GitHub Actions failures

[jGaboardi]

Question in regarding current GitHub Actions failures:

https://github.community/t5/GitHub-Actions/Error-in-Python-testing-environment/m-p/51781

[sjsrey]

If we skip decorate the two voronoi tests, then the job passes

[jGaboardi]

This a bizarre that it passed without issue yesterday and with weirdness today. But seems like we should have that skip test anyway since geopandas is not hard dependency? Shall we go ahead and do a PR including the skip?

[sjsrey]

For now I would say we keep testing for gp until we can figure out what is going on with the actions infrastructure. I was skipping them to see if there were other problems with GHA, so this at lease narrows it down to the missing geopandas import.

[jGaboardi]

After more reviewing and testing, this appears to be another libgdal/fiona issue causing hiccups in installing geopandas properly. Our SKIPIF check sets geopandas to not be available on ImportError, but does not check the specific message that is thrown. Maybe a ModuleNotFoundError would be more appropriate for the unavailability of geopandas, where ImportError is reserved for an actual problem with the install?

See full trace of test environment creation below.

(base) user:~ user$ conda create -n GEOTEST python=3.7
Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /Users/user/miniconda3/envs/GEOTEST

  added / updated specs:
    - python=3.7


The following NEW packages will be INSTALLED:

  ca-certificates    conda-forge/osx-64::ca-certificates-2019.11.28-hecc5488_0
  certifi            conda-forge/osx-64::certifi-2019.11.28-py37hc8dfbb8_1
  libcxx             conda-forge/osx-64::libcxx-9.0.1-1
  libffi             conda-forge/osx-64::libffi-3.2.1-h4a8c4bd_1007
  ncurses            conda-forge/osx-64::ncurses-6.1-h0a44026_1002
  openssl            conda-forge/osx-64::openssl-1.1.1e-h0b31af3_0
  pip                conda-forge/noarch::pip-20.0.2-py_2
  python             conda-forge/osx-64::python-3.7.6-h90870a6_5_cpython
  python_abi         conda-forge/osx-64::python_abi-3.7-1_cp37m
  readline           conda-forge/osx-64::readline-8.0-hcfe32e1_0
  setuptools         conda-forge/osx-64::setuptools-46.1.3-py37hc8dfbb8_0
  sqlite             conda-forge/osx-64::sqlite-3.30.1-h93121df_0
  tk                 conda-forge/osx-64::tk-8.6.10-hbbe82c9_0
  wheel              conda-forge/noarch::wheel-0.34.2-py_1
  xz                 conda-forge/osx-64::xz-5.2.4-h0b31af3_1002
  zlib               conda-forge/osx-64::zlib-1.2.11-h0b31af3_1006


Preparing transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate GEOTEST
#
# To deactivate an active environment, use
#
#     $ conda deactivate

(base) user:~ user$ conda activate GEOTEST
INFO: deactivate-gfortran_osx-64.sh made the following environmental changes:
-DEBUG_FFLAGS=-march=nocona -mtune=core2 -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem /Users/user/miniconda3/include -march=nocona -mtune=core2 -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments
-DEBUG_FORTRANFLAGS=-march=nocona -mtune=core2 -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem /Users/user/miniconda3/include -march=nocona -mtune=core2 -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments
-F77=/Users/user/miniconda3/bin/x86_64-apple-darwin13.4.0-gfortran
-F90=/Users/user/miniconda3/bin/x86_64-apple-darwin13.4.0-gfortran
-F95=/Users/user/miniconda3/bin/x86_64-apple-darwin13.4.0-gfortran
-FC=/Users/user/miniconda3/bin/x86_64-apple-darwin13.4.0-gfortran
-FFLAGS=-march=nocona -mtune=core2 -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem /Users/user/miniconda3/include
-FORTRANFLAGS=-march=nocona -mtune=core2 -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem /Users/user/miniconda3/include
-GFORTRAN=/Users/user/miniconda3/bin/x86_64-apple-darwin13.4.0-gfortran
(GEOTEST) user:~ user$ conda install geopandas
Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /Users/user/miniconda3/envs/GEOTEST

  added / updated specs:
    - geopandas


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    libnetcdf-4.7.4            |nompi_he461dc0_100         1.2 MB  conda-forge
    ------------------------------------------------------------
                                           Total:         1.2 MB

The following NEW packages will be INSTALLED:

  attrs              conda-forge/noarch::attrs-19.3.0-py_0
  boost-cpp          conda-forge/osx-64::boost-cpp-1.72.0-hdf9ef73_0
  bzip2              conda-forge/osx-64::bzip2-1.0.8-h0b31af3_2
  cairo              conda-forge/osx-64::cairo-1.16.0-hec6a9b0_1003
  cfitsio            conda-forge/osx-64::cfitsio-3.470-h84d2f63_2
  click              conda-forge/noarch::click-7.1.1-pyh8c360ce_0
  click-plugins      conda-forge/noarch::click-plugins-1.1.1-py_0
  cligj              conda-forge/noarch::cligj-0.5.0-py_0
  curl               conda-forge/osx-64::curl-7.68.0-h8754def_0
  expat              conda-forge/osx-64::expat-2.2.9-h4a8c4bd_2
  fiona              conda-forge/osx-64::fiona-1.8.13-py37he71f6a4_0
  fontconfig         conda-forge/osx-64::fontconfig-2.13.1-h6b1039f_1001
  freetype           conda-forge/osx-64::freetype-2.10.1-h8da9a1a_0
  freexl             conda-forge/osx-64::freexl-1.0.5-h1de35cc_1002
  gdal               conda-forge/osx-64::gdal-3.0.4-py37h08e9697_2
  geopandas          conda-forge/noarch::geopandas-0.7.0-py_1
  geos               conda-forge/osx-64::geos-3.8.1-h4a8c4bd_0
  geotiff            conda-forge/osx-64::geotiff-1.5.1-h4bdff65_9
  gettext            conda-forge/osx-64::gettext-0.19.8.1-h46ab8bc_1002
  giflib             conda-forge/osx-64::giflib-5.2.1-h0b31af3_2
  glib               conda-forge/osx-64::glib-2.58.3-py37h7c187be_1003
  hdf4               conda-forge/osx-64::hdf4-4.2.13-h84186c3_1003
  hdf5               conda-forge/osx-64::hdf5-1.10.5-nompi_h3e39495_1104
  icu                conda-forge/osx-64::icu-64.2-h6de7cb9_1
  jpeg               conda-forge/osx-64::jpeg-9c-h1de35cc_1001
  json-c             conda-forge/osx-64::json-c-0.13.1-h1de35cc_1001
  kealib             conda-forge/osx-64::kealib-1.4.12-h2324030_0
  krb5               conda-forge/osx-64::krb5-1.16.4-h1752a42_0
  libblas            conda-forge/osx-64::libblas-3.8.0-16_openblas
  libcblas           conda-forge/osx-64::libcblas-3.8.0-16_openblas
  libcurl            conda-forge/osx-64::libcurl-7.68.0-h709d2b2_0
  libdap4            conda-forge/osx-64::libdap4-3.20.4-habf5908_0
  libedit            conda-forge/osx-64::libedit-3.1.20170329-hcfe32e1_1001
  libgdal            conda-forge/osx-64::libgdal-3.0.4-hbf8f8d6_2
  libgfortran        conda-forge/osx-64::libgfortran-4.0.0-2
  libiconv           conda-forge/osx-64::libiconv-1.15-h0b31af3_1006
  libkml             conda-forge/osx-64::libkml-1.3.0-h169b8f9_1011
  liblapack          conda-forge/osx-64::liblapack-3.8.0-16_openblas
  libnetcdf          conda-forge/osx-64::libnetcdf-4.7.4-nompi_he461dc0_100
  libopenblas        conda-forge/osx-64::libopenblas-0.3.9-h3d69b6c_0
  libpng             conda-forge/osx-64::libpng-1.6.37-hbbe82c9_1
  libpq              conda-forge/osx-64::libpq-12.2-h554dc5a_0
  libspatialindex    conda-forge/osx-64::libspatialindex-1.9.3-h4a8c4bd_3
  libspatialite      conda-forge/osx-64::libspatialite-4.3.0a-hbcd37d4_1037
  libssh2            conda-forge/osx-64::libssh2-1.8.2-hcdc9a53_2
  libtiff            conda-forge/osx-64::libtiff-4.1.0-ha78913b_3
  libwebp            conda-forge/osx-64::libwebp-1.0.2-hd3bf737_5
  libxml2            conda-forge/osx-64::libxml2-2.9.10-h53d96d6_0
  llvm-openmp        conda-forge/osx-64::llvm-openmp-9.0.1-h28b9765_2
  lz4-c              conda-forge/osx-64::lz4-c-1.8.3-h6de7cb9_1001
  munch              conda-forge/noarch::munch-2.5.0-py_0
  numpy              conda-forge/osx-64::numpy-1.18.1-py37h7687784_1
  openjpeg           conda-forge/osx-64::openjpeg-2.3.1-h254dc36_3
  pandas             conda-forge/osx-64::pandas-1.0.3-py37h94625e5_0
  pcre               conda-forge/osx-64::pcre-8.44-h4a8c4bd_0
  pixman             conda-forge/osx-64::pixman-0.38.0-h01d97ff_1003
  poppler            conda-forge/osx-64::poppler-0.67.0-h16886b5_8
  poppler-data       conda-forge/noarch::poppler-data-0.4.9-1
  postgresql         conda-forge/osx-64::postgresql-12.2-h16d8c28_0
  proj               conda-forge/osx-64::proj-6.3.1-h773a61f_1
  pyproj             conda-forge/osx-64::pyproj-2.6.0-py37hf6d6e9e_0
  python-dateutil    conda-forge/noarch::python-dateutil-2.8.1-py_0
  pytz               conda-forge/noarch::pytz-2019.3-py_0
  rtree              conda-forge/osx-64::rtree-0.9.4-py37h8526d28_1
  shapely            conda-forge/osx-64::shapely-1.7.0-py37hfcf0db4_2
  six                conda-forge/noarch::six-1.14.0-py_1
  tbb                conda-forge/osx-64::tbb-2018.0.5-h2d50403_0
  tiledb             conda-forge/osx-64::tiledb-1.7.0-hd5e958f_2
  tzcode             conda-forge/osx-64::tzcode-2019a-h01d97ff_1002
  xerces-c           conda-forge/osx-64::xerces-c-3.2.2-h8f8adb3_1004
  zstd               conda-forge/osx-64::zstd-1.4.4-hed8d7c8_2



Downloading and Extracting Packages
libnetcdf-4.7.4      | 1.2 MB    | ##################################################################################### | 100% 
Preparing transaction: done
Executing transaction: done
(GEOTEST) user:~ user $ python -c 'import geopandas'
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/Users/user/miniconda3/envs/GEOTEST/lib/python3.7/site-packages/geopandas/__init__.py", line 5, in <module>
    from geopandas.io.file import read_file  # noqa
  File "/Users/user/miniconda3/envs/GEOTEST/lib/python3.7/site-packages/geopandas/io/file.py", line 6, in <module>
    import fiona
  File "/Users/user/miniconda3/envs/GEOTEST/lib/python3.7/site-packages/fiona/__init__.py", line 84, in <module>
    from fiona.collection import BytesCollection, Collection
  File "/Users/user/miniconda3/envs/GEOTEST/lib/python3.7/site-packages/fiona/collection.py", line 9, in <module>
    from fiona.ogrext import Iterator, ItemsIterator, KeysIterator
ImportError: dlopen(/Users/user/miniconda3/envs/GEOTEST/lib/python3.7/site-packages/fiona/ogrext.cpython-37m-darwin.so, 2): Library not loaded: @rpath/libnetcdf.15.dylib
  Referenced from: /Users/user/miniconda3/envs/GEOTEST/lib/libgdal.26.dylib
  Reason: image not found

[jGaboardi]

Being addressed upstream. See conda-forge/fiona-feedstock#159

[jGaboardi]

This appears to be resolved. Tests needing geopandas are being skipped in spaghetti.

[jGaboardi]

voronoi tests that were failing (or being skipped) previously are now passing.