Release v2.4.0

[peterk87]

Change log for v2.4.0 release:

• added scheme metadata table to Python package data (Fix to include metadata when installing with pip/conda #109)
• typing scheme name change from tb_speciation to tb_lineage (Rename tb_speciation to tb_lineage  #110)
• updated README (Readme Update #111)
• updated default low coverage depth value for SE scheme from 50 to 20, max kmer frequency from 1000 to 10,000 and updated help/usage docs (Update default coverage values and clarify help statement #114)
• improved reverse complement function performance (Faster reverse complement using translation table #118)
• fixed merging of subtyping results with subtype result metadata table (Fix metadata NA value issue #120)
• added CI testing for Python 3.7, cleaned up setup.py (Prepare release v2.4.0 #119)

[DarianHole]

Hi @peterk87,

Everything seems to be in order on the code side. Pytests run on both 3.6 and 3.7 as expected.

Although I think I've found an installation issue I missed last time (or I don't know how to install). Currently I pip install from the branch (pip install .) and when I do that, the aho_corasick and qc directories are not being copied with the data (no issue when I tried 2.3 or 2.2 in this).

I'll see if its on my end a bit more as well

[DarianHole]

Just the one comment to fix the issue I was having and two small potential wording changes I would recommend.

Otherwise good!

As an aside question, will this auto-deploy to pypi?

[peterk87]

Thanks a lot @DarianHole for taking a look at this PR! I fixed the packaging issue and made the suggested changes.

I think it should auto-deploy when a release tag is created.

biohansel/.travis.yml

Lines 13 to 23 in f653c2f

	deploy:
	provider: pypi
	distributions: sdist bdist_wheel
	user: peterk87
	deployment: bio-hansel
	password:
	secure: 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
	on:
	tags: true
	repo: phac-nml/biohansel
	python: 3.6

The user and secure password could be changed to the phac-nml and a secure password generated by the travis-ci cli tool. I've added the phac-nml user as a project owner on PyPI.

[DarianHole]

Changes are good. Testing shows that everything is working as expected for python 3.6 and 3.7

[DarianHole]

@peterk87 I am not authorized to merge this one but its good. Let me know if anything else is needed!

[peterk87]

Thanks a lot @DarianHole! I'll create a v2.4.0 release and make sure it's up on PyPI

[glabbe]

Thanks a lot @peterk87 and @DarianHole for this new version release, much appreciated!