tweaks for build compatibility

.devcontainer/Dockerfile

@@ -0,0 +1,18 @@
+FROM mcr.microsoft.com/devcontainers/cpp:1-debian-11
+
+ARG REINSTALL_CMAKE_VERSION_FROM_SOURCE="none"
+
+# Optionally install the cmake for vcpkg
+COPY ./reinstall-cmake.sh /tmp/
+
+RUN if [ "${REINSTALL_CMAKE_VERSION_FROM_SOURCE}" != "none" ]; then \
+ chmod +x /tmp/reinstall-cmake.sh && /tmp/reinstall-cmake.sh ${REINSTALL_CMAKE_VERSION_FROM_SOURCE}; \
+ fi \
+ && rm -f /tmp/reinstall-cmake.sh
+
+# [Optional] Uncomment this section to install additional vcpkg ports.
+# RUN su vscode -c "${VCPKG_ROOT}/vcpkg install <your-port-name-here>"
+
+# [Optional] Uncomment this section to install additional packages.
+# RUN apt-get update && export DEBIAN_FRONTEND=noninteractive \
+# && apt-get -y install --no-install-recommends <your-package-list-here>

.devcontainer/devcontainer.json

@@ -0,0 +1,26 @@
+// For format details, see https://aka.ms/devcontainer.json.
+{
+ "name": "C++",
+ "build": {
+ "dockerfile": "Dockerfile"
+ },
+ "features": {
+ "ghcr.io/devcontainers/features/python:1": {},
+ "ghcr.io/devcontainers-contrib/features/meson-asdf:2": {}
+ }
+
+ // Features to add to the dev container. More info: https://containers.dev/features.
+ // "features": {},
+
+ // Use 'forwardPorts' to make a list of ports inside the container available locally.
+ // "forwardPorts": [],
+
+ // Use 'postCreateCommand' to run commands after the container is created.
+ // "postCreateCommand": "gcc -v",
+
+ // Configure tool-specific properties.
+ // "customizations": {},
+
+ // Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
+ // "remoteUser": "root"
+}

.devcontainer/reinstall-cmake.sh

@@ -0,0 +1,59 @@
+#!/usr/bin/env bash
+#-------------------------------------------------------------------------------------------------------------
+# Copyright (c) Microsoft Corporation. All rights reserved.
+# Licensed under the MIT License. See https://go.microsoft.com/fwlink/?linkid=2090316 for license information.
+#-------------------------------------------------------------------------------------------------------------
+#
+set -e
+
+CMAKE_VERSION=${1:-"none"}
+
+if [ "${CMAKE_VERSION}" = "none" ]; then
+ echo "No CMake version specified, skipping CMake reinstallation"
+ exit 0
+fi
+
+# Cleanup temporary directory and associated files when exiting the script.
+cleanup() {
+ EXIT_CODE=$?
+ set +e
+ if [[ -n "${TMP_DIR}" ]]; then
+ echo "Executing cleanup of tmp files"
+ rm -Rf "${TMP_DIR}"
+ fi
+ exit $EXIT_CODE
+}
+trap cleanup EXIT
+
+
+echo "Installing CMake..."
+apt-get -y purge --auto-remove cmake
+mkdir -p /opt/cmake
+
+architecture=$(dpkg --print-architecture)
+case "${architecture}" in
+ arm64)
+ ARCH=aarch64 ;;
+ amd64)
+ ARCH=x86_64 ;;
+ *)
+ echo "Unsupported architecture ${architecture}."
+ exit 1
+ ;;
+esac
+
+CMAKE_BINARY_NAME="cmake-${CMAKE_VERSION}-linux-${ARCH}.sh"
+CMAKE_CHECKSUM_NAME="cmake-${CMAKE_VERSION}-SHA-256.txt"
+TMP_DIR=$(mktemp -d -t cmake-XXXXXXXXXX)
+
+echo "${TMP_DIR}"
+cd "${TMP_DIR}"
+
+curl -sSL "https://github.com/Kitware/CMake/releases/download/v${CMAKE_VERSION}/${CMAKE_BINARY_NAME}" -O
+curl -sSL "https://github.com/Kitware/CMake/releases/download/v${CMAKE_VERSION}/${CMAKE_CHECKSUM_NAME}" -O
+
+sha256sum -c --ignore-missing "${CMAKE_CHECKSUM_NAME}"
+sh "${TMP_DIR}/${CMAKE_BINARY_NAME}" --prefix=/opt/cmake --skip-license
+
+ln -s /opt/cmake/bin/cmake /usr/local/bin/cmake
+ln -s /opt/cmake/bin/ctest /usr/local/bin/ctest

.github/workflows/build_macos.yml

@@ -29,7 +29,10 @@ jobs:
  export LDFLAGS="-L/usr/local/opt/llvm/lib"
  export CPPFLAGS="-I/usr/local/opt/llvm/include"
  echo 'export PATH="/usr/local/opt/llvm/bin:$PATH"' >> ~/.bash_profile
+ echo 'export PATH="/usr/local/opt/llvm/bin:$PATH"' >> /Users/runner/.bash_profile
  source ~/.bash_profile
+ - name: Verify Clang version 
+ run: | 
  clang --version
  - name: Install OpenBLAS
  run: |
@@ -48,6 +51,9 @@ jobs:
  - name: Install package
  run: |
  pip install --verbose .
+ env:
+ CC: /usr/local/opt/llvm/bin/clang
+ CXX: /usr/local/opt/llvm/bin/clang
  - name: Test with pytest
  run: |
  python -m pytest tests/ --cov=primate --benchmark-skip

Dockerfile

@@ -0,0 +1 @@
+FROM cibuildwheel/manylinux1_x86_64:latest

pyproject.toml

@@ -4,7 +4,7 @@ requires = ['meson-python', 'wheel', 'ninja', 'pybind11', 'numpy', 'pythran-open
 
 [project]
 name = "primate"
-version = '0.2.2'
+version = "0.2.3"
 readme = "README.md"
 classifiers = [
  "Intended Audience :: Science/Research",
@@ -18,7 +18,7 @@ authors = [
 requires-python = ">=3.8"
 dependencies = [
  "numpy", 
- "scipy >= 1.11.3",
+ "scipy",
  "more_itertools"
 ]
 license = {file = "LICENSE"}

src/primate/_lanczos.cpp

@@ -39,6 +39,8 @@ using py_array = py::array_t< F, py::array::f_style | py::array::forcecast >;
 
 template< std::floating_point F > 
 auto param_spectral_func(const py::kwargs& kwargs) -> std::function< F(F) >{
+ constexpr F SQRT2_REC = 0.70710678118654752440; // 1 / sqrt(2)
+ constexpr F SQRT2_RECPI = 1.12837916709551257390; // 2 / sqrt(pi)
  auto kwargs_map = kwargs.cast< std::unordered_map< std::string, py::object > >();
  std::function< F(F) > f = std::identity();
  if (kwargs_map.contains("function")){
@@ -68,7 +70,7 @@ auto param_spectral_func(const py::kwargs& kwargs) -> std::function< F(F) >{
  F sigma = kwargs_map.contains("sigma") ? kwargs_map["sigma"].cast< F >() : 1.0;
  f = [mu, sigma](F eigenvalue) -> F { 
  auto x = (mu - eigenvalue) / sigma;
- return (0.5 * M_SQRT1_2 * M_2_SQRTPI / sigma) * exp(-0.5 * x * x); 
+ return (0.5 * SQRT2_REC * SQRT2_RECPI / sigma) * exp(-0.5 * x * x); 
  }; 
  } else if (matrix_func == "numrank"){
  F threshold = kwargs_map.contains("threshold") ? kwargs_map["threshold"].cast< F >() : 0.000001;

src/primate/trace.py

@@ -1,6 +1,6 @@
 from typing import * 
 import numpy as np
-from scipy.sparse import issparse, sparray
+from scipy.sparse import issparse
 from scipy.sparse.linalg import LinearOperator
 
 ## Package imports
@@ -11,7 +11,7 @@
 _builtin_matrix_functions = ["identity", "sqrt", "exp", "pow", "log", "numrank", "smoothstep", "gaussian"]
 
 def sl_trace (
- A: Union[LinearOperator, sparray, np.ndarray],
+ A: Union[LinearOperator, np.ndarray],
  fun: Union[str, Callable] = "identity", 
  maxiter: int = 200,
  deg: int = 20,
@@ -77,7 +77,6 @@ def sl_trace (
  [1] Ubaru, S., Chen, J., & Saad, Y. (2017). Fast estimation of tr(f(A)) via stochastic Lanczos quadrature. 
  SIAM Journal on Matrix Analysis and Applications, 38(4), 1075-1099.
  """
- # assert isinstance(A, spmatrix) or isinstance(A, sparray), "A must be a sparse matrix, for now."
  attr_checks = [hasattr(A, "__matmul__"), hasattr(A, "matmul"), hasattr(A, "dot"), hasattr(A, "matvec")]
  assert any(attr_checks), "Invalid operator; must have an overloaded 'matvec' or 'matmul' method" 
  assert hasattr(A, "shape") and len(A.shape) >= 2, "Operator must be at least two dimensional."
@@ -242,7 +241,7 @@ def sl_trace (
 
 
 def sl_gauss(
- A: Union[LinearOperator, sparray, np.ndarray],
+ A: Union[LinearOperator, np.ndarray],
  n: int = 150,
  deg: int = 20,
  pdf: str = "rademacher",