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project.py
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project.py
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# Copyright (c) 2019 The Regents of the University of Michigan
# All rights reserved.
# This software is licensed under the BSD 3-Clause License.
"""Workflow definition with the FlowProject.
The FlowProject is a signac Project that allows the user to define a workflow.
"""
import argparse
import contextlib
import functools
import inspect
import json
import logging
import multiprocessing
import os
import random
import re
import shlex
import subprocess
import sys
import textwrap
import threading
import time
import warnings
from collections import Counter, defaultdict
from copy import deepcopy
from enum import IntFlag
from hashlib import md5, sha1
from itertools import chain, count, groupby, islice
from multiprocessing import Event, Pool, TimeoutError, cpu_count
from multiprocessing.pool import ThreadPool
import cloudpickle
import jinja2
import jsonschema
import signac
from jinja2 import TemplateNotFound as Jinja2TemplateNotFound
from signac.filterparse import parse_filter_arg
from .aggregates import (
_AggregatesCursor,
_AggregateStore,
_AggregateStoresCursor,
_JobAggregateCursor,
aggregator,
get_aggregate_id,
)
from .directives import _document_directive
from .environment import ComputeEnvironment, get_environment, registered_environments
from .errors import (
ConfigKeyError,
FlowProjectDefinitionError,
NoSchedulerError,
SubmitError,
TemplateError,
UserConditionError,
UserOperationError,
)
from .hooks import _Hooks
from .labels import _is_label_func, classlabel, label, staticlabel
from .render_status import _render_status
from .scheduling.base import ClusterJob, JobStatus
from .util import config as flow_config
from .util import template_filters
from .util.misc import (
_add_cwd_to_environment_pythonpath,
_bidict,
_cached_partial,
_get_parallel_executor,
_positive_int,
_roundrobin,
_switch_to_directory,
_to_hashable,
_TrackGetItemDict,
tqdm,
)
from .util.translate import abbreviate, shorten
logger = logging.getLogger(__name__)
# The TEMPLATE_HELP can be shown with the --template-help option available to all
# command line subcommands that use the templating system.
TEMPLATE_HELP = """Execution and submission scripts are generated with the jinja2 template files.
Standard files are shipped with the package, but maybe replaced or extended with
custom templates provided within a project.
The default template directory can be configured with the 'template_dir' configuration
variable, for example in the project configuration file. The current template directory is:
{template_dir}
All template variables can be placed within a template using the standard jinja2
syntax, e.g., the project root directory can be written as: {{{{ project.path }}}}.
The available template variables are:
{template_vars}
Filter functions can be used to format template variables in a specific way.
For example: {{{{ project.id | capitalize }}}}.
The available filters are:
{filters}"""
_FMT_SCHEDULER_STATUS = {
JobStatus.unknown: "U",
JobStatus.registered: "R",
JobStatus.inactive: "I",
JobStatus.submitted: "S",
JobStatus.held: "H",
JobStatus.queued: "Q",
JobStatus.active: "A",
JobStatus.error: "E",
JobStatus.group_registered: "GR",
JobStatus.group_inactive: "GI",
JobStatus.group_submitted: "GS",
JobStatus.group_held: "GH",
JobStatus.group_queued: "GQ",
JobStatus.group_active: "GA",
JobStatus.group_error: "GE",
JobStatus.placeholder: " ",
}
class IgnoreConditions(IntFlag):
"""Flags that determine which conditions are used to determine job eligibility."""
# The __invert__ operator must be defined since IntFlag simply performs an
# integer bitwise not on the underlying enum value, which is problematic in
# two's-complement arithmetic. What we want is to only flip valid bits.
def __invert__(self):
# Compute the largest number of bits used to represent one of the flags
# so that we can XOR the appropriate number.
max_bits = len(bin(max(elem.value for elem in type(self)))) - 2
return self.__class__((2**max_bits - 1) ^ self._value_)
NONE = 0
"""Check all conditions."""
PRE = 1
"""Ignore preconditions."""
POST = 2
"""Ignore postconditions."""
ALL = PRE | POST
"""Ignore all conditions."""
def __str__(self):
return {
IgnoreConditions.PRE: "pre",
IgnoreConditions.POST: "post",
IgnoreConditions.ALL: "all",
IgnoreConditions.NONE: "none",
}[self]
class _IgnoreConditionsConversion(argparse.Action):
def __init__(self, option_strings, dest, nargs=None, **kwargs):
if nargs is not None:
raise ValueError("nargs not allowed")
super().__init__(option_strings, dest, **kwargs)
def __call__(self, parser, namespace, values, option_string=None):
setattr(namespace, self.dest, getattr(IgnoreConditions, values.upper()))
class _condition:
# This counter should be incremented each time a "never" condition
# is created, and the value should be used as the tag for that
# condition to ensure that no pair of "never" conditions
# are found to be equal by the graph detection algorithm.
current_arbitrary_tag = 0
def __init__(self, condition, tag=None):
"""Add tag to differentiate built-in conditions during graph detection."""
if tag is None:
try:
tag = condition.__code__.co_code
except AttributeError:
logger.warning(f"Condition {condition} could not autogenerate tag.")
condition._flow_tag = tag
self.condition = condition
@classmethod
def isfile(cls, filename):
"""Determine if the specified file exists for the job(s)."""
def _isfile(*jobs):
return all(job.isfile(filename) for job in jobs)
return cls(_isfile, "isfile_" + filename)
@classmethod
def true(cls, key):
"""Evaluate if a document key is True for the job(s).
Returns True if the specified key is present in the job document(s) and
evaluates to True.
"""
def _document(*jobs):
return all(job.document.get(key, False) for job in jobs)
return cls(_document, "true_" + key)
@classmethod
def false(cls, key):
"""Evaluate if a document key is False for the job(s).
Returns True if the specified key is present in the job document(s) and
evaluates to False.
"""
def _no_document(*jobs):
return all(not job.document.get(key, False) for job in jobs)
return cls(_no_document, "false_" + key)
@classmethod
def never(cls, func):
"""Return False."""
cls.current_arbitrary_tag += 1
return cls(lambda _: False, str(cls.current_arbitrary_tag))(func)
@classmethod
def not_(cls, condition):
"""Return ``not condition(*jobs)`` for the provided condition function."""
def _not(*jobs):
return not condition(*jobs)
return cls(_not, b"not_" + condition.__code__.co_code)
def _create_all_metacondition(condition_dict, *other_funcs):
"""Generate metacondition requiring all provided conditions to be true.
This function generates an aggregate metaconditions that requires *all*
provided conditions to be met. The resulting metacondition is constructed
with appropriate information for graph detection.
"""
condition_list = [c for f in other_funcs for c in condition_dict[f]]
def _flow_metacondition(*jobs):
return all(c(*jobs) for c in condition_list)
_flow_metacondition._composed_of = condition_list
return _flow_metacondition
def _make_bundles(operations, size=None):
"""Slice an iterable of operations into equally sized bundles.
This utility function splits an iterable of operations into equally sized
bundles. The final bundle may be smaller than the specified size.
Parameters
----------
operations : iterable
Iterable of operations.
size : int
Size of bundles. (Default value = None)
Yields
------
list
Bundles of operations with specified size.
"""
if size == 0:
size = None
operations = iter(operations)
while True:
bundle = list(islice(operations, size))
if bundle:
yield bundle
else:
break
class _JobOperation:
"""Class containing execution information for one group and one job.
The execution or submission of a :class:`~.FlowGroup` uses a passed-in command
which can either be a string or function with no arguments that returns a shell
executable command. The shell executable command won't be used if it is
determined that the group can be executed without forking.
.. note::
This class is used by the :class:`~.FlowGroup` class for the execution and
submission process and should not be instantiated by users themselves.
Parameters
----------
id : str
The id of this _JobOperation instance. The id should be unique.
name : str
The name of the _JobOperation.
jobs : tuple of :class:`~signac.job.Job`
The jobs associated with this operation.
cmd : callable or str
The command that executes this operation. Can be a callable that when
evaluated returns a string.
directives : dict
A `dict` object of additional parameters that provide instructions on
how to execute this operation, e.g., specifically required resources.
user_directives : set
Keys in ``directives`` that correspond to user-specified directives
that are not part of the environment's standard directives.
"""
def __init__(self, id, name, jobs, cmd, directives, user_directives):
self._id = id
self.name = name
self._jobs = jobs
if not (callable(cmd) or isinstance(cmd, str)):
raise ValueError("cmd must be a callable or string.")
self._cmd = cmd
# We use a special dictionary that tracks all keys that have been
# evaluated by the template engine and compare them to those explicitly
# set by the user. See also comment below.
self.directives = _TrackGetItemDict(directives)
# Keys which were explicitly set by the user, but are not evaluated by
# the template engine are cause for concern and might hint at a bug in
# the template script or ill-defined directives. We are therefore
# keeping track of all keys set by the user and check whether they have
# been evaluated by the template script engine later.
self.directives._keys_set_by_user = user_directives
def __str__(self):
aggregate_id = get_aggregate_id(self._jobs)
return f"{self.name}({aggregate_id})"
def __repr__(self):
return "{type}(name='{name}', jobs='{jobs}', cmd={cmd}, directives={directives})".format(
type=type(self).__name__,
name=self.name,
jobs="(" + ", ".join(map(repr, self._jobs)) + ")",
cmd=repr(self.cmd),
directives=self.directives,
)
def __hash__(self):
return hash(self.id)
def __eq__(self, other):
return self.id == other.id
@property
def id(self):
return self._id
@property
def cmd(self):
if callable(self._cmd):
# We allow cmd to be 'lazy' or an unevaluated function because
# in cases where a user uses the Python API without specifying
# a project entrypoint, running many operations is still valid.
# If we need to fork this will fail to generate a command and
# error, but not until then. If we don't fork then nothing errors,
# and the user gets the expected result.
return self._cmd()
return self._cmd
class _SubmissionJobOperation(_JobOperation):
r"""Class containing submission information for one group and one job.
This class extends :class:`_JobOperation` to include a set of groups
that will be executed via the "run" command. These groups are known at
submission time.
Parameters
----------
\*args
Passed to the constructor of :class:`_JobOperation`.
eligible_operations : list
A list of :class:`_JobOperation` that will be executed when this
submitted job is executed.
operations_with_unmet_preconditions : list
A list of :class:`_JobOperation` that will not be executed in the
first pass of :meth:`FlowProject.run` due to unmet preconditions. These
operations may be executed in subsequent iterations of the run loop.
operations_with_met_postconditions : list
A list of :class:`_JobOperation` that will not be executed in the
first pass of :meth:`FlowProject.run` because all postconditions are
met. These operations may be executed in subsequent iterations of the
run loop.
\*\*kwargs
Passed to the constructor of :class:`_JobOperation`.
"""
def __init__(
self,
*args,
eligible_operations=None,
operations_with_unmet_preconditions=None,
operations_with_met_postconditions=None,
**kwargs,
):
super().__init__(*args, **kwargs)
if eligible_operations is None:
eligible_operations = []
self.eligible_operations = eligible_operations
if operations_with_unmet_preconditions is None:
operations_with_unmet_preconditions = []
self.operations_with_unmet_preconditions = operations_with_unmet_preconditions
if operations_with_met_postconditions is None:
operations_with_met_postconditions = []
self.operations_with_met_postconditions = operations_with_met_postconditions
class _FlowCondition:
"""A _FlowCondition represents a condition as a function of a signac job.
The ``__call__()`` method of a _FlowCondition object may return either True
or False, representing whether the condition is met or not. This can be
used to build a graph of conditions and operations.
Parameters
----------
callback : callable
A callable with one positional argument (the job).
"""
def __init__(self, callback):
self._callback = callback
def __call__(self, jobs):
try:
return self._callback(*jobs)
except Exception as error:
assert len(jobs) == 1
raise UserConditionError(
"An exception was raised while evaluating the condition {name} "
"for job {jobs}.".format(
name=self._callback.__name__, jobs=", ".join(map(str, jobs))
)
) from error
def __hash__(self):
return hash(self._callback)
def __eq__(self, other):
return self._callback == other._callback
class BaseFlowOperation:
"""A :class:`~.BaseFlowOperation` represents a data space operation acting on any job.
Every :class:`~.BaseFlowOperation` is associated with a specific command.
Preconditions (pre) and postconditions (post) can be used to trigger an
operation only when certain conditions are met. Conditions are unary
callables, which expect an instance of job as their first and only
positional argument and return either True or False.
An operation is considered "eligible" for execution when all preconditions
are met and when at least one of the postconditions is not met.
Preconditions are always met when the list of preconditions is empty.
Postconditions are never met when the list of postconditions is empty.
.. note::
This class should not be instantiated directly.
Parameters
----------
pre : sequence of callables
List of preconditions.
post : sequence of callables
List of postconditions.
"""
def __init__(self, pre=None, post=None):
if pre is None:
pre = []
if post is None:
post = []
self._preconditions = [_FlowCondition(cond) for cond in pre]
self._postconditions = [_FlowCondition(cond) for cond in post]
def _eligible(self, aggregate, ignore_conditions=IgnoreConditions.NONE):
"""Determine eligibility of an aggregate.
An aggregate is eligible when all preconditions are true and at least
one postcondition is false, or corresponding conditions are ignored.
Parameters
----------
aggregate : tuple of :class:`~signac.job.Job`
The aggregate of signac jobs.
ignore_conditions : :class:`~.IgnoreConditions`
Specify if preconditions and/or postconditions are to be ignored
when determining eligibility. The default is
:class:`IgnoreConditions.NONE`.
Returns
-------
bool
Whether the aggregate is eligible.
"""
if not isinstance(ignore_conditions, IgnoreConditions):
raise ValueError(
"The ignore_conditions argument of FlowProject.run() "
"must be a member of class IgnoreConditions."
)
# len(self._preconditions) check for speed optimization
met_preconditions = (
(len(self._preconditions) == 0)
or (ignore_conditions & IgnoreConditions.PRE)
or all(cond(aggregate) for cond in self._preconditions)
)
if met_preconditions and len(self._postconditions) > 0:
unmet_postconditions = (ignore_conditions & IgnoreConditions.POST) or any(
not cond(aggregate) for cond in self._postconditions
)
else:
unmet_postconditions = True
return met_preconditions and unmet_postconditions
def _complete(self, jobs):
"""Check if all postconditions are met."""
if len(self._postconditions) > 0:
return all(cond(jobs) for cond in self._postconditions)
return False
class FlowCmdOperation(BaseFlowOperation):
"""An operation that executes a shell command.
When an operation has the ``FlowProject.operation(cmd=True)`` directive specified, it is
instantiated as a :class:`~.FlowCmdOperation`. The operation should be a
function of one or more positional arguments that are instances of
:class:`~signac.job.Job`. The command (cmd) may either be a
callable that expects one or more instances of
:class:`~signac.job.Job` as positional arguments and returns a
string containing valid shell commands, or the string of commands itself.
In either case, the resulting string may contain any attributes of the
job (or jobs) placed in curly braces, which will then be substituted by
Python string formatting.
.. note::
This class should not be instantiated directly.
Parameters
----------
cmd : str or callable
The command to execute the operation. Callable values will be
provided one or more positional arguments that are
instances of :class:`~signac.job.Job`. String values will be
formatted with ``cmd.format(jobs=jobs)`` where ``jobs`` is a tuple of
:class:`~signac.job.Job`, or ``cmd.format(jobs=jobs,
job=job)`` if only one job is provided.
pre : sequence of callables
List of preconditions.
post : sequence of callables
List of postconditions.
"""
def __init__(self, cmd, pre=None, post=None):
super().__init__(pre=pre, post=post)
self._cmd = cmd
def __str__(self):
return f"{type(self).__name__}(cmd='{self._cmd}')"
def __call__(self, *jobs):
"""Return the command formatted with the supplied job(s)."""
return self._cmd(*jobs) if callable(self._cmd) else self._cmd
class FlowOperation(BaseFlowOperation):
"""An operation that executes a Python function.
All operations without the ``FlowProject.operation(cmd=True)`` directive use this class. The
callable ``op_func`` should be a function of one or more instances of
:class:`~signac.job.Job`.
.. note::
This class should not be instantiated directly.
Parameters
----------
op_func : callable
A callable function of ``*jobs``.
pre : sequence of callables
List of preconditions.
post : sequence of callables
List of postconditions.
"""
def __init__(self, op_func, pre=None, post=None):
super().__init__(pre=pre, post=post)
self._op_func = op_func
def __str__(self):
"""Return string representing operation."""
return f"{type(self).__name__}(op_func='{self._op_func}')"
def __call__(self, *jobs):
r"""Call the operation on the provided jobs.
Parameters
----------
\*jobs : One or more instances of :class:`~signac.job.Job`.
The jobs passed to the operation.
Returns
-------
object
The result of the operation function.
"""
return self._op_func(*jobs)
class FlowGroupEntry:
"""A FlowGroupEntry registers operations for inclusion into a :class:`FlowGroup`.
Application developers should not directly instantiate this class, but
use :meth:`~.FlowProject.make_group` instead.
Operation functions can be marked for inclusion into a :class:`FlowGroup`
by decorating the functions with a corresponding :class:`FlowGroupEntry`.
If the operation requires group specific directives, calling the
:class:`FlowGroupEntry` with the keyword argument ``directives`` allows the
setting of directives for the exclusively for the group. Doing this overrides
the default directives specified by :meth:`FlowProject.operation`.
Parameters
----------
name : str
The name of the :class:`FlowGroup` to be created.
project : flow.FlowProject
The project the group is associated with.
submit_options : str
The :meth:`FlowProject.run` options to pass when submitting the group.
These will be included in all submissions. Submissions use run
commands to execute.
run_options : str
The options to pass to ``entrypoint exec`` when running the group. Specifying this will
cause the operation to be forked even if it otherwise would run in the current Python
interpreter.
group_aggregator : :class:`~.aggregator`
aggregator object associated with the :class:`FlowGroup` (Default value = None).
"""
def __init__(
self, name, project, submit_options="", run_options="", group_aggregator=None
):
self.name = name
self._project = project
self.submit_options = submit_options
self.run_options = run_options
self.group_aggregator = group_aggregator
def __call__(self, func=None, /, *, directives=None):
"""Add the function into the group's operations.
This call operator allows the class to be used as a decorator.
Parameters
----------
func : callable
The function to decorate.
directives : dict
Directives to use for resource requests and execution.
The directives specified in this decorator are only applied when
executing the operation through the :class:`FlowGroup`.
To apply directives to an individual operation executed outside of the
group, see :meth:`.FlowProject.operation`.
Returns
-------
func
The decorated function.
"""
if directives is not None:
warnings.warn(
"The current directives (e.g. nranks, np) are deprecated as of flow 0.27. "
"When updating flow please look at the documentation for the new style "
"(https://docs.signac.io/en/latest/cluster_submission.html#submission-directives).",
DeprecationWarning,
)
if func is None:
return functools.partial(self._internal_call, directives=directives)
return self._internal_call(func, directives=directives)
def _internal_call(self, func, /, *, directives):
if not any(
func == op_func for _, op_func in self._project._OPERATION_FUNCTIONS
):
raise FlowProjectDefinitionError(
f"Cannot add function '{func}' to group without making the function an "
f"operation. Add @MyProjectClass.operation below group decorator."
)
if self.name in func._flow_groups[self._project]:
raise FlowProjectDefinitionError(
f"Cannot reregister operation '{func}' with the group '{self.name}'."
)
func._flow_groups[self._project].add(self.name)
if directives is None:
return func
if hasattr(func, "_flow_group_operation_directives"):
func._flow_group_operation_directives[self.name] = directives
else:
func._flow_group_operation_directives = {self.name: directives}
return func
def _set_directives(self, func, directives):
if hasattr(func, "_flow_group_operation_directives"):
if self.name in func._flow_group_operation_directives:
raise FlowProjectDefinitionError(
"Cannot set directives because directives already exist "
f"for operation '{func}' in group '{self.name}'."
)
func._flow_group_operation_directives[self.name] = directives
else:
func._flow_group_operation_directives = {self.name: directives}
class FlowGroup:
"""A :class:`~.FlowGroup` represents a subset of a workflow for a project.
A :class:`FlowGroup` is associated with one or more instances of
:class:`~.BaseFlowOperation`.
Examples
--------
In the example below, the directives will be ``{'nranks': 4}`` for op1 and
``{'nranks': 2, 'executable': 'python3'}`` for op2.
.. code-block:: python
group = FlowProject.make_group(name='example_group')
@group(directives={"nranks": 4})
@FlowProject.operation({"nranks": 2, "executable": "python3"})
def op1(job):
pass
@group
@FlowProject.operation({"nranks": 2, "executable": "python3"})
def op2(job):
pass
Parameters
----------
name : str
The name of the group to be used when calling from the command line.
operations : dict
A dictionary of operations where the keys are operation names and
each value is a :class:`~.BaseFlowOperation`.
operation_directives : dict
A dictionary of additional parameters that provide instructions on how
to execute a particular operation, e.g., specifically required
resources. Operation names are keys and the dictionaries of directives
are values. If an operation does not have directives specified, then
the directives of the singleton group containing that operation are
used. To prevent this, set the directives to an empty dictionary for
that operation.
submit_options : str
The :meth:`FlowProject.run` options to pass when submitting the group. These will be
included in all submissions. Submissions use run commands to execute.
run_options : str
The options to pass to ``entrypoint exec`` when running the group. Specifying this will
cause the operation to be forked even if it otherwise would run in the current Python
interpreter.
"""
MAX_LEN_ID = 100
def __init__(
self,
name,
operations=None,
operation_directives=None,
submit_options="",
run_options="",
):
if operation_directives is not None:
warnings.warn(
"The current directives (e.g. nranks, np) are deprecated as of flow 0.27. "
"When updating flow please look at the documentation for the new style "
"(https://docs.signac.io/en/latest/cluster_submission.html#submission-directives).",
DeprecationWarning,
)
self.name = name
self.submit_options = submit_options
self.run_options = run_options
# Requires Python >=3.6: dict must be ordered to ensure consistent
# pretend submission output for templates.
self.operations = {} if operations is None else dict(operations)
if operation_directives is None:
self.operation_directives = {}
else:
self.operation_directives = operation_directives
def _set_entrypoint_item(self, entrypoint, directives, key, default, jobs):
"""Set a value (executable, path) for entrypoint in command.
Order of priority is the operation directives specified and
then the project specified value.
"""
entrypoint[key] = directives.get(key, entrypoint.get(key, default))
if callable(entrypoint[key]):
entrypoint[key] = entrypoint[key](*jobs)
def _determine_entrypoint(self, entrypoint, directives, jobs):
"""Get the entrypoint for creating a _JobOperation.
If path cannot be determined, then raise a RuntimeError since we do not
know where to point to.
"""
entrypoint = entrypoint.copy()
self._set_entrypoint_item(
entrypoint, directives, "executable", sys.executable, jobs
)
# If a path is not provided, default to the path to the file where the
# FlowProject (subclass) is defined.
# We are assuming that all the jobs belong to the same project
default_path = inspect.getfile(jobs[0]._project.__class__)
self._set_entrypoint_item(entrypoint, directives, "path", default_path, jobs)
return "{} {}".format(entrypoint["executable"], entrypoint["path"]).lstrip()
def _resolve_directives(self, name, defaults, env):
all_directives = env._get_default_directives()
if name in self.operation_directives:
all_directives.update(self.operation_directives[name])
else:
all_directives.update(defaults.get(name, {}))
return all_directives
def _submit_cmd(self, entrypoint, ignore_conditions, jobs):
entrypoint = self._determine_entrypoint(entrypoint, {}, jobs)
cmd = f"{entrypoint} run -o {self.name}"
cmd = cmd if jobs is None else cmd + f" -j {get_aggregate_id(jobs)}"
options = self.submit_options
if ignore_conditions != IgnoreConditions.NONE:
options += " --ignore-conditions=" + str(ignore_conditions)
return " ".join((cmd, options)).strip()
def _run_cmd(self, entrypoint, operation_name, operation, directives, jobs):
if isinstance(operation, FlowCmdOperation):
return operation(*jobs).lstrip()
entrypoint = self._determine_entrypoint(entrypoint, directives, jobs)
cmd = f"{entrypoint} exec {operation_name} {get_aggregate_id(jobs)} {self.run_options}"
return cmd.strip()
def __iter__(self):
yield from self.operations.values()
def __repr__(self):
return (
f"{type(self).__name__}(name={repr(self.name)}, operations='"
f"{' '.join(list(self.operations))}',"
f"operation_directives={self.operation_directives}, "
f"submit_options={repr(self.submit_options)}, run_options={repr(self.run_options)})"
)
def _eligible(self, aggregate, ignore_conditions=IgnoreConditions.NONE):
"""Determine if at least one operation is eligible.
A :class:`~.FlowGroup` is eligible for execution if at least one of
its associated operations is eligible.
Parameters
----------
aggregate : tuple of :class:`~signac.job.Job`
The aggregate of signac jobs.
ignore_conditions : :class:`~.IgnoreConditions`
Specify if preconditions and/or postconditions are to be ignored
while checking eligibility. The default is
:class:`IgnoreConditions.NONE`.
Returns
-------
bool
Whether the group is eligible.
"""
return any(op._eligible(aggregate, ignore_conditions) for op in self)
def _complete(self, jobs):
"""Check if postconditions are met for all operations in the group.
Parameters
----------
jobs : tuple
The signac job handles.
Returns
-------
bool
Whether the group is complete (all contained operations are
complete).
"""
return all(op._complete(jobs) for op in self)
def add_operation(self, name, operation, directives=None):
"""Add an operation to the :class:`~.FlowGroup`.
Parameters
----------
name : str
The name of the operation.
operation : :class:`~.BaseFlowOperation`
The workflow operation to add to the :class:`~.FlowGroup`.
directives : dict
The operation specific directives. (Default value = None)
"""
self.operations[name] = operation
if directives is not None:
self.operation_directives[name] = directives
def isdisjoint(self, group):
"""Return whether two groups are disjoint.
Groups are disjoint if they do not share any common operations.
Parameters
----------
group : :class:`~.FlowGroup`
The other :class:`~.FlowGroup` to compare to.
Returns
-------
bool
Returns ``True`` if ``group`` and ``self`` share no operations,
otherwise returns ``False``.
"""
return set(self).isdisjoint(set(group))
def _generate_id(self, aggregate, operation_name=None):
"""Generate a unique id which identifies this group and job(s).
The generated value is used to identify interactions with the
scheduler.
Parameters
----------
aggregate : tuple of :class:`signac.job.Job`
The aggregate of signac jobs.
operation_name : str
Operation name defining the unique id. (Default value = None)
Returns
-------
str
The unique id.
"""
project = aggregate[0]._project
# The full name is designed to be truly unique for each job-group.
if operation_name is None:
op_string = "".join(sorted(list(self.operations)))
else:
op_string = operation_name
aggregate_id = get_aggregate_id(aggregate)
full_name = f"{project.path}%{aggregate_id}%{op_string}"
# The job_op_id is a hash computed from the unique full name.
job_op_id = md5(full_name.encode("utf-8")).hexdigest()
# The actual job id is then constructed from a readable part and the
# job_op_id, ensuring that the job-op is still somewhat identifiable,
# but guaranteed to be unique. The readable name is based on the
# project id, aggregate id, and operation name. All names and the id
# itself are restricted in length to guarantee that the id does not get
# too long.
max_len = self.MAX_LEN_ID - len(job_op_id)
if max_len < len(job_op_id):
raise ValueError(f"Value for MAX_LEN_ID is too small ({self.MAX_LEN_ID}).")
separator = getattr(project._environment, "JOB_ID_SEPARATOR", "/")
readable_name = "{project}{sep}{aggregate_id}{sep}{op_string}{sep}".format(
sep=separator,
project=project.__class__.__name__[:12],
aggregate_id=aggregate_id,
op_string=op_string[:12],