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pynio causes dependency conflicts in py36 CI build #3154

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crusaderky opened this issue Jul 20, 2019 · 9 comments
Closed

pynio causes dependency conflicts in py36 CI build #3154

crusaderky opened this issue Jul 20, 2019 · 9 comments

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@crusaderky
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On Saturday night, all Python 3.6 CI builds started failing. Python 3.7 is unaffected.
See https://dev.azure.com/xarray/xarray/_build/results?buildId=362&view=logs

MacOSX py36:

UnsatisfiableError: The following specifications were found to be in conflict:
  - pynio
  - python=3.6
  - rasterio

Linux py36:

UnsatisfiableError: The following specifications were found to be in conflict:
  - cfgrib[version='>=0.9.2']
  - h5netcdf
  - pynio
@HasanAhmadQ7
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I am getting a different error for linux py36

Linux py36

UnsatisfiableError: The following specifications were found to be in conflict:
  - cfgrib[version='>=0.9.2']
  - h5py
  - pynio

@shoyer
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shoyer commented Jul 21, 2019

I can reproduce this issue locally:

$ conda create -n xarray-tmp -c conda-forge python=3 pynio h5py
Collecting package metadata (current_repodata.json): done
Solving environment: failed with current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed

UnsatisfiableError: The following specifications were found to be incompatible with each other:



Package hdfeos5 conflicts for:
pynio -> hdfeos5==5.1.15=0
Package zlib conflicts for:
pynio -> zlib
python=3 -> zlib[version='1.2.*|1.2.11|1.2.8|>=1.2.11,<1.3.0a0']
Package hdfeos2 conflicts for:
pynio -> hdfeos2
Package libgfortran conflicts for:
pynio -> libgfortran[version='>=3.0,<4.0.0.a0|>=3.0.1,<4.0.0.a0']
Package libuuid conflicts for:
pynio -> libuuid[version='>=2.32.1,<3.0a0']
Package hdf5 conflicts for:
pynio -> hdf5[version='1.10.1|1.8.15.1|>=1.10.2,<1.10.3.0a0|>=1.10.4,<1.10.5.0a0|>=1.10.5,<1.10.6.0a0']
h5py -> hdf5[version='1.10.1|1.10.1.*|1.10.2.*|1.8.15.*|1.8.17.*|1.10.2.*,>=1.10.2,<1.10.3.0a0|1.8.17|1.8.17.*|1.8.18|1.8.18.*|>=1.10.2,<1.10.3.0a0|>=1.10.3,<1.10.4.0a0|>=1.10.4,<1.10.5.0a0|>=1.10.4,<1.10.5.0a0|>=1.10.4,<1.10.5.0a0',build='mpi_mpich_*|mpi_openmpi_*']
Package jpeg conflicts for:
pynio -> jpeg
Package python conflicts for:
pynio -> python[version='2.7.*|>=2.7,<2.8.0a0|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0']
h5py -> python[version='2.7.*|3.4.*|3.5.*|3.6.*|>=2.7,<2.8.0a0|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0']
Package proj4 conflicts for:
pynio -> proj4[version='4.9.3|>=4.9.3,<4.9.4.0a0|>=5.2.0,<5.2.1.0a0|>=6.0.0,<6.0.1.0a0|>=6.1.0,<6.1.1.0a0']
Package libgcc conflicts for:
pynio -> libgcc
Package krb5 conflicts for:
pynio -> krb5
Package mpich conflicts for:
h5py -> mpich[version='>=3.2,<3.3.0a0']
Package curl conflicts for:
pynio -> curl
Package openmpi conflicts for:
h5py -> openmpi[version='>=3.1,<3.2.0a0']
Package readline conflicts for:
python=3 -> readline[version='6.2.*|7.0|>=7.0,<8.0a0|>=8.0,<9.0a0']
Package numpy conflicts for:
h5py -> numpy[version='1.10.*|1.11.*|1.12.*|1.13.*|>=1.8|>=1.8,<1.14|>=1.9.3,<2.0a0']
pynio -> numpy[version='1.10.*|1.11.*|1.12.*|1.13.*|1.9.*|>=1.11|>=1.14|>=1.7']
Package pip conflicts for:
python=3 -> pip
Package mpi4py conflicts for:
h5py -> mpi4py
Package ncurses conflicts for:
python=3 -> ncurses[version='>=6.1,<6.2.0a0']
Package libgdal conflicts for:
pynio -> libgdal[version='2.1.*|2.2.*|>=2.2.4,<2.3.0a0|>=2.4.0,<2.5.0a0|>=2.4.1,<2.5.0a0']
Package libiconv conflicts for:
pynio -> libiconv
Package tk conflicts for:
python=3 -> tk[version='8.5.*|8.6.*|>=8.6.8,<8.7.0a0|>=8.6.9,<8.7.0a0']
Package libcxx conflicts for:
python=3 -> libcxx[version='>=4.0.1']
pynio -> libcxx[version='>=4.0.1']
Package hdf4 conflicts for:
pynio -> hdf4[version='>=4.2.13,<4.3.0a0']
Package jasper conflicts for:
pynio -> jasper[version='>=1.900.1,<2.0a0']
Package xz conflicts for:
python=3 -> xz[version='5.0.*|5.2.*|>=5.2.3,<5.3.0a0|>=5.2.4,<5.3.0a0']
Package libpng conflicts for:
pynio -> libpng
Package bzip2 conflicts for:
python=3 -> bzip2[version='>=1.0.6,<2.0a0']
Package sqlite conflicts for:
python=3 -> sqlite[version='3.13.*|3.20.*|3.9.*|>=3.24.0,<4.0a0|>=3.25.1,<4.0a0|>=3.25.2,<4.0a0|>=3.25.3,<4.0a0|>=3.26.0,<4.0a0|>=3.28.0,<4.0a0']
Package six conflicts for:
h5py -> six
Package libnetcdf conflicts for:
pynio -> libnetcdf[version='4.4.*|>=4.5|>=4.6.1,<4.7.0a0|>=4.6.2,<4.6.3.0a0|>=4.6.2,<4.7.0a0']
Package libffi conflicts for:
python=3 -> libffi[version='>=3.2.1,<3.3.0a0']
Package openssl conflicts for:
python=3 -> openssl[version='1.0.*|>=1.0.2o,<1.0.3a|>=1.0.2p,<1.0.3a|>=1.1.1a,<1.1.2a']
Package unittest2 conflicts for:
h5py -> unittest2
Package gdal conflicts for:
pynio -> gdal[version='1.11.*|2.1.*|2.2.*|1.11.4']
Package g2clib conflicts for:
pynio -> g2clib[version='1.5.*|1.6.*']
Note that strict channel priority may have removed packages required for satisfiability.

Maybe hdf5 is the problem? h5py seems to want the mpi version, but pynio doesn't.

Perhaps one of our friendly conda-forge experts can help diagnose the issue? @ocefpaf any ideas?

@akrherz
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akrherz commented Jul 21, 2019

I am not an expert, but will chime in. Verify that you have conda-forge before the defaults channel and that you have strict channel priority enabled.

@shoyer
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shoyer commented Jul 22, 2019

Verify that you have conda-forge before the defaults channel and that you have strict channel priority enabled.

I'm not 100% sure what this looks like, but we use conda env to make our build environments and only list conda-forge under channels.

@ocefpaf
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ocefpaf commented Jul 22, 2019

The problem here is that we had to remove some old builds of gdal (a pynio dependency) due to an incompatibility with a newer icu. However, the new builds are using hdf5 1.10.5 but h5py is not ready for it yet. (h5py still uses hdf 1.10.4.)

@shoyer
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shoyer commented Jul 22, 2019

OK, this is fixed for now by removing pynio from the CI builds.

@max-sixty
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Should we close? Or wait for the dependencies to update?

@shoyer shoyer changed the title CI broken for py36 pynio causes dependency conflicts in py36 CI build Aug 5, 2019
@shoyer
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shoyer commented Aug 5, 2019

I renamed the issue -- let's leave it open for now until we can restore pynio.

@crusaderky
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Closed by #3340

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