Looper

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)

**This version introduced backwards-incompatible changes.**

Added
- Commands:
- `init`; initializes `.looper.yaml` file
- `inspect`; inspects `Project` or `Sample` objects
- `table`; writes summary stats table
- `runp`; runs project level pipelines
- Input schemas and output schemas
- `--settings` argument to specify compute resources as a YAML file
- Option to preset CLI options in a dotfile
- `--command-extra` and `--command-extra-override` arguments that append specified string to pipeline commands. These functions supercede the previous `pipeline_config` and `pipeline_args` sections, which are now deprecated. The new method is more universal, and can accomplish the same functionality but more simply, using the built-in PEP machinery to selectively apply commands to samples.
- Option to specify destination of sample YAML in pipeline interface
- `--pipeline_interfaces` argument that allows pipeline interface specification via CLI

Changed
- `looper summarize` to `looper report`
- Pipeline interface format changed drastically
- The PyPi name changed from 'loopercli' to 'looper'
- resources section in pipeline interface replaced with `size_dependent_attributes` or `dynamic_variables_command_template`.
- `--compute` can be used to specify arguments other than resources
- `all_input_files` and `required_input_files` keys in pipeline interface moved to the input schema and renamed to `files` and `required_files`
- pipeline interface specification

Added
- possibility to execute library module as a script: `python -m looper ...`

Changed
- in the summary page account for missing values when plotting; the value is disregarded in such a case and plot is still created
- show 50 rows in the summary table
- make links to the summary page relative
- long entries in the sample stats table are truncated with an option to see original value in a popover

Fixed
- inactive jQuery dependent components in the status page
- project objects layout in the summary index page
- inactivation of popovers after Bootstrap Table events
- non-homogeneous status flags appearance

Changed
- reduce verbosity of missing options; [Issue 174](https://github.com/pepkit/looper/issues/174)
- switch to [Bootstrap Table](https://bootstrap-table.com/) in the summary index page table and sample status tables