New features
- Added the `s1_name` and `s2_name` parameters to `viz_imshow()` and `viz_spy()` ([17](https://github.com/fedarko/wotplot/issues/17)).
- You can use these parameters to adjust the sequence name shown on the x or y axis, respectively.
Performance
- Updated the default algorithm for finding shared _k_-mers between two strings. Rather than manually iterating through the suffix arrays produced by `pydivsufsort.divsufsort()` to identify shared _k_-mers, we now instead use [`pydivsufsort.common_substrings()`](https://github.com/louisabraham/pydivsufsort/issues/42) -- which accomplishes the same thing much faster.
- For example, creating a dot plot of two random 1 Mbp sequences (using _k_ = 20) takes **26.52 seconds** (max memory usage 563.09 MiB) using the old method and **2.16 seconds** (max memory usage 617.53 MiB) using the new method.
- The new method does have higher memory usage for long sequences -- to the point where some test cases crash Jupyter Notebook with the new method, but succeed (albeit after taking a long time) with the old method. If desired, you can choose to use the old method ("suff-only") by passing `suff_only=True` to the `DotPlotMatrix()` constructor.
- When using the old shared-_k_-mer-finding method ("suff-only") and creating a self dot plot (i.e. comparing a sequence with itself), wotplot will now detect if the sequences are identical and reuse the sequence's suffix array (rather than unnecessarily creating the same suffix array twice).
- Note that there are still other, more dramatic ways to speed up the creation of self dot plots; this is a relatively small improvement.
Maintenance
- **Breaking change:** Removed the `binary` parameter of the `DotPlotMatrix()` constructor.
- Now, all matrices are "not binary" by default. If you want to visualize a matrix in a binary way, you can now set `binary=True` when calling `viz_imshow()` or `viz_spy()` (this is analogous to the `force_binary` parameter in wotplot 0.3.0). Matrix visualization defaults to visualizing the matrix in color.
- This change was motivated by benchmarking -- making the matrix "not binary" didn't seem to impact construction speed. It does impact visualization speed slightly, but the effects of this can be (entirely, I think?) offset by using `binary=True` during visualization.
- Sorry for the breaking change. I think this makes the interface a lot more natural to use.
- Abstracted code from the benchmarking notebook to a separate file in the `docs/` folder, and tried to tidy it up.
- Restructured and tested the SciPy version checking code.
- Additional tests.
- Added [`pytest-mock`](https://github.com/pytest-dev/pytest-mock) as a development dependency.
Bug fixes
- Fixed a bug where, if every single cell in the dot plot matrix was a match cell, the resulting dot plot would be empty ([19](https://github.com/fedarko/wotplot/issues/19)).
Documentation
- Add better documentation to `wotplot._make._get_row()` and `wotplot._make._make()`.
- Various updates to the README, tutorial notebook, and benchmarking notebook.
- The tutorial now includes a more complex example of creating a grid of dot plots. The example (shown below) creates a grid figure comparing all pairs of sequences with each other.
Fancy screenshot of a grid of dot plots from the tutorial
