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Include bdgenomics.adam-0.23.0_SNAPSHOT-py2.7.egg in distribution tarball #1667

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heuermh opened this issue Aug 15, 2017 · 9 comments
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Include bdgenomics.adam-0.23.0_SNAPSHOT-py2.7.egg in distribution tarball #1667

heuermh opened this issue Aug 15, 2017 · 9 comments
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@heuermh
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@heuermh heuermh commented Aug 15, 2017

I don't believe pyadam will work out of the box after downloading and decompressing the distribution tarball.

@akmorrow13
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@akmorrow13 akmorrow13 commented Aug 23, 2017

Going off of this @heuermh , what is the best way to use ADAM python APIs in an external project? bigdatagenomics/mango#307 depends on the ADAM python apis, but it is not accessible through pip. Is there a plan to add these to pip, or is there an alternative way in which we can access adam python in an alternative project?

@heuermh
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@heuermh heuermh commented Aug 23, 2017

I don't know. Who are our go-to python experts? ;) @pbashyal-nmdp may also be interested.

@akmorrow13
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@akmorrow13 akmorrow13 commented Aug 23, 2017

I can definitely set up a PyPl account and push it so it is accessible by pip (see here: http://peterdowns.com/posts/first-time-with-pypi.html) The process seems quite painless. The only issue with putting this library on pip is that is it relatively useless without the jars. Should we put it up there anyways @heuermh and @fnothaft ?

@fnothaft
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@fnothaft fnothaft commented Aug 23, 2017

How do you have your packaging set up? I assume you're using a virtualenv? We will push to pip at the release. In the intermediate, once you've activated your virtualenv, you can cd into adam-python and run make develop, which will install the bindings into the virtualenv.

@fnothaft
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@fnothaft fnothaft commented Aug 23, 2017

WRT pip, PySpark is pushed to pip and has some fancy logic that moves the Spark jars into a python package. We need to play around with that a bit, but it is doable.

@akmorrow13
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@akmorrow13 akmorrow13 commented Aug 24, 2017

Yes, I have been cding into adam-python and running pip install and that is working for testing. I am just trying to figure the best way to handle things when we merge into the Mango master branch. We don't need the jars because those are built into the mango jar, we just need the python APIs.

@fnothaft
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@fnothaft fnothaft commented Aug 24, 2017

Ah, gotcha. In the PiPy config, we should be able to make it so that installing the JARs is optional, if that would help.

@pbashyal-nmdp
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@pbashyal-nmdp pbashyal-nmdp commented Aug 24, 2017

When I run make sdist it produces dist/bdgenomics.adam-0.23.0-SNAPSHOT.tar.gz When I try to pip install the distribution, it fails not finding the version module.

(venv) > pip install dist/bdgenomics.adam-0.23.0-SNAPSHOT.tar.gz
Processing ./dist/bdgenomics.adam-0.23.0-SNAPSHOT.tar.gz
    Complete output from command python setup.py egg_info:
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/private/var/folders/7l/5w7957112mjb8yjf6lf13c2cycqhx4/T/pip-qQtkk4-build/setup.py", line 20, in <module>
        from version import version as adam_version
    ImportError: No module named version

    ----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /private/var/folders/7l/5w7957112mjb8yjf6lf13c2cycqhx4/T/pip-qQtkk4-build/
@pbashyal-nmdp
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@pbashyal-nmdp pbashyal-nmdp commented Aug 24, 2017

I'd like the dist/bdgenomics.adam-0.23.0-SNAPSHOT.tar.gz to be part of the release. I can then download the release, use pip install to install the python package as well as install the packages for R etc..

@heuermh heuermh modified the milestone: 0.23.0 Sep 1, 2017
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 Nov 6, 2017
fnothaft added a commit to fnothaft/adam that referenced this issue Nov 7, 2017
@heuermh heuermh closed this in #1765 Nov 7, 2017
heuermh added a commit that referenced this issue Nov 7, 2017
@heuermh heuermh added this to Completed in Release 0.23.0 Jan 4, 2018
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