selinv 1.0.0__tar.gz

selinv-1.0.0/.gitignore

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+# Python
+__pycache__/
+*.py[cod]
+*$py.class
+*.pyc
+*.pyo
+*.pyd
+.Python
+*.egg
+*.egg-info/
+dist/
+build/
+eggs/
+parts/
+var/
+sdist/
+develop-eggs/
+.installed.cfg
+lib/
+lib64/
+MANIFEST
+
+# Virtual environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Distribution / packaging
+.eggs/
+pip-wheel-metadata/
+share/python-wheels/
+*.whl
+
+# C / C++ / Fortran
+*.o
+*.a
+*.so
+*.so.*
+*.dylib
+*.dll
+*.mod
+*.smod
+
+# CMake
+CMakeCache.txt
+CMakeFiles/
+CMakeScripts/
+Testing/
+Makefile
+cmake_install.cmake
+install_manifest.txt
+compile_commands.json
+CTestTestfile.cmake
+_deps/
+*.cmake
+!cmake/*.cmake
+
+# scikit-build
+_skbuild/
+
+# pytest
+.pytest_cache/
+.coverage
+htmlcov/
+.tox/
+nosetests.xml
+coverage.xml
+*.cover
+*.hypothesis/
+
+# Jupyter Notebooks
+.ipynb_checkpoints
+*.ipynb
+
+# Editor / IDE
+.vscode/
+.idea/
+*.swp
+*.swo
+*~
+.DS_Store
+Thumbs.db
+
+# Sphinx docs build
+docs/_build/
+docs/api/_autosummary/
+
+# MyPy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Ruff / linters
+.ruff_cache/
+
+# CI artifacts
+*.log
+*.out
+.gitlab-ci-local
+
+# Local env files
+.env.local
+.env.*.local

selinv-1.0.0/.gitlab-ci.yml

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+# --- selinv GitLab CI --------------------------------------------------------
+#
+# Stages
+#   test         – pytest for each supported Python version
+#   build-wheels – binary wheels + sdist (version tags only)
+#   publish      – upload to PyPI (version tags only)
+#
+# Required CI/CD variables
+#   PYPI_TOKEN             – PyPI API token (masked, protected)
+#
+# Optional CI/CD variables
+#   TWINE_REPOSITORY_URL   – custom PyPI registry URL (defaults to pypi.org)
+
+default:
+  image: ghcr.io/prefix-dev/pixi:latest
+
+stages:
+  - test
+  - build-wheels
+  - publish
+
+# --- test --------------------------------------------------------------------
+
+test:
+  stage: test
+  script:
+    - pixi run -e $PIXI_ENVIRONMENT test -v
+  parallel:
+    matrix:
+      - PIXI_ENVIRONMENT: [py310, py311, py312, py313, py314]
+
+
+# --- build-wheels ------------------------------------------------------------
+
+build-wheel:
+  stage: build-wheels
+  rules:
+    - if: $CI_COMMIT_TAG =~ /^v\d+\.\d+\.\d+/
+  script:
+    - pixi run -e $PIXI_ENVIRONMENT wheel
+  parallel:
+    matrix:
+      - PIXI_ENVIRONMENT: [py310, py311, py312, py313, py314]
+  artifacts:
+    paths:
+      - dist/*.whl
+    expire_in: 1 month
+
+build-sdist:
+  stage: build-wheels
+  rules:
+    - if: $CI_COMMIT_TAG =~ /^v\d+\.\d+\.\d+/
+  script:
+    - pixi run -e dev sdist
+  artifacts:
+    paths:
+      - dist/*.tar.gz
+    expire_in: 1 month
+
+# --- publish -----------------------------------------------------------------
+
+publish:
+  stage: publish
+  rules:
+    - if: $CI_COMMIT_TAG =~ /^v\d+\.\d+\.\d+/
+  needs:
+    - build-wheel
+    - build-sdist
+  script:
+    - pixi run -e dev twine upload --verbose --non-interactive --repository pypi dist/*
+  artifacts:
+    paths:
+      - dist/
+    expire_in: 1 month

selinv-1.0.0/CHANGELOG.md

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+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [Unreleased]
+
+## [0.1.0] 
+
+### Added
+- Initial release of the `selinv` Python package.
+- Python bindings for the SelInv selected-inversion algorithm (Lin, Yang et al., 2011)
+  via [nanobind](https://github.com/wjakob/nanobind).
+- `selinv(A)` — compute the diagonal of A⁻¹ for a sparse symmetric positive-definite
+  matrix `A` given in CSC/CSR format.
+- `selinvfull(A, P)` — compute selected off-diagonal elements of A⁻¹ specified by the
+  sparsity pattern `P`.
+- CMake-based build system using `scikit-build-core` for installation via `pip`.
+- Support for BLAS/LAPACK backends (OpenBLAS on Linux; Accelerate on macOS).
+- Optional METIS reordering support (disabled by default; enable with
+  `-DSELINV_USE_METIS=ON`).
+- Test suite under `tests/` exercising correctness against dense
+  reference inverses from NumPy/SciPy.
+- Sphinx documentation with mathematical background, installation guide, and API
+  reference.
+- GitLab CI pipeline for automated testing, wheel building (via `cibuildwheel`), and
+  publishing to a private PyPI registry.
+
+### Dependencies
+- Python ≥ 3.9
+- NumPy ≥ 1.21
+- SciPy ≥ 1.7
+- A Fortran compiler (gfortran ≥ 7) and CMake ≥ 3.15 are required at build time.
+- BLAS and LAPACK libraries are required at build time.
+
+[Unreleased]: https://gitlab.in2p3.fr/lemaitre/selinv/-/compare/v0.1.0...HEAD
+[0.1.0]: https://gitlab.in2p3.fr/lemaitre/selinv/-/tags/v0.1.0

selinv-1.0.0/CMakeLists.txt

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+cmake_minimum_required(VERSION 3.18)
+
+# ---------------------------------------------------------------------------
+# scikit-build-core calls CMake before the project() command to detect the
+# Python interpreter; the actual languages are declared below.
+# ---------------------------------------------------------------------------
+project(selinv LANGUAGES C CXX Fortran)
+
+set(CMAKE_CXX_STANDARD 17)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+set(CMAKE_CXX_EXTENSIONS OFF)
+
+# ---------------------------------------------------------------------------
+# Dependencies
+# ---------------------------------------------------------------------------
+
+# Python – must be found BEFORE nanobind (nanobind's cmake config requires it).
+# scikit-build-core sets this up automatically; for a plain cmake invocation
+# the interpreter and development headers must be on PATH / in the prefix.
+find_package(Python 3.9
+    REQUIRED COMPONENTS Interpreter Development.Module
+    OPTIONAL_COMPONENTS Development.SABIModule
+)
+
+# nanobind – provided as a build requirement via scikit-build-core.
+# In a plain CMake build outside scikit-build-core, run:
+#   pip install nanobind
+# and CMake will find it through the Python site-packages.
+find_package(nanobind CONFIG REQUIRED)
+
+# BLAS / LAPACK – required by the Fortran solver.
+find_package(BLAS REQUIRED)
+find_package(LAPACK REQUIRED)
+
+# ---------------------------------------------------------------------------
+# Optional: METIS reordering (Node Nested Dissection)
+# ---------------------------------------------------------------------------
+option(SELINV_USE_METIS "Enable METIS reordering support" OFF)
+
+if(SELINV_USE_METIS)
+    find_library(METIS_LIB NAMES metis REQUIRED
+        DOC "Path to the METIS library (libmetis)")
+    find_path(METIS_INCLUDE_DIR NAMES metis.h REQUIRED
+        DOC "Path to the METIS include directory")
+    if(NOT METIS_LIB OR NOT METIS_INCLUDE_DIR)
+        message(FATAL_ERROR
+            "METIS requested but not found.  "
+            "Set METIS_LIB and METIS_INCLUDE_DIR manually or disable "
+            "SELINV_USE_METIS.")
+    endif()
+    message(STATUS "selinv: METIS support enabled (${METIS_LIB})")
+endif()
+
+# ---------------------------------------------------------------------------
+# Fortran sources – all .f files in extern/selinv/
+# ---------------------------------------------------------------------------
+file(GLOB FORTRAN_SOURCES
+    "${CMAKE_CURRENT_SOURCE_DIR}/extern/selinv/*.f"
+)
+
+if(NOT FORTRAN_SOURCES)
+    message(FATAL_ERROR "No Fortran sources found in extern/selinv/")
+endif()
+
+# ---------------------------------------------------------------------------
+# Static library: Fortran core (supernodal LDL' + SelInv)
+# ---------------------------------------------------------------------------
+add_library(selinv_fortran STATIC
+    ${FORTRAN_SOURCES}
+)
+
+# Position-independent code is required for shared libraries / Python extensions
+set_target_properties(selinv_fortran PROPERTIES
+    POSITION_INDEPENDENT_CODE ON
+)
+
+target_link_libraries(selinv_fortran PUBLIC
+    ${LAPACK_LIBRARIES}
+    ${BLAS_LIBRARIES}
+)
+
+# On macOS use Accelerate instead of the separately-found BLAS/LAPACK when the
+# detected libraries resolve to the Accelerate framework (cmake ≥ 3.22 sets the
+# BLA_VENDOR to Apple for this case).
+if(APPLE)
+    target_link_options(selinv_fortran PUBLIC -framework Accelerate)
+endif()
+
+# ---------------------------------------------------------------------------
+# Static library: thread-safe C interface (replaces C2Finterface.c)
+# ---------------------------------------------------------------------------
+add_library(selinv_c_interface STATIC
+    "${CMAKE_CURRENT_SOURCE_DIR}/csrc/selinv_interface.c"
+)
+
+target_include_directories(selinv_c_interface PUBLIC
+    "${CMAKE_CURRENT_SOURCE_DIR}/csrc"
+)
+
+target_link_libraries(selinv_c_interface PUBLIC selinv_fortran)
+
+set_target_properties(selinv_c_interface PROPERTIES
+    POSITION_INDEPENDENT_CODE ON
+)
+
+if(SELINV_USE_METIS)
+    target_compile_definitions(selinv_c_interface PRIVATE METIS)
+    target_include_directories(selinv_c_interface PRIVATE "${METIS_INCLUDE_DIR}")
+    target_link_libraries(selinv_c_interface PUBLIC "${METIS_LIB}")
+endif()
+
+# ---------------------------------------------------------------------------
+# nanobind Python extension: _selinv_core
+# ---------------------------------------------------------------------------
+nanobind_add_module(_selinv_core
+    NB_STATIC          # link nanobind statically → fewer runtime dependencies
+    "${CMAKE_CURRENT_SOURCE_DIR}/csrc/selinv_bind.cpp"
+)
+
+# On Linux, bind all function references inside _selinv_core.so to the definitions
+# inside the same .so (i.e. our local 3-argument dscal_ from dscal.f), so
+# that MKL's 4-argument dscal_ — which is loaded transitively via numpy/scipy
+# at runtime — cannot override them and cause a segfault.
+# The equivalent on macOS (two-level namespace) is not needed because dylibs
+# resolve symbols at link time rather than load time.
+target_link_options(_selinv_core PRIVATE
+    $<$<PLATFORM_ID:Linux>:-Wl,-Bsymbolic-functions>
+)
+
+target_include_directories(_selinv_core PRIVATE
+    "${CMAKE_CURRENT_SOURCE_DIR}/csrc"
+)
+
+target_link_libraries(_selinv_core PRIVATE selinv_c_interface)
+
+if(SELINV_USE_METIS)
+    target_compile_definitions(_selinv_core PRIVATE SELINV_HAS_METIS)
+endif()
+
+# Install the extension alongside the Python package sources
+install(TARGETS _selinv_core
+    LIBRARY DESTINATION selinv
+    RUNTIME DESTINATION selinv
+)
+
+# ---------------------------------------------------------------------------
+# Summary
+# ---------------------------------------------------------------------------
+message(STATUS "")
+message(STATUS "selinv configuration summary")
+message(STATUS "  Fortran compiler : ${CMAKE_Fortran_COMPILER_ID} ${CMAKE_Fortran_COMPILER_VERSION}")
+message(STATUS "  C   compiler     : ${CMAKE_C_COMPILER_ID} ${CMAKE_C_COMPILER_VERSION}")
+message(STATUS "  C++ compiler     : ${CMAKE_CXX_COMPILER_ID} ${CMAKE_CXX_COMPILER_VERSION}")
+message(STATUS "  BLAS             : ${BLAS_LIBRARIES}")
+message(STATUS "  LAPACK           : ${LAPACK_LIBRARIES}")
+message(STATUS "  METIS support    : ${SELINV_USE_METIS}")
+message(STATUS "")

selinv-1.0.0/LICENSE

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+BSD 3-Clause License
+
+Copyright (c) 2025, Mathieu Bernard
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice,
+   this list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from this
+   software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGE.
+
+
+==============================================================================
+The Fortran sources in extern/selinv/ are part of the SelInv package and are
+distributed under the following license:
+==============================================================================
+
+Selected Inversion Package (SelInv)
+
+Copyright (c) 2011, The Regents of the University of California,
+Department of Energy contract-operators of the Lawrence Berkeley
+National Laboratory.  All rights reserved.
+
+1. Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+   (1) Redistributions of source code must retain the copyright notice,
+this list of conditions and the following disclaimer.
+
+   (2) Redistributions in binary form must reproduce the copyright
+notice, this list of conditions and the following disclaimer in the
+documentation and/or other materials provided with the distribution.
+
+   (3) Neither the name of the University of California, Lawrence
+Berkeley National Laboratory, U.S. Dept. of Energy nor the names of its
+contributors may be used to endorse or promote products derived from
+this software without specific prior written permission.
+
+2. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER
+OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+3. You are under no obligation whatsoever to provide any bug fixes,
+patches, or upgrades to the features, functionality or performance of
+the source code ("Enhancements") to anyone; however, if you choose to
+make your Enhancements available either publicly, or directly to
+Lawrence Berkeley National Laboratory, without imposing a separate
+written license agreement for such Enhancements, then you hereby grant
+the following license: a non-exclusive, royalty-free perpetual license
+to install, use, modify, prepare derivative works, incorporate into
+other computer software, distribute, and sublicense such enhancements or
+derivative works thereof, in binary and source code form.