def main(args=None):
if which('git') is None:
print('Error: git was not found. Quit')
return
if which('mvn') is None:
print('Error: mvn was not found. Quit')
return
git_retrieve('https://github.com/pdp10/simqueue.git')
compile_simqueue()
print('cleanup!')
rmtree(os.path.join('.', 'simqueue'), ignore_errors=True)
def run_copasi_model(infile):
"""
Run a Copasi model
:param infile: the input file
"""
command = which("CopasiSE") + " " + infile
run_cmd(command)
def __init__(self):
__doc__ = Simul.__init__.__doc__
Simul.__init__(self)
self._copasi_not_found_msg = "CopasiSE not found! Please check that CopasiSE is installed and in the PATH " \
"environmental variable."
self._copasi = which("CopasiSE")
if self._copasi is None:
logger.error(self._copasi_not_found_msg)
def run_generic_model(infile):
"""
Run a generic model
:param infile: the input file
"""
command = which("python") + " " + infile + \
" " + os.path.basename(infile)[:-4] + ".csv"
run_cmd(command)
def setUpClass(cls):
sbpipe_snake_folder = 'sbpipe_snake'
orig_wd = os.getcwd()
os.chdir('snakemake')
if which('git') is None and os.path.isdir(sbpipe_snake_folder):
cls._output = 'git was not found. SKIP snakemake tests'
return
print('retrieving Snakemake workflows for SBpipe')
git_retrieve('https://github.com/pdp10/sbpipe_snake.git')
source = os.listdir(sbpipe_snake_folder)
destination = os.getcwd()
for f in source:
if f.endswith('.snake'):
shutil.move(os.path.join(os.path.abspath(sbpipe_snake_folder), f),
os.path.join(destination, f))
shutil.rmtree(sbpipe_snake_folder)
os.chdir(orig_wd)
def __init__(self,
lang=None,
lang_err_msg="No programming language is set!",
options=""):
"""
A constructor for a simulator of models coded in a programming language
:param lang: the programming language name (e.g. python, Copasi)
:param lang_err_msg: the message to print if lang is not found.
:param options: the options to use when invoking the command (e.g. "" for python).
"""
__doc__ = Simul.__init__.__doc__
Simul.__init__(self)
self._language = which(lang)
self._language_not_found_msg = lang_err_msg
self._options = options
logger.debug("Invoking simulator " + self._language +
" with options " + self._options)
if self._language is None:
logger.error(self._language_not_found_msg)
def pdf_report(outputdir, filename):
"""
Generate a PDF report from LaTeX report using pdflatex.
:param outputdir: the output directory
:param filename: the LaTeX file name
"""
pdflatex = which("pdflatex")
if pdflatex is None:
logger.error(
"pdflatex not found! pdflatex must be installed for pdf reports.")
return
currdir = os.getcwd()
os.chdir(outputdir)
logger.info(filename.replace('tex', 'pdf'))
logger.debug(pdflatex + " -halt-on-error " + filename)
# We suppress the output of pdflatex completely
try:
from subprocess import DEVNULL # python3
except ImportError:
DEVNULL = open(os.devnull, 'wb')
if sys.version_info > (3, ):
with subprocess.Popen([pdflatex, "-halt-on-error", filename],
stdout=DEVNULL,
stderr=subprocess.STDOUT) as p:
p.communicate()[0]
with subprocess.Popen([pdflatex, "-halt-on-error", filename],
stdout=DEVNULL,
stderr=subprocess.STDOUT) as p:
p.communicate()[0]
else:
p = subprocess.Popen([pdflatex, "-halt-on-error", filename],
stdout=DEVNULL,
stderr=subprocess.STDOUT)
p = subprocess.Popen([pdflatex, "-halt-on-error", filename],
stdout=DEVNULL,
stderr=subprocess.STDOUT)
p.communicate()[0]
os.chdir(currdir)