Snakemake

Changed

- Improved warning on wildcard constraints (jheuel)
- Improved logging from the new scheduler
implementation (johanneskoester)
- Restored Python 3.5 compatibility by removing f-strings (mbhall88)
- Snakemake now automatically adds a global wildcard constraint for
{scatteritem}, when scatter/gather support is used.
- The zip variant of Snakemake reports is now compressed
(FelixMoelder).
- Improved docs (ctb).
- Make output file removal in cluster mode more robust (sebschmi).

Changed

- Handle accidental use of GLS backend with singularity (vsoch).
- Improved and extended WMS-monitor implementation (vsoch).
- Display index and total count in `{scatteritem}` when using the
scatter-gather helper (johanneskoester).
- Fixed problems with jobid display when handling checkpoint updates
(johanneskoester, jmeppley).
- Fixed bug when checking for directory containment of output files
(jmeppley).
- Implement --no-subworkflows treatment in combination with --cluster
(goi42).

Changed

- added wget again to the container image

Added

- The `Paramspace` helper for automatically exploring parameter spaces
given as Pandas dataframes.
- A new directive `name:` for setting rule names from variables.

Changed

- Various small bug fixes for scheduling and checkpoint handling.
- Automatically block R_LIBS, PYTHONPATH, PERL5LIB, and PERLLIB when
using conda with --use-conda. This behavior can be deactivated with
--conda-not-block-envvars.
- Update container image to latest singularity.

Changed

- Fix permission issues with jobscripts on some systems (Phhere).
- Added notes on WSL to the tutorial (RomainFeron).
- Scheduler fixes (johanneskoester).
- Fixed a bug in checkpoint handling that led to hanging workflow
execution (jmeppley).
- Pass cluster nodes to subworkflows (votti).
- Fix start time recording in metadata (lparsons).
- Fix time retrieval in reports (johanneskoester).
- Fix error when returning a Path from an input function (sappjw).
- Extending monitoring docs with some notes about future api changes
(vsoch).

Added

- Benchmarks now also report CPU time (natir).

Changed

- Fixed a reauthentication bug in Kubernetes support (haizi-zh).