Option to skip plotting wall in equilibrium_CX

[eldond]

• This is useful when trying to cycle through different limiter files
• Might not want to edit the ODS itself to put them in (keep the original in there)
• Needed to support https://github.com/gafusion/OMFIT-source/pull/4411
• Also fix sample data and close #97

[eldond]

@orso82 I don't know what to do about the travis failure. It looks like a netcdf4 installation problem, or something. Not sure.

[eldond]

@orso82 Do you have any suggestions for how to fix this?

[orso82]

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.

[eldond]

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

[eldond]

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

[eldond]

Changes to package versions between a good travis run (for #94) and now:

• boto3 changed from 1.12.18 to 1.12.27
• matplotlib changed from 3.2.0 to 3.2.1
• xarray from 0.15.0 to 0.15.1
• cftime from 1.1.0 to 1.1.1.2
• botocore from 1.15.18 to 1.15.27
• pandas 1.0.1 to 1.03

[codecov[bot]]

Codecov Report

Merging #96 into master will increase coverage by 0.01%. The diff coverage is 100.00%.

@@            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:

---

Continue to review full report at Codecov.

Legend - Click here to learn more Δ = absolute <relative> (impact), ø = not affected, ? = missing data Powered by Codecov. Last update 810660f...2aa7ab8. Read the comment docs.

[eldond]

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.

[eldond]

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)

[eldond]

THANKS, NUMPY

[eldond]

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.

[eldond]

@orso82 It's ready

[orso82]

@eldond cannot thank you enough 🥇