Snakemake

Changed

- Add missing import in rules.py.
- Use threading only in cluster jobs.

Changed

- Snakemake now warns when using relative paths starting with "./".
- The option -R now also accepts an empty list of arguments.
- Bug fix when handling benchmark directive.
- Jobscripts exit with code 1 in case of failure. This should improve
the error messages of cluster system.
- Fixed a bug in SFTP remote provider.

Added

- Wildcards can now be constrained by rule and globally via the new
`wildcard_constraints` directive (see the
[docs](https://bitbucket.org/snakemake/snakemake/wiki/Documentation#markdown-header-wildcards)).
- Subworkflows now allow to overwrite their config file via the
configfile directive in the calling Snakefile.
- A method `log_fmt_shell` in the snakemake proxy object that is
available in scripts and wrappers allows to obtain a formatted
string to redirect logging output from STDOUT or STDERR.
- Functions given to resources can now optionally contain an
additional argument `input` that refers to the input files.
- Functions given to params can now optionally contain additional
arguments `input` (see above) and `resources`. The latter refers to
the resources.
- It is now possible to let items in shell commands be automatically
quoted (see the
[docs](https://bitbucket.org/snakemake/snakemake/wiki/Documentation#markdown-header-rules)).
This is useful when dealing with filenames that contain
whitespaces.

Changed

- Snakemake now deletes output files before job execution. Further, it
touches output files after job execution. This solves various
problems with slow NFS filesystems.
- A bug was fixed that caused dynamic output rules to be executed
multiple times when forcing their execution with -R.
- A bug causing double uploads with remote files was fixed. Various
additional bug fixes related to remote files.
- Various minor bug fixes.

Changed

- Fixed a missing import of the multiprocessing module.

Added

- The entries in `resources` and the `threads` job attribute can now
be callables that must return `int` values.
- Multiple `--cluster-config` arguments can be given to the Snakemake
command line. Later one override earlier ones.
- In the API, multiple `cluster_config` paths can be given as a list,
alternatively to the previous behaviour of expecting one string for
this parameter.
- When submitting cluster jobs (either through `--cluster` or
`--drmaa`), you can now use `--max-jobs-per-second` to limit the
number of jobs being submitted (also available through Snakemake
API). Some cluster installations have problems with too many jobs
per second.
- Wildcard values are now printed upon job execution in addition to
input and output files. Changed
- Fixed a bug with HTTP remote providers.

Changed

- Work around missing RecursionError in Python \< 3.5
- Improved conversion of numpy and pandas data structures to R
scripts.
- Fixed locking of working directory.