testing numpy 1.16.4 as minimal pin to pass travis

[turbach]

Minimal pin to get fitgrid 0.4.4.X to pass

During testing the unpinned environment I installed the i-rkernel, which downgraded pbdzmq and zeromzq and pytest started passing.

I don't know what's causing the problem, but pinning numpy<=1.16.4 is sufficient to get pytest passing again and numpy==1.16.5 fails.

1.16.5 is a bright line for numpy, the last series to support Python 2.7 and only good for 3.5-3.7

https://numpy.org/devdocs/release/1.16.5-notes.html

So for fitgrid, 4.X.Y just maintenance patches for Python 3.5-3.7 for now.

The next series can work to Python 3.8

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Here is the sequence ...

Additions and downgrades that allowed fitgrid pytest pass

2019-09-16 07:02:47  (rev 2)
     openssl  {1.1.1c -> 1.1.1d}
     pyzmq  {18.1.0 -> 17.1.2}
     zeromq  {4.3.1 -> 4.2.5}
    +r-base64enc-0.1_3
    +r-evaluate-0.13
    +r-htmltools-0.3.6
    +r-irdisplay-0.7.0
    +r-irkernel-0.8.15
    +r-jsonlite-1.6
    +r-pbdzmq-0.3_3
    +r-repr-0.19.2
    +r-uuid-0.1_2

Could be an addition that filled in a missing dependency or the zeromq related downgrades

First (unlikely) thing to check is a missing dependency

Candidates ... all missing from default fitgrid_compat environment

• r-repr # import rbase64enc
• r-base64enc
• r-pdbzmq # big data zmq wrapper
• r-evaluate r/noarch::r-evaluate-0.13-r36h6115d3f_0
• r-uuid r/linux-64::r-uuid-0.1_2-r36h96ca727_4
• r-irkernel r/noarch::r-irkernel-0.8.15-r36_0
• r-irdisplay r/noarch::r-irdisplay-0.7.0-r36h6115d3f_0

Test 1

conda install -c r r-base64enc

The following NEW packages will be INSTALLED:

r-base64enc        r/linux-64::r-base64enc-0.1_3-r36h96ca727_4

pytest FAILED

Test 2

conda install -c r r-repr

The following NEW packages will be INSTALLED:

 r-htmltools        r/linux-64::r-htmltools-0.3.6-r36h29659fb_0
 r-jsonlite         r/linux-64::r-jsonlite-1.6-r36h96ca727_0
 r-repr             r/noarch::r-repr-0.19.2-r36h6115d3f_0

pytest FAILED

Test 3

conda install -c r r-pbdzmq 

The following NEW packages will be INSTALLED:

libsodium          pkgs/main/linux-64::libsodium-1.0.16-h1bed415_0
r-pbdzmq           r/linux-64::r-pbdzmq-0.3_3-r36h29659fb_0
zeromq             pkgs/main/linux-64::zeromq-4.2.5-hf484d3e_1

pytest FAILED

Test 4

 conda install -c r r-evaluate

 The following NEW packages will be INSTALLED:

  r-evaluate         r/noarch::r-evaluate-0.13-r36h6115d3f_0

pytest FAILED

Test 5

conda install -c r r-uuid

The following NEW packages will be INSTALLED:

r-uuid             r/linux-64::r-uuid-0.1_2-r36h96ca727_4

pytest FAILED

Test 6

conda install -c r r-irkernel

The following NEW packages will be INSTALLED:

r-irdisplay        r/noarch::r-irdisplay-0.7.0-r36h6115d3f_0
r-irkernel         r/noarch::r-irkernel-0.8.15-r36_0

pytest FAILED

Interim Conclusion

Problem was not missing r-* dependencies. As expected.

Problem seems to be pyzmq and/or zeromq

Note: pyzmq and zerozmq are not in the fitgrid env by default

Test 7

conda install pyzmq

The following NEW packages will be INSTALLED:

pyzmq              pkgs/main/linux-64::pyzmq-17.1.2-py36h14c3975_0

pytest FAILED

Notes:

• comparison of fitgrid_refresh (pytests pass) with fitgrid_0.4.4.dev0 shows same versions of r-* including downgraded zero mq related python packages.

• numpy versions differ

Test 8

downgraded numpy from 1.17.2 to 1.16.4 with previously downgraded zmq friends.

numpy                     1.16.4           py36h7e9f1db_0  
numpy-base                1.16.4           py36hde5b4d6_0  

pytests PASS

Test 9

candidate minimal pin for fitgrid 0.4.4

numpy<1.17
zeromq<4.3

pytest FAILED

Note

numpy==1.16.5
zeromq==4.2.5

So zeromq<4.3 is not sufficient

Test 10

candidate minimal pin for fitgrid 0.4.4

numpy<=1.16.4

pytest PASS

Note: pinning numpy 1.16.4 also holds zeromq at 4.2.5

[codecov[bot]]

Codecov Report

Merging #157 into refresh will not change coverage. The diff coverage is n/a.

@@           Coverage Diff            @@
##           refresh     #157   +/-   ##
========================================
  Coverage    87.86%   87.86%           
========================================
  Files           14       14           
  Lines          898      898           
========================================
  Hits           789      789           
  Misses         109      109

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