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Update environment #14

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lesserwhirls opened this issue Jan 8, 2020 · 12 comments
Closed

Update environment #14

lesserwhirls opened this issue Jan 8, 2020 · 12 comments

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@lesserwhirls
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We should update our environment to mimic what is in the python-training repo. See https://github.com/Unidata/python-training/blob/master/environment.yml

@lesserwhirls
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Outside of more packages, the biggest differences between the two are that in the python-training environment:

  1. Python version is more strongly pinned
  2. No sphinx stuff
  3. pint isn't explicitly listed
  4. python-awips is pulled in

I think we just go with python-training wholesale, but possibly leaving out python-awips (I think so). Also, should we explicitly include pint? @dopplershift - what's your feeling on pint?

@dopplershift
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If you're installing MetPy, then it's going to pull in pint. Unless you're planning on doing stand-alone teaching on Pint, I'd just leave it as a transitive dependency of MetPy.

@julienchastang
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julienchastang commented Jan 8, 2020

Note that if we are going to update the conda environment, I would like to know about this, sooner rather than later -- or at least not right before the workshop. The material in this repo will get automagically propagated to the user via nbgitpuller. But that is not the case for the environment. I will actually have to build a new container, push it out, and refer to it in a configuration file. So heads up there. That said, any adjustments you wish to make can be made by a PR to the environment.yml in this repo.

Edit: I would also try to keep the environment to what is essential. That might improve kernel start time issues.

@lesserwhirls
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Julien - we will need to update the environment. I will get a PR in with that asap.

@lesserwhirls
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lesserwhirls commented Jan 8, 2020

Closed by #15

-- edit --
wrong repo! Changed python-training to pyaos-ams-2020.

@jthielen
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@julienchastang One environment-related question I had: are the current installed versions of the packages what will be present on Sunday for the workshop, or will they be updated beforehand? My notebook (#19) has some version dependence between the current MetPy v0.12 and upcoming v1.0.

@julienchastang
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Below is the latest and greatest. Metpy is at 0.12.0. Is this sufficient for your needs? Whatever we end up installing, it has to be available via a standard conda install -- or at least that is my strong preference.

# packages in environment at /opt/conda/envs/pyaos-ams-2020:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
appdirs                   1.4.3                      py_1    conda-forge
attrs                     19.3.0                     py_0    conda-forge
backcall                  0.1.0                      py_0    conda-forge
beautifulsoup4            4.8.2                    py37_0    conda-forge
bleach                    3.1.0                      py_0    conda-forge
boto3                     1.10.48                    py_0    conda-forge
botocore                  1.13.48                    py_0    conda-forge
bzip2                     1.0.8                h516909a_2    conda-forge
ca-certificates           2019.11.28           hecc5488_0    conda-forge
cartopy                   0.17.0          py37h423102d_1009    conda-forge
certifi                   2019.11.28               py37_0    conda-forge
cffi                      1.13.2           py37h8022711_0    conda-forge
cftime                    1.0.4.2          py37hc1659b7_0    conda-forge
chardet                   3.0.4                 py37_1003    conda-forge
cryptography              2.8              py37h72c5cf5_1    conda-forge
curl                      7.65.3               hf8cf82a_0    conda-forge
cycler                    0.10.0                     py_2    conda-forge
dbus                      1.13.6               he372182_0    conda-forge
decorator                 4.4.1                      py_0    conda-forge
defusedxml                0.6.0                      py_0    conda-forge
docutils                  0.15.2                   py37_0    conda-forge
entrypoints               0.3                   py37_1000    conda-forge
expat                     2.2.5             he1b5a44_1004    conda-forge
ffmpeg                    4.2                  h167e202_0    conda-forge
fontconfig                2.13.1            h86ecdb6_1001    conda-forge
freetype                  2.10.0               he983fc9_1    conda-forge
geos                      3.8.0                he1b5a44_0    conda-forge
gettext                   0.19.8.1          hc5be6a0_1002    conda-forge
glib                      2.58.3          py37h6f030ca_1002    conda-forge
gmp                       6.1.2             hf484d3e_1000    conda-forge
gnutls                    3.6.5             hd3a4fd2_1002    conda-forge
gst-plugins-base          1.14.5               h0935bb2_0    conda-forge
gstreamer                 1.14.5               h36ae1b5_0    conda-forge
hdf4                      4.2.13            hf30be14_1003    conda-forge
hdf5                      1.10.5          nompi_h3c11f04_1104    conda-forge
icu                       64.2                 he1b5a44_1    conda-forge
idna                      2.8                   py37_1000    conda-forge
importlib_metadata        1.3.0                    py37_0    conda-forge
ipykernel                 5.1.3            py37h5ca1d4c_0    conda-forge
ipython                   7.11.1           py37h5ca1d4c_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
ipywidgets                7.5.1                      py_0    conda-forge
jedi                      0.15.2                   py37_0    conda-forge
jinja2                    2.10.3                     py_0    conda-forge
jmespath                  0.9.4                      py_0    conda-forge
jpeg                      9c                h14c3975_1001    conda-forge
json5                     0.8.5                      py_0    conda-forge
jsonschema                3.2.0                    py37_0    conda-forge
jupyter                   1.0.0                      py_2    conda-forge
jupyter_client            5.3.4                    py37_0    conda-forge
jupyter_console           6.0.0                      py_0    conda-forge
jupyter_core              4.6.1                    py37_0    conda-forge
jupyterlab                1.2.4                      py_0    conda-forge
jupyterlab_server         1.0.6                      py_0    conda-forge
kiwisolver                1.1.0            py37hc9558a2_0    conda-forge
krb5                      1.16.4               h2fd8d38_0    conda-forge
lame                      3.100             h14c3975_1001    conda-forge
ld_impl_linux-64          2.33.1               h53a641e_7    conda-forge
libblas                   3.8.0               14_openblas    conda-forge
libcblas                  3.8.0               14_openblas    conda-forge
libclang                  9.0.1           default_hde54327_0    conda-forge
libcurl                   7.65.3               hda55be3_0    conda-forge
libedit                   3.1.20170329      hf8c457e_1001    conda-forge
libffi                    3.2.1             he1b5a44_1006    conda-forge
libgcc-ng                 9.2.0                h24d8f2e_1    conda-forge
libgfortran-ng            7.3.0                hdf63c60_3    conda-forge
libgomp                   9.2.0                h24d8f2e_1    conda-forge
libiconv                  1.15              h516909a_1005    conda-forge
liblapack                 3.8.0               14_openblas    conda-forge
libllvm9                  9.0.1                hc9558a2_0    conda-forge
libnetcdf                 4.7.3           nompi_h94020b1_100    conda-forge
libopenblas               0.3.7                h5ec1e0e_6    conda-forge
libpng                    1.6.37               hed695b0_0    conda-forge
libprotobuf               3.11.2               h8b12597_0    conda-forge
libsodium                 1.0.17               h516909a_0    conda-forge
libssh2                   1.8.2                h22169c7_2    conda-forge
libstdcxx-ng              9.2.0                hdf63c60_1    conda-forge
libtiff                   4.1.0                hc3755c2_3    conda-forge
libuuid                   2.32.1            h14c3975_1000    conda-forge
libxcb                    1.13              h14c3975_1002    conda-forge
libxkbcommon              0.9.1                hebb1f50_0    conda-forge
libxml2                   2.9.10               hee79883_0    conda-forge
lz4-c                     1.8.3             he1b5a44_1001    conda-forge
markupsafe                1.1.1            py37h516909a_0    conda-forge
matplotlib                3.1.2                    py37_1    conda-forge
matplotlib-base           3.1.2            py37h250f245_1    conda-forge
metpy                     0.12.0                     py_0    conda-forge
mistune                   0.8.4           py37h516909a_1000    conda-forge
more-itertools            8.0.2                      py_0    conda-forge
nbconvert                 5.6.1                    py37_0    conda-forge
nbformat                  5.0.3                      py_0    conda-forge
ncurses                   6.1               hf484d3e_1002    conda-forge
netcdf4                   1.5.3           nompi_py37hd35fb8e_102    conda-forge
nettle                    3.4.1             h1bed415_1002    conda-forge
notebook                  6.0.1                    py37_0    conda-forge
nspr                      4.24                 he1b5a44_0    conda-forge
nss                       3.47                 he751ad9_0    conda-forge
numpy                     1.17.3           py37h95a1406_0    conda-forge
olefile                   0.46                       py_0    conda-forge
openh264                  1.8.0             hdbcaa40_1000    conda-forge
openmp_impl               4.5                       0_gnu    conda-forge
openssl                   1.1.1d               h516909a_0    conda-forge
owslib                    0.19.0                     py_2    conda-forge
packaging                 20.0                       py_0    conda-forge
pandas                    0.25.3           py37hb3f55d8_0    conda-forge
pandoc                    2.9.1.1                       0    conda-forge
pandocfilters             1.4.2                      py_1    conda-forge
parso                     0.5.2                      py_0    conda-forge
pcre                      8.43                 he1b5a44_0    conda-forge
pexpect                   4.7.0                    py37_0    conda-forge
pickleshare               0.7.5                 py37_1000    conda-forge
pillow                    7.0.0            py37hefe7db6_0    conda-forge
pint                      0.10.1                     py_0    conda-forge
pip                       19.3.1                   py37_0    conda-forge
pooch                     0.7.0                      py_0    conda-forge
proj                      6.2.1                hc80f0dc_0    conda-forge
prometheus_client         0.7.1                      py_0    conda-forge
prompt_toolkit            2.0.10                     py_0    conda-forge
protobuf                  3.11.2           py37he1b5a44_0    conda-forge
pthread-stubs             0.4               h14c3975_1001    conda-forge
ptyprocess                0.6.0                   py_1001    conda-forge
pycparser                 2.19                     py37_1    conda-forge
pyepsg                    0.4.0                      py_0    conda-forge
pygments                  2.5.2                      py_0    conda-forge
pykdtree                  1.3.1           py37hc1659b7_1002    conda-forge
pyopenssl                 19.1.0                   py37_0    conda-forge
pyparsing                 2.4.6                      py_0    conda-forge
pyproj                    2.4.2.post1      py37h12732c1_0    conda-forge
pyqt                      5.12.3           py37hcca6a23_1    conda-forge
pyqt5-sip                 4.19.18                  pypi_0    pypi
pyqtwebengine             5.12.1                   pypi_0    pypi
pyrsistent                0.15.7           py37h516909a_0    conda-forge
pyshp                     2.1.0                      py_0    conda-forge
pysocks                   1.7.1                    py37_0    conda-forge
python                    3.7.6                h357f687_2    conda-forge
python-dateutil           2.8.1                      py_0    conda-forge
pytz                      2019.3                     py_0    conda-forge
pyzmq                     18.1.1           py37h1768529_0    conda-forge
qt                        5.12.5               hd8c4c69_1    conda-forge
qtconsole                 4.6.0                      py_0    conda-forge
readline                  8.0                  hf8c457e_0    conda-forge
requests                  2.22.0                   py37_1    conda-forge
s3transfer                0.2.1                    py37_0    conda-forge
scipy                     1.4.1            py37h921218d_0    conda-forge
send2trash                1.5.0                      py_0    conda-forge
setuptools                44.0.0                   py37_0    conda-forge
shapely                   1.6.4           py37h5d51c17_1007    conda-forge
siphon                    0.8.0                 py37_1002    conda-forge
six                       1.13.0                   py37_0    conda-forge
soupsieve                 1.9.4                    py37_0    conda-forge
sqlite                    3.30.1               hcee41ef_0    conda-forge
terminado                 0.8.3                    py37_0    conda-forge
testpath                  0.4.4                      py_0    conda-forge
tk                        8.6.10               hed695b0_0    conda-forge
tornado                   6.0.3            py37h516909a_0    conda-forge
traitlets                 4.3.3                    py37_0    conda-forge
urllib3                   1.25.7                   py37_0    conda-forge
wcwidth                   0.1.8                      py_0    conda-forge
webencodings              0.5.1                      py_1    conda-forge
wheel                     0.33.6                   py37_0    conda-forge
widgetsnbextension        3.5.1                    py37_0    conda-forge
x264                      1!152.20180806       h14c3975_0    conda-forge
xarray                    0.14.1                     py_1    conda-forge
xorg-libxau               1.0.9                h14c3975_0    conda-forge
xorg-libxdmcp             1.1.3                h516909a_0    conda-forge
xz                        5.2.4             h14c3975_1001    conda-forge
zeromq                    4.3.2                he1b5a44_2    conda-forge
zipp                      0.6.0                      py_0    conda-forge
zlib                      1.2.11            h516909a_1006    conda-forge
zstd                      1.4.4                h3b9ef0a_1    conda-forge

@julienchastang
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Sounds obvious, but it is worth mentioning: make sure your committed notebooks work in http://pyaos-workshop.unidata.ucar.edu/.

@dopplershift
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@jthielen 1.0 won’t be available for the workshop. If you have a critical fix I can cut 0.12.1, but that’s not planned at the moment.

@jthielen
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jthielen commented Jan 10, 2020

@julienchastang @dopplershift Thanks, that's what I needed to know! No critical fixes, I just wanted to know what level of "xarray compatibility" I should target in the notebook. I'll be sure to include the more manual broadcasting and type casting required with the current version.

@jthielen
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Although, @dopplershift if you don't mind me asking, when is the current target for 1.0? Knowing that may help re-prioritize my current work here and in MetPy (xarray compat in kinematics Unidata/MetPy#1260 / Unidata/MetPy#893 (comment), xarray compat in general functions Unidata/MetPy#1223, coordinate and projection helpers, etc.).

@dopplershift
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Hard pencils down time is Monday night (ahem early Tuesday morning).

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