Running Tests about piff

[rmjarvis]

My best guess is that you have python <= 2.7.8. There was a bug related to this that was fixed in python 2.7.9.

[jmeyers314]

Sounds like you're also missing the nosetests package. You should be able to install this via pip install nose, or if you're using Anaconda python, conda install nose.

@rmjarvis, is it worth adding nose to requirements.txt? It's not strictly required outside of tests I suppose, but I think it's unlikely to cause problems if we do add it.

[rmjarvis]

I think technically, that kind of thing should be in a dev-requirements.txt file.

cf. http://setupext-pip.readthedocs.io/en/latest/requirements-files.html

I have no objection to adding it there.

[areshernandez]

I was using the version of python that came with my mac (which was 2.7.6). I installed python version 2.7.13 from the python website. It seems that Galsim and other python packages from my old python did not migrate to the new version of python I just installed.

If I decide to install Galsim (and all of the python packages it requires) again is there anything I have to do when re-installing it to make sure it will install on python 2.7.13 rather than the old 2.7.6 (which already has Galsim)? Alternatively, is there a way to automatically migrate all of the python packages I have from python 2.7.6 (which came with my mac) to the new version of python I just installed?

[aaronroodman]

Ares, you need to have your PYTHONPATH (and PATH) setup to point to the version of python you are using Aaron

[rmjarvis]

Yes, the PYTHONPATH environment variable should be set correctly.

And you will need to reinstall all the various packages you need. numpy, fitsio, astropy, etc. Using pip is usually a good way to go with that, since many of the more popular packages have binary installations, so it's not usually too onerous to install them.

While you're at it, install nose as well, so you can use nosetests to run the tests.

[areshernandez]

Galsim, Piff, and Nose packages are successfully installed. I ran the nosetests for Piff. It mostly worked but it failed one test out of 56. Specifically,

FAIL: Initial simple test of Gaussian, Kolmogorov, and Moffat PSFs.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/areshernandez/lsstsw/miniconda/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/Users/areshernandez/Piff-master/tests/piff_test_helper.py", line 78, in f2
    result = f(*args, **kwargs)
  File "/Users/areshernandez/Piff-master/tests/test_gsobject_model.py", line 189, in test_simple
    np.testing.assert_allclose(fit.params[2], g2, rtol=0, atol=1e-6)
  File "/Users/areshernandez/lsstsw/miniconda/lib/python2.7/site-packages/numpy/testing/utils.py", line 1392, in assert_allclose
    verbose=verbose, header=header)
  File "/Users/areshernandez/lsstsw/miniconda/lib/python2.7/site-packages/numpy/testing/utils.py", line 739, in assert_array_compare
    raise AssertionError(msg)
AssertionError: 
Not equal to tolerance rtol=0, atol=1e-06

(mismatch 100.0%)
 x: array(-0.16999878078849628)
 y: array(-0.17)

It seems that this failure was due to something being only slightly off (but out of the strict tolerance range it had). Do you have an idea as to why this test failed? Have you encountered this nosetest failure before?

[rmjarvis]

Do you have an idea as to why this test failed?

Yes. This was related to a change in the precision of some GalSim operations. I ran into this and fixed it on branch alternate_wcs, currently in PR. If you want to install that branch, feel free. Or just ignore this error, since it will eventually be merged into master.

[areshernandez]

After installing Piff on my personal laptop I tried installing it on my work computer as well. I tried to do it using the LSST stack method. I ran (in my home directory):

git clone https://github.com/lsst/lsstsw.git
cd lsstsw
./bin/deploy

I confirmed that a new lsstsw directory appeared in my home directory, as expected. However, something went wrong when I used "./bin/deploy." It gave me this error:

Output written on eups.pdf (43 pages, 351429 bytes).
Transcript written on eups.log.
Running latex2html
/bin/sh: latex2html: command not found
latex2html failed; writing dummy eups.html
make[1]: Leaving directory `/afs/slac.stanford.edu/u/ec/aresh/lsstsw/sources/eups-2.1.3/doc'
cp Makefile README  Release_Notes gpl.txt "/u/ec/aresh/lsstsw/eups/2.1.3"
echo "`env EUPS_DIR=. PYTHONPATH=python bin/eups --version 2>&1 | awk '/Version/ {print $3}'`" > "/u/ec/aresh/lsstsw/eups/2.1.3/git.version"
Remember to source /u/ec/aresh/lsstsw/eups/2.1.3/bin/setups.{c,z,}sh
::: Making eups 2.1.3 the default
::: Deploying manifest.remap
::: Deploying versiondb
Cloning into 'versiondb'...
remote: Counting objects: 117813, done.
remote: Compressing objects: 100% (325/325), done.
remote: Total 117813 (delta 252), reused 253 (delta 100), pack-reused 117388
Receiving objects: 100% (117813/117813), 57.73 MiB | 18.86 MiB/s, done.
Resolving deltas: 100% (108096/108096), done.
fatal: fsync error on '/afs/slac.stanford.edu/u/ec/aresh/lsstsw/versiondb/.git/objects/pack/tmp_pack_5JldJf': Disk quota exceeded
fatal: index-pack failed

I'm not sure what went wrong. It said "disk quota exceeded." Does that mean there was not enough room remaining on the computer for something from lsst?

[cpadavis]

afs at slac has a pretty small limit, like hundreds of megs or maybe one gig. Do you have access to any of the nfs disks? If so, I would put as much stuff there as possible. I'll be in tomorrow and we can chat about this in person if you need more help.

…

On Thu, Jun 29, 2017 at 21:28 Ares Hernandez ***@***.***> wrote: After installing Piff on my personal laptop I tried installing it on my work computer as well. I tried to do it using the LSST stack method. I ran (in my home directory): git clone https://github.com/lsst/lsstsw.git cd lsstsw ./bin/deploy I confirmed that a new lsstsw directory appeared in my home directory, as expected. However, something went wrong when I used "./bin/deploy." It gave me this error: Output written on eups.pdf (43 pages, 351429 bytes). Transcript written on eups.log. Running latex2html /bin/sh: latex2html: command not found latex2html failed; writing dummy eups.html make[1]: Leaving directory `/afs/slac.stanford.edu/u/ec/aresh/lsstsw/sources/eups-2.1.3/doc' cp Makefile README Release_Notes gpl.txt "/u/ec/aresh/lsstsw/eups/2.1.3" echo "`env EUPS_DIR=. PYTHONPATH=python bin/eups --version 2>&1 | awk '/Version/ {print $3}'`" > "/u/ec/aresh/lsstsw/eups/2.1.3/git.version" Remember to source /u/ec/aresh/lsstsw/eups/2.1.3/bin/setups.{c,z,}sh ::: Making eups 2.1.3 the default ::: Deploying manifest.remap ::: Deploying versiondb Cloning into 'versiondb'... remote: Counting objects: 117813, done. remote: Compressing objects: 100% (325/325), done. remote: Total 117813 (delta 252), reused 253 (delta 100), pack-reused 117388 Receiving objects: 100% (117813/117813), 57.73 MiB | 18.86 MiB/s, done. Resolving deltas: 100% (108096/108096), done. fatal: fsync error on '/afs/slac.stanford.edu/u/ec/aresh/lsstsw/versiondb/.git/objects/pack/tmp_pack_5JldJf': Disk quota exceeded fatal: index-pack failed I'm not sure what went wrong. It said "disk quota exceeded." Does that mean there was not enough room remaining on the computer for something from lsst? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#52 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABsw5J5u4IhbUhRGzO5dB_l2qinCyWS0ks5sJAjjgaJpZM4OAVgM> .

[jmeyers314]

There's a GalSim installation at slac at /nfs/slac/g/ki/ki19/jmeyers3/src/GalSim/. If you add

export PATH=/nfs/slac/g/ki/ki19/jmeyers3/miniconda2/bin:$PATH
source eups-setups.sh
setup galsim

to your .bash_profile, I think it should work. I too will be in tomorrow for potential debugging if that doesn't do it.

[rmjarvis]

I'm not sure what any of this has to do with Piff. Piff doesn't require the lsst stack. Aside from GalSim, you should be able to get all dependencies of Piff installed with pip install piff. (And GalSim will soon be similarly installable...)