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bdgenomics.adam vs bdg.adam for R/Python APIs #1655

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fnothaft opened this Issue Aug 3, 2017 · 10 comments

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fnothaft commented Aug 3, 2017

I put the package name for the Python library as bdgenomics.adam while the R library lives at bdg.adam. What are folks thoughts about which one is preferable? bdgenomics.adam is more consistent with the Scala/Java side of the house, but bdg.adam is shorter.

I'd like this to be consistent across any Python libraries we make available, e.g., bigdatagenomics/workflows#12.

@fnothaft fnothaft added the discussion label Aug 3, 2017

@fnothaft fnothaft added this to the 0.23.0 milestone Aug 3, 2017

@fnothaft fnothaft self-assigned this Aug 3, 2017

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heuermh Aug 3, 2017

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+1 to bdgenomics.adam with future migration to bigdatagenomics.adam if/when we obtain the .org domain name and change all the Scala/Java package names and groupIds.

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heuermh commented Aug 3, 2017

+1 to bdgenomics.adam with future migration to bigdatagenomics.adam if/when we obtain the .org domain name and change all the Scala/Java package names and groupIds.

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pbashyal-nmdp Aug 15, 2017

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+1 to bdgenomics.adam

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pbashyal-nmdp commented Aug 15, 2017

+1 to bdgenomics.adam

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heuermh Aug 18, 2017

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@fnothaft do you want to make this change in #1651 or would you prefer I do this in a separate PR?

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heuermh commented Aug 18, 2017

@fnothaft do you want to make this change in #1651 or would you prefer I do this in a separate PR?

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Referencing issue #1691, then should the name be bdgenomics-adam for python?

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akmorrow13 commented Aug 30, 2017

Referencing issue #1691, then should the name be bdgenomics-adam for python?

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Is bdgenomics-adam valid for both python and R?

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heuermh commented Aug 30, 2017

Is bdgenomics-adam valid for both python and R?

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pbashyal-nmdp Aug 30, 2017

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You can't have dash - in the package name in python. You could change it to underscore _ instead. See PEP 423 for Python package standard.

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pbashyal-nmdp commented Aug 30, 2017

You can't have dash - in the package name in python. You could change it to underscore _ instead. See PEP 423 for Python package standard.

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PEP 8 is also has a recommendation for package/module names.

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pbashyal-nmdp commented Aug 30, 2017

PEP 8 is also has a recommendation for package/module names.

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What I see there is that ${community}.${project} seems to be reasonable. Why does that prevent ${community}.${other project} from working (#1691)?

https://www.python.org/dev/peps/pep-0423/#id81
https://www.python.org/dev/peps/pep-0423/#id87
Yes:
Package name: "kheops.pyramid", i.e. import kheops.pyramid
Project name: "kheops.pyramid", i.e. pip install kheops.pyramid

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heuermh commented Aug 30, 2017

What I see there is that ${community}.${project} seems to be reasonable. Why does that prevent ${community}.${other project} from working (#1691)?

https://www.python.org/dev/peps/pep-0423/#id81
https://www.python.org/dev/peps/pep-0423/#id87
Yes:
Package name: "kheops.pyramid", i.e. import kheops.pyramid
Project name: "kheops.pyramid", i.e. pip install kheops.pyramid

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Ah, so IIRC, @akmorrow13 was seeing that the packages would pip install in incompatible ways. I'm wondering if the culprit is the way we're structuring our directories. E.g., if we do adam-python/src/bdg.adam instead of adam-python/src/bdg/adam, does that resolve the problem?

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fnothaft commented Aug 30, 2017

Ah, so IIRC, @akmorrow13 was seeing that the packages would pip install in incompatible ways. I'm wondering if the culprit is the way we're structuring our directories. E.g., if we do adam-python/src/bdg.adam instead of adam-python/src/bdg/adam, does that resolve the problem?

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I don't think so, this project used as an example in the packaging doc is src/${community}/${project}
https://bitbucket.org/gawel/gpfileupload/src/54887f3493542b392156178d403c49a9cda27ba2/gp/fileupload/?at=default

And shouldn't it be src/bdgenomics/adam?

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heuermh commented Aug 30, 2017

I don't think so, this project used as an example in the packaging doc is src/${community}/${project}
https://bitbucket.org/gawel/gpfileupload/src/54887f3493542b392156178d403c49a9cda27ba2/gp/fileupload/?at=default

And shouldn't it be src/bdgenomics/adam?

fnothaft added a commit to fnothaft/adam that referenced this issue Oct 17, 2017

fnothaft added a commit to fnothaft/adam that referenced this issue Oct 17, 2017

heuermh added a commit that referenced this issue Oct 17, 2017

@heuermh heuermh added this to Completed in Release 0.23.0 Jan 4, 2018

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