importing error when testing

Trying to install oggm on a Mac Machine using conda, following the installation instruction.

The installation went smooth. However, when I ran pytest --pyargs oggm, it shows the following message:

============================= test session starts ============================== platform darwin – Python 3.6.7, pytest-4.3.0, py-1.8.0, pluggy-0.9.0 rootdir: /Users/Larry/anaconda3/envs/oggm, inifile: collected 0 items / 7 errors

==================================== ERRORS ==================================== __ ERROR collecting lib/python3.6/site-packages/oggm/tests/test_benchmarks.py __ ImportError while importing test module ‘/Users/Larry/anaconda3/envs/oggm/lib/python3.6/site-packages/oggm/tests/test_benchmarks.py’. Hint: make sure your test modules/packages have valid Python names. Traceback: lib/python3.6/site-packages/oggm/init.py:34: in <module> from oggm.utils import GlacierDirectory, entity_task, global_task lib/python3.6/site-packages/oggm/utils.py:29: in <module> import geopandas as gpd lib/python3.6/site-packages/geopandas/init.py:4: in <module> from geopandas.io.file import read_file lib/python3.6/site-packages/geopandas/io/file.py:3: in <module> import fiona lib/python3.6/site-packages/fiona/init.py:69: in <module> from fiona.collection import Collection, BytesCollection, vsi_path lib/python3.6/site-packages/fiona/collection.py:9: in <module> from fiona.ogrext import Iterator, ItemsIterator, KeysIterator E ImportError: dlopen(/Users/Larry/anaconda3/envs/oggm/lib/python3.6/site-packages/fiona/ogrext.cpython-36m-darwin.so, 2): Library not loaded: @rpath/libpoppler.71.dylib E Referenced from: /Users/Larry/anaconda3/envs/oggm/lib/libgdal.20.dylib E Reason: image not found ___ ERROR collecting lib/python3.6/site-packages/oggm/tests/test_graphics.py ___ ImportError while importing test module ‘/Users/Larry/anaconda3/envs/oggm/lib/python3.6/site-packages/oggm/tests/test_graphics.py’. Hint: make sure your test modules/packages have valid Python names. Traceback: lib/python3.6/site-packages/oggm/init.py:34: in <module> from oggm.utils import GlacierDirectory, entity_task, global_task lib/python3.6/site-packages/oggm/utils.py:29: in <module> import geopandas as gpd lib/python3.6/site-packages/geopandas/init.py:4: in <module> from geopandas.io.file import read_file lib/python3.6/site-packages/geopandas/io/file.py:3: in <module> import fiona lib/python3.6/site-packages/fiona/init.py:69: in <module> from fiona.collection import Collection, BytesCollection, vsi_path lib/python3.6/site-packages/fiona/collection.py:9: in <module> from fiona.ogrext import Iterator, ItemsIterator, KeysIterator E ImportError: dlopen(/Users/Larry/anaconda3/envs/oggm/lib/python3.6/site-packages/fiona/ogrext.cpython-36m-darwin.so, 2): Library not loaded: @rpath/libpoppler.71.dylib E Referenced from: /Users/Larry/anaconda3/envs/oggm/lib/libgdal.20.dylib E Reason: image not found ____ ERROR collecting lib/python3.6/site-packages/oggm/tests/test_models.py ____ ImportError while importing test module ‘/Users/Larry/anaconda3/envs/oggm/lib/python3.6/site-packages/oggm/tests/test_models.py’. Hint: make sure your test modules/packages have valid Python names. Traceback: lib/python3.6/site-packages/oggm/init.py:34: in <module> from oggm.utils import GlacierDirectory, entity_task, global_task lib/python3.6/site-packages/oggm/utils.py:29: in <module> import geopandas as gpd lib/python3.6/site-packages/geopandas/init.py:4: in <module> from geopandas.io.file import read_file lib/python3.6/site-packages/geopandas/io/file.py:3: in <module> import fiona lib/python3.6/site-packages/fiona/init.py:69: in <module> from fiona.collection import Collection, BytesCollection, vsi_path lib/python3.6/site-packages/fiona/collection.py:9: in <module> from fiona.ogrext import Iterator, ItemsIterator, KeysIterator E ImportError: dlopen(/Users/Larry/anaconda3/envs/oggm/lib/python3.6/site-packages/fiona/ogrext.cpython-36m-darwin.so, 2): Library not loaded: @rpath/libpoppler.71.dylib E Referenced from: /Users/Larry/anaconda3/envs/oggm/lib/libgdal.20.dylib E Reason: image not found ___ ERROR collecting lib/python3.6/site-packages/oggm/tests/test_numerics.py ___ ImportError while importing test module ‘/Users/Larry/anaconda3/envs/oggm/lib/python3.6/site-packages/oggm/tests/test_numerics.py’. Hint: make sure your test modules/packages have valid Python names. Traceback: lib/python3.6/site-packages/oggm/init.py:34: in <module> from oggm.utils import GlacierDirectory, entity_task, global_task lib/python3.6/site-packages/oggm/utils.py:29: in <module> import geopandas as gpd lib/python3.6/site-packages/geopandas/init.py:4: in <module> from geopandas.io.file import read_file lib/python3.6/site-packages/geopandas/io/file.py:3: in <module> import fiona lib/python3.6/site-packages/fiona/init.py:69: in <module> from fiona.collection import Collection, BytesCollection, vsi_path lib/python3.6/site-packages/fiona/collection.py:9: in <module> from fiona.ogrext import Iterator, ItemsIterator, KeysIterator E ImportError: dlopen(/Users/Larry/anaconda3/envs/oggm/lib/python3.6/site-packages/fiona/ogrext.cpython-36m-darwin.so, 2): Library not loaded: @rpath/libpoppler.71.dylib E Referenced from: /Users/Larry/anaconda3/envs/oggm/lib/libgdal.20.dylib E Reason: image not found ____ ERROR collecting lib/python3.6/site-packages/oggm/tests/test_prepro.py ____ ImportError while importing test module ‘/Users/Larry/anaconda3/envs/oggm/lib/python3.6/site-packages/oggm/tests/test_prepro.py’. Hint: make sure your test modules/packages have valid Python names. Traceback: lib/python3.6/site-packages/oggm/init.py:34: in <module> from oggm.utils import GlacierDirectory, entity_task, global_task lib/python3.6/site-packages/oggm/utils.py:29: in <module> import geopandas as gpd lib/python3.6/site-packages/geopandas/init.py:4: in <module> from geopandas.io.file import read_file lib/python3.6/site-packages/geopandas/io/file.py:3: in <module> import fiona lib/python3.6/site-packages/fiona/init.py:69: in <module> from fiona.collection import Collection, BytesCollection, vsi_path lib/python3.6/site-packages/fiona/collection.py:9: in <module> from fiona.ogrext import Iterator, ItemsIterator, KeysIterator E ImportError: dlopen(/Users/Larry/anaconda3/envs/oggm/lib/python3.6/site-packages/fiona/ogrext.cpython-36m-darwin.so, 2): Library not loaded: @rpath/libpoppler.71.dylib E Referenced from: /Users/Larry/anaconda3/envs/oggm/lib/libgdal.20.dylib E Reason: image not found ____ ERROR collecting lib/python3.6/site-packages/oggm/tests/test_utils.py _____ ImportError while importing test module ‘/Users/Larry/anaconda3/envs/oggm/lib/python3.6/site-packages/oggm/tests/test_utils.py’. Hint: make sure your test modules/packages have valid Python names. Traceback: lib/python3.6/site-packages/oggm/init.py:34: in <module> from oggm.utils import GlacierDirectory, entity_task, global_task lib/python3.6/site-packages/oggm/utils.py:29: in <module> import geopandas as gpd lib/python3.6/site-packages/geopandas/init.py:4: in <module> from geopandas.io.file import read_file lib/python3.6/site-packages/geopandas/io/file.py:3: in <module> import fiona lib/python3.6/site-packages/fiona/init.py:69: in <module> from fiona.collection import Collection, BytesCollection, vsi_path lib/python3.6/site-packages/fiona/collection.py:9: in <module> from fiona.ogrext import Iterator, ItemsIterator, KeysIterator E ImportError: dlopen(/Users/Larry/anaconda3/envs/oggm/lib/python3.6/site-packages/fiona/ogrext.cpython-36m-darwin.so, 2): Library not loaded: @rpath/libpoppler.71.dylib E Referenced from: /Users/Larry/anaconda3/envs/oggm/lib/libgdal.20.dylib E Reason: image not found ___ ERROR collecting lib/python3.6/site-packages/oggm/tests/test_workflow.py ___ ImportError while importing test module ‘/Users/Larry/anaconda3/envs/oggm/lib/python3.6/site-packages/oggm/tests/test_workflow.py’. Hint: make sure your test modules/packages have valid Python names. Traceback: lib/python3.6/site-packages/oggm/init.py:34: in <module> from oggm.utils import GlacierDirectory, entity_task, global_task lib/python3.6/site-packages/oggm/utils.py:29: in <module> import geopandas as gpd lib/python3.6/site-packages/geopandas/init.py:4: in <module> from geopandas.io.file import read_file lib/python3.6/site-packages/geopandas/io/file.py:3: in <module> import fiona lib/python3.6/site-packages/fiona/init.py:69: in <module> from fiona.collection import Collection, BytesCollection, vsi_path lib/python3.6/site-packages/fiona/collection.py:9: in <module> from fiona.ogrext import Iterator, ItemsIterator, KeysIterator E ImportError: dlopen(/Users/Larry/anaconda3/envs/oggm/lib/python3.6/site-packages/fiona/ogrext.cpython-36m-darwin.so, 2): Library not loaded: @rpath/libpoppler.71.dylib E Referenced from: /Users/Larry/anaconda3/envs/oggm/lib/libgdal.20.dylib E Reason: image not found !!! Interrupted: 7 errors during collection !!! =========================== 7 error in 1.42 seconds ============================

[TimoRoth]

I managed to build some environment again that pass the tests at least: https://github.com/OGGM/OGGM-dependency-list/tree/master/linux-64

For installation to work, your conda root environment needs to be up to date. So run conda update conda and conda update --all before trying to install those environments. You then also might need to enforce strict channel ordering, because otherwise it will download some of the packages from the default channel instead of conda-forge, which will result in random crashes.

The oggm-1.1 environments come with oggm-1.1 installed. The oggmdev ones do not contain oggm itself, but only all of the dependencies tested to be working at the date the environment was generated. So you need to pip install -e your clone of oggm into them.

[larry-lu]

@TimoRoth I appreciate your time.

I just tried on my Mac, and both the pytest part and using OGGM seem to be functional again.