Bailey Harrington

Episode 10 Defensive Programming — Using the assert statement to validate data is bad practice

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# Relating to [Episode 10 — Defensive Programming](https://github.com/swcarpentry/python-novice-inflammation/blob/gh-pages/_episodes/10-defensive.md) The first half of this lesson advocates using Python's `assert` statement to do data validation. While this may be *common* (I don't...

Issue #378: Add `alembic` support for database migrations

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This PR adds `alembic` for `pyani`, making it possible to upgrade and downgrade existing databases to accommodate otherwise breaking changes to the ORM, as with the addition of `fastANI` capabilities....

Update `get_version()` tests based on discussion surrounding Issue #405

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Makes changes to the `get_version()` tests discussed in Issue #405 in the other subcommand APIs. ## Type of change - [ ] Bug fix (non-breaking change that fixes an issue)...

Addition of a new test case to address some previously uncovered code. Closes #405. ## Type of change (not quite a bug fix, really, but this is the closest option)...

Untested code in `fastani.py`

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#### Summary: Lines 97–99 in `pyani/fastani.py`: ```python if fastani_path is None: return f"{fastani_exe} is not found in $PATH" ``` are missed by testing, and likely redundant. `fastani_path` is defined a...

Use `--noextend` in NUCmer as a rule

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#### Summary: Make `--noextend` the default NUCmer behaviour for v0.3, and implement an `--extend` option for `pyani anim` that allows us to use `pyani` compare to see what the damage...

Issue #373: ANIm should not be symmetric

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With this PR, ANIm is no longer treated as symmetric. Comparisons between each pair of genomes are run in both directions; enforced sorting of output file names has been disabled;...

Add `try/except` around extraction to accommodate failing uncompression in `pyani download`

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Fixes problem where failure to extract the contents of individual zip files from `pyani download` triggers a `SystemExit`. Closes #383. Please include a summary of the change and which issue...

Issue #123: Add `anib`

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Adds `anib` subcommand to v3. Closes #123. ## Type of change - [ ] Bug fix (non-breaking change that fixes an issue) - [x] New feature (non-breaking change that adds...

Issue #402: Fix tests that fail as a result of running `pytest` with no flags

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CLI parsing in `pyani_script.py` and some test files made the implicit assumption that they were dealing with a `pyani` command; however, these files also parse the command line when a...