Pytest-workflow

---------------------------
+ Added ``--kwd`` as alias for ``--keep-workflow-wd``. Notify the user of
deletion of temporary directories and logs.
+ Released pytest-workflow as a `conda package on bioconda
<https://bioconda.github.io/recipes/pytest-workflow/README.html>`_.

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+ Enabled custom tests on workflow files.

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Lots of small fixes that improve the usability of pytest-workflow are included
in version 1.0.0.

+ Gzipped files can now also be checked for contents. Files with '.gz' as
extension are automatically decompressed.
+ ``stdout`` and ``stderr`` of workflows are now streamed to a file instead of
being kept in memory. This means you can check the progress of a workflow by
running ``tail -f <stdout or stderr>``. The location of ``stdout`` and
``stderr`` is now reported at the start of each worflow. If the
``--keep-workflow-wd`` is not set the ``stdout`` and ``stderr`` files will be
deleted with the rest of the workflow files.
+ The log reports now when a workflow is starting, instead of when it is added
to the queue. This makes it easier to see which workflows are currently
running and if you forgot to use the ``--workflow-threads`` or ``--wt`` flag.
+ Workflow exit code failures now mention the name of the workflow. Previously
the generic name "Workflow" was used, which made it harder to figure out
which workflows failed.
+ When tests of file content fail because the file does not exist, a different
error message is given compared to when the file exist, but the content is
not there, which makes debugging easier. Also the accompanying
"FileNotFound" error stacktrace is now suppressed, which keeps the test
output more pleasant.
+ When tests of stdout/stderr content or file content fail a more informative
error message is given to allow for easier debugging.
+ All workflows now get their own folder within the `same` temporary directory.
This fixes a bug where if ``basetemp`` was not set, each workflow would get
its own folder in a separate temp directory. For example running workflows
'workflow1' and 'workflow2' would create two temporary folders:

'/tmp/pytest_workflow\_\ **33mrz5a5**/workflow1' and
'/tmp/pytest_workflow\_\ **b8m1wzuf**/workflow2'

This is now changed to have all workflows in one temporary directory per
pytest run:

'/tmp/pytest_workflow\_\ **33mrz5a5**/workflow1' and
'/tmp/pytest_workflow\_\ **33mrz5a5**/workflow2'

+ Disallow empty ``command`` and ``name`` keys. An empty ``command`` caused
pytest-workflow to hang. Empty names are also disallowed.

---------------------------
+ Added more information to the manual on how to debug pipelines and use
``pytest-workflow`` outside a virtual environment.
+ Reworked code to use ``tempfile.mkdtemp`` to create a truly unique
temporary working directory if the ``--basetemp`` flag is not used. This
replaces the old code which dependeded on pytest internal code which was
flagged as deprecated. Also more information was added to the manual about
the use of ``--basetemp``.
+ Added a test case for WDL pipelines run with Cromwell and wrote an example
for using WDL+Cromwell in the manual.
+ Added ``--tag`` flag to allow for easier selection of workflows during
testing.
+ Added a test case for snakemake pipelines and wrote an example for using
pytest-workflow with snakemake in the manual.

---------------------------
+ Improved the log output to look nicer and make workflow log paths easier to
find in the test output.
+ Fixed an error that polluted the log message with a pytest stacktrace when
running more than one workflow. Measures are taken in our test framework to
detect such issues in the future.
+ Added the possibility to run multiple workflows simultaneously with the
``--workflow-threads`` or ``--wt`` flag.
+ Made code easier to maintain by using stdlib instead of pytest's ``py`` lib
in all of the code.
+ Added a schema check to ensure that tests have unique names when whitespace
is removed.

---------------------------
+ Cleanup the readme and move advanced usage documentation to our readthedocs
page.
+ Start using sphinx and readthedocs.org for creating project documentation.
+ The temporary directories in which workflows are run are automatically
cleaned up at the end of each workflow test. You can disable this behaviour
by using the ``--keep-workflow-wd`` flag, which allows you to inspect the
working directory after the workflow tests have run. This is useful for
debugging workflows.
+ The temporary directories in which workflows are run can now be
changed by using the ``--basetemp`` flag. This is because pytest-workflow now
uses the built-in tmpdir capabilities of pytest.
+ Save stdout and stderr of each workflow to a file and report their locations
to stdout when running ``pytest``.
+ Comprehensible failure messages were added to make debugging workflows
easier.