Pyani

- major changes to the command-line API
- the new API now uses a subcommand system: `pyani <cmd> <arguments>`
- major changes to result storage
- results are now stored in an SQLite database, rather than reported to `.tab` files
- enables reuse of previously calculated results in new analyses
- enables generation of multiple output files from the same analysis, after the analysis is complete
- more output formats
- tabular output is available as HTML tables, as well as plain text
- new documentation
- documentation is now available at [ReadTheDocs](https://pyani.readthedocs.io/en/development/)
- papers citing or referring to `pyani` are now listed
- `pyani download` (replacing `genbank_get_genomes_by_taxon.py`) allows use of an NCBI API key for faster/more stable downloads
- `genbank_get_genomes_by_taxon.py` label/class file output updated to include a hash, matching the `pyani download` output format
- `pyani plot` now produces distribution plots in addition to heatmaps
- A number of bug fixes were implemented, including:
- consistent handling of filenames as `Path`s
- alignment length calculation for ANIm was corrected
- major refactoring of code ported from v0.2
- static typing implemented
- testing converted to `pytest` conventions from `unittest`

- Fix for issue 97 where numeric arguments to the GenBank download script were not recognised
- GenBank download script now insists on integer input for `--batchsize`, `--retries`, and `--timeout`
- Added `setup.cfg` that points to README.md
- Fix issue 97 where valid input arguments were not recognised in the download script

- update legacy BLAST download location in TravisCI
- update concordance tests (issue 105)
- extend test suites (issue 104)
- modify ANIm concordance test to accommodate new command structure
- add `delta-filter` wrapper for compatibility with SGE/OGE schedulers

- Add Dockerfiles for making Docker images

- `ANIm` now uses `delta-filter` to remove alignments of repeat regions (issue 91)
- added `--filter_exe` option to specify location of `delta-filter` utility (issue 91)
- fixed `--format` option so that GenBank downloads work again (issue 89)
- add `--SGEargs` option to `average_nucleotide_identity.py` for custom qsub settings
- `README.md` badges now clickable
- `--version` switch added to `average_nucleotide_identity.py`
- FTP timeouts are now caught differently in `genbank_get_genomes_by_taxon.py`
- Additional characters in NCBI FTP URIs now escaped in `genbank_get_genomes_by_taxon.py` - should be fewer failed downloads
- Modified error messaging when `NUCmer` alignment fails
- `average_nucleotide_identity.py` argument documentation improvements
- Script now fails immediately if label or class files missing (issue 78)
- Changes to `--noclobber` log behaviour (issue 79)
- fixed `--rerender` code (issue 85)

- fixes a bug in the installed scripts where the shebang (`!`) in wheel and egg packages pointed to a development Python