"
 
-          cargo test --no-run
+          cargo test --no-run --workspace --exclude pecos-quest --exclude pecos-decoders --features llvm
+          cargo test --no-run -p pecos-quest --features cpu
+          cargo test --no-run -p pecos-decoders --all-features
 
       - name: Compile tests (Linux/Windows)
         if: matrix.os != 'macos-latest'
-        run: cargo test --no-run
+        run: |
+          cargo test --no-run --workspace --exclude pecos-quest --exclude pecos-decoders --features llvm
+          cargo test --no-run -p pecos-quest --features cpu
+          cargo test --no-run -p pecos-decoders --all-features
 
       - name: Run tests (macOS)
         if: matrix.os == 'macos-latest'
@@ -222,23 +275,32 @@ jobs:
           unset PKG_CONFIG_PATH
           export LIBRARY_PATH=/usr/lib
 
-          cargo test --workspace
+          cargo test --workspace --exclude pecos-quest --exclude pecos-decoders --features llvm
+          cargo test -p pecos-quest --features cpu
+          cargo test -p pecos-decoders --all-features
 
       - name: Run tests (Linux)
         if: matrix.os == 'ubuntu-latest'
-        run: cargo test --workspace
+        run: |
+          cargo test --workspace --exclude pecos-quest --exclude pecos-decoders --features llvm
+          cargo test -p pecos-quest --features cpu
+          cargo test -p pecos-decoders --all-features
 
       - name: Run tests (Windows)
         if: matrix.os == 'windows-latest'
         run: |
           # Run all non-doctest tests
-          cargo test --workspace --exclude pecos-rslib --lib --bins --tests --examples
+          cargo test --workspace --exclude pecos-quest --exclude pecos-decoders --exclude pecos-rslib --features llvm --lib --bins --tests --examples
+          cargo test -p pecos-quest --features cpu --lib --bins --tests --examples
+          cargo test -p pecos-decoders --all-features --lib --bins --tests --examples
 
           # For Windows, we need to run doctests for the pecos crate specially
           # to ensure they run from the crate directory
           cd crates/pecos
-          cargo test --doc
+          cargo test --doc --features llvm
           cd ../..
 
           # Run doctests for other crates normally
-          cargo test --workspace --exclude pecos-rslib --exclude pecos --doc
+          cargo test --workspace --exclude pecos-quest --exclude pecos-decoders --exclude pecos-rslib --exclude pecos --features llvm --doc
+          cargo test -p pecos-quest --doc
+          cargo test -p pecos-decoders --all-features --doc