Remove FlowProject.add_operation (#487)

* Fix FlowProject.add_operation docstring error * Make FlowProject.add_operation a classmethod * Add test for FlowProject.add_operation classmethod * Update changelog for `FlowProject.add_operation`. * Remove ``FlowProject.add_operation`` * Add documentation for directives. (#480) * Add documentation for directives. * Fix directives docs, add _FORK directive. * Update changelog. * Bump pre-commit from 2.10.1 to 2.11.1 (#489) Bumps [pre-commit](https://github.com/pre-commit/pre-commit) from 2.10.1 to 2.11.1. - [Release notes](https://github.com/pre-commit/pre-commit/releases) - [Changelog](https://github.com/pre-commit/pre-commit/blob/master/CHANGELOG.md) - [Commits](pre-commit/pre-commit@v2.10.1...v2.11.1) Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Change default status_parallelization to "none". (#486) * Change default status_parallelization to process. * Update changelog. * Change default status_parallelization to "none". * Bump ruamel-yaml from 0.16.12 to 0.17.2 (#490) Bumps [ruamel-yaml](https://sourceforge.net/p/ruamel-yaml/code/ci/default/tree) from 0.16.12 to 0.17.2. Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Bradley Dice <[email protected]> * Deprecate and remove references to add_operation. * Fix import. * Default memory requests to integer values (#484) * converting to int * updating docstring * switching to int output for M and G * Update flow/util/template_filters.py Co-authored-by: Bradley Dice <[email protected]> * fixing formatting * Update template reference data.s * Minor edits. * Update changelog. * Add support for "GB" suffixes. * Update memory tests. Co-authored-by: Bradley Dice <[email protected]> * Changed TORQUE to PBS (#491) Renamed TORQUE scheduler related classes, objects, templates, etc to PBS in code and documentation. * changed torque to pbs * fixed isort error * changed torque to pbs * rename PBSScheduler * rename PBSScheduler * rename PBSScheduler * Add changelog entry. * Rename Torque -> PBS in more places. * Update contributors.yaml * Added back deprecated class for DefaultTorqueEnvironment. * Remove extra line in contributors.yaml. * Fix import. Co-authored-by: Bradley Dice <[email protected]> * Add submission summary feature. (#488) * Add submission summary feature. * Update changelog. * Sort status counts by status code. Co-authored-by: Bradley Dice <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Alyssa Travitz <[email protected]> Co-authored-by: Charlottez112 <[email protected]>
glotzerlab · Apr 12, 2021 · c51bbc2 · c51bbc2
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commit c51bbc2
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diff --git a/changelog.txt b/changelog.txt
@@ -32,6 +32,7 @@ Fixed
 Removed
 +++++++
 
+- Removed ``FlowProject.add_operation`` (#487).
 - Removed deprecated ``--walltime`` argument (#478).
 - Removed deprecated ``flow.run`` interface (#478).
 - Removed deprecated ``FlowProject.export_job_statuses`` (#478).

diff --git a/doc/api.rst b/doc/api.rst
@@ -27,7 +27,6 @@ The FlowProject
 .. autosummary::
 
     FlowProject.ALIASES
-    FlowProject.add_operation
     FlowProject.completed_operations
     FlowProject.get_job_status
     FlowProject.label

diff --git a/flow/project.py b/flow/project.py
@@ -31,6 +31,7 @@
 import cloudpickle
 import jinja2
 import signac
+from deprecation import deprecated
 from jinja2 import TemplateNotFound as Jinja2TemplateNotFound
 from signac.contrib.filterparse import parse_filter_arg
 from tqdm.auto import tqdm
@@ -62,6 +63,7 @@
     switch_to_directory,
 )
 from .util.translate import abbreviate, shorten
+from .version import __version__
 
 logger = logging.getLogger(__name__)
 
@@ -3927,75 +3929,18 @@ def labels(self, job):
             elif bool(label_value) is True:
                 yield label_name
 
-    def add_operation(self, name, cmd, pre=None, post=None, **kwargs):
-        r"""Add an operation to the workflow.
-
-        This method will add an instance of :class:`~.FlowOperation` to the
-        operations of this project.
-
-        .. seealso::
-
-            A Python function may be defined as an operation function directly
-            using the :meth:`~.operation` decorator.
-
-        Any FlowOperation is associated with a specific command, which should
-        be a function of :class:`~signac.contrib.job.Job`. The command (cmd)
-        can be stated as function, either by using str-substitution based on a
-        job's attributes, or by providing a unary callable, which expects an
-        instance of job as its first and only positional argument.
-
-        For example, if we wanted to define a command for a program called
-        'hello', which expects a job id as its first argument, we could
-        construct the following two equivalent operations:
-
-        .. code-block:: python
-
-            op = FlowOperation('hello', cmd='hello {job.id}')
-            op = FlowOperation('hello', cmd=lambda 'hello {}'.format(job.id))
-
-        Here are some more useful examples for str-substitutions:
-
-        .. code-block:: python
-
-            # Substitute job state point parameters:
-            op = FlowOperation('hello', cmd='cd {job.ws}; hello {job.sp.a}')
-
-        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.
-
-        Please note, eligibility in this contexts refers only to the workflow
-        pipeline and not to other contributing factors, such as whether the
-        job-operation is currently running or queued.
-
-        Parameters
-        ----------
-        name : str
-            A unique identifier for this operation, which may be freely chosen.
-        cmd : str or callable
-            The command to execute operation; should be a function of job.
-        pre : sequence of callables
-            List of preconditions. (Default value = None)
-        post : sequence of callables
-            List of postconditions. (Default value = None)
-        \*\*kwargs
-            Keyword arguments passed as directives.
-
-        """
-        if name in self.operations:
-            raise KeyError("An operation with this identifier is already added.")
-        op = self.operations[name] = FlowCmdOperation(cmd=cmd, pre=pre, post=post)
-        if name in self._groups:
-            raise KeyError("A group with this identifier already exists.")
-        self._groups[name] = FlowGroup(
-            name, operations={name: op}, operation_directives=dict(name=kwargs)
+    @deprecated(
+        deprecated_in="0.14",
+        removed_in="0.16",
+        current_version=__version__,
+        details="Method has been removed.",
+    )
+    def add_operation(*args, **kwargs):  # noqa: D102
+        raise AttributeError(
+            "The add_operation() method was removed in version 0.14. "
+            "Please see https://docs.signac.io/en/latest/flow-project.html#defining-a-workflow "
+            "for instructions on how to define operations using the current API. This message "
+            "will be removed in version 0.16."
         )
 
     def completed_operations(self, job):
@@ -4070,8 +4015,6 @@ def operation(cls, func, name=None):
             def hello(job):
                 print('Hello', job)
 
-        See also: :meth:`~.flow.FlowProject.add_operation`.
-
         Parameters
         ----------
         func : callable