Closed eldond closed 4 years ago
@orso82 I don't know what to do about the travis failure. It looks like a netcdf4 installation problem, or something. Not sure.
@orso82 Do you have any suggestions for how to fix this?
Not sure. Something must have changed on the Travis side. Perhaps we can try to lock the version of NetCDF4 in the setup.py script https://github.com/gafusion/omas/blob/master/setup.py to a previous version.
just having Cython version x.y installed on your system is entirely irrelevant if a certain package that you install was built with an older Cython version that has a bug.
https://github.com/cython/cython/issues/1953#issuecomment-398128940
This failed run has
Collecting netCDF4 (from omas==0.55.2)
Downloading https://files.pythonhosted.org/packages/bf/da/79d6762e0ef66f913249684122d567bddfada6b83cdf9e96c82550fd2d14/netCDF4-1.5.3-cp37-cp37m-manylinux1_x86_64.whl (4.1MB)
vs. a previous successful run:
Collecting netCDF4 (from omas==0.55.1)
Downloading https://files.pythonhosted.org/packages/bf/da/79d6762e0ef66f913249684122d567bddfada6b83cdf9e96c82550fd2d14/netCDF4-1.5.3-cp37-cp37m-manylinux1_x86_64.whl (4.1MB)
It's the same netcdf4 version
Changes to package versions between a good travis run (for #94) and now:
Merging #96 into master will increase coverage by
0.01%
. The diff coverage is100.00%
.
@@ Coverage Diff @@
## master #96 +/- ##
==========================================
+ Coverage 79.84% 79.85% +0.01%
==========================================
Files 45 45
Lines 7869 7869
==========================================
+ Hits 6283 6284 +1
+ Misses 1586 1585 -1
Impacted Files | Coverage Δ | |
---|---|---|
omas/omas_plot.py | 73.31% <100.00%> (ø) |
|
omas/omas_utils.py | 80.84% <0.00%> (+0.22%) |
:arrow_up: |
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The error we're facing is
AttributeError: type object 'netCDF4._netCDF4._MemBuf' has no attribute '__reduce_cython__'
I found https://github.com/pynbody/pynbody/issues/503:
Update: the issue was that when I updated cython, I did it using conda update. I redid it by pip install --upgrading, then I installed pynbody from GitHub, and finally, pip install --upgrade numpy. Now I can import the package without any problems. I guess the bottom line is that updating with pip works better than with conda.
MAybe that's not it.
In the travis log, I found
xarray 0.15.1 has requirement setuptools>=41.2, but you'll have setuptools 40.8.0 which is incompatible.
First mention of old setup tools is in
Requirement already satisfied: setuptools in /home/travis/virtualenv/python3.7.1/lib/python3.7/site-packages (from pint->omas==0.55.2) (40.8.0)
THANKS, NUMPY
With the partial rollback, I get this error in pip again:
xarray 0.15.1 has requirement setuptools>=41.2, but you'll have setuptools 40.8.0 which is incompatible.
So maybe I should put setuptools back. It looks like it's going to pass anyway, though.
@orso82 It's ready
@eldond cannot thank you enough 🥇