Merge pull request #23094 from veprbl/for_upstream

pythonPackages: add pyhepmc, graphviz; bump rootpy

3 files changed, 226 insertions, 2 deletions

diff --git a/pkgs/development/libraries/physics/herwig/default.nix b/pkgs/development/libraries/physics/herwig/default.nix
index cb765f761d78e..737565d298e08 100644
--- a/pkgs/development/libraries/physics/herwig/default.nix
+++ b/pkgs/development/libraries/physics/herwig/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   name = "herwig-${version}";
-  version = "7.0.3";
+  version = "7.0.4";
 
   src = fetchurl {
     url = "http://www.hepforge.org/archive/herwig/Herwig-${version}.tar.bz2";
-    sha256 = "0v7b84n0v3dhjpx0vfk5p8g87kivgg9svfivnih1yrfm749269m2";
+    sha256 = "1vac5y5cyyn1z1ii1a6x1ysx2znxmfq9a51gxqib0i19mrn5y9p6";
   };
 
   patches = [
diff --git a/pkgs/development/python-modules/pyhepmc_export_edges.patch b/pkgs/development/python-modules/pyhepmc_export_edges.patch
new file mode 100644
index 0000000000000..5c6e56566a34d
--- /dev/null
+++ b/pkgs/development/python-modules/pyhepmc_export_edges.patch
@@ -0,0 +1,204 @@
+# HG changeset patch
+# User Lukas Heinrich <lukas.heinrich@gmail.com>
+# Date 1430606843 14400
+# Node ID 325f89b7b72922e9add9ca9dd0f7ca4a6c83bf00
+# Parent  e4fd953257e0d38511f2177de7ffaef662358af2
+add incoming/outgoing generators for GenVertex
+
+diff --git a/hepmc/generators.i b/hepmc/generators.i
+new file mode 100644
+--- /dev/null
++++ b/hepmc/generators.i
+@@ -0,0 +1,171 @@
++/*!
++ * \file   generators.i
++ * \author Seth R. Johnson
++ * \brief  Define generator/iterator for any type
++
++Example:
++\code
++    SETUP_GENERATOR( std::vector<Cell>::const_iterator )
++    ADD_GENERATOR( Mesh, cells,
++    std::vector<Cell>::const_iterator, Cell, beginCells, endCells)
++\endcode
++would be a method to add a \c cells generator method method to the Python class
++\c Mesh, when the C++ class \c Mesh has a \c std::vector<Cell> accessed through
++methods \c beginCells and \c endCells.
++
++The macro \c ADD_GENERATOR_P would be if the underlying storage were \c
++std::vector<Cell*> instead.
++
++Alternatively, for containers of regular objects that provide \c begin(), \c end(), and \c const_iterator, you can use the \c ADD_CONTAINER_ITERATOR macro:
++\code
++ADD_CONTAINER_ITERATOR( QuadratureSet )
++\endcode
++
++\section License
++
++Copyright (c) 2010, Seth R. Johnson
++All rights reserved.
++
++Redistribution and use in source and binary forms, with or without
++modification, are permitted provided that the following conditions are met:
++ * Redistributions of source code must retain the above copyright notice, this
++   list of conditions and the following disclaimer.
++ * Redistributions in binary form must reproduce the above copyright notice,
++   this list of conditions and the following disclaimer in the documentation
++   and/or other materials provided with the distribution.
++ * Neither the name of the this project nor the names of its contributors
++   may be used to endorse or promote products derived from this software
++   without specific prior written permission.
++
++THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
++ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
++WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
++DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
++ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
++(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
++LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
++ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
++(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
++SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
++
++ This material is based upon work supported under a National Science
++ Foundation Graduate Research Fellowship. Any opinions, findings, conclusions
++ or recommendations expressed in this publication are those of the author
++ and do not necessarily reflect the views of the National Science
++ Foundation.
++*/
++#ifndef tools_SWIG_generators_i
++#define tools_SWIG_generators_i
++/*----------------------------------------------------------------------------*/
++
++// Add a Python class to provide iterator objects
++%insert("python") %{
++class GenericIterator:
++    def __init__(self, begin_iter_method, deref_method, incr_method):
++        self.it = begin_iter_method()
++        self.incr   = incr_method
++        self.deref  = deref_method
++
++    def __iter__(self):
++        return self
++
++    def next(self):
++        obj = self.deref( self.it )
++        if obj is not None:
++            self.incr( self.it )
++            return obj
++        else:
++            raise StopIteration
++%}
++
++//============== GENERIC GENERATOR/ITERATOR WRAPPER SUPPORT ============
++//! Thin wrapper for incrementing a certain type of iterator
++// only need to define once per iterator type, and we can use the same name
++// thanks to overloading (even though this may decrease efficiency)
++%define SETUP_GENERATOR( ITERATOR... )
++%inline %{
++void _iter_incr( ITERATOR* iter )
++{
++    ++(*iter);
++}
++%}
++%enddef
++
++/*----------------------------------------------------------------------------*/
++// Internal method for adding common parts of the generator
++%define PYTRT_BASE_ADD_GENERATOR( CLASS, PYMETHOD, ITERATOR, CBEGIN )
++    %extend CLASS {
++%insert("python") %{
++    def PYMETHOD(self):
++        "Returns an iterator for PYMETHOD."
++        return GenericIterator(
++                self._begin_ ## PYMETHOD,
++                self._deref_ ## PYMETHOD,
++                _iter_incr
++                 )
++%}
++// get the first element in the vector
++ITERATOR* _begin_ ## PYMETHOD()
++{
++    return new ITERATOR( ($self)->CBEGIN() );
++}
++    }
++%enddef
++/*----------------------------------------------------------------------------*/
++// If the dereferenced iterator is an object
++%define ADD_GENERATOR( CLASS, PYMETHOD, ITERATOR, RVALUE, CBEGIN, CEND )
++
++// add the python and begin method
++PYTRT_BASE_ADD_GENERATOR( CLASS, PYMETHOD, ITERATOR, CBEGIN )
++
++    %extend CLASS {
++//! Dereference the iterator; return NULL if at the end
++const RVALUE* _deref_ ## PYMETHOD ## ( const ITERATOR* iter )
++{
++    // if at the end, return NULL
++    if (*iter == ($self)->CEND() ) {
++        return NULL;
++    }
++    // otherwise, return the POINTER to the dereferenced iterator
++    return &(**iter);
++}
++    }
++%enddef
++/*----------------------------------------------------------------------------*/
++// If the dereferenced iterator is a pointer
++%define ADD_GENERATOR_P( CLASS, PYMETHOD, ITERATOR, RVALUE, CBEGIN, CEND )
++
++// add the python and begin method
++PYTRT_BASE_ADD_GENERATOR( CLASS, PYMETHOD, ITERATOR, CBEGIN )
++
++    %extend CLASS {
++//! Dereference the iterator; return NULL if at the end
++const RVALUE* _deref_ ## PYMETHOD ## ( const ITERATOR* iter )
++{
++    // if at the end, return NULL
++    if (*iter == ($self)->CEND() ) {
++        return NULL;
++    }
++    // otherwise, return the dereferenced iterator (a pointer)
++    return **iter;
++}
++    }
++%enddef
++/*----------------------------------------------------------------------------*/
++//! For a regular container with "begin" and "end" and "size"
++%define ADD_CONTAINER_ITERATOR( CLASS )
++    SETUP_GENERATOR( CLASS::const_iterator );
++    ADD_GENERATOR( CLASS, __iter__,
++            CLASS ## ::const_iterator, CLASS ## ::value_type,
++            begin, end)
++    %extend CLASS {
++    %insert("python") %{
++    def __len__(self):
++        return self.size()
++    %}
++    }
++%enddef
++
++/*============================================================================*/
++#endif
++
+diff --git a/hepmc/hepmcwrap.i b/hepmc/hepmcwrap.i
+--- a/hepmc/hepmcwrap.i
++++ b/hepmc/hepmcwrap.i
+@@ -1,5 +1,7 @@
+ %module hepmcwrap
+ 
++%include generators.i
++
+ %{
+   #include "HepMC/GenEvent.h"
+   #include "HepMC/GenVertex.h"
+@@ -251,3 +253,9 @@
+     return ss.str();
+   }
+ }
++
++SETUP_GENERATOR( std::vector< HepMC::GenParticle* >::const_iterator )
++ADD_GENERATOR_P( HepMC::GenVertex, incoming,
++std::vector< HepMC::GenParticle* >::const_iterator, HepMC::GenParticle, particles_in_const_begin, particles_in_const_end)
++ADD_GENERATOR_P( HepMC::GenVertex, outgoing,
++std::vector< HepMC::GenParticle* >::const_iterator, HepMC::GenParticle, particles_out_const_begin, particles_out_const_end)
diff --git a/pkgs/development/python-modules/pyhepmc_export_flow.patch b/pkgs/development/python-modules/pyhepmc_export_flow.patch
new file mode 100644
index 0000000000000..85e26a1a16077
--- /dev/null
+++ b/pkgs/development/python-modules/pyhepmc_export_flow.patch
@@ -0,0 +1,20 @@
+diff --git a/hepmc/hepmcwrap.i b/hepmc/hepmcwrap.i
+index cf35c1b..b94fbe2 100644
+--- a/hepmc/hepmcwrap.i
++++ b/hepmc/hepmcwrap.i
+@@ -1,6 +1,7 @@
+ %module hepmcwrap
+ 
+ %{
++  #include "HepMC/Flow.h"
+   #include "HepMC/GenEvent.h"
+   #include "HepMC/GenVertex.h"
+   #include "HepMC/GenParticle.h"
+@@ -93,6 +94,7 @@ namespace HepMC {
+ // headers before importing headers that use those classes.
+ // Result is that headers should probably be %included in an order
+ // which sees "contents before containers"
++%include "HepMC/Flow.h"
+ %include "HepMC/HepMCDefs.h"
+ %include "HepMC/SimpleVector.h"
+ // #ifdef HEPMC_HAS_ITERATOR_RANGES