def build_regex_win32(): # pragma: windows
r"""Build the regex_win32 library using cmake."""
# Configure project
cmd = ['cmake', '-H.', '-Bbuild']
comp_process = tools.popen_nobuffer(cmd, cwd=_regex_win32_dir)
output, err = comp_process.communicate()
exit_code = comp_process.returncode
if exit_code != 0: # pragma: debug
print(' '.join(cmd))
tools.print_encoded(output, end="")
raise RuntimeError("Could not config regex_win32")
# Build project
cmd = ['cmake', '--build', 'build', '--clean-first']
comp_process = tools.popen_nobuffer(cmd, cwd=_regex_win32_dir)
output, err = comp_process.communicate()
exit_code = comp_process.returncode
if exit_code != 0: # pragma: debug
print(' '.join(cmd))
tools.print_encoded(output, end="")
raise RuntimeError("Could not build regex_win32")
assert (os.path.isfile(_regex_win32_lib))
def pprint_diff(x, y): # pragma: no cover
r"""Get the diff between the pprint.pformat string for two objects."""
tools.print_encoded('\n'.join(
difflib.ndiff(
pprint.pformat(x).splitlines(),
pprint.pformat(y).splitlines())))
# If the receive was not succesful, send the end-of-file message to
# close the output file.
print("End of file input (Python)")
out_file.send_eof()
# Read rows from ASCII table until end of file is reached.
# As each row is received, it is then sent to the output ASCII table
print('ascii_io(P): Receiving/sending ASCII table.')
ret = True
while ret:
# Receive a single row
(ret, line) = in_table.recv()
if ret:
# If the receive was succesful, send the values to output.
# Formatting is taken care of on the output driver side.
print_encoded("Table: %s, %d, %3.1f, %s" % tuple(line))
# print("Table: %s, %d, %3.1f, %s" % line)
ret = out_table.send(*line)
if not ret:
raise RuntimeError("ascii_io(P): ERROR SENDING ROW")
else:
# If the receive was not succesful, send the end-of-file message to
# close the output file.
print("End of table input (Python)")
out_table.send_eof()
# Read entire array from ASCII table into numpy array
ret = True
while ret:
ret, arr = in_array.recv_array()
if ret:
if args.yggdrasil:
from yggdrasil.interface import YggInput, YggOutput
from yggdrasil.units import add_units
from yggdrasil.tools import print_encoded
input = YggInput('photosynthesis_rate')
output = YggOutput('growth_rate', '%f\n')
while True:
flag, prate = input.recv()
if not flag:
print('growth: No more input.')
break
grate = calculate_growth(*prate)
grate *= add_units(1.0, "cm*m**2/umol")
print_encoded(
f'growth: photosynthesis rate = {prate[0]} ---> '
f'growth rate = {grate}')
flag = output.send(grate)
if not flag:
print('growth: Error sending growth rate.')
sys.exit(-1)
else:
parser.add_argument('input_file', help='Input file.', nargs=1)
parser.add_argument('output_file', help='Output file.', nargs=1)
args = parser.parse_known_args()[0]
input_fd = open(args.input_file[0], newline='')
output_fd = open(args.output_file[0], 'w', newline='')
output = []
input_reader = csv.reader(filter(lambda row: row[0] != '#', input_fd),
def call_link(obj,
out=None,
flags=[],
overwrite=False,
verbose=False,
cpp=False,
shared=False,
static=False,
working_dir=None):
r"""Compile a source file, checking for errors.
Args:
obj (list): Object files that should be linked.
out (str, optional): Full path to output file that should be created.
If None, the path will be determined from the path to the first
object file provided. Defaults to False.
flags (list, optional): Compilation flags. Defaults to [].
overwrite (bool, optional): If True, the existing compile file will be
overwritten. Otherwise, it will be kept and this function will
return without recompiling the source file.
verbose (bool, optional): If True, the linking command and any output
produced by the command will be displayed on success. Defaults to
False.
cpp (bool, optional): If True, value is returned assuming the source
is written in C++. Defaults to False.
shared (bool, optional): If True, the object files are combined into a
shared library. Defaults to False.
static (bool, optional): If True, the object files are combined into a
static library. Defaults to False.
working_dir (str, optional): Working directory that input file paths are
relative to. Defaults to current working directory.
Returns:
str: Full path to compiled source.
"""
# Set defaults
if working_dir is None:
working_dir = os.getcwd()
flags = copy.deepcopy(flags)
if not isinstance(obj, list):
obj = [obj]
# Set path if not provided
if out is None:
obase = os.path.splitext(obj[0])[0]
if platform._is_win: # pragma: windows
oext = '.exe'
else:
oext = '.out'
out = obase + oext
if not os.path.isabs(out):
out = os.path.normpath(os.path.join(working_dir, out))
# Check for file
if os.path.isfile(out):
if overwrite:
os.remove(out)
else:
return out
# Check extension for information about the result
if out.endswith('.so') or out.endswith('.dll') or out.endswith('.dylib'):
shared = True
elif out.endswith('.a') or out.endswith('.lib'):
static = True
# Get compiler
cc = get_cc(shared=shared, static=static, cpp=cpp, linking=True)
# Construct arguments
args = [cc]
if shared:
if platform._is_win: # pragma: windows
flags.append('/DLL')
elif platform._is_mac:
flags.append('-dynamiclib')
else:
flags.append('-shared')
args += flags
elif static:
if platform._is_win: # pragma: windows
pass
elif platform._is_mac:
flags += ['-static']
else:
flags += ['-rcs', out]
args += flags
if platform._is_win: # pragma: windows
args += ['/OUT:%s' % out]
elif platform._is_mac:
if shared:
args += ["-o", out]
else:
args += ["-o", out]
else:
if static:
args += [out]
else:
args += ["-o", out]
args += obj
if not (shared or static):
args += flags
# Call linker
comp_process = tools.popen_nobuffer(args)
output, err = comp_process.communicate()
exit_code = comp_process.returncode
if exit_code != 0: # pragma: debug
print(' '.join(args))
tools.print_encoded(output, end="")
raise RuntimeError("Linking of %s failed with code %d." %
(out, exit_code))
if not os.path.isfile(out): # pragma: debug
print(' '.join(args))
raise RuntimeError("Linking failed to produce result '%s'" % out)
logging.info("Linked %s" % out)
if verbose: # pragma: debug
print(' '.join(args))
tools.print_encoded(output, end="")
return out
def call_compile(src,
out=None,
flags=[],
overwrite=False,
verbose=False,
cpp=None,
working_dir=None):
r"""Compile a source file, checking for errors.
Args:
src (str): Full path to source file.
out (str, optional): Full path to the output object file that should
be created. Defaults to None and is created from the provided source
file.
flags (list, optional): Compilation flags. Defaults to [].
overwrite (bool, optional): If True, the existing compile file will be
overwritten. Otherwise, it will be kept and this function will
return without recompiling the source file.
verbose (bool, optional): If True, the compilation command and any output
produced by the command will be displayed on success. Defaults to
False.
cpp (bool, optional): If True, value is returned assuming the source
is written in C++. Defaults to False.
working_dir (str, optional): Working directory that input file paths are
relative to. Defaults to current working directory.
Returns:
str: Full path to compiled source.
"""
# Set defaults
if working_dir is None:
working_dir = os.getcwd()
flags = copy.deepcopy(flags)
if platform._is_win: # pragma: windows
flags = ['/W4', '/Zi', "/EHsc"] + flags
else:
flags = ['-g', '-Wall'] + flags
src_base, src_ext = os.path.splitext(src)
if cpp is None:
cpp = False
if src_ext in ['.hpp', '.cpp']:
cpp = True
if platform._is_win: # pragma: windows
if cpp:
flags.insert(2, '/TP')
else:
flags.insert(2, '/TP')
# TODO: Currently everything compiled as C++ on windows to allow use of
# complex types
# flags.insert(2, '/TC')
# Add standard library flag
std_flag = None
for i, a in enumerate(flags):
if a.startswith('-std='):
std_flag = i
break
if cpp and (not platform._is_win):
if std_flag is None:
flags.append('-std=c++11')
else:
if std_flag is not None:
flags.pop(i)
# Get compiler command
cc = get_cc(cpp=cpp)
# Get output if not provided
if out is None:
if platform._is_win: # pragma: windows
out_ext = '.obj'
else:
out_ext = '.o'
out = src_base + '_' + src_ext[1:] + out_ext
if not os.path.isabs(out):
out = os.path.normpath(os.path.join(working_dir, out))
# Construct arguments
args = [cc, "-c"] + flags + [src]
if not platform._is_win:
args += ["-o", out]
else: # pragma: windows
args.insert(1, '/Fo%s' % out)
# Check for file
if os.path.isfile(out):
if overwrite:
os.remove(out)
else:
return out
# Call compiler
comp_process = tools.popen_nobuffer(args)
output, err = comp_process.communicate()
exit_code = comp_process.returncode
if exit_code != 0: # pragma: debug
print(' '.join(args))
tools.print_encoded(output, end="")
raise RuntimeError("Compilation of %s failed with code %d." %
(out, exit_code))
if not os.path.isfile(out): # pragma: debug
print(' '.join(args))
raise RuntimeError("Compilation failed to produce result '%s'" % out)
logging.info("Compiled %s" % out)
if verbose: # pragma: debug
print(' '.join(args))
tools.print_encoded(output, end="")
return out