Don't import biopandas during install

[ecederstrand]

Getting the version during install is more safely done by reading init as text.

The reason is that init may at some point include code that requires importing packages that have not yet been installed. Installing a package should always be possible using pip install biopython in an empty virtualenv.

Description

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Related issues or pull requests

Link related issues/pull requests here

Pull Request requirements

For new features or bug fixes, pleas consider the following to-do list:

• Added appropriate unit test functions in the ./biopandas/*/tests directories
• Ran nosetests ./biopandas -sv and make sure that all unit tests pass
• Checked the test coverage by running nosetests ./biopandas --with-coverage
• Checked for style issues by running flake8 ./biopandas
• Added a note about the modification or contribution to the ./docs/sources/CHANGELOG.md` file
• Modified documentation in the appropriate location under biopandas/docs/sources/ (optional)
• Checked that the Travis-CI build passed at https://travis-ci.org/rasbt/biopandas

[pep8speaks]

Hello @ecederstrand! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

There are currently no PEP 8 issues detected in this Pull Request. Cheers! 🍻

Comment last updated at 2019-10-10 18:09:48 UTC

[rasbt]

Thanks for the PR. Just making sure that I understand the rationale correctly. So, the argument is that if we accumulate a lot of stuff in the __init__.py file, we may have problems getting the version in pip due to import issues?

I am not sure if this is an issue here, because we do not import external packages in the __init__.py

[ecederstrand]

It's correct that this isn't an issue right now because the init doesn't contain any import statements. But if you start adding import helpers so you can do biopandas import Foo then you start getting problems. It's quite difficult to debug and only shows up in a fresh virtualenv, so developers usually don't notice before some user complains.

Anyway, I just wanted to raise the issue here since I've wasted countless hours due to this in other projects :-)

[rasbt]

It's correct that this isn't an issue right now because the init doesn't contain any import statements. But if you start adding import helpers so you can do biopandas import Foo then you start getting problems. It's quite difficult to debug and only shows up in a fresh virtualenv, so developers usually don't notice before some user complains.

Anyway, I just wanted to raise the issue here since I've wasted countless hours due to this in other projects :-)

Yeah, it certainly doesn't hurt to add this. I'd be happy to merge this once the issues are fixed.

[coveralls]

Coverage remained the same at 94.236% when pulling 993f6be on ecederstrand:patch-1 into 83d1b65 on rasbt:master.

[ecederstrand]

Wow, I really botched this PR. Sorry. Copy-pasting code and editing files online on GitHub is not a good combination :-)

[rasbt]

Looks good, thx! Doc updates etc are not required, because these are just changes under the hood. Will merge. Thanks!