New release including fix for qa script in Python 3?

[jrderuiter]

I am getting the following error in the qa script in Python 3 using version 0.7.2:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/Julian/Anaconda/envs/imfusion-dev/lib/python3.5/site-packages/HTSeq/scripts/qa.py", line 148
    print i, "reads processed"
          ^
SyntaxError: Missing parentheses in call to 'print'

I saw that this issue was fixed in a recent commit. Will there be a new version that includes this fix?

[yhoogstrate]

Is it possible there is an old installation of the HTSeq library present? I don't think this error can be produced with the current version of HTSeq (https://github.com/simon-anders/htseq/blob/master/python3/HTSeq/scripts/qa.py#L145) - print() seems to be applied appropriately over the entire file

[iosonofabio]

Thanks Julian, that's a known regression that I fixed but not yet made a release for. Will try this week...

On May 1, 2017 1:37:11 AM PDT, Julian de Ruiter notifications@github.com wrote:

I am getting the following error in the qa script in Python 3 using version 0.7.2:

Traceback (most recent call last):
 File "<stdin>", line 1, in <module>
File
"/Users/Julian/Anaconda/envs/imfusion-dev/lib/python3.5/site-packages/HTSeq/scripts/qa.py",
line 148
   print i, "reads processed"
         ^
SyntaxError: Missing parentheses in call to 'print'

I saw that this issue was fixed in a recent commit. Will there be a new version that includes this fix?

-- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/simon-anders/htseq/issues/24

[jrderuiter]

@iosonofabio That would be great! Are you also planning to supply wheels for HTSeq? That would make HTSeq easier and faster to install for many people. (HTSeq is currently my only dependency that doesn't have a wheel and takes long to install in a CI environment.)

[iosonofabio]

I tried and failed for now. Wheels don't really support Linux which is my OS, and pysam does not offer Windows wheels either, so until pysam starts supporting it we probably won't either.

But if you want to try implementing it yourself, please keep me posted! Ideally we would have an AppVeyor CI that runs​and makes wheels as well :-)

On May 2, 2017 12:26:09 AM PDT, Julian de Ruiter notifications@github.com wrote:

@iosonofabio That would be great! Are you also planning to supply wheels for HTSeq? That would make HTSeq easier and faster to install for many people.

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[iosonofabio]

Sorry I forgot: another way to make installation faster and easier for people is non-wheel binaries, e.g. from your Linux distribution, Homebrew/macports, Conda, or whatever. But it's hard for me to cover all those cases...

On May 2, 2017 12:26:09 AM PDT, Julian de Ruiter notifications@github.com wrote:

@iosonofabio That would be great! Are you also planning to supply wheels for HTSeq? That would make HTSeq easier and faster to install for many people.

-- You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub: https://github.com/simon-anders/htseq/issues/24#issuecomment-298524531

[jrderuiter]

I have already added the most recent release in bioconda: https://github.com/bioconda/bioconda-recipes/pull/4571.

[iosonofabio]

Awesome thanks! Does that cover both Python 2 and 3?

On May 4, 2017 7:46:50 AM PDT, Julian de Ruiter notifications@github.com wrote:

I have already added the most recent release in bioconda: https://github.com/bioconda/bioconda-recipes/pull/4571

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[jrderuiter]

Jep! (Except for the qa script in Python 3, which is why I was asking about a new release!) Currently bioconda builds for Python 2.7, 3.4 and 3.5 I think.

[iosonofabio]

Great thanks, does bioconda provide binaries for OSX?

On May 4, 2017 12:53:32 PM PDT, Julian de Ruiter notifications@github.com wrote:

Jep! (Except for the qa script in Python 3, which is why I was asking about a new release!) Currently bioconda builds for Python 2.7, 3.4 and 3.5 I think.

-- You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub: https://github.com/simon-anders/htseq/issues/24#issuecomment-299291239

[yhoogstrate]

Yes, they do (https://travis-ci.org/bioconda/bioconda-recipes/jobs/227564351)

[iosonofabio]

qa script is fixed in 0.8.0, wheels is under way and another issue altogether