def __init__(self, sim=None, params=None):
self.sim = sim
try:
self.name_solver = sim.info.solver.short_name
except AttributeError:
pass
else:
self.package = get_solver_package(self.name_solver)
self.root = self.get_root()
# Check configfile early
self.get_configfile()
if sim:
self.oper = sim.oper
self.params = sim.params.output
# Same as package name __name__
super().__init__(sim)
dict_classes = sim.info.solver.classes.Output.import_classes()
# initialize objects
for cls_name, Class in dict_classes.items():
# only initialize if Class is not the Output class
if not isinstance(self, Class):
setattr(self, underscore(cls_name), Class(self))
elif params:
# At least initialize params
self.params = params.output
else:
self.params = None
logger.warning(
"Initializing Output class without sim or params might lead to errors."
)
def get_configfile(cls, host=None):
"""Get path of the Snakemake configuration file for the current machine.
All configuration files are stored under ``etc`` sub-package.
"""
if not host:
host = os.getenv("SNIC_RESOURCE",
os.getenv("GITHUB_WORKFLOW", gethostname()))
root = cls.get_root()
configfile = root / "etc" / f"{host}.yml"
if not configfile.exists():
logger.warning(
"Expected a configuration file describing compilers and flags: "
f"{configfile}")
configfile = Path(get_asset("default_configfile.yml"))
logger.info(f"Using default configuration instead: {configfile}")
return configfile
def copy(self, new_dir, force=False):
"""Copy case files to a new directory. The directory does not have to be present.
:param new_dir: A str or Path-like instance pointing to the new directory.
:param force: Force copy would overwrite if files already exist.
"""
# Avoid race conditions! Should be only executed by rank 0.
if mpi.rank != 0:
return
abs_paths = self.get_paths()
subpackages = self._get_subpackages()
root = self.root
def conditional_ignore(src, names):
"""Ignore if not found in ``abs_paths``."""
src = Path(src)
include = abs_paths + [root / subpkg for subpkg in subpackages]
exclude = tuple(name for name in names if not any(
(src / name) == path for path in include))
logger.debug("".join((
f"- src: {src}",
"\n- include:\n",
"\n ".join(str(name) for name in include),
"\n- exclude:\n",
"\n ".join(exclude),
"\n----",
)))
return exclude
new_root = Path(new_dir)
try:
logger.info("Copying with shutil.copytree ...")
copytree_kwargs = dict(src=root,
dst=new_root,
symlinks=False,
ignore=conditional_ignore)
# Python 3.8+
shutil.copytree(**copytree_kwargs, dirs_exist_ok=True)
except (TypeError, shutil.Error):
try:
logger.warning(
"Python < 3.8: shutil.copytree may not proceed if directories exist."
)
# Hoping that new_root has not been created
shutil.copytree(**copytree_kwargs)
except FileExistsError as e:
logger.warning(e)
logger.info("Copying with shutil.copy2 ...")
# Copy one by one from the scratch
if not new_root.exists():
logger.debug(f"Creating {new_root} ...")
os.makedirs(new_root, exist_ok=True)
for abs_path in abs_paths:
rel_path = abs_path.relative_to(root)
new_path = new_root / rel_path
if not new_path.parent.exists():
os.makedirs(new_path.parent)
logger.debug(f"Copying {new_path}")
if new_path.exists():
if force:
logger.warning(
f"{new_path} would be overwritten ...")
else:
logger.warning(
f"{new_path} exists, skipping. Use force=True to overwrite."
)
continue
shutil.copy2(abs_path, new_path)
finally:
logger.info(f"Copied: {root} -> {new_root}")