Upgrade to using uv instead of pip

.github/workflows/python-release.yml

@@ -66,13 +66,20 @@ jobs:
         with:
           python-version: ${{ env.PYTHON_VERSION }}
 
+      - name: Install the latest version of uv
+        uses: astral-sh/setup-uv@v4
+        with:
+          enable-cache: true
+          ignore-nothing-to-cache: true
+          cache-dependency-glob: |
+            **/pyproject.toml
+            **/requirements*.txt
+            **/uv.lock
+
       - name: Remove conflicting README.md
         run: |
           if [ -f crates/pecos-python/README.md ]; then
             mv crates/pecos-python/README.md crates/pecos-python/README.md.bak
-            echo "Moved conflicting README.md to README.md.bak"
-          else
-            echo "No conflicting README.md found"
           fi
 
       - name: Build pecos-rslib SDist
@@ -87,15 +94,13 @@ jobs:
         run: |
           if [ -f crates/pecos-python/README.md.bak ]; then
             mv crates/pecos-python/README.md.bak crates/pecos-python/README.md
-            echo "Restored README.md from backup"
-          else
-            echo "No README.md backup found"
           fi
 
-      - name: Test pecos-rslib SDist
+      - name: Install and test pecos-rslib SDist
         run: |
-          pip install --force-reinstall --verbose python/pecos-rslib/dist/*.tar.gz
-          python -c 'import pecos_rslib; print(pecos_rslib.__version__)'
+          uv sync --project .
+          uv pip install --force-reinstall python/pecos-rslib/dist/*.tar.gz
+          uv run python -c 'import pecos_rslib; print(pecos_rslib.__version__)'
 
       - name: Upload pecos-rslib SDist
         uses: actions/upload-artifact@v4
@@ -130,13 +135,15 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
+      - name: Install the latest version of uv
+        uses: astral-sh/setup-uv@v4
+        with:
+          enable-cache: true
+
       - name: Remove conflicting README.md
         run: |
           if [ -f crates/pecos-python/README.md ]; then
             mv crates/pecos-python/README.md crates/pecos-python/README.md.bak
-            echo "Moved conflicting README.md to README.md.bak"
-          else
-            echo "No conflicting README.md found"
           fi
 
       - name: Build wheel
@@ -153,16 +160,14 @@ jobs:
         run: |
           if [ -f crates/pecos-python/README.md.bak ]; then
             mv crates/pecos-python/README.md.bak crates/pecos-python/README.md
-            echo "Restored README.md from backup"
-          else
-            echo "No README.md backup found"
           fi
 
       - name: Test wheel
         if: ${{ !(matrix.architecture == 'x86_64' && matrix.os == 'macos-latest') && matrix.architecture != 'aarch64' }}
         run: |
-          pip install --force-reinstall --verbose python/pecos-rslib/dist/*.whl
-          python -c 'import pecos_rslib; print(pecos_rslib.__version__)'
+          uv sync --project .
+          uv pip install --force-reinstall python/pecos-rslib/dist/*.whl
+          uv run python -c 'import pecos_rslib; print(pecos_rslib.__version__)'
 
       - name: Upload wheel
         uses: actions/upload-artifact@v4
@@ -187,29 +192,33 @@ jobs:
         with:
           python-version: ${{ env.PYTHON_VERSION }}
 
+      - name: Install the latest version of uv
+        uses: astral-sh/setup-uv@v4
+        with:
+          enable-cache: true
+
       - name: Download pecos-rslib wheel
         uses: actions/download-artifact@v4
         with:
           name: wheel-pecos-rslib-ubuntu-latest-x86_64-py${{ env.PYTHON_VERSION }}
           path: ./pecos-rslib-wheel
 
-      - name: Install pecos-rslib
-        run: pip install ./pecos-rslib-wheel/*.whl
-
-      - name: Install build dependencies
+      - name: Setup environment and install dependencies
         run: |
-          python -m pip install --upgrade pip
-          pip install build
+          uv sync --project .
+          uv pip install ./pecos-rslib-wheel/*.whl
+          uv pip install build
 
       - name: Build quantum-pecos SDist
         run: |
           cd python/quantum-pecos
+          uv pip install --system build
           python -m build --sdist --outdir dist
 
       - name: Test quantum-pecos SDist
         run: |
-          pip install python/quantum-pecos/dist/*.tar.gz
-          python -c 'import pecos; print(pecos.__version__)'
+          uv pip install python/quantum-pecos/dist/*.tar.gz
+          uv run python -c 'import pecos; print(pecos.__version__)'
 
       - name: Upload quantum-pecos SDist
         uses: actions/upload-artifact@v4
@@ -233,24 +242,25 @@ jobs:
         with:
           ref: ${{ inputs.sha || github.sha }}
 
-      - name: Set up Python ${{ matrix.python-version }}
+      - name: Set up Python
         uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
+      - name: Install the latest version of uv
+        uses: astral-sh/setup-uv@v4
+        with:
+          enable-cache: true
+
       - name: Download pecos-rslib wheel
         uses: actions/download-artifact@v4
         with:
           name: wheel-pecos-rslib-ubuntu-latest-x86_64-py${{ matrix.python-version }}
           path: ./pecos-rslib-wheel
 
-      - name: Install pecos-rslib
-        run: pip install ./pecos-rslib-wheel/*.whl
-
-      - name: Install build dependencies
+      - name: Setup environment and install dependencies
         run: |
-          python -m pip install --upgrade pip
-          pip install build
+          uv pip install --system ./pecos-rslib-wheel/*.whl build
 
       - name: Build quantum-pecos wheel
         run: |
@@ -259,8 +269,9 @@ jobs:
 
       - name: Test quantum-pecos wheel
         run: |
-          pip install python/quantum-pecos/dist/*.whl
-          python -c 'import pecos; print(pecos.__version__)'
+          uv sync  # This will use the workspace config correctly
+          uv pip install python/quantum-pecos/dist/*.whl
+          uv run python -c 'import pecos; print(pecos.__version__)'
 
       - name: Upload quantum-pecos wheel
         uses: actions/upload-artifact@v4

.github/workflows/python-test.yml

@@ -1,5 +1,4 @@
 name: Python test / linting
-
 on:
   push:
     branches: [ "master", "development" ]
@@ -22,7 +21,6 @@ concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
 
-
 env:
   RUSTFLAGS: -C debuginfo=0
   RUST_BACKTRACE: 1
@@ -34,7 +32,6 @@ defaults:
 
 jobs:
   python-test:
-
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
@@ -50,25 +47,10 @@ 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 +60,34 @@ 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

development.md → DEVELOPMENT.md

@@ -10,38 +10,14 @@ For developers who want to contribute or modify PECOS:
    cd PECOS
    ```
 
-3. Set up the development environment either using the `Makefile` (Note: for Windows to use the `Makefile` you may need to use a shell that has access to Linux commands such as utilizing [git bash](https://gitforwindows.org/)):
-   ```sh
-   make venv
-   ```
-   <details>
-   <summary>or manually set up a Python virtual environment for develop of this project's code.</summary>
-
-   On Linux/Mac:
-
-   ```sh
-   python -m venv .venv
-   source .venv/bin/activate
-   pip install -U pip setuptools
-   pip install -r python/quantum-pecos/requirements.txt
-   make metadeps
-   pre-commit install
-   ```
-
-   On Windows:
+3. [Install `uv` for your system](https://docs.astral.sh/uv/getting-started/installation/).
+   And run the following at the root of the project to create a development environment, which will be stored in `.venv/`:
 
    ```sh
-   python -m venv .venv
-   .\venv\Scripts\activate
-   pip install -U pip setuptools
-   pip install -r python/quantum-pecos/requirements.txt
-   make metadeps
-   pre-commit install
+   uv sync
    ```
-   </details>
-
 
-4. When developing in the development environment, be sure to activate the venv:
+4. You may wish to explicitly activate the environment for development. To do so:
 
     On Linux/Mac:
     ```sh
@@ -50,24 +26,21 @@ For developers who want to contribute or modify PECOS:
 
     On Windows:
     ```sh
-    .\venv\Scripts\activate
+    .\.venv\Scripts\activate
     ```
 
-
 5. Build the project in editable mode
     ```sh
    make build
    ```
    See other build options in the `Makefile`.
 
-
 6. Run all Python and Rust tests:
    ```sh
    make test
    ```
    Note: Make sure you have run a build command before running tests.
 
-
 7. Run linters using pre-commit (after [installing it](https://pre-commit.com/)) to make sure all everything is properly linted/formated
    ```sh
    make lint
@@ -78,4 +51,6 @@ For developers who want to contribute or modify PECOS:
     deactivate
     ```
 
+Before pull requests are merged, they must pass linting and the test.
+
 Note: For the Rust side of the project, you can use `cargo` to run tests, benchmarks, formatting, etc.