Set autoinstall to True by default

setup.py

@@ -53,7 +53,7 @@ def run(self):
  cmdclass = cmdclass,
  package_dir = {'dsc': 'src'},
  install_requires = ['numpy', 'pandas>=0.23.4', 'sympy', 'numexpr',
- 'sos>=0.16.11', 'sos-pbs>=0.9.16.0', 'h5py', 'PTable',
+ 'sos>=0.17.3', 'sos-pbs>=0.9.17.0', 'h5py', 'PTable',
  'pyarrow>=0.5.0', 'sqlalchemy', 'tzlocal',
  'msgpack-python']
  )

src/dsc_translator.py

@@ -141,9 +141,9 @@ def __init__(self, workflows, runtime, rerun = False, n_cpu = 4, try_catch = Fal
  self.install_libs(runtime.rlib, "R_library")
  self.install_libs([x for x in runtime.pymodule if x != 'dsc'], "Python_Module")
  else:
- self.lib_depends.extend([f'if not R_library({repr(l[0])}, {repr(l[1]) if l[1] is not None else "None"}).target_exists():\n raise RuntimeError("Automatic installation failed. Please login and manually install {repr(l[0])}.")'
+ self.lib_depends.extend([f'if not R_library({repr(l[0])}, version={repr(l[1]) if l[1] is not None else "None"}, autoinstall=True).target_exists():\n raise RuntimeError("Automatic installation failed. Please login and manually install {repr(l[0])}.")'
  for l in [install_r_lib(x, dryrun = True) for x in runtime.rlib]])
- self.lib_depends.extend([f'if not Py_Module("{l}").target_exists():\n raise RuntimeError("Automatic installation failed. Please login and manually install {repr(l)}.")'
+ self.lib_depends.extend([f'if not Py_Module("{l}", autoinstall=True).target_exists():\n raise RuntimeError("Automatic installation failed. Please login and manually install {repr(l)}.")'
  for l in (runtime.pymodule + ['msgpack'])])
 
  def write_pipeline(self, arg):

src/utils.py

@@ -485,14 +485,14 @@ def install_r_lib(lib, dryrun = False):
  versions = None
  if not dryrun:
  logger.info("Checking R library {} ...".format(lib))
- return R_library(lib, versions).target_exists()
+ return R_library(lib, version=versions, autoinstall=True).target_exists()
  else:
  return(lib, versions)
 
 def install_py_module(lib):
  from sos.targets_python import Py_Module
  logger.info("Checking Python module {} ...".format(lib))
- return Py_Module(lib).target_exists()
+ return Py_Module(lib, autoinstall=True).target_exists()
 
 def make_html_name(value):
  return "".join(x for x in value.replace(' ', '-') if x.isalnum() or x in ['-', '_']).lower()