Merge branch 'master' into github-actions

.pre-commit-config.yaml

@@ -5,29 +5,29 @@ exclude: '(?:^flow/util/mistune/)'
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: 'v4.3.0'
+    rev: 'v4.4.0'
     hooks:
       - id: end-of-file-fixer
         exclude: 'setup.cfg'
       - id: trailing-whitespace
         exclude: 'setup.cfg'
       - id: debug-statements
   - repo: https://github.com/asottile/pyupgrade
-    rev: 'v2.38.2'
+    rev: 'v3.3.1'
     hooks:
       - id: pyupgrade
         args:
           - --py38-plus
   - repo: https://github.com/PyCQA/isort
-    rev: '5.10.1'
+    rev: '5.11.4'
     hooks:
       - id: isort
   - repo: https://github.com/psf/black
-    rev: '22.8.0'
+    rev: '22.12.0'
     hooks:
       - id: black
   - repo: https://github.com/PyCQA/flake8
-    rev: '5.0.4'
+    rev: '6.0.0'
     hooks:
       - id: flake8
   - repo: https://github.com/PyCQA/pydocstyle

.zenodo.json

@@ -184,5 +184,5 @@
     },
     "title": "signac-flow",
     "upload_type": "software",
-    "version": "0.22.0"
+    "version": "0.23.0"
 }

CITATION.cff

@@ -2,7 +2,7 @@
 ---
 cff-version: "1.0.3"
 title: signac-flow
-version: 0.22.0
+version: 0.23.0
 abstract: |
     The signac-flow tool provides the basic components to set up simple to complex workflows for projects as part of the signac framework. That includes the definition of data pipelines, execution of data space operations and the submission of operations to high-performance super computers.
 authors:

changelog.txt

@@ -5,40 +5,62 @@ Changelog
 The **signac-flow** package follows `semantic versioning <https://semver.org/>`_.
 The numbers in brackets denote the related GitHub issue and/or pull request.
 
+Version 0.24
+============
+
+[0.24.0] -- 20xx-xx-xx
+----------------------
+
+Changed
++++++++
+
+- Placing ``@FlowProject.pre`` and ``@FlowProject.post`` before the ``FlowProject.operation`` decorator raises an error (#700).
+- Updated CI to use GitHub Actions (#698).
+
+Removed
++++++++
+
+- ``@flow.aggregates.aggregator()`` use ``FlowProject.operation(aggregator=...)`` instead (#700).
+- ``alias`` CLI argument to ``flow init`` (#700).
+- ``FlowGroupEntry.with_directives`` use directives keyword argument in ``FlowGroupEntry()``(#700).
+
 Version 0.23
 ============
 
-[0.23.0] -- 20xx-xx-xx
+[0.23.0] -- 2022-12-09
 ----------------------
 
 Added
 +++++
 
-- Add official support for Python version 3.11 (#697).
+- Official Python 3.11 support (#697).
+- The ``flow.FlowProject.operation`` decorator now has an ``aggregator`` keyword argument: ``@FlowProject.operation(aggregator=aggregator.groupsof(2))`` (#681).
+- The ``FlowGroupEntry`` class can be called with a ``directives`` keyword argument: ``FlowGroupEntry(directives={...})`` (#696).
 
 Changed
 +++++++
 
+- Deprecated using ``flow.aggregates.aggregator`` as a decorator.
 - Deprecated placing ``@FlowProject.pre`` and ``@FlowProject.post`` before the ``FlowProject.operation`` decorator (#690).
 - Require ``signac`` version 1.8.0 (#693).
 - Deprecated ``alias`` CLI argument to ``flow init`` (#693).
 - Algorithm for computing cluster job ids (#695).
-- Updated CI to use GitHub Actions (#698).
+- Deprecated ``FlowGroupEntry.with_directives`` in favor of a directives keyword argument in ``FlowGroupEntry()``(#696).
 
 Fixed
 +++++
 
 - Detecting correct environment on Delta GPU nodes (#682).
-- Identical aggregates are used only once in submission and running (#694).
+- Identical aggregates are used only once in submission and running (#694, #688).
 
 Removed
 +++++++
 
 - ``show_traceback`` from CLI and config (#690).
 - Formatting the output of a ``FlowCmdOperation`` (#686).
-- ``@flow.cmd`` and ``flow.with_job`` (#686).
+- ``@flow.cmd`` and ``flow.with_job`` (#686, #669).
 - ``@FlowProject.operation.with_directives`` (#686).
-- The ``flow.testing`` module (#691).
+- The ``flow.testing`` module (#691, #692).
 
 Version 0.22
 ============

doc/conf.py

@@ -78,9 +78,9 @@ def __getattr__(cls, name):
 # built documents.
 #
 # The short X.Y version.
-version = "0.22.0"
+version = "0.23.0"
 # The full version, including alpha/beta/rc tags.
-release = "0.22.0"
+release = "0.23.0"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

flow/__main__.py

@@ -19,7 +19,6 @@
 from signac import get_project, init_project
 
 from . import __version__, environment, template
-from .util.misc import _deprecated_warning
 
 logger = logging.getLogger(__name__)
 
@@ -32,13 +31,6 @@ def main_init(args):
     try:
         get_project()
     except LookupError:
-        if args.alias != "":
-            _deprecated_warning(
-                deprecation="alias",
-                alternative="",
-                deprecated_in="0.23.0",
-                removed_in="0.24.0",
-            )
         init_project()
         print("Initialized signac project in current directory.", file=sys.stderr)
     try:
@@ -115,13 +107,6 @@ def main():
         "init", help="Initialize a signac-flow project."
     )
     parser_init.set_defaults(func=main_init)
-    parser_init.add_argument(
-        "alias",
-        type=str,
-        nargs="?",
-        default="",
-        help="Unused, will be removed in flow 0.24.0.",
-    )
     parser_init.add_argument(
         "-t",
         "--template",

flow/aggregates.py

@@ -12,9 +12,6 @@
 from collections.abc import Collection, Iterable, Mapping
 from hashlib import md5
 
-from .errors import FlowProjectDefinitionError
-from .util.misc import _deprecated_warning
-
 
 def _get_unique_function_id(func):
     """Generate unique id for the provided function.
@@ -335,40 +332,6 @@ def _create_AggregateStore(self, project):
         else:
             return _AggregateStore(self, project)
 
-    def __call__(self, func=None):
-        """Add this aggregator to a provided operation.
-
-        This call operator allows the class to be used as a decorator.
-
-        Parameters
-        ----------
-        func : callable
-            The function to decorate.
-
-        """
-        _deprecated_warning(
-            deprecation="@aggregator(...)",
-            alternative="Use FlowProject.operation(aggregator=aggregator(...)) instead.",
-            deprecated_in="0.23.0",
-            removed_in="0.24.0",
-        )
-        if not callable(func):
-            raise FlowProjectDefinitionError(
-                "Invalid argument passed while calling the aggregate "
-                f"instance. Expected a callable, got {type(func)}."
-            )
-        if getattr(func, "_flow_with_job", False):
-            raise FlowProjectDefinitionError(
-                "The with_job option cannot be used with aggregation."
-            )
-        current_agg = getattr(func, "_flow_aggregate", None)
-        if current_agg is not None and current_agg != aggregator.groupsof(1):
-            raise FlowProjectDefinitionError(
-                "Cannot specify aggregates in function and decorator."
-            )
-        setattr(func, "_flow_aggregate", self)
-        return func
-
 
 class _BaseAggregateStore(Mapping):
     """Base abstract class for aggregate stores.

flow/project.py

@@ -65,7 +65,6 @@
     _add_cwd_to_environment_pythonpath,
     _bidict,
     _cached_partial,
-    _deprecated_warning,
     _get_parallel_executor,
     _positive_int,
     _roundrobin,
@@ -634,12 +633,10 @@ class FlowGroupEntry:
 
     Operation functions can be marked for inclusion into a :class:`FlowGroup`
     by decorating the functions with a corresponding :class:`FlowGroupEntry`.
-    If the operation requires specific directives, :meth:`~.with_directives`
-    accepts keyword arguments that are mapped to directives and returns a
-    decorator that can be applied to the operation to mark it for inclusion in
-    the group and indicate that it should be executed using the specified
-    directives. This overrides the default directives specified by
-    :meth:`flow.directives`.
+    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
     ----------
@@ -673,7 +670,7 @@ def __init__(
         # `@operation`.
         self.group_aggregator = group_aggregator
 
-    def __call__(self, func):
+    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.
@@ -683,12 +680,23 @@ def __call__(self, func):
         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
         -------
-        callable
+        func
             The decorated function.
-
         """
+        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
         ):
@@ -702,6 +710,13 @@ def __call__(self, func):
                 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):
@@ -715,38 +730,6 @@ def _set_directives(self, func, directives):
         else:
             func._flow_group_operation_directives = {self.name: directives}
 
-    def with_directives(self, directives):
-        """Decorate an operation to provide additional execution directives for this group.
-
-        Directives can be used to provide information about required resources
-        such as the number of processors required for execution of parallelized
-        operations. For a list of supported directives, see
-        :meth:`.FlowProject.operation.with_directives`. For more information,
-        see :ref:`signac-docs:cluster_submission_directives`.
-
-        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`.
-
-        Parameters
-        ----------
-        directives : dict
-            Directives to use for resource requests and execution.
-
-        Returns
-        -------
-        function
-            A decorator which registers the operation with the group using the
-            specified directives.
-        """
-
-        def decorator(func):
-            self._set_directives(func, directives)
-            return self(func)
-
-        return decorator
-
 
 class FlowGroup:
     """A :class:`~.FlowGroup` represents a subset of a workflow for a project.
@@ -763,7 +746,7 @@ class FlowGroup:
 
         group = FlowProject.make_group(name='example_group')
 
-        @group.with_directives({"nranks": 4})
+        @group(directives={"nranks": 4})
         @FlowProject.operation({"nranks": 2, "executable": "python3"})
         def op1(job):
             pass
@@ -1291,13 +1274,8 @@ def __call__(self, func):
                     func for name, func in self._parent_class._collect_operations()
                 ]
                 if func not in operation_functions:
-                    _deprecated_warning(
-                        deprecation="Placing conditions below the @FlowProject.operation "
-                        "decorator.",
-                        alternative="Place decorator above @FlowProject.operation to remove the "
-                        "warning.",
-                        deprecated_in="0.23.0",
-                        removed_in="0.24.0",
+                    raise FlowProjectDefinitionError(
+                        "Conditions must come after (above) @FlowProject.operation."
                     )
                 if self.condition in operation_functions:
                     raise FlowProjectDefinitionError(
@@ -1391,13 +1369,8 @@ def __call__(self, func):
                     func for name, func in self._parent_class._collect_operations()
                 ]
                 if func not in operation_functions:
-                    _deprecated_warning(
-                        deprecation="Placing conditions below the @FlowProject.operation "
-                        "decorator.",
-                        alternative="Place decorator above @FlowProject.operation to remove the "
-                        "warning.",
-                        deprecated_in="0.23.0",
-                        removed_in="0.24.0",
+                    raise FlowProjectDefinitionError(
+                        "Conditions must come after (above) @FlowProject.operation."
                     )
                 if self.condition in operation_functions:
                     raise FlowProjectDefinitionError(

flow/version.py

@@ -3,6 +3,6 @@
 # This software is licensed under the BSD 3-Clause License.
 """Define the signac-flow version."""
 
-__version__ = "0.22.0"
+__version__ = "0.23.0"
 
 __all__ = ["__version__"]

requirements/requirements-dev.txt

@@ -1,3 +1,3 @@
 click>=7.0
 ruamel.yaml>=0.16.12
-pre-commit==2.20.0
+pre-commit==2.21.0

requirements/requirements-test.txt

@@ -1,5 +1,5 @@
 click==8.1.3
-coverage==6.5.0
+coverage==7.0.1
 pytest-cov==4.0.0
 pytest==7.2.0
 ruamel.yaml==0.17.21

setup.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.22.0
+current_version = 0.23.0
 commit = True
 tag = False
 message = Bump up to version {new_version}.