travis: update Miniconda to 4.3.21

[mbargull]

Error reported by @nsoranzo:

I think something broke bioconda-utils lint (and probably more): https://travis-ci.org/bioconda/bioconda-recipes/jobs/295247753

The reason is that pytz was changed to be a noarch: python package but for Bioconda Miniconda 4.2.12 has been used as the starting point on Travis. noarch: python support is a conda 4.3 things hence pytz=2017.3=1 somehow wasn't correctly installed by conda 4.2.12 when trying to update itself.

conda ==4.3.21 is specified in bioconda_utils-requirements.txt. So, I guess it might be ok to use Miniconda 4.3.21 for Travis?

[mbargull]

noarch: python change for pytz happend in conda-forge/pytz-feedstock#13

[mbargull]

Just checked locally (Linux) which packages get installed:

# packages in environment at /home/maba/code/miniconda3-4.2.12:
#
conda                     4.2.12                   py35_0
conda-env                 2.6.0                         0
openssl                   1.0.2j                        0
pip                       8.1.2                    py35_0
pycosat                   0.6.1                    py35_1
pycrypto                  2.6.1                    py35_4
python                    3.5.2                         0
readline                  6.2                           2
requests                  2.11.1                   py35_0
ruamel_yaml               0.11.14                  py35_0
setuptools                27.2.0                   py35_0
sqlite                    3.13.0                        0
tk                        8.5.18                        0
wheel                     0.29.0                   py35_0
xz                        5.2.2                         0
yaml                      0.1.6                         0
zlib                      1.2.8                         3

# packages in environment at /home/maba/code/miniconda3-4.3.21:
#
asn1crypto                0.22.0                   py36_0
cffi                      1.10.0                   py36_0
conda                     4.3.21                   py36_0
conda-env                 2.6.0                         0
cryptography              1.8.1                    py36_0
idna                      2.5                      py36_0
libffi                    3.2.1                         1
openssl                   1.0.2l                        0
packaging                 16.8                     py36_0
pip                       9.0.1                    py36_1
pycosat                   0.6.2                    py36_0
pycparser                 2.17                     py36_0
pyopenssl                 17.0.0                   py36_0
pyparsing                 2.1.4                    py36_0
python                    3.6.1                         2
readline                  6.2                           2
requests                  2.14.2                   py36_0
ruamel_yaml               0.11.14                  py36_1
setuptools                27.2.0                   py36_0
six                       1.10.0                   py36_0
sqlite                    3.13.0                        0
tk                        8.5.18                        0
wheel                     0.29.0                   py36_0
xz                        5.2.2                         1
yaml                      0.1.6                         0
zlib                      1.2.8                         3

So Miniconda 4.3.21 uses python=3.6 but I guess that should be fine since it should be downgraded by

conda install -y --file bioconda_utils/bioconda_utils-requirements.txt

EDIT: ok, all build logs show successful downgrade to python=3.5.2!

[daler]

I don't think it's a bad thing to update the miniconda to use the version of conda we're already using. However I'm not sure it will solve the problem -- the travis error is happening after the env is updated to conda 4.3, and pytz appears to be installed: https://travis-ci.org/bioconda/bioconda-recipes/jobs/295247753#L736. I'm unable to reproduce locally using:

./simulate-travis.py --bootstrap /tmp/minconda --overwrite
/tmp/miniconda/bin/bioconda-utils lint recipes config.yml --git-range HEAD

Maybe there's something temporarily strange on travis? There are other errors I can't explain in recent builds:

https://travis-ci.org/bioconda/bioconda-recipes/jobs/295191691
https://travis-ci.org/bioconda/bioconda-recipes/jobs/295053232
https://travis-ci.org/bioconda/bioconda-recipes/jobs/295225731

[mbargull]

The problem is that pytz got installed by conda 4.2.12. If you do a conda update conda for conda 4.2.12 it will get pulled in as a dependency and will be installed in a broken state. If you the force re-install it with conda 4.3.21 the problem goes away.
I could successfully reproduce this locally.

[mbargull]

The logs

https://travis-ci.org/bioconda/bioconda-recipes/jobs/295053232
https://travis-ci.org/bioconda/bioconda-recipes/jobs/295225731

could show the same error as the one reported by @nsoranzo. But it is indeed strange that they are truncated.. The other log, well, even more strange oO.

Nonetheless the reasons why those logs are truncated are unrelated to the fact that the error was caused by the pytz noarch:python update.

[mbargull]

Go ahead and merge this as well as bioconda/bioconda-recipes#6555 as soon as you see fit 😉

[daler]

@mbargull I see, so Miniconda bump should fix this then.

I can now reproduce. I had a working version of pytz that wasn't updated, but removing the install dir and re-installing let me reproduce. ./simulate-travis.py --overwrite should really do a complete removal of the directory. After that, bumping Miniconda version in bioconda-recipes/.travis.yml fixed the problem locally.

Sorry being slow, still waiting for caffeine to percolate through my system . . .

I'll merge them both. Thanks!

[mbargull]

May the power of caffeine be with you! Thanks for merging.

[bgruening]

Thanks all for fixing this!