numpy package requirements

[jnyhuis]

python 2.7.3

I was trying to install pyDNase using pip, and it was erroring out on the numpy version. While numpy was installed, pyDNase was failing the numpy requirement.

I corrected the issue with: pip install numpy --upgrade, which brought numpy to version 1.7.1 after which pyDNase installed normally.

It would be nice if you listed your numpy version requirement in your docs.

for reference:

[root@lebowski ~]# pip install numpy
Requirement already satisfied (use --upgrade to upgrade): numpy in /net/lebowski/vol1/sw/python/2.7.3/lib/python2.7/site-packages
Cleaning up...
[root@lebowski ~]# pip install pyDNase
Downloading/unpacking pyDNase
Downloading pyDNase-0.1.2.tar.gz (201kB): 201kB downloaded
Running setup.py egg_info for package pyDNase
Traceback (most recent call last):
File "", line 16, in
File "/tmp/pip_build_root/pyDNase/setup.py", line 9, in
raise ImportError("Due to a quirk with pip, pyDNase requires numpy to be installed before starting setup")
ImportError: Due to a quirk with pip, pyDNase requires numpy to be installed before starting setup
Complete output from command python setup.py egg_info:
Traceback (most recent call last):

File "", line 16, in

File "/tmp/pip_build_root/pyDNase/setup.py", line 9, in

raise ImportError("Due to a quirk with pip, pyDNase requires numpy to be installed before starting setup")

ImportError: Due to a quirk with pip, pyDNase requires numpy to be installed before starting setup

---

Cleaning up...
Command python setup.py egg_info failed with error code 1 in /tmp/pip_build_root/pyDNase
Storing complete log in /root/.pip/pip.log

Thanks Much!
John N.

[jpiper]

Hi John,

I'll have to go through and work out which version of NumPy is required - I never actually tested how far you can go back before it breaks! I imagine this is also a bit of dependency hell, as scipy depends on NumPy to compile, so these will be linked.

I haven't actually hardcoded a numpy version into the NumPy install checker (it just attempts to import numpy, and raises that error if it fails to), which makes your bug report confusing, as NumPy should have imported if it was a valid install of any version. Do you happen to know if your old NumPy install was still working?

Jason

[jnyhuis]

Well, none of the informatics staff (who use python daily) reported numpy as broken, so I assume it was working... :-)
Sorry, I failed to pull the numpy version we were using before the upgrade, and I don't think pip logs the old version number during an upgrade.

Thanks,
John Nyhuis
IT Manager, Stam Lab
2211 Elliott Avenue
6th Floor, 6S139
Seattle, WA 98121
O: (206)-267-1097 ext 220
F: (206)-441-3033

On 12/10/2013 01:07 AM, Jason Piper wrote:

Hi John,

I'll have to go through and work out which version of NumPy is required - I never actually tested how far you can go back before it breaks! I
imagine this is also a bit of dependency hell, as scipy depends on NumPy to compile, so these will be linked.

I haven't actually hardcoded a numpy version into the NumPy install checker (it just attempts to import numpy, and raises that error if it fails
to), which makes your bug report confusing, as NumPy should have imported if it was a valid install of any version. Do you happen to know if
your old NumPy install was still working?

Jason

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Reply to this email directly or view it on GitHub #3 (comment).

[jpiper]

Thanks for the extra info John - I'll try and see if I can break pyDNase with some old NumPy installs, although I've had some other people look at the code and we're not sure what would cause it, so this may be unreproducible.

Barring this little hiccup, I hope you've managed to get everything up and running. If you need any more help with anything pyDNase/Wellington related (or if anyone in the lab has any questions), feel free to raise an issue here, or email me directly on j.piper@warwick.ac.uk

J

[jpiper]

Unable to reproduce.