Signac-flow

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

Added
+++++

- The ``--job-output`` command line flag for submission can be set for SLURM, PBS, and LSF schedulers (550).
- Added a ``custom_content`` block to templates for user customization (553, 520).
- Added official support for XSEDE Expanse cluster (537).
- Added ``FlowProjectDefinitionError`` for exceptions involving ``FlowProject`` definitions (549).
- Added official support for Drexel University's Picotte cluster (561).

Changed
+++++++

- Improved documentation of directives (554).
- Raise ``FlowProjectDefinitionError`` error for inaccurate ``FlowProject`` definitions (549).

Removed
+++++++

- Removed deprecated environment classes (556).
- Removed support for signac < 1.3.0 (558).
- Removed support for decommissioned XSEDE Comet cluster (537).
- Removed ``--memory`` option from University of Michigan Great Lakes cluster submission. Use directives instead (563).

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

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

Added
+++++

- Add support for aggregation (operations acting on multiple jobs) via ``flow.aggregator`` (464, 516, 542).
- Add official support for Andes cluster (500).
- Decorator for setting directives while registering operation function ``FlowProject.operation.with_directives`` (309, 502).
- Add new flow command ``flow template create`` for automatic creation of custom templates (520, 534).

Changed
+++++++

- Jinja templates are indented for easier reading (461, 495).
- ``flow.directives`` is deprecated in favor of ``flow.FlowProject.operation.with_directives`` (309, 502).
- All environments require a scheduler in order to submit, even in pretend mode (533).
- Submitting in pretend mode will show additional scheduler command information (533).
- Support fractional timeout value in Python and command line interface (541).

Fixed
+++++

- Errors raised during submission were not being shown to users (517, 518).
- Fixed dependency flag for SLURM submissions (530, 531).

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

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

Added
+++++

- Documentation for all directives (480).
- Defined validators for the ``fork`` directive (480).
- Submission summary now appears in ``FlowProject`` status output, showing the number of queued, running, unknown statuses. (472, 488).
- Status overview now shows the number of jobs with incomplete operations and totals for the label overviews (481, 501).

Changed
+++++++

- Renamed TorqueEnvironment and related classes to PBSEnvironment (388, 491).
- LSF and SLURM schedulers will appear to be present if the respective commands ``bjobs -V`` or ``sbatch --version`` exit with a non-zero error code (498).
- Only known JobStatus values will be written to the project document, to save space and writing time (503).

Fixed
+++++

- Strictly enforce that operation functions cannot be used as condition functions (and vice-versa) and prevent the registration of two operations with the same name (496).
- Changed default value of ``status_parallelization`` to none, to avoid bugs in user code caused by thread parallelism and overhead in process parallelism (486).
- Memory directives are converted to an integer number of gigabytes or megabytes in submission scripts (482, 484).
- Fixed behavior of ``--only-incomplete-operations`` (481, 501).

Removed
+++++++

- Removed ``FlowProject.add_operation`` (479, 487).
- Removed deprecated ``--walltime`` argument (478).
- Removed deprecated ``flow.run`` interface (478).
- Removed deprecated ``FlowProject.export_job_statuses`` (478).
- Removed deprecated ``script`` feature, use ``submit --pretend`` instead (478).
- Removed deprecated ``CPUEnvironment``, ``GPUEnvironment`` classes (478).

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