Numpy req

.github/workflows/python-release.yml

@@ -1,7 +1,7 @@
 name: Python Artifacts
 
 env:
-  TRIGGER_ON_PR_PUSH: false  # Set to true to enable triggers on PR pushes
+  TRIGGER_ON_PR_PUSH: true  # Set to true to enable triggers on PR pushes
   PYTHON_VERSION: '3.10'
 
 on:

.github/workflows/python-test.yml

@@ -1,5 +1,11 @@
 name: Python test / linting
 
+env:
+  TRIGGER_ON_PR_PUSH: true  # Set to true to enable triggers on PR pushes
+  RUSTFLAGS: -C debuginfo=0
+  RUST_BACKTRACE: 1
+  PYTHONUTF8: 1
+
 on:
   push:
     branches: [ "master", "development" ]
@@ -22,19 +28,12 @@ concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
 
-
-env:
-  RUSTFLAGS: -C debuginfo=0
-  RUST_BACKTRACE: 1
-  PYTHONUTF8: 1
-
 defaults:
   run:
     shell: bash
 
 jobs:
   python-test:
-
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
@@ -50,25 +49,10 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
 
-    - name: Create and activate virtual environment
-      env:
-        BIN: ${{ matrix.os == 'windows-latest' && 'Scripts' || 'bin' }}
-      run: |
-          python -m venv .venv
-          source .venv/$BIN/activate
-          echo "$GITHUB_WORKSPACE/.venv/$BIN" >> $GITHUB_PATH
-          echo "VIRTUAL_ENV=$GITHUB_WORKSPACE/.venv" >> $GITHUB_ENV
-
-    - name: Install Python dependencies
-      run: |
-        python -m pip install --upgrade pip setuptools
-        pip install maturin pre-commit
-        echo "Temporarily removing pecos-rslib from requirements... because we need to build it"
-        grep -v "pecos-rslib" python/quantum-pecos/requirements.txt > temp_requirements.txt
-        echo "Installing project requirements (excluding pecos-rslib)..."
-        pip install -r temp_requirements.txt
-        echo "Cleaning up temporary files..."
-        rm temp_requirements.txt
+    - name: Install the latest version of uv
+      uses: astral-sh/setup-uv@v4
+      with:
+        enable-cache: true
 
     - name: Set up Rust
       run: rustup show
@@ -78,23 +62,34 @@ jobs:
       with:
           workspaces: python/pecos-rslib
 
-    - name: Install pecos-rslib with maturin develop
+    - name: Generate lockfile and install dependencies
+      run: |
+        uv lock --project .
+        uv sync --project .
+
+    - name: Install pecos-rslib with maturin
       run: |
         cd python/pecos-rslib
-        maturin develop
+        uv run maturin develop --uv
 
-    - name: Install pure Python PECOS
-      run: pip install ./python/quantum-pecos/
+    - name: Install quantum-pecos
+      run: |
+        cd python/quantum-pecos
+        uv pip install -e .
 
     - name: Run pre-commit checks
+      run: uv run pre-commit run --all-files --show-diff-on-failure
+
+    - name: Install test dependencies
       run: |
-        pre-commit run --all-files --show-diff-on-failure
+        cd python/quantum-pecos
+        uv pip install -e .[all,test]  # Install with both all and test extras
+        uv pip install pytest pytest-cov  # Explicitly install test requirements
 
     - name: Run standard tests
       run: |
-        pytest ./python/tests --doctest-modules --junitxml=junit/test-results.xml --cov=com --cov-report=xml --cov-report=html
+        uv run pytest ./python/tests --doctest-modules --junitxml=junit/test-results.xml --cov=com --cov-report=xml --cov-report=html
 
-    - name: Run tests with optional dependencies
+    - name: Run optional dependency tests
       run: |
-        pip install ./python/quantum-pecos/[all]
-        pytest ./python/tests --doctest-modules --junitxml=junit/test-results.xml --cov=com --cov-report=xml --cov-report=html -m optional_dependency
+        uv run pytest ./python/tests --doctest-modules --junitxml=junit/test-results.xml --cov=com --cov-report=xml --cov-report=html -m optional_dependency

.github/workflows/rust-test.yml

@@ -1,5 +1,10 @@
 name: Rust test / linting
 
+env:
+  TRIGGER_ON_PR_PUSH: true  # Set to true to enable triggers on PR pushes
+  RUSTFLAGS: -C debuginfo=0
+  RUST_BACKTRACE: 1
+
 on:
   push:
     branches: [ "master", "development" ]
@@ -22,16 +27,18 @@ concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
 
-env:
-  RUSTFLAGS: -C debuginfo=0
-  RUST_BACKTRACE: 1
-
 jobs:
   rust-lint:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
 
+      - name: Install Rust (for local testing)
+        run: |
+          curl https://sh.rustup.rs -sSf | sh -s -- -y
+          echo "$HOME/.cargo/bin" >> $GITHUB_PATH
+          export PATH="$HOME/.cargo/bin:$PATH"
+
       - name: Set up Rust
         run: rustup override set stable && rustup update
 
@@ -76,6 +83,21 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
+      - name: Install Rust (for local testing)
+        if: matrix.os == 'windows-latest'
+        run: |
+          curl -sSf -o rustup-init.exe https://win.rustup.rs
+          ./rustup-init.exe -y --default-toolchain stable --profile minimal
+          echo "$HOME\.cargo\bin" | Out-File -FilePath $env:GITHUB_PATH -Encoding utf8 -Append
+          $env:Path += ";$HOME\.cargo\bin"
+
+      - name: Install Rust (for local testing)
+        if: matrix.os != 'windows-latest'
+        run: |
+          curl https://sh.rustup.rs -sSf | sh -s -- -y
+          echo "$HOME/.cargo/bin" >> $GITHUB_PATH
+          export PATH="$HOME/.cargo/bin:$PATH"
+
       - name: Set up Rust
         run: rustup show
 
@@ -84,8 +106,132 @@ jobs:
         with:
           save-if: ${{ github.ref_name == 'master' || github.ref_name == 'development' }}
 
+      - name: Install LLVM Tools (Ubuntu)
+        if: matrix.os == 'ubuntu-latest'
+        run: |
+          sudo apt-get update
+          # Add LLVM 14 repository
+          wget -O - https://apt.llvm.org/llvm-snapshot.gpg.key | sudo apt-key add -
+          sudo add-apt-repository "deb http://apt.llvm.org/jammy/ llvm-toolchain-jammy-14 main"
+          sudo apt-get update
+          # Install LLVM 14 specifically
+          sudo apt-get install -y llvm-14 clang-14
+          # Create symlinks for llc and clang
+          sudo update-alternatives --install /usr/bin/llc llc /usr/bin/llc-14 100
+          sudo update-alternatives --install /usr/bin/clang clang /usr/bin/clang-14 100
+          # Verify installation
+          which llc
+          llc --version
+
+      - name: Install LLVM Tools (macOS)
+        if: matrix.os == 'macos-latest'
+        run: |
+          brew install llvm@14
+          echo "$(brew --prefix llvm@14)/bin" >> $GITHUB_PATH
+          # Make sure it's available in the current step too
+          export PATH="$(brew --prefix llvm@14)/bin:$PATH"
+          which llc
+          llc --version
+
+      - name: Install LLVM Tools (Windows)
+        if: matrix.os == 'windows-latest'
+        uses: KyleMayes/install-llvm-action@v2
+        with:
+          version: "14.0"
+          directory: ${{ runner.temp }}/llvm
+          env: true
+
+      - name: Setup LLVM Path (Windows)
+        if: matrix.os == 'windows-latest'
+        run: |
+          Write-Host "Setting up LLVM in PATH..."
+
+          # Display LLVM_PATH environment variable set by the action
+          Write-Host "LLVM_PATH environment variable: $env:LLVM_PATH"
+
+          # Add LLVM bin directory to PATH for this and subsequent steps
+          $llvmBinDir = Join-Path -Path $env:LLVM_PATH -ChildPath "bin"
+
+          # Verify the directory exists
+          if (Test-Path -Path $llvmBinDir) {
+            Write-Host "LLVM bin directory exists at $llvmBinDir"
+            # List contents to verify what's available
+            Write-Host "LLVM bin directory contents:"
+            Get-ChildItem -Path $llvmBinDir | Select-Object -First 10 | ForEach-Object {
+              Write-Host "  $($_.Name)"
+            }
+
+            # Add to PATH
+            echo "$llvmBinDir" | Out-File -FilePath $env:GITHUB_PATH -Encoding utf8 -Append
+            $env:PATH = "$llvmBinDir;$env:PATH"
+
+            # Verify llc is available
+            $llcPath = Join-Path -Path $llvmBinDir -ChildPath "llc.exe"
+            if (Test-Path -Path $llcPath) {
+              Write-Host "Found llc.exe at $llcPath"
+              Write-Host "Testing llc.exe:"
+              & "$llcPath" --version
+            } else {
+              Write-Host "WARNING: llc.exe not found at $llcPath"
+              # Display all exe files to help diagnose what might be available
+              Write-Host "Available executables in bin directory:"
+              Get-ChildItem -Path $llvmBinDir -Filter "*.exe" | ForEach-Object {
+                Write-Host "  $($_.Name)"
+              }
+            }
+          } else {
+            Write-Host "ERROR: LLVM bin directory does not exist at $llvmBinDir"
+            Write-Host "LLVM_PATH contents:"
+            Get-ChildItem -Path $env:LLVM_PATH | ForEach-Object {
+              Write-Host "  $($_.Name)"
+            }
+            exit 1
+          }
+
+      - name: Verify LLVM PATH (Windows)
+        if: matrix.os == 'windows-latest'
+        run: |
+          Write-Host "PATH environment variable:"
+          $env:PATH -split ';' | ForEach-Object { Write-Host "  $_" }
+
+          Write-Host "Checking for llc command:"
+          try {
+            $llcCommand = Get-Command llc -ErrorAction Stop
+            Write-Host "Found llc at location $($llcCommand.Source)"
+            & $llcCommand.Source --version
+          } catch {
+            Write-Host "llc command not found in PATH. This may cause tests to fail."
+
+            # Look for llc.exe in LLVM_PATH
+            if ($env:LLVM_PATH) {
+              $llcPath = Join-Path -Path $env:LLVM_PATH -ChildPath "bin\llc.exe"
+              if (Test-Path -Path $llcPath) {
+                Write-Host "Found llc.exe at $llcPath, but it's not in PATH. Adding it now."
+                $llvmBinDir = Join-Path -Path $env:LLVM_PATH -ChildPath "bin"
+                $env:PATH = "$llvmBinDir;$env:PATH"
+                echo "PATH=$env:PATH" | Out-File -FilePath $env:GITHUB_ENV -Encoding utf8 -Append
+              }
+            }
+          }
+
       - name: Compile tests
         run: cargo test --no-run
 
-      - name: Run tests
-        run: cargo test
+      - name: Run tests (Linux/macOS)
+        if: matrix.os != 'windows-latest'
+        run: cargo test --workspace
+
+      - 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
+
+          # 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
+          cd ../..
+
+          # Run doctests for other crates normally
+          cargo test --workspace --exclude pecos-rslib --exclude pecos --doc

.github/workflows/rust-version-consistency.yml

@@ -1,5 +1,7 @@
 name: Rust Version Consistency Check
 
+# bump
+
 on:
   push:
     paths:

.github/workflows/test-docs-examples.yml

@@ -0,0 +1,70 @@
+name: Documentation Tests & Build
+
+on:
+  push:
+    branches: [ master, development ]
+    paths:
+      - 'docs/**'
+  pull_request:
+    branches: [ master, development ]
+    paths:
+      - 'docs/**'
+  workflow_dispatch:
+
+env:
+  RUSTFLAGS: -C debuginfo=0
+  RUST_BACKTRACE: 1
+  PYTHONUTF8: 1
+
+jobs:
+  docs-ci:
+    name: Test and build documentation
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.10'
+
+      - name: Install the latest version of uv
+        uses: astral-sh/setup-uv@v4
+        with:
+          enable-cache: true
+
+      - name: Set up Rust
+        run: rustup show
+
+      - name: Cache Rust
+        uses: Swatinem/rust-cache@v2
+        with:
+          workspaces: python/pecos-rslib
+
+      - name: Generate lockfile and install dependencies
+        run: |
+          uv lock --project .
+          uv sync --project .
+
+      - name: Install pecos-rslib with maturin
+        run: |
+          cd python/pecos-rslib
+          uv run maturin develop --uv
+
+      - name: Install quantum-pecos from local source
+        run: |
+          cd python/quantum-pecos
+          uv pip install -e .
+
+      - name: Test working documentation examples
+        run: |
+          uv run python scripts/docs/test_working_examples.py
+
+      - name: Test all code examples
+        run: |
+          uv run python scripts/docs/test_code_examples.py
+
+      - name: Build documentation
+        if: success()
+        run: |
+          uv run mkdocs build