two version of R2R are here HEAD master

3 files changed, 575 insertions, 0 deletions

diff --git a/.venv/lib/python3.12/site-packages/numpy/doc/__init__.py b/.venv/lib/python3.12/site-packages/numpy/doc/__init__.py
new file mode 100644
index 00000000..8a944fec
--- /dev/null
+++ b/.venv/lib/python3.12/site-packages/numpy/doc/__init__.py
@@ -0,0 +1,26 @@
+import os
+
+ref_dir = os.path.join(os.path.dirname(__file__))
+
+__all__ = sorted(f[:-3] for f in os.listdir(ref_dir) if f.endswith('.py') and
+           not f.startswith('__'))
+
+for f in __all__:
+    __import__(__name__ + '.' + f)
+
+del f, ref_dir
+
+__doc__ = """\
+Topical documentation
+=====================
+
+The following topics are available:
+%s
+
+You can view them by
+
+>>> help(np.doc.TOPIC)                                      #doctest: +SKIP
+
+""" % '\n- '.join([''] + __all__)
+
+__all__.extend(['__doc__'])
diff --git a/.venv/lib/python3.12/site-packages/numpy/doc/constants.py b/.venv/lib/python3.12/site-packages/numpy/doc/constants.py
new file mode 100644
index 00000000..4db5c639
--- /dev/null
+++ b/.venv/lib/python3.12/site-packages/numpy/doc/constants.py
@@ -0,0 +1,412 @@
+"""
+=========
+Constants
+=========
+
+.. currentmodule:: numpy
+
+NumPy includes several constants:
+
+%(constant_list)s
+"""
+#
+# Note: the docstring is autogenerated.
+#
+import re
+import textwrap
+
+# Maintain same format as in numpy.add_newdocs
+constants = []
+def add_newdoc(module, name, doc):
+    constants.append((name, doc))
+
+add_newdoc('numpy', 'pi',
+    """
+    ``pi = 3.1415926535897932384626433...``
+
+    References
+    ----------
+    https://en.wikipedia.org/wiki/Pi
+
+    """)
+
+add_newdoc('numpy', 'e',
+    """
+    Euler's constant, base of natural logarithms, Napier's constant.
+
+    ``e = 2.71828182845904523536028747135266249775724709369995...``
+
+    See Also
+    --------
+    exp : Exponential function
+    log : Natural logarithm
+
+    References
+    ----------
+    https://en.wikipedia.org/wiki/E_%28mathematical_constant%29
+
+    """)
+
+add_newdoc('numpy', 'euler_gamma',
+    """
+    ``γ = 0.5772156649015328606065120900824024310421...``
+
+    References
+    ----------
+    https://en.wikipedia.org/wiki/Euler-Mascheroni_constant
+
+    """)
+
+add_newdoc('numpy', 'inf',
+    """
+    IEEE 754 floating point representation of (positive) infinity.
+
+    Returns
+    -------
+    y : float
+        A floating point representation of positive infinity.
+
+    See Also
+    --------
+    isinf : Shows which elements are positive or negative infinity
+
+    isposinf : Shows which elements are positive infinity
+
+    isneginf : Shows which elements are negative infinity
+
+    isnan : Shows which elements are Not a Number
+
+    isfinite : Shows which elements are finite (not one of Not a Number,
+    positive infinity and negative infinity)
+
+    Notes
+    -----
+    NumPy uses the IEEE Standard for Binary Floating-Point for Arithmetic
+    (IEEE 754). This means that Not a Number is not equivalent to infinity.
+    Also that positive infinity is not equivalent to negative infinity. But
+    infinity is equivalent to positive infinity.
+
+    `Inf`, `Infinity`, `PINF` and `infty` are aliases for `inf`.
+
+    Examples
+    --------
+    >>> np.inf
+    inf
+    >>> np.array([1]) / 0.
+    array([ Inf])
+
+    """)
+
+add_newdoc('numpy', 'nan',
+    """
+    IEEE 754 floating point representation of Not a Number (NaN).
+
+    Returns
+    -------
+    y : A floating point representation of Not a Number.
+
+    See Also
+    --------
+    isnan : Shows which elements are Not a Number.
+
+    isfinite : Shows which elements are finite (not one of
+    Not a Number, positive infinity and negative infinity)
+
+    Notes
+    -----
+    NumPy uses the IEEE Standard for Binary Floating-Point for Arithmetic
+    (IEEE 754). This means that Not a Number is not equivalent to infinity.
+
+    `NaN` and `NAN` are aliases of `nan`.
+
+    Examples
+    --------
+    >>> np.nan
+    nan
+    >>> np.log(-1)
+    nan
+    >>> np.log([-1, 1, 2])
+    array([        NaN,  0.        ,  0.69314718])
+
+    """)
+
+add_newdoc('numpy', 'newaxis',
+    """
+    A convenient alias for None, useful for indexing arrays.
+
+    Examples
+    --------
+    >>> newaxis is None
+    True
+    >>> x = np.arange(3)
+    >>> x
+    array([0, 1, 2])
+    >>> x[:, newaxis]
+    array([[0],
+    [1],
+    [2]])
+    >>> x[:, newaxis, newaxis]
+    array([[[0]],
+    [[1]],
+    [[2]]])
+    >>> x[:, newaxis] * x
+    array([[0, 0, 0],
+    [0, 1, 2],
+    [0, 2, 4]])
+
+    Outer product, same as ``outer(x, y)``:
+
+    >>> y = np.arange(3, 6)
+    >>> x[:, newaxis] * y
+    array([[ 0,  0,  0],
+    [ 3,  4,  5],
+    [ 6,  8, 10]])
+
+    ``x[newaxis, :]`` is equivalent to ``x[newaxis]`` and ``x[None]``:
+
+    >>> x[newaxis, :].shape
+    (1, 3)
+    >>> x[newaxis].shape
+    (1, 3)
+    >>> x[None].shape
+    (1, 3)
+    >>> x[:, newaxis].shape
+    (3, 1)
+
+    """)
+
+add_newdoc('numpy', 'NZERO',
+    """
+    IEEE 754 floating point representation of negative zero.
+
+    Returns
+    -------
+    y : float
+        A floating point representation of negative zero.
+
+    See Also
+    --------
+    PZERO : Defines positive zero.
+
+    isinf : Shows which elements are positive or negative infinity.
+
+    isposinf : Shows which elements are positive infinity.
+
+    isneginf : Shows which elements are negative infinity.
+
+    isnan : Shows which elements are Not a Number.
+
+    isfinite : Shows which elements are finite - not one of
+               Not a Number, positive infinity and negative infinity.
+
+    Notes
+    -----
+    NumPy uses the IEEE Standard for Binary Floating-Point for Arithmetic
+    (IEEE 754). Negative zero is considered to be a finite number.
+
+    Examples
+    --------
+    >>> np.NZERO
+    -0.0
+    >>> np.PZERO
+    0.0
+
+    >>> np.isfinite([np.NZERO])
+    array([ True])
+    >>> np.isnan([np.NZERO])
+    array([False])
+    >>> np.isinf([np.NZERO])
+    array([False])
+
+    """)
+
+add_newdoc('numpy', 'PZERO',
+    """
+    IEEE 754 floating point representation of positive zero.
+
+    Returns
+    -------
+    y : float
+        A floating point representation of positive zero.
+
+    See Also
+    --------
+    NZERO : Defines negative zero.
+
+    isinf : Shows which elements are positive or negative infinity.
+
+    isposinf : Shows which elements are positive infinity.
+
+    isneginf : Shows which elements are negative infinity.
+
+    isnan : Shows which elements are Not a Number.
+
+    isfinite : Shows which elements are finite - not one of
+               Not a Number, positive infinity and negative infinity.
+
+    Notes
+    -----
+    NumPy uses the IEEE Standard for Binary Floating-Point for Arithmetic
+    (IEEE 754). Positive zero is considered to be a finite number.
+
+    Examples
+    --------
+    >>> np.PZERO
+    0.0
+    >>> np.NZERO
+    -0.0
+
+    >>> np.isfinite([np.PZERO])
+    array([ True])
+    >>> np.isnan([np.PZERO])
+    array([False])
+    >>> np.isinf([np.PZERO])
+    array([False])
+
+    """)
+
+add_newdoc('numpy', 'NAN',
+    """
+    IEEE 754 floating point representation of Not a Number (NaN).
+
+    `NaN` and `NAN` are equivalent definitions of `nan`. Please use
+    `nan` instead of `NAN`.
+
+    See Also
+    --------
+    nan
+
+    """)
+
+add_newdoc('numpy', 'NaN',
+    """
+    IEEE 754 floating point representation of Not a Number (NaN).
+
+    `NaN` and `NAN` are equivalent definitions of `nan`. Please use
+    `nan` instead of `NaN`.
+
+    See Also
+    --------
+    nan
+
+    """)
+
+add_newdoc('numpy', 'NINF',
+    """
+    IEEE 754 floating point representation of negative infinity.
+
+    Returns
+    -------
+    y : float
+        A floating point representation of negative infinity.
+
+    See Also
+    --------
+    isinf : Shows which elements are positive or negative infinity
+
+    isposinf : Shows which elements are positive infinity
+
+    isneginf : Shows which elements are negative infinity
+
+    isnan : Shows which elements are Not a Number
+
+    isfinite : Shows which elements are finite (not one of Not a Number,
+    positive infinity and negative infinity)
+
+    Notes
+    -----
+    NumPy uses the IEEE Standard for Binary Floating-Point for Arithmetic
+    (IEEE 754). This means that Not a Number is not equivalent to infinity.
+    Also that positive infinity is not equivalent to negative infinity. But
+    infinity is equivalent to positive infinity.
+
+    Examples
+    --------
+    >>> np.NINF
+    -inf
+    >>> np.log(0)
+    -inf
+
+    """)
+
+add_newdoc('numpy', 'PINF',
+    """
+    IEEE 754 floating point representation of (positive) infinity.
+
+    Use `inf` because `Inf`, `Infinity`, `PINF` and `infty` are aliases for
+    `inf`. For more details, see `inf`.
+
+    See Also
+    --------
+    inf
+
+    """)
+
+add_newdoc('numpy', 'infty',
+    """
+    IEEE 754 floating point representation of (positive) infinity.
+
+    Use `inf` because `Inf`, `Infinity`, `PINF` and `infty` are aliases for
+    `inf`. For more details, see `inf`.
+
+    See Also
+    --------
+    inf
+
+    """)
+
+add_newdoc('numpy', 'Inf',
+    """
+    IEEE 754 floating point representation of (positive) infinity.
+
+    Use `inf` because `Inf`, `Infinity`, `PINF` and `infty` are aliases for
+    `inf`. For more details, see `inf`.
+
+    See Also
+    --------
+    inf
+
+    """)
+
+add_newdoc('numpy', 'Infinity',
+    """
+    IEEE 754 floating point representation of (positive) infinity.
+
+    Use `inf` because `Inf`, `Infinity`, `PINF` and `infty` are aliases for
+    `inf`. For more details, see `inf`.
+
+    See Also
+    --------
+    inf
+
+    """)
+
+
+if __doc__:
+    constants_str = []
+    constants.sort()
+    for name, doc in constants:
+        s = textwrap.dedent(doc).replace("\n", "\n    ")
+
+        # Replace sections by rubrics
+        lines = s.split("\n")
+        new_lines = []
+        for line in lines:
+            m = re.match(r'^(\s+)[-=]+\s*$', line)
+            if m and new_lines:
+                prev = textwrap.dedent(new_lines.pop())
+                new_lines.append('%s.. rubric:: %s' % (m.group(1), prev))
+                new_lines.append('')
+            else:
+                new_lines.append(line)
+        s = "\n".join(new_lines)
+
+        # Done.
+        constants_str.append(""".. data:: %s\n    %s""" % (name, s))
+    constants_str = "\n".join(constants_str)
+
+    __doc__ = __doc__ % dict(constant_list=constants_str)
+    del constants_str, name, doc
+    del line, lines, new_lines, m, s, prev
+
+del constants, add_newdoc
diff --git a/.venv/lib/python3.12/site-packages/numpy/doc/ufuncs.py b/.venv/lib/python3.12/site-packages/numpy/doc/ufuncs.py
new file mode 100644
index 00000000..c99e9abc
--- /dev/null
+++ b/.venv/lib/python3.12/site-packages/numpy/doc/ufuncs.py
@@ -0,0 +1,137 @@
+"""
+===================
+Universal Functions
+===================
+
+Ufuncs are, generally speaking, mathematical functions or operations that are
+applied element-by-element to the contents of an array. That is, the result
+in each output array element only depends on the value in the corresponding
+input array (or arrays) and on no other array elements. NumPy comes with a
+large suite of ufuncs, and scipy extends that suite substantially. The simplest
+example is the addition operator: ::
+
+ >>> np.array([0,2,3,4]) + np.array([1,1,-1,2])
+ array([1, 3, 2, 6])
+
+The ufunc module lists all the available ufuncs in numpy. Documentation on
+the specific ufuncs may be found in those modules. This documentation is
+intended to address the more general aspects of ufuncs common to most of
+them. All of the ufuncs that make use of Python operators (e.g., +, -, etc.)
+have equivalent functions defined (e.g. add() for +)
+
+Type coercion
+=============
+
+What happens when a binary operator (e.g., +,-,\\*,/, etc) deals with arrays of
+two different types? What is the type of the result? Typically, the result is
+the higher of the two types. For example: ::
+
+ float32 + float64 -> float64
+ int8 + int32 -> int32
+ int16 + float32 -> float32
+ float32 + complex64 -> complex64
+
+There are some less obvious cases generally involving mixes of types
+(e.g. uints, ints and floats) where equal bit sizes for each are not
+capable of saving all the information in a different type of equivalent
+bit size. Some examples are int32 vs float32 or uint32 vs int32.
+Generally, the result is the higher type of larger size than both
+(if available). So: ::
+
+ int32 + float32 -> float64
+ uint32 + int32 -> int64
+
+Finally, the type coercion behavior when expressions involve Python
+scalars is different than that seen for arrays. Since Python has a
+limited number of types, combining a Python int with a dtype=np.int8
+array does not coerce to the higher type but instead, the type of the
+array prevails. So the rules for Python scalars combined with arrays is
+that the result will be that of the array equivalent the Python scalar
+if the Python scalar is of a higher 'kind' than the array (e.g., float
+vs. int), otherwise the resultant type will be that of the array.
+For example: ::
+
+  Python int + int8 -> int8
+  Python float + int8 -> float64
+
+ufunc methods
+=============
+
+Binary ufuncs support 4 methods.
+
+**.reduce(arr)** applies the binary operator to elements of the array in
+  sequence. For example: ::
+
+ >>> np.add.reduce(np.arange(10))  # adds all elements of array
+ 45
+
+For multidimensional arrays, the first dimension is reduced by default: ::
+
+ >>> np.add.reduce(np.arange(10).reshape(2,5))
+     array([ 5,  7,  9, 11, 13])
+
+The axis keyword can be used to specify different axes to reduce: ::
+
+ >>> np.add.reduce(np.arange(10).reshape(2,5),axis=1)
+ array([10, 35])
+
+**.accumulate(arr)** applies the binary operator and generates an
+equivalently shaped array that includes the accumulated amount for each
+element of the array. A couple examples: ::
+
+ >>> np.add.accumulate(np.arange(10))
+ array([ 0,  1,  3,  6, 10, 15, 21, 28, 36, 45])
+ >>> np.multiply.accumulate(np.arange(1,9))
+ array([    1,     2,     6,    24,   120,   720,  5040, 40320])
+
+The behavior for multidimensional arrays is the same as for .reduce(),
+as is the use of the axis keyword).
+
+**.reduceat(arr,indices)** allows one to apply reduce to selected parts
+  of an array. It is a difficult method to understand. See the documentation
+  at:
+
+**.outer(arr1,arr2)** generates an outer operation on the two arrays arr1 and
+  arr2. It will work on multidimensional arrays (the shape of the result is
+  the concatenation of the two input shapes.: ::
+
+ >>> np.multiply.outer(np.arange(3),np.arange(4))
+ array([[0, 0, 0, 0],
+        [0, 1, 2, 3],
+        [0, 2, 4, 6]])
+
+Output arguments
+================
+
+All ufuncs accept an optional output array. The array must be of the expected
+output shape. Beware that if the type of the output array is of a different
+(and lower) type than the output result, the results may be silently truncated
+or otherwise corrupted in the downcast to the lower type. This usage is useful
+when one wants to avoid creating large temporary arrays and instead allows one
+to reuse the same array memory repeatedly (at the expense of not being able to
+use more convenient operator notation in expressions). Note that when the
+output argument is used, the ufunc still returns a reference to the result.
+
+ >>> x = np.arange(2)
+ >>> np.add(np.arange(2),np.arange(2.),x)
+ array([0, 2])
+ >>> x
+ array([0, 2])
+
+and & or as ufuncs
+==================
+
+Invariably people try to use the python 'and' and 'or' as logical operators
+(and quite understandably). But these operators do not behave as normal
+operators since Python treats these quite differently. They cannot be
+overloaded with array equivalents. Thus using 'and' or 'or' with an array
+results in an error. There are two alternatives:
+
+ 1) use the ufunc functions logical_and() and logical_or().
+ 2) use the bitwise operators & and \\|. The drawback of these is that if
+    the arguments to these operators are not boolean arrays, the result is
+    likely incorrect. On the other hand, most usages of logical_and and
+    logical_or are with boolean arrays. As long as one is careful, this is
+    a convenient way to apply these operators.
+
+"""