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conda-forge / pygraphblas-feedstock

A conda-smithy repository for pygraphblas.
BSD 3-Clause "New" or "Revised" License
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Importing pygraphblas fails due to (supposedly) missing numba.core dependency #1

Open szarnyasg opened 4 years ago

szarnyasg commented 4 years ago

Issue:


Environment (conda list):

``` $ conda list # packages in environment at /root/anaconda3: # # Name Version Build Channel _ipyw_jlab_nb_ext_conf 0.1.0 py37_0 _libgcc_mutex 0.1 main alabaster 0.7.12 py37_0 anaconda 2020.02 py37_0 anaconda-client 1.7.2 py37_0 anaconda-navigator 1.9.12 py37_0 anaconda-project 0.8.4 py_0 argh 0.26.2 py37_0 asn1crypto 1.3.0 py37_0 astroid 2.3.3 py37_0 astropy 4.0 py37h7b6447c_0 atomicwrites 1.3.0 py37_1 attrs 19.3.0 py_0 autopep8 1.4.4 py_0 babel 2.8.0 py_0 backcall 0.1.0 py37_0 backports 1.0 py_2 backports.functools_lru_cache 1.6.1 py_0 backports.shutil_get_terminal_size 1.0.0 py37_2 backports.tempfile 1.0 py_1 backports.weakref 1.0.post1 py_1 beautifulsoup4 4.8.2 py37_0 bitarray 1.2.1 py37h7b6447c_0 bkcharts 0.2 py37_0 blas 1.0 mkl bleach 3.1.0 py37_0 blosc 1.16.3 hd408876_0 bokeh 1.4.0 py37_0 boto 2.49.0 py37_0 bottleneck 1.3.2 py37heb32a55_0 bzip2 1.0.8 h7b6447c_0 ca-certificates 2020.1.1 0 cairo 1.14.12 h8948797_3 certifi 2019.11.28 py37_0 cffi 1.14.0 py37h2e261b9_0 chardet 3.0.4 py37_1003 click 7.0 py37_0 cloudpickle 1.3.0 py_0 clyent 1.2.2 py37_1 colorama 0.4.3 py_0 conda 4.8.5 py37he5f6b98_2 conda-forge conda-build 3.18.11 py37_0 conda-env 2.6.0 1 conda-package-handling 1.6.0 py37h7b6447c_0 conda-verify 3.4.2 py_1 contextlib2 0.6.0.post1 py_0 cryptography 2.8 py37h1ba5d50_0 curl 7.68.0 hbc83047_0 cycler 0.10.0 py37_0 cython 0.29.15 py37he6710b0_0 cytoolz 0.10.1 py37h7b6447c_0 dask 2.11.0 py_0 dask-core 2.11.0 py_0 dbus 1.13.12 h746ee38_0 decorator 4.4.1 py_0 defusedxml 0.6.0 py_0 diff-match-patch 20181111 py_0 distributed 2.11.0 py37_0 docutils 0.16 py37_0 entrypoints 0.3 py37_0 et_xmlfile 1.0.1 py37_0 expat 2.2.6 he6710b0_0 fastcache 1.1.0 py37h7b6447c_0 filelock 3.0.12 py_0 flake8 3.7.9 py37_0 flask 1.1.1 py_0 fontconfig 2.13.0 h9420a91_0 freetype 2.9.1 h8a8886c_1 fribidi 1.0.5 h7b6447c_0 fsspec 0.6.2 py_0 future 0.18.2 py37_0 get_terminal_size 1.0.0 haa9412d_0 gevent 1.4.0 py37h7b6447c_0 glib 2.63.1 h5a9c865_0 glob2 0.7 py_0 gmp 6.1.2 h6c8ec71_1 gmpy2 2.0.8 py37h10f8cd9_2 graphblas 3.3.3 he1b5a44_1 conda-forge graphite2 1.3.13 h23475e2_0 greenlet 0.4.15 py37h7b6447c_0 gst-plugins-base 1.14.0 hbbd80ab_1 gstreamer 1.14.0 hb453b48_1 h5py 2.10.0 py37h7918eee_0 harfbuzz 1.8.8 hffaf4a1_0 hdf5 1.10.4 hb1b8bf9_0 heapdict 1.0.1 py_0 html5lib 1.0.1 py37_0 hypothesis 5.5.4 py_0 icu 58.2 h9c2bf20_1 idna 2.8 py37_0 imageio 2.6.1 py37_0 imagesize 1.2.0 py_0 importlib_metadata 1.5.0 py37_0 intel-openmp 2020.0 166 intervaltree 3.0.2 py_0 ipykernel 5.1.4 py37h39e3cac_0 ipython 7.12.0 py37h5ca1d4c_0 ipython_genutils 0.2.0 py37_0 ipywidgets 7.5.1 py_0 isort 4.3.21 py37_0 itsdangerous 1.1.0 py37_0 jbig 2.1 hdba287a_0 jdcal 1.4.1 py_0 jedi 0.14.1 py37_0 jeepney 0.4.2 py_0 jinja2 2.11.1 py_0 joblib 0.14.1 py_0 jpeg 9b h024ee3a_2 json5 0.9.1 py_0 jsonschema 3.2.0 py37_0 jupyter 1.0.0 py37_7 jupyter_client 5.3.4 py37_0 jupyter_console 6.1.0 py_0 jupyter_core 4.6.1 py37_0 jupyterlab 1.2.6 pyhf63ae98_0 jupyterlab_server 1.0.6 py_0 keyring 21.1.0 py37_0 kiwisolver 1.1.0 py37he6710b0_0 krb5 1.17.1 h173b8e3_0 lazy-object-proxy 1.4.3 py37h7b6447c_0 ld_impl_linux-64 2.33.1 h53a641e_7 libarchive 3.3.3 h5d8350f_5 libcurl 7.68.0 h20c2e04_0 libedit 3.1.20181209 hc058e9b_0 libffi 3.2.1 hd88cf55_4 libgcc-ng 9.1.0 hdf63c60_0 libgfortran-ng 7.3.0 hdf63c60_0 liblief 0.9.0 h7725739_2 libpng 1.6.37 hbc83047_0 libsodium 1.0.16 h1bed415_0 libspatialindex 1.9.3 he6710b0_0 libssh2 1.8.2 h1ba5d50_0 libstdcxx-ng 9.1.0 hdf63c60_0 libtiff 4.1.0 h2733197_0 libtool 2.4.6 h7b6447c_5 libuuid 1.0.3 h1bed415_2 libxcb 1.13 h1bed415_1 libxml2 2.9.9 hea5a465_1 libxslt 1.1.33 h7d1a2b0_0 llvm-openmp 8.0.1 hc9558a2_0 conda-forge llvmlite 0.31.0 py37hd408876_0 locket 0.2.0 py37_1 lxml 4.5.0 py37hefd8a0e_0 lz4-c 1.8.1.2 h14c3975_0 lzo 2.10 h49e0be7_2 markupsafe 1.1.1 py37h7b6447c_0 matplotlib 3.1.3 py37_0 matplotlib-base 3.1.3 py37hef1b27d_0 mccabe 0.6.1 py37_1 mistune 0.8.4 py37h7b6447c_0 mkl 2020.0 166 mkl-service 2.3.0 py37he904b0f_0 mkl_fft 1.0.15 py37ha843d7b_0 mkl_random 1.1.0 py37hd6b4f25_0 mock 4.0.1 py_0 more-itertools 8.2.0 py_0 mpc 1.1.0 h10f8cd9_1 mpfr 4.0.1 hdf1c602_3 mpmath 1.1.0 py37_0 msgpack-python 0.6.1 py37hfd86e86_1 multipledispatch 0.6.0 py37_0 navigator-updater 0.2.1 py37_0 nbconvert 5.6.1 py37_0 nbformat 5.0.4 py_0 ncurses 6.2 he6710b0_0 networkx 2.4 py_0 nltk 3.4.5 py37_0 nose 1.3.7 py37_2 notebook 6.0.3 py37_0 numba 0.48.0 py37h0573a6f_0 numexpr 2.7.1 py37h423224d_0 numpy 1.18.1 py37h4f9e942_0 numpy-base 1.18.1 py37hde5b4d6_1 numpydoc 0.9.2 py_0 olefile 0.46 py37_0 openmp 8.0.1 0 conda-forge openpyxl 3.0.3 py_0 openssl 1.1.1d h7b6447c_4 packaging 20.1 py_0 pandas 1.0.1 py37h0573a6f_0 pandoc 2.2.3.2 0 pandocfilters 1.4.2 py37_1 pango 1.42.4 h049681c_0 parso 0.5.2 py_0 partd 1.1.0 py_0 patchelf 0.10 he6710b0_0 path 13.1.0 py37_0 path.py 12.4.0 0 pathlib2 2.3.5 py37_0 pathtools 0.1.2 py_1 patsy 0.5.1 py37_0 pcre 8.43 he6710b0_0 pep8 1.7.1 py37_0 pexpect 4.8.0 py37_0 pickleshare 0.7.5 py37_0 pillow 7.0.0 py37hb39fc2d_0 pip 20.0.2 py37_1 pixman 0.38.0 h7b6447c_0 pkginfo 1.5.0.1 py37_0 pluggy 0.13.1 py37_0 ply 3.11 py37_0 prometheus_client 0.7.1 py_0 prompt_toolkit 3.0.3 py_0 psutil 5.6.7 py37h7b6447c_0 ptyprocess 0.6.0 py37_0 py 1.8.1 py_0 py-lief 0.9.0 py37h7725739_2 pycodestyle 2.5.0 py37_0 pycosat 0.6.3 py37h7b6447c_0 pycparser 2.19 py37_0 pycrypto 2.6.1 py37h14c3975_9 pycurl 7.43.0.5 py37h1ba5d50_0 pydocstyle 4.0.1 py_0 pyflakes 2.1.1 py37_0 pygments 2.5.2 py_0 pygraphblas 3.4.0 py37h8f50634_0 conda-forge pylint 2.4.4 py37_0 pyodbc 4.0.30 py37he6710b0_0 pyopenssl 19.1.0 py37_0 pyparsing 2.4.6 py_0 pyqt 5.9.2 py37h05f1152_2 pyrsistent 0.15.7 py37h7b6447c_0 pysocks 1.7.1 py37_0 pytables 3.6.1 py37h71ec239_0 pytest 5.3.5 py37_0 pytest-arraydiff 0.3 py37h39e3cac_0 pytest-astropy 0.8.0 py_0 pytest-astropy-header 0.1.2 py_0 pytest-doctestplus 0.5.0 py_0 pytest-openfiles 0.4.0 py_0 pytest-remotedata 0.3.2 py37_0 python 3.7.6 h0371630_2 python-dateutil 2.8.1 py_0 python-jsonrpc-server 0.3.4 py_0 python-language-server 0.31.7 py37_0 python-libarchive-c 2.8 py37_13 python_abi 3.7 1_cp37m conda-forge pytz 2019.3 py_0 pywavelets 1.1.1 py37h7b6447c_0 pyxdg 0.26 py_0 pyyaml 5.3 py37h7b6447c_0 pyzmq 18.1.1 py37he6710b0_0 qdarkstyle 2.8 py_0 qt 5.9.7 h5867ecd_1 qtawesome 0.6.1 py_0 qtconsole 4.6.0 py_1 qtpy 1.9.0 py_0 readline 7.0 h7b6447c_5 requests 2.22.0 py37_1 ripgrep 11.0.2 he32d670_0 rope 0.16.0 py_0 rtree 0.9.3 py37_0 ruamel_yaml 0.15.87 py37h7b6447c_0 scikit-image 0.16.2 py37h0573a6f_0 scikit-learn 0.22.1 py37hd81dba3_0 scipy 1.4.1 py37h0b6359f_0 seaborn 0.10.0 py_0 secretstorage 3.1.2 py37_0 send2trash 1.5.0 py37_0 setuptools 45.2.0 py37_0 simplegeneric 0.8.1 py37_2 singledispatch 3.4.0.3 py37_0 sip 4.19.8 py37hf484d3e_0 six 1.14.0 py37_0 snappy 1.1.7 hbae5bb6_3 snowballstemmer 2.0.0 py_0 sortedcollections 1.1.2 py37_0 sortedcontainers 2.1.0 py37_0 soupsieve 1.9.5 py37_0 sphinx 2.4.0 py_0 sphinxcontrib 1.0 py37_1 sphinxcontrib-applehelp 1.0.1 py_0 sphinxcontrib-devhelp 1.0.1 py_0 sphinxcontrib-htmlhelp 1.0.2 py_0 sphinxcontrib-jsmath 1.0.1 py_0 sphinxcontrib-qthelp 1.0.2 py_0 sphinxcontrib-serializinghtml 1.1.3 py_0 sphinxcontrib-websupport 1.2.0 py_0 spyder 4.0.1 py37_0 spyder-kernels 1.8.1 py37_0 sqlalchemy 1.3.13 py37h7b6447c_0 sqlite 3.31.1 h7b6447c_0 statsmodels 0.11.0 py37h7b6447c_0 sympy 1.5.1 py37_0 tbb 2020.0 hfd86e86_0 tblib 1.6.0 py_0 terminado 0.8.3 py37_0 testpath 0.4.4 py_0 tk 8.6.8 hbc83047_0 toolz 0.10.0 py_0 tornado 6.0.3 py37h7b6447c_3 tqdm 4.42.1 py_0 traitlets 4.3.3 py37_0 ujson 1.35 py37h14c3975_0 unicodecsv 0.14.1 py37_0 unixodbc 2.3.7 h14c3975_0 urllib3 1.25.8 py37_0 watchdog 0.10.2 py37_0 wcwidth 0.1.8 py_0 webencodings 0.5.1 py37_1 werkzeug 1.0.0 py_0 wheel 0.34.2 py37_0 widgetsnbextension 3.5.1 py37_0 wrapt 1.11.2 py37h7b6447c_0 wurlitzer 2.0.0 py37_0 xlrd 1.2.0 py37_0 xlsxwriter 1.2.7 py_0 xlwt 1.3.0 py37_0 xmltodict 0.12.0 py_0 xz 5.2.4 h14c3975_4 yaml 0.1.7 had09818_2 yapf 0.28.0 py_0 zeromq 4.3.1 he6710b0_3 zict 1.0.0 py_0 zipp 2.2.0 py_0 zlib 1.2.11 h7b6447c_3 zstd 1.3.7 h0b5b093_0 ```


Details about conda and system ( conda info ):

``` $ conda info active environment : base active env location : /root/anaconda3 shell level : 1 user config file : /root/.condarc populated config files : /root/.condarc conda version : 4.8.5 conda-build version : 3.18.11 python version : 3.7.6.final.0 virtual packages : __glibc=2.31 base environment : /root/anaconda3 (writable) channel URLs : https://conda.anaconda.org/conda-forge/linux-64 https://conda.anaconda.org/conda-forge/noarch https://repo.anaconda.com/pkgs/main/linux-64 https://repo.anaconda.com/pkgs/main/noarch https://repo.anaconda.com/pkgs/r/linux-64 https://repo.anaconda.com/pkgs/r/noarch package cache : /root/anaconda3/pkgs /root/.conda/pkgs envs directories : /root/anaconda3/envs /root/.conda/envs platform : linux-64 user-agent : conda/4.8.5 requests/2.22.0 CPython/3.7.6 Linux/5.8.13-200.fc32.x86_64 ubuntu/20.04 glibc/2.31 UID:GID : 0:0 netrc file : None offline mode : False ```

I created a fresh Conda install in an Ubuntu 20.04 Docker image:

bash Anaconda3-2020.02-Linux-x86_64.sh
. ~/.bashrc
conda config --add channels conda-forge
conda install pygraphblas
python

When importing pygraphblas, I got an error message even though the numba package is installed (as confirmed by conda list):

Python 3.7.6 (default, Jan  8 2020, 19:59:22) 
[GCC 7.3.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import pygraphblas
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/root/anaconda3/lib/python3.7/site-packages/pygraphblas/__init__.py", line 5, in <module>
    from .matrix import Matrix
  File "/root/anaconda3/lib/python3.7/site-packages/pygraphblas/matrix.py", line 18, in <module>
    from . import types, binaryop, monoid, unaryop, semiring as _semiring
  File "/root/anaconda3/lib/python3.7/site-packages/pygraphblas/types.py", line 7, in <module>
    from numba.core.typing import cffi_utils as cffi_support
ModuleNotFoundError: No module named 'numba.core'
eriknw commented 4 years ago

Upgrade numba. The use of numba.core requires numba >=0.49. This constraint should be added to the requirements.

szarnyasg commented 4 years ago

Thanks, conda update --all solved it. Leaving the issue open to get the requirement fixed.