Adding some configurations

.clang-format

@@ -0,0 +1,94 @@
+---
+Language:        Cpp
+# BasedOnStyle:  LLVM
+AccessModifierOffset: -2
+AlignAfterOpenBracket: Align
+AlignConsecutiveAssignments: false
+AlignConsecutiveDeclarations: false
+AlignEscapedNewlinesLeft: false
+AlignOperands:   true
+AlignTrailingComments: true
+AllowAllParametersOfDeclarationOnNextLine: true
+AllowShortBlocksOnASingleLine: false
+AllowShortCaseLabelsOnASingleLine: false
+AllowShortFunctionsOnASingleLine: All
+AllowShortIfStatementsOnASingleLine: false
+AllowShortLoopsOnASingleLine: false
+AlwaysBreakAfterDefinitionReturnType: None
+AlwaysBreakAfterReturnType: None
+AlwaysBreakBeforeMultilineStrings: false
+AlwaysBreakTemplateDeclarations: true
+BinPackArguments: true
+BinPackParameters: true
+BraceWrapping:
+  AfterClass:      false
+  AfterControlStatement: false
+  AfterEnum:       false
+  AfterFunction:   false
+  AfterNamespace:  false
+  AfterObjCDeclaration: false
+  AfterStruct:     false
+  AfterUnion:      false
+  BeforeCatch:     false
+  BeforeElse:      false
+  IndentBraces:    false
+BreakBeforeBinaryOperators: All
+BreakBeforeBraces: Allman
+BreakBeforeTernaryOperators: true
+BreakConstructorInitializersBeforeComma: false
+BreakAfterJavaFieldAnnotations: false
+BreakStringLiterals: true
+ColumnLimit:     80
+CommentPragmas:  '^ IWYU pragma:'
+ConstructorInitializerAllOnOneLineOrOnePerLine: false
+ConstructorInitializerIndentWidth: 4
+ContinuationIndentWidth: 4
+Cpp11BracedListStyle: true
+DerivePointerAlignment: false
+DisableFormat:   false
+ExperimentalAutoDetectBinPacking: false
+ForEachMacros:   [ foreach, Q_FOREACH, BOOST_FOREACH ]
+IncludeCategories:
+  - Regex:           '^"(llvm|llvm-c|clang|clang-c)/'
+    Priority:        2
+  - Regex:           '^(<|"(gtest|isl|json)/)'
+    Priority:        3
+  - Regex:           '.*'
+    Priority:        1
+IncludeIsMainRegex: '$'
+IndentCaseLabels: false
+IndentWidth:     2
+IndentWrappedFunctionNames: false
+JavaScriptQuotes: Leave
+JavaScriptWrapImports: true
+KeepEmptyLinesAtTheStartOfBlocks: true
+MacroBlockBegin: ''
+MacroBlockEnd:   ''
+MaxEmptyLinesToKeep: 1
+NamespaceIndentation: None
+ObjCBlockIndentWidth: 2
+ObjCSpaceAfterProperty: false
+ObjCSpaceBeforeProtocolList: true
+PenaltyBreakBeforeFirstCallParameter: 19
+PenaltyBreakComment: 300
+PenaltyBreakFirstLessLess: 120
+PenaltyBreakString: 1000
+PenaltyExcessCharacter: 1000000
+PenaltyReturnTypeOnItsOwnLine: 60
+PointerAlignment: Left
+ReflowComments:  true
+SortIncludes:    true
+SpaceAfterCStyleCast: false
+SpaceAfterTemplateKeyword: true
+SpaceBeforeAssignmentOperators: true
+SpaceBeforeParens: ControlStatements
+SpaceInEmptyParentheses: false
+SpacesBeforeTrailingComments: 1
+SpacesInAngles:  false
+SpacesInContainerLiterals: true
+SpacesInCStyleCastParentheses: false
+SpacesInParentheses: false
+SpacesInSquareBrackets: false
+Standard:        Cpp11
+TabWidth:        8
+UseTab:          Never

.github/dependabot.yml

@@ -0,0 +1,11 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+
+version: 2
+updates:
+  - package-ecosystem: "github-actions" # See documentation for possible values
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "weekly"

.github/workflows/pre-commit.yml

@@ -0,0 +1,14 @@
+name: pre-commit
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
+    - uses: pre-commit/[email protected]

.github/workflows/pypi.yml

@@ -0,0 +1,42 @@
+name: Release
+
+on: [push, pull_request]
+
+jobs:
+  dist:
+    runs-on: ubuntu-latest
+    container: ghcr.io/fenics/dolfinx/dolfinx:nightly
+    env:
+      DEB_PYTHON_INSTALL_LAYOUT: deb_system
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Install build dependencies
+      run: python3 -m pip install --upgrade build twine
+
+    - name: Build SDist and wheel
+      run: python3 -m build --no-isolation --sdist
+
+    - uses: actions/upload-artifact@v4
+      with:
+        path: dist/*
+
+    - name: Check metadata
+      run: python3 -m twine check dist/*
+
+  publish:
+    needs: [dist]
+    runs-on: ubuntu-latest
+    if: startsWith(github.ref, 'refs/tags')
+    environment: pypi
+    permissions:
+      id-token: write
+
+    steps:
+    - uses: actions/download-artifact@v4
+      with:
+        name: artifact
+        path: dist
+
+    - uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/tests.yml

@@ -23,4 +23,4 @@ jobs:
         run: python3 -m pytest -v
 
       - name: Run tests in parallel
-        run: mpiexec -n 4 python3 -m pytest -v
+        run: mpiexec -n 4 python3 -m pytest -v

.pre-commit-config.yaml

@@ -0,0 +1,36 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-added-large-files
+      - id: check-docstring-first
+      - id: debug-statements
+      - id: check-toml
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: 'v0.6.5'
+    hooks:
+       # Run the linter.
+      - id: ruff
+        args: [ --fix ]
+      # Run the formatter.
+      - id: ruff-format
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.11.2
+    hooks:
+      - id: mypy
+        files: ^src/|^tests/
+        args: ["--config-file", "pyproject.toml"]
+
+
+  - repo: https://github.com/pre-commit/mirrors-clang-format
+    rev: 'v14.0.6'  # Use the sha / tag you want to point at
+    hooks:
+      - id: clang-format

CMakeLists.txt

@@ -60,4 +60,4 @@ target_link_libraries(_scifem PRIVATE dolfinx)
 set_target_properties(_scifem PROPERTIES INSTALL_RPATH_USE_LINK_PATH TRUE)
 
 # Install directive for scikit-build-core
-install(TARGETS _scifem LIBRARY DESTINATION ${PROJECT_NAME})
+install(TARGETS _scifem LIBRARY DESTINATION ${PROJECT_NAME})

README.md

@@ -3,7 +3,7 @@ This package contains a collection of tools for scientific computing with a focu
 
 Many users that are transitioning from legacy FEniCS to FEniCSx may find the transition difficult due to the lack of some functionalities in FEniCSx.
 This package aims to provide some of the functionalities that are missing in FEniCSx.
-The package is still in its early stages and many functionalities are still missing. 
+The package is still in its early stages and many functionalities are still missing.
 
 ## Features
 - Real-space implementation for usage in DOLFINx (>=v0.8.0)
@@ -28,6 +28,3 @@ python3 -m pip install --no-build-isolation git+https://github.com/scientificcom
 ## Having issues or want to contribute?
 
 If you are having issues, feature request or would like to contribute, please let us know. You can do so by opening an issue on the [issue tracker](https://github.com/scientificcomputing/scifem/issues).
-
-
-

pyproject.toml

@@ -20,6 +20,7 @@ repository = "https://github.com/scientificcomputing/scifem.git"
 
 [project.optional-dependencies]
 docs = []
+dev = ["ruff", "mypy", "bump-my-version", "pre-commit"]
 test = ["pytest", "petsc4py"]
 
 
@@ -88,3 +89,43 @@ max-complexity = 10
 
 [tool.ruff.lint.pydocstyle]
 convention = "google"
+
+
+[tool.ruff.lint.isort]
+known-first-party = ["scifem"]
+known-third-party = [
+    "basix",
+    "dolfinx",
+    "ffcx",
+    "ufl",
+    "gmsh",
+    "numpy",
+    "pytest",
+]
+section-order = [
+    "future",
+    "standard-library",
+    "mpi",
+    "third-party",
+    "first-party",
+    "local-folder",
+]
+[tool.ruff.lint.isort.sections]
+"mpi" = ["mpi4py", "petsc4py"]
+
+
+[tool.bumpversion]
+allow_dirty = false
+commit = true
+message = "Bump version: {current_version} → {new_version}"
+tag = true
+sign_tags = false
+tag_name = "v{new_version}"
+tag_message = "Bump version: {current_version} → {new_version}"
+current_version = "0.1.0"
+
+
+[[tool.bumpversion.files]]
+filename = "pyproject.toml"
+search = 'version = "{current_version}"'
+replace = 'version = "{new_version}"'