Homelette

Added
- Added CITATION.cff
- Added citation to README.md
- Added citation to documentation
- Added option to test installation by running tutorials in docker image and locally.
- Added standard user `homelette` to docker image.

Fixed
- Updated the RCSB PDB Search API from v1 to v2.
- Implemented fallback method in `AlignmentGenerator.get_pdbs` for increasing chances of correct alignment when structures in PDB have unconventional number schemes. (4)
- Fixed issue with long target names in `AlignmentGenerator`s. (5)
- Fixed issue with `extension.extension_foldx.Evaluation_foldx_alascan_buildmodels`.

Changed
- Adapted working directories in homelette docker image: `/home/homelette/workdir/`, `/home/homelette/templates/`, and `/home/homelette/alignments/`.

Added
- Added loop modelling routines: `routines.Routine_loopmodel_default` and `Routine_loopmodel_slow`, build on the base class `routines.Routine_loopmodel`
- Added functionality for, given a target sequence, automatically searching for
potential templates and generating alignments using different methods:
- Base class: `alignment.AlignmentGenerator`
- Classes for application: `alignment.AlignmentGenerator_pdb`, `alignment.AlignmentGenerator_hhblits`, `alignment.AlignmentGenerator_from_aln`
- Added Tutorial 8 about automatic generation of alignments.
- Methods for checking coverage between sequences in alignments:
- `alignment.Alignment.calc_coverage`
- `alignment.Alignment.calc_coverage_target`
- `alignment.Alignment.calc_pairwise_coverage_all`
- `pdb_io` submodule for pooling functionality that is internally used to handle PDB files.
- Added .gitignore file.

Fixed
- Fixed mistake in docstring for `alignment.Alignment.calc_identity()`.

Changed
- `alignment.Alignment.calc_identity_target()` and
`alignment.Alignment.calc_pairwise_identity_all()` do not calculate
identities between sequences of the same identifier anymore.