Signac-flow

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

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Added
+++++

- Add ``FlowGroup`` (one or more operations can be grouped within an execution environment) (114).
- Add official support for University of Michigan Great Lakes cluster (185).
- Add official support for Bridges AI cluster (222).
- Add ``IgnoreConditions`` option for ``submit()``, ``run()`` and ``script()`` (38, 209).
- Add pytest support for testing framework (227, 232).
- Add markdown and html format support for ``print_status()`` (113, 163).
- Add memory flag option for default Slurm scheduler (256).
- Add optional environment variable to specify submission script separator (262).
- Add ``status_parallelization`` configuration to specify the parallelization used for fetching status (264, 271).

Changed
+++++++

- Raises ``ValueError`` when an operation function is passed to ``FlowProject.pre()`` and ``FlowProject.post()``, or a non-operation function passed to ``FlowProject.pre.after()`` (248, 249).
- The option to provide the ``env`` argument to ``submit`` and ``submit_operations`` has been deprecated (245).
- The command line option ``--cmd`` for ``script`` has been deprecated and will trigger a ``DeprecationWarning`` upon use until removed (243, 218).
- Raises ``ValueError`` when ``--job-name`` is passed by the user because that interferes with status checking (164, 241).
- Submitting with ``--memory`` no longer assumes a unit of gigabytes on Bridges and Comet clusters (257).
- Buffering is enabled by default, improving the performance of status checks (273).
- Deprecate the use of ``no_parallelize`` argument while printing status (264, 271).
- Submission via the command-line interface now calls the ``FlowProject.submit`` function instead of bypassing it for ``FlowProject.submit_operations`` (238, 286).
- Updated Great Lakes GPU request syntax (299).

Fixed
+++++

- Ensure that label names are used when displaying status (263).
- Fix node counting for large resource sets on Summit (294).

Removed
+++++++

- Removed ``ENVIRONMENT`` global variable in the ``flow.environment`` module (245).
- Removed vendored ``tqdm`` module and replaced it with a requirement (247).

===========

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

Added
+++++

- Add official support for Python version 3.8 (190, 210).
- Add descriptive error message when tag is not set and cannot be autogenerated for conditions (195).
- Add "fork" directive to enforce the execution of operations within a subprocess (159).
- Operation graph detection based on function comparison (178).
- Exceptions raised during operations always show tracebacks of user code (169, 171).

Changed
+++++++

- Raise a warning when a condition's tag is not set and raise an error if this occurs during graph detection (195).
- Raise errors if a forked process or ``cmd`` operation returns a non-zero exit code. (170, 172).

Removed
+++++++

- Drop support for Python version 2.7 (157, 158, 201).
- The "always" condition has been deprecated and will trigger a ``DeprecationWarning`` upon use until removed (179).
- Removed deprecated ``UnknownEnvironment`` in favor of ``StandardEnvironment`` (204).
- Removed support for decommissioned INCITE Titan and Eos computers (204).
- Removed support for the legacy Python-based submission script generation (200).
- Removed legacy compatibility layers for Python 2, signac < 1.0, and soft dependencies (205).
- Removed deprecated support for implied operation names with the ``run`` command (205).

===========

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

Added
+++++

- Add feature for integrated profiling of status updates (``status --profile``) to aid with the optimization of a FlowProject implementation (107, 110).
- The status view is generated with Jinja2 templates and thus more easily customizable (67, 111).
- Automatically show an overview of the number of eligible jobs for each operation in status view (134).
- Allow the provision of multiple operation-functions to the ``pre.after`` and ``*.copy_from`` conditions (120).
- Add option to specify the operation execution order (121).
- Add a testing module to easily initialize a test project (130).
- Enable option to always show the full traceback with ``show_traceback = on`` within the ``[flow]`` section of the signac configuration (61, 144).
- Add full launcher support for job submission on XSEDE Stampede2 for large parallel single processor jobs (85, 91).

Fixed
+++++

- Both the ``nranks`` and ``omp_num_threads`` directives properly support callables (118).
- Show submission error messages in combination with a TORQUE scheduler (103, 104).
- Fix issue that caused the "Fetching operation status" progress bar to be inaccurate (108).
- Fix erroneous line in the torque submission template (126).
- Ensure default parameter range detection in status printing succeeds for nested state points (154).
- Fix issue with the resource set calculation on INCITE Summit (101).

Changed
+++++++

- Packaged environments are now available by default. Set ``import_packaged_environments = off`` within the ``[flow]`` section of the signac configuration to revert to previous behavior.
- The following methods of the ``FlowProject`` class have been deprecated and will trigger a ``DeprecationWarning`` upon use until their removal:

+ ``classify`` (use ``labels()`` instead)
+ ``next_operation`` (use ``next_operations()`` instead)
+ ``export_job_stati`` (replaced by ``export_job_statuses``)
+ ``eligible_for_submission`` (removed without replacement)
+ ``update_aliases`` (removed without replacement)

- The support for Python version 2.7 is deprecated.

Removed
+++++++

- The support for Python version 3.4 has been dropped.
- Support for signac version 0.9 has been dropped.