Update codebase to python 3 #15
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tncowart
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tncowart
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In addition to my comments I don't think you should check in the symlinks.
ggr_cwl_ipynb_gen/__init__.py
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| if __name__ == '__main__': | |||
| ggr-main() | |||
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ggr-main() isn't a valid identifier. I think you can just delete this.
setup.cfg
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| [metadata] | |||
| name = ggr-cwl-ipynb-gen-alexbarrera | |||
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should you remove -alexbarrera?
setup.cfg
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| description = IPython notebook generator for GGR CWL processing pipelines of genomic data | ||
| long_description = file: README.md | ||
| long_description_content_type = text/markdown | ||
| url = https://github.com/alexbarrera/ggr-cwl-ipynb-gen |
setup.py
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| url='https://github.com/alexbarrera/ggr-cwl-ipynb-gen', | ||
| author='Alejandro Barrera', | ||
| author_email='alejandro.barrera@duke.edu', | ||
| classifiers=[ |
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This list doesn't match the list in setup.cfg
setup.py
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| ('templates', ['ggr_cwl_ipynb_gen/templates/ungzip_fastq_files.j2']), | ||
| ], # Optional | ||
| project_urls={ | ||
| 'Bug Reports': 'https://github.com/alexbarrera/ggr-cwl-ipynb-gen/issues', |
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these urls should be updated to the new location in reddylab.
requirements.txt
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| ruamel.yaml >=0.11.11 | ||
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| setuptools | ||
| pymongo No newline at end of file |
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Shouldn't pymongo be versioned too?
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I didn't versioned pymongo because I'm not sure where to draw the line of the oldest version that should be accepted
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Your initial commit was 4/26/2017 and it looks like the newest version of pymongo at the time was 3.4.0, so probably that version (it's only at 3.11 now, 4 years later).
requirements.txt
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| xlrd >=1.0.0 | ||
| ruamel.yaml >=0.11.11 | ||
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| setuptools |
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I don't think you need setup tools here because it's mentioned in pyproject.toml
MANIFEST.in
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| include templates/* No newline at end of file | |||
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I don't think you need a manifest file because you use data_files in setup.py
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What's the argument to remove the |
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Just to declutter the repo. I don't feel super strongly about it though. |
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Got it, yeah, I imagined that was it. I also feel like symlinks are prob something that can stay away from the repo, not common to find them committed. I just removed them. Thanks for all the comments!! |
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Closes #11 |
This
devbranch addresses a couple things needed moving forward:setup.pyand some other necessary file for packaging the tool and make it installable withpip install /path/to/ggr-cwl-ipynb-genSince we don't have unittests or CI yet, it might be one for one of the reviewers to download and test before merging (if you haven't yet)