Looper

Added

- preliminary support for [pipestat](http://pipestat.databio.org).
- ability to skip samples using `-k` or `--skip` [367](https://github.com/pepkit/looper/pull/367)
- ability to input a range into `limit` and `skip`[367](https://github.com/pepkit/looper/pull/367)
- `limit` and `skip` are now both usable with Destroy and Run. [367](https://github.com/pepkit/looper/pull/367)
- ability to generate generic pipeline interface using `init -p` or `init --piface` [368](https://github.com/pepkit/looper/pull/368)
- Fixed ability to use custom sample index
- Added `write_custom_template`, a built-in pre-submit plugin for writing templates

Changed
- looper now returns nonzero if any samples fail submission
- various other developer changes

Deprecated
- `path` variable will be deprecated in favor of `var_templates` [322](https://github.com/pepkit/looper/issues/322)

Changed
- Fixed bug with use_2to3 for setuptools compatibility.

Changed
- If remote schemas are not accessible, the job submission doesn't fail anymore
- Fixed a bug where looper stated "No failed flag found" when a failed flag was found

Deprecated
- Fixed and deprecated `looper inspect`. Use `eido inspect` from now on.

Added
- New plugin system for pre-submission hooks
- Included plugin functions: `write_sample_yaml`, `write_sample_yaml_prj`, `write_sample_yaml_cwl` and `write_submission_yaml`
- New `var_templates` section for defining variables in the pipeline interface

Changed
- Pipeline interface specification was updated to accommodate new `var_templates` section and pre-submission hooks

Deprecated
- pipeline interface sections:
- `dynamic_variables_command_template`, which can now be more simply accomplished with a pre-submission hook
- `path`, which is replaced by a more generic `var_templates` section

Added
- Environment variables expansion in custom sample YAML paths; [Issue 273](https://github.com/pepkit/looper/issues/273)
- `dynamic_variables_script_path` key in the pipeline interface. Path, absolute or relative to the pipeline interface file; [Issue 276](https://github.com/pepkit/looper/issues/276)
Changed
- Resolve project pipeline interface path by making it relative to the config not current directory; [Issue 268](https://github.com/pepkit/looper/issues/268)
Fixed
- Unclear error when `output_dir` was not provided in a config `looper` section; [Issue 286](https://github.com/pepkit/looper/issues/286)