xcoll 0.3.6__py3-none-any.whl → 0.5.0__py3-none-any.whl

xcoll/scattering_routines/geant4/collimasim/lib/pybind11/docs/Makefile

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+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+PAPER         =
+BUILDDIR      = .build
+
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+ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)
+$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/)
+endif
+
+# Internal variables.
+PAPEROPT_a4     = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+# the i18n builder cannot share the environment and doctrees with the others
+I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+
+.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest coverage gettext
+
+help:
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+
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+
+html:
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+	@echo
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+
+dirhtml:
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+
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+	@echo
+	@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
+
+pickle:
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+	@echo
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+
+json:
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+	@echo
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+	@echo
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+	      ".hhp project file in $(BUILDDIR)/htmlhelp."
+
+qthelp:
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+	@echo
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+	@echo "To view the help file:"
+	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/pybind11.qhc"
+
+applehelp:
+	$(SPHINXBUILD) -b applehelp $(ALLSPHINXOPTS) $(BUILDDIR)/applehelp
+	@echo
+	@echo "Build finished. The help book is in $(BUILDDIR)/applehelp."
+	@echo "N.B. You won't be able to view it unless you put it in" \
+	      "~/Library/Documentation/Help or install it in your application" \
+	      "bundle."
+
+devhelp:
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+	@echo
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+
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+
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+
+texinfo:
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+	@echo
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+	      "(use \`make info' here to do that automatically)."
+
+info:
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+	@echo "Running Texinfo files through makeinfo..."
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+
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+	@echo
+	@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
+
+changes:
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+	@echo
+	@echo "The overview file is in $(BUILDDIR)/changes."
+
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+	$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
+	@echo
+	@echo "Link check complete; look for any errors in the above output " \
+	      "or in $(BUILDDIR)/linkcheck/output.txt."
+
+doctest:
+	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
+	@echo "Testing of doctests in the sources finished, look at the " \
+	      "results in $(BUILDDIR)/doctest/output.txt."
+
+coverage:
+	$(SPHINXBUILD) -b coverage $(ALLSPHINXOPTS) $(BUILDDIR)/coverage
+	@echo "Testing of coverage in the sources finished, look at the " \
+	      "results in $(BUILDDIR)/coverage/python.txt."
+
+xml:
+	$(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
+	@echo
+	@echo "Build finished. The XML files are in $(BUILDDIR)/xml."
+
+pseudoxml:
+	$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
+	@echo
+	@echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."

xcoll/scattering_routines/geant4/collimasim/lib/pybind11/docs/_static/theme_overrides.css

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+.wy-table-responsive table td,
+.wy-table-responsive table th {
+    white-space: initial !important;
+}
+.rst-content table.docutils td {
+    vertical-align: top !important;
+}
+div[class^='highlight'] pre {
+    white-space: pre;
+    white-space: pre-wrap;
+}

xcoll/scattering_routines/geant4/collimasim/lib/pybind11/docs/advanced/cast/chrono.rst

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+Chrono
+======
+
+When including the additional header file :file:`pybind11/chrono.h` conversions
+from C++11 chrono datatypes to python datetime objects are automatically enabled.
+This header also enables conversions of python floats (often from sources such
+as ``time.monotonic()``, ``time.perf_counter()`` and ``time.process_time()``)
+into durations.
+
+An overview of clocks in C++11
+------------------------------
+
+A point of confusion when using these conversions is the differences between
+clocks provided in C++11. There are three clock types defined by the C++11
+standard and users can define their own if needed. Each of these clocks have
+different properties and when converting to and from python will give different
+results.
+
+The first clock defined by the standard is ``std::chrono::system_clock``. This
+clock measures the current date and time. However, this clock changes with to
+updates to the operating system time. For example, if your time is synchronised
+with a time server this clock will change. This makes this clock a poor choice
+for timing purposes but good for measuring the wall time.
+
+The second clock defined in the standard is ``std::chrono::steady_clock``.
+This clock ticks at a steady rate and is never adjusted. This makes it excellent
+for timing purposes, however the value in this clock does not correspond to the
+current date and time. Often this clock will be the amount of time your system
+has been on, although it does not have to be. This clock will never be the same
+clock as the system clock as the system clock can change but steady clocks
+cannot.
+
+The third clock defined in the standard is ``std::chrono::high_resolution_clock``.
+This clock is the clock that has the highest resolution out of the clocks in the
+system. It is normally a typedef to either the system clock or the steady clock
+but can be its own independent clock. This is important as when using these
+conversions as the types you get in python for this clock might be different
+depending on the system.
+If it is a typedef of the system clock, python will get datetime objects, but if
+it is a different clock they will be timedelta objects.
+
+Provided conversions
+--------------------
+
+.. rubric:: C++ to Python
+
+- ``std::chrono::system_clock::time_point`` → ``datetime.datetime``
+    System clock times are converted to python datetime instances. They are
+    in the local timezone, but do not have any timezone information attached
+    to them (they are naive datetime objects).
+
+- ``std::chrono::duration`` → ``datetime.timedelta``
+    Durations are converted to timedeltas, any precision in the duration
+    greater than microseconds is lost by rounding towards zero.
+
+- ``std::chrono::[other_clocks]::time_point`` → ``datetime.timedelta``
+    Any clock time that is not the system clock is converted to a time delta.
+    This timedelta measures the time from the clocks epoch to now.
+
+.. rubric:: Python to C++
+
+- ``datetime.datetime`` or ``datetime.date`` or ``datetime.time`` → ``std::chrono::system_clock::time_point``
+    Date/time objects are converted into system clock timepoints. Any
+    timezone information is ignored and the type is treated as a naive
+    object.
+
+- ``datetime.timedelta`` → ``std::chrono::duration``
+    Time delta are converted into durations with microsecond precision.
+
+- ``datetime.timedelta`` → ``std::chrono::[other_clocks]::time_point``
+    Time deltas that are converted into clock timepoints are treated as
+    the amount of time from the start of the clocks epoch.
+
+- ``float`` → ``std::chrono::duration``
+    Floats that are passed to C++ as durations be interpreted as a number of
+    seconds. These will be converted to the duration using ``duration_cast``
+    from the float.
+
+- ``float`` → ``std::chrono::[other_clocks]::time_point``
+    Floats that are passed to C++ as time points will be interpreted as the
+    number of seconds from the start of the clocks epoch.

xcoll/scattering_routines/geant4/collimasim/lib/pybind11/docs/advanced/cast/custom.rst

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+Custom type casters
+===================
+
+In very rare cases, applications may require custom type casters that cannot be
+expressed using the abstractions provided by pybind11, thus requiring raw
+Python C API calls. This is fairly advanced usage and should only be pursued by
+experts who are familiar with the intricacies of Python reference counting.
+
+The following snippets demonstrate how this works for a very simple ``inty``
+type that that should be convertible from Python types that provide a
+``__int__(self)`` method.
+
+.. code-block:: cpp
+
+    struct inty { long long_value; };
+
+    void print(inty s) {
+        std::cout << s.long_value << std::endl;
+    }
+
+The following Python snippet demonstrates the intended usage from the Python side:
+
+.. code-block:: python
+
+    class A:
+        def __int__(self):
+            return 123
+
+
+    from example import print
+
+    print(A())
+
+To register the necessary conversion routines, it is necessary to add an
+instantiation of the ``pybind11::detail::type_caster<T>`` template.
+Although this is an implementation detail, adding an instantiation of this
+type is explicitly allowed.
+
+.. code-block:: cpp
+
+    namespace pybind11 { namespace detail {
+        template <> struct type_caster<inty> {
+        public:
+            /**
+             * This macro establishes the name 'inty' in
+             * function signatures and declares a local variable
+             * 'value' of type inty
+             */
+            PYBIND11_TYPE_CASTER(inty, _("inty"));
+
+            /**
+             * Conversion part 1 (Python->C++): convert a PyObject into a inty
+             * instance or return false upon failure. The second argument
+             * indicates whether implicit conversions should be applied.
+             */
+            bool load(handle src, bool) {
+                /* Extract PyObject from handle */
+                PyObject *source = src.ptr();
+                /* Try converting into a Python integer value */
+                PyObject *tmp = PyNumber_Long(source);
+                if (!tmp)
+                    return false;
+                /* Now try to convert into a C++ int */
+                value.long_value = PyLong_AsLong(tmp);
+                Py_DECREF(tmp);
+                /* Ensure return code was OK (to avoid out-of-range errors etc) */
+                return !(value.long_value == -1 && !PyErr_Occurred());
+            }
+
+            /**
+             * Conversion part 2 (C++ -> Python): convert an inty instance into
+             * a Python object. The second and third arguments are used to
+             * indicate the return value policy and parent object (for
+             * ``return_value_policy::reference_internal``) and are generally
+             * ignored by implicit casters.
+             */
+            static handle cast(inty src, return_value_policy /* policy */, handle /* parent */) {
+                return PyLong_FromLong(src.long_value);
+            }
+        };
+    }} // namespace pybind11::detail
+
+.. note::
+
+    A ``type_caster<T>`` defined with ``PYBIND11_TYPE_CASTER(T, ...)`` requires
+    that ``T`` is default-constructible (``value`` is first default constructed
+    and then ``load()`` assigns to it).
+
+.. warning::
+
+    When using custom type casters, it's important to declare them consistently
+    in every compilation unit of the Python extension module. Otherwise,
+    undefined behavior can ensue.

xcoll/scattering_routines/geant4/collimasim/lib/pybind11/docs/advanced/cast/eigen.rst

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+Eigen
+#####
+
+`Eigen <http://eigen.tuxfamily.org>`_ is C++ header-based library for dense and
+sparse linear algebra. Due to its popularity and widespread adoption, pybind11
+provides transparent conversion and limited mapping support between Eigen and
+Scientific Python linear algebra data types.
+
+To enable the built-in Eigen support you must include the optional header file
+:file:`pybind11/eigen.h`.
+
+Pass-by-value
+=============
+
+When binding a function with ordinary Eigen dense object arguments (for
+example, ``Eigen::MatrixXd``), pybind11 will accept any input value that is
+already (or convertible to) a ``numpy.ndarray`` with dimensions compatible with
+the Eigen type, copy its values into a temporary Eigen variable of the
+appropriate type, then call the function with this temporary variable.
+
+Sparse matrices are similarly copied to or from
+``scipy.sparse.csr_matrix``/``scipy.sparse.csc_matrix`` objects.
+
+Pass-by-reference
+=================
+
+One major limitation of the above is that every data conversion implicitly
+involves a copy, which can be both expensive (for large matrices) and disallows
+binding functions that change their (Matrix) arguments.  Pybind11 allows you to
+work around this by using Eigen's ``Eigen::Ref<MatrixType>`` class much as you
+would when writing a function taking a generic type in Eigen itself (subject to
+some limitations discussed below).
+
+When calling a bound function accepting a ``Eigen::Ref<const MatrixType>``
+type, pybind11 will attempt to avoid copying by using an ``Eigen::Map`` object
+that maps into the source ``numpy.ndarray`` data: this requires both that the
+data types are the same (e.g. ``dtype='float64'`` and ``MatrixType::Scalar`` is
+``double``); and that the storage is layout compatible.  The latter limitation
+is discussed in detail in the section below, and requires careful
+consideration: by default, numpy matrices and Eigen matrices are *not* storage
+compatible.
+
+If the numpy matrix cannot be used as is (either because its types differ, e.g.
+passing an array of integers to an Eigen parameter requiring doubles, or
+because the storage is incompatible), pybind11 makes a temporary copy and
+passes the copy instead.
+
+When a bound function parameter is instead ``Eigen::Ref<MatrixType>`` (note the
+lack of ``const``), pybind11 will only allow the function to be called if it
+can be mapped *and* if the numpy array is writeable (that is
+``a.flags.writeable`` is true).  Any access (including modification) made to
+the passed variable will be transparently carried out directly on the
+``numpy.ndarray``.
+
+This means you can can write code such as the following and have it work as
+expected:
+
+.. code-block:: cpp
+
+    void scale_by_2(Eigen::Ref<Eigen::VectorXd> v) {
+        v *= 2;
+    }
+
+Note, however, that you will likely run into limitations due to numpy and
+Eigen's difference default storage order for data; see the below section on
+:ref:`storage_orders` for details on how to bind code that won't run into such
+limitations.
+
+.. note::
+
+    Passing by reference is not supported for sparse types.
+
+Returning values to Python
+==========================
+
+When returning an ordinary dense Eigen matrix type to numpy (e.g.
+``Eigen::MatrixXd`` or ``Eigen::RowVectorXf``) pybind11 keeps the matrix and
+returns a numpy array that directly references the Eigen matrix: no copy of the
+data is performed.  The numpy array will have ``array.flags.owndata`` set to
+``False`` to indicate that it does not own the data, and the lifetime of the
+stored Eigen matrix will be tied to the returned ``array``.
+
+If you bind a function with a non-reference, ``const`` return type (e.g.
+``const Eigen::MatrixXd``), the same thing happens except that pybind11 also
+sets the numpy array's ``writeable`` flag to false.
+
+If you return an lvalue reference or pointer, the usual pybind11 rules apply,
+as dictated by the binding function's return value policy (see the
+documentation on :ref:`return_value_policies` for full details).  That means,
+without an explicit return value policy, lvalue references will be copied and
+pointers will be managed by pybind11.  In order to avoid copying, you should
+explicitly specify an appropriate return value policy, as in the following
+example:
+
+.. code-block:: cpp
+
+    class MyClass {
+        Eigen::MatrixXd big_mat = Eigen::MatrixXd::Zero(10000, 10000);
+    public:
+        Eigen::MatrixXd &getMatrix() { return big_mat; }
+        const Eigen::MatrixXd &viewMatrix() { return big_mat; }
+    };
+
+    // Later, in binding code:
+    py::class_<MyClass>(m, "MyClass")
+        .def(py::init<>())
+        .def("copy_matrix", &MyClass::getMatrix) // Makes a copy!
+        .def("get_matrix", &MyClass::getMatrix, py::return_value_policy::reference_internal)
+        .def("view_matrix", &MyClass::viewMatrix, py::return_value_policy::reference_internal)
+        ;
+
+.. code-block:: python
+
+    a = MyClass()
+    m = a.get_matrix()  # flags.writeable = True,  flags.owndata = False
+    v = a.view_matrix()  # flags.writeable = False, flags.owndata = False
+    c = a.copy_matrix()  # flags.writeable = True,  flags.owndata = True
+    # m[5,6] and v[5,6] refer to the same element, c[5,6] does not.
+
+Note in this example that ``py::return_value_policy::reference_internal`` is
+used to tie the life of the MyClass object to the life of the returned arrays.
+
+You may also return an ``Eigen::Ref``, ``Eigen::Map`` or other map-like Eigen
+object (for example, the return value of ``matrix.block()`` and related
+methods) that map into a dense Eigen type.  When doing so, the default
+behaviour of pybind11 is to simply reference the returned data: you must take
+care to ensure that this data remains valid!  You may ask pybind11 to
+explicitly *copy* such a return value by using the
+``py::return_value_policy::copy`` policy when binding the function.  You may
+also use ``py::return_value_policy::reference_internal`` or a
+``py::keep_alive`` to ensure the data stays valid as long as the returned numpy
+array does.
+
+When returning such a reference of map, pybind11 additionally respects the
+readonly-status of the returned value, marking the numpy array as non-writeable
+if the reference or map was itself read-only.
+
+.. note::
+
+    Sparse types are always copied when returned.
+
+.. _storage_orders:
+
+Storage orders
+==============
+
+Passing arguments via ``Eigen::Ref`` has some limitations that you must be
+aware of in order to effectively pass matrices by reference.  First and
+foremost is that the default ``Eigen::Ref<MatrixType>`` class requires
+contiguous storage along columns (for column-major types, the default in Eigen)
+or rows if ``MatrixType`` is specifically an ``Eigen::RowMajor`` storage type.
+The former, Eigen's default, is incompatible with ``numpy``'s default row-major
+storage, and so you will not be able to pass numpy arrays to Eigen by reference
+without making one of two changes.
+
+(Note that this does not apply to vectors (or column or row matrices): for such
+types the "row-major" and "column-major" distinction is meaningless).
+
+The first approach is to change the use of ``Eigen::Ref<MatrixType>`` to the
+more general ``Eigen::Ref<MatrixType, 0, Eigen::Stride<Eigen::Dynamic,
+Eigen::Dynamic>>`` (or similar type with a fully dynamic stride type in the
+third template argument).  Since this is a rather cumbersome type, pybind11
+provides a ``py::EigenDRef<MatrixType>`` type alias for your convenience (along
+with EigenDMap for the equivalent Map, and EigenDStride for just the stride
+type).
+
+This type allows Eigen to map into any arbitrary storage order.  This is not
+the default in Eigen for performance reasons: contiguous storage allows
+vectorization that cannot be done when storage is not known to be contiguous at
+compile time.  The default ``Eigen::Ref`` stride type allows non-contiguous
+storage along the outer dimension (that is, the rows of a column-major matrix
+or columns of a row-major matrix), but not along the inner dimension.
+
+This type, however, has the added benefit of also being able to map numpy array
+slices.  For example, the following (contrived) example uses Eigen with a numpy
+slice to multiply by 2 all coefficients that are both on even rows (0, 2, 4,
+...) and in columns 2, 5, or 8:
+
+.. code-block:: cpp
+
+    m.def("scale", [](py::EigenDRef<Eigen::MatrixXd> m, double c) { m *= c; });
+
+.. code-block:: python
+
+    # a = np.array(...)
+    scale_by_2(myarray[0::2, 2:9:3])
+
+The second approach to avoid copying is more intrusive: rearranging the
+underlying data types to not run into the non-contiguous storage problem in the
+first place.  In particular, that means using matrices with ``Eigen::RowMajor``
+storage, where appropriate, such as:
+
+.. code-block:: cpp
+
+    using RowMatrixXd = Eigen::Matrix<double, Eigen::Dynamic, Eigen::Dynamic, Eigen::RowMajor>;
+    // Use RowMatrixXd instead of MatrixXd
+
+Now bound functions accepting ``Eigen::Ref<RowMatrixXd>`` arguments will be
+callable with numpy's (default) arrays without involving a copying.
+
+You can, alternatively, change the storage order that numpy arrays use by
+adding the ``order='F'`` option when creating an array:
+
+.. code-block:: python
+
+    myarray = np.array(source, order="F")
+
+Such an object will be passable to a bound function accepting an
+``Eigen::Ref<MatrixXd>`` (or similar column-major Eigen type).
+
+One major caveat with this approach, however, is that it is not entirely as
+easy as simply flipping all Eigen or numpy usage from one to the other: some
+operations may alter the storage order of a numpy array.  For example, ``a2 =
+array.transpose()`` results in ``a2`` being a view of ``array`` that references
+the same data, but in the opposite storage order!
+
+While this approach allows fully optimized vectorized calculations in Eigen, it
+cannot be used with array slices, unlike the first approach.
+
+When *returning* a matrix to Python (either a regular matrix, a reference via
+``Eigen::Ref<>``, or a map/block into a matrix), no special storage
+consideration is required: the created numpy array will have the required
+stride that allows numpy to properly interpret the array, whatever its storage
+order.
+
+Failing rather than copying
+===========================
+
+The default behaviour when binding ``Eigen::Ref<const MatrixType>`` Eigen
+references is to copy matrix values when passed a numpy array that does not
+conform to the element type of ``MatrixType`` or does not have a compatible
+stride layout.  If you want to explicitly avoid copying in such a case, you
+should bind arguments using the ``py::arg().noconvert()`` annotation (as
+described in the :ref:`nonconverting_arguments` documentation).
+
+The following example shows an example of arguments that don't allow data
+copying to take place:
+
+.. code-block:: cpp
+
+    // The method and function to be bound:
+    class MyClass {
+        // ...
+        double some_method(const Eigen::Ref<const MatrixXd> &matrix) { /* ... */ }
+    };
+    float some_function(const Eigen::Ref<const MatrixXf> &big,
+                        const Eigen::Ref<const MatrixXf> &small) {
+        // ...
+    }
+
+    // The associated binding code:
+    using namespace pybind11::literals; // for "arg"_a
+    py::class_<MyClass>(m, "MyClass")
+        // ... other class definitions
+        .def("some_method", &MyClass::some_method, py::arg().noconvert());
+
+    m.def("some_function", &some_function,
+        "big"_a.noconvert(), // <- Don't allow copying for this arg
+        "small"_a            // <- This one can be copied if needed
+    );
+
+With the above binding code, attempting to call the the ``some_method(m)``
+method on a ``MyClass`` object, or attempting to call ``some_function(m, m2)``
+will raise a ``RuntimeError`` rather than making a temporary copy of the array.
+It will, however, allow the ``m2`` argument to be copied into a temporary if
+necessary.
+
+Note that explicitly specifying ``.noconvert()`` is not required for *mutable*
+Eigen references (e.g. ``Eigen::Ref<MatrixXd>`` without ``const`` on the
+``MatrixXd``): mutable references will never be called with a temporary copy.
+
+Vectors versus column/row matrices
+==================================
+
+Eigen and numpy have fundamentally different notions of a vector.  In Eigen, a
+vector is simply a matrix with the number of columns or rows set to 1 at
+compile time (for a column vector or row vector, respectively).  NumPy, in
+contrast, has comparable 2-dimensional 1xN and Nx1 arrays, but *also* has
+1-dimensional arrays of size N.
+
+When passing a 2-dimensional 1xN or Nx1 array to Eigen, the Eigen type must
+have matching dimensions: That is, you cannot pass a 2-dimensional Nx1 numpy
+array to an Eigen value expecting a row vector, or a 1xN numpy array as a
+column vector argument.
+
+On the other hand, pybind11 allows you to pass 1-dimensional arrays of length N
+as Eigen parameters.  If the Eigen type can hold a column vector of length N it
+will be passed as such a column vector.  If not, but the Eigen type constraints
+will accept a row vector, it will be passed as a row vector.  (The column
+vector takes precedence when both are supported, for example, when passing a
+1D numpy array to a MatrixXd argument).  Note that the type need not be
+explicitly a vector: it is permitted to pass a 1D numpy array of size 5 to an
+Eigen ``Matrix<double, Dynamic, 5>``: you would end up with a 1x5 Eigen matrix.
+Passing the same to an ``Eigen::MatrixXd`` would result in a 5x1 Eigen matrix.
+
+When returning an Eigen vector to numpy, the conversion is ambiguous: a row
+vector of length 4 could be returned as either a 1D array of length 4, or as a
+2D array of size 1x4.  When encountering such a situation, pybind11 compromises
+by considering the returned Eigen type: if it is a compile-time vector--that
+is, the type has either the number of rows or columns set to 1 at compile
+time--pybind11 converts to a 1D numpy array when returning the value.  For
+instances that are a vector only at run-time (e.g. ``MatrixXd``,
+``Matrix<float, Dynamic, 4>``), pybind11 returns the vector as a 2D array to
+numpy.  If this isn't want you want, you can use ``array.reshape(...)`` to get
+a view of the same data in the desired dimensions.
+
+.. seealso::
+
+    The file :file:`tests/test_eigen.cpp` contains a complete example that
+    shows how to pass Eigen sparse and dense data types in more detail.