Add linters and formatters, and workflows for checking and uploading …

…to pypi

.clang-format

@@ -0,0 +1,94 @@
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+# BasedOnStyle:  LLVM
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+AlignAfterOpenBracket: Align
+AlignConsecutiveAssignments: false
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+AlwaysBreakAfterReturnType: None
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+AlwaysBreakTemplateDeclarations: true
+BinPackArguments: true
+BinPackParameters: true
+BraceWrapping:
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+BreakBeforeBraces: Allman
+BreakBeforeTernaryOperators: true
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+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: ''
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+MaxEmptyLinesToKeep: 1
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+Standard:        Cpp11
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+UseTab:          Never

.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

@@ -21,4 +21,3 @@ jobs:
 
       - name: Run tests
         run: python3 -m pytest
-

.pre-commit-config.yaml

@@ -0,0 +1,30 @@
+# 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"]

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

@@ -2,7 +2,7 @@
 
 This package contains a collection of tools for scientific computing with a focus on finite element methods. The tools are written in Python and are intended to be used in conjunction with the [dolfinx](https://github.com/FEniCS/dolfinx).
 
-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. 
+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.
 
 
 ## Installation
@@ -21,4 +21,4 @@ If you are having issues, feature request or would like to contribute, please le
 
 
 ## LICENSE
-MIT
+MIT

pyproject.toml

@@ -21,6 +21,7 @@ repository = "https://github.com/scientificcomputing/scifem.git"
 [project.optional-dependencies]
 docs = []
 test = ["pytest"]
+dev = ["ruff", "mypy", "bump-my-version", "pre-commit"]
 
 
 [tool.pytest.ini_options]
@@ -87,4 +88,44 @@ max-complexity = 10
 
 
 [tool.ruff.lint.pydocstyle]
-convention = "google"
+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}"'

src/scifem.cpp

@@ -8,64 +8,74 @@
 #include <dolfinx/fem/FiniteElement.h>
 #include <dolfinx/fem/FunctionSpace.h>
 #include <dolfinx/mesh/Mesh.h>
+#include <memory>
 #include <nanobind/nanobind.h>
 #include <nanobind/stl/shared_ptr.h>
-#include <memory>
 using namespace dolfinx;
 
 namespace scifem
 {
-    template <typename T>
-    dolfinx::fem::FunctionSpace<T> create_real_functionspace(std::shared_ptr<const dolfinx::mesh::Mesh<T>> mesh)
-    {
+template <typename T>
+dolfinx::fem::FunctionSpace<T>
+create_real_functionspace(std::shared_ptr<const dolfinx::mesh::Mesh<T>> mesh)
+{
 
-        basix::FiniteElement e_v = basix::create_element<T>(
-            basix::element::family::P, mesh::cell_type_to_basix_type(mesh->topology()->cell_type()), 0,
-            basix::element::lagrange_variant::unset, basix::element::dpc_variant::unset, true);
+  basix::FiniteElement e_v = basix::create_element<T>(
+      basix::element::family::P,
+      mesh::cell_type_to_basix_type(mesh->topology()->cell_type()), 0,
+      basix::element::lagrange_variant::unset,
+      basix::element::dpc_variant::unset, true);
 
-        // NOTE: Optimize input source/dest later as we know this a priori
-        std::int32_t num_dofs = (dolfinx::MPI::rank(MPI_COMM_WORLD) == 0) ? 1 : 0;
-        std::int32_t num_ghosts = (dolfinx::MPI::rank(MPI_COMM_WORLD) != 0) ? 1 : 0;
-        std::vector<std::int64_t> ghosts(num_ghosts, 0);
-        ghosts.reserve(1);
-        std::vector<int> owners(num_ghosts, 0);
-        owners.reserve(1);
-        std::shared_ptr<const dolfinx::common::IndexMap> imap =
-            std::make_shared<const dolfinx::common::IndexMap>(MPI_COMM_WORLD, num_dofs, ghosts, owners);
-        int index_map_bs = 1;
-        int bs = 1;
-        // Element dof layout
-        fem::ElementDofLayout dof_layout(1, e_v.entity_dofs(), e_v.entity_closure_dofs(), {}, {});
-        std::size_t num_cells_on_process = mesh->topology()->index_map(mesh->topology()->dim())->size_local() +
-                                           mesh->topology()->index_map(mesh->topology()->dim())->num_ghosts();
+  // NOTE: Optimize input source/dest later as we know this a priori
+  std::int32_t num_dofs = (dolfinx::MPI::rank(MPI_COMM_WORLD) == 0) ? 1 : 0;
+  std::int32_t num_ghosts = (dolfinx::MPI::rank(MPI_COMM_WORLD) != 0) ? 1 : 0;
+  std::vector<std::int64_t> ghosts(num_ghosts, 0);
+  ghosts.reserve(1);
+  std::vector<int> owners(num_ghosts, 0);
+  owners.reserve(1);
+  std::shared_ptr<const dolfinx::common::IndexMap> imap
+      = std::make_shared<const dolfinx::common::IndexMap>(
+          MPI_COMM_WORLD, num_dofs, ghosts, owners);
+  int index_map_bs = 1;
+  int bs = 1;
+  // Element dof layout
+  fem::ElementDofLayout dof_layout(1, e_v.entity_dofs(),
+                                   e_v.entity_closure_dofs(), {}, {});
+  std::size_t num_cells_on_process
+      = mesh->topology()->index_map(mesh->topology()->dim())->size_local()
+        + mesh->topology()->index_map(mesh->topology()->dim())->num_ghosts();
 
-        std::vector<std::int32_t> dofmap(num_cells_on_process, 0);
-        dofmap.reserve(1);
-        std::shared_ptr<const dolfinx::fem::DofMap> real_dofmap =
-            std::make_shared<const dolfinx::fem::DofMap>(dof_layout, imap, index_map_bs, dofmap, bs);
-        std::vector<std::size_t> value_shape(0);
+  std::vector<std::int32_t> dofmap(num_cells_on_process, 0);
+  dofmap.reserve(1);
+  std::shared_ptr<const dolfinx::fem::DofMap> real_dofmap
+      = std::make_shared<const dolfinx::fem::DofMap>(dof_layout, imap,
+                                                     index_map_bs, dofmap, bs);
+  std::vector<std::size_t> value_shape(0);
 
-        std::shared_ptr<const dolfinx::fem::FiniteElement<T>> d_el =
-            std::make_shared<const dolfinx::fem::FiniteElement<T>>(e_v, 1, false);
+  std::shared_ptr<const dolfinx::fem::FiniteElement<T>> d_el
+      = std::make_shared<const dolfinx::fem::FiniteElement<T>>(e_v, 1, false);
 
-        return dolfinx::fem::FunctionSpace<T>(mesh, d_el, real_dofmap, value_shape);
-    }
+  return dolfinx::fem::FunctionSpace<T>(mesh, d_el, real_dofmap, value_shape);
 }
+} // namespace scifem
 
 namespace scifem_wrapper
 {
-    template <typename T>
-    void declare_real_function_space(nanobind::module_ &m, std::string type)
-    {
-        std::string pyfunc_name = "create_real_functionspace_" + type;
-        m.def(pyfunc_name.c_str(), [](std::shared_ptr<const dolfinx::mesh::Mesh<T>> mesh)
-              { return scifem::create_real_functionspace<T>(mesh); }, "Create a real function space");
-    }
+template <typename T>
+void declare_real_function_space(nanobind::module_& m, std::string type)
+{
+  std::string pyfunc_name = "create_real_functionspace_" + type;
+  m.def(
+      pyfunc_name.c_str(),
+      [](std::shared_ptr<const dolfinx::mesh::Mesh<T>> mesh)
+      { return scifem::create_real_functionspace<T>(mesh); },
+      "Create a real function space");
+}
 
 } // namespace scifem_wrapper
 
 NB_MODULE(_scifem, m)
 {
-    scifem_wrapper::declare_real_function_space<double>(m, "float64");
-    scifem_wrapper::declare_real_function_space<float>(m, "float32");
-}
+  scifem_wrapper::declare_real_function_space<double>(m, "float64");
+  scifem_wrapper::declare_real_function_space<float>(m, "float32");
+}