Update HDF5 ecosystem to 1.8.18

[qwhelan]

After merging #68, I realized that almost all conda-forge packages have pinned their recipes to 1.8.17|1.8.17.*. As hdf5 is cautious and checks that version numbers are the same for headers and shared objects, we'll need to update the pinned versions to allow a user to use 1.8.18.

I identified all conda-forge packages using hdf5 by checking out https://github.com/conda-forge/feedstocks, running git submodule init && git submodule update, and then executing the following:

grep hdf5 * -R | awk -F/ '{print $1}' | sort | uniq > hdf5.txt

I will be creating PRs for each library below and checking them off as they get merged:

• alps Upgrade to hdf5 1.8.18 alps-feedstock#13
• armadillo
• bob.io.base Upgrade to hdf5 1.8.18 bob.io.base-feedstock#20
• caffe Upgrade to hdf5 1.8.18 caffe-feedstock#28
• calliope Upgrade to hdf5 1.8.18 calliope-feedstock#4
• casacore Upgrade to hdf5 1.8.18 casacore-feedstock#4
• cdo
• cyclus Upgrade to hdf5 1.8.18 cyclus-feedstock#21
• cyclus-build-deps Upgrade to hdf5 1.8.18 cyclus-build-deps-feedstock#9
• flann Upgrade to hdf5 1.8.18 flann-feedstock#12
• gdal Upgrade to hdf5 1.8.18 gdal-feedstock#157
• gmt Upgrade to hdf5 1.8.18 gmt-feedstock#6
• graph Upgrade to hdf5 1.8.18 graph-feedstock#1
• h5py Upgrade to hdf5 1.8.18 h5py-feedstock#23
• hdf5 Bump version to 1.8.18 to resolve multiple CVEs #68
• hdfeos5 Upgrade to hdf5 1.8.18 hdfeos5-feedstock#14
• hyperion-fortran Upgrade to hdf5 1.8.18 hyperion-fortran-feedstock#7
• itk Rebuild for Python 3.7, GCC 7, R 3.5.1, openBLAS 0.3.2 itk-feedstock#5
  • The one library pinned to 1.8.* rather than 1.8.17|1.8.17.*
• kealib Pin hdf5 kealib-feedstock#11
• libcdms Upgrade to hdf5 1.8.18 libcdms-feedstock#3
• libcf Pin hdf5 libcf-feedstock#6
• libmatio Upgrade to hdf5 1.8.18 libmatio-feedstock#10
• libnetcdf Upgrade to hdf5 1.8.18 libnetcdf-feedstock#21
• marray Upgrade to hdf5 1.8.18 marray-feedstock#2
• moab Upgrade to hdf5 1.8.18 moab-feedstock#6
• ncl pin hdf5 ncl-feedstock#11
• nco pin hdf5 nco-feedstock#37
• netcdf4 Upgrade to hdf5 1.8.18 netcdf4-feedstock#32
• opencv Upgrade to hdf5 1.8.18 opencv-feedstock#76
• openmc Upgrade to hdf5 1.8.18 openmc-feedstock#8
• pyne Upgrade to hdf5 1.8.18 pyne-feedstock#10
• pytables Update hdf5 to 1.8.18 pytables-feedstock#15
• vigra Upgrade to hdf5 1.8.18 vigra-feedstock#26
• vtk Upgrade to hdf5 1.8.18 vtk-feedstock#32
• yaafe Upgrade to hdf5 1.8.18 yaafe-feedstock#2

[gillins]

II don't know much about it, but I thought updating https://github.com/conda-forge/conda-forge.github.io/blob/master/scripts/pin_the_slow_way.py would achieve the same result in a more automated fashion. cc @ocefpaf @jakirkham

[jakirkham]

That would be the place to start. Yes the bot should do this, but it is broken of late.

Still we should first send a PR to that script and only then PR the feedstocks after the pinning change has been accepted.

[qwhelan]

@gillins Thanks for pointing that out - definitely looked for something like this but didn't see any traces of it in most feedstocks I sampled.

Handling the upstream pin in conda-forge/conda-forge.github.io#394

[jakirkham]

Thank you for doing that @qwhelan and putting in the time to make all these PRs. It's definitely appreciated.

[jakirkham]

Are we good to close this out? I think everything either got rebuilt with 1.8.18, got rebuilt with 1.10.1, or is simply lagging behind.