GITENV file updated 15

cgpenv/Lib/site-packages/scipy/INSTALL.rst.txt

+Building and installing SciPy
++++++++++++++++++++++++++++++
+
+See https://www.scipy.org/install.html
+
+.. Contents::
+
+
+INTRODUCTION
+============
+
+It is *strongly* recommended that you use either a complete scientific Python
+distribution or binary packages on your platform if they are available, in
+particular on Windows and Mac OS X. You should not attempt to build SciPy if
+you are not familiar with compiling software from sources.
+
+Recommended distributions are:
+
+  - Enthought Canopy (https://www.enthought.com/products/canopy/)
+  - Anaconda (https://www.anaconda.com)
+  - Python(x,y) (https://python-xy.github.io/)
+  - WinPython (https://winpython.github.io/)
+
+The rest of this install documentation summarizes how to build Scipy.  Note
+that more extensive (and possibly more up-to-date) build instructions are
+maintained at https://scipy.github.io/devdocs/building/
+
+
+PREREQUISITES
+=============
+
+SciPy requires the following software installed for your platform:
+
+1) Python__ >= 3.7
+
+__ https://www.python.org
+
+2) NumPy__ >= 1.16.5
+
+__ https://www.numpy.org/
+
+If building from source, SciPy also requires:
+
+3) setuptools__
+
+__ https://github.com/pypa/setuptools
+
+4) pybind11__ >= 2.4.3
+
+__ https://github.com/pybind/pybind11
+
+5) If you want to build the documentation: Sphinx__ >= 2.4.0 and < 3.1.0
+
+__ http://www.sphinx-doc.org/
+
+6) If you want to build SciPy master or other unreleased version from source
+   (Cython-generated C sources are included in official releases):
+   Cython__ >= 0.29.18
+
+__ http://cython.org/
+
+Windows
+-------
+
+Compilers
+~~~~~~~~~
+
+There are two ways to build SciPy on Windows:
+
+1. Use Intel MKL, and Intel compilers or ifort + MSVC.  This is what Anaconda
+   and Enthought Canopy use.
+2. Use MSVC + GFortran with OpenBLAS.  This is how the SciPy Windows wheels are
+   built.
+
+Mac OS X
+--------
+
+It is recommended to use GCC or Clang, both work fine. Gcc is available for
+free when installing Xcode, the developer toolsuite on Mac OS X. You also
+need a Fortran compiler, which is not included with Xcode: you should use a
+recent GFortran from an OS X package manager (like Homebrew).
+
+Please do NOT use GFortran from `hpc.sourceforge.net <http://hpc.sourceforge.net>`_,
+it is known to generate buggy SciPy binaries.
+
+You should also use a BLAS/LAPACK library from an OS X package manager.
+ATLAS, OpenBLAS, and MKL all work.
+
+As of SciPy version 1.2.0, we do not support compiling against the system
+Accelerate library for BLAS and LAPACK. It does not support a sufficiently
+recent LAPACK interface.
+
+Linux
+-----
+
+Most common distributions include all the dependencies.  You will need to
+install a BLAS/LAPACK (all of ATLAS, OpenBLAS, MKL work fine) including
+development headers, as well as development headers for Python itself.  Those
+are typically packaged as python-dev.
+
+
+INSTALLING SCIPY
+================
+
+For the latest information, see the website:
+
+  https://www.scipy.org
+
+
+Development version from Git
+----------------------------
+Use the command::
+
+  git clone https://github.com/scipy/scipy.git
+
+  cd scipy
+  git clean -xdf
+  python setup.py install --user
+
+Documentation
+-------------
+Type::
+
+  cd scipy/doc
+  make html
+
+From tarballs
+-------------
+Unpack ``SciPy-<version>.tar.gz``, change to the ``SciPy-<version>/``
+directory, and run::
+
+  pip install . -v --user
+
+This may take several minutes to half an hour depending on the speed of your
+computer.
+
+
+TESTING
+=======
+
+To test SciPy after installation (highly recommended), execute in Python::
+
+   >>> import scipy
+   >>> scipy.test()
+
+To run the full test suite use::
+
+   >>> scipy.test('full')
+
+If you are upgrading from an older SciPy release, please test your code for any
+deprecation warnings before and after upgrading to avoid surprises:
+
+   $ python -Wd -c my_code_that_shouldnt_break.py
+
+Please note that you must have version 1.0 or later of the Pytest test
+framework installed in order to run the tests.  More information about Pytest is
+available on the website__.
+
+__ https://pytest.org/
+
+COMPILER NOTES
+==============
+
+You can specify which Fortran compiler to use by using the following
+install command::
+
+  python setup.py config_fc --fcompiler=<Vendor> install
+
+To see a valid list of <Vendor> names, run::
+
+  python setup.py config_fc --help-fcompiler
+
+IMPORTANT: It is highly recommended that all libraries that SciPy uses (e.g.
+BLAS and ATLAS libraries) are built with the same Fortran compiler. In most
+cases, if you mix compilers, you will not be able to import SciPy at best, and will have
+crashes and random results at worst.
+
+UNINSTALLING
+============
+
+When installing with ``python setup.py install`` or a variation on that, you do
+not get proper uninstall behavior for an older already installed SciPy version.
+In many cases that's not a problem, but if it turns out to be an issue, you
+need to manually uninstall it first (remove from e.g. in
+``/usr/lib/python3.4/site-packages/scipy`` or
+``$HOME/lib/python3.4/site-packages/scipy``).
+
+Alternatively, you can use ``pip install . --user`` instead of ``python
+setup.py install --user`` in order to get reliable uninstall behavior.
+The downside is that ``pip`` doesn't show you a build log and doesn't support
+incremental rebuilds (it copies the whole source tree to a tempdir).
+
+TROUBLESHOOTING
+===============
+
+If you experience problems when building/installing/testing SciPy, you
+can ask help from scipy-user@python.org or scipy-dev@python.org mailing
+lists. Please include the following information in your message:
+
+NOTE: You can generate some of the following information (items 1-5,7)
+in one command::
+
+  python -c 'from numpy.f2py.diagnose import run; run()'
+
+1) Platform information::
+
+     python -c 'import os, sys; print(os.name, sys.platform)'
+     uname -a
+     OS, its distribution name and version information
+     etc.
+
+2) Information about C, C++, Fortran compilers/linkers as reported by
+   the compilers when requesting their version information, e.g.,
+   the output of
+   ::
+
+     gcc -v
+     g77 --version
+
+3) Python version::
+
+     python -c 'import sys; print(sys.version)'
+
+4) NumPy version::
+
+     python -c 'import numpy; print(numpy.__version__)'
+
+5) ATLAS version, the locations of atlas and lapack libraries, building
+   information if any. If you have ATLAS version 3.3.6 or newer, then
+   give the output of the last command in
+   ::
+
+     cd scipy/Lib/linalg
+     python setup_atlas_version.py build_ext --inplace --force
+     python -c 'import atlas_version'
+
+7) The output of the following commands
+   ::
+
+     python INSTALLDIR/numpy/distutils/system_info.py
+
+   where INSTALLDIR is, for example, /usr/lib/python3.4/site-packages/.
+
+8) Feel free to add any other relevant information.
+   For example, the full output (both stdout and stderr) of the SciPy
+   installation command can be very helpful. Since this output can be
+   rather large, ask before sending it into the mailing list (or
+   better yet, to one of the developers, if asked).
+
+9) In case of failing to import extension modules, the output of
+   ::
+
+     ldd /path/to/ext_module.so
+
+   can be useful.

cgpenv/Lib/site-packages/scipy/__config__.py

+# This file is generated by numpy's setup.py
+# It contains system_info results at the time of building this package.
+__all__ = ["get_info","show"]
+
+
+import os
+import sys
+
+extra_dll_dir = os.path.join(os.path.dirname(__file__), '.libs')
+
+if sys.platform == 'win32' and os.path.isdir(extra_dll_dir):
+    if sys.version_info >= (3, 8):
+        os.add_dll_directory(extra_dll_dir)
+    else:
+        os.environ.setdefault('PATH', '')
+        os.environ['PATH'] += os.pathsep + extra_dll_dir
+
+lapack_mkl_info={}
+openblas_lapack_info={'library_dirs': ['C:\\projects\\scipy-wheels\\scipy\\build\\openblas_lapack_info'], 'libraries': ['openblas_lapack_info'], 'language': 'f77', 'define_macros': [('HAVE_CBLAS', None)]}
+lapack_opt_info={'library_dirs': ['C:\\projects\\scipy-wheels\\scipy\\build\\openblas_lapack_info'], 'libraries': ['openblas_lapack_info'], 'language': 'f77', 'define_macros': [('HAVE_CBLAS', None)]}
+blas_mkl_info={}
+blis_info={}
+openblas_info={'library_dirs': ['C:\\projects\\scipy-wheels\\scipy\\build\\openblas_info'], 'libraries': ['openblas_info'], 'language': 'f77', 'define_macros': [('HAVE_CBLAS', None)]}
+blas_opt_info={'library_dirs': ['C:\\projects\\scipy-wheels\\scipy\\build\\openblas_info'], 'libraries': ['openblas_info'], 'language': 'f77', 'define_macros': [('HAVE_CBLAS', None)]}
+
+def get_info(name):
+    g = globals()
+    return g.get(name, g.get(name + "_info", {}))
+
+def show():
+    """
+    Show libraries in the system on which NumPy was built.
+
+    Print information about various resources (libraries, library
+    directories, include directories, etc.) in the system on which
+    NumPy was built.
+
+    See Also
+    --------
+    get_include : Returns the directory containing NumPy C
+                  header files.
+
+    Notes
+    -----
+    Classes specifying the information to be printed are defined
+    in the `numpy.distutils.system_info` module.
+
+    Information may include:
+
+    * ``language``: language used to write the libraries (mostly
+      C or f77)
+    * ``libraries``: names of libraries found in the system
+    * ``library_dirs``: directories containing the libraries
+    * ``include_dirs``: directories containing library header files
+    * ``src_dirs``: directories containing library source files
+    * ``define_macros``: preprocessor macros used by
+      ``distutils.setup``
+
+    Examples
+    --------
+    >>> np.show_config()
+    blas_opt_info:
+        language = c
+        define_macros = [('HAVE_CBLAS', None)]
+        libraries = ['openblas', 'openblas']
+        library_dirs = ['/usr/local/lib']
+    """
+    for name,info_dict in globals().items():
+        if name[0] == "_" or type(info_dict) is not type({}): continue
+        print(name + ":")
+        if not info_dict:
+            print("  NOT AVAILABLE")
+        for k,v in info_dict.items():
+            v = str(v)
+            if k == "sources" and len(v) > 200:
+                v = v[:60] + " ...\n... " + v[-60:]
+            print("    %s = %s" % (k,v))

cgpenv/Lib/site-packages/scipy/__init__.py

+"""
+SciPy: A scientific computing package for Python
+================================================
+
+Documentation is available in the docstrings and
+online at https://docs.scipy.org.
+
+Contents
+--------
+SciPy imports all the functions from the NumPy namespace, and in
+addition provides:
+
+Subpackages
+-----------
+Using any of these subpackages requires an explicit import. For example,
+``import scipy.cluster``.
+
+::
+
+ cluster                      --- Vector Quantization / Kmeans
+ fft                          --- Discrete Fourier transforms
+ fftpack                      --- Legacy discrete Fourier transforms
+ integrate                    --- Integration routines
+ interpolate                  --- Interpolation Tools
+ io                           --- Data input and output
+ linalg                       --- Linear algebra routines
+ linalg.blas                  --- Wrappers to BLAS library
+ linalg.lapack                --- Wrappers to LAPACK library
+ misc                         --- Various utilities that don't have
+                                  another home.
+ ndimage                      --- N-D image package
+ odr                          --- Orthogonal Distance Regression
+ optimize                     --- Optimization Tools
+ signal                       --- Signal Processing Tools
+ signal.windows               --- Window functions
+ sparse                       --- Sparse Matrices
+ sparse.linalg                --- Sparse Linear Algebra
+ sparse.linalg.dsolve         --- Linear Solvers
+ sparse.linalg.dsolve.umfpack --- :Interface to the UMFPACK library:
+                                  Conjugate Gradient Method (LOBPCG)
+ sparse.linalg.eigen          --- Sparse Eigenvalue Solvers
+ sparse.linalg.eigen.lobpcg   --- Locally Optimal Block Preconditioned
+                                  Conjugate Gradient Method (LOBPCG)
+ spatial                      --- Spatial data structures and algorithms
+ special                      --- Special functions
+ stats                        --- Statistical Functions
+
+Utility tools
+-------------
+::
+
+ test              --- Run scipy unittests
+ show_config       --- Show scipy build configuration
+ show_numpy_config --- Show numpy build configuration
+ __version__       --- SciPy version string
+ __numpy_version__ --- Numpy version string
+
+"""
+
+
+def __dir__():
+    return ['test']
+
+
+__all__ = __dir__()
+
+from numpy import show_config as show_numpy_config
+if show_numpy_config is None:
+    raise ImportError(
+        "Cannot import SciPy when running from NumPy source directory.")
+from numpy import __version__ as __numpy_version__
+
+# Import numpy symbols to scipy name space (DEPRECATED)
+from ._lib.deprecation import _deprecated
+import numpy as _num
+linalg = None
+_msg = ('scipy.{0} is deprecated and will be removed in SciPy 2.0.0, '
+        'use numpy.{0} instead')
+# deprecate callable objects, skipping classes
+for _key in _num.__all__:
+    _fun = getattr(_num, _key)
+    if callable(_fun) and not isinstance(_fun, type):
+        _fun = _deprecated(_msg.format(_key))(_fun)
+    globals()[_key] = _fun
+from numpy.random import rand, randn
+_msg = ('scipy.{0} is deprecated and will be removed in SciPy 2.0.0, '
+        'use numpy.random.{0} instead')
+rand = _deprecated(_msg.format('rand'))(rand)
+randn = _deprecated(_msg.format('randn'))(randn)
+# fft is especially problematic, so was removed in SciPy 1.6.0
+from numpy.fft import ifft
+ifft = _deprecated('scipy.ifft is deprecated and will be removed in SciPy '
+                   '2.0.0, use scipy.fft.ifft instead')(ifft)
+import numpy.lib.scimath as _sci
+_msg = ('scipy.{0} is deprecated and will be removed in SciPy 2.0.0, '
+        'use numpy.lib.scimath.{0} instead')
+for _key in _sci.__all__:
+    _fun = getattr(_sci, _key)
+    if callable(_fun):
+        _fun = _deprecated(_msg.format(_key))(_fun)
+    globals()[_key] = _fun
+
+__all__ += _num.__all__
+__all__ += ['randn', 'rand', 'ifft']
+
+del _num
+# Remove the linalg imported from NumPy so that the scipy.linalg package can be
+# imported.
+del linalg
+__all__.remove('linalg')
+
+# We first need to detect if we're being called as part of the SciPy
+# setup procedure itself in a reliable manner.
+try:
+    __SCIPY_SETUP__
+except NameError:
+    __SCIPY_SETUP__ = False
+
+
+if __SCIPY_SETUP__:
+    import sys as _sys
+    _sys.stderr.write('Running from SciPy source directory.\n')
+    del _sys
+else:
+    try:
+        from scipy.__config__ import show as show_config
+    except ImportError as e:
+        msg = """Error importing SciPy: you cannot import SciPy while
+        being in scipy source directory; please exit the SciPy source
+        tree first and relaunch your Python interpreter."""
+        raise ImportError(msg) from e
+
+    from scipy.version import version as __version__
+
+    # Allow distributors to run custom init code
+    from . import _distributor_init
+
+    from scipy._lib import _pep440
+    # In maintenance branch, change to np_maxversion N+3 if numpy is at N
+    # See setup.py for more details
+    np_minversion = '1.16.5'
+    np_maxversion = '1.23.0'
+    if (_pep440.parse(__numpy_version__) < _pep440.Version(np_minversion) or
+            _pep440.parse(__numpy_version__) >= _pep440.Version(np_maxversion)):
+        import warnings
+        warnings.warn(f"A NumPy version >={np_minversion} and <{np_maxversion}"
+                      f" is required for this version of SciPy (detected "
+                      f"version {__numpy_version__}",
+                      UserWarning)
+
+    del _pep440
+
+    from scipy._lib._ccallback import LowLevelCallable
+
+    from scipy._lib._testutils import PytestTester
+    test = PytestTester(__name__)
+    del PytestTester
+
+    # This makes "from scipy import fft" return scipy.fft, not np.fft
+    del fft

cgpenv/Lib/site-packages/scipy/_build_utils/__init__.py

+import os
+
+import numpy as np
+from ._fortran import *
+from .system_info import combine_dict
+
+
+# Don't use the deprecated NumPy C API. Define this to a fixed version instead of
+# NPY_API_VERSION in order not to break compilation for released SciPy versions
+# when NumPy introduces a new deprecation. Use in setup.py::
+#
+#   config.add_extension('_name', sources=['source_fname'], **numpy_nodepr_api)
+#
+numpy_nodepr_api = dict(define_macros=[("NPY_NO_DEPRECATED_API",
+                                        "NPY_1_9_API_VERSION")])
+
+
+def uses_blas64():
+    return (os.environ.get("NPY_USE_BLAS_ILP64", "0") != "0")
+
+def import_file(folder, module_name):
+    """Import a file directly, avoiding importing scipy"""
+    import importlib
+    import pathlib
+
+    fname = pathlib.Path(folder) / f'{module_name}.py'
+    spec = importlib.util.spec_from_file_location(module_name, str(fname))
+    module = importlib.util.module_from_spec(spec)
+    spec.loader.exec_module(module)
+    return module
+
+
+from scipy._lib._testutils import PytestTester
+test = PytestTester(__name__)
+del PytestTester

cgpenv/Lib/site-packages/scipy/_build_utils/compiler_helper.py

+"""
+Helpers for detection of compiler features
+"""
+import tempfile
+import os
+import sys
+from numpy.distutils.system_info import dict_append
+
+def try_compile(compiler, code=None, flags=[], ext=None):
+    """Returns True if the compiler is able to compile the given code"""
+    from distutils.errors import CompileError
+    from numpy.distutils.fcompiler import FCompiler
+
+    if code is None:
+        if isinstance(compiler, FCompiler):
+            code = "      program main\n      return\n      end"
+        else:
+            code = 'int main (int argc, char **argv) { return 0; }'
+
+    ext = ext or compiler.src_extensions[0]
+
+    with tempfile.TemporaryDirectory() as temp_dir:
+        fname = os.path.join(temp_dir, 'main'+ext)
+        with open(fname, 'w') as f:
+            f.write(code)
+
+        try:
+            compiler.compile([fname], output_dir=temp_dir, extra_postargs=flags)
+        except CompileError:
+            return False
+    return True
+
+
+def has_flag(compiler, flag, ext=None):
+    """Returns True if the compiler supports the given flag"""
+    return try_compile(compiler, flags=[flag], ext=ext)
+
+
+def get_cxx_std_flag(compiler):
+    """Detects compiler flag for c++14, c++11, or None if not detected"""
+    # GNU C compiler documentation uses single dash:
+    #    https://gcc.gnu.org/onlinedocs/gcc/Standards.html
+    # but silently understands two dashes, like --std=c++11 too.
+    # Other GCC compatible compilers, like Intel C Compiler on Linux do not.
+    gnu_flags = ['-std=c++14', '-std=c++11']
+    flags_by_cc = {
+        'msvc': ['/std:c++14', None],
+        'intelw': ['/Qstd=c++14', '/Qstd=c++11'],
+        'intelem': ['-std=c++14', '-std=c++11']
+    }
+    flags = flags_by_cc.get(compiler.compiler_type, gnu_flags)
+
+    for flag in flags:
+        if flag is None:
+            return None
+
+        if has_flag(compiler, flag, ext='.cpp'):
+            return flag
+
+    from numpy.distutils import log
+    log.warn('Could not detect c++ standard flag')
+    return None
+
+
+def get_c_std_flag(compiler):
+    """Detects compiler flag to enable C99"""
+    gnu_flag = '-std=c99'
+    flag_by_cc = {
+        'msvc': None,
+        'intelw': '/Qstd=c99',
+        'intelem': '-std=c99'
+    }
+    flag = flag_by_cc.get(compiler.compiler_type, gnu_flag)
+
+    if flag is None:
+        return None
+
+    if has_flag(compiler, flag, ext='.c'):
+        return flag
+
+    from numpy.distutils import log
+    log.warn('Could not detect c99 standard flag')
+    return None
+
+
+def try_add_flag(args, compiler, flag, ext=None):
+    """Appends flag to the list of arguments if supported by the compiler"""
+    if try_compile(compiler, flags=args+[flag], ext=ext):
+        args.append(flag)
+
+
+def set_c_flags_hook(build_ext, ext):
+    """Sets basic compiler flags for compiling C99 code"""
+    std_flag = get_c_std_flag(build_ext.compiler)
+    if std_flag is not None:
+        ext.extra_compile_args.append(std_flag)
+
+
+def set_cxx_flags_hook(build_ext, ext):
+    """Sets basic compiler flags for compiling C++11 code"""
+    cc = build_ext._cxx_compiler
+    args = ext.extra_compile_args
+
+    std_flag = get_cxx_std_flag(cc)
+    if std_flag is not None:
+        args.append(std_flag)
+
+    if sys.platform == 'darwin':
+        # Set min macOS version
+        min_macos_flag = '-mmacosx-version-min=10.9'
+        if has_flag(cc, min_macos_flag):
+            args.append(min_macos_flag)
+            ext.extra_link_args.append(min_macos_flag)
+
+
+def set_cxx_flags_clib_hook(build_clib, build_info):
+    cc = build_clib.compiler
+    new_args = []
+    new_link_args = []
+
+    std_flag = get_cxx_std_flag(cc)
+    if std_flag is not None:
+        new_args.append(std_flag)
+
+    if sys.platform == 'darwin':
+        # Set min macOS version
+        min_macos_flag = '-mmacosx-version-min=10.9'
+        if has_flag(cc, min_macos_flag):
+            new_args.append(min_macos_flag)
+            new_link_args.append(min_macos_flag)
+
+    dict_append(build_info, extra_compiler_args=new_args,
+                extra_link_args=new_link_args)
+

cgpenv/Lib/site-packages/scipy/_build_utils/setup.py

+
+def configuration(parent_package='', top_path=None):
+    from numpy.distutils.misc_util import Configuration
+    config = Configuration('_build_utils', parent_package, top_path)
+    config.add_data_dir('tests')
+    return config
+
+
+if __name__ == '__main__':
+    from numpy.distutils.core import setup
+    setup(**configuration(top_path='').todict())

cgpenv/Lib/site-packages/scipy/_build_utils/system_info.py

+import warnings
+
+import numpy as np
+import numpy.distutils.system_info
+
+from numpy.distutils.system_info import (system_info,
+                                         numpy_info,
+                                         NotFoundError,
+                                         BlasNotFoundError,
+                                         LapackNotFoundError,
+                                         AtlasNotFoundError,
+                                         LapackSrcNotFoundError,
+                                         BlasSrcNotFoundError,
+                                         dict_append,
+                                         get_info as old_get_info)
+
+from scipy._lib import _pep440
+
+
+def combine_dict(*dicts, **kw):
+    """
+    Combine Numpy distutils style library configuration dictionaries.
+
+    Parameters
+    ----------
+    *dicts
+        Dictionaries of keys. List-valued keys will be concatenated.
+        Otherwise, duplicate keys with different values result to
+        an error. The input arguments are not modified.
+    **kw
+        Keyword arguments are treated as an additional dictionary
+        (the first one, i.e., prepended).
+
+    Returns
+    -------
+    combined
+        Dictionary with combined values.
+    """
+    new_dict = {}
+
+    for d in (kw,) + dicts:
+        for key, value in d.items():
+            if new_dict.get(key, None) is not None:
+                old_value = new_dict[key]
+                if isinstance(value, (list, tuple)):
+                    if isinstance(old_value, (list, tuple)):
+                        new_dict[key] = list(old_value) + list(value)
+                        continue
+                elif value == old_value:
+                    continue
+
+                raise ValueError("Conflicting configuration dicts: {!r} {!r}"
+                                 "".format(new_dict, d))
+            else:
+                new_dict[key] = value
+
+    return new_dict
+
+
+if _pep440.parse(np.__version__) >= _pep440.Version("1.15.0.dev"):
+    # For new enough numpy.distutils, the ACCELERATE=None environment
+    # variable in the top-level setup.py is enough, so no need to
+    # customize BLAS detection.
+    get_info = old_get_info
+else:
+    # For NumPy < 1.15.0, we need overrides.
+
+    def get_info(name, notfound_action=0):
+        # Special case our custom *_opt_info.
+        cls = {'lapack_opt': lapack_opt_info,
+               'blas_opt': blas_opt_info}.get(name.lower())
+        if cls is None:
+            return old_get_info(name, notfound_action)
+        return cls().get_info(notfound_action)
+
+    #
+    # The following is copypaste from numpy.distutils.system_info, with
+    # OSX Accelerate-related parts removed.
+    #
+
+    class lapack_opt_info(system_info):
+
+        notfounderror = LapackNotFoundError
+
+        def calc_info(self):
+
+            lapack_mkl_info = get_info('lapack_mkl')
+            if lapack_mkl_info:
+                self.set_info(**lapack_mkl_info)
+                return
+
+            openblas_info = get_info('openblas_lapack')
+            if openblas_info:
+                self.set_info(**openblas_info)
+                return
+
+            openblas_info = get_info('openblas_clapack')
+            if openblas_info:
+                self.set_info(**openblas_info)
+                return
+
+            atlas_info = get_info('atlas_3_10_threads')
+            if not atlas_info:
+                atlas_info = get_info('atlas_3_10')
+            if not atlas_info:
+                atlas_info = get_info('atlas_threads')
+            if not atlas_info:
+                atlas_info = get_info('atlas')
+
+            need_lapack = 0
+            need_blas = 0
+            info = {}
+            if atlas_info:
+                l = atlas_info.get('define_macros', [])
+                if ('ATLAS_WITH_LAPACK_ATLAS', None) in l \
+                       or ('ATLAS_WITHOUT_LAPACK', None) in l:
+                    need_lapack = 1
+                info = atlas_info
+
+            else:
+                warnings.warn(AtlasNotFoundError.__doc__, stacklevel=2)
+                need_blas = 1
+                need_lapack = 1
+                dict_append(info, define_macros=[('NO_ATLAS_INFO', 1)])
+
+            if need_lapack:
+                lapack_info = get_info('lapack')
+                #lapack_info = {} ## uncomment for testing
+                if lapack_info:
+                    dict_append(info, **lapack_info)
+                else:
+                    warnings.warn(LapackNotFoundError.__doc__, stacklevel=2)
+                    lapack_src_info = get_info('lapack_src')
+                    if not lapack_src_info:
+                        warnings.warn(LapackSrcNotFoundError.__doc__, stacklevel=2)
+                        return
+                    dict_append(info, libraries=[('flapack_src', lapack_src_info)])
+
+            if need_blas:
+                blas_info = get_info('blas')
+                if blas_info:
+                    dict_append(info, **blas_info)
+                else:
+                    warnings.warn(BlasNotFoundError.__doc__, stacklevel=2)
+                    blas_src_info = get_info('blas_src')
+                    if not blas_src_info:
+                        warnings.warn(BlasSrcNotFoundError.__doc__, stacklevel=2)
+                        return
+                    dict_append(info, libraries=[('fblas_src', blas_src_info)])
+
+            self.set_info(**info)
+            return
+
+    class blas_opt_info(system_info):
+
+        notfounderror = BlasNotFoundError
+
+        def calc_info(self):
+
+            blas_mkl_info = get_info('blas_mkl')
+            if blas_mkl_info:
+                self.set_info(**blas_mkl_info)
+                return
+
+            blis_info = get_info('blis')
+            if blis_info:
+                self.set_info(**blis_info)
+                return
+
+            openblas_info = get_info('openblas')
+            if openblas_info:
+                self.set_info(**openblas_info)
+                return
+
+            atlas_info = get_info('atlas_3_10_blas_threads')
+            if not atlas_info:
+                atlas_info = get_info('atlas_3_10_blas')
+            if not atlas_info:
+                atlas_info = get_info('atlas_blas_threads')
+            if not atlas_info:
+                atlas_info = get_info('atlas_blas')
+
+            need_blas = 0
+            info = {}
+            if atlas_info:
+                info = atlas_info
+            else:
+                warnings.warn(AtlasNotFoundError.__doc__, stacklevel=2)
+                need_blas = 1
+                dict_append(info, define_macros=[('NO_ATLAS_INFO', 1)])
+
+            if need_blas:
+                blas_info = get_info('blas')
+                if blas_info:
+                    dict_append(info, **blas_info)
+                else:
+                    warnings.warn(BlasNotFoundError.__doc__, stacklevel=2)
+                    blas_src_info = get_info('blas_src')
+                    if not blas_src_info:
+                        warnings.warn(BlasSrcNotFoundError.__doc__, stacklevel=2)
+                        return
+                    dict_append(info, libraries=[('fblas_src', blas_src_info)])
+
+            self.set_info(**info)
+            return

cgpenv/Lib/site-packages/scipy/_build_utils/tempita.py

+import sys
+import os
+
+from Cython import Tempita as tempita
+# XXX: If this import ever fails (does it really?), vendor either
+# cython.tempita or numpy/npy_tempita.
+
+
+def process_tempita(fromfile):
+    """Process tempita templated file and write out the result.
+
+    The template file is expected to end in `.c.in` or `.pyx.in`:
+    E.g. processing `template.c.in` generates `template.c`.
+
+    """
+    if not fromfile.endswith('.in'):
+        raise ValueError("Unexpected extension: %s" % fromfile)
+
+    from_filename = tempita.Template.from_filename
+    template = from_filename(fromfile,
+                             encoding=sys.getdefaultencoding())    
+
+    content = template.substitute()
+
+    outfile = os.path.splitext(fromfile)[0]
+    with open(outfile, 'w') as f:
+        f.write(content)
+
+
+if __name__ == "__main__":
+    process_tempita(sys.argv[1])
+    

cgpenv/Lib/site-packages/scipy/_build_utils/tests/test_scipy_version.py

+import re
+
+import scipy
+from numpy.testing import assert_
+
+
+def test_valid_scipy_version():
+    # Verify that the SciPy version is a valid one (no .post suffix or other
+    # nonsense). See NumPy issue gh-6431 for an issue caused by an invalid
+    # version.
+    version_pattern = r"^[0-9]+\.[0-9]+\.[0-9]+(|a[0-9]|b[0-9]|rc[0-9])"
+    dev_suffix = r"(\.dev0\+.+([0-9a-f]{7}|Unknown))"
+    if scipy.version.release:
+        res = re.match(version_pattern, scipy.__version__)
+    else:
+        res = re.match(version_pattern + dev_suffix, scipy.__version__)
+
+    assert_(res is not None, scipy.__version__)

cgpenv/Lib/site-packages/scipy/_distributor_init.py

+""" Distributor init file
+
+Distributors: you can add custom code here to support particular distributions
+of scipy.
+
+For example, this is a good place to put any checks for hardware requirements.
+
+The scipy standard source distribution will not put code in this file, so you
+can safely replace this file with your own version.
+"""
+
+import os
+
+# on Windows SciPy loads important DLLs
+# and the code below aims to alleviate issues with DLL
+# path resolution portability with an absolute path DLL load
+if os.name == 'nt':
+    from ctypes import WinDLL
+    import glob
+    # convention for storing / loading the DLL from
+    # scipy/.libs/, if present
+    libs_path = os.path.abspath(os.path.join(os.path.dirname(__file__),
+                                             '.libs'))
+    if os.path.isdir(libs_path):
+        # for Python >= 3.8, DLL resolution ignores the PATH variable
+        # and the current working directory; see release notes:
+        # https://docs.python.org/3/whatsnew/3.8.html#bpo-36085-whatsnew
+        # Only the system paths, the directory containing the DLL, and 
+        # directories added with add_dll_directory() are searched for 
+        # load-time dependencies with Python >= 3.8
+
+        # this module was originally added to support DLL resolution in
+        # Python 3.8 because of the changes described above--providing the
+        # absolute paths to the DLLs allowed for proper resolution/loading
+
+        # however, we also started to receive reports of problems with DLL
+        # resolution with Python 3.7 that were sometimes alleviated with
+        # inclusion of the _distributor_init.py module; see SciPy main 
+        # repo gh-11826
+
+        # we noticed in scipy-wheels repo gh-70 that inclusion of
+        # _distributor_init.py in 32-bit wheels for Python 3.7 resulted
+        # in failures in DLL resolution (64-bit 3.7 did not)
+        # as a result, we decided to combine both the old (working directory)
+        # and new (absolute path to DLL location) DLL resolution mechanisms
+        # to improve the chances of resolving DLLs across a wider range of
+        # Python versions
+
+        # we did not experiment with manipulating the PATH environment variable
+        # to include libs_path; it is not immediately clear if this would have
+        # robustness or security advantages over changing working directories
+        # as done below
+
+        # we should remove the working directory shims when our minimum supported
+        # Python version is 3.8 and trust the improvements to secure DLL loading
+        # in the standard lib for Python >= 3.8
+        try:
+            owd = os.getcwd()
+            os.chdir(libs_path)
+            for filename in glob.glob(os.path.join(libs_path, '*dll')):
+                WinDLL(os.path.abspath(filename))
+        finally:
+            os.chdir(owd)

cgpenv/Lib/site-packages/scipy/_lib/__init__.py

+"""
+Module containing private utility functions
+===========================================
+
+The ``scipy._lib`` namespace is empty (for now). Tests for all
+utilities in submodules of ``_lib`` can be run with::
+
+    from scipy import _lib
+    _lib.test()
+
+"""
+from scipy._lib._testutils import PytestTester
+test = PytestTester(__name__)
+del PytestTester

cgpenv/Lib/site-packages/scipy/_lib/_boost_utils.py

+'''Helper functions to get location of header files.'''
+
+import pathlib
+from typing import Union
+
+
+def _boost_dir(ret_path: bool = False) -> Union[pathlib.Path, str]:
+    '''Directory where root Boost/ directory lives.'''
+    p = pathlib.Path(__file__).parent / 'boost'
+    return p if ret_path else str(p)

cgpenv/Lib/site-packages/scipy/_lib/_bunch.py

+
+import sys as _sys
+from keyword import iskeyword as _iskeyword
+
+
+def _validate_names(typename, field_names, extra_field_names):
+    """
+    Ensure that all the given names are valid Python identifiers that
+    do not start with '_'.  Also check that there are no duplicates
+    among field_names + extra_field_names.
+    """
+    for name in [typename] + field_names + extra_field_names:
+        if type(name) is not str:
+            raise TypeError('typename and all field names must be strings')
+        if not name.isidentifier():
+            raise ValueError('typename and all field names must be valid '
+                             f'identifiers: {name!r}')
+        if _iskeyword(name):
+            raise ValueError('typename and all field names cannot be a '
+                             f'keyword: {name!r}')
+
+    seen = set()
+    for name in field_names + extra_field_names:
+        if name.startswith('_'):
+            raise ValueError('Field names cannot start with an underscore: '
+                             f'{name!r}')
+        if name in seen:
+            raise ValueError(f'Duplicate field name: {name!r}')
+        seen.add(name)
+
+
+# Note: This code is adapted from CPython:Lib/collections/__init__.py
+def _make_tuple_bunch(typename, field_names, extra_field_names=None,
+                      module=None):
+    """
+    Create a namedtuple-like class with additional attributes.
+
+    This function creates a subclass of tuple that acts like a namedtuple
+    and that has additional attributes.
+
+    The additional attributes are listed in `extra_field_names`.  The
+    values assigned to these attributes are not part of the tuple.
+
+    The reason this function exists is to allow functions in SciPy
+    that currently return a tuple or a namedtuple to returned objects
+    that have additional attributes, while maintaining backwards
+    compatibility.
+
+    This should only be used to enhance *existing* functions in SciPy.
+    New functions are free to create objects as return values without
+    having to maintain backwards compatibility with an old tuple or
+    namedtuple return value.
+
+    Parameters
+    ----------
+    typename : str
+        The name of the type.
+    field_names : list of str
+        List of names of the values to be stored in the tuple. These names
+        will also be attributes of instances, so the values in the tuple
+        can be accessed by indexing or as attributes.  At least one name
+        is required.  See the Notes for additional restrictions.
+    extra_field_names : list of str, optional
+        List of names of values that will be stored as attributes of the
+        object.  See the notes for additional restrictions.
+
+    Returns
+    -------
+    cls : type
+        The new class.
+
+    Notes
+    -----
+    There are restrictions on the names that may be used in `field_names`
+    and `extra_field_names`:
+
+    * The names must be unique--no duplicates allowed.
+    * The names must be valid Python identifiers, and must not begin with
+      an underscore.
+    * The names must not be Python keywords (e.g. 'def', 'and', etc., are
+      not allowed).
+
+    Examples
+    --------
+    >>> from scipy._lib._bunch import _make_tuple_bunch
+
+    Create a class that acts like a namedtuple with length 2 (with field
+    names `x` and `y`) that will also have the attributes `w` and `beta`:
+
+    >>> Result = _make_tuple_bunch('Result', ['x', 'y'], ['w', 'beta'])
+
+    `Result` is the new class.  We call it with keyword arguments to create
+    a new instance with given values.
+
+    >>> result1 = Result(x=1, y=2, w=99, beta=0.5)
+    >>> result1
+    Result(x=1, y=2, w=99, beta=0.5)
+
+    `result1` acts like a tuple of length 2:
+
+    >>> len(result1)
+    2
+    >>> result1[:]
+    (1, 2)
+
+    The values assigned when the instance was created are available as
+    attributes:
+
+    >>> result1.y
+    2
+    >>> result1.beta
+    0.5
+    """
+    if len(field_names) == 0:
+        raise ValueError('field_names must contain at least one name')
+
+    if extra_field_names is None:
+        extra_field_names = []
+    _validate_names(typename, field_names, extra_field_names)
+
+    typename = _sys.intern(str(typename))
+    field_names = tuple(map(_sys.intern, field_names))
+    extra_field_names = tuple(map(_sys.intern, extra_field_names))
+
+    all_names = field_names + extra_field_names
+    arg_list = ', '.join(field_names)
+    full_list = ', '.join(all_names)
+    repr_fmt = ''.join(('(',
+                        ', '.join(f'{name}=%({name})r' for name in all_names),
+                        ')'))
+    tuple_new = tuple.__new__
+    _dict, _tuple, _zip = dict, tuple, zip
+
+    # Create all the named tuple methods to be added to the class namespace
+
+    s = f"""\
+def __new__(_cls, {arg_list}, **extra_fields):
+    return _tuple_new(_cls, ({arg_list},))
+
+def __init__(self, {arg_list}, **extra_fields):
+    for key in self._extra_fields:
+        if key not in extra_fields:
+            raise TypeError("missing keyword argument '%s'" % (key,))
+    for key, val in extra_fields.items():
+        if key not in self._extra_fields:
+            raise TypeError("unexpected keyword argument '%s'" % (key,))
+        self.__dict__[key] = val
+
+def __setattr__(self, key, val):
+    raise AttributeError("can't set attribute %r of class %r"
+                         % (key, self.__class__.__name__))
+"""
+    del arg_list
+    namespace = {'_tuple_new': tuple_new,
+                 '__builtins__': dict(TypeError=TypeError,
+                                      AttributeError=AttributeError),
+                 '__name__': f'namedtuple_{typename}'}
+    exec(s, namespace)
+    __new__ = namespace['__new__']
+    __new__.__doc__ = f'Create new instance of {typename}({full_list})'
+    __init__ = namespace['__init__']
+    __init__.__doc__ = f'Instantiate instance of {typename}({full_list})'
+    __setattr__ = namespace['__setattr__']
+
+    def __repr__(self):
+        'Return a nicely formatted representation string'
+        return self.__class__.__name__ + repr_fmt % self._asdict()
+
+    def _asdict(self):
+        'Return a new dict which maps field names to their values.'
+        out = _dict(_zip(self._fields, self))
+        out.update(self.__dict__)
+        return out
+
+    def __getnewargs_ex__(self):
+        'Return self as a plain tuple.  Used by copy and pickle.'
+        return _tuple(self), self.__dict__
+
+    # Modify function metadata to help with introspection and debugging
+    for method in (__new__, __repr__, _asdict, __getnewargs_ex__):
+        method.__qualname__ = f'{typename}.{method.__name__}'
+
+    # Build-up the class namespace dictionary
+    # and use type() to build the result class
+    class_namespace = {
+        '__doc__': f'{typename}({full_list})',
+        '_fields': field_names,
+        '__new__': __new__,
+        '__init__': __init__,
+        '__repr__': __repr__,
+        '__setattr__': __setattr__,
+        '_asdict': _asdict,
+        '_extra_fields': extra_field_names,
+        '__getnewargs_ex__': __getnewargs_ex__,
+    }
+    for index, name in enumerate(field_names):
+        doc = _sys.intern(f'Alias for field number {index}')
+
+        def _get(self, index=index):
+            return self[index]
+        class_namespace[name] = property(_get, doc=doc)
+    for name in extra_field_names:
+        doc = _sys.intern(f'Alias for name {name}')
+
+        def _get(self, name=name):
+            return self.__dict__[name]
+        class_namespace[name] = property(_get, doc=doc)
+
+    result = type(typename, (tuple,), class_namespace)
+
+    # For pickling to work, the __module__ variable needs to be set to the
+    # frame where the named tuple is created.  Bypass this step in environments
+    # where sys._getframe is not defined (Jython for example) or sys._getframe
+    # is not defined for arguments greater than 0 (IronPython), or where the
+    # user has specified a particular module.
+    if module is None:
+        try:
+            module = _sys._getframe(1).f_globals.get('__name__', '__main__')
+        except (AttributeError, ValueError):
+            pass
+    if module is not None:
+        result.__module__ = module
+        __new__.__module__ = module
+
+    return result

cgpenv/Lib/site-packages/scipy/_lib/_ccallback.py

+from . import _ccallback_c
+
+import ctypes
+
+PyCFuncPtr = ctypes.CFUNCTYPE(ctypes.c_void_p).__bases__[0]
+
+ffi = None
+
+class CData:
+    pass
+
+def _import_cffi():
+    global ffi, CData
+
+    if ffi is not None:
+        return
+
+    try:
+        import cffi
+        ffi = cffi.FFI()
+        CData = ffi.CData
+    except ImportError:
+        ffi = False
+
+
+class LowLevelCallable(tuple):
+    """
+    Low-level callback function.
+
+    Parameters
+    ----------
+    function : {PyCapsule, ctypes function pointer, cffi function pointer}
+        Low-level callback function.
+    user_data : {PyCapsule, ctypes void pointer, cffi void pointer}
+        User data to pass on to the callback function.
+    signature : str, optional
+        Signature of the function. If omitted, determined from *function*,
+        if possible.
+
+    Attributes
+    ----------
+    function
+        Callback function given.
+    user_data
+        User data given.
+    signature
+        Signature of the function.
+
+    Methods
+    -------
+    from_cython
+        Class method for constructing callables from Cython C-exported
+        functions.
+
+    Notes
+    -----
+    The argument ``function`` can be one of:
+
+    - PyCapsule, whose name contains the C function signature
+    - ctypes function pointer
+    - cffi function pointer
+
+    The signature of the low-level callback must match one of those expected
+    by the routine it is passed to.
+
+    If constructing low-level functions from a PyCapsule, the name of the
+    capsule must be the corresponding signature, in the format::
+
+        return_type (arg1_type, arg2_type, ...)
+
+    For example::
+
+        "void (double)"
+        "double (double, int *, void *)"
+
+    The context of a PyCapsule passed in as ``function`` is used as ``user_data``,
+    if an explicit value for ``user_data`` was not given.
+
+    """
+
+    # Make the class immutable
+    __slots__ = ()
+
+    def __new__(cls, function, user_data=None, signature=None):
+        # We need to hold a reference to the function & user data,
+        # to prevent them going out of scope
+        item = cls._parse_callback(function, user_data, signature)
+        return tuple.__new__(cls, (item, function, user_data))
+
+    def __repr__(self):
+        return "LowLevelCallable({!r}, {!r})".format(self.function, self.user_data)
+
+    @property
+    def function(self):
+        return tuple.__getitem__(self, 1)
+
+    @property
+    def user_data(self):
+        return tuple.__getitem__(self, 2)
+
+    @property
+    def signature(self):
+        return _ccallback_c.get_capsule_signature(tuple.__getitem__(self, 0))
+
+    def __getitem__(self, idx):
+        raise ValueError()
+
+    @classmethod
+    def from_cython(cls, module, name, user_data=None, signature=None):
+        """
+        Create a low-level callback function from an exported Cython function.
+
+        Parameters
+        ----------
+        module : module
+            Cython module where the exported function resides
+        name : str
+            Name of the exported function
+        user_data : {PyCapsule, ctypes void pointer, cffi void pointer}, optional
+            User data to pass on to the callback function.
+        signature : str, optional
+            Signature of the function. If omitted, determined from *function*.
+
+        """
+        try:
+            function = module.__pyx_capi__[name]
+        except AttributeError as e:
+            raise ValueError("Given module is not a Cython module with __pyx_capi__ attribute") from e
+        except KeyError as e:
+            raise ValueError("No function {!r} found in __pyx_capi__ of the module".format(name)) from e
+        return cls(function, user_data, signature)
+
+    @classmethod
+    def _parse_callback(cls, obj, user_data=None, signature=None):
+        _import_cffi()
+
+        if isinstance(obj, LowLevelCallable):
+            func = tuple.__getitem__(obj, 0)
+        elif isinstance(obj, PyCFuncPtr):
+            func, signature = _get_ctypes_func(obj, signature)
+        elif isinstance(obj, CData):
+            func, signature = _get_cffi_func(obj, signature)
+        elif _ccallback_c.check_capsule(obj):
+            func = obj
+        else:
+            raise ValueError("Given input is not a callable or a low-level callable (pycapsule/ctypes/cffi)")
+
+        if isinstance(user_data, ctypes.c_void_p):
+            context = _get_ctypes_data(user_data)
+        elif isinstance(user_data, CData):
+            context = _get_cffi_data(user_data)
+        elif user_data is None:
+            context = 0
+        elif _ccallback_c.check_capsule(user_data):
+            context = user_data
+        else:
+            raise ValueError("Given user data is not a valid low-level void* pointer (pycapsule/ctypes/cffi)")
+
+        return _ccallback_c.get_raw_capsule(func, signature, context)
+
+
+#
+# ctypes helpers
+#
+
+def _get_ctypes_func(func, signature=None):
+    # Get function pointer
+    func_ptr = ctypes.cast(func, ctypes.c_void_p).value
+
+    # Construct function signature
+    if signature is None:
+        signature = _typename_from_ctypes(func.restype) + " ("
+        for j, arg in enumerate(func.argtypes):
+            if j == 0:
+                signature += _typename_from_ctypes(arg)
+            else:
+                signature += ", " + _typename_from_ctypes(arg)
+        signature += ")"
+
+    return func_ptr, signature
+
+
+def _typename_from_ctypes(item):
+    if item is None:
+        return "void"
+    elif item is ctypes.c_void_p:
+        return "void *"
+
+    name = item.__name__
+
+    pointer_level = 0
+    while name.startswith("LP_"):
+        pointer_level += 1
+        name = name[3:]
+
+    if name.startswith('c_'):
+        name = name[2:]
+
+    if pointer_level > 0:
+        name += " " + "*"*pointer_level
+
+    return name
+
+
+def _get_ctypes_data(data):
+    # Get voidp pointer
+    return ctypes.cast(data, ctypes.c_void_p).value
+
+
+#
+# CFFI helpers
+#
+
+def _get_cffi_func(func, signature=None):
+    # Get function pointer
+    func_ptr = ffi.cast('uintptr_t', func)
+
+    # Get signature
+    if signature is None:
+        signature = ffi.getctype(ffi.typeof(func)).replace('(*)', ' ')
+
+    return func_ptr, signature
+
+
+def _get_cffi_data(data):
+    # Get pointer
+    return ffi.cast('uintptr_t', data)

cgpenv/Lib/site-packages/scipy/_lib/_disjoint_set.py

+"""
+Disjoint set data structure
+"""
+
+
+class DisjointSet:
+    """ Disjoint set data structure for incremental connectivity queries.
+
+    .. versionadded:: 1.6.0
+
+    Attributes
+    ----------
+    n_subsets : int
+        The number of subsets.
+
+    Methods
+    -------
+    add
+    merge
+    connected
+    subset
+    subsets
+    __getitem__
+
+    Notes
+    -----
+    This class implements the disjoint set [1]_, also known as the *union-find*
+    or *merge-find* data structure. The *find* operation (implemented in
+    `__getitem__`) implements the *path halving* variant. The *merge* method
+    implements the *merge by size* variant.
+
+    References
+    ----------
+    .. [1] https://en.wikipedia.org/wiki/Disjoint-set_data_structure
+
+    Examples
+    --------
+    >>> from scipy.cluster.hierarchy import DisjointSet
+
+    Initialize a disjoint set:
+
+    >>> disjoint_set = DisjointSet([1, 2, 3, 'a', 'b'])
+
+    Merge some subsets:
+
+    >>> disjoint_set.merge(1, 2)
+    True
+    >>> disjoint_set.merge(3, 'a')
+    True
+    >>> disjoint_set.merge('a', 'b')
+    True
+    >>> disjoint_set.merge('b', 'b')
+    False
+
+    Find root elements:
+
+    >>> disjoint_set[2]
+    1
+    >>> disjoint_set['b']
+    3
+
+    Test connectivity:
+
+    >>> disjoint_set.connected(1, 2)
+    True
+    >>> disjoint_set.connected(1, 'b')
+    False
+
+    List elements in disjoint set:
+
+    >>> list(disjoint_set)
+    [1, 2, 3, 'a', 'b']
+
+    Get the subset containing 'a':
+
+    >>> disjoint_set.subset('a')
+    {'a', 3, 'b'}
+
+    Get all subsets in the disjoint set:
+
+    >>> disjoint_set.subsets()
+    [{1, 2}, {'a', 3, 'b'}]
+    """
+    def __init__(self, elements=None):
+        self.n_subsets = 0
+        self._sizes = {}
+        self._parents = {}
+        # _nbrs is a circular linked list which links connected elements.
+        self._nbrs = {}
+        # _indices tracks the element insertion order in `__iter__`.
+        self._indices = {}
+        if elements is not None:
+            for x in elements:
+                self.add(x)
+
+    def __iter__(self):
+        """Returns an iterator of the elements in the disjoint set.
+
+        Elements are ordered by insertion order.
+        """
+        return iter(self._indices)
+
+    def __len__(self):
+        return len(self._indices)
+
+    def __contains__(self, x):
+        return x in self._indices
+
+    def __getitem__(self, x):
+        """Find the root element of `x`.
+
+        Parameters
+        ----------
+        x : hashable object
+            Input element.
+
+        Returns
+        -------
+        root : hashable object
+            Root element of `x`.
+        """
+        if x not in self._indices:
+            raise KeyError(x)
+
+        # find by "path halving"
+        parents = self._parents
+        while self._indices[x] != self._indices[parents[x]]:
+            parents[x] = parents[parents[x]]
+            x = parents[x]
+        return x
+
+    def add(self, x):
+        """Add element `x` to disjoint set
+        """
+        if x in self._indices:
+            return
+
+        self._sizes[x] = 1
+        self._parents[x] = x
+        self._nbrs[x] = x
+        self._indices[x] = len(self._indices)
+        self.n_subsets += 1
+
+    def merge(self, x, y):
+        """Merge the subsets of `x` and `y`.
+
+        The smaller subset (the child) is merged into the larger subset (the
+        parent). If the subsets are of equal size, the root element which was
+        first inserted into the disjoint set is selected as the parent.
+
+        Parameters
+        ----------
+        x, y : hashable object
+            Elements to merge.
+
+        Returns
+        -------
+        merged : bool
+            True if `x` and `y` were in disjoint sets, False otherwise.
+        """
+        xr = self[x]
+        yr = self[y]
+        if self._indices[xr] == self._indices[yr]:
+            return False
+
+        sizes = self._sizes
+        if (sizes[xr], self._indices[yr]) < (sizes[yr], self._indices[xr]):
+            xr, yr = yr, xr
+        self._parents[yr] = xr
+        self._sizes[xr] += self._sizes[yr]
+        self._nbrs[xr], self._nbrs[yr] = self._nbrs[yr], self._nbrs[xr]
+        self.n_subsets -= 1
+        return True
+
+    def connected(self, x, y):
+        """Test whether `x` and `y` are in the same subset.
+
+        Parameters
+        ----------
+        x, y : hashable object
+            Elements to test.
+
+        Returns
+        -------
+        result : bool
+            True if `x` and `y` are in the same set, False otherwise.
+        """
+        return self._indices[self[x]] == self._indices[self[y]]
+
+    def subset(self, x):
+        """Get the subset containing `x`.
+
+        Parameters
+        ----------
+        x : hashable object
+            Input element.
+
+        Returns
+        -------
+        result : set
+            Subset containing `x`.
+        """
+        if x not in self._indices:
+            raise KeyError(x)
+
+        result = [x]
+        nxt = self._nbrs[x]
+        while self._indices[nxt] != self._indices[x]:
+            result.append(nxt)
+            nxt = self._nbrs[nxt]
+        return set(result)
+
+    def subsets(self):
+        """Get all the subsets in the disjoint set.
+
+        Returns
+        -------
+        result : list
+            Subsets in the disjoint set.
+        """
+        result = []
+        visited = set()
+        for x in self:
+            if x not in visited:
+                xset = self.subset(x)
+                visited.update(xset)
+                result.append(xset)
+        return result

cgpenv/Lib/site-packages/scipy/_lib/_gcutils.py

+"""
+Module for testing automatic garbage collection of objects
+
+.. autosummary::
+   :toctree: generated/
+
+   set_gc_state - enable or disable garbage collection
+   gc_state - context manager for given state of garbage collector
+   assert_deallocated - context manager to check for circular references on object
+
+"""
+import weakref
+import gc
+
+from contextlib import contextmanager
+from platform import python_implementation
+
+__all__ = ['set_gc_state', 'gc_state', 'assert_deallocated']
+
+
+IS_PYPY = python_implementation() == 'PyPy'
+
+
+class ReferenceError(AssertionError):
+    pass
+
+
+def set_gc_state(state):
+    """ Set status of garbage collector """
+    if gc.isenabled() == state:
+        return
+    if state:
+        gc.enable()
+    else:
+        gc.disable()
+
+
+@contextmanager
+def gc_state(state):
+    """ Context manager to set state of garbage collector to `state`
+
+    Parameters
+    ----------
+    state : bool
+        True for gc enabled, False for disabled
+
+    Examples
+    --------
+    >>> with gc_state(False):
+    ...     assert not gc.isenabled()
+    >>> with gc_state(True):
+    ...     assert gc.isenabled()
+    """
+    orig_state = gc.isenabled()
+    set_gc_state(state)
+    yield
+    set_gc_state(orig_state)
+
+
+@contextmanager
+def assert_deallocated(func, *args, **kwargs):
+    """Context manager to check that object is deallocated
+
+    This is useful for checking that an object can be freed directly by
+    reference counting, without requiring gc to break reference cycles.
+    GC is disabled inside the context manager.
+
+    This check is not available on PyPy.
+
+    Parameters
+    ----------
+    func : callable
+        Callable to create object to check
+    \\*args : sequence
+        positional arguments to `func` in order to create object to check
+    \\*\\*kwargs : dict
+        keyword arguments to `func` in order to create object to check
+
+    Examples
+    --------
+    >>> class C: pass
+    >>> with assert_deallocated(C) as c:
+    ...     # do something
+    ...     del c
+
+    >>> class C:
+    ...     def __init__(self):
+    ...         self._circular = self # Make circular reference
+    >>> with assert_deallocated(C) as c: #doctest: +IGNORE_EXCEPTION_DETAIL
+    ...     # do something
+    ...     del c
+    Traceback (most recent call last):
+        ...
+    ReferenceError: Remaining reference(s) to object
+    """
+    if IS_PYPY:
+        raise RuntimeError("assert_deallocated is unavailable on PyPy")
+
+    with gc_state(False):
+        obj = func(*args, **kwargs)
+        ref = weakref.ref(obj)
+        yield obj
+        del obj
+        if ref() is not None:
+            raise ReferenceError("Remaining reference(s) to object")

cgpenv/Lib/site-packages/scipy/_lib/_testutils.py

+"""
+Generic test utilities.
+
+"""
+
+import os
+import re
+import sys
+
+
+__all__ = ['PytestTester', 'check_free_memory']
+
+
+class FPUModeChangeWarning(RuntimeWarning):
+    """Warning about FPU mode change"""
+    pass
+
+
+class PytestTester:
+    """
+    Pytest test runner entry point.
+    """
+
+    def __init__(self, module_name):
+        self.module_name = module_name
+
+    def __call__(self, label="fast", verbose=1, extra_argv=None, doctests=False,
+                 coverage=False, tests=None, parallel=None):
+        import pytest
+
+        module = sys.modules[self.module_name]
+        module_path = os.path.abspath(module.__path__[0])
+
+        pytest_args = ['--showlocals', '--tb=short']
+
+        if doctests:
+            raise ValueError("Doctests not supported")
+
+        if extra_argv:
+            pytest_args += list(extra_argv)
+
+        if verbose and int(verbose) > 1:
+            pytest_args += ["-" + "v"*(int(verbose)-1)]
+
+        if coverage:
+            pytest_args += ["--cov=" + module_path]
+
+        if label == "fast":
+            pytest_args += ["-m", "not slow"]
+        elif label != "full":
+            pytest_args += ["-m", label]
+
+        if tests is None:
+            tests = [self.module_name]
+
+        if parallel is not None and parallel > 1:
+            if _pytest_has_xdist():
+                pytest_args += ['-n', str(parallel)]
+            else:
+                import warnings
+                warnings.warn('Could not run tests in parallel because '
+                              'pytest-xdist plugin is not available.')
+
+        pytest_args += ['--pyargs'] + list(tests)
+
+        try:
+            code = pytest.main(pytest_args)
+        except SystemExit as exc:
+            code = exc.code
+
+        return (code == 0)
+
+
+def _pytest_has_xdist():
+    """
+    Check if the pytest-xdist plugin is installed, providing parallel tests
+    """
+    # Check xdist exists without importing, otherwise pytests emits warnings
+    from importlib.util import find_spec
+    return find_spec('xdist') is not None
+
+
+def check_free_memory(free_mb):
+    """
+    Check *free_mb* of memory is available, otherwise do pytest.skip
+    """
+    import pytest
+
+    try:
+        mem_free = _parse_size(os.environ['SCIPY_AVAILABLE_MEM'])
+        msg = '{0} MB memory required, but environment SCIPY_AVAILABLE_MEM={1}'.format(
+            free_mb, os.environ['SCIPY_AVAILABLE_MEM'])
+    except KeyError:
+        mem_free = _get_mem_available()
+        if mem_free is None:
+            pytest.skip("Could not determine available memory; set SCIPY_AVAILABLE_MEM "
+                        "variable to free memory in MB to run the test.")
+        msg = '{0} MB memory required, but {1} MB available'.format(
+            free_mb, mem_free/1e6)
+
+    if mem_free < free_mb * 1e6:
+        pytest.skip(msg)
+
+
+def _parse_size(size_str):
+    suffixes = {'': 1e6,
+                'b': 1.0,
+                'k': 1e3, 'M': 1e6, 'G': 1e9, 'T': 1e12,
+                'kb': 1e3, 'Mb': 1e6, 'Gb': 1e9, 'Tb': 1e12,
+                'kib': 1024.0, 'Mib': 1024.0**2, 'Gib': 1024.0**3, 'Tib': 1024.0**4}
+    m = re.match(r'^\s*(\d+)\s*({0})\s*$'.format('|'.join(suffixes.keys())),
+                 size_str,
+                 re.I)
+    if not m or m.group(2) not in suffixes:
+        raise ValueError("Invalid size string")
+
+    return float(m.group(1)) * suffixes[m.group(2)]
+
+
+def _get_mem_available():
+    """
+    Get information about memory available, not counting swap.
+    """
+    try:
+        import psutil
+        return psutil.virtual_memory().available
+    except (ImportError, AttributeError):
+        pass
+
+    if sys.platform.startswith('linux'):
+        info = {}
+        with open('/proc/meminfo', 'r') as f:
+            for line in f:
+                p = line.split()
+                info[p[0].strip(':').lower()] = float(p[1]) * 1e3
+
+        if 'memavailable' in info:
+            # Linux >= 3.14
+            return info['memavailable']
+        else:
+            return info['memfree'] + info['cached']
+
+    return None

cgpenv/Lib/site-packages/scipy/_lib/_threadsafety.py

+import threading
+
+import scipy._lib.decorator
+
+
+__all__ = ['ReentrancyError', 'ReentrancyLock', 'non_reentrant']
+
+
+class ReentrancyError(RuntimeError):
+    pass
+
+
+class ReentrancyLock:
+    """
+    Threading lock that raises an exception for reentrant calls.
+
+    Calls from different threads are serialized, and nested calls from the
+    same thread result to an error.
+
+    The object can be used as a context manager or to decorate functions
+    via the decorate() method.
+
+    """
+
+    def __init__(self, err_msg):
+        self._rlock = threading.RLock()
+        self._entered = False
+        self._err_msg = err_msg
+
+    def __enter__(self):
+        self._rlock.acquire()
+        if self._entered:
+            self._rlock.release()
+            raise ReentrancyError(self._err_msg)
+        self._entered = True
+
+    def __exit__(self, type, value, traceback):
+        self._entered = False
+        self._rlock.release()
+
+    def decorate(self, func):
+        def caller(func, *a, **kw):
+            with self:
+                return func(*a, **kw)
+        return scipy._lib.decorator.decorate(func, caller)
+
+
+def non_reentrant(err_msg=None):
+    """
+    Decorate a function with a threading lock and prevent reentrant calls.
+    """
+    def decorator(func):
+        msg = err_msg
+        if msg is None:
+            msg = "%s is not re-entrant" % func.__name__
+        lock = ReentrancyLock(msg)
+        return lock.decorate(func)
+    return decorator

cgpenv/Lib/site-packages/scipy/_lib/_tmpdirs.py

+''' Contexts for *with* statement providing temporary directories
+'''
+import os
+from contextlib import contextmanager
+from shutil import rmtree
+from tempfile import mkdtemp
+
+
+@contextmanager
+def tempdir():
+    """Create and return a temporary directory. This has the same
+    behavior as mkdtemp but can be used as a context manager.
+
+    Upon exiting the context, the directory and everything contained
+    in it are removed.
+
+    Examples
+    --------
+    >>> import os
+    >>> with tempdir() as tmpdir:
+    ...     fname = os.path.join(tmpdir, 'example_file.txt')
+    ...     with open(fname, 'wt') as fobj:
+    ...         _ = fobj.write('a string\\n')
+    >>> os.path.exists(tmpdir)
+    False
+    """
+    d = mkdtemp()
+    yield d
+    rmtree(d)
+
+
+@contextmanager
+def in_tempdir():
+    ''' Create, return, and change directory to a temporary directory
+
+    Examples
+    --------
+    >>> import os
+    >>> my_cwd = os.getcwd()
+    >>> with in_tempdir() as tmpdir:
+    ...     _ = open('test.txt', 'wt').write('some text')
+    ...     assert os.path.isfile('test.txt')
+    ...     assert os.path.isfile(os.path.join(tmpdir, 'test.txt'))
+    >>> os.path.exists(tmpdir)
+    False
+    >>> os.getcwd() == my_cwd
+    True
+    '''
+    pwd = os.getcwd()
+    d = mkdtemp()
+    os.chdir(d)
+    yield d
+    os.chdir(pwd)
+    rmtree(d)
+
+
+@contextmanager
+def in_dir(dir=None):
+    """ Change directory to given directory for duration of ``with`` block
+
+    Useful when you want to use `in_tempdir` for the final test, but
+    you are still debugging. For example, you may want to do this in the end:
+
+    >>> with in_tempdir() as tmpdir:
+    ...     # do something complicated which might break
+    ...     pass
+
+    But, indeed, the complicated thing does break, and meanwhile, the
+    ``in_tempdir`` context manager wiped out the directory with the
+    temporary files that you wanted for debugging. So, while debugging, you
+    replace with something like:
+
+    >>> with in_dir() as tmpdir: # Use working directory by default
+    ...     # do something complicated which might break
+    ...     pass
+
+    You can then look at the temporary file outputs to debug what is happening,
+    fix, and finally replace ``in_dir`` with ``in_tempdir`` again.
+    """
+    cwd = os.getcwd()
+    if dir is None:
+        yield cwd
+        return
+    os.chdir(dir)
+    yield dir
+    os.chdir(cwd)

cgpenv/Lib/site-packages/scipy/_lib/_uarray/LICENSE

+BSD 3-Clause License
+
+Copyright (c) 2018, Quansight-Labs
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* 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.
+
+* 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 HOLDER 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.

cgpenv/Lib/site-packages/scipy/_lib/_uarray/__init__.py

+"""
+.. note::
+    If you are looking for overrides for NumPy-specific methods, see the
+    documentation for :obj:`unumpy`. This page explains how to write
+    back-ends and multimethods.
+
+``uarray`` is built around a back-end protocol and overridable multimethods.
+It is necessary to define multimethods for back-ends to be able to override them.
+See the documentation of :obj:`generate_multimethod` on how to write multimethods.
+
+
+
+Let's start with the simplest:
+
+``__ua_domain__`` defines the back-end *domain*. The domain consists of period-
+separated string consisting of the modules you extend plus the submodule. For
+example, if a submodule ``module2.submodule`` extends ``module1``
+(i.e., it exposes dispatchables marked as types available in ``module1``),
+then the domain string should be ``"module1.module2.submodule"``.
+
+
+For the purpose of this demonstration, we'll be creating an object and setting
+its attributes directly. However, note that you can use a module or your own type
+as a backend as well.
+
+>>> class Backend: pass
+>>> be = Backend()
+>>> be.__ua_domain__ = "ua_examples"
+
+It might be useful at this point to sidetrack to the documentation of
+:obj:`generate_multimethod` to find out how to generate a multimethod
+overridable by :obj:`uarray`. Needless to say, writing a backend and
+creating multimethods are mostly orthogonal activities, and knowing
+one doesn't necessarily require knowledge of the other, although it
+is certainly helpful. We expect core API designers/specifiers to write the
+multimethods, and implementors to override them. But, as is often the case,
+similar people write both.
+
+Without further ado, here's an example multimethod:
+
+>>> import uarray as ua
+>>> from uarray import Dispatchable
+>>> def override_me(a, b):
+...   return Dispatchable(a, int),
+>>> def override_replacer(args, kwargs, dispatchables):
+...     return (dispatchables[0], args[1]), {}
+>>> overridden_me = ua.generate_multimethod(
+...     override_me, override_replacer, "ua_examples"
+... )
+
+Next comes the part about overriding the multimethod. This requires
+the ``__ua_function__`` protocol, and the ``__ua_convert__``
+protocol. The ``__ua_function__`` protocol has the signature
+``(method, args, kwargs)`` where ``method`` is the passed
+multimethod, ``args``/``kwargs`` specify the arguments and ``dispatchables``
+is the list of converted dispatchables passed in.
+
+>>> def __ua_function__(method, args, kwargs):
+...     return method.__name__, args, kwargs
+>>> be.__ua_function__ = __ua_function__
+
+The other protocol of interest is the ``__ua_convert__`` protocol. It has the
+signature ``(dispatchables, coerce)``. When ``coerce`` is ``False``, conversion
+between the formats should ideally be an ``O(1)`` operation, but it means that
+no memory copying should be involved, only views of the existing data.
+
+>>> def __ua_convert__(dispatchables, coerce):
+...     for d in dispatchables:
+...         if d.type is int:
+...             if coerce and d.coercible:
+...                 yield str(d.value)
+...             else:
+...                 yield d.value
+>>> be.__ua_convert__ = __ua_convert__
+
+Now that we have defined the backend, the next thing to do is to call the multimethod.
+
+>>> with ua.set_backend(be):
+...      overridden_me(1, "2")
+('override_me', (1, '2'), {})
+
+Note that the marked type has no effect on the actual type of the passed object.
+We can also coerce the type of the input.
+
+>>> with ua.set_backend(be, coerce=True):
+...     overridden_me(1, "2")
+...     overridden_me(1.0, "2")
+('override_me', ('1', '2'), {})
+('override_me', ('1.0', '2'), {})
+
+Another feature is that if you remove ``__ua_convert__``, the arguments are not
+converted at all and it's up to the backend to handle that.
+
+>>> del be.__ua_convert__
+>>> with ua.set_backend(be):
+...     overridden_me(1, "2")
+('override_me', (1, '2'), {})
+
+You also have the option to return ``NotImplemented``, in which case processing moves on
+to the next back-end, which, in this case, doesn't exist. The same applies to
+``__ua_convert__``.
+
+>>> be.__ua_function__ = lambda *a, **kw: NotImplemented
+>>> with ua.set_backend(be):
+...     overridden_me(1, "2")
+Traceback (most recent call last):
+    ...
+uarray.backend.BackendNotImplementedError: ...
+
+The last possibility is if we don't have ``__ua_convert__``, in which case the job is left
+up to ``__ua_function__``, but putting things back into arrays after conversion will not be
+possible.
+"""
+
+from ._backend import *
+
+__version__ = '0.5.1+49.g4c3f1d7.scipy'

cgpenv/Lib/site-packages/scipy/_lib/_uarray/setup.py

+
+def pre_build_hook(build_ext, ext):
+    from scipy._build_utils.compiler_helper import (
+        set_cxx_flags_hook, try_add_flag)
+    cc = build_ext._cxx_compiler
+    args = ext.extra_compile_args
+
+    set_cxx_flags_hook(build_ext, ext)
+
+    if cc.compiler_type == 'msvc':
+        args.append('/EHsc')
+    else:
+        try_add_flag(args, cc, '-fvisibility=hidden')
+
+
+def configuration(parent_package='', top_path=None):
+    from numpy.distutils.misc_util import Configuration
+
+    config = Configuration('_uarray', parent_package, top_path)
+    config.add_data_files('LICENSE')
+    ext = config.add_extension('_uarray',
+                               sources=['_uarray_dispatch.cxx'],
+                               language='c++')
+    ext._pre_build_hook = pre_build_hook
+    return config
+
+
+if __name__ == '__main__':
+    from numpy.distutils.core import setup
+    setup(**configuration(top_path='').todict())

cgpenv/Lib/site-packages/scipy/_lib/deprecation.py

+import functools
+import warnings
+
+__all__ = ["_deprecated"]
+
+
+def _deprecated(msg, stacklevel=2):
+    """Deprecate a function by emitting a warning on use."""
+    def wrap(fun):
+        if isinstance(fun, type):
+            warnings.warn(
+                "Trying to deprecate class {!r}".format(fun),
+                category=RuntimeWarning, stacklevel=2)
+            return fun
+
+        @functools.wraps(fun)
+        def call(*args, **kwargs):
+            warnings.warn(msg, category=DeprecationWarning,
+                          stacklevel=stacklevel)
+            return fun(*args, **kwargs)
+        call.__doc__ = msg
+        return call
+
+    return wrap
+
+
+class _DeprecationHelperStr:
+    """
+    Helper class used by deprecate_cython_api
+    """
+    def __init__(self, content, message):
+        self._content = content
+        self._message = message
+
+    def __hash__(self):
+        return hash(self._content)
+
+    def __eq__(self, other):
+        res = (self._content == other)
+        if res:
+            warnings.warn(self._message, category=DeprecationWarning,
+                          stacklevel=2)
+        return res
+
+
+def deprecate_cython_api(module, routine_name, new_name=None, message=None):
+    """
+    Deprecate an exported cdef function in a public Cython API module.
+
+    Only functions can be deprecated; typedefs etc. cannot.
+
+    Parameters
+    ----------
+    module : module
+        Public Cython API module (e.g. scipy.linalg.cython_blas).
+    routine_name : str
+        Name of the routine to deprecate. May also be a fused-type
+        routine (in which case its all specializations are deprecated).
+    new_name : str
+        New name to include in the deprecation warning message
+    message : str
+        Additional text in the deprecation warning message
+
+    Examples
+    --------
+    Usually, this function would be used in the top-level of the
+    module ``.pyx`` file:
+
+    >>> from scipy._lib.deprecation import deprecate_cython_api
+    >>> import scipy.linalg.cython_blas as mod
+    >>> deprecate_cython_api(mod, "dgemm", "dgemm_new",
+    ...                      message="Deprecated in Scipy 1.5.0")
+    >>> del deprecate_cython_api, mod
+
+    After this, Cython modules that use the deprecated function emit a
+    deprecation warning when they are imported.
+
+    """
+    old_name = "{}.{}".format(module.__name__, routine_name)
+
+    if new_name is None:
+        depdoc = "`%s` is deprecated!" % old_name
+    else:
+        depdoc = "`%s` is deprecated, use `%s` instead!" % \
+                 (old_name, new_name)
+
+    if message is not None:
+        depdoc += "\n" + message
+
+    d = module.__pyx_capi__
+
+    # Check if the function is a fused-type function with a mangled name
+    j = 0
+    has_fused = False
+    while True:
+        fused_name = "__pyx_fuse_{}{}".format(j, routine_name)
+        if fused_name in d:
+            has_fused = True
+            d[_DeprecationHelperStr(fused_name, depdoc)] = d.pop(fused_name)
+            j += 1
+        else:
+            break
+
+    # If not, apply deprecation to the named routine
+    if not has_fused:
+        d[_DeprecationHelperStr(routine_name, depdoc)] = d.pop(routine_name)
+

cgpenv/Lib/site-packages/scipy/_lib/setup.py

+import os
+import pathlib
+
+
+def check_boost_submodule():
+    from scipy._lib._boost_utils import _boost_dir
+
+    if not os.path.exists(_boost_dir(ret_path=True) / 'README.md'):
+        raise RuntimeError("Missing the `boost` submodule! Run `git submodule "
+                           "update --init` to fix this.")
+
+
+def build_clib_pre_build_hook(cmd, ext):
+    from scipy._build_utils.compiler_helper import get_cxx_std_flag
+    std_flag = get_cxx_std_flag(cmd.compiler)
+    ext.setdefault('extra_compiler_args', [])
+    if std_flag is not None:
+        ext['extra_compiler_args'].append(std_flag)
+
+
+def configuration(parent_package='',top_path=None):
+    from numpy.distutils.misc_util import Configuration
+    from scipy._lib._boost_utils import _boost_dir
+
+    check_boost_submodule()
+
+    config = Configuration('_lib', parent_package, top_path)
+    config.add_data_files('tests/*.py')
+
+    include_dir = os.path.abspath(os.path.join(os.path.dirname(__file__), 'src'))
+    depends = [os.path.join(include_dir, 'ccallback.h')]
+
+    config.add_extension("_ccallback_c",
+                         sources=["_ccallback_c.c"],
+                         depends=depends,
+                         include_dirs=[include_dir])
+
+    config.add_extension("_test_ccallback",
+                         sources=["src/_test_ccallback.c"],
+                         depends=depends,
+                         include_dirs=[include_dir])
+
+    config.add_extension("_fpumode",
+                         sources=["_fpumode.c"])
+
+    def get_messagestream_config(ext, build_dir):
+        # Generate a header file containing defines
+        config_cmd = config.get_config_cmd()
+        defines = []
+        if config_cmd.check_func('open_memstream', decl=True, call=True):
+            defines.append(('HAVE_OPEN_MEMSTREAM', '1'))
+        target = os.path.join(os.path.dirname(__file__), 'src',
+                              'messagestream_config.h')
+        with open(target, 'w') as f:
+            for name, value in defines:
+                f.write('#define {0} {1}\n'.format(name, value))
+
+    depends = [os.path.join(include_dir, 'messagestream.h')]
+    config.add_extension("messagestream",
+                         sources=["messagestream.c"] + [get_messagestream_config],
+                         depends=depends,
+                         include_dirs=[include_dir])
+
+    config.add_extension("_test_deprecation_call",
+                         sources=["_test_deprecation_call.c"],
+                         include_dirs=[include_dir])
+
+    config.add_extension("_test_deprecation_def",
+                         sources=["_test_deprecation_def.c"],
+                         include_dirs=[include_dir])
+
+    config.add_subpackage('_uarray')
+
+    # ensure Boost was checked out and builds
+    config.add_library(
+        'test_boost_build',
+        sources=['tests/test_boost_build.cpp'],
+        include_dirs=_boost_dir(),
+        language='c++',
+        _pre_build_hook=build_clib_pre_build_hook)
+
+    return config
+
+
+if __name__ == '__main__':
+    from numpy.distutils.core import setup
+
+    setup(**configuration(top_path='').todict())

cgpenv/Lib/site-packages/scipy/_lib/tests/test__testutils.py

+import sys
+from scipy._lib._testutils import _parse_size, _get_mem_available
+import pytest
+
+
+def test__parse_size():
+    expected = {
+        '12': 12e6,
+        '12 b': 12,
+        '12k': 12e3,
+        '  12  M  ': 12e6,
+        '  12  G  ': 12e9,
+        ' 12Tb ': 12e12,
+        '12  Mib ': 12 * 1024.0**2,
+        '12Tib': 12 * 1024.0**4,
+    }
+
+    for inp, outp in sorted(expected.items()):
+        if outp is None:
+            with pytest.raises(ValueError):
+                _parse_size(inp)
+        else:
+            assert _parse_size(inp) == outp
+
+
+def test__mem_available():
+    # May return None on non-Linux platforms
+    available = _get_mem_available()
+    if sys.platform.startswith('linux'):
+        assert available >= 0
+    else:
+        assert available is None or available >= 0

cgpenv/Lib/site-packages/scipy/_lib/tests/test_deprecation.py

+import pytest
+
+
+def test_cython_api_deprecation():
+    match = ("`scipy._lib._test_deprecation_def.foo_deprecated` "
+             "is deprecated, use `foo` instead!\n"
+             "Deprecated in Scipy 42.0.0")
+    with pytest.warns(DeprecationWarning, match=match):
+        from .. import _test_deprecation_call
+    assert _test_deprecation_call.call() == (1, 1)