Add --system to all uv pip install/list calls in CI

CI workflows run without a virtual environment, so uv pip requires
--system to install into the system Python. Also rebase on latest
main to resolve merge conflicts (.gitattributes, .pre-commit-config).

Co-authored-by: Cursor <cursoragent@cursor.com>

Author: kkraus14

.github/workflows/build-docs.yml

@@ -184,18 +184,18 @@ jobs:
       - name: Install all packages
         run: |
           pushd cuda_pathfinder
-          uv pip install *.whl
+          uv pip install --system *.whl
           popd
 
           pushd "${CUDA_BINDINGS_ARTIFACTS_DIR}"
-          uv pip install *.whl
+          uv pip install --system *.whl
           popd
 
           pushd "${CUDA_CORE_ARTIFACTS_DIR}"
-          uv pip install *.whl
+          uv pip install --system *.whl
           popd
 
-          uv pip install cuda_python*.whl
+          uv pip install --system cuda_python*.whl
 
       # This step sets the PR_NUMBER/BUILD_LATEST/BUILD_PREVIEW env vars.
       - name: Get PR number

.github/workflows/build-wheel.yml

@@ -111,7 +111,7 @@ jobs:
 
       - name: Install twine
         run: |
-          uv pip install twine
+          uv pip install --system twine
 
       # To keep the build workflow simple, all matrix jobs will build a wheel for later use within this workflow.
       - name: Build and check cuda.pathfinder wheel
@@ -320,11 +320,11 @@ jobs:
 
       - name: Install cuda.pathfinder (required for next step)
         run: |
-          uv pip install cuda_pathfinder/dist/*.whl
+          uv pip install --system cuda_pathfinder/dist/*.whl
 
       - name: Build cuda.bindings Cython tests
         run: |
-          uv pip install ${{ env.CUDA_BINDINGS_ARTIFACTS_DIR }}/*.whl
+          uv pip install --system ${{ env.CUDA_BINDINGS_ARTIFACTS_DIR }}/*.whl
           uv sync --package cuda-bindings --only-group test --no-install-project
           pushd ${{ env.CUDA_BINDINGS_CYTHON_TESTS_DIR }}
           bash build_tests.sh
@@ -339,7 +339,7 @@ jobs:
 
       - name: Build cuda.core Cython tests
         run: |
-          uv pip install ${{ env.CUDA_CORE_ARTIFACTS_DIR }}/"cu${BUILD_CUDA_MAJOR}"/*.whl
+          uv pip install --system ${{ env.CUDA_CORE_ARTIFACTS_DIR }}/"cu${BUILD_CUDA_MAJOR}"/*.whl
           uv sync --package cuda-core --only-group test --no-install-project
           pushd ${{ env.CUDA_CORE_CYTHON_TESTS_DIR }}
           bash build_tests.sh
@@ -454,7 +454,7 @@ jobs:
 
       - name: Merge cuda.core wheels
         run: |
-          uv pip install wheel
+          uv pip install --system wheel
           python ci/tools/merge_cuda_core_wheels.py \
             "${{ env.CUDA_CORE_ARTIFACTS_DIR }}"/cu"${BUILD_CUDA_MAJOR}"/cuda_core*.whl \
             "${{ env.CUDA_CORE_ARTIFACTS_DIR }}"/cu"${BUILD_PREV_CUDA_MAJOR}"/cuda_core*.whl \

.github/workflows/test-wheel-linux.yml

@@ -282,18 +282,18 @@ jobs:
       - name: Ensure cuda-python installable
         run: |
           if [[ "${{ matrix.LOCAL_CTK }}" == 1 ]]; then
-            uv pip install cuda_python*.whl
+            uv pip install --system cuda_python*.whl
           else
-            uv pip install $(ls cuda_python*.whl)[all]
+            uv pip install --system $(ls cuda_python*.whl)[all]
           fi
 
       - name: Install cuda.pathfinder extra wheels for testing
         run: |
           set -euo pipefail
           pushd cuda_pathfinder
-          uv pip install -v ./*.whl
+          uv pip install --system -v ./*.whl
           uv sync --package cuda-pathfinder --only-group "test-cu${TEST_CUDA_MAJOR}" --no-install-project
-          uv pip list
+          uv pip list --system
           popd
 
       - name: Run cuda.pathfinder tests with all_must_work

.github/workflows/test-wheel-windows.yml

@@ -260,18 +260,18 @@ jobs:
         shell: bash --noprofile --norc -xeuo pipefail {0}
         run: |
           if [[ "${{ matrix.LOCAL_CTK }}" == 1 ]]; then
-            uv pip install cuda_python*.whl
+            uv pip install --system cuda_python*.whl
           else
-            uv pip install $(ls cuda_python*.whl)[all]
+            uv pip install --system $(ls cuda_python*.whl)[all]
           fi
 
       - name: Install cuda.pathfinder extra wheels for testing
         shell: bash --noprofile --norc -xeuo pipefail {0}
         run: |
           pushd cuda_pathfinder
-          uv pip install -v ./*.whl
+          uv pip install --system -v ./*.whl
           uv sync --package cuda-pathfinder --only-group "test-cu${TEST_CUDA_MAJOR}" --no-install-project
-          uv pip list
+          uv pip list --system
           popd
 
       - name: Run cuda.pathfinder tests with all_must_work

.pre-commit-config.yaml

@@ -55,9 +55,12 @@ repos:
     - id: check-yaml
     - id: debug-statements
     - id: end-of-file-fixer
+      exclude: &gen_exclude '^(?:cuda_python/README\.md|cuda_bindings/cuda/bindings/.*\.in?|cuda_bindings/docs/source/module/.*\.rst?)$'
     - id: mixed-line-ending
     - id: trailing-whitespace
+      exclude: *gen_exclude
 
+  # Checking for common mistakes
   - repo: https://github.com/pre-commit/pygrep-hooks
     rev: "3a6eb0fadf60b3cccfd80bad9dbb6fae7e47b316"  # frozen: v1.10.0
     hooks:
@@ -66,22 +69,27 @@ repos:
     - id: rst-inline-touching-normal
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: "3fa3bf0572b3af5e0b2fba0b6e76a1e0c4e1fdee"  # frozen: v1.16.1
+    rev: a66e98df7b4aeeb3724184b332785976d062b92e  # frozen: v1.19.1
     hooks:
-    - id: mypy
-      name: mypy-pathfinder
-      args: ["--config-file=cuda_pathfinder/pyproject.toml"]
-      files: "^cuda_pathfinder/"
-      exclude: "^cuda_pathfinder/tests/"
+      - id: mypy
+        name: mypy-pathfinder
+        files: ^cuda_pathfinder/cuda/.*\.py$  # Exclude tests directory
+        args: [--config-file=cuda_pathfinder/pyproject.toml]
 
   - repo: https://github.com/rhysd/actionlint
-    rev: "a1bcb27e3e8727e0b92d7d36c5a6f4b076b32b34"  # frozen: v1.7.7
+    rev: "0933c147c9d6587653d45fdcb4c497c57a65f9af"  # frozen: v1.7.10
     hooks:
       - id: actionlint
-        name: Lint GitHub Actions workflow files
+        args: ["-shellcheck="]
+        exclude: ^\.github/workflows/coverage.yml$
 
   - repo: https://github.com/MarcoGorelli/cython-lint
-    rev: "48ca7bf3eb3d0bba6c3e76ba43b0a9e0a1f9bcc9"  # frozen: v0.16.6
+    rev: "d9ff7ce99ef4f2ae8fba93079ca9d76c4651d4ac"  # frozen: v0.18.0
     hooks:
-    - id: cython-lint
-      args: ['--max-line-length=320']
+      - id: cython-lint
+        args: [--no-pycodestyle]
+        exclude: ^cuda_bindings/
+
+
+default_language_version:
+      python: python3

ci/tools/run-tests

@@ -24,7 +24,7 @@ test_module=${1}
 # (it is a direct dependency of bindings, and a transitive dependency of core)
 pushd ./cuda_pathfinder
 echo "Installing pathfinder wheel"
-uv pip install ./*.whl
+uv pip install --system ./*.whl
 uv sync --package cuda-pathfinder --only-group test --no-install-project
 popd
 
@@ -42,9 +42,9 @@ elif [[ "${test_module}" == "bindings" ]]; then
   echo "Installing bindings wheel"
   pushd ./cuda_bindings
   if [[ "${LOCAL_CTK}" == 1 ]]; then
-    uv pip install "${CUDA_BINDINGS_ARTIFACTS_DIR}"/*.whl
+    uv pip install --system "${CUDA_BINDINGS_ARTIFACTS_DIR}"/*.whl
   else
-    uv pip install $(ls "${CUDA_BINDINGS_ARTIFACTS_DIR}"/*.whl)[all]
+    uv pip install --system $(ls "${CUDA_BINDINGS_ARTIFACTS_DIR}"/*.whl)[all]
   fi
   uv sync --package cuda-bindings --only-group test --no-install-project
   echo "Running bindings tests"
@@ -59,9 +59,9 @@ elif [[ "${test_module}" == "core" ]]; then
   if [[ "${SKIP_CUDA_BINDINGS_TEST}" == 1 ]]; then
     echo "Installing bindings wheel"
     if [[ "${LOCAL_CTK}" == 1 ]]; then
-      uv pip install "${CUDA_BINDINGS_ARTIFACTS_DIR}"/*.whl
+      uv pip install --system "${CUDA_BINDINGS_ARTIFACTS_DIR}"/*.whl
     else
-      uv pip install $(ls "${CUDA_BINDINGS_ARTIFACTS_DIR}"/*.whl)[all]
+      uv pip install --system $(ls "${CUDA_BINDINGS_ARTIFACTS_DIR}"/*.whl)[all]
     fi
   fi
   TEST_CUDA_MAJOR="$(cut -d '.' -f 1 <<< ${CUDA_VER})"
@@ -76,9 +76,9 @@ elif [[ "${test_module}" == "core" ]]; then
   if [[ "${LOCAL_CTK}" == 1 ]]; then
     # We already installed cuda-bindings, and all CTK components exist locally,
     # so just install the test dependencies.
-    uv pip install "${CUDA_CORE_ARTIFACTS_DIR}"/*.whl
+    uv pip install --system "${CUDA_CORE_ARTIFACTS_DIR}"/*.whl
   else
-    uv pip install $(ls "${CUDA_CORE_ARTIFACTS_DIR}"/*.whl)["cu${TEST_CUDA_MAJOR}"]
+    uv pip install --system $(ls "${CUDA_CORE_ARTIFACTS_DIR}"/*.whl)["cu${TEST_CUDA_MAJOR}"]
   fi
   uv sync --package cuda-core --only-group "test-cu${TEST_CUDA_MAJOR}${FREE_THREADING}" --no-install-project
   echo "Running core tests"