diff env/lib/python3.9/site-packages/cwltool/mpi.py @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/env/lib/python3.9/site-packages/cwltool/mpi.py	Mon Mar 22 18:12:50 2021 +0000
@@ -0,0 +1,77 @@
+"""Experimental support for MPI."""
+import inspect
+import os
+import re
+from typing import List, Mapping, MutableMapping, Optional, Type, TypeVar, Union
+
+from ruamel import yaml
+
+MpiConfigT = TypeVar("MpiConfigT", bound="MpiConfig")
+
+MPIRequirementName = "http://commonwl.org/cwltool#MPIRequirement"
+
+
+class MpiConfig:
+    def __init__(
+        self,
+        runner: str = "mpirun",
+        nproc_flag: str = "-n",
+        default_nproc: Union[int, str] = 1,
+        extra_flags: Optional[List[str]] = None,
+        env_pass: Optional[List[str]] = None,
+        env_pass_regex: Optional[List[str]] = None,
+        env_set: Optional[Mapping[str, str]] = None,
+    ) -> None:
+        """
+        Initialize from the argument mapping.
+
+        Defaults are:
+        runner: "mpirun"
+        nproc_flag: "-n"
+        default_nproc: 1
+        extra_flags: []
+        env_pass: []
+        env_pass_regex: []
+        env_set: {}
+
+        Any unknown keys will result in an exception.
+        """
+        self.runner = runner
+        self.nproc_flag = nproc_flag
+        self.default_nproc = int(default_nproc)
+        self.extra_flags = extra_flags or []
+        self.env_pass = env_pass or []
+        self.env_pass_regex = env_pass_regex or []
+        self.env_set = env_set or {}
+
+    @classmethod
+    def load(cls: Type[MpiConfigT], config_file_name: str) -> MpiConfigT:
+        """Create the MpiConfig object from the contents of a YAML file.
+
+        The file must contain exactly one object, whose attributes must
+        be in the list allowed in the class initialiser (all are
+        optional).
+        """
+        with open(config_file_name) as cf:
+            data = yaml.main.round_trip_load(cf)
+        try:
+            return cls(**data)
+        except TypeError as e:
+            unknown = set(data.keys()) - set(inspect.signature(cls).parameters)
+            raise ValueError(f"Unknown key(s) in MPI configuration: {unknown}")
+
+    def pass_through_env_vars(self, env: MutableMapping[str, str]) -> None:
+        """Take the configured list of environment variables and pass them to the executed process."""
+        for var in self.env_pass:
+            if var in os.environ:
+                env[var] = os.environ[var]
+
+        for var_re in self.env_pass_regex:
+            r = re.compile(var_re)
+            for k in os.environ:
+                if r.match(k):
+                    env[k] = os.environ[k]
+
+    def set_env_vars(self, env: MutableMapping[str, str]) -> None:
+        """Set some variables to the value configured."""
+        env.update(self.env_set)