Rpbp

Fixed

- Pandas `str.split` API in `summarize_rpbp_predictions.py`

Changed

- Requires pbiotools >= 4.0.2

Added

- `riboseq_sample_name_map`, `riboseq_condition_name_map` to `rpbp_predictions_dashboard.py`
- Exception for duplicated transcript ids with _de novo_ annotation.

Fixed

- STAR output
- Redundant transcripts with _de novo_ annotation in `summarize_rpbp_predictions.py`
- ORF numbers in labels

Changed

- I/O: ensure bool in config, remove symlinks
- Documentation

Fixed

- Missing GTF attributes

Added

- Dash assets to MANIFEST

Changed

- Upgrade all dependencies/required packages, install via bioconda
- Location of (compiled) Stan models
- PyStan 2 to CmdStanPy API
- Handling of ORF labels
- Documentation

Removed

- PyStan dependency
- Fitted parameters from output `_location` and `_scale`
- `orf_type` filtering for translation prediction
- GFF3 support
- Unfiltered predictions, unless [--write-unfiltered] is set
- QTI-seq, various plotting/reporting scripts, notebooks

Fixed

- Stan models transformed data/parameters name/definition (no-periodicity.stan, gaussian-naive-bayes.stan)
- CmdStanPy logging

Added

- Regression tests, pre-commit, GitHub CI workflow, etc.
- Options handling for `prepare_rpbp_genome`
- Retrieve gene_id, etc. from annotations
- Dashboad applications to replace PDF reports
- Data wrangling: `summarize_rpbp_profile_construction.py`, and `summarize_rpbp_predictions.py`
- ribo_utils
- orf_profile_construction scripts from pbiotools.ribo

Changed

- Configure setup() using setup.cfg, add `pbio`, update install via requirements.

Added

- Config file for RTD
- Module with all defaults parameters, handling options for external dependencies
- Add option to force the pickling of the Stan models during installation
[ISSUE 88](https://github.com/dieterich-lab/rp-bp/issues/88).

Fixed

- Build RTD documentation (add `autodoc_mock_imports`, empty `docs/requirements.txt`)
- Missing parameters in function calls, hard coded defaults
- [YAMLLoadWarning](https://msg.pyyaml.org/load)
- Fall back to multiprocessing in `estimate_orf_bayes_factors`, and
`extract_orf_profiles`
- Stan assignment operator in models
- ORF labels in `prepare_rpbp_genome`, `label_orfs` and `extract_orf_coordinates`, see
[ISSUE 96](https://github.com/dieterich-lab/rp-bp/issues/96).

Removed

- Transcript exons file (unused)