Scikick

Fixes

- Add support for new snakemake versions requiring wildcards in benchmark

Changes

- Benchmark directory now created by default under `report/benchmark`

New Features

- Project Maps - embed the scikick workflow into each page as a graph with nodes linking to pages
- Added experimental support for `.ipynb`
- Website menus are processed to be more human readable (1)
- Individual page log files stored in report/logs
- Allow for global rmarkdown/pandoc yaml in scikick.yml
- Dump full logs after snakemake error
- Add `sk run --quiet` argument
- Include the default homepage in sk status

Changes

- Remove internal custom CSS for rmarkdown::html_document
- Snakemake requirement bumped to >= 5.9 due to use of custom logger
- New sk status message (detect unknown execution reasons)
- Fix issue 2 for sk add -d usage
- More checks for scikick.yml state (e.g. sk version in use)
- Minor changes to footer/homepage content (include scikick.yml)
- Reduce outputs in sk init and other
- New sk init template
- Fix conda env usage with `sk config --conda` and `sk run -s --use-conda`

New Features

- Allow for convenient single page runs with `sk run my.Rmd` usage
- Single page status usage as `sk status my.Rmd`
- Add `--copy-deps` to `sk add` for duplicating file dependencies
- Index page is now defined by user with `sk add <path to index file>`
instead of auto-detected
- Add git SHA to site git logs

Changes

- Many sk status adjustments
- More detailed `sk add -d` output
- Better outputs for errors and warnings during `sk run`
- Tested and fixed renv compatibility
- Default index page is appended to any added index page
- Requirement of git2r version >= 0.27.1
- Fix git warnings and other outputs
- Add checks for scikick.yml format
- Other bug fixes

- Initial release