Gwf

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

Added
-----

* Backend for Sun Grid Engine (SGE). The backend does not support all target
options supported by the Slurm backend, so workflows can not necessarily
run with the SGE backend without changes. See the documentation for a list
of supported options.

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

Fixed
-----

* Made the ``touch`` command faster.

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

Added
-----

* The ``gwf status`` command now accepts multiple ``-s/--status`` flags and will show
targets matching any of the given states. E.g. ``gwf status -s completed -s running``
will show all completed and running targets.
* A new command ``gwf touch`` has been introduced. The command touches all files in
the workflow in order, creating missing files and updating timestamps, such that
*gwf* thinks that the workflow has been run.
* When specifying the workflow attribute in the workflow path, e.g.
``gwf -f workflow.py:foo``, the filename part can now be left out and will default
to `workflow.py`. For example, ``gwf -f :foo`` will access the ``foo`` workflow
object in `workflow.py`.
* Documentation describing advanced patterns for *gwf* workflows.

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

This release contains a bunch of new features and plenty of bug fixes. Most
noteworthy is the removal of the progress bars in the status command. The status
bars were often confusing and didn't communicate much more than a simple
"percentage completion". The status command now outputs a table with target
name, target status, and percentage completion (see the tutorial for examples).
Additionally, the status command now shows all targets by default (not only
endpoints). For users who wish to only see endpoints, there's now a
``--endpoints`` flag.

We aim to make *gwf* a good cluster citizen. Thus, logs from targets that no
no longer exist in the workflow will now be removed when running ``gwf run``.
This ensures that *gwf* doesn't unnecessarily accumulate logs over time.

Fixed
-----

* Add missing import to documentation for function templates (4eddcac).
* Remove reference to ``--not-endpoints`` flag (d7ed251).
* Remove broken badges in README (e352f09).
* Remove pre-1.0 upgrade documentation (bfa03da6).
* Fixed bug in scheduler that caused an exception when a target's input file did
not exist, but the output file did (reported by Jonas Berglund) (92301ef3).

Changed
-------

* Dots have been removed from logging output to make copy-pasting target names
easier (f33f7195).
* Now uses pipenv to fix development environment.
* Improved coloring of logging output when running with ``-v debug`` (ab4ac7e3).
* Remove status bars in ``gwf status`` command (47cb7b50).

Added
-----

* Added undocumented API which allows core and plugins to register validation
functions for configuration keys. This fixes issues like 226 (c8c57d7c7).
* The ``gwf clean`` command now shows how much data will be removed (d81f143f1).
* Remove log files for targets that are no longer defined in the workflow
(beb912bd).
* Note in tutorial on how to terminate the local workers (a long with other
updates to the tutorial) (34421498).

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

Fixed
-----

* Bug when returning an ``AnonymousTarget`` from a template function without
specifying the *working_dir* in the constructor (212). Thanks to Steffen
Møller-Larsen for reporting this.

===========

Fixed
-----

* Bug when using ``--format table`` and no targets were found (203).
* Bug when cancelling a target running on the Slurm backend (199).
* Link to documentation in error message when unable to connect to local
workers.
* Fixed bug in the *FileLogManager* where the wrong exception was raised when no
log was found.

Changed
-------

* Moved checking of file timestamps to the scheduler. This means that creating a
``Graph`` object will never touch the file system, and thus won't raise an
exception if a target depends on a file that doesn't exist and that's not
provided a target. Instead, unresolved paths are added to
``Graph.unresolved``. They will then be checked by the scheduler (if
necessary). For end users, this means that many commands have become
substantially faster.

Added
-----

* Added ``AnonymousTarget`` which represents an unnamed target. ``Target`` now
inherits from this class and templates may now return an ``AnonymousTarget``
instead of a tuple.
* Added *backend.slurm.log_mode* option, see the documentation for the Slurm
backend for usage (202).