NESTML dependency astropy not happy with new numpy

This issue was found in current 23.09-rc when trying NESTML (py-nestml), but is related to an upstream dependency. Maybe this can be solved by downgrading py-numpy, but developers are notified in issue https://github.com/nest/nestml/issues/967 to fix the root of the problem.

File /srv/main-spack-instance-2309/spack/var/spack/environments/ebrains-23-09/.spack-env/view/lib/python3.8/site-packages/astropy/units/quantity_helper/function_helpers.py:126
    118 UNSUPPORTED_FUNCTIONS |= {np.linalg.slogdet}
    120 # The following are not just unsupported, but so unlikely to be thought
    121 # to be supported that we ignore them in testing.  (Kept in a separate
    122 # variable so that we can check consistency in the test routine -
    123 # test_quantity_non_ufuncs.py)
    124 IGNORED_FUNCTIONS = {
    125     # Deprecated
--> 126     np.asscalar,
    127     # I/O - useless for Quantity, since no way to store the unit.
    128     np.save, np.savez, np.savetxt, np.savez_compressed,
    129     # Polynomials
    130     np.poly, np.polyadd, np.polyder, np.polydiv, np.polyfit, np.polyint,
    131     np.polymul, np.polysub, np.polyval, np.roots, np.vander,
    132     # financial
    133     np.fv, np.ipmt, np.irr, np.mirr, np.nper, np.npv, np.pmt, np.ppmt,
    134     np.pv, np.rate}
    135 if NUMPY_LT_1_18:
    136     IGNORED_FUNCTIONS |= {np.rank}

File /srv/main-spack-instance-2309/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-10.3.0/py-numpy-1.23.5-rm3niouf5xjbvqy74ubkcuewixomy5ds/lib/python3.8/site-packages/numpy/__init__.py:311, in __getattr__(attr)
    308     from .testing import Tester
    309     return Tester
--> 311 raise AttributeError("module {!r} has no attribute "
    312                      "{!r}".format(__name__, attr))

AttributeError: module 'numpy' has no attribute 'asscalar'

added test-error label

Updating to py-astropy@5.1 should fix it. It needed a small edit to the py-astropy Spack package because a (very) specific py-cython version was required for 5.1, I relaxed the version range a bit to allow the update, let's hope that's OK.

Can you check in the lab-int, in the EBRAINS-test kernel?

@terhorst did you get a chance to test that? should I update the rc?

Hey, yes that works! This specific error goes away, but now I get a different one. :/

Seems there is a dependency definition missing in py-nestml package.

WARNING:root:PyGSL is not available. The stiffness test will be skipped.
WARNING:root:Error when importing: No module named 'pygsl'

I'm trying to reach the developers directly for a faster interaction than issues and mails... I know they can fix it the minute they see it.

ok, thanks :) maybe when adding the missing dependency, you could also add whatever tests you are running as installation-time tests (to catch this kind of issues next time)?

Yes, we already started discussing if the test could be prepared as a wf- example, but it might require a bit more extras so not for this release. We'll first recheck all dependencies are defined, then look at implementing the test. It requires at least two files to be available at test time, should those go into this repo?!

it depends, but normally that should not be necessary.. where are the files stored now?

mentioned in merge request !444 (merged)

mentioned in merge request !447 (merged)

mentioned in commit f1ad0f76

closed with merge request !447 (merged)

reopened

@terhorst this specific issue was solved with !443 (merged). Could you open a new issue to keep track of any other problems with the wf- example?

closed