Merge for 2.6.1 release.

salilab · Apr 8, 2016 · e487c2c · e487c2c
2 parents bcebf55 + eb3a1c5
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diff --git a/ChangeLog.md b/ChangeLog.md
@@ -1,6 +1,12 @@
 ChangeLog {#changelog}
 =========
 
+# 2.6.1 - 2016-04-14 # {#changelog_2_6_1}
+- The 'cluster' binary is now called 'rmsd_cluster' to avoid conflicts with
+  other packages (e.g. graphviz also provides a 'cluster' binary).
+- Minor bug fixes to PMI.
+- Minor documentation fixes.
+
 # 2.6.0 - 2016-03-28 # {#changelog_2_6_0}
 - This release includes most of the functionality of PMI2. This is an improved
   version of PMI that is faster than PMI1, more modular, and easier to use.

diff --git a/VERSION b/VERSION
@@ -1 +1 @@
-2.6.0
+2.6.1
diff --git a/doc/manual/biosystem.md b/doc/manual/biosystem.md
@@ -29,7 +29,8 @@ for an example):
    representatives).
  - a top-level `%README.md` file describing the system and explaining how to
    run the protocol.
- - a `test` directory containing one or more Python scripts. It should be
+ - a `test` directory containing one or more Python scripts with names starting
+   with `test`. It should be
    possible to run these scripts without any "special" setup (e.g. they should
    not require any input arguments or environment variables, or use
    hard-coded paths). These scripts should run as much of your modeling

diff --git a/doc/manual/installation.md b/doc/manual/installation.md
@@ -23,12 +23,12 @@ to see if the code is currently stable enough for your purposes.
 In order to build %IMP from source, you will need:
 
 - [CMake](http://www.cmake.org) (2.8 or later)
-- [Boost](http://www.boost.org) (1.40 or later; note that 1.60 does not
-  [currently work](https://svn.boost.org/trac/boost/ticket/11880))
+- [Boost](http://www.boost.org) (1.40 or later)
 - [HDF5](http://www.hdfgroup.org/HDF5/) (1.8 or later)
 - [Python](http://www.python.org) (2.6 or later, or any version of Python 3)
 - [SWIG](http://www.swig.org) (1.3.40 or later; 2.0.4 or later is needed
-  if you want to use Python 3)
+  if you want to use Python 3; note that 3.0.8 does not
+  [currently work](https://github.com/swig/swig/issues/583))
 
 The following prerequisites are _optional_; without them some parts of %IMP
 will not build, and some will not function optimally.
@@ -53,9 +53,8 @@ will not build, and some will not function optimally.
 - An [MPI](@ref IMP::mpi) library is needed to use the IMP.mpi module.
 - The [numpy, scipy](http://www.scipy.org/scipylib/download.html),
   [scikit-learn](http://scikit-learn.org/stable/install.html),
-  [matplotlib](http://matplotlib.org/downloads.html) and
-  [biopython](http://biopython.org/wiki/Download) Python libraries are also
-  recommended.
+  and [matplotlib](http://matplotlib.org/downloads.html)
+  Python libraries are also recommended.
 - [Chimera](https://www.cgl.ucsf.edu/chimera/download.html) is recommended
   for visualization of results.
 

diff --git a/doc/manual/rnapolii_stalk.dox b/doc/manual/rnapolii_stalk.dox
@@ -29,19 +29,16 @@ packages installed in addition to [IMP itself](@ref installation):
 - [matplotlib](http://matplotlib.org/downloads.html)
   for plotting results
 
-- [biopython](http://biopython.org/wiki/Download)
-  for reading FASTA sequence files
-
 - [Chimera](https://www.cgl.ucsf.edu/chimera/download.html)
   for visualization of results
 
 (If you are using [Anaconda Python](https://store.continuum.io/cshop/anaconda/),
 you can get the Python packages above by simply running
-`conda install numpy scipy scikit-learn matplotlib biopython`.
+`conda install numpy scipy scikit-learn matplotlib`.
 On a Mac you can get them using the
 [pip](https://pypi.python.org/pypi/pip) tool, e.g. by running a command like
 `sudo easy_install pip`, then install the packages with something like
-`sudo pip install scikit-learn; sudo pip install matplotlib; sudo pip install biopython`. `numpy` and `scipy` are already installed on modern Macs. Something
+`sudo pip install scikit-learn; sudo pip install matplotlib`. `numpy` and `scipy` are already installed on modern Macs. Something
 similar may also work on a Linux box, although it's probably better to install
 the packages using the distribution's package manager, such as `yum` or
 `apt-get`.)

diff --git a/modules/algebra/include/GridD.h b/modules/algebra/include/GridD.h
@@ -25,30 +25,30 @@
 
 IMPALGEBRA_BEGIN_NAMESPACE
 
-//! A voxel grid in d-dimensional space space.
+//! A voxel grid in d-dimensional space.
 /**
    First some terminology:
-   - a voxel is the data stored at a given location is space
+   - a voxel is the data stored at a given location in space
    - an Index is a way of identifying a particular voxel. That is, given
-   an index, it is easy to get the voxel, but not vice-versa
+     an index, it is easy to get the voxel, but not vice-versa.
    - an ExtendedIndex identifies a particular region in space, but
-   it may not have a corresponding voxel (if it is outside of the
-   region the grid is built on or if that voxel has not yet been
-   added to the sparse grid).
+     it may not have a corresponding voxel (if it is outside of the
+     region the grid is built on or if that voxel has not yet been
+     added to the sparse grid).
 
    \imp provides support for a variety of spatial grids. The grid support in
    C++ is implemented by combining several different layers to specify
    what capabilities are desired. These layers are:
-   - Data: any type of data can be stored in a voxel of the grid
+   - Data: any type of data can be stored in a voxel of the grid.
    - Boundedness: By using UnboundedGridStorage3D or BoundedGridStorage3D,
-   one can choose whether you want a grid over a finite region of space
-   or over the whole space.
+     one can choose whether you want a grid over a finite region of space
+     or over the whole space.
    - Storage: by choosing SparseGridStorage3D or DenseGridStorage3D, you can
-   choose whether you want to store all voxels or only a subset of the
-   voxels. The former is faster and more compact when most of the voxels are
-   used, the latter when only a few are used (say <1/4).]
+     choose whether you want to store all voxels or only a subset of the
+     voxels. The former is faster and more compact when most of the voxels are
+     used, the latter when only a few are used (say <1/4).
    - Geometry: The Grid3D class itself provides a geometric layer, mapping
-   Vector3D objects into voxels in the grid.
+     Vector3D objects into voxels in the grid.
 
    These are implemented as mix-ins, so each layer provides a set of accessible
    functionality as methods/types in the final class.

diff --git a/modules/atom/src/hierarchy_tools.cpp b/modules/atom/src/hierarchy_tools.cpp
@@ -260,7 +260,8 @@ Hierarchy create_approximation_of_residues(const Hierarchies &t) {
     }
     catch (ValueException) {
       IMP_WARN_ONCE(rt.get_string(),
-                    "Computing volume for non-standard residue " << rt, wc);
+                    "Computing volume for non-standard residue " << rt
+                    << std::endl, wc);
       algebra::Sphere3Ds ss;
       Hierarchies gl = get_leaves(t[i]);
       for (unsigned int i = 0; i < gl.size(); ++i) {

diff --git a/modules/atom/test/test_representation.py b/modules/atom/test/test_representation.py
@@ -229,10 +229,10 @@ def test_show(self):
         tmp20 = IMP.atom.create_simplified_along_backbone(ch,20)
         density_frag = IMP.atom.Fragment.setup_particle(IMP.Particle(mdl),idxs)
         for frag in tmp20.get_children():
-           gp = frag.get_particle()
-           xyzr = IMP.core.XYZR(gp)
-           g = bead2gaussian(xyzr.get_coordinates(),xyzr.get_radius(),mdl)
-           density_frag.add_child(g)
+            gp = frag.get_particle()
+            xyzr = IMP.core.XYZR(gp)
+            g = bead2gaussian(xyzr.get_coordinates(),xyzr.get_radius(),mdl)
+            density_frag.add_child(g)
         density_frag.set_name("Density:20")
         rep.add_representation(density_frag.get_particle(),IMP.atom.DENSITIES,20)
 

diff --git a/modules/container/include/AllBipartitePairContainer.h b/modules/container/include/AllBipartitePairContainer.h
@@ -2,9 +2,6 @@
  *  \file IMP/container/AllBipartitePairContainer.h
  *  \brief Return all pairs from a SingletonContainer
  *
- *  This file is generated by a script (core/tools/make-container).
- *  Do not edit directly.
- *
  *  Copyright 2007-2016 IMP Inventors. All rights reserved.
  */
 

diff --git a/modules/container/include/AllPairContainer.h b/modules/container/include/AllPairContainer.h
@@ -2,9 +2,6 @@
  *  \file IMP/container/AllPairContainer.h
  *  \brief Return all pairs from a SingletonContainer
  *
- *  This file is generated by a script (core/tools/make-container).
- *  Do not edit directly.
- *
  *  Copyright 2007-2016 IMP Inventors. All rights reserved.
  */
 

diff --git a/modules/container/include/CloseBipartitePairContainer.h b/modules/container/include/CloseBipartitePairContainer.h
@@ -2,9 +2,6 @@
  *  \file IMP/container/CloseBipartitePairContainer.h
  *  \brief Return all pairs from a SingletonContainer
  *
- *  This file is generated by a script (core/tools/make-container).
- *  Do not edit directly.
- *
  *  Copyright 2007-2016 IMP Inventors. Close rights reserved.
  */
 

diff --git a/modules/container/include/ClosePairContainer.h b/modules/container/include/ClosePairContainer.h
@@ -2,9 +2,6 @@
  *  \file IMP/container/ClosePairContainer.h
  *  \brief Return all pairs from a SingletonContainer
  *
- *  This file is generated by a script (core/tools/make-container).
- *  Do not edit directly.
- *
  *  Copyright 2007-2016 IMP Inventors. Close rights reserved.
  */
 

diff --git a/modules/container/src/AllBipartitePairContainer.cpp b/modules/container/src/AllBipartitePairContainer.cpp
@@ -2,9 +2,6 @@
  *  \file AllBipartitePairContainer.cpp   \brief A list of
  *ParticlePairs.
  *
- *  This file is generated by a script (core/tools/make-container).
- *  Do not edit directly.
- *
  *  Copyright 2007-2016 IMP Inventors. All rights reserved.
  *
  */

diff --git a/modules/container/src/AllPairContainer.cpp b/modules/container/src/AllPairContainer.cpp
@@ -1,9 +1,6 @@
 /**
  *  \file AllPairContainer.cpp   \brief A list of ParticlePairs.
  *
- *  This file is generated by a script (core/tools/make-container).
- *  Do not edit directly.
- *
  *  Copyright 2007-2016 IMP Inventors. All rights reserved.
  *
  */

diff --git a/modules/container/src/CloseBipartitePairContainer.cpp b/modules/container/src/CloseBipartitePairContainer.cpp
@@ -2,9 +2,6 @@
  *  \file CloseBipartitePairContainer.cpp   \brief A list of
  *ParticlePairs.
  *
- *  This file is generated by a script (core/tools/make-container).
- *  Do not edit directly.
- *
  *  Copyright 2007-2016 IMP Inventors. Close rights reserved.
  *
  */

diff --git a/modules/container/src/ClosePairContainer.cpp b/modules/container/src/ClosePairContainer.cpp
@@ -1,9 +1,6 @@
 /**
  *  \file ClosePairContainer.cpp   \brief A list of ParticlePairs.
  *
- *  This file is generated by a script (core/tools/make-container).
- *  Do not edit directly.
- *
  *  Copyright 2007-2016 IMP Inventors. Close rights reserved.
  *
  */

diff --git a/modules/container/src/ConnectingPairContainer.cpp b/modules/container/src/ConnectingPairContainer.cpp
@@ -1,9 +1,6 @@
 /**
  *  \file ConnectingPairContainer.cpp   \brief A list of ParticlePairs.
  *
- *  This file is generated by a script (core/tools/make-container).
- *  Do not edit directly.
- *
  *  Copyright 2007-2016 IMP Inventors. Connecting rights reserved.
  *
  */
@@ -19,6 +16,13 @@
 #include <IMP/container_macros.h>
 #include <algorithm>
 
+// Work around Boost bug with adjacency_matrix in 1.60:
+// https://svn.boost.org/trac/boost/ticket/11880
+#include <boost/version.hpp>
+#if BOOST_VERSION == 106000
+# include <boost/type_traits/ice.hpp>
+#endif
+
 #include <boost/graph/kruskal_min_spanning_tree.hpp>
 #include <boost/graph/prim_minimum_spanning_tree.hpp>
 #include <boost/graph/adjacency_list.hpp>

diff --git a/modules/core/include/internal/CoreCloseBipartitePairContainer.h b/modules/core/include/internal/CoreCloseBipartitePairContainer.h
@@ -2,9 +2,6 @@
  *  \file CloseBipartitePairContainer.h
  *  \brief Return all pairs from a SingletonContainer
  *
- *  This file is generated by a script (core/tools/make-container).
- *  Do not edit directly.
- *
  *  Copyright 2007-2016 IMP Inventors. Close rights reserved.
  */
 

diff --git a/modules/core/include/internal/CoreClosePairContainer.h b/modules/core/include/internal/CoreClosePairContainer.h
@@ -2,9 +2,6 @@
  *  \file core/internal/CoreClosePairContainer.h
  *  \brief Return all pairs from a SingletonContainer
  *
- *  This file is generated by a script (core/tools/make-container).
- *  Do not edit directly.
- *
  *  Copyright 2007-2016 IMP Inventors. Close rights reserved.
  */
 

diff --git a/modules/core/include/internal/container_helpers.h b/modules/core/include/internal/container_helpers.h
@@ -2,9 +2,6 @@
  *  \file internal/particle_helpers.h
  *  \brief A container for Singletons.
  *
- *  This file is generated by a script (core/tools/make-container).
- *  Do not edit directly.
- *
  *  Copyright 2007-2016 IMP Inventors. All rights reserved.
  */
 

diff --git a/modules/core/src/ConnectivityRestraint.cpp b/modules/core/src/ConnectivityRestraint.cpp
@@ -21,6 +21,13 @@
 
 #include <climits>
 
+// Work around Boost bug with adjacency_matrix in 1.60:
+// https://svn.boost.org/trac/boost/ticket/11880
+#include <boost/version.hpp>
+#if BOOST_VERSION == 106000
+# include <boost/type_traits/ice.hpp>
+#endif
+
 #include <boost/graph/kruskal_min_spanning_tree.hpp>
 #include <boost/graph/prim_minimum_spanning_tree.hpp>
 #include <boost/graph/adjacency_list.hpp>

diff --git a/modules/core/src/MSConnectivityRestraint.cpp b/modules/core/src/MSConnectivityRestraint.cpp
@@ -24,6 +24,13 @@
 
 #include <climits>
 
+// Work around Boost bug with adjacency_matrix in 1.60:
+// https://svn.boost.org/trac/boost/ticket/11880
+#include <boost/version.hpp>
+#if BOOST_VERSION == 106000
+# include <boost/type_traits/ice.hpp>
+#endif
+
 #include <boost/graph/kruskal_min_spanning_tree.hpp>
 #include <boost/graph/prim_minimum_spanning_tree.hpp>
 #include <boost/graph/adjacency_list.hpp>

diff --git a/modules/core/src/internal/CoreCloseBipartitePairContainer.cpp b/modules/core/src/internal/CoreCloseBipartitePairContainer.cpp
@@ -2,9 +2,6 @@
  *  \file CloseBipartitePairContainer.cpp   \brief A list of
  *ParticlePairs.
  *
- *  This file is generated by a script (core/tools/make-container).
- *  Do not edit directly.
- *
  *  Copyright 2007-2016 IMP Inventors. Close rights reserved.
  *
  */

diff --git a/modules/core/src/internal/CoreClosePairContainer.cpp b/modules/core/src/internal/CoreClosePairContainer.cpp
@@ -1,9 +1,6 @@
 /**
  *  \file ClosePairContainer.cpp   \brief A list of ParticlePairs.
  *
- *  This file is generated by a script (core/tools/make-container).
- *  Do not edit directly.
- *
  *  Copyright 2007-2016 IMP Inventors. Close rights reserved.
  *
  */