Spacemake

- Added support for multiple references per species (`genome`, `rRNA`, `mirgenedb` etc).
- The multiple species references are controlled through the `map_strategy` variable (e.g. `rRNA->genome`).
- Implemented an optimized algorithm for binning (meshing) coordinate systems.
- Added support for easy addition of custom rules into the workflow.
- Added unit tests.
- Updated the `environment.yaml` to pin the OpenJDK version.
- Fixed several bugs and errors.

- fixed issue with --version introduced in v0.5.4
- fixed command line error where updating a sample from the command line would remove puck_ids

- Each sample can have multiple barcode files
- Added a novosparc tutorial
- Bugfixes:
- read-only `project_df.csv` during spacemake run
- adding new puck command

- Further bugfixes
- Completed docs with longread tutorial

- Fixed errors during initialization and species download
- Updated docs

- Added H&E integration
- Updated documentation
- Bugfixes