cannot import TiggerSkyModel because of astropy 2.0.4? #86

lord-blueberry · 2018-11-15T10:57:16Z

I can reproduce this behaviour in a clean 18.04 install. After adding the KERN repo, I use:

sudo apt-get install python
sudo apt-get install meqtrees
sudo apt-get install python-astropy

It installs astropy version 2.0.4-4 and meqtrees

When using the meqtree browser, turbo-sim.py fails to load tigger with the following stack trace:

Traceback (most recent call last):
  File "/usr/lib/python2.7/dist-packages/Cattery/Siamese/turbo-sim.py", line 80, in <module>
    models.insert(0,TiggerSkyModel());
  File "/usr/lib/python2.7/dist-packages/Cattery/Siamese/OMS/tigger_lsm.py", line 44, in TiggerSkyModel
    classobj = importTigger(verbose=verbose);
  File "/usr/lib/python2.7/dist-packages/Cattery/Siamese/OMS/tigger_lsm.py", line 14, in importTigger
    import Tigger.SiameseInterface
  File "/usr/lib/python2.7/dist-packages/Tigger/SiameseInterface.py", line 49, in <module>
    from Tigger.Models.Formats import ModelHTML
  File "/usr/lib/python2.7/dist-packages/Tigger/Models/Formats/ModelHTML.py", line 39, in <module>
    from Tigger.Models import SkyModel
  File "/usr/lib/python2.7/dist-packages/Tigger/Models/SkyModel.py", line 32, in <module>
    from Tigger.Coordinates import angular_dist_pos_angle,DEG
  File "/usr/lib/python2.7/dist-packages/Tigger/Coordinates.py", line 62, in <module>
    from astLib.astWCS import WCS
  File "/usr/lib/python2.7/dist-packages/astLib/astWCS.py", line 27, in <module>
    from astropy.io import fits as pyfits
  File "/usr/lib/python2.7/dist-packages/astropy/__init__.py", line 116, in <module>
    _check_numpy()
  File "/usr/lib/python2.7/dist-packages/astropy/__init__.py", line 105, in _check_numpy
    requirement_met = minversion(numpy, __minimum_numpy_version__)
  File "/usr/lib/python2.7/dist-packages/astropy/utils/introspection.py", line 156, in minversion
    from pkg_resources import parse_version
  File "/usr/lib/python2.7/dist-packages/pkg_resources/__init__.py", line 50, in <module>
    from pkg_resources.extern import six
  File "/usr/lib/python2.7/dist-packages/pkg_resources/extern/__init__.py", line 44, in load_module
    mod = sys.modules[extant]
AttributeError: 'NoneType' object has no attribute 'modules'

This seems related to the issue reported here: ratt-ru/tigger#74 . But now with astropy/numpy as the culprit, as far as I can tell.

I've found an ugly hack for init.py, which is inserting import sys to line 43. It "fixes" the issue in pkg_resources, but fails later on the astropy package with the trace:

Traceback (most recent call last):
  File "/usr/lib/python2.7/dist-packages/Cattery/Siamese/turbo-sim.py", line 80, in <module>
    models.insert(0,TiggerSkyModel());
  File "/usr/lib/python2.7/dist-packages/Cattery/Siamese/OMS/tigger_lsm.py", line 44, in TiggerSkyModel
    classobj = importTigger(verbose=verbose);
  File "/usr/lib/python2.7/dist-packages/Cattery/Siamese/OMS/tigger_lsm.py", line 14, in importTigger
    import Tigger.SiameseInterface
  File "/usr/lib/python2.7/dist-packages/Tigger/SiameseInterface.py", line 49, in <module>
    from Tigger.Models.Formats import ModelHTML
  File "/usr/lib/python2.7/dist-packages/Tigger/Models/Formats/ModelHTML.py", line 39, in <module>
    from Tigger.Models import SkyModel
  File "/usr/lib/python2.7/dist-packages/Tigger/Models/SkyModel.py", line 32, in <module>
    from Tigger.Coordinates import angular_dist_pos_angle,DEG
  File "/usr/lib/python2.7/dist-packages/Tigger/Coordinates.py", line 62, in <module>
    from astLib.astWCS import WCS
  File "/usr/lib/python2.7/dist-packages/astLib/astWCS.py", line 27, in <module>
    from astropy.io import fits as pyfits
  File "/usr/lib/python2.7/dist-packages/astropy/__init__.py", line 287, in <module>
    log = _init_log()
  File "/usr/lib/python2.7/dist-packages/astropy/logger.py", line 100, in _init_log
    log._set_defaults()
  File "/usr/lib/python2.7/dist-packages/astropy/logger.py", line 484, in _set_defaults
    self.disable_warnings_logging()
  File "/usr/lib/python2.7/dist-packages/astropy/logger.py", line 253, in disable_warnings_logging
    if warnings.showwarning != self._showwarning:
AttributeError: 'NoneType' object has no attribute 'showwarning'

Something seems royally screwed. Did I install everything correctly?

The text was updated successfully, but these errors were encountered:

o-smirnov · 2018-11-17T11:58:50Z

Yeah it does smell like ratt-ru/tigger#74. @gijzelaerr @sjperkins any comments? This is some kind of python2/3 shizzle going badly wrong.

Feeling very astropy-irritated just now 😠 See this too: ratt-ru/montblanc#261

sjperkins · 2018-11-17T12:04:05Z

See my comments in the montblanc issue

…

On Sat, 17 Nov 2018, 13:58 Oleg Smirnov ***@***.*** wrote: Yeah it does smell like ratt-ru/tigger#74 <ratt-ru/tigger#74>. @gijzelaerr <https://github.com/gijzelaerr> @sjperkins <https://github.com/sjperkins> any comments? This is some kind of python2/3 shizzle going badly wrong. Feeling very astropy-irritated just now 😠 See this too: ratt-ru/montblanc#261 <ratt-ru/montblanc#261> — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#86 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ADXd5HANE4-kHTev1AFged4nQOUM_jHuks5uv_n8gaJpZM4Yfjqa> .

o-smirnov · 2018-11-19T13:41:05Z

Actually it's this issue here again: ratt-ru/meqtrees-timba#34

The 18.04 version of astropy obviously pulls in pkg_resources, which somehow triggers the bug. Gawd I hate this setuptools shizzle. In fact, looking at the current astropy code, looks like they share my high esteem of it, because they've taken that crap out: https://github.com/astropy/astropy/blob/master/astropy/utils/introspection.py

Question is @gijzelaerr, can we still ship a compatible astropy in KERN-4? The latest version is Python3-only...

o-smirnov · 2018-11-19T14:06:04Z

@lord-blueberry, could you give it a go with the issue-7 branch of https://github.com/ska-sa/tigger-lsm?

git clone https://github.com/ska-sa/tigger-lsm -b issue-7
Add the cloned tigger-lsm directory to the front of your PYTHONPATH

If this works for you, we can push out a new release.

lord-blueberry · 2018-12-02T10:30:46Z

Finally got around to it: Almost there. But the tigger-lsm issue-7 fails to import the Tigger package with this error

Traceback (most recent call last):
  File "/usr/lib/python2.7/dist-packages/Cattery/Siamese/turbo-sim.py", line 89, in <module>
    models.insert(0,TiggerSkyModel());
  File "/usr/lib/python2.7/dist-packages/Cattery/Siamese/OMS/tigger_lsm.py", line 42, in TiggerSkyModel
    classobj = importTigger(verbose=verbose);
  File "/usr/lib/python2.7/dist-packages/Cattery/Siamese/OMS/tigger_lsm.py", line 13, in importTigger
    import Tigger.SiameseInterface
  File "Tigger/SiameseInterface.py", line 46, in <module>
    from Tigger.Models.Formats import ModelHTML
  File "Tigger/Models/Formats/ModelHTML.py", line 29, in <module>
    from html.parser import HTMLParser
ImportError: No module named html.parser

AFAIK html.parser is a python3 package, but I run it from python2. Or is this a package from Cattery missing?

gijzelaerr · 2018-12-02T12:04:37Z

i'll fix this next week.

twillis449 · 2018-12-18T17:43:51Z

I seem to be hitting the tigger-lsm issue myself. I'm not sure if astropy is the culprit. I deleted astropy from my ubuntu 16.04 system and I still get the error message:

Failure to import TiggerSkyModel module
Is the location of Tigger defined in your PYTHONPATH environment variable?

(I still had a version of pyfits in my system so fits calls were still handled OK.)

gijzelaerr · 2018-12-19T07:52:44Z

working on these issues as we speak, I hope the situation is solved soon.

gijzelaerr · 2018-12-20T14:44:39Z

This is probably because for some package the name used to request the version number from pkg_resources doesn't match the package name. Some package had to be renamed (like tigger to astro-tigger) since they already existed on pypi.

gijzelaerr · 2018-12-21T11:21:39Z

This should be solved with the release of tigger-lsm 1.5.0 https://github.com/ska-sa/tigger-lsm/releases/tag/1.5.0 and kittens 1.4.0 https://github.com/ska-sa/kittens/releases/tag/v1.4.0.

please let me know if you still experience issues.

bmerry · 2019-03-05T07:53:25Z

@gijzelaerr I'm using KERN-4 and running into this issue. Is it expected to work there or do I need to upgrade to KERN-5?

gijzelaerr · 2019-03-05T08:00:29Z

It is not expected to work with KERN-4, if you can switch to KERN-5.

o-smirnov mentioned this issue Nov 19, 2018

defer import of astropy & co until necessary ratt-ru/tigger-lsm#7

Closed

gijzelaerr self-assigned this Dec 2, 2018

gijzelaerr closed this as completed Dec 21, 2018

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cannot import TiggerSkyModel because of astropy 2.0.4? #86

cannot import TiggerSkyModel because of astropy 2.0.4? #86

lord-blueberry commented Nov 15, 2018

o-smirnov commented Nov 17, 2018

sjperkins commented Nov 17, 2018 via email

o-smirnov commented Nov 19, 2018

o-smirnov commented Nov 19, 2018

lord-blueberry commented Dec 2, 2018

gijzelaerr commented Dec 2, 2018

twillis449 commented Dec 18, 2018

gijzelaerr commented Dec 19, 2018

gijzelaerr commented Dec 20, 2018 •

edited

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gijzelaerr commented Dec 21, 2018

bmerry commented Mar 5, 2019

gijzelaerr commented Mar 5, 2019

cannot import TiggerSkyModel because of astropy 2.0.4? #86

cannot import TiggerSkyModel because of astropy 2.0.4? #86

Comments

lord-blueberry commented Nov 15, 2018

o-smirnov commented Nov 17, 2018

sjperkins commented Nov 17, 2018 via email

o-smirnov commented Nov 19, 2018

o-smirnov commented Nov 19, 2018

lord-blueberry commented Dec 2, 2018

gijzelaerr commented Dec 2, 2018

twillis449 commented Dec 18, 2018

gijzelaerr commented Dec 19, 2018

gijzelaerr commented Dec 20, 2018 • edited Loading

gijzelaerr commented Dec 21, 2018

bmerry commented Mar 5, 2019

gijzelaerr commented Mar 5, 2019

gijzelaerr commented Dec 20, 2018 •

edited

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