Pyrodigal

Stable version, to be published in the [Journal of Open-Source Software](https://joss.theoj.org/).

Added
- `pickle` protocol implementation for `Nodes`, `TrainingInfo`, `OrfFinder`, `Sequence`, `Masks` and `Genes` objects.
- Buffer protocol implementation for `Sequence`, allowing access to raw digits.
- `__eq__` and `__repr__` magic methods to `Mask` objects.

Changed
- Optimized code used for region masking to avoid searching for the same mask repeatedly.
- `TRANSLATION_TABLES` and `METAGENOMIC_BINS` are now exposed as constants in the top `pyrodigal` module.
- Refactored connection scoring into different functions based on the type (start/stop) and strand (direct/reverse) of the node being scored.
- Changed the growth factor for dynamic arrays to be the same as the one used in CPython `list` buffers.

Added
- `Gene.score` property to get the gene score as reported in the score data string.

Fixed
- `OrfFinder.find_genes` not producing consistent results across runs in *meta* mode ([13](https://github.com/althonos/pyrodigal/issues/13)).
- `OrfFinder.find_genes` returning `Nodes` with incomplete score information.

Changed
- Improve performance of `mer_ndx` and `score_connection` using dedicated implementations with better branch prediction.
- Mark arguments as `const` in C code where possible.

Fixed
- Signatures of Cython classes not displaying properly because of the `embedsignature` directive.
- `_sequence.h` functions not being inlined as expected.

Changed
- Rewrite internal `Sequence` code using inlined functions to increase performance when the strand is known.

Fixed
- `Nodes.copy` potentially failing on empty collections after trying to allocate 0 bytes.
- `TestGenes.test_write_scores` failing on some machines because of float rounding issues.
- `Gene.translate` ignoring the `unknown_residue` argument value and always using `"X"`.
- Memory leak in `Pyrodigal.train` cause by memory not being freed after building the GC frame plot.

Added
- Support for setting a custom minimum gene length in `pyrodigal.OrfFinder`.
- `Genes.write_scores` method to write the node scores to a file.
- `Gene.__repr__` and `Node.__repr__` methods to display some useful attributes.
- `Sequence.__str__` method to get back a nucleotide string from a `Sequence` object.

Changed
- Use a more compact data structure to store `Gene` data.

Fixed
- `Nodes._calc_orf_gc` reading nucleotides after the sequence end when computing GC content for edge nodes.

Removed
- `pyrodigal.Pyrodigal` class (use `pyrodigal.OrfFinder` instead).
- `pyrodigal.Predictions` class (functionality merged into `pyrodigal.Genes`).

Added
- `load` and `dump` methods to `TrainingInfo` for storing and loading a raw training info structure.
- Support for creating an `OrfFinder` pre-configured with a training info.
- `-t` and `-n` flags to the CLI.