Signac-flow

----------------------

Added
+++++

- Add official support for Bridges-2 cluster (441).
- Add support for memory requests via ``directives`` (258, 466).
- Add support for walltime requests via ``directives``, deprecated ``--walltime`` argument to ``submit`` (240, 476).

Fixed
+++++

- Support for multi-line ``flow.cmd`` operations (451, 453).
- ``FlowProject`` status shows labels and correct number of jobs for projects with zero operations (454, 460).

Removed
+++++++

- Removed public API of deprecated class ``JobOperation`` (445).
- Removed public API of deprecated methods ``eligible`` and ``complete`` of ``BaseFlowOperation`` and ``FlowGroup`` (445).
- Removed configuration option ``use_buffered_mode`` (445).
- Removed public API of ``script``, ``next_operations`` and ``submit_operations`` of ``FlowProject`` (445).
- Removed support for decommissioned Bridges cluster (441).
- Removed support for ``memory`` command line argument in ``submit`` (466).

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

----------------------

Added
+++++

- Code is formatted with ``black`` and ``isort`` pre-commit hooks (365).
- Add official support for Python version 3.9 (365).
- Documentation has been added for all public classes and methods (387, 389).
- Added internal support for aggregates of jobs (334, 348, 351, 364, 383, 390, 415, 422, 430).
- Added code coverage to continuous integration (405).

Changed
+++++++

- Command line interface always uses ``--job-id`` instead of ``--jobid`` (363, 386).
- ``CPUEnvironment`` and ``GPUEnvironment`` classes are deprecated (381).
- Docstrings are now written in `numpydoc style <https://numpydoc.readthedocs.io/en/latest/format.html>`__ (#392).
- Default environment for the University of Minnesota Mangi cluster changed from Torque to SLURM (393).
- Run commands are evaluted lazily (70, 396).
- Deprecated method ``export_job_statuses`` (402).
- Improved internal caching of scheduler status (410).
- Refactored status fetching code (368, 417).
- Optimization: Directives are no longer deep-copied (420, 421).
- The ``use_buffered_mode`` config option is deprecated. Buffering is always internally enabled (425).
- Evaluate directives when called instead of when defined (398, 402).
- Various internal refactorings and optimizations (371, 373, 374, 375, 376, 377, 378, 379, 380, 400, 410, 416, 423, 426).
- ``Scheduler`` is now an abstract base class (426).
- ``flow.scheduling.fakescheduler`` has been renamed to ``flow.scheduling.fake_scheduler`` (426).
- Arguments to ``submit`` have been changed for all scheduler classes (426).
- Python 3.6 is only tested with oldest dependencies (436).
- Drop support for `tqdm <https://github.com/tqdm/tqdm>`__ versions older than `4.48.1` (#436, 440).
- Drop support for `Jinja2 <https://palletsprojects.com/p/jinja/>`__ versions older than `2.10.0` (#436).
- Deprecated ``operations.py`` method ``flow.run`` (221, 463, 467).

Fixed
+++++

- Ensure that directives are always evaluated before running or submitting (408, 409).
- Cache the fully qualified domain name during environment detection to fix a performance issue on macOS (339, 394).
- Ensure that ``next`` CLI command displays eligible jobs for the exact operation name provided (443).
- Display warning when a non-existing operation/group is passed to ``run``, ``submit``, or ``next`` commands (291, 442).

Removed
+++++++

- Removed the deprecated method ``flow.util.misc.write_human_readable_statepoints`` (397).
- Removed the deprecated argument ``--no-parallelize`` (424).
- Removed the deprecated ``env`` argument from submission methods (424).
- ``flow.render_status.Renderer`` class has been removed. ``FlowProject.print_status`` no longer returns the renderer (426).
- Removed deprecated ``status.py`` module (426).
- Removed the ``--test`` argument from ``FlowProject.submit`` (439).

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

----------------------

Added
+++++

- Added classes ``_Directives`` and ``_Directive`` that serve as a smart mapping for directives specified by the environment or user (265, 283).
- Added support for `pre-commit hooks <https://pre-commit.com/>`__ (#333).
- Add environment profile for University of Minnesota, Minnesota Supercomputing Institute, Mangi supercomputer (353).

Changed
+++++++

- Make ``FlowCondition`` class private (307, 315).
- Deprecate ``JobOperation`` class, make ``SubmissionJobOperation`` a private class and deprecate the following methods of ``FlowProject``: ``script``, ``run_operations``, ``submit_operations``, ``next_operations``. (313)
- Deprecate the following methods: ``FlowGroup.eligible``, ``FlowGroup.complete``, ``BaseFlowOperation.eligible``, ``BaseFlowOperation.complete`` (337).

Fixed
+++++

- Serial execution on Summit correctly counts total node requirements (342).
- Fixed performance regression in job submission in large workspaces (354).

Removed
+++++++

- Drop support for Python 3.5 (305). The signac project will follow the `NEP 29 deprecation policy <https://numpy.org/neps/nep-0029-deprecation_policy.html>`_ going forward.
- Remove the deprecated methods ``always``, ``make_bundles``, and ``JobOperation.get_id`` (312).

----------------------

Fixed
+++++

- Fix issue with the submission of bundled operations on cluster environments that do not allow slashes ('/') in cluster scheduler job names (343).