Issues in setup.py - Githubissues

ukhsa-collaboration / PHEnix

Public Health England SNP calling pipeline.

http://phenix.readthedocs.io/en/latest/

GNU General Public License v3.0

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Issues in setup.py #37

Open mbargull opened 6 years ago

mbargull commented 6 years ago

Hi there, I found a couple issues in your setup.py file:

You should use from setuptools import setup instead of from distutils.core import setup since you use the install_requires keyword, which is a setuptools addition.
The package parameter should be named packages.
There should be no need to use pip.req.parse_requirements. A simple
```
with open("requirements.txt") as requirements_file:
  requirements = requirements_file.read().split("\n")
```
However I'd advice against using it at all, see: https://packaging.python.org/discussions/install-requires-vs-requirements/. install_requires should list compatible versions, e.g., package>=1.0 or package>=1.0,<2.0, which are usually not exact == requirements as in requirements.txt

mbargull commented 6 years ago

Additionally, the requirements which are used for the tests or to build the docs needn't be install_requires. Test requirements can use the tests_require parameter to setup(...).

ulfschaefer commented 6 years ago

To be honest, you seem to know more about it than I do. We have been aware that there are issues with the setup on some systems. If you just clone the repository, put the scripts folder in your PATH and the basepath in your PYTHONPATH, and install the Python dependencies with pip and somehow install the required mappers and variant callers, you should be OK. Sorry for not being as helpful as I could have been.

mbargull commented 6 years ago

Hi @ulfschaefer, sorry for not providing more context upfront. I'm coming from over at https://github.com/bioconda/bioconda-recipes, where someone (@pvanheus) is looking into making PHEnix available to Conda / Bioconda users (and thus make your software more easily accessible, i.e., let a single conda install phenix install everything -- including those non-Python mapper/var. caller dependencies -- for the user). My comments are meant as suggestions/improvements to make PHEnix behave more like "conventional/standard" Python package which would ease user installation as well as packaging in Bioconda & co. Happy to help if you need any assistance or more information!

ulfschaefer commented 6 years ago

Sure. I know @pvanheus and I have spoken to him separately. Thank you to you both for looking into doing this.