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guix/gnu/packages/patches/avogadro-python-eigen-lib.patch
Kei Kebreau 7d01ee66d4
gnu: Add avogadro. 
* gnu/packages/chemistry.scm (avogadro): New variable.
* gnu/packages/patches/avogadro-boost148.patch,
gnu/packages/patches/avogadro-eigen3-update.patch,
gnu/packages/patches/avogadro-python-eigen-lib.patch: New files.
* gnu/local.mk (dist_patch_DATA): Add them.
2018-08-25 17:05:30 -04:00

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From 2d4be7ede177a8df7340fe3b209698d591ee8a04 Mon Sep 17 00:00:00 2001
From: Claudio Fernandes <claudiosf.claudio@gmail.com>
Date: Mon, 16 Jan 2017 19:48:23 -0200
Subject: [PATCH] Adapt libavogadro/python to Eigen 3.3
---
libavogadro/src/python/camera.cpp | 2 +-
libavogadro/src/python/eigen.cpp | 60 +++++++++++++++++++--------------------
2 files changed, 31 insertions(+), 31 deletions(-)
diff --git a/libavogadro/src/python/camera.cpp b/libavogadro/src/python/camera.cpp
index 69ca87bf8..30b32af7d 100644
--- a/libavogadro/src/python/camera.cpp
+++ b/libavogadro/src/python/camera.cpp
@@ -10,7 +10,7 @@ using namespace Avogadro;
void export_Camera()
{
- const Eigen::Transform3d& (Camera::*modelview_ptr)() const = &Camera::modelview;
+ const Eigen::Projective3d& (Camera::*modelview_ptr)() const = &Camera::modelview;
Eigen::Vector3d (Camera::*unProject_ptr1)(const Eigen::Vector3d&) const = &Camera::unProject;
Eigen::Vector3d (Camera::*unProject_ptr2)(const QPoint&, const Eigen::Vector3d&) const = &Camera::unProject;
Eigen::Vector3d (Camera::*unProject_ptr3)(const QPoint&) const = &Camera::unProject;
diff --git a/libavogadro/src/python/eigen.cpp b/libavogadro/src/python/eigen.cpp
index c1faedbcc..20b4e719d 100644
--- a/libavogadro/src/python/eigen.cpp
+++ b/libavogadro/src/python/eigen.cpp
@@ -305,9 +305,9 @@ template <> struct ScalarTraits<double>
struct innerclass
{
//
- // Eigen::Transform3d --> python array (4x4)
+ // Eigen::Projective3d --> python array (4x4)
//
- static PyObject* convert(Eigen::Transform3d const &trans)
+ static PyObject* convert(Eigen::Projective3d const &trans)
{
npy_intp dims[2] = { 4, 4 };
PyObject *result = PyArray_SimpleNew(2, dims, PyArray_DOUBLE);
@@ -321,9 +321,9 @@ template <> struct ScalarTraits<double>
return incref(result);
}
//
- // Eigen::Transform3d* --> python array (4x4)
+ // Eigen::Projective3d* --> python array (4x4)
//
- static PyObject* convert(Eigen::Transform3d *trans)
+ static PyObject* convert(Eigen::Projective3d *trans)
{
npy_intp dims[2] = { 4, 4 };
PyObject *result = PyArray_SimpleNew(2, dims, PyArray_DOUBLE);
@@ -337,9 +337,9 @@ template <> struct ScalarTraits<double>
return incref(result);
}
//
- // const Eigen::Transform3d* --> python array (4x4)
+ // const Eigen::Projective3d* --> python array (4x4)
//
- static PyObject* convert(const Eigen::Transform3d *trans)
+ static PyObject* convert(const Eigen::Projective3d *trans)
{
npy_intp dims[2] = { 4, 4 };
PyObject *result = PyArray_SimpleNew(2, dims, PyArray_DOUBLE);
@@ -358,10 +358,10 @@ template <> struct ScalarTraits<double>
Transform3d_to_python_array()
{
#ifndef WIN32
- to_python_converter<Eigen::Transform3d, innerclass>();
+ to_python_converter<Eigen::Projective3d, innerclass>();
#endif
- to_python_converter<Eigen::Transform3d*, innerclass>();
- to_python_converter<const Eigen::Transform3d*, innerclass>();
+ to_python_converter<Eigen::Projective3d*, innerclass>();
+ to_python_converter<const Eigen::Projective3d*, innerclass>();
}
};
@@ -373,17 +373,17 @@ template <> struct ScalarTraits<double>
// Insert an rvalue from_python converter at the tail of the
// chain. Used for implicit conversions
//
- // python array --> Eigen::Transform3d
+ // python array --> Eigen::Projective3d
//
// used for:
//
- // void function(Eigen::Transform3d vec)
- // void function(Eigen::Transform3d & vec)
- // void function(const Eigen::Transform3d & vec)
+ // void function(Eigen::Projective3d vec)
+ // void function(Eigen::Projective3d & vec)
+ // void function(const Eigen::Projective3d & vec)
//
- converter::registry::push_back( &convertible, &construct, type_id<Eigen::Transform3d>() );
+ converter::registry::push_back( &convertible, &construct, type_id<Eigen::Projective3d>() );
- converter::registry::insert( &convert, type_id<Eigen::Transform3d>() );
+ converter::registry::insert( &convert, type_id<Eigen::Projective3d>() );
}
static void* convert(PyObject *obj_ptr)
@@ -401,7 +401,7 @@ template <> struct ScalarTraits<double>
throw_error_already_set(); // the 1D array does not have exactly 3 elements
double *values = reinterpret_cast<double*>(array->data);
- Eigen::Transform3d *c_obj = new Eigen::Transform3d();
+ Eigen::Projective3d *c_obj = new Eigen::Projective3d();
double *dataPtr = c_obj->data();
for (int i = 0; i < 16; ++i)
@@ -432,7 +432,7 @@ template <> struct ScalarTraits<double>
// I think this is a better way to get at the double array, where is this
// deleted though? Does Boost::Python do it?
double *values = reinterpret_cast<double*>(array->data);
- Eigen::Transform3d *storage = new Eigen::Transform3d();
+ Eigen::Projective3d *storage = new Eigen::Projective3d();
double *dataPtr = storage->data();
for (int i = 0; i < 16; ++i)
@@ -467,21 +467,21 @@ class EigenUnitTestHelper
void set_vector3d_ptr(Eigen::Vector3d* vec) { m_vector3d = *vec; }
void set_const_vector3d_ptr(const Eigen::Vector3d* const vec) { m_vector3d = *vec; }
- //Eigen::Transform3d transform3d() { return m_transform3d; }
- //Eigen::Transform3d& transform3d_ref() { return m_transform3d; }
- const Eigen::Transform3d& const_transform3d_ref() { return m_transform3d; }
- Eigen::Transform3d* transform3d_ptr() { return &m_transform3d; }
- const Eigen::Transform3d* const_transform3d_ptr() { return &m_transform3d; }
-
- //void set_transform3d(Eigen::Transform3d vec) { m_transform3d = vec; }
- //void set_transform3d_ref(Eigen::Transform3d& vec) { m_transform3d = vec; }
- void set_const_transform3d_ref(const Eigen::Transform3d& vec) { m_transform3d = vec; }
- void set_transform3d_ptr(Eigen::Transform3d* vec) { m_transform3d = *vec; }
- void set_const_transform3d_ptr(const Eigen::Transform3d* const vec) { m_transform3d = *vec; }
+ //Eigen::Projective3d transform3d() { return m_transform3d; }
+ //Eigen::Projective3d& transform3d_ref() { return m_transform3d; }
+ const Eigen::Projective3d& const_transform3d_ref() { return m_transform3d; }
+ Eigen::Projective3d* transform3d_ptr() { return &m_transform3d; }
+ const Eigen::Projective3d* const_transform3d_ptr() { return &m_transform3d; }
+
+ //void set_transform3d(Eigen::Projective3d vec) { m_transform3d = vec; }
+ //void set_transform3d_ref(Eigen::Projective3d& vec) { m_transform3d = vec; }
+ void set_const_transform3d_ref(const Eigen::Projective3d& vec) { m_transform3d = vec; }
+ void set_transform3d_ptr(Eigen::Projective3d* vec) { m_transform3d = *vec; }
+ void set_const_transform3d_ptr(const Eigen::Projective3d* const vec) { m_transform3d = *vec; }
private:
Eigen::Vector3d m_vector3d;
- Eigen::Transform3d m_transform3d;
+ Eigen::Projective3d m_transform3d;
};
#endif
@@ -529,6 +529,6 @@ void export_Eigen()
Vector3x_to_python_array<Eigen::Vector3i>();
Vector3x_from_python_array<Eigen::Vector3i>();
- // Eigen::Transform3d
+ // Eigen::Projective3d
Transform3d_to_python_array();
Transform3d_from_python_array();
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