Signac-flow

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Added
+++++

- Added the OLCF Crusher environment (708).
- Added `TrackOperations` as a built in hook (739).

Changed
+++++++

- Switched to a pyproject.toml based build (704).
- Placing ``FlowProject.pre`` and ``FlowProject.post`` before the ``FlowProject.operation`` decorator raises an error (700).
- Updated CI to use GitHub Actions (698).

Fixed
+++++

- Bumped ``isort`` to 5.12.0 in the pre-commit configuration file (715).
- Fixed bundle status information not being correctly read for subclasses of ``FlowProject`` (718, 720).

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).

============

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Added
+++++

- 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).
- 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, 688).

Removed
+++++++

- ``show_traceback`` from CLI and config (690).
- Formatting the output of a ``FlowCmdOperation`` (686).
- ``flow.cmd`` and ``flow.with_job`` (686, 669).
- ``FlowProject.operation.with_directives`` (686).
- The ``flow.testing`` module (691, 692).

============

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Added
+++++

- Support for formatting with operation function arguments for ``FlowCmdOperation`` (666, 630).
- The CLI ``status`` command can show document parameters by using flag ``-p doc.PARAM`` (667).
- ``FlowProject.operation`` now has ``cmd``, ``with_job``, and ``directives`` keyword only arguments (679, 655, 669).

Changed
+++++++

- Deprecated formatting the output of a ``FlowCmdOperation`` (666, 630).
- ``flow.cmd`` and ``flow.with_job`` are deprecated (679, 669, 665).
- ``FlowProject.operation.with_directives`` is deprecated (679, 665).
- Deprecated the ``--show-traceback`` for ``flow``'s CLI ``run`` and ``submit`` commands (674, 169).
- ``flow`` CLI ``run`` and ``submit`` show tracebacks by default (674, 169).
- Broke ``TestBidict`` and ``TestTemplateFilters`` into smaller and simpler functions (626).