[ci] Use pixi and pre-commit for all linting jobs

.ci/lint-cpp.sh → .ci/lint/lint-openmp-pragmas.sh

@@ -2,26 +2,6 @@
 
 set -e -E -u -o pipefail
 
-echo "running cpplint"
-cpplint \
-    --filter=-build/c++11,-build/include_subdir,-build/header_guard,-whitespace/line_length \
-    --recursive ./src ./include ./R-package ./swig ./tests \
-|| exit 1
-echo "done running cpplint"
-
-echo "running cmakelint"
-find \
-    . \
-    -type f \
-    \( -name CMakeLists.txt -o -path "./cmake/*.cmake" \) \
-    -not -path './external_libs/*' \
-    -exec cmakelint \
-    --linelength=120 \
-    --filter=-convention/filename,-package/stdargs,-readability/wonkycase \
-    {} \+ \
-|| exit 1
-echo "done running cmakelint"
-
 echo "checking that all OpenMP pragmas specify num_threads()"
 get_omp_pragmas_without_num_threads() {
     grep \
@@ -52,4 +32,3 @@ if test "${PROBLEMATIC_LINES}" != ""; then
     echo "For details, see https://www.openmp.org/spec-html/5.0/openmpse14.html#x54-800002.6"
     exit 1
 fi
-echo "done checking OpenMP pragmas"

.ci/lint-powershell.ps1 → .ci/lint/lint-powershell.ps1

@@ -1,56 +1,57 @@
-$settings = @{
-    Severity = @(
-        'Information',
-        'Warning',
-        'Error'
-    )
-    IncludeDefaultRules = $true
-    # Additional rules that are disabled by default
-    Rules = @{
-        PSAvoidExclaimOperator = @{
-            Enable = $true
-        }
-        PSAvoidLongLines = @{
-            Enable = $true
-            MaximumLineLength = 120
-        }
-        PSAvoidSemicolonsAsLineTerminators = @{
-            Enable = $true
-        }
-        PSPlaceCloseBrace = @{
-            Enable = $true
-            NoEmptyLineBefore = $true
-            IgnoreOneLineBlock = $true
-            NewLineAfter = $false
-        }
-        PSPlaceOpenBrace = @{
-            Enable = $true
-            OnSameLine = $true
-            NewLineAfter = $true
-            IgnoreOneLineBlock = $true
-        }
-        PSUseConsistentIndentation = @{
-            Enable = $true
-            IndentationSize = 4
-            PipelineIndentation = 'IncreaseIndentationAfterEveryPipeline'
-            Kind = 'space'
-        }
-        PSUseConsistentWhitespace = @{
-            Enable = $true
-            CheckInnerBrace = $true
-            CheckOpenBrace = $true
-            CheckOpenParen = $true
-            CheckOperator = $true
-            CheckSeparator = $true
-            CheckPipe = $true
-            CheckPipeForRedundantWhitespace = $true
-            CheckParameter = $true
-            IgnoreAssignmentOperatorInsideHashTable = $false
-        }
-        PSUseCorrectCasing = @{
-            Enable = $true
-        }
-    }
-}
-
-Invoke-ScriptAnalyzer -Path ./ -Recurse -EnableExit -Settings $settings
+$settings = @{
+    Severity = @(
+        'Information',
+        'Warning',
+        'Error'
+    )
+    IncludeDefaultRules = $true
+    # Additional rules that are disabled by default
+    Rules = @{
+        PSAvoidExclaimOperator = @{
+            Enable = $true
+        }
+        PSAvoidLongLines = @{
+            Enable = $true
+            MaximumLineLength = 120
+        }
+        PSAvoidSemicolonsAsLineTerminators = @{
+            Enable = $true
+        }
+        PSPlaceCloseBrace = @{
+            Enable = $true
+            NoEmptyLineBefore = $true
+            IgnoreOneLineBlock = $true
+            NewLineAfter = $false
+        }
+        PSPlaceOpenBrace = @{
+            Enable = $true
+            OnSameLine = $true
+            NewLineAfter = $true
+            IgnoreOneLineBlock = $true
+        }
+        PSUseConsistentIndentation = @{
+            Enable = $true
+            IndentationSize = 4
+            PipelineIndentation = 'IncreaseIndentationAfterEveryPipeline'
+            Kind = 'space'
+        }
+        PSUseConsistentWhitespace = @{
+            Enable = $true
+            CheckInnerBrace = $true
+            CheckOpenBrace = $true
+            CheckOpenParen = $true
+            CheckOperator = $true
+            CheckSeparator = $true
+            CheckPipe = $true
+            CheckPipeForRedundantWhitespace = $true
+            CheckParameter = $true
+            IgnoreAssignmentOperatorInsideHashTable = $false
+        }
+        PSUseCorrectCasing = @{
+            Enable = $true
+        }
+    }
+}
+
+Install-Module -Name PSScriptAnalyzer -Scope CurrentUser -SkipPublisherCheck
+Invoke-ScriptAnalyzer -Path ./.ci -Recurse -EnableExit -Settings $settings

.ci/lint-r-code.R → .ci/lint/lint-r-code.R

@@ -14,6 +14,7 @@ FILES_TO_LINT <- list.files(
     , recursive = TRUE
     , include.dirs = FALSE
 )
+FILES_TO_LINT <- FILES_TO_LINT[!grepl(paste0("^", file.path(".", ".pixi", "")), FILES_TO_LINT)]
 
 # text to use for pipe operators from packages like 'magrittr'
 pipe_text <- paste0(

.ci/test.sh

@@ -98,34 +98,6 @@ if [[ $TASK == "swig" ]]; then
     exit 0
 fi
 
-if [[ $TASK == "lint" ]]; then
-    pwsh -command "Install-Module -Name PSScriptAnalyzer -Scope CurrentUser -SkipPublisherCheck"
-    echo "Linting PowerShell code"
-    pwsh -file ./.ci/lint-powershell.ps1 || exit 1
-    conda create -q -y -n "${CONDA_ENV}" \
-        "${CONDA_PYTHON_REQUIREMENT}" \
-        'biome>=1.9.3' \
-        'cmakelint>=1.4.3' \
-        'cpplint>=1.6.0' \
-        'matplotlib-base>=3.9.1' \
-        'mypy>=1.11.1' \
-        'pre-commit>=3.8.0' \
-        'pyarrow-core>=17.0' \
-        'scikit-learn>=1.5.2' \
-        'r-lintr>=3.1.2'
-    # shellcheck disable=SC1091
-    source activate "${CONDA_ENV}"
-    echo "Linting Python and bash code"
-    bash ./.ci/lint-python-bash.sh || exit 1
-    echo "Linting R code"
-    Rscript ./.ci/lint-r-code.R "${BUILD_DIRECTORY}" || exit 1
-    echo "Linting C++ code"
-    bash ./.ci/lint-cpp.sh || exit 1
-    echo "Linting JavaScript code"
-    bash ./.ci/lint-js.sh || exit 1
-    exit 0
-fi
-
 if [[ $TASK == "check-docs" ]] || [[ $TASK == "check-links" ]]; then
     conda env create \
         -n "${CONDA_ENV}" \

.envrc

@@ -0,0 +1,2 @@
+watch_file pixi.toml pixi.lock
+eval "$(pixi shell-hook)"

.gitattributes

@@ -0,0 +1,2 @@
+# SCM syntax highlighting & preventing 3-way merges
+pixi.lock merge=binary linguist-language=YAML linguist-generated=true

.github/workflows/static_analysis.yml

@@ -16,22 +16,33 @@ concurrency:
   cancel-in-progress: true
 
 env:
-  COMPILER: 'gcc'
-  MAKEFLAGS: '-j4'
-  OS_NAME: 'linux'
-  PYTHON_VERSION: '3.13'
+  COMPILER: "gcc"
+  MAKEFLAGS: "-j4"
+  OS_NAME: "linux"
+  PYTHON_VERSION: "3.13"
 
 jobs:
-  test:
-    name: ${{ matrix.task }}
+  lint:
+    name: lint
+    runs-on: ubuntu-latest
+    timeout-minutes: 60
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 5
+          submodules: false
+      - name: Setup pixi
+        uses: prefix-dev/[email protected]
+        with:
+          environments: lint
+      - name: Run pre-commit
+        run: pixi run lint
+
+  python-check-docs:
+    name: python-check-docs
     runs-on: ubuntu-latest
     timeout-minutes: 60
-    strategy:
-      fail-fast: false
-      matrix:
-        include:
-          - task: lint
-          - task: check-docs
     steps:
       - name: Checkout repository
         uses: actions/checkout@v4
@@ -41,12 +52,13 @@ jobs:
       - name: Setup and run tests
         shell: bash
         run: |
-          export TASK="${{ matrix.task }}"
+          export TASK="check-docs"
           export BUILD_DIRECTORY="$GITHUB_WORKSPACE"
           export CONDA=${HOME}/miniforge
           export PATH=${CONDA}/bin:$HOME/.local/bin:${PATH}
           $GITHUB_WORKSPACE/.ci/setup.sh || exit 1
           $GITHUB_WORKSPACE/.ci/test.sh || exit 1
+
   r-check-docs:
     name: r-package-check-docs
     timeout-minutes: 60
@@ -83,10 +95,11 @@ jobs:
               echo ""
               exit 1
           fi
+
   all-static-analysis-jobs-successful:
     if: always()
     runs-on: ubuntu-latest
-    needs: [test, r-check-docs]
+    needs: [lint, python-check-docs, r-check-docs]
     steps:
       - name: Note that all tests succeeded
         uses: re-actors/[email protected]

.gitignore

@@ -463,3 +463,7 @@ dask-worker-space/
 *.pub
 *.rdp
 *_rsa
+
+# pixi environments
+.pixi
+*.egg-info