def link_swig(source):
target = os.path.join("swig")
tools.mkdir(target)
for module, g in tools.get_modules(source):
# they all go in the same dir, so don't remove old links
tools.link_dir(
os.path.join(g,
"pyext"),
target,
match=["*.i"],
clean=False)
if os.path.exists(os.path.join(g, "pyext", "include")):
tools.link_dir(
os.path.join(g,
"pyext",
"include"),
target,
match=["*.i"],
clean=False)
tools.link(
os.path.join(
g,
"pyext",
"swig.i-in"),
os.path.join(
target,
"IMP_%s.impl.i" %
module))
def run_swig(outputdir, options):
args = [options.swig]
args.append("-castmode")
args.extend(["-interface", "_IMP_%s" % options.module])
args.append("-DPySwigIterator=IMP_%s_PySwigIterator" %
options.module.upper())
args.append("-DSwigPyIterator=IMP_%s_SwigPyIterator" %
options.module.upper())
args.append("-python")
args.append("-c++")
args.append("-naturalvar")
args.append("-modern")
args.append("-fvirtual")
args.append("-Wextra")
args.append("-I" + os.path.join("..", "..", "include"))
args.append("-I" + os.path.join("..", "..", "swig"))
args.extend(["-oh", "wrap.h-in"])
args.extend(["-o", "wrap.cpp-in"])
if options.module == "base":
args.append("-DIMP_SWIG_BASE")
for p in options.swigpath:
args.append("-I%s" % tools.from_cmake_path(p))
for p in options.includepath:
args.append("-I%s" % tools.from_cmake_path(p))
args.append(os.path.abspath("./swig/IMP_%s.i" % options.module))
ret = tools.run_subprocess(args, cwd=outputdir)
if len(
open("src/%s_swig/IMP.%s.py" %
(options.module, options.module), "r").read()) < 10:
raise IOError("Empty swig wrapper file")
tools.link("src/%s_swig/IMP.%s.py" % (options.module, options.module),
"lib/IMP/%s/__init__.py" % options.module)
def run_swig(outputdir, options):
args = [options.swig]
args.append("-castmode")
args.extend(["-interface", "_IMP_%s" % options.module])
args.append(
"-DPySwigIterator=IMP_%s_PySwigIterator" %
options.module.upper())
args.append(
"-DSwigPyIterator=IMP_%s_SwigPyIterator" %
options.module.upper())
args.append("-python")
args.append("-c++")
args.append("-naturalvar")
args.append("-modern")
args.append("-fvirtual")
args.append("-Wextra")
args.append("-I" + os.path.join("..", "..", "include"))
args.append("-I" + os.path.join("..", "..", "swig"))
args.extend(["-oh", "wrap.h-in"])
args.extend(["-o", "wrap.cpp-in"])
if options.module == "base":
args.append("-DIMP_SWIG_BASE")
for p in options.swigpath:
args.append("-I%s" % tools.from_cmake_path(p))
for p in options.includepath:
args.append("-I%s" % tools.from_cmake_path(p))
args.append(os.path.abspath("./swig/IMP_%s.i" % options.module))
ret = tools.run_subprocess(args, cwd=outputdir)
if len(open("src/%s_swig/IMP.%s.py" % (options.module, options.module), "r").read()) < 10:
raise IOError("Empty swig wrapper file")
tools.link("src/%s_swig/IMP.%s.py" % (options.module, options.module),
"lib/IMP/%s/__init__.py" % options.module)
def main():
alias_headers(
os.path.join('include', 'IMP'), os.path.join('include', 'IMP',
'kernel'),
os.path.join('include', 'IMP', 'base'), 'IMP', [
'AttributeOptimizer.h', 'base_types.h', 'Configuration.h',
'ConfigurationSet.h', 'constants.h', 'Constraint.h',
'container_base.h', 'container_macros.h', 'Decorator.h',
'decorator_macros.h', 'dependency_graph.h',
'DerivativeAccumulator.h', 'doxygen.h', 'FloatIndex.h',
'functor.h', 'generic.h', 'input_output.h', 'io.h', 'Key.h',
'macros.h', 'Model.h', 'ModelObject.h', 'model_object_helpers.h',
'Optimizer.h', 'OptimizerState.h', 'Particle.h',
'particle_index.h', 'ParticleTuple.h', 'python_only.h',
'Refiner.h', 'Restraint.h', 'RestraintSet.h', 'Sampler.h',
'scoped.h', 'ScoreAccumulator.h', 'ScoreState.h',
'ScoringFunction.h', 'UnaryFunction.h', 'Undecorator.h',
'utility.h'
], {'base_utility.h': 'utility.h'})
alias_headers(
os.path.join('include', 'IMP', 'internal'),
os.path.join('include', 'IMP', 'kernel', 'internal'),
os.path.join('include', 'IMP', 'base', 'internal'), 'IMP/internal', [
'AccumulatorScoreModifier.h', 'AttributeTable.h',
'attribute_tables.h', 'constants.h', 'ContainerConstraint.h',
'container_helpers.h', 'ContainerRestraint.h',
'ContainerScoreState.h', 'create_decomposition.h',
'DynamicListContainer.h', 'evaluate_utility.h',
'ExponentialNumber.h', 'functors.h', 'graph_utility.h',
'IndexingIterator.h', 'input_output_exception.h', 'key_helpers.h',
'ListLikeContainer.h', 'NestedIterator.h', 'pdb.h',
'PrefixStream.h', 'restraint_evaluation.h',
'RestraintsScoringFunction.h', 'scoring_functions.h', 'static.h',
'StaticListContainer.h', 'swig.h', 'swig_helpers.h',
'TupleConstraint.h', 'TupleRestraint.h', 'Unit.h', 'units.h',
'utility.h'
], {
'base_graph_utility.h': 'graph_utility.h',
'base_static.h': 'static.h',
'swig_base.h': 'swig.h',
'swig_helpers_base.h': 'swig_helpers.h'
})
tools.rewrite(os.path.join('include', 'IMP', 'base', 'base_config.h'),
get_header_contents('IMP', 'kernel_config.h'))
tools.link(os.path.join('include', 'IMP.h'),
os.path.join('include', 'IMP', 'kernel.h'))
tools.link(os.path.join('include', 'IMP.h'),
os.path.join('include', 'IMP', 'base.h'))
for mod in ('base', 'kernel'):
subdir = os.path.join('lib', 'IMP', mod)
if not os.path.exists(subdir):
os.mkdir(subdir)
pymod = os.path.join(subdir, '__init__.py')
with open(pymod, 'w') as fh:
fh.write("""import sys
sys.stderr.write('IMP.%s is deprecated - use "import IMP" instead\\n')
from IMP import *
""" % mod)
def main():
alias_headers(os.path.join('include', 'IMP'),
os.path.join('include', 'IMP', 'kernel'),
os.path.join('include', 'IMP', 'base'),
'IMP', [ 'AttributeOptimizer.h', 'base_types.h',
'Configuration.h', 'ConfigurationSet.h', 'constants.h',
'Constraint.h', 'container_base.h', 'container_macros.h',
'Decorator.h', 'decorator_macros.h', 'dependency_graph.h',
'DerivativeAccumulator.h', 'doxygen.h', 'FloatIndex.h',
'functor.h', 'generic.h', 'input_output.h', 'io.h', 'Key.h',
'macros.h', 'Model.h', 'ModelObject.h', 'model_object_helpers.h',
'Optimizer.h', 'OptimizerState.h', 'Particle.h', 'particle_index.h',
'ParticleTuple.h', 'python_only.h', 'Refiner.h', 'Restraint.h',
'RestraintSet.h', 'Sampler.h', 'scoped.h', 'ScoreAccumulator.h',
'ScoreState.h', 'ScoringFunction.h', 'UnaryFunction.h',
'Undecorator.h', 'utility.h' ],
{'base_utility.h': 'utility.h' })
alias_headers(os.path.join('include', 'IMP', 'internal'),
os.path.join('include', 'IMP', 'kernel', 'internal'),
os.path.join('include', 'IMP', 'base', 'internal'),
'IMP/internal', [ 'AccumulatorScoreModifier.h',
'AttributeTable.h', 'attribute_tables.h', 'constants.h',
'ContainerConstraint.h', 'container_helpers.h', 'ContainerRestraint.h',
'ContainerScoreState.h', 'create_decomposition.h',
'DynamicListContainer.h', 'evaluate_utility.h', 'ExponentialNumber.h',
'functors.h', 'graph_utility.h', 'IndexingIterator.h',
'input_output_exception.h', 'key_helpers.h', 'ListLikeContainer.h',
'NestedIterator.h', 'pdb.h', 'PrefixStream.h',
'restraint_evaluation.h', 'RestraintsScoringFunction.h',
'scoring_functions.h', 'static.h', 'StaticListContainer.h', 'swig.h',
'swig_helpers.h', 'TupleConstraint.h', 'TupleRestraint.h',
'Unit.h', 'units.h', 'utility.h' ],
{'base_graph_utility.h': 'graph_utility.h',
'base_static.h': 'static.h',
'swig_base.h': 'swig.h',
'swig_helpers_base.h': 'swig_helpers.h'})
tools.rewrite(os.path.join('include', 'IMP', 'base', 'base_config.h'),
get_header_contents('IMP', 'kernel_config.h'))
tools.link(os.path.join('include', 'IMP.h'),
os.path.join('include', 'IMP', 'kernel.h'))
tools.link(os.path.join('include', 'IMP.h'),
os.path.join('include', 'IMP', 'base.h'))
for mod in ('base', 'kernel'):
subdir = os.path.join('lib', 'IMP', mod)
if not os.path.exists(subdir):
os.mkdir(subdir)
pymod = os.path.join(subdir, '__init__.py')
with open(pymod, 'w') as fh:
fh.write("""import sys
sys.stderr.write('IMP.%s is deprecated - use "import IMP" instead\\n')
from IMP import *
""" % mod)
def link_swig(source):
target = os.path.join("swig")
tools.mkdir(target)
for module, g in tools.get_modules(source):
# they all go in the same dir, so don't remove old links
tools.link_dir(os.path.join(g, "pyext"),
target,
match=["*.i"],
clean=False)
if os.path.exists(os.path.join(g, "pyext", "include")):
tools.link_dir(os.path.join(g, "pyext", "include"),
target,
match=["*.i"],
clean=False)
tools.link(os.path.join(g, "pyext", "swig.i-in"),
os.path.join(target, "IMP_%s.impl.i" % module))
def main():
name_template = "simple_graph{0}"
simple_parser = argparse.ArgumentParser(
formatter_class=argparse.RawTextHelpFormatter,
description="""Create a simple graph""",
epilog=textwrap.dedent("""
The test set is generated in the following way:
1. shuffles vertices
Example:
num_vertices = 8
[0, 1, 2, 3, 4, 5, 6, 7] ->
[3, 4, 1, 2, 6, 0, 7, 5]
2. splits them according to 'd' ...
first method
d[0] = 2, d[1] = 3, d[2] = 3
a = [3, 4]
b = [1, 2, 6]
c = [7, 5, 0]
d[0] = 0.25, d[1] = 0.5 (implicitly d[2] = 0.25)
a = [3, 4]
b = [1, 2, 6]
c = [7, 5, 0]
3. links them
edges[0] = [(3,4)]
edges[1] = [(1,2), (2,6)]
edges[2] = [(7,5), (5,0)]
4. adds e additional edges
first method
e = 0 1 1
edges[1] = [(1,2), (2,6), (1,6)]
edges[2] = [(7,5), (5,0), (7,0)]
second method
2 0 0.5
edges[1] = [(1,2), (2,6), (1,6)]
edges[2] = [(7,5), (5,0), (7,0)]
5. Generates two files
c = 1, 6 [ vertex intial and vertex final ]
simple_graphx.in
x increments if there already exists prior .in
Also order of edges are shuffled
Also all values are increased by one as vertices start from 1
according to course specification
simple_graph2.in [ if for example simple_graph1.in already exists ]
8 10 [num vertices, num edges]
2 3
2 7
...
4 5
1 6 [ vertices you want to go from and to specified by -c can be blank]
test number for .group will match test number for .in
will overwrite any .group with same number
simple_graph2.group
3, 4
1, 2, 6
7, 5, 0
""")
)
graph_parser(simple_parser)
simple_parser.add_argument(
'-c',
type=int,
help="inital and destination vertex",
nargs='*'
)
simple_parser.add_argument(
'-s',
"--show",
help=textwrap.dedent("""
If included creates image using graphviz
""".format(name_template)),
action="store_true"
)
args = simple_parser.parse_args()
num_vertices, ranges, vertices, split_vertices, additional_edges = create_graph(args)
edges = link(split_vertices, linker)
add_extra_edges(edges, split_vertices, additional_edges)
edges_str = edges_to_str(edges)
in_str = first_line(num_vertices, edges) + edges_str
if args.c is not None:
if len(args.c) != 2:
raise ValueError(
"num -c args is {0}, should be 2".format(len(args.c)))
in_str += last_line(args.c)
split_vertices_str = split_vertices_to_str(split_vertices)
i = write_in_and_group(in_str, split_vertices_str, file_dir, args.o, name_template)
flat_edges = [ list(edge) for edgesli in edges for edge in edgesli ]
s = bool(args.show)
if s:
image_filename = name_template.format(i) + ".png"
dot_str = to_dot(flat_edges, directed=False)
create_image(dot_str, image_filename)
