Leighton Pritchard

Rationalise documentation

2

#### Summary: We'd like to rationalise the documentation to make our lives, and users' lives, easier. #### Description: Some of the existing documentation is possibly overlong/in the "wrong" place, so...

`pyani anim` loads sequences into database before checking class/label files

3

#### Summary: The `pyani anim` command should check for correct formatting before committing sequences to the database - this would save time #### Description: Currently, all sequences are processed and...

Use JSON for labels/classes files

2

The *ad hoc* tab-separated text format for label/class files works, but JSON may be more exchangeable and enhancement-friendly.

Use `alembic` to manage SQLite schema changes?

41

#### Summary: Use [`alembic`](https://alembic.sqlalchemy.org/en/latest/batch.html) or similar to manage database migration. #### Description: In discussions with users, modifications to the SQLite database schema have caused issues where updating their v0.3 installation...

Ensure ANIm identity scores are true metrics

14

#### Summary: It's not precisely established that ANIm identities are true metrics - we need to demonstrate and ensure this, otherwise the clique-based classification is not as sound as we'd...

Add SLURM support

10

#### Summary: `pyani` currently only supports SGE/OGE-like systems, but SLURM is very popular. It would be useful to support SLURM scheduling.

Have `pyani` use a user-controlled config file

4

#### Summary: The current config arrangement is hacky and awful. It would be better to have a user-controlled config file that specifies colour palettes, application locations and so on. This...

Add explicit warnings for zero-identity comparison runs

4

#### Summary: Several issues have been raised (#93 #72 #73 etc.) where the main issue is that a comparison has given a zero identity, and errors have been thrown downstream....

Make `version_0_2` the default branch and rename `master` to `version_0_3`

5

Many users who install `pyani` v0.2.x through `conda` or `PyPI` come to GitHub for documentation, and find the default branch `master`, which refers to v0.3+. The CLIs are different, and...

#### Summary: The new Python3 `concurrent.futures` interface can replace `multiprocessing` with a cleaner interface and more control/usability.