scikit-misc 0.4.0__tar.gz → 0.5.0__tar.gz

{scikit_misc-0.4.0 → scikit_misc-0.5.0}/.spin/cmds.py

@@ -100,3 +100,26 @@ def sdist():
         "--sdist",
         ".",
     ], replace=True)
+
+
+@click.option(
+    "--clean", is_flag=True,
+    help="Clean build directory before build"
+)
+@click.option(
+    "-v", "--verbose", is_flag=True,
+    help="Print all build output, even installation"
+)
+@click.argument("meson_args", nargs=-1)
+@click.pass_context
+def build(
+    ctx,
+    meson_args,
+    jobs=None,
+    clean=False,
+    verbose=False,
+    quiet=False,
+    *args,
+    **kwargs
+):
+    ctx.forward(meson.build)

{scikit_misc-0.4.0 → scikit_misc-0.5.0}/Makefile

@@ -43,7 +43,7 @@ ruff:
 	ruff check . $(args)
 
 ruff-isort:
-	ruff --select I001 --quiet . $(args)
+	ruff check --select I001 --quiet . $(args)
 
 
 lint: ruff ruff-isort

{scikit_misc-0.4.0 → scikit_misc-0.5.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: scikit-misc
-Version: 0.4.0
+Version: 0.5.0
 Summary: Miscellaneous tools for scientific computing.
 Home-page: https://has2k1.github.io/scikit-misc/stable
 Author-Email: Hassan Kibirige <has2k1@gmail.com>
@@ -42,6 +42,7 @@ Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 Classifier: Topic :: Scientific/Engineering
 Project-URL: Homepage, https://has2k1.github.io/scikit-misc/stable
 Project-URL: Repository, https://github.com/has2k1/scikit-misc

{scikit_misc-0.4.0 → scikit_misc-0.5.0}/doc/changelog.rst

@@ -1,6 +1,12 @@
 Changelog
 =========
 
+v0.5.0
+------
+*(2024-07-25)*
+
+- Fixed support for numpy 2.0
+
 v0.4.0
 ------
 *(2024-06-22)*

{scikit_misc-0.4.0 → scikit_misc-0.5.0}/doc/index.rst

@@ -7,7 +7,8 @@ A collection of scientific algorithms missing from scipy.
 At some point some of the procedures were present in scipy in an
 unstable form, hence their removal. These procedures have been
 cleaned up some and the code made more stable. Please report issues
-and file corrections `at <https://github.com/has2k1/scikit-misc>`_.
+and file corrections at `scikit-misc GitHub repository <https://github.com/has2k1/scikit-misc>`_.
+
 
 Documentation
 -------------

{scikit_misc-0.4.0 → scikit_misc-0.5.0}/meson.build

@@ -4,84 +4,39 @@ project(
   'c', 'cython',
   version: run_command('skmisc/_build_utils/version_please.py', check: true).stdout().strip(),
   license: 'BSD-3',
-  meson_version: '>= 1.1.0',
+  meson_version: '>= 1.2.99',
   default_options: [
     'buildtype=debugoptimized',
     'c_std=c99',
     'fortran_std=legacy',
-    'blas=openblas',
-    'lapack=openblas'
+    'pkgconfig.relocatable=true',
   ],
 )
 
-# Adding at project level causes many spurious -lgfortran flags.
-add_languages('fortran', native: false)
-###
-
-#### Configuration Information
-conf_data = configuration_data()
-
-# The object above is stored so that we can write it to
-# a file.
-conf_data.set('VERSION', meson.project_version())
 ###
 
 #### Setup Python
 # https://mesonbuild.com/Python-module.html
-py_mod = import('python')
-py = py_mod.find_installation(pure: false)
-py_dep = py.dependency()
-
-skmisc_dir = py.get_install_dir() / 'skmisc'
-
-conf_data.set('PYTHON_PATH', py.full_path())
-conf_data.set('PYTHON_VERSION', py.language_version())
+py3 = import('python').find_installation(pure: false)
+py3_dep = py3.dependency()
 ###
 
-#### Setup Compilers
+#### Define Compilers
 cc = meson.get_compiler('c')
-ff = meson.get_compiler('fortran')
-# generator() doesn't accept compilers, only found programs. Cast it.
 cy = meson.get_compiler('cython')
+# generator() doesn't accept compilers, only found programs. Cast it.
 cython = find_program(cy.cmd_array()[0])
-
-compilers = {
-  'C': cc,
-  'CYTHON': cy,
-  'FORTRAN': ff
-}
-
-foreach name, compiler : compilers
-  # conf_data.set(name + '_COMP_CMD_ARRAY', compiler.cmd_array())
-  conf_data.set(name + '_COMP_CMD_ARRAY', compiler.get_id())
-  conf_data.set(name + '_COMP', compiler.get_id())
-  conf_data.set(name + '_COMP_LINKER_ID', compiler.get_linker_id())
-  conf_data.set(name + '_COMP_VERSION', compiler.version())
-  conf_data.set(name + '_COMP_CMD_ARRAY', ', '.join(compiler.cmd_array()))
-endforeach
-###
-
-#### Setup Machine CPU & System Information
-machines = {
-  'HOST': host_machine,
-  'BUILD': build_machine,
-}
-
-foreach name, machine : machines
-  conf_data.set(name + '_CPU', machine.cpu())
-  conf_data.set(name + '_CPU_FAMILY', machine.cpu_family())
-  conf_data.set(name + '_CPU_ENDIAN', machine.endian())
-  conf_data.set(name + '_CPU_SYSTEM', machine.system())
-endforeach
-
-conf_data.set('CROSS_COMPILED', meson.is_cross_build())
 ###
 
 #### Compiler Arguments and Settings
 # Check compiler is recent enough (see "Toolchain Roadmap" for details)
 if cc.get_id() == 'gcc'
-  if not cc.version().version_compare('>=8.0')
-    error('scikit-misc requires GCC >= 8.0')
+  if not cc.version().version_compare('>=9.1')
+    error('scikit-misc requires GCC >= 9.1')
+  endif
+elif cc.get_id() == 'clang' or cc.get_id() == 'clang-cl'
+  if not cc.version().version_compare('>=12.0')
+    error('scikit-misc requires clang >= 12.0')
   endif
 elif cc.get_id() == 'msvc'
   if not cc.version().version_compare('>=19.20')
@@ -90,21 +45,39 @@ elif cc.get_id() == 'msvc'
   endif
 endif
 
+if not cy.version().version_compare('>=3.0.6')
+  error('NumPy requires Cython >= 3.0.6')
+endif
+
+# Add default compile flags for any compiler that supports them.
+# Note that MSVC does not support strict aliasing at all, and neither do the
+# Intel compilers on Windows, so the `-fno` flavor of the flag should be fine.
+add_project_arguments(
+  cc.get_supported_arguments( '-fno-strict-aliasing'), language : 'c'
+)
+
 # link against the standard math library since we use it in c
 m_dep = cc.find_library('m', required : false)
 if m_dep.found()
   add_project_link_arguments('-lm', language : 'c')
 endif
 
+# Adding at project level causes many spurious -lgfortran flags.
 add_languages('fortran', native: false)
+ff = meson.get_compiler('fortran')
 if ff.has_argument('-Wno-conversion')
   add_project_arguments('-Wno-conversion', language: 'fortran')
 endif
 
-
 is_windows = host_machine.system() == 'windows'
 is_macos = host_machine.system() == 'darwin'
 
+if is_macos and cc.has_link_argument('-Wl,-ld_classic')
+  # New linker introduced in macOS 14 not working yet with at least OpenBLAS in Spack,
+  # see gh-24964 (and linked scipy issue from there).
+  add_project_link_arguments('-Wl,-ld_classic', language : ['c', 'cpp'])
+endif
+
 # Intel compilers default to fast-math, so disable it if we detect Intel
 # compilers. A word of warning: this may not work with the conda-forge
 # compilers, because those have the annoying habit of including lots of flags
@@ -113,18 +86,18 @@ is_macos = host_machine.system() == 'darwin'
 # is actually needed, everything else shouldn't be there).
 _intel_cflags = []
 _intel_fflags = []
-if cc.get_id() == 'intel'
+if cc.get_id() in ['intel', 'intel-llvm']
   _intel_cflags += cc.get_supported_arguments('-fp-model=strict')
-elif cc.get_id() == 'intel-cl'
+elif cc.get_id() in ['intel-cl', 'intel-llvm-cl']
   _intel_cflags += cc.get_supported_arguments('/fp:strict')
 endif
-if ff.get_id() == 'intel'
+if ff.get_id() in ['intel', 'intel-llvm']
   _intel_fflags = ff.get_supported_arguments('-fp-model=strict')
   minus0_arg = ['-assume', 'minus0']
   if ff.has_multi_arguments(minus0_arg)
     _intel_fflags += minus0_arg
   endif
-elif ff.get_id() == 'intel-cl'
+elif ff.get_id() in ['intel-cl', 'intel-llvm-cl']
   # Intel Fortran on Windows does things differently, so deal with that
   # (also specify dynamic linking and the right name mangling)
   _intel_fflags = ff.get_supported_arguments(
@@ -134,10 +107,6 @@ elif ff.get_id() == 'intel-cl'
 endif
 add_project_arguments(_intel_cflags, language: ['c'])
 add_project_arguments(_intel_fflags, language: 'fortran')
-
-cython_c_args = []
-cython_args = ['-3', '--fast-fail', '--output-file', '@OUTPUT@', '--include-dir', '@BUILD_ROOT@', '@INPUT@']
-cython_c_link_args = []
 ###
 
 #### Include Main Package

{scikit_misc-0.4.0 → scikit_misc-0.5.0}/meson_options.txt

@@ -1,7 +1,3 @@
-option('blas', type: 'string', value: 'openblas',
-        description: 'option for BLAS library switching')
-option('lapack', type: 'string', value: 'openblas',
-        description: 'option for LAPACK library switching')
 option('use-g77-abi', type: 'boolean', value: false,
         description: 'If set to true, forces using g77 compatibility wrappers ' +
                      'for LAPACK functions. The default is to use gfortran ' +

{scikit_misc-0.4.0 → scikit_misc-0.5.0}/pyproject.toml

@@ -25,6 +25,7 @@ classifiers = [
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
     "Topic :: Scientific/Engineering",
 ]
 
@@ -75,7 +76,7 @@ changelog = "https://has2k1.github.io/scikit-misc/stable/changelog.html"
 build-backend = 'mesonpy'
 requires = [
     "meson-python>=0.15.0",
-    "Cython>=3.0.8",  # when updating version, also update check in meson.build
+    "Cython>=3.0.8",
     "setuptools",
     "wheel",
 
@@ -148,33 +149,47 @@ Environments = [
 
 ########## Tool - CIBuildWheel ##########
 [tool.cibuildwheel]
-skip = "pp* *_ppc64le *_i686 *_s390x *-musllinux*"
-build-verbosity = "3"
-# gmpy2 and scikit-umfpack are usually added for testing. However, there are
-# currently wheels missing that make the test script fail.
-test-requires = ["pytest", "pytest-cov"]
+# Note: the below skip command doesn't do much currently, the platforms to
+# build wheels for in CI are controlled in `.github/workflows/wheels.yml` and
+# `tools/ci/cirrus_wheels.yml`.
+build-frontend = "build"
+skip = "cp36-* cp37-* cp-38* pp37-* *-manylinux_i686 *_ppc64le *_s390x *_universal2"
+before-build = "bash {project}/tools/wheels/cibw_before_build.sh {project}"
 test-command = "bash {project}/tools/wheels/cibw_test_command.sh {project}"
+test-requires = [
+    "pytest",
+    "pytest-cov",
+]
 
 [tool.cibuildwheel.linux]
 manylinux-x86_64-image = "manylinux2014"
 manylinux-aarch64-image = "manylinux2014"
-before-build = "bash {project}/tools/wheels/cibw_before_build_linux.sh {project}"
+
+[tool.cibuildwheel.linux.environment]
+# RUNNER_OS is a GitHub Actions specific env var; define it here so it works on Cirrus CI too
+RUNNER_OS="Linux"
+
 
 [tool.cibuildwheel.macos]
-before-build = "bash {project}/tools/wheels/cibw_before_build_macos.sh {project}"
+# universal2 wheels are not supported (see gh-21233), use `delocate-fuse` if you need them
+# note that universal2 wheels are not built, they're listed in the tool.cibuildwheel.skip
+# section
+# Not clear why the DYLD_LIBRARY_PATH is not passed through from the environment
+repair-wheel-command = [
+  "echo DYLD_LIBRARY_PATH $DYLD_LIBRARY_PATH",
+  "delocate-wheel --require-archs {delocate_archs} -w {dest_dir} -v {wheel}",
+]
+
+
+[tool.cibuildwheel.macos.environment]
+PKG_CONFIG_PATH="{project}"
 
 [tool.cibuildwheel.windows]
-before-build = "bash {project}/tools/wheels/cibw_before_build_win.sh {project}"
-repair-wheel-command = "bash ./tools/wheels/repair_windows.sh {wheel} {dest_dir}"
+# This does not work, use CIBW_ENVIRONMENT_WINDOWS
+config-settings = "setup-args=--vsenv build-dir=build"
+repair-wheel-command = "bash -el ./tools/wheels/repair_windows.sh {wheel} {dest_dir}"
 
 [[tool.cibuildwheel.overrides]]
 select = "*-win32"
-
-[[tool.cibuildwheel.overrides]]
-select = "*-win_amd64"
-# can use pkg-config detection for win_amd64 because the installed rtools
-# provide a working pkg-config.
-# An alternative is to set CMAKE_PREFIX_PATH="c:/opt/openblas/if_32/32"
-# Don't use double backslash for path separators, they don't get passed
-# to the build correctly
-environment = { PKG_CONFIG_PATH="c:/opt/64/lib/pkgconfig" }
+config-settings = "setup-args=--vsenv build-dir=build"
+repair-wheel-command = ""

scikit_misc-0.5.0/requirements/ci_requirements.txt

@@ -0,0 +1,3 @@
+spin
+# Keep this in sync with ci32_requirements.txt
+scipy-openblas64==0.3.27.44.3

scikit_misc-0.5.0/requirements/openblas.txt

@@ -0,0 +1 @@
+scipy-openblas32==0.3.27.63.1

{scikit_misc-0.4.0 → scikit_misc-0.5.0}/skmisc/__config__.py.in

@@ -45,26 +45,6 @@ CONFIG = _cleanup(
             },
         },
         "Build Dependencies": {
-            "blas": {
-                "name": "@BLAS_NAME@",
-                "found": bool("@BLAS_FOUND@".lower().replace('false', '')),
-                "version": "@BLAS_VERSION@",
-                "detection method": "@BLAS_TYPE_NAME@",
-                "include directory": r"@BLAS_INCLUDEDIR@",
-                "lib directory": r"@BLAS_LIBDIR@",
-                "openblas configuration": "@BLAS_OPENBLAS_CONFIG@",
-                "pc file directory": r"@BLAS_PCFILEDIR@",
-            },
-            "lapack": {
-                "name": "@LAPACK_NAME@",
-                "found": bool("@LAPACK_FOUND@".lower().replace('false', '')),
-                "version": "@LAPACK_VERSION@",
-                "detection method": "@LAPACK_TYPE_NAME@",
-                "include directory": r"@LAPACK_INCLUDEDIR@",
-                "lib directory": r"@LAPACK_LIBDIR@",
-                "openblas configuration": "@LAPACK_OPENBLAS_CONFIG@",
-                "pc file directory": r"@LAPACK_PCFILEDIR@",
-            },
         },
         "Machine Information": {
             "host": {

{scikit_misc-0.4.0 → scikit_misc-0.5.0}/skmisc/_version.py

@@ -1,4 +1,4 @@
 # This file is dynamically generated by the build system to support
 # versioning with source control. Do not edit by hand
 
-__version__ = "0.4.0"
+__version__ = "0.5.0"

{scikit_misc-0.4.0 → scikit_misc-0.5.0}/skmisc/loess/meson.build

@@ -16,21 +16,21 @@ loess_cython_gen = generator(
 ###
 
 #### Fortran Loess into a static library
-floess_sources = [
-  'src/loessf.f',
-  'src/linpack_lite.f'
-]
 
 floess_lib = static_library(
   'floess',
-  floess_sources,
-  fortran_args: [fortran_ignore_warnings],
-  dependencies: [blas, lapack]
+  sources: [
+    'src/loessf.f',
+    'src/linpack_lite.f',
+    'src/blas_lite.f'
+  ],
+  fortran_args: [fortran_args, fortran_ignore_warnings],
+  link_args: [fortran_link_args],
 )
 ###
 
 #### Loess Extenstion Module
-py.extension_module(
+py3.extension_module(
   '_loess',
    sources: [
      'src/loess.c',
@@ -39,8 +39,8 @@ py.extension_module(
      'src/predict.c',
      loess_cython_gen.process('src/_loess.pyx')
    ],
-   c_args: [cython_c_args],
-   dependencies: [py_dep, npymath_lib, np_dep],
+   c_args: [c_args, cython_c_args],
+   dependencies: [py3_dep, npymath_lib, np_dep],
    link_with: [floess_lib],
    link_args: [cython_c_link_args],
    link_language: 'c',
@@ -55,7 +55,7 @@ python_sources = [
   '__init__.py'
 ]
 
-py.install_sources(
+py3.install_sources(
   python_sources,
   subdir: 'skmisc/loess'
 )

{scikit_misc-0.4.0 → scikit_misc-0.5.0}/skmisc/loess/src/S.h

@@ -12,21 +12,16 @@
  * handed to the local loader; e.g., "x_" in system V, Berkeley & 9th edition
  */
 
-#ifdef lint
-#define F77_SUB(x) x
-#define F77_COM(x) x
+#ifdef _MSC_VER
+  // Microsoft Visual C++
+  #define F77_SUB(x) x##_
 #else
-#ifdef __STDC__
-#define F77_SUB(x) x##_
-#define F77_COM(x) x##_
-#else
-#define F77_SUB(x) x/**/_
-#define F77_COM(x) x/**/_
-#endif
+  // Other compilers
+  #ifdef __STDC__
+    #define F77_SUB(x) x##_
+  #else
+    #define F77_SUB(x) x/**/_
+  #endif
 #endif
 
 #define NULL_ENTRY          ((int *)NULL)
-
-
-
-