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