def __call__(self, assumptions=None):
"""
Run 'command' and collect output.
INPUT:
- ``assumptions`` - ignored, accepted for compatibility with
other solvers (default: ``None``)
TESTS:
This class is not meant to be called directly::
sage: from sage.sat.solvers.dimacs import DIMACS
sage: fn = tmp_filename()
sage: solver = DIMACS(filename=fn)
sage: solver.add_clause( (1, -2 , 3) )
sage: solver()
Traceback (most recent call last):
...
ValueError: No SAT solver command selected.
"""
if assumptions is not None:
raise NotImplementedError("Assumptions are not supported for DIMACS based solvers.")
self.write()
output_filename = None
self._output = []
command = self._command.strip()
if not command:
raise ValueError("No SAT solver command selected.")
if "{output}" in command:
output_filename = tmp_filename()
command = command.format(input=self._headname, output=output_filename)
args = shlex.split(command)
try:
process = subprocess.Popen(args, stdout=subprocess.PIPE)
except OSError:
raise OSError("Could run '%s', perhaps you need to add your SAT solver to $PATH?"%(" ".join(args)))
try:
while process.poll() is None:
for line in iter(process.stdout.readline,''):
if get_verbose() or self._verbosity:
print line,
sys.stdout.flush()
self._output.append(line)
sleep(0.1)
if output_filename:
self._output.extend(open(output_filename).readlines())
except KeyboardInterrupt:
process.kill()
raise KeyboardInterrupt
def __call__(self, model, outfile='sage.png',
verbose=1, block=True, extra_opts=''):
modelfile = tmp_filename() + '.dat'
open(modelfile,'w').write(model)
opts = ''
ext = outfile[-4:].lower()
if ext == '.png':
opts += ' -format PNG '
elif ext == '.tga':
opts += ' -format TARGA '
elif ext == '.bmp':
opts += ' -format BMP '
elif ext == '.ppm':
opts += ' -format PPM '
elif ext == '.rgb':
opts += ' -format RGB '
opts += ' -o %s '%outfile
opts += ' ' + extra_opts + ' '
if verbose >= 2:
opts += ' +V '
elif verbose == 0:
opts += ' 1>/dev/null'
cmd = 'tachyon %s %s; rm -f "%s"'%(modelfile,opts, modelfile)
if not block:
cmd += ' &'
if verbose:
print cmd
os.system(cmd)
def __call__(self,
model,
outfile='sage.png',
verbose=1,
block=True,
extra_opts=''):
"""
This executes the tachyon program, given a scene file input.
The default is to return the result as a PNG file called 'sage.png'.
TESTS::
sage: from sage.interfaces.tachyon import TachyonRT
sage: tgen = Tachyon()
sage: tgen.texture('t1')
sage: tgen.sphere((0,0,0),1,'t1')
sage: tgen.str()[30:40]
'resolution'
sage: t = TachyonRT()
sage: import os
sage: t(tgen.str(), outfile = os.devnull)
tachyon ...
Tachyon Parallel/Multiprocessor Ray Tracer...
"""
modelfile = tmp_filename(ext='.dat')
open(modelfile, 'w').write(model)
opts = ''
ext = outfile[-4:].lower()
if ext == '.png':
opts += ' -format PNG '
elif ext == '.tga':
opts += ' -format TARGA '
elif ext == '.bmp':
opts += ' -format BMP '
elif ext == '.ppm':
opts += ' -format PPM '
elif ext == '.rgb':
opts += ' -format RGB '
opts += ' -o %s ' % outfile
opts += ' ' + extra_opts + ' '
if verbose >= 2:
opts += ' +V '
elif verbose == 0:
opts += ' 1>/dev/null'
cmd = 'tachyon %s %s; rm -f "%s"' % (modelfile, opts, modelfile)
if not block:
cmd = '( ' + cmd + ' ) &'
if verbose:
print cmd
# One should always flush before system()
sys.stdout.flush()
sys.stderr.flush()
os.system(cmd)
def __init__(self, command=None, filename=None, verbosity=0, **kwds):
"""
Construct a new generic DIMACS solver.
INPUT:
- ``command`` - a named format string with the command to
run. The string must contain {input} and may contain
{output} if the solvers writes the solution to an output
file. For example "sat-solver {input}" is a valid
command. If ``None`` then the class variable ``command`` is
used. (default: ``None``)
- ``filename`` - a filename to write clauses to in DIMACS
format, must be writable. If ``None`` a temporary filename
is chosen automatically. (default: ``None``)
- ``verbosity`` - a verbosity level, where zero means silent
and anything else means verbose output. (default: ``0``)
- ``**kwds`` - accepted for compatibility with other solves,
ignored.
TESTS::
sage: from sage.sat.solvers.dimacs import DIMACS
sage: DIMACS()
DIMACS Solver: ''
"""
if filename is None:
filename = tmp_filename()
self._headname = filename
self._verbosity = verbosity
if command is not None:
self._command = command
else:
self._command = self.__class__.command
self._tail = open(tmp_filename(), 'w')
self._var = 0
self._lit = 0
def __init__(self, command=None, filename=None, verbosity=0, **kwds):
"""
Construct a new generic DIMACS solver.
INPUT:
- ``command`` - a named format string with the command to
run. The string must contain {input} and may contain
{output} if the solvers writes the solution to an output
file. For example "sat-solver {input}" is a valid
command. If ``None`` then the class variable ``command`` is
used. (default: ``None``)
- ``filename`` - a filename to write clauses to in DIMACS
format, must be writable. If ``None`` a temporary filename
is chosen automatically. (default: ``None``)
- ``verbosity`` - a verbosity level, where zero means silent
and anything else means verbose output. (default: ``0``)
- ``**kwds`` - accepted for compatibility with other solves,
ignored.
TESTS::
sage: from sage.sat.solvers.dimacs import DIMACS
sage: DIMACS()
DIMACS Solver: ''
"""
if filename is None:
filename = tmp_filename()
self._headname = filename
self._verbosity = verbosity
if command is not None:
self._command = command
else:
self._command = self.__class__.command
self._tail = open(tmp_filename(), "w")
self._var = 0
self._lit = 0
def __call__(self, model, outfile='sage.png',
verbose=1, block=True, extra_opts=''):
"""
This executes the tachyon program, given a scene file input.
The default is to return the result as a PNG file called 'sage.png'.
TESTS::
sage: from sage.interfaces.tachyon import TachyonRT
sage: tgen = Tachyon()
sage: tgen.texture('t1')
sage: tgen.sphere((0,0,0),1,'t1')
sage: tgen.str()[30:40]
'resolution'
sage: t = TachyonRT()
sage: import os
sage: t(tgen.str(), outfile = os.devnull)
tachyon ...
Tachyon Parallel/Multiprocessor Ray Tracer...
"""
modelfile = tmp_filename(ext='.dat')
open(modelfile,'w').write(model)
opts = ''
ext = outfile[-4:].lower()
if ext == '.png':
opts += ' -format PNG '
elif ext == '.tga':
opts += ' -format TARGA '
elif ext == '.bmp':
opts += ' -format BMP '
elif ext == '.ppm':
opts += ' -format PPM '
elif ext == '.rgb':
opts += ' -format RGB '
opts += ' -o %s '%outfile
opts += ' ' + extra_opts + ' '
if verbose >= 2:
opts += ' +V '
elif verbose == 0:
opts += ' 1>/dev/null'
cmd = 'tachyon %s %s; rm -f "%s"'%(modelfile,opts, modelfile)
if not block:
cmd = '( ' + cmd + ' ) &'
if verbose:
print cmd
# One should always flush before system()
sys.stdout.flush()
sys.stderr.flush()
os.system(cmd)
def runsnake(command):
"""
Graphical profiling with ``runsnake``
INPUT:
- ``command`` -- the command to be run as a string.
EXAMPLES::
sage: runsnake("list(SymmetricGroup(3))") # optional - runsnake
``command`` is first preparsed (see :func:`preparse`)::
sage: runsnake('for x in range(1,4): print x^2') # optional - runsnake
1
4
9
:func:`runsnake` requires the program ``runsnake``. Due to non
trivial dependencies (python-wxgtk, ...), installing it within the
Sage distribution is unpractical. Hence, we recommend installing
it with the system wide Python. On Ubuntu 10.10, this can be done
with::
> sudo apt-get install python-profiler python-wxgtk2.8 python-setuptools
> sudo easy_install RunSnakeRun
See the ``runsnake`` website for instructions for other platforms.
:func:`runsnake` further assumes that the system wide Python is
installed in ``/usr/bin/python``.
.. seealso::
- `The runsnake website <http://www.vrplumber.com/programming/runsnakerun/>`_
- ``%prun``
- :class:`Profiler`
"""
import cProfile, os
from sage.misc.misc import tmp_filename, get_main_globals
from sage.misc.preparser import preparse
tmpfile = tmp_filename()
cProfile.runctx(preparse(command.lstrip().rstrip()),
get_main_globals(),
locals(),
filename=tmpfile)
os.system("/usr/bin/python -E `which runsnake` %s &" % tmpfile)
def dump_to_tmpfile(s):
"""
Utility function to dump a string to a temporary file.
EXAMPLE:
sage: from spherical import *
sage: file_loc = dump_to_tmpfile("boo")
sage: os.remove(file_loc)
"""
file_loc = tmp_filename()
f = open(file_loc,"w")
f.write(s)
f.close()
return file_loc
def dump_to_tmpfile(s):
"""
Utility function to dump a string to a temporary file.
EXAMPLE::
sage: from sage.combinat.designs import ext_rep
sage: file_loc = ext_rep.dump_to_tmpfile("boo")
sage: os.remove(file_loc)
"""
file_loc = tmp_filename()
f = open(file_loc, "w")
f.write(v2_b2_k2_icgsa)
f.close()
return file_loc
def dump_to_tmpfile(s):
"""
Utility function to dump a string to a temporary file.
EXAMPLE::
sage: from sage.combinat.designs import ext_rep
sage: file_loc = ext_rep.dump_to_tmpfile("boo")
sage: os.remove(file_loc)
"""
file_loc = tmp_filename()
f = open(file_loc,"w")
f.write(v2_b2_k2_icgsa)
f.close()
return file_loc
def runsnake(command):
"""
Graphical profiling with ``runsnake``
INPUT:
- ``command`` -- the command to be run as a string.
EXAMPLES::
sage: runsnake("list(SymmetricGroup(3))") # optional - runsnake
``command`` is first preparsed (see :func:`preparse`)::
sage: runsnake('for x in range(1,4): print x^2') # optional - runsnake
1
4
9
:func:`runsnake` requires the program ``runsnake``. Due to non
trivial dependencies (python-wxgtk, ...), installing it within the
Sage distribution is unpractical. Hence, we recommend installing
it with the system wide Python. On Ubuntu 10.10, this can be done
with::
> sudo apt-get install python-profiler python-wxgtk2.8 python-setuptools
> sudo easy_install RunSnakeRun
See the ``runsnake`` website for instructions for other platforms.
:func:`runsnake` further assumes that the system wide Python is
installed in ``/usr/bin/python``.
.. seealso::
- `The runsnake website <http://www.vrplumber.com/programming/runsnakerun/>`_
- ``%prun``
- :class:`Profiler`
"""
import cProfile, os
from sage.misc.misc import tmp_filename, get_main_globals
from sage.misc.preparser import preparse
tmpfile = tmp_filename()
cProfile.runctx(preparse(command.lstrip().rstrip()), get_main_globals(), locals(), filename=tmpfile)
os.system("/usr/bin/python -E `which runsnake` %s &"%tmpfile)
def __call__(self, n, watch=False):
n = Integer(n)
self._validate(n)
cmd = 'echo "%s" | %s'%(n, self.__cmd)
if watch:
t = tmp_filename()
os.system('%s | tee %s'%(cmd, t))
ou = open(t).read()
os.unlink(t)
else:
i,o,e = os.popen3(cmd)
i.close()
ou = e.read() + '\n' + o.read()
if 'command not found' in ou:
err = ou + '\n' + 'You must install GMP-ECM.\n'
err += sage.misc.package.package_mesg('ecm-6.1.3')
raise RuntimeError, err
return ou
def __call__(self, n, watch=False):
n = Integer(n)
self._validate(n)
cmd = 'echo "%s" | %s' % (n, self.__cmd)
if watch:
t = tmp_filename()
os.system("%s | tee %s" % (cmd, t))
ou = open(t).read()
os.unlink(t)
else:
i, o, e = os.popen3(cmd)
i.close()
ou = e.read() + "\n" + o.read()
if "command not found" in ou:
err = ou + "\n" + "You must install GMP-ECM.\n"
err += sage.misc.package.package_mesg("ecm-6.1.3")
raise RuntimeError, err
return ou
def __call__(self, n, watch=False):
n = Integer(n)
self._validate(n)
cmd = 'echo "%s" | %s'%(n, self.__cmd)
if watch:
t = tmp_filename()
os.system('%s | tee %s'%(cmd, t))
ou = open(t).read()
os.unlink(t)
else:
from subprocess import Popen, PIPE
x = Popen(cmd, shell=True,
stdin=PIPE, stdout=PIPE, stderr=PIPE, close_fds=True)
x.stdin.close()
ou = x.stderr.read() + '\n' + x.stdout.read()
if 'command not found' in ou:
err = ou + '\n' + 'You must install GMP-ECM.\n'
err += sage.misc.package.package_mesg('ecm-6.1.3')
raise RuntimeError, err
return ou
def __call__(self, n, watch=False):
n = Integer(n)
self._validate(n)
cmd = 'echo "%s" | %s'%(n, self.__cmd)
if watch:
t = tmp_filename()
os.system('%s | tee %s'%(cmd, t))
ou = open(t).read()
os.unlink(t)
else:
from subprocess import Popen, PIPE
x = Popen(cmd, shell=True,
stdin=PIPE, stdout=PIPE, stderr=PIPE, close_fds=True)
x.stdin.close()
ou = x.stderr.read() + '\n' + x.stdout.read()
if 'command not found' in ou:
err = ou + '\n' + 'You must install GMP-ECM.\n'
err += sage.misc.package.package_mesg('ecm-6.1.3')
raise RuntimeError, err
return ou
def compile_and_load(code):
r"""
INPUT:
- ``code`` -- string containing code that could be in a .pyx file
that is attached or put in a %cython block in the notebook.
OUTPUT: a module, which results from compiling the given code and
importing it
EXAMPLES::
sage: module = sage.misc.cython.compile_and_load("def f(int n):\n return n*n")
sage: module.f(10)
100
"""
from sage.misc.misc import tmp_filename
file = tmp_filename() + ".pyx"
open(file, 'w').write(code)
from sage.server.support import cython_import
return cython_import(file, create_local_c_file=False)
def tmp_filename():
"""
Return a temporary file.
OUTPUT:
String. The absolute filename of the temporary file.
EXAMPLES::
sage: from sage.dev.misc import tmp_filename
sage: tmp_filename().startswith(str(SAGE_TMP))
True
"""
try:
from sage.misc.misc import tmp_filename
return tmp_filename()
except ImportError:
from tempfile import NamedTemporaryFile
f = NamedTemporaryFile(dir=get_sage_tmp())
f.close()
return f.name
def __call__(self,
model,
outfile='sage.png',
verbose=1,
block=True,
extra_opts=''):
modelfile = tmp_filename() + '.dat'
open(modelfile, 'w').write(model)
opts = ''
ext = outfile[-4:].lower()
if ext == '.png':
opts += ' -format PNG '
elif ext == '.tga':
opts += ' -format TARGA '
elif ext == '.bmp':
opts += ' -format BMP '
elif ext == '.ppm':
opts += ' -format PPM '
elif ext == '.rgb':
opts += ' -format RGB '
opts += ' -o %s ' % outfile
opts += ' ' + extra_opts + ' '
if verbose >= 2:
opts += ' +V '
elif verbose == 0:
opts += ' 1>/dev/null'
cmd = 'tachyon %s %s; rm -f "%s"' % (modelfile, opts, modelfile)
if not block:
cmd += ' &'
if verbose:
print cmd
os.system(cmd)
def compile_and_load(code):
r"""
INPUT:
- ``code`` -- string containing code that could be in a .pyx file
that is attached or put in a %cython block in the notebook.
OUTPUT: a module, which results from compiling the given code and
importing it
EXAMPLES::
sage: module = sage.misc.cython.compile_and_load("def f(int n):\n return n*n")
sage: module.f(10)
100
"""
from sage.misc.misc import tmp_filename
file = tmp_filename() + ".pyx"
open(file, "w").write(code)
from sage.server.support import cython_import
return cython_import(file, create_local_c_file=False)
def __call__(self, program, complex, subcomplex=None, **kwds):
"""
Call a CHomP program to compute the homology of a chain
complex, simplicial complex, or cubical complex.
See :class:`CHomP` for full documentation.
EXAMPLES::
sage: from sage.interfaces.chomp import CHomP
sage: T = cubical_complexes.Torus()
sage: CHomP()('homcubes', T) # indirect doctest, optional - CHomP
{0: 0, 1: Z x Z, 2: Z}
"""
from sage.misc.misc import tmp_filename
from sage.homology.all import CubicalComplex, cubical_complexes
from sage.homology.all import SimplicialComplex, Simplex
from sage.homology.cubical_complex import Cube
from sage.homology.chain_complex import HomologyGroup, ChainComplex
from subprocess import Popen, PIPE
from sage.rings.all import QQ, ZZ
from sage.modules.all import VectorSpace, vector
from sage.combinat.free_module import CombinatorialFreeModule
if not have_chomp(program):
raise OSError, "Program %s not found" % program
verbose = kwds.get('verbose', False)
generators = kwds.get('generators', False)
extra_opts = kwds.get('extra_opts', '')
base_ring = kwds.get('base_ring', ZZ)
if extra_opts:
extra_opts = extra_opts.split()
else:
extra_opts = []
# type of complex:
cubical = False
simplicial = False
chain = False
# CHomP seems to have problems with cubical complexes if the
# first interval in the first cube defining the complex is
# degenerate. So replace the complex X with [0,1] x X.
if isinstance(complex, CubicalComplex):
cubical = True
edge = cubical_complexes.Cube(1)
original_complex = complex
complex = edge.product(complex)
if verbose:
print "Cubical complex"
elif isinstance(complex, SimplicialComplex):
simplicial = True
if verbose:
print "Simplicial complex"
else:
chain = True
base_ring = kwds.get('base_ring', complex.base_ring())
if verbose:
print "Chain complex over %s" % base_ring
if base_ring == QQ:
raise ValueError, "CHomP doesn't compute over the rationals, only over Z or F_p."
if base_ring.is_prime_field():
p = base_ring.characteristic()
extra_opts.append('-p%s' % p)
mod_p = True
else:
mod_p = False
#
# complex
#
try:
data = complex._chomp_repr_()
except AttributeError:
raise AttributeError, "Complex can not be converted to use with CHomP."
datafile = tmp_filename()
f = open(datafile, 'w')
f.write(data)
f.close()
#
# subcomplex
#
if subcomplex is None:
if cubical:
subcomplex = CubicalComplex([complex.n_cells(0)[0]])
elif simplicial:
m = re.search(r'\(([^,]*),', data)
v = int(m.group(1))
subcomplex = SimplicialComplex([[v]])
else:
# replace subcomplex with [0,1] x subcomplex.
if cubical:
subcomplex = edge.product(subcomplex)
#
# generators
#
if generators:
genfile = tmp_filename()
extra_opts.append('-g%s' % genfile)
#
# call program
#
if subcomplex is not None:
try:
sub = subcomplex._chomp_repr_()
except AttributeError:
raise AttributeError, "Subcomplex can not be converted to use with CHomP."
subfile = tmp_filename()
f = open(subfile, 'w')
f.write(sub)
f.close()
else:
subfile = ''
if verbose:
print "Popen called with arguments",
print [program, datafile, subfile] + extra_opts
print
print "CHomP output:"
print
# output = Popen([program, datafile, subfile, extra_opts],
cmd = [program, datafile]
if subfile:
cmd.append(subfile)
if extra_opts:
cmd.extend(extra_opts)
output = Popen(cmd, stdout=PIPE).communicate()[0]
if verbose:
print output
print "End of CHomP output"
print
if generators:
gens = open(genfile, 'r').read()
if verbose:
print "Generators:"
print gens
#
# process output
#
# output contains substrings of one of the forms
# "H_1 = Z", "H_1 = Z_2 + Z", "H_1 = Z_2 + Z^2",
# "H_1 = Z + Z_2 + Z"
if output.find('trivial') != -1:
if mod_p:
return {0: VectorSpace(base_ring, 0)}
else:
return {0: HomologyGroup(0)}
d = {}
h = re.compile("^H_([0-9]*) = (.*)$", re.M)
tors = re.compile("Z_([0-9]*)")
#
# homology groups
#
for m in h.finditer(output):
if verbose:
print m.groups()
# dim is the dimension of the homology group
dim = int(m.group(1))
# hom_str is the right side of the equation "H_n = Z^r + Z_k + ..."
hom_str = m.group(2)
# need to read off number of summands and their invariants
if hom_str.find("0") == 0:
if mod_p:
hom = VectorSpace(base_ring, 0)
else:
hom = HomologyGroup(0)
else:
rk = 0
if hom_str.find("^") != -1:
rk_srch = re.search(r'\^([0-9]*)\s?', hom_str)
rk = int(rk_srch.group(1))
rk += len(re.findall("(Z$)|(Z\s)", hom_str))
if mod_p:
rk = rk if rk != 0 else 1
if verbose:
print "dimension = %s, rank of homology = %s" % (dim, rk)
hom = VectorSpace(base_ring, rk)
else:
n = rk
invts = []
for t in tors.finditer(hom_str):
n += 1
invts.append(int(t.group(1)))
for i in range(rk):
invts.append(0)
if verbose:
print "dimension = %s, number of factors = %s, invariants = %s" %(dim, n, invts)
hom = HomologyGroup(n, invts)
#
# generators
#
if generators:
if cubical:
g = process_generators_cubical(gens, dim)
if verbose:
print "raw generators: %s" % g
if g:
module = CombinatorialFreeModule(base_ring,
original_complex.n_cells(dim),
prefix="",
bracket=True)
basis = module.basis()
output = []
for x in g:
v = module(0)
for term in x:
v += term[0] * basis[term[1]]
output.append(v)
g = output
elif simplicial:
g = process_generators_simplicial(gens, dim, complex)
if verbose:
print "raw generators: %s" % gens
if g:
module = CombinatorialFreeModule(base_ring,
complex.n_cells(dim),
prefix="",
bracket=False)
basis = module.basis()
output = []
for x in g:
v = module(0)
for term in x:
if complex._numeric:
v += term[0] * basis[term[1]]
else:
# if not numeric: have to
# translate vertices from numbers
# to their original form.
translate = dict([(b,a) for (a,b) in complex._numeric_translation])
simplex = Simplex([translate[a] for a in tuple(term[1])])
v += term[0] * basis[simplex]
output.append(v)
g = output
elif chain:
g = process_generators_chain(gens, dim, base_ring)
if verbose:
print "raw generators: %s" % gens
if g:
d[dim] = (hom, g)
else:
d[dim] = hom
else:
d[dim] = hom
if chain:
new_d = {}
bottom = min(complex.differential())
top = max(complex.differential())
for dim in d:
if complex._degree == -1: # chain complex
new_dim = bottom + dim
else: # cochain complex
new_dim = top - dim
if isinstance(d[dim], tuple):
# generators included.
group = d[dim][0]
gens = d[dim][1]
new_gens = []
dimension = complex.differential(new_dim).ncols()
# make sure that each vector is embedded in the
# correct ambient space: pad with a zero if
# necessary.
for v in gens:
v_dict = v.dict()
if dimension - 1 not in v.dict():
v_dict[dimension - 1] = 0
new_gens.append(vector(base_ring, v_dict))
else:
new_gens.append(v)
new_d[new_dim] = (group, new_gens)
else:
new_d[new_dim] = d[dim]
d = new_d
return d
def eval(self,x,globals=None, locals=None):
"""
EXAMPLES::
sage: from sage.misc.inline_fortran import InlineFortran, _example
sage: test_fortran = InlineFortran(globals()) # optional -- fortran
sage: test_fortran(_example) # optional -- fortran
sage: import numpy
sage: n = numpy.array(range(10),dtype=float)
sage: fib(n,int(10)) # optional -- fortran
sage: n # optional -- fortran
array([ 0., 1., 1., 2., 3., 5., 8., 13., 21., 34.])
"""
if len(x.splitlines()) == 1 and os.path.exists(x):
filename = x
x = open(x).read()
if filename.lower().endswith('.f90'):
x = '!f90\n' + x
global count
# On linux g77_shared should be a script that runs sage_fortran -shared
# On OS X it should be a script that runs gfortran -bundle -undefined dynamic_lookup
path = os.environ['SAGE_LOCAL']+'/bin/sage-g77_shared'
from numpy import f2py
old_import_path=os.sys.path
cwd=os.getcwd()
os.sys.path.append(cwd)
#name = tmp_dir() + '/fortran_module_%d'%count
name = 'fortran_module_%d'%count
if os.path.exists(name):
os.unlink(name)
s_lib_path=""
s_lib=""
for s in self.library_paths:
s_lib_path=s_lib_path+"-L"+s+" "
for s in self.libraries:
s_lib=s_lib +"-l"+s + " "
# if the first line has !f90 as a comment gfortran will treat it as
# fortran 90 code
if x.startswith('!f90'):
fname = os.path.join(tmp_filename() +'.f90')
else:
fname = os.path.join(tmp_filename() +'.f')
log = tmp_filename()
extra_args = '--quiet --f77exec=%s --f90exec=%s %s %s 1>&2 >"%s"'%(
path, path, s_lib_path, s_lib, log)
f2py.compile(x, name, extra_args = extra_args, source_fn=fname)
log_string = open(log).read()
os.unlink(log)
os.unlink(fname)
if self.verbose:
print log_string
count += 1
try:
m=__builtin__.__import__(name)
except ImportError:
if not self.verbose:
print log_string
return
finally:
os.sys.path=old_import_path
os.unlink(name + '.so')
for k, x in m.__dict__.iteritems():
if k[0] != '_':
self.globals[k] = x
def __call__(self, program, complex, subcomplex=None, **kwds):
"""
Call a CHomP program to compute the homology of a chain
complex, simplicial complex, or cubical complex.
See :class:`CHomP` for full documentation.
EXAMPLES::
sage: from sage.interfaces.chomp import CHomP
sage: T = cubical_complexes.Torus()
sage: CHomP()('homcubes', T) # indirect doctest, optional - CHomP
{0: 0, 1: Z x Z, 2: Z}
"""
from sage.misc.misc import tmp_filename
from sage.homology.all import CubicalComplex, cubical_complexes
from sage.homology.all import SimplicialComplex, Simplex
from sage.homology.cubical_complex import Cube
from sage.homology.chain_complex import HomologyGroup, ChainComplex
from subprocess import Popen, PIPE
from sage.rings.all import QQ, ZZ
from sage.modules.all import VectorSpace, vector
from sage.combinat.free_module import CombinatorialFreeModule
if not have_chomp(program):
raise OSError("Program %s not found" % program)
verbose = kwds.get('verbose', False)
generators = kwds.get('generators', False)
extra_opts = kwds.get('extra_opts', '')
base_ring = kwds.get('base_ring', ZZ)
if extra_opts:
extra_opts = extra_opts.split()
else:
extra_opts = []
# type of complex:
cubical = False
simplicial = False
chain = False
# CHomP seems to have problems with cubical complexes if the
# first interval in the first cube defining the complex is
# degenerate. So replace the complex X with [0,1] x X.
if isinstance(complex, CubicalComplex):
cubical = True
edge = cubical_complexes.Cube(1)
original_complex = complex
complex = edge.product(complex)
if verbose:
print "Cubical complex"
elif isinstance(complex, SimplicialComplex):
simplicial = True
if verbose:
print "Simplicial complex"
else:
chain = True
base_ring = kwds.get('base_ring', complex.base_ring())
if verbose:
print "Chain complex over %s" % base_ring
if base_ring == QQ:
raise ValueError(
"CHomP doesn't compute over the rationals, only over Z or F_p."
)
if base_ring.is_prime_field():
p = base_ring.characteristic()
extra_opts.append('-p%s' % p)
mod_p = True
else:
mod_p = False
#
# complex
#
try:
data = complex._chomp_repr_()
except AttributeError:
raise AttributeError(
"Complex can not be converted to use with CHomP.")
datafile = tmp_filename()
f = open(datafile, 'w')
f.write(data)
f.close()
#
# subcomplex
#
if subcomplex is None:
if cubical:
subcomplex = CubicalComplex([complex.n_cells(0)[0]])
elif simplicial:
m = re.search(r'\(([^,]*),', data)
v = int(m.group(1))
subcomplex = SimplicialComplex([[v]])
else:
# replace subcomplex with [0,1] x subcomplex.
if cubical:
subcomplex = edge.product(subcomplex)
#
# generators
#
if generators:
genfile = tmp_filename()
extra_opts.append('-g%s' % genfile)
#
# call program
#
if subcomplex is not None:
try:
sub = subcomplex._chomp_repr_()
except AttributeError:
raise AttributeError(
"Subcomplex can not be converted to use with CHomP.")
subfile = tmp_filename()
f = open(subfile, 'w')
f.write(sub)
f.close()
else:
subfile = ''
if verbose:
print "Popen called with arguments",
print[program, datafile, subfile] + extra_opts
print
print "CHomP output:"
print
# output = Popen([program, datafile, subfile, extra_opts],
cmd = [program, datafile]
if subfile:
cmd.append(subfile)
if extra_opts:
cmd.extend(extra_opts)
output = Popen(cmd, stdout=PIPE).communicate()[0]
if verbose:
print output
print "End of CHomP output"
print
if generators:
gens = open(genfile, 'r').read()
if verbose:
print "Generators:"
print gens
#
# process output
#
# output contains substrings of one of the forms
# "H_1 = Z", "H_1 = Z_2 + Z", "H_1 = Z_2 + Z^2",
# "H_1 = Z + Z_2 + Z"
if output.find('trivial') != -1:
if mod_p:
return {0: VectorSpace(base_ring, 0)}
else:
return {0: HomologyGroup(0, ZZ)}
d = {}
h = re.compile("^H_([0-9]*) = (.*)$", re.M)
tors = re.compile("Z_([0-9]*)")
#
# homology groups
#
for m in h.finditer(output):
if verbose:
print m.groups()
# dim is the dimension of the homology group
dim = int(m.group(1))
# hom_str is the right side of the equation "H_n = Z^r + Z_k + ..."
hom_str = m.group(2)
# need to read off number of summands and their invariants
if hom_str.find("0") == 0:
if mod_p:
hom = VectorSpace(base_ring, 0)
else:
hom = HomologyGroup(0, ZZ)
else:
rk = 0
if hom_str.find("^") != -1:
rk_srch = re.search(r'\^([0-9]*)\s?', hom_str)
rk = int(rk_srch.group(1))
rk += len(re.findall("(Z$)|(Z\s)", hom_str))
if mod_p:
rk = rk if rk != 0 else 1
if verbose:
print "dimension = %s, rank of homology = %s" % (dim,
rk)
hom = VectorSpace(base_ring, rk)
else:
n = rk
invts = []
for t in tors.finditer(hom_str):
n += 1
invts.append(int(t.group(1)))
for i in range(rk):
invts.append(0)
if verbose:
print "dimension = %s, number of factors = %s, invariants = %s" % (
dim, n, invts)
hom = HomologyGroup(n, ZZ, invts)
#
# generators
#
if generators:
if cubical:
g = process_generators_cubical(gens, dim)
if verbose:
print "raw generators: %s" % g
if g:
module = CombinatorialFreeModule(
base_ring,
original_complex.n_cells(dim),
prefix="",
bracket=True)
basis = module.basis()
output = []
for x in g:
v = module(0)
for term in x:
v += term[0] * basis[term[1]]
output.append(v)
g = output
elif simplicial:
g = process_generators_simplicial(gens, dim, complex)
if verbose:
print "raw generators: %s" % gens
if g:
module = CombinatorialFreeModule(base_ring,
complex.n_cells(dim),
prefix="",
bracket=False)
basis = module.basis()
output = []
for x in g:
v = module(0)
for term in x:
if complex._is_numeric():
v += term[0] * basis[term[1]]
else:
translate = complex._translation_from_numeric(
)
simplex = Simplex(
[translate[a] for a in term[1]])
v += term[0] * basis[simplex]
output.append(v)
g = output
elif chain:
g = process_generators_chain(gens, dim, base_ring)
if verbose:
print "raw generators: %s" % gens
if g:
if not mod_p:
# sort generators to match up with corresponding invariant
g = [
_[1]
for _ in sorted(zip(invts, g), key=lambda x: x[0])
]
d[dim] = (hom, g)
else:
d[dim] = hom
else:
d[dim] = hom
if chain:
new_d = {}
diff = complex.differential()
if len(diff) == 0:
return {}
bottom = min(diff)
top = max(diff)
for dim in d:
if complex._degree_of_differential == -1: # chain complex
new_dim = bottom + dim
else: # cochain complex
new_dim = top - dim
if isinstance(d[dim], tuple):
# generators included.
group = d[dim][0]
gens = d[dim][1]
new_gens = []
dimension = complex.differential(new_dim).ncols()
# make sure that each vector is embedded in the
# correct ambient space: pad with a zero if
# necessary.
for v in gens:
v_dict = v.dict()
if dimension - 1 not in v.dict():
v_dict[dimension - 1] = 0
new_gens.append(vector(base_ring, v_dict))
else:
new_gens.append(v)
new_d[new_dim] = (group, new_gens)
else:
new_d[new_dim] = d[dim]
d = new_d
return d
def __call__(self, assumptions=None):
"""
Run 'command' and collect output.
INPUT:
- ``assumptions`` - ignored, accepted for compatibility with
other solvers (default: ``None``)
TESTS:
This class is not meant to be called directly::
sage: from sage.sat.solvers.dimacs import DIMACS
sage: fn = tmp_filename()
sage: solver = DIMACS(filename=fn)
sage: solver.add_clause( (1, -2 , 3) )
sage: solver()
Traceback (most recent call last):
...
ValueError: No SAT solver command selected.
"""
if assumptions is not None:
raise NotImplementedError(
"Assumptions are not supported for DIMACS based solvers.")
self.write()
output_filename = None
self._output = []
command = self._command.strip()
if not command:
raise ValueError("No SAT solver command selected.")
if "{output}" in command:
output_filename = tmp_filename()
command = command.format(input=self._headname, output=output_filename)
args = shlex.split(command)
try:
process = subprocess.Popen(args, stdout=subprocess.PIPE)
except OSError:
raise OSError(
"Could run '%s', perhaps you need to add your SAT solver to $PATH?"
% (" ".join(args)))
try:
while process.poll() is None:
for line in iter(process.stdout.readline, ''):
if get_verbose() or self._verbosity:
print line,
sys.stdout.flush()
self._output.append(line)
sleep(0.1)
if output_filename:
self._output.extend(open(output_filename).readlines())
except KeyboardInterrupt:
process.kill()
raise KeyboardInterrupt