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Commits on Aug 16, 2017
  1. Suppress 'was not used' warning.

    Since we do "use" these objects, we should set the
    was-used flag, otherwise we'll get a warning on
    every single score evaluation.
    benmwebb committed Aug 16, 2017
Commits on Aug 14, 2017
  1. Start working on next release.

    benmwebb committed Aug 14, 2017
Commits on Aug 11, 2017
  1. Don't use 'typename' outside of a template.

    While newer gcc will accept this usage, the old gcc that
    we use to build conda packages doesn't like it.
    benmwebb committed Aug 11, 2017
  2. Remove unused function.

    benmwebb committed Aug 11, 2017
Commits on Aug 10, 2017
  1. Remove functions that were deprecated in 2.7.

    benmwebb committed Aug 10, 2017
Commits on Aug 9, 2017
  1. Prepare for 2.8.0 release.

    benmwebb committed Aug 9, 2017
Commits on Aug 8, 2017
  1. Squashed 'modules/rmf/dependency/RMF/' changes from e6ced6c4c5..8d8fa…

    …22672
    
    8d8fa22672 Work around Windows #define of "ALTERNATE".
    
    git-subtree-dir: modules/rmf/dependency/RMF
    git-subtree-split: 8d8fa226726fd721833d68783e1f21f1d9ecd2d0
    benmwebb committed Aug 8, 2017
  2. Only use mpiexec in tests if it was found.

    Currently our Windows builds build OK with MS-MPI, but its
    mpiexec doesn't work in our Wine environment for some
    reason, so in this case we'll just test on one processor.
    benmwebb committed Aug 8, 2017
  3. Don't complain about unbundled msmpi.dll.

    MPI-enabled modules will require msmpi.dll on Windows
    systems, but we're relying on the user to install MS-MPI
    themselves, so don't complain about it not being bundled.
    benmwebb committed Aug 8, 2017
  4. Don't use C99 round() function.

    MSVC doesn't support the C99 round() function, so
    add a simple workaround.
    benmwebb committed Aug 8, 2017
  5. Look for mpi.h in system paths first.

    We should look for mpi.h in system paths *before* the
    current directory, as otherwise when building the SWIG
    wrappers the compiler may find IMP/mpi.h rather than the
    'real' MPI header file we want.
    benmwebb committed Aug 8, 2017
  6. Fix generation of Python search path file.

    We can't use simple globbing here since the file doesn't
    exist yet, but we *can* glob the directory.
    benmwebb committed Aug 8, 2017
  7. We don't currently provide MPI for Python 3.

    Our RPMs don't currently include a Python 3 & MPI
    package, so we should skip Python 3 tests of MPI
    components for now.
    benmwebb committed Aug 8, 2017
  8. Initialize members in declared order.

    While in this case it shouldn't make any difference in what
    order members are initialized, it's probably best to initialize
    them in the same order that they're declared in the header
    file, if only to avoid a compiler warning.
    benmwebb committed Aug 8, 2017
  9. Don't use C99 variable-sized arrays.

    C99-style variable-sized arrays aren't supported by
    all of our compilers (e.g. MSVC) so use the C++
    std::vector equivalent.
    benmwebb committed Aug 8, 2017
Commits on Aug 7, 2017
  1. Add MPI-dependent location to Python search path.

    On Fedora this is handled by the python2-mpich package, while in RHEL7
    the mpich modulefile sets PYTHONPATH, but nothing appears to handle it
    in RHEL6, so we'll do it ourselves.
    benmwebb committed Aug 7, 2017
  2. Fix package name.

    benmwebb committed Aug 7, 2017
  3. Prefer https for links.

    benmwebb committed Aug 7, 2017
  4. Use MPI-specific location for spb binaries.

    Since all of the SPB binaries use MPI, they should
    go into an MPI-specific location so that they don't
    conflict between MPI implementations.
    benmwebb committed Aug 7, 2017
  5. Make sure mpich subdir is in Python path on Fedora.

    On RHEL7, the mpich module adds the mpich-specific Python
    module directory to $PYTHONPATH, but on Fedora we need
    to pull in a special python-mpich package which adds a
    .pth file to extend sys.path.
    benmwebb committed Aug 7, 2017
Commits on Aug 5, 2017
  1. Add function name exceptions

    sdaxen committed Aug 5, 2017
Commits on Aug 4, 2017
  1. Squashed 'modules/pmi/' changes from 6e9dda042d..7807950f08

    7807950f08 fixing a test
    1f2c0fd412 new MapCrossLinkDataBaseOnStructure class (removed from xltable)
    d4c3bb9198 forgot to add the test data file
    688f2ac619 fixing dof test
    072189109d added a class to gather score values from replicas
    906ae173f0 save_coordinates_mode for ReplicaExchange0
    3b8c40a8ae have the RMSD deal with dynamic or static trajectories
    f55e076a8e add state function of build macro now accepts a fasta name conversion dict
    8b958df064 added comment to the get fields function
    b2ebfa850c added support for monolink parsing
    
    git-subtree-dir: modules/pmi
    git-subtree-split: 7807950f0843d0d68b95b0b3971c722f2402c8b3
    benmwebb committed Aug 4, 2017
Commits on Aug 3, 2017
Commits on Aug 2, 2017
  1. We actually need Boost 1.41, as per installation docs.

    benmwebb committed Aug 2, 2017