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.

1 files changed, 161 insertions, 0 deletions

diff --git a/gnu/packages/patches/avogadro-python-eigen-lib.patch b/gnu/packages/patches/avogadro-python-eigen-lib.patch
new file mode 100644
index 0000000000..ac9f2e30af
--- /dev/null
+++ b/gnu/packages/patches/avogadro-python-eigen-lib.patch
@@ -0,0 +1,161 @@
+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();