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holoviz / datashader

Quickly and accurately render even the largest data.
http://datashader.org
BSD 3-Clause "New" or "Revised" License
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Installing datashader via pip and/or conda breaks jupyter #790

Closed jolespin closed 3 years ago

jolespin commented 4 years ago

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Description

Things to consider including:

I first broke my Jupyter (the python kernel will not load) using conda install datashader then I recreated a conda environment b/c I was unable to fix jupyter. Then I tried this: pip install datashader

Both broke my jupyter beyond repair.

Errors and warnings

If relevant, please include:

Note this happened for Jupyter notebooks and Jupyter lab

How to reproduce

Ideally, please include a complete, minimal, self-contained python script or notebook that reproduces the issue (in the environment you describe below). http://matthewrocklin.com/blog/work/2018/02/28/minimal-bug-reports contains useful guidance on doing this if you are unsure.

Above

Your environment

If your version of datashader is neither the latest release (https://github.com/bokeh/datashader/releases/latest) nor the latest GitHub master, please consider upgrading before filing your issue.

Please tell us how to reproduce your environment:

# CLICK DROPDOWN FOR: conda list and conda info ``` (soothsayer_testing_env) jespinozlt-osx:~ jespinoz$ conda list # packages in environment at /Users/jespinoz/anaconda3/envs/soothsayer_testing_env: # # Name Version Build Channel _r-mutex 1.0.1 anacondar_1 conda-forge adjusttext 0.7.3.1 py_0 conda-forge appnope 0.1.0 py36_1000 conda-forge astropy 3.2.1 py36h01d97ff_0 conda-forge atomicwrites 1.3.0 py_0 conda-forge attrs 19.1.0 py_0 conda-forge backcall 0.1.0 py_0 conda-forge bids-validator 1.2.4 pypi_0 pypi bioconductor-annotationdbi 1.46.0 r36_1 bioconda bioconductor-biobase 2.44.0 r36h01d97ff_1 bioconda bioconductor-biocgenerics 0.30.0 r36_1 bioconda bioconductor-biomformat 1.12.0 r36_1 bioconda bioconductor-biostrings 2.52.0 r36h01d97ff_1 bioconda bioconductor-edger 3.26.5 r36h6de7cb9_0 bioconda bioconductor-ggtree 1.16.3 r36_0 bioconda bioconductor-go.db 3.8.2 r36_1 bioconda bioconductor-ihw 1.12.0 r36_1 bioconda bioconductor-impute 1.58.0 r36hd44dcd8_1 bioconda bioconductor-iranges 2.18.2 r36h01d97ff_0 bioconda bioconductor-limma 3.40.2 r36h01d97ff_0 bioconda bioconductor-lpsymphony 1.12.0 r36h6de7cb9_1 bioconda bioconductor-metagenomeseq 1.26.2 r36_0 bioconda bioconductor-multtest 2.40.0 r36h01d97ff_1 bioconda bioconductor-philr 1.10.0 r36_1 bioconda bioconductor-phyloseq 1.28.0 r36_1 bioconda bioconductor-preprocesscore 1.46.0 r36h01d97ff_1 bioconda bioconductor-rhdf5 2.28.0 r36h6de7cb9_1 bioconda bioconductor-rhdf5lib 1.6.0 r36h01d97ff_1 bioconda bioconductor-s4vectors 0.22.0 r36h01d97ff_1 bioconda bioconductor-treeio 1.8.1 r36_0 bioconda bioconductor-wrench 1.2.0 r36_1 bioconda bioconductor-xvector 0.24.0 r36h01d97ff_1 bioconda bioconductor-zlibbioc 1.30.0 r36h01d97ff_1 bioconda biom-format 2.1.7 py36h917ab60_1002 conda-forge biopython 1.74 py36h01d97ff_0 conda-forge bleach 3.1.0 pypi_0 pypi bokeh 1.3.4 py36_0 conda-forge bwidget 1.9.11 0 conda-forge bzip2 1.0.8 h01d97ff_1 conda-forge ca-certificates 2019.9.11 hecc5488_0 conda-forge cachecontrol 0.12.5 py_0 conda-forge cairo 1.16.0 h0ab9d94_1001 conda-forge cctools 895 1 conda-forge certifi 2016.9.26 py36_0 conda-forge clang 4.0.1 1 conda-forge clang_osx-64 4.0.1 h1ce6c1d_17 conda-forge clangxx 4.0.1 1 conda-forge clangxx_osx-64 4.0.1 h22b1bf0_17 conda-forge click 7.0 py_0 conda-forge cloudpickle 1.2.2 pypi_0 pypi colorcet 2.0.2 pypi_0 pypi compiler-rt 4.0.1 hcfea43d_1 curl 7.65.3 ha441bb4_0 cycler 0.10.0 py_1 conda-forge cython 0.29.13 py36h6de7cb9_0 conda-forge dask 2.4.0 pypi_0 pypi datashader 0.7.0 pypi_0 pypi datashape 0.5.2 pypi_0 pypi dbus 1.13.6 h2f22bb5_0 conda-forge decorator 4.4.0 py_0 conda-forge defusedxml 0.6.0 pypi_0 pypi distributed 2.4.0 pypi_0 pypi docopt 0.6.2 pypi_0 pypi entrypoints 0.3 pypi_0 pypi et-xmlfile 1.0.1 pypi_0 pypi ete3 3.1.1 py36_0 bioconda expat 2.2.5 h6de7cb9_1003 conda-forge fastcluster 1.1.25 py36h1702cab_1000 conda-forge fontconfig 2.13.1 h1027ab8_1000 conda-forge freetype 2.10.0 h24853df_1 conda-forge fribidi 1.0.5 h01d97ff_1002 conda-forge fsspec 0.5.1 pypi_0 pypi future 0.17.1 py36_1000 conda-forge gettext 0.19.8.1 h46ab8bc_1002 conda-forge gfortran_osx-64 4.8.5 h22b1bf0_8 conda-forge glib 2.58.3 h9d45998_1002 conda-forge gneiss 0.4.5 py_0 bioconda graphite2 1.3.13 h2098e52_1000 conda-forge graphviz 2.38.0 hc6cc99f_1011 conda-forge gsl 2.4 ha2d443c_1006 conda-forge harfbuzz 2.4.0 h92b87b8_1 conda-forge hdmedians 0.13 py36heacc8b8_1001 conda-forge heapdict 1.0.1 pypi_0 pypi icu 58.2 h0a44026_1000 conda-forge imageio 2.5.0 pypi_0 pypi importlib_metadata 0.23 py36_0 conda-forge ipykernel 5.1.2 pypi_0 pypi ipython 7.8.0 py36h5ca1d4c_0 conda-forge ipython_genutils 0.2.0 py_1 conda-forge jdcal 1.4.1 pypi_0 pypi jedi 0.15.1 py36_0 conda-forge jinja2 2.10.1 py_0 conda-forge joblib 0.13.2 py_0 conda-forge jpeg 9c h1de35cc_1001 conda-forge json5 0.8.5 pypi_0 pypi jsonschema 3.0.2 pypi_0 pypi jupyter-client 5.3.3 pypi_0 pypi jupyter-core 4.5.0 pypi_0 pypi jupyterlab 1.1.4 pypi_0 pypi jupyterlab-server 1.0.6 pypi_0 pypi kiwisolver 1.1.0 py36h770b8ee_0 conda-forge krb5 1.16.1 hddcf347_7 ld64 274.2 1 libblas 3.8.0 12_openblas conda-forge libcblas 3.8.0 12_openblas conda-forge libcurl 7.65.3 h051b688_0 libcxx 4.0.1 hcfea43d_1 conda-forge libcxxabi 4.0.1 hcfea43d_1 conda-forge libedit 3.1.20181209 hb402a30_0 libffi 3.2.1 h475c297_4 libgfortran 3.0.1 0 conda-forge libiconv 1.15 h01d97ff_1005 conda-forge liblapack 3.8.0 12_openblas conda-forge libopenblas 0.3.7 hd44dcd8_1 conda-forge libpng 1.6.37 h2573ce8_0 conda-forge libssh2 1.8.2 hcdc9a53_2 conda-forge libtiff 4.0.10 hd08fb8f_1003 conda-forge libxcb 1.13 h1de35cc_1002 conda-forge libxml2 2.9.9 hd80cff7_2 conda-forge libxslt 1.1.33 h33a18ac_0 llvm 4.0.1 1 conda-forge llvm-lto-tapi 4.0.1 1 conda-forge llvm-openmp 9.0.0 h40edb58_0 conda-forge llvmlite 0.29.0 pypi_0 pypi locket 0.2.0 pypi_0 pypi lockfile 0.12.2 py_1 conda-forge lxml 4.4.1 py36h08abf6f_0 conda-forge lz4-c 1.8.3 h6de7cb9_1001 conda-forge make 4.2.1 h1de35cc_2004 conda-forge 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pypi_0 pypi patsy 0.5.1 py_0 conda-forge pcre 8.43 h0a44026_0 pexpect 4.7.0 py36_0 conda-forge pickleshare 0.7.5 py36_1000 conda-forge pillow 6.1.0 py36hb68e598_0 pip 19.2.3 py36_0 conda-forge pixman 0.38.0 h01d97ff_1003 conda-forge pluggy 0.12.0 py_0 conda-forge prometheus-client 0.7.1 pypi_0 pypi prompt_toolkit 2.0.9 py_0 conda-forge psutil 5.6.3 py36h01d97ff_0 conda-forge pthread-stubs 0.4 h1de35cc_1001 conda-forge ptyprocess 0.6.0 py_1001 conda-forge py 1.8.0 py_0 conda-forge pybids 0.9.4 pypi_0 pypi pyct 0.4.6 pypi_0 pypi pydot 1.4.1 py36_1001 conda-forge pygments 2.4.2 py_0 conda-forge pygraphviz 1.5 py36h01d97ff_1001 conda-forge pyhamcrest 1.9.0 py_2 conda-forge pyparsing 2.4.2 py_0 conda-forge pyqt 5.9.2 py36h2a560b1_4 conda-forge pyrsistent 0.15.4 pypi_0 pypi pytest 5.1.2 py36_0 conda-forge pytest-arraydiff 0.3 py_0 conda-forge pytest-astropy 0.5.0 py_0 conda-forge pytest-doctestplus 0.4.0 py_0 conda-forge pytest-openfiles 0.4.0 py_0 conda-forge pytest-remotedata 0.3.1 py_0 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r-tidytree 0.2.5 r36h6115d3f_0 conda-forge r-usethis 1.5.0 r36h6115d3f_0 r r-utf8 1.1.4 r36h46e59ec_0 r r-vegan 2.5_6 r36haf69682_0 conda-forge r-viridis 0.5.1 r36h6115d3f_1003 conda-forge r-viridislite 0.3.0 r36h6115d3f_1002 conda-forge r-wgcna 1.68 r36hf99fc2c_1 bioconda r-whisker 0.3_2 r36h6115d3f_4 r r-withr 2.1.2 r36h6115d3f_0 r r-xfun 0.9 r36h6115d3f_0 conda-forge r-xopen 1.0.0 r36h6115d3f_0 r r-yaml 2.2.0 r36h46e59ec_0 r readline 7.0 h1de35cc_5 requests 2.12.5 py36_0 conda-forge rpy2 2.9.4 py36r36h1d22016_0 r scikit-bio 0.5.5 py36h917ab60_1000 conda-forge scikit-image 0.15.0 pypi_0 pypi scikit-learn 0.21.3 py36hd4ffd6c_0 conda-forge scipy 1.3.1 py36hab3da7d_2 conda-forge seaborn 0.9.0 py_1 conda-forge send2trash 1.5.0 pypi_0 pypi setuptools 41.2.0 py36_0 conda-forge sip 4.19.8 py36h0a44026_1000 conda-forge six 1.12.0 py36_1000 conda-forge soothsayer 2019.8 pypi_0 pypi sortedcontainers 2.1.0 pypi_0 pypi sqlalchemy 1.3.8 pypi_0 pypi sqlite 3.29.0 ha441bb4_0 statsmodels 0.10.1 py36heacc8b8_0 conda-forge tblib 1.4.0 pypi_0 pypi templateflow 0.4.1 pypi_0 pypi teneto 0.4.5 pypi_0 pypi terminado 0.8.2 pypi_0 pypi testpath 0.3.1 pypi_0 pypi tk 8.6.8 ha441bb4_0 conda-forge tktable 2.10 h1de35cc_0 toolz 0.10.0 pypi_0 pypi tornado 6.0.3 py36h01d97ff_0 conda-forge tqdm 4.36.1 py_0 conda-forge traitlets 4.3.2 py36_1000 conda-forge tzlocal 2.0.0 py_0 conda-forge wcwidth 0.1.7 py_1 conda-forge webencodings 0.5.1 pypi_0 pypi wheel 0.33.6 py36_0 conda-forge xarray 0.13.0 py_0 conda-forge xorg-kbproto 1.0.7 h1de35cc_1002 conda-forge xorg-libice 1.0.10 h01d97ff_0 conda-forge xorg-libsm 1.2.3 h01d97ff_1000 conda-forge xorg-libx11 1.6.8 h01d97ff_0 conda-forge xorg-libxau 1.0.9 h1de35cc_0 conda-forge xorg-libxdmcp 1.1.3 h01d97ff_0 conda-forge xorg-libxext 1.3.4 h01d97ff_0 conda-forge xorg-libxrender 0.9.10 h01d97ff_1002 conda-forge xorg-renderproto 0.11.1 h1de35cc_1002 conda-forge xorg-xextproto 7.3.0 h1de35cc_1002 conda-forge xorg-xproto 7.0.31 h1de35cc_1007 conda-forge xz 5.2.4 h1de35cc_4 yaml 0.1.7 h1de35cc_1001 conda-forge zict 1.0.0 pypi_0 pypi zipp 0.6.0 py_0 conda-forge zlib 1.2.11 h1de35cc_3 zstd 1.4.0 ha9f0a20_0 conda-forge (soothsayer_testing_env) jespinozlt-osx:~ jespinoz$ conda info active environment : soothsayer_testing_env active env location : /Users/jespinoz/anaconda3/envs/soothsayer_testing_env shell level : 2 user config file : /Users/jespinoz/.condarc populated config files : /Users/jespinoz/.condarc conda version : 4.7.10 conda-build version : 3.18.8 python version : 3.7.3.final.0 virtual packages : base environment : /Users/jespinoz/anaconda3 (writable) channel URLs : https://conda.anaconda.org/bioconda/osx-64 https://conda.anaconda.org/bioconda/noarch https://conda.anaconda.org/conda-forge/osx-64 https://conda.anaconda.org/conda-forge/noarch https://repo.anaconda.com/pkgs/main/osx-64 https://repo.anaconda.com/pkgs/main/noarch https://repo.anaconda.com/pkgs/r/osx-64 https://repo.anaconda.com/pkgs/r/noarch https://conda.anaconda.org/jolespin/osx-64 https://conda.anaconda.org/jolespin/noarch package cache : /Users/jespinoz/anaconda3/pkgs /Users/jespinoz/.conda/pkgs envs directories : /Users/jespinoz/anaconda3/envs /Users/jespinoz/.conda/envs platform : osx-64 user-agent : conda/4.7.10 requests/2.22.0 CPython/3.7.3 Darwin/18.7.0 OSX/10.14.6 UID:GID : 3456:63 netrc file : None offline mode : False ``` * If using pip, the output of `pip freeze`. * What operating system and version? OSX 10.14.6 * If relevant, which browser and version? Chrome Version 76.0.3809.132
philippjfr commented 4 years ago

It's very unclear how installing a package (and specifically datashader which is a pure python package) could cause this. Did installing datashader upgrade (or downgrade) any other packages?

jolespin commented 4 years ago

What would be the best way to test it? Should I do conda list and info before and after?

philippjfr commented 4 years ago

Sure, that will work, or the output you get when running the install command.

jolespin commented 4 years ago

Hope this helps. I'd really like to use this package. Especially the bundled layouts! They look great.

Before installation

conda info ``` (soothsayer_testing_env) jespinozlt-osx:~ jespinoz$ conda info active environment : soothsayer_testing_env active env location : /Users/jespinoz/anaconda3/envs/soothsayer_testing_env shell level : 2 user config file : /Users/jespinoz/.condarc populated config files : /Users/jespinoz/.condarc conda version : 4.7.10 conda-build version : 3.18.8 python version : 3.7.3.final.0 virtual packages : base environment : /Users/jespinoz/anaconda3 (writable) channel URLs : https://conda.anaconda.org/bioconda/osx-64 https://conda.anaconda.org/bioconda/noarch https://conda.anaconda.org/conda-forge/osx-64 https://conda.anaconda.org/conda-forge/noarch https://repo.anaconda.com/pkgs/main/osx-64 https://repo.anaconda.com/pkgs/main/noarch https://repo.anaconda.com/pkgs/r/osx-64 https://repo.anaconda.com/pkgs/r/noarch https://conda.anaconda.org/jolespin/osx-64 https://conda.anaconda.org/jolespin/noarch package cache : /Users/jespinoz/anaconda3/pkgs /Users/jespinoz/.conda/pkgs envs directories : /Users/jespinoz/anaconda3/envs /Users/jespinoz/.conda/envs platform : osx-64 user-agent : conda/4.7.10 requests/2.22.0 CPython/3.7.3 Darwin/18.7.0 OSX/10.14.6 UID:GID : 3456:63 netrc file : None offline mode : False ```
conda list ``` (soothsayer_testing_env) jespinozlt-osx:~ jespinoz$ conda list # packages in environment at /Users/jespinoz/anaconda3/envs/soothsayer_testing_env: # # Name Version Build Channel _r-mutex 1.0.1 anacondar_1 conda-forge adjusttext 0.7.3.1 py_0 conda-forge appnope 0.1.0 py36_1000 conda-forge astropy 3.2.1 py36h01d97ff_0 conda-forge atomicwrites 1.3.0 py_0 conda-forge attrs 19.1.0 py_0 conda-forge backcall 0.1.0 py_0 conda-forge bids-validator 1.2.4 pypi_0 pypi bioconductor-annotationdbi 1.46.0 r36_1 bioconda bioconductor-biobase 2.44.0 r36h01d97ff_1 bioconda bioconductor-biocgenerics 0.30.0 r36_1 bioconda bioconductor-biomformat 1.12.0 r36_1 bioconda bioconductor-biostrings 2.52.0 r36h01d97ff_1 bioconda bioconductor-edger 3.26.5 r36h6de7cb9_0 bioconda bioconductor-ggtree 1.16.3 r36_0 bioconda bioconductor-go.db 3.8.2 r36_1 bioconda bioconductor-ihw 1.12.0 r36_1 bioconda bioconductor-impute 1.58.0 r36hd44dcd8_1 bioconda bioconductor-iranges 2.18.2 r36h01d97ff_0 bioconda bioconductor-limma 3.40.2 r36h01d97ff_0 bioconda bioconductor-lpsymphony 1.12.0 r36h6de7cb9_1 bioconda bioconductor-metagenomeseq 1.26.2 r36_0 bioconda bioconductor-multtest 2.40.0 r36h01d97ff_1 bioconda bioconductor-philr 1.10.0 r36_1 bioconda bioconductor-phyloseq 1.28.0 r36_1 bioconda bioconductor-preprocesscore 1.46.0 r36h01d97ff_1 bioconda bioconductor-rhdf5 2.28.0 r36h6de7cb9_1 bioconda bioconductor-rhdf5lib 1.6.0 r36h01d97ff_1 bioconda bioconductor-s4vectors 0.22.0 r36h01d97ff_1 bioconda bioconductor-treeio 1.8.1 r36_0 bioconda bioconductor-wrench 1.2.0 r36_1 bioconda bioconductor-xvector 0.24.0 r36h01d97ff_1 bioconda bioconductor-zlibbioc 1.30.0 r36h01d97ff_1 bioconda biom-format 2.1.7 py36h917ab60_1002 conda-forge biopython 1.74 py36h01d97ff_0 conda-forge bleach 3.1.0 pypi_0 pypi bokeh 1.3.4 py36_0 conda-forge bwidget 1.9.11 0 conda-forge bzip2 1.0.8 h01d97ff_1 conda-forge ca-certificates 2019.9.11 hecc5488_0 conda-forge cachecontrol 0.12.5 py_0 conda-forge cairo 1.16.0 h0ab9d94_1001 conda-forge cctools 895 1 conda-forge certifi 2016.9.26 py36_0 conda-forge clang 4.0.1 1 conda-forge clang_osx-64 4.0.1 h1ce6c1d_17 conda-forge clangxx 4.0.1 1 conda-forge clangxx_osx-64 4.0.1 h22b1bf0_17 conda-forge click 7.0 py_0 conda-forge compiler-rt 4.0.1 hcfea43d_1 curl 7.65.3 ha441bb4_0 cycler 0.10.0 py_1 conda-forge cython 0.29.13 py36h6de7cb9_0 conda-forge dbus 1.13.6 h2f22bb5_0 conda-forge decorator 4.4.0 py_0 conda-forge defusedxml 0.6.0 pypi_0 pypi docopt 0.6.2 pypi_0 pypi entrypoints 0.3 pypi_0 pypi et-xmlfile 1.0.1 pypi_0 pypi ete3 3.1.1 py36_0 bioconda expat 2.2.5 h6de7cb9_1003 conda-forge fastcluster 1.1.25 py36h1702cab_1000 conda-forge fontconfig 2.13.1 h1027ab8_1000 conda-forge freetype 2.10.0 h24853df_1 conda-forge fribidi 1.0.5 h01d97ff_1002 conda-forge future 0.17.1 py36_1000 conda-forge gettext 0.19.8.1 h46ab8bc_1002 conda-forge gfortran_osx-64 4.8.5 h22b1bf0_8 conda-forge glib 2.58.3 h9d45998_1002 conda-forge gneiss 0.4.5 py_0 bioconda graphite2 1.3.13 h2098e52_1000 conda-forge graphviz 2.38.0 hc6cc99f_1011 conda-forge gsl 2.4 ha2d443c_1006 conda-forge harfbuzz 2.4.0 h92b87b8_1 conda-forge hdmedians 0.13 py36heacc8b8_1001 conda-forge icu 58.2 h0a44026_1000 conda-forge importlib_metadata 0.23 py36_0 conda-forge ipykernel 5.1.2 pypi_0 pypi ipython 7.8.0 py36h5ca1d4c_0 conda-forge ipython_genutils 0.2.0 py_1 conda-forge jdcal 1.4.1 pypi_0 pypi jedi 0.15.1 py36_0 conda-forge jinja2 2.10.1 py_0 conda-forge joblib 0.13.2 py_0 conda-forge jpeg 9c h1de35cc_1001 conda-forge json5 0.8.5 pypi_0 pypi jsonschema 3.0.2 pypi_0 pypi jupyter-client 5.3.3 pypi_0 pypi jupyter-core 4.5.0 pypi_0 pypi jupyterlab 1.1.4 pypi_0 pypi jupyterlab-server 1.0.6 pypi_0 pypi kiwisolver 1.1.0 py36h770b8ee_0 conda-forge krb5 1.16.1 hddcf347_7 ld64 274.2 1 libblas 3.8.0 12_openblas conda-forge libcblas 3.8.0 12_openblas conda-forge libcurl 7.65.3 h051b688_0 libcxx 4.0.1 hcfea43d_1 conda-forge libcxxabi 4.0.1 hcfea43d_1 conda-forge libedit 3.1.20181209 hb402a30_0 libffi 3.2.1 h475c297_4 libgfortran 3.0.1 0 conda-forge libiconv 1.15 h01d97ff_1005 conda-forge liblapack 3.8.0 12_openblas conda-forge libopenblas 0.3.7 hd44dcd8_1 conda-forge libpng 1.6.37 h2573ce8_0 conda-forge libssh2 1.8.2 hcdc9a53_2 conda-forge libtiff 4.0.10 hd08fb8f_1003 conda-forge libxcb 1.13 h1de35cc_1002 conda-forge libxml2 2.9.9 hd80cff7_2 conda-forge libxslt 1.1.33 h33a18ac_0 llvm 4.0.1 1 conda-forge llvm-lto-tapi 4.0.1 1 conda-forge llvm-openmp 9.0.0 h40edb58_0 conda-forge lockfile 0.12.2 py_1 conda-forge lxml 4.4.1 py36h08abf6f_0 conda-forge lz4-c 1.8.3 h6de7cb9_1001 conda-forge make 4.2.1 h1de35cc_2004 conda-forge markupsafe 1.1.1 py36h1de35cc_0 conda-forge matplotlib 3.1.1 py36_1 conda-forge matplotlib-base 3.1.1 py36h3a684a6_1 conda-forge matplotlib-venn 0.11.5 py_1 conda-forge mistune 0.8.4 pypi_0 pypi more-itertools 7.2.0 py_0 conda-forge msgpack-python 0.6.2 py36h770b8ee_0 conda-forge natsort 6.0.0 py_0 conda-forge nbconvert 5.6.0 pypi_0 pypi nbformat 4.4.0 pypi_0 pypi ncurses 6.1 h0a44026_1 networkx 2.3 py_0 conda-forge nibabel 2.5.1 pypi_0 pypi nilearn 0.5.2 pypi_0 pypi nose 1.3.7 py36_1002 conda-forge notebook 6.0.1 pypi_0 pypi num2words 0.5.10 pypi_0 pypi numpy 1.17.2 py36h6b0580a_0 conda-forge olefile 0.46 py_0 conda-forge openpyxl 2.6.3 pypi_0 pypi openssl 1.1.1c h01d97ff_0 conda-forge packaging 19.2 py_0 conda-forge palettable 3.3.0 py_0 conda-forge pandas 0.25.1 py36h86efe34_0 conda-forge pandocfilters 1.4.2 pypi_0 pypi pango 1.42.4 h6691c8e_1 conda-forge parso 0.5.1 py_0 conda-forge patsy 0.5.1 py_0 conda-forge pcre 8.43 h0a44026_0 pexpect 4.7.0 py36_0 conda-forge pickleshare 0.7.5 py36_1000 conda-forge pillow 6.1.0 py36hb68e598_0 pip 19.2.3 py36_0 conda-forge pixman 0.38.0 h01d97ff_1003 conda-forge pluggy 0.12.0 py_0 conda-forge prometheus-client 0.7.1 pypi_0 pypi prompt_toolkit 2.0.9 py_0 conda-forge psutil 5.6.3 py36h01d97ff_0 conda-forge pthread-stubs 0.4 h1de35cc_1001 conda-forge ptyprocess 0.6.0 py_1001 conda-forge py 1.8.0 py_0 conda-forge pybids 0.9.4 pypi_0 pypi pydot 1.4.1 py36_1001 conda-forge pygments 2.4.2 py_0 conda-forge pygraphviz 1.5 py36h01d97ff_1001 conda-forge pyhamcrest 1.9.0 py_2 conda-forge pyparsing 2.4.2 py_0 conda-forge pyqt 5.9.2 py36h2a560b1_4 conda-forge pyrsistent 0.15.4 pypi_0 pypi pytest 5.1.2 py36_0 conda-forge pytest-arraydiff 0.3 py_0 conda-forge pytest-astropy 0.5.0 py_0 conda-forge pytest-doctestplus 0.4.0 py_0 conda-forge pytest-openfiles 0.4.0 py_0 conda-forge pytest-remotedata 0.3.1 py_0 conda-forge python 3.6.9 h359304d_0 python-dateutil 2.8.0 py_0 conda-forge python-louvain 0.13 pypi_0 pypi python-ternary 1.0.6 py_0 conda-forge pytz 2019.2 py_0 conda-forge pyyaml 5.1.2 py36h01d97ff_0 conda-forge pyzmq 18.1.0 pypi_0 pypi qt 5.9.7 h93ee506_2 conda-forge r-acepack 1.4.1 r36haf69682_1004 conda-forge r-ade4 1.7_13 r36h159158b_1001 conda-forge r-ape 5.3 r36hf99fc2c_1 conda-forge r-askpass 1.0 r36h1de35cc_0 r r-assertthat 0.2.1 r36h6115d3f_0 r r-backports 1.1.4 r36h46e59ec_0 r r-base 3.6.1 hcb44179_0 r r-base64enc 0.1_3 r36h159158b_1003 conda-forge r-bh 1.69.0_1 r36h6115d3f_0 r r-bit 1.1_14 r36h46e59ec_0 r r-bit64 0.9_7 r36h46e59ec_0 r r-bitops 1.0_6 r36h159158b_1003 conda-forge r-blob 1.1.1 r36h6115d3f_0 r r-callr 3.2.0 r36h6115d3f_0 r r-catools 1.17.1.2 r36hf99fc2c_1 conda-forge r-checkmate 1.9.4 r36h159158b_1 conda-forge r-cli 1.1.0 r36h6115d3f_0 r r-clipr 0.6.0 r36h6115d3f_0 r r-clisymbols 1.2.0 r36h6115d3f_0 r r-cluster 2.1.0 r36haf69682_2 conda-forge r-codetools 0.2_16 r36h6115d3f_1001 conda-forge r-colorspace 1.4_1 r36h159158b_1 conda-forge r-crayon 1.3.4 r36h6115d3f_0 r r-curl 3.3 r36h46e59ec_0 r r-data.table 1.12.2 r36h159158b_1 conda-forge r-dbi 1.0.0 r36h6115d3f_0 r r-dbplyr 1.4.0 r36h6115d3f_0 r r-deoptimr 1.0_8 r36h6115d3f_1002 conda-forge r-desc 1.2.0 r36h6115d3f_0 r r-devtools 2.0.2 r36h6115d3f_0 r r-digest 0.6.18 r36h46e59ec_0 r r-doparallel 1.0.15 r36h6115d3f_0 conda-forge r-dplyr 0.8.0.1 r36h466af19_0 r r-dynamictreecut 1.63_1 r36h6115d3f_1002 conda-forge r-evaluate 0.14 r36h6115d3f_1 conda-forge r-fansi 0.4.0 r36h46e59ec_0 r r-fastcluster 1.1.25 r36ha90c164_1002 conda-forge r-fastmatch 1.1_0 r36h159158b_1004 conda-forge r-fdrtool 1.2.15 r36h159158b_1002 conda-forge r-fit.models 0.5_14 r36h6115d3f_1002 conda-forge r-foreach 1.4.7 r36h6115d3f_0 conda-forge r-foreign 0.8_72 r36h159158b_0 conda-forge r-formula 1.2_3 r36h6115d3f_1002 conda-forge r-fs 1.2.7 r36h466af19_0 r r-gdata 2.18.0 r36h6115d3f_1002 conda-forge r-ggplot2 3.2.1 r36h6115d3f_0 conda-forge r-gh 1.0.1 r36h6115d3f_0 r r-git2r 0.25.2 r36h46e59ec_0 r r-glmnet 2.0_18 r36haf69682_2 conda-forge r-glue 1.3.1 r36h46e59ec_0 r r-gplots 3.0.1.1 r36h6115d3f_1 conda-forge r-gridextra 2.3 r36h6115d3f_1002 conda-forge r-gtable 0.3.0 r36h6115d3f_2 conda-forge r-gtools 3.8.1 r36h159158b_1003 conda-forge r-highr 0.8 r36h6115d3f_1 conda-forge r-hmisc 4.2_0 r36haf69682_2 conda-forge r-htmltable 1.13.2 r36h6115d3f_0 conda-forge r-htmltools 0.3.6 r36h6de7cb9_1003 conda-forge r-htmlwidgets 1.3 r36h6115d3f_1001 conda-forge r-httr 1.4.0 r36h6115d3f_0 r r-igraph 1.2.4.1 r36h75781db_2 conda-forge r-ini 0.3.1 r36h6115d3f_0 r r-iterators 1.0.12 r36h6115d3f_0 conda-forge r-jsonlite 1.6 r36h46e59ec_0 r r-kernsmooth 2.23_15 r36haf69682_1004 conda-forge r-knitr 1.25 r36h6115d3f_0 conda-forge r-labeling 0.3 r36h6115d3f_1002 conda-forge r-lattice 0.20_38 r36h159158b_1002 conda-forge r-latticeextra 0.6_28 r36h6115d3f_1002 conda-forge r-lazyeval 0.2.2 r36h159158b_1 conda-forge r-locfit 1.5_9.1 r36h01d97ff_1004 conda-forge r-magrittr 1.5 r36h6115d3f_4 r r-markdown 1.1 r36h159158b_0 conda-forge r-mass 7.3_51.4 r36h159158b_1 conda-forge r-matrix 1.2_17 r36h159158b_1 conda-forge r-matrixstats 0.55.0 r36h159158b_0 conda-forge r-memoise 1.1.0 r36h6115d3f_0 r r-mgcv 1.8_29 r36h159158b_0 conda-forge r-mime 0.6 r36h46e59ec_0 r r-munsell 0.5.0 r36h6115d3f_1002 conda-forge r-mvtnorm 1.0_11 r36haf69682_2 conda-forge r-nlme 3.1_141 r36haf69682_1 conda-forge r-nnet 7.3_12 r36h159158b_1003 conda-forge r-openssl 1.3 r36h46e59ec_0 r r-pcapp 1.9_73 r36hf99fc2c_1001 conda-forge r-permute 0.9_5 r36_1 conda-forge r-phangorn 2.5.5 r36hf99fc2c_1 conda-forge r-pillar 1.3.1 r36h6115d3f_0 r r-pkgbuild 1.0.3 r36h6115d3f_0 r r-pkgconfig 2.0.2 r36h6115d3f_0 r r-pkgload 1.0.2 r36h466af19_0 r r-plogr 0.2.0 r36h6115d3f_0 r r-plyr 1.8.4 r36hf99fc2c_1003 conda-forge r-prettyunits 1.0.2 r36h6115d3f_0 r r-processx 3.3.0 r36h46e59ec_0 r r-ps 1.3.0 r36h46e59ec_0 r r-purrr 0.3.2 r36h46e59ec_0 r r-quadprog 1.5_7 r36haf69682_2 conda-forge r-r6 2.4.0 r36h6115d3f_0 r r-rcmdcheck 1.3.2 r36h6115d3f_0 r r-rcolorbrewer 1.1_2 r36h6115d3f_1002 conda-forge r-rcpp 1.0.1 r36h466af19_0 r r-remotes 2.0.4 r36h6115d3f_0 r r-reshape2 1.4.3 r36hf99fc2c_1004 conda-forge r-rlang 0.3.4 r36h46e59ec_0 r r-robust 0.4_18.1 r36haf69682_2 conda-forge r-robustbase 0.93_5 r36haf69682_2 conda-forge r-rpart 4.1_15 r36h159158b_1 conda-forge r-rprojroot 1.3_2 r36h6115d3f_0 r r-rrcov 1.4_7 r36haf69682_2 conda-forge r-rsqlite 2.1.1 r36h466af19_0 r r-rstudioapi 0.10 r36h6115d3f_0 r r-rvcheck 0.1.3 r36_1001 conda-forge r-scales 1.0.0 r36hf99fc2c_1002 conda-forge r-sessioninfo 1.1.1 r36h6115d3f_0 r r-slam 0.1_45 r36h159158b_1 conda-forge r-stringi 1.4.3 r36h466af19_0 r r-stringr 1.4.0 r36h6115d3f_1 conda-forge r-survival 2.44_1.1 r36h159158b_1 conda-forge r-sys 3.2 r36h46e59ec_0 r r-tibble 2.1.1 r36h46e59ec_0 r r-tidyr 0.8.3 r36h466af19_0 r r-tidyselect 0.2.5 r36h466af19_0 r r-tidytree 0.2.5 r36h6115d3f_0 conda-forge r-usethis 1.5.0 r36h6115d3f_0 r r-utf8 1.1.4 r36h46e59ec_0 r r-vegan 2.5_6 r36haf69682_0 conda-forge r-viridis 0.5.1 r36h6115d3f_1003 conda-forge r-viridislite 0.3.0 r36h6115d3f_1002 conda-forge r-wgcna 1.68 r36hf99fc2c_1 bioconda r-whisker 0.3_2 r36h6115d3f_4 r r-withr 2.1.2 r36h6115d3f_0 r r-xfun 0.9 r36h6115d3f_0 conda-forge r-xopen 1.0.0 r36h6115d3f_0 r r-yaml 2.2.0 r36h46e59ec_0 r readline 7.0 h1de35cc_5 requests 2.12.5 py36_0 conda-forge rpy2 2.9.4 py36r36h1d22016_0 r scikit-bio 0.5.5 py36h917ab60_1000 conda-forge scikit-learn 0.21.3 py36hd4ffd6c_0 conda-forge scipy 1.3.1 py36hab3da7d_2 conda-forge seaborn 0.9.0 py_1 conda-forge send2trash 1.5.0 pypi_0 pypi setuptools 41.2.0 py36_0 conda-forge sip 4.19.8 py36h0a44026_1000 conda-forge six 1.12.0 py36_1000 conda-forge soothsayer 2019.8 pypi_0 pypi sqlalchemy 1.3.8 pypi_0 pypi sqlite 3.29.0 ha441bb4_0 statsmodels 0.10.1 py36heacc8b8_0 conda-forge templateflow 0.4.1 pypi_0 pypi teneto 0.4.5 pypi_0 pypi terminado 0.8.2 pypi_0 pypi testpath 0.4.2 pypi_0 pypi tk 8.6.8 ha441bb4_0 conda-forge tktable 2.10 h1de35cc_0 tornado 6.0.3 py36h01d97ff_0 conda-forge tqdm 4.36.1 py_0 conda-forge traitlets 4.3.2 py36_1000 conda-forge tzlocal 2.0.0 py_0 conda-forge wcwidth 0.1.7 py_1 conda-forge webencodings 0.5.1 pypi_0 pypi wheel 0.33.6 py36_0 conda-forge xarray 0.13.0 py_0 conda-forge xorg-kbproto 1.0.7 h1de35cc_1002 conda-forge xorg-libice 1.0.10 h01d97ff_0 conda-forge xorg-libsm 1.2.3 h01d97ff_1000 conda-forge xorg-libx11 1.6.8 h01d97ff_0 conda-forge xorg-libxau 1.0.9 h1de35cc_0 conda-forge xorg-libxdmcp 1.1.3 h01d97ff_0 conda-forge xorg-libxext 1.3.4 h01d97ff_0 conda-forge xorg-libxrender 0.9.10 h01d97ff_1002 conda-forge xorg-renderproto 0.11.1 h1de35cc_1002 conda-forge xorg-xextproto 7.3.0 h1de35cc_1002 conda-forge xorg-xproto 7.0.31 h1de35cc_1007 conda-forge xz 5.2.4 h1de35cc_4 yaml 0.1.7 h1de35cc_1001 conda-forge zipp 0.6.0 py_0 conda-forge zlib 1.2.11 h1de35cc_3 zstd 1.4.0 ha9f0a20_0 conda-forge ```
jupyter lab ``` (soothsayer_testing_env) jespinozlt-osx:~ jespinoz$ jupyter lab [I 12:36:08.950 LabApp] The port 8888 is already in use, trying another port. [I 12:36:08.963 LabApp] JupyterLab extension loaded from /Users/jespinoz/anaconda3/envs/soothsayer_testing_env/lib/python3.6/site-packages/jupyterlab [I 12:36:08.963 LabApp] JupyterLab application directory is /Users/jespinoz/anaconda3/envs/soothsayer_testing_env/share/jupyter/lab [I 12:36:08.965 LabApp] Serving notebooks from local directory: /Users/jespinoz [I 12:36:08.965 LabApp] The Jupyter Notebook is running at: [I 12:36:08.965 LabApp] http://localhost:8889/?token=a0759888e2730f5921c80f256556c40b10542f35b9d59ccb [I 12:36:08.965 LabApp] or http://127.0.0.1:8889/?token=a0759888e2730f5921c80f256556c40b10542f35b9d59ccb [I 12:36:08.965 LabApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation). [C 12:36:08.973 LabApp] To access the notebook, open this file in a browser: file:///Users/jespinoz/Library/Jupyter/runtime/nbserver-36880-open.html Or copy and paste one of these URLs: http://localhost:8889/?token=a0759888e2730f5921c80f256556c40b10542f35b9d59ccb or http://127.0.0.1:8889/?token=a0759888e2730f5921c80f256556c40b10542f35b9d59ccb [I 12:36:12.462 LabApp] Build is up to date [W 12:36:12.505 LabApp] 404 GET /api/contents/Clinical_Multi-Omics/Notebooks/ipnet_multiomics.ipynb?content=0&1569440172487 (::1): No such file or directory: Clinical_Multi-Omics/Notebooks/ipnet_multiomics.ipynb [W 12:36:12.505 LabApp] No such file or directory: Clinical_Multi-Omics/Notebooks/ipnet_multiomics.ipynb [W 12:36:12.506 LabApp] 404 GET /api/contents/Clinical_Multi-Omics/Notebooks/ipnet_multiomics.ipynb?content=0&1569440172487 (::1) 5.98ms referer=http://localhost:8889/lab?reset=&token=a0759888e2730f5921c80f256556c40b10542f35b9d59ccb [W 12:36:12.506 LabApp] 404 GET /api/contents/Clinical_Multi-Omics/Notebooks/feature_selection_edges.ipynb?content=0&1569440172484 (::1): No such file or directory: Clinical_Multi-Omics/Notebooks/feature_selection_edges.ipynb [W 12:36:12.506 LabApp] No such file or directory: Clinical_Multi-Omics/Notebooks/feature_selection_edges.ipynb [W 12:36:12.507 LabApp] 404 GET /api/contents/Clinical_Multi-Omics/Notebooks/feature_selection_edges.ipynb?content=0&1569440172484 (::1) 5.50ms referer=http://localhost:8889/lab?reset=&token=a0759888e2730f5921c80f256556c40b10542f35b9d59ccb [W 12:36:12.507 LabApp] 404 GET /api/contents/Clinical_Multi-Omics/Notebooks/biomarkers.ipynb?content=0&1569440172481 (::1): No such file or directory: Clinical_Multi-Omics/Notebooks/biomarkers.ipynb [W 12:36:12.507 LabApp] No such file or directory: Clinical_Multi-Omics/Notebooks/biomarkers.ipynb [W 12:36:12.508 LabApp] 404 GET /api/contents/Clinical_Multi-Omics/Notebooks/biomarkers.ipynb?content=0&1569440172481 (::1) 5.24ms referer=http://localhost:8889/lab?reset=&token=a0759888e2730f5921c80f256556c40b10542f35b9d59ccb [W 12:36:12.508 LabApp] 404 GET /api/contents/SCV/Notebooks/Untitled.ipynb?content=0&1569440172479 (::1): No such file or directory: SCV/Notebooks/Untitled.ipynb [W 12:36:12.509 LabApp] No such file or directory: SCV/Notebooks/Untitled.ipynb [W 12:36:12.509 LabApp] 404 GET /api/contents/SCV/Notebooks/Untitled.ipynb?content=0&1569440172479 (::1) 5.47ms referer=http://localhost:8889/lab?reset=&token=a0759888e2730f5921c80f256556c40b10542f35b9d59ccb [W 12:36:12.509 LabApp] 404 GET /api/contents/Clinical_Multi-Omics/Notebooks?1569440172478 (::1): No such file or directory: Clinical_Multi-Omics/Notebooks [W 12:36:12.510 LabApp] No such file or directory: Clinical_Multi-Omics/Notebooks [W 12:36:12.510 LabApp] 404 GET /api/contents/Clinical_Multi-Omics/Notebooks?1569440172478 (::1) 5.95ms referer=http://localhost:8889/lab?reset=&token=a0759888e2730f5921c80f256556c40b10542f35b9d59ccb [I 12:36:25.094 LabApp] Creating new notebook in / [I 12:36:25.446 LabApp] Kernel started: a6c0e964-0325-47c8-ba86-8eeb0946f4c0 ```

Installation

pip install datashader ``` (soothsayer_testing_env) jespinozlt-osx:~ jespinoz$ pip install datashader Collecting datashader Using cached https://files.pythonhosted.org/packages/c0/e1/abee9d9a960f42658e230ea243955ea19bda58de1d39d2476cf54abc3156/datashader-0.7.0-py2.py3-none-any.whl Requirement already satisfied: bokeh in ./anaconda3/envs/soothsayer_testing_env/lib/python3.6/site-packages (from datashader) (1.3.4) Requirement already satisfied: numpy>=1.7 in ./anaconda3/envs/soothsayer_testing_env/lib/python3.6/site-packages (from datashader) (1.17.2) Collecting param>=1.6.0 (from datashader) Using cached https://files.pythonhosted.org/packages/48/d9/3b08717fd06542b6df8fb9db98054db371c8d138178b4309cdd317910659/param-1.9.1-py2.py3-none-any.whl Requirement already satisfied: pandas>=0.20.3 in ./anaconda3/envs/soothsayer_testing_env/lib/python3.6/site-packages (from datashader) (0.25.1) Collecting testpath<0.4 (from datashader) Using cached https://files.pythonhosted.org/packages/15/19/d7bc380c479a184e4a5a9ce516e4e2a773165f89b445f7cdced83d94de25/testpath-0.3.1-py2.py3-none-any.whl Requirement already satisfied: xarray>=0.9.6 in ./anaconda3/envs/soothsayer_testing_env/lib/python3.6/site-packages (from datashader) (0.13.0) Collecting scikit-image (from datashader) Using cached https://files.pythonhosted.org/packages/c5/7c/c61e0bdb02fecd1e801d34fb534839f74055873eb935a05d96a8831d4448/scikit_image-0.15.0-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl Collecting dask[complete]>=0.18.0 (from datashader) Using cached https://files.pythonhosted.org/packages/19/39/5f782ac9cfc00cd7d2eae10e72e1bff2f0b396ec31961257acda55e0ef36/dask-2.4.0-py3-none-any.whl Requirement already satisfied: pillow>=3.1.1 in ./anaconda3/envs/soothsayer_testing_env/lib/python3.6/site-packages (from datashader) (6.1.0) Collecting colorcet>=0.9.0 (from datashader) Using cached https://files.pythonhosted.org/packages/b5/a4/8a5a364492af01c8b689987ce792d0d00835bbb1203a5cd5e49798a41fbd/colorcet-2.0.2-py2.py3-none-any.whl Collecting pyct[cmd] (from datashader) Using cached https://files.pythonhosted.org/packages/eb/76/cdf8ba7edc7be2a26d418ff8d1ff695a7ac024761bda1ad6f8e269a90434/pyct-0.4.6-py2.py3-none-any.whl Requirement already satisfied: scipy in ./anaconda3/envs/soothsayer_testing_env/lib/python3.6/site-packages (from datashader) (1.3.1) Collecting numba>=0.37.0 (from datashader) Using cached https://files.pythonhosted.org/packages/3c/17/5b841c36980a417d0ef9470a1ad83b31b483550c41f7f66ad50a0d91131f/numba-0.45.1-cp36-cp36m-macosx_10_9_x86_64.whl Collecting toolz>=0.7.4 (from datashader) Collecting datashape>=0.5.1 (from datashader) Requirement already satisfied: packaging>=16.8 in ./anaconda3/envs/soothsayer_testing_env/lib/python3.6/site-packages (from bokeh->datashader) (19.2) Requirement already satisfied: python-dateutil>=2.1 in ./anaconda3/envs/soothsayer_testing_env/lib/python3.6/site-packages (from bokeh->datashader) (2.8.0) Requirement already satisfied: six>=1.5.2 in ./anaconda3/envs/soothsayer_testing_env/lib/python3.6/site-packages (from bokeh->datashader) (1.12.0) Requirement already satisfied: PyYAML>=3.10 in ./anaconda3/envs/soothsayer_testing_env/lib/python3.6/site-packages (from bokeh->datashader) (5.1.2) Requirement already satisfied: tornado>=4.3 in ./anaconda3/envs/soothsayer_testing_env/lib/python3.6/site-packages (from bokeh->datashader) (6.0.3) Requirement already satisfied: Jinja2>=2.7 in ./anaconda3/envs/soothsayer_testing_env/lib/python3.6/site-packages (from bokeh->datashader) (2.10.1) Requirement already satisfied: pytz>=2017.2 in ./anaconda3/envs/soothsayer_testing_env/lib/python3.6/site-packages (from pandas>=0.20.3->datashader) (2019.2) Requirement already satisfied: matplotlib!=3.0.0,>=2.0.0 in ./anaconda3/envs/soothsayer_testing_env/lib/python3.6/site-packages (from scikit-image->datashader) (3.1.1) Requirement already satisfied: networkx>=2.0 in ./anaconda3/envs/soothsayer_testing_env/lib/python3.6/site-packages (from scikit-image->datashader) (2.3) Collecting PyWavelets>=0.4.0 (from scikit-image->datashader) Using cached https://files.pythonhosted.org/packages/1c/66/0bdb59713833391d90b605ccf53003c41175e1fcc75dade52383cc6436b9/PyWavelets-1.0.3-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl Collecting imageio>=2.0.1 (from scikit-image->datashader) Using cached https://files.pythonhosted.org/packages/af/0a/943c965d372dae0b1f1482677d29030ab834351a61a9a632fd62f27f1523/imageio-2.5.0-py3-none-any.whl Collecting distributed>=2.0; extra == "complete" (from dask[complete]>=0.18.0->datashader) Using cached https://files.pythonhosted.org/packages/28/b4/a3fd1be0026fcea8cf3e963bff7ba098dd2e2ff52dd6a709481ec78e587c/distributed-2.4.0-py3-none-any.whl Collecting fsspec>=0.3.3; extra == "complete" (from dask[complete]>=0.18.0->datashader) Using cached https://files.pythonhosted.org/packages/95/2c/31fce3889ce89ec13e47201c71a0cb6d2ff6e5c7b5fed066fe0ac5c5e22b/fsspec-0.5.1-py3-none-any.whl Collecting cloudpickle>=0.2.1; extra == "complete" (from dask[complete]>=0.18.0->datashader) Using cached https://files.pythonhosted.org/packages/c1/49/334e279caa3231255725c8e860fa93e72083567625573421db8875846c14/cloudpickle-1.2.2-py2.py3-none-any.whl Collecting partd>=0.3.10; extra == "complete" (from dask[complete]>=0.18.0->datashader) Using cached https://files.pythonhosted.org/packages/8b/17/09c352519da1db31634979c3aa9126078e9ece0f561c5f641e0649b78905/partd-1.0.0-py2.py3-none-any.whl Requirement already satisfied: requests; extra == "cmd" in ./anaconda3/envs/soothsayer_testing_env/lib/python3.6/site-packages (from pyct[cmd]->datashader) (2.12.5) Collecting llvmlite>=0.29.0dev0 (from numba>=0.37.0->datashader) Using cached https://files.pythonhosted.org/packages/c4/75/0a330b7f888485f070f7d79a10d1e07234e6870c15791ecc015f73206e51/llvmlite-0.29.0-cp36-cp36m-macosx_10_9_x86_64.whl Collecting multipledispatch>=0.4.7 (from datashape>=0.5.1->datashader) Using cached https://files.pythonhosted.org/packages/89/79/429ecef45fd5e4504f7474d4c3c3c4668c267be3370e4c2fd33e61506833/multipledispatch-0.6.0-py3-none-any.whl Requirement already satisfied: pyparsing>=2.0.2 in ./anaconda3/envs/soothsayer_testing_env/lib/python3.6/site-packages (from packaging>=16.8->bokeh->datashader) (2.4.2) Requirement already satisfied: MarkupSafe>=0.23 in ./anaconda3/envs/soothsayer_testing_env/lib/python3.6/site-packages (from Jinja2>=2.7->bokeh->datashader) (1.1.1) Requirement already satisfied: kiwisolver>=1.0.1 in ./anaconda3/envs/soothsayer_testing_env/lib/python3.6/site-packages (from matplotlib!=3.0.0,>=2.0.0->scikit-image->datashader) (1.1.0) Requirement already satisfied: cycler>=0.10 in ./anaconda3/envs/soothsayer_testing_env/lib/python3.6/site-packages (from matplotlib!=3.0.0,>=2.0.0->scikit-image->datashader) (0.10.0) Requirement already satisfied: decorator>=4.3.0 in ./anaconda3/envs/soothsayer_testing_env/lib/python3.6/site-packages (from networkx>=2.0->scikit-image->datashader) (4.4.0) Requirement already satisfied: msgpack in ./anaconda3/envs/soothsayer_testing_env/lib/python3.6/site-packages (from distributed>=2.0; extra == "complete"->dask[complete]>=0.18.0->datashader) (0.6.2) Collecting tblib (from distributed>=2.0; extra == "complete"->dask[complete]>=0.18.0->datashader) Using cached https://files.pythonhosted.org/packages/64/b5/ebb1af4d843047ccd7292b92f5e5f8643153e8b95d14508d9fe3b35f7004/tblib-1.4.0-py2.py3-none-any.whl Collecting zict>=0.1.3 (from distributed>=2.0; extra == "complete"->dask[complete]>=0.18.0->datashader) Using cached https://files.pythonhosted.org/packages/64/b4/a904be4184814adb9dfc2e679c4e611392080a32726a657a34cab93b38c2/zict-1.0.0-py2.py3-none-any.whl Requirement already satisfied: psutil>=5.0 in ./anaconda3/envs/soothsayer_testing_env/lib/python3.6/site-packages (from distributed>=2.0; extra == "complete"->dask[complete]>=0.18.0->datashader) (5.6.3) Requirement already satisfied: click>=6.6 in ./anaconda3/envs/soothsayer_testing_env/lib/python3.6/site-packages (from distributed>=2.0; extra == "complete"->dask[complete]>=0.18.0->datashader) (7.0) Collecting sortedcontainers!=2.0.0,!=2.0.1 (from distributed>=2.0; extra == "complete"->dask[complete]>=0.18.0->datashader) Using cached https://files.pythonhosted.org/packages/13/f3/cf85f7c3a2dbd1a515d51e1f1676d971abe41bba6f4ab5443240d9a78e5b/sortedcontainers-2.1.0-py2.py3-none-any.whl Collecting locket (from partd>=0.3.10; extra == "complete"->dask[complete]>=0.18.0->datashader) Requirement already satisfied: setuptools in ./anaconda3/envs/soothsayer_testing_env/lib/python3.6/site-packages (from kiwisolver>=1.0.1->matplotlib!=3.0.0,>=2.0.0->scikit-image->datashader) (41.2.0) Collecting heapdict (from zict>=0.1.3->distributed>=2.0; extra == "complete"->dask[complete]>=0.18.0->datashader) Using cached https://files.pythonhosted.org/packages/b6/9d/cd4777dbcf3bef9d9627e0fe4bc43d2e294b1baeb01d0422399d5e9de319/HeapDict-1.0.1-py3-none-any.whl Installing collected packages: param, testpath, PyWavelets, imageio, scikit-image, tblib, heapdict, zict, cloudpickle, sortedcontainers, toolz, distributed, fsspec, locket, partd, dask, pyct, colorcet, llvmlite, numba, multipledispatch, datashape, datashader Found existing installation: testpath 0.4.2 Uninstalling testpath-0.4.2: Successfully uninstalled testpath-0.4.2 Successfully installed PyWavelets-1.0.3 cloudpickle-1.2.2 colorcet-2.0.2 dask-2.4.0 datashader-0.7.0 datashape-0.5.2 distributed-2.4.0 fsspec-0.5.1 heapdict-1.0.1 imageio-2.5.0 llvmlite-0.29.0 locket-0.2.0 multipledispatch-0.6.0 numba-0.45.1 param-1.9.1 partd-1.0.0 pyct-0.4.6 scikit-image-0.15.0 sortedcontainers-2.1.0 tblib-1.4.0 testpath-0.3.1 toolz-0.10.0 zict-1.0.0 ```

After installation

conda info ``` (soothsayer_testing_env) jespinozlt-osx:~ jespinoz$ conda info active environment : soothsayer_testing_env active env location : /Users/jespinoz/anaconda3/envs/soothsayer_testing_env shell level : 2 user config file : /Users/jespinoz/.condarc populated config files : /Users/jespinoz/.condarc conda version : 4.7.10 conda-build version : 3.18.8 python version : 3.7.3.final.0 virtual packages : base environment : /Users/jespinoz/anaconda3 (writable) channel URLs : https://conda.anaconda.org/bioconda/osx-64 https://conda.anaconda.org/bioconda/noarch https://conda.anaconda.org/conda-forge/osx-64 https://conda.anaconda.org/conda-forge/noarch https://repo.anaconda.com/pkgs/main/osx-64 https://repo.anaconda.com/pkgs/main/noarch https://repo.anaconda.com/pkgs/r/osx-64 https://repo.anaconda.com/pkgs/r/noarch https://conda.anaconda.org/jolespin/osx-64 https://conda.anaconda.org/jolespin/noarch package cache : /Users/jespinoz/anaconda3/pkgs /Users/jespinoz/.conda/pkgs envs directories : /Users/jespinoz/anaconda3/envs /Users/jespinoz/.conda/envs platform : osx-64 user-agent : conda/4.7.10 requests/2.22.0 CPython/3.7.3 Darwin/18.7.0 OSX/10.14.6 UID:GID : 3456:63 netrc file : None offline mode : False ```
conda list ``` (soothsayer_testing_env) jespinozlt-osx:~ jespinoz$ conda list # packages in environment at /Users/jespinoz/anaconda3/envs/soothsayer_testing_env: # # Name Version Build Channel _r-mutex 1.0.1 anacondar_1 conda-forge adjusttext 0.7.3.1 py_0 conda-forge appnope 0.1.0 py36_1000 conda-forge astropy 3.2.1 py36h01d97ff_0 conda-forge atomicwrites 1.3.0 py_0 conda-forge attrs 19.1.0 py_0 conda-forge backcall 0.1.0 py_0 conda-forge bids-validator 1.2.4 pypi_0 pypi bioconductor-annotationdbi 1.46.0 r36_1 bioconda bioconductor-biobase 2.44.0 r36h01d97ff_1 bioconda bioconductor-biocgenerics 0.30.0 r36_1 bioconda bioconductor-biomformat 1.12.0 r36_1 bioconda bioconductor-biostrings 2.52.0 r36h01d97ff_1 bioconda bioconductor-edger 3.26.5 r36h6de7cb9_0 bioconda bioconductor-ggtree 1.16.3 r36_0 bioconda bioconductor-go.db 3.8.2 r36_1 bioconda bioconductor-ihw 1.12.0 r36_1 bioconda bioconductor-impute 1.58.0 r36hd44dcd8_1 bioconda bioconductor-iranges 2.18.2 r36h01d97ff_0 bioconda bioconductor-limma 3.40.2 r36h01d97ff_0 bioconda bioconductor-lpsymphony 1.12.0 r36h6de7cb9_1 bioconda bioconductor-metagenomeseq 1.26.2 r36_0 bioconda bioconductor-multtest 2.40.0 r36h01d97ff_1 bioconda bioconductor-philr 1.10.0 r36_1 bioconda bioconductor-phyloseq 1.28.0 r36_1 bioconda bioconductor-preprocesscore 1.46.0 r36h01d97ff_1 bioconda bioconductor-rhdf5 2.28.0 r36h6de7cb9_1 bioconda bioconductor-rhdf5lib 1.6.0 r36h01d97ff_1 bioconda bioconductor-s4vectors 0.22.0 r36h01d97ff_1 bioconda bioconductor-treeio 1.8.1 r36_0 bioconda bioconductor-wrench 1.2.0 r36_1 bioconda bioconductor-xvector 0.24.0 r36h01d97ff_1 bioconda bioconductor-zlibbioc 1.30.0 r36h01d97ff_1 bioconda biom-format 2.1.7 py36h917ab60_1002 conda-forge biopython 1.74 py36h01d97ff_0 conda-forge bleach 3.1.0 pypi_0 pypi bokeh 1.3.4 py36_0 conda-forge bwidget 1.9.11 0 conda-forge bzip2 1.0.8 h01d97ff_1 conda-forge ca-certificates 2019.9.11 hecc5488_0 conda-forge cachecontrol 0.12.5 py_0 conda-forge cairo 1.16.0 h0ab9d94_1001 conda-forge cctools 895 1 conda-forge certifi 2016.9.26 py36_0 conda-forge clang 4.0.1 1 conda-forge clang_osx-64 4.0.1 h1ce6c1d_17 conda-forge clangxx 4.0.1 1 conda-forge clangxx_osx-64 4.0.1 h22b1bf0_17 conda-forge click 7.0 py_0 conda-forge cloudpickle 1.2.2 pypi_0 pypi colorcet 2.0.2 pypi_0 pypi compiler-rt 4.0.1 hcfea43d_1 curl 7.65.3 ha441bb4_0 cycler 0.10.0 py_1 conda-forge cython 0.29.13 py36h6de7cb9_0 conda-forge dask 2.4.0 pypi_0 pypi datashader 0.7.0 pypi_0 pypi datashape 0.5.2 pypi_0 pypi dbus 1.13.6 h2f22bb5_0 conda-forge decorator 4.4.0 py_0 conda-forge defusedxml 0.6.0 pypi_0 pypi distributed 2.4.0 pypi_0 pypi docopt 0.6.2 pypi_0 pypi entrypoints 0.3 pypi_0 pypi et-xmlfile 1.0.1 pypi_0 pypi ete3 3.1.1 py36_0 bioconda expat 2.2.5 h6de7cb9_1003 conda-forge fastcluster 1.1.25 py36h1702cab_1000 conda-forge fontconfig 2.13.1 h1027ab8_1000 conda-forge freetype 2.10.0 h24853df_1 conda-forge fribidi 1.0.5 h01d97ff_1002 conda-forge fsspec 0.5.1 pypi_0 pypi future 0.17.1 py36_1000 conda-forge gettext 0.19.8.1 h46ab8bc_1002 conda-forge gfortran_osx-64 4.8.5 h22b1bf0_8 conda-forge glib 2.58.3 h9d45998_1002 conda-forge gneiss 0.4.5 py_0 bioconda graphite2 1.3.13 h2098e52_1000 conda-forge graphviz 2.38.0 hc6cc99f_1011 conda-forge gsl 2.4 ha2d443c_1006 conda-forge harfbuzz 2.4.0 h92b87b8_1 conda-forge hdmedians 0.13 py36heacc8b8_1001 conda-forge heapdict 1.0.1 pypi_0 pypi icu 58.2 h0a44026_1000 conda-forge imageio 2.5.0 pypi_0 pypi importlib_metadata 0.23 py36_0 conda-forge ipykernel 5.1.2 pypi_0 pypi ipython 7.8.0 py36h5ca1d4c_0 conda-forge ipython_genutils 0.2.0 py_1 conda-forge jdcal 1.4.1 pypi_0 pypi jedi 0.15.1 py36_0 conda-forge jinja2 2.10.1 py_0 conda-forge joblib 0.13.2 py_0 conda-forge jpeg 9c h1de35cc_1001 conda-forge json5 0.8.5 pypi_0 pypi jsonschema 3.0.2 pypi_0 pypi jupyter-client 5.3.3 pypi_0 pypi jupyter-core 4.5.0 pypi_0 pypi jupyterlab 1.1.4 pypi_0 pypi jupyterlab-server 1.0.6 pypi_0 pypi kiwisolver 1.1.0 py36h770b8ee_0 conda-forge krb5 1.16.1 hddcf347_7 ld64 274.2 1 libblas 3.8.0 12_openblas conda-forge libcblas 3.8.0 12_openblas conda-forge libcurl 7.65.3 h051b688_0 libcxx 4.0.1 hcfea43d_1 conda-forge libcxxabi 4.0.1 hcfea43d_1 conda-forge libedit 3.1.20181209 hb402a30_0 libffi 3.2.1 h475c297_4 libgfortran 3.0.1 0 conda-forge libiconv 1.15 h01d97ff_1005 conda-forge liblapack 3.8.0 12_openblas conda-forge libopenblas 0.3.7 hd44dcd8_1 conda-forge libpng 1.6.37 h2573ce8_0 conda-forge libssh2 1.8.2 hcdc9a53_2 conda-forge libtiff 4.0.10 hd08fb8f_1003 conda-forge libxcb 1.13 h1de35cc_1002 conda-forge libxml2 2.9.9 hd80cff7_2 conda-forge libxslt 1.1.33 h33a18ac_0 llvm 4.0.1 1 conda-forge llvm-lto-tapi 4.0.1 1 conda-forge llvm-openmp 9.0.0 h40edb58_0 conda-forge llvmlite 0.29.0 pypi_0 pypi locket 0.2.0 pypi_0 pypi lockfile 0.12.2 py_1 conda-forge lxml 4.4.1 py36h08abf6f_0 conda-forge lz4-c 1.8.3 h6de7cb9_1001 conda-forge make 4.2.1 h1de35cc_2004 conda-forge markupsafe 1.1.1 py36h1de35cc_0 conda-forge matplotlib 3.1.1 py36_1 conda-forge matplotlib-base 3.1.1 py36h3a684a6_1 conda-forge matplotlib-venn 0.11.5 py_1 conda-forge mistune 0.8.4 pypi_0 pypi more-itertools 7.2.0 py_0 conda-forge msgpack-python 0.6.2 py36h770b8ee_0 conda-forge multipledispatch 0.6.0 pypi_0 pypi natsort 6.0.0 py_0 conda-forge nbconvert 5.6.0 pypi_0 pypi nbformat 4.4.0 pypi_0 pypi ncurses 6.1 h0a44026_1 networkx 2.3 py_0 conda-forge nibabel 2.5.1 pypi_0 pypi nilearn 0.5.2 pypi_0 pypi nose 1.3.7 py36_1002 conda-forge notebook 6.0.1 pypi_0 pypi num2words 0.5.10 pypi_0 pypi numba 0.45.1 pypi_0 pypi numpy 1.17.2 py36h6b0580a_0 conda-forge olefile 0.46 py_0 conda-forge openpyxl 2.6.3 pypi_0 pypi openssl 1.1.1c h01d97ff_0 conda-forge packaging 19.2 py_0 conda-forge palettable 3.3.0 py_0 conda-forge pandas 0.25.1 py36h86efe34_0 conda-forge pandocfilters 1.4.2 pypi_0 pypi pango 1.42.4 h6691c8e_1 conda-forge param 1.9.1 pypi_0 pypi parso 0.5.1 py_0 conda-forge partd 1.0.0 pypi_0 pypi patsy 0.5.1 py_0 conda-forge pcre 8.43 h0a44026_0 pexpect 4.7.0 py36_0 conda-forge pickleshare 0.7.5 py36_1000 conda-forge pillow 6.1.0 py36hb68e598_0 pip 19.2.3 py36_0 conda-forge pixman 0.38.0 h01d97ff_1003 conda-forge pluggy 0.12.0 py_0 conda-forge prometheus-client 0.7.1 pypi_0 pypi prompt_toolkit 2.0.9 py_0 conda-forge psutil 5.6.3 py36h01d97ff_0 conda-forge pthread-stubs 0.4 h1de35cc_1001 conda-forge ptyprocess 0.6.0 py_1001 conda-forge py 1.8.0 py_0 conda-forge pybids 0.9.4 pypi_0 pypi pyct 0.4.6 pypi_0 pypi pydot 1.4.1 py36_1001 conda-forge pygments 2.4.2 py_0 conda-forge pygraphviz 1.5 py36h01d97ff_1001 conda-forge pyhamcrest 1.9.0 py_2 conda-forge pyparsing 2.4.2 py_0 conda-forge pyqt 5.9.2 py36h2a560b1_4 conda-forge pyrsistent 0.15.4 pypi_0 pypi pytest 5.1.2 py36_0 conda-forge pytest-arraydiff 0.3 py_0 conda-forge pytest-astropy 0.5.0 py_0 conda-forge pytest-doctestplus 0.4.0 py_0 conda-forge pytest-openfiles 0.4.0 py_0 conda-forge pytest-remotedata 0.3.1 py_0 conda-forge python 3.6.9 h359304d_0 python-dateutil 2.8.0 py_0 conda-forge python-louvain 0.13 pypi_0 pypi python-ternary 1.0.6 py_0 conda-forge pytz 2019.2 py_0 conda-forge pywavelets 1.0.3 pypi_0 pypi pyyaml 5.1.2 py36h01d97ff_0 conda-forge pyzmq 18.1.0 pypi_0 pypi qt 5.9.7 h93ee506_2 conda-forge r-acepack 1.4.1 r36haf69682_1004 conda-forge r-ade4 1.7_13 r36h159158b_1001 conda-forge r-ape 5.3 r36hf99fc2c_1 conda-forge r-askpass 1.0 r36h1de35cc_0 r r-assertthat 0.2.1 r36h6115d3f_0 r r-backports 1.1.4 r36h46e59ec_0 r r-base 3.6.1 hcb44179_0 r r-base64enc 0.1_3 r36h159158b_1003 conda-forge r-bh 1.69.0_1 r36h6115d3f_0 r r-bit 1.1_14 r36h46e59ec_0 r r-bit64 0.9_7 r36h46e59ec_0 r r-bitops 1.0_6 r36h159158b_1003 conda-forge r-blob 1.1.1 r36h6115d3f_0 r r-callr 3.2.0 r36h6115d3f_0 r r-catools 1.17.1.2 r36hf99fc2c_1 conda-forge r-checkmate 1.9.4 r36h159158b_1 conda-forge r-cli 1.1.0 r36h6115d3f_0 r r-clipr 0.6.0 r36h6115d3f_0 r r-clisymbols 1.2.0 r36h6115d3f_0 r r-cluster 2.1.0 r36haf69682_2 conda-forge r-codetools 0.2_16 r36h6115d3f_1001 conda-forge r-colorspace 1.4_1 r36h159158b_1 conda-forge r-crayon 1.3.4 r36h6115d3f_0 r r-curl 3.3 r36h46e59ec_0 r r-data.table 1.12.2 r36h159158b_1 conda-forge r-dbi 1.0.0 r36h6115d3f_0 r r-dbplyr 1.4.0 r36h6115d3f_0 r r-deoptimr 1.0_8 r36h6115d3f_1002 conda-forge r-desc 1.2.0 r36h6115d3f_0 r r-devtools 2.0.2 r36h6115d3f_0 r r-digest 0.6.18 r36h46e59ec_0 r r-doparallel 1.0.15 r36h6115d3f_0 conda-forge r-dplyr 0.8.0.1 r36h466af19_0 r r-dynamictreecut 1.63_1 r36h6115d3f_1002 conda-forge r-evaluate 0.14 r36h6115d3f_1 conda-forge r-fansi 0.4.0 r36h46e59ec_0 r r-fastcluster 1.1.25 r36ha90c164_1002 conda-forge r-fastmatch 1.1_0 r36h159158b_1004 conda-forge r-fdrtool 1.2.15 r36h159158b_1002 conda-forge r-fit.models 0.5_14 r36h6115d3f_1002 conda-forge r-foreach 1.4.7 r36h6115d3f_0 conda-forge r-foreign 0.8_72 r36h159158b_0 conda-forge r-formula 1.2_3 r36h6115d3f_1002 conda-forge r-fs 1.2.7 r36h466af19_0 r r-gdata 2.18.0 r36h6115d3f_1002 conda-forge r-ggplot2 3.2.1 r36h6115d3f_0 conda-forge r-gh 1.0.1 r36h6115d3f_0 r r-git2r 0.25.2 r36h46e59ec_0 r r-glmnet 2.0_18 r36haf69682_2 conda-forge r-glue 1.3.1 r36h46e59ec_0 r r-gplots 3.0.1.1 r36h6115d3f_1 conda-forge r-gridextra 2.3 r36h6115d3f_1002 conda-forge r-gtable 0.3.0 r36h6115d3f_2 conda-forge r-gtools 3.8.1 r36h159158b_1003 conda-forge r-highr 0.8 r36h6115d3f_1 conda-forge r-hmisc 4.2_0 r36haf69682_2 conda-forge r-htmltable 1.13.2 r36h6115d3f_0 conda-forge r-htmltools 0.3.6 r36h6de7cb9_1003 conda-forge r-htmlwidgets 1.3 r36h6115d3f_1001 conda-forge r-httr 1.4.0 r36h6115d3f_0 r r-igraph 1.2.4.1 r36h75781db_2 conda-forge r-ini 0.3.1 r36h6115d3f_0 r r-iterators 1.0.12 r36h6115d3f_0 conda-forge r-jsonlite 1.6 r36h46e59ec_0 r r-kernsmooth 2.23_15 r36haf69682_1004 conda-forge r-knitr 1.25 r36h6115d3f_0 conda-forge r-labeling 0.3 r36h6115d3f_1002 conda-forge r-lattice 0.20_38 r36h159158b_1002 conda-forge r-latticeextra 0.6_28 r36h6115d3f_1002 conda-forge r-lazyeval 0.2.2 r36h159158b_1 conda-forge r-locfit 1.5_9.1 r36h01d97ff_1004 conda-forge r-magrittr 1.5 r36h6115d3f_4 r r-markdown 1.1 r36h159158b_0 conda-forge r-mass 7.3_51.4 r36h159158b_1 conda-forge r-matrix 1.2_17 r36h159158b_1 conda-forge r-matrixstats 0.55.0 r36h159158b_0 conda-forge r-memoise 1.1.0 r36h6115d3f_0 r r-mgcv 1.8_29 r36h159158b_0 conda-forge r-mime 0.6 r36h46e59ec_0 r r-munsell 0.5.0 r36h6115d3f_1002 conda-forge r-mvtnorm 1.0_11 r36haf69682_2 conda-forge r-nlme 3.1_141 r36haf69682_1 conda-forge r-nnet 7.3_12 r36h159158b_1003 conda-forge r-openssl 1.3 r36h46e59ec_0 r r-pcapp 1.9_73 r36hf99fc2c_1001 conda-forge r-permute 0.9_5 r36_1 conda-forge r-phangorn 2.5.5 r36hf99fc2c_1 conda-forge r-pillar 1.3.1 r36h6115d3f_0 r r-pkgbuild 1.0.3 r36h6115d3f_0 r r-pkgconfig 2.0.2 r36h6115d3f_0 r r-pkgload 1.0.2 r36h466af19_0 r r-plogr 0.2.0 r36h6115d3f_0 r r-plyr 1.8.4 r36hf99fc2c_1003 conda-forge r-prettyunits 1.0.2 r36h6115d3f_0 r r-processx 3.3.0 r36h46e59ec_0 r r-ps 1.3.0 r36h46e59ec_0 r r-purrr 0.3.2 r36h46e59ec_0 r r-quadprog 1.5_7 r36haf69682_2 conda-forge r-r6 2.4.0 r36h6115d3f_0 r r-rcmdcheck 1.3.2 r36h6115d3f_0 r r-rcolorbrewer 1.1_2 r36h6115d3f_1002 conda-forge r-rcpp 1.0.1 r36h466af19_0 r r-remotes 2.0.4 r36h6115d3f_0 r r-reshape2 1.4.3 r36hf99fc2c_1004 conda-forge r-rlang 0.3.4 r36h46e59ec_0 r r-robust 0.4_18.1 r36haf69682_2 conda-forge r-robustbase 0.93_5 r36haf69682_2 conda-forge r-rpart 4.1_15 r36h159158b_1 conda-forge r-rprojroot 1.3_2 r36h6115d3f_0 r r-rrcov 1.4_7 r36haf69682_2 conda-forge r-rsqlite 2.1.1 r36h466af19_0 r r-rstudioapi 0.10 r36h6115d3f_0 r r-rvcheck 0.1.3 r36_1001 conda-forge r-scales 1.0.0 r36hf99fc2c_1002 conda-forge r-sessioninfo 1.1.1 r36h6115d3f_0 r r-slam 0.1_45 r36h159158b_1 conda-forge r-stringi 1.4.3 r36h466af19_0 r r-stringr 1.4.0 r36h6115d3f_1 conda-forge r-survival 2.44_1.1 r36h159158b_1 conda-forge r-sys 3.2 r36h46e59ec_0 r r-tibble 2.1.1 r36h46e59ec_0 r r-tidyr 0.8.3 r36h466af19_0 r r-tidyselect 0.2.5 r36h466af19_0 r r-tidytree 0.2.5 r36h6115d3f_0 conda-forge r-usethis 1.5.0 r36h6115d3f_0 r r-utf8 1.1.4 r36h46e59ec_0 r r-vegan 2.5_6 r36haf69682_0 conda-forge r-viridis 0.5.1 r36h6115d3f_1003 conda-forge r-viridislite 0.3.0 r36h6115d3f_1002 conda-forge r-wgcna 1.68 r36hf99fc2c_1 bioconda r-whisker 0.3_2 r36h6115d3f_4 r r-withr 2.1.2 r36h6115d3f_0 r r-xfun 0.9 r36h6115d3f_0 conda-forge r-xopen 1.0.0 r36h6115d3f_0 r r-yaml 2.2.0 r36h46e59ec_0 r readline 7.0 h1de35cc_5 requests 2.12.5 py36_0 conda-forge rpy2 2.9.4 py36r36h1d22016_0 r scikit-bio 0.5.5 py36h917ab60_1000 conda-forge scikit-image 0.15.0 pypi_0 pypi scikit-learn 0.21.3 py36hd4ffd6c_0 conda-forge scipy 1.3.1 py36hab3da7d_2 conda-forge seaborn 0.9.0 py_1 conda-forge send2trash 1.5.0 pypi_0 pypi setuptools 41.2.0 py36_0 conda-forge sip 4.19.8 py36h0a44026_1000 conda-forge six 1.12.0 py36_1000 conda-forge soothsayer 2019.8 pypi_0 pypi sortedcontainers 2.1.0 pypi_0 pypi sqlalchemy 1.3.8 pypi_0 pypi sqlite 3.29.0 ha441bb4_0 statsmodels 0.10.1 py36heacc8b8_0 conda-forge tblib 1.4.0 pypi_0 pypi templateflow 0.4.1 pypi_0 pypi teneto 0.4.5 pypi_0 pypi terminado 0.8.2 pypi_0 pypi testpath 0.3.1 pypi_0 pypi tk 8.6.8 ha441bb4_0 conda-forge tktable 2.10 h1de35cc_0 toolz 0.10.0 pypi_0 pypi tornado 6.0.3 py36h01d97ff_0 conda-forge tqdm 4.36.1 py_0 conda-forge traitlets 4.3.2 py36_1000 conda-forge tzlocal 2.0.0 py_0 conda-forge wcwidth 0.1.7 py_1 conda-forge webencodings 0.5.1 pypi_0 pypi wheel 0.33.6 py36_0 conda-forge xarray 0.13.0 py_0 conda-forge xorg-kbproto 1.0.7 h1de35cc_1002 conda-forge xorg-libice 1.0.10 h01d97ff_0 conda-forge xorg-libsm 1.2.3 h01d97ff_1000 conda-forge xorg-libx11 1.6.8 h01d97ff_0 conda-forge xorg-libxau 1.0.9 h1de35cc_0 conda-forge xorg-libxdmcp 1.1.3 h01d97ff_0 conda-forge xorg-libxext 1.3.4 h01d97ff_0 conda-forge xorg-libxrender 0.9.10 h01d97ff_1002 conda-forge xorg-renderproto 0.11.1 h1de35cc_1002 conda-forge xorg-xextproto 7.3.0 h1de35cc_1002 conda-forge xorg-xproto 7.0.31 h1de35cc_1007 conda-forge xz 5.2.4 h1de35cc_4 yaml 0.1.7 h1de35cc_1001 conda-forge zict 1.0.0 pypi_0 pypi zipp 0.6.0 py_0 conda-forge zlib 1.2.11 h1de35cc_3 zstd 1.4.0 ha9f0a20_0 conda-forge ```
jupyter lab ``` (soothsayer_testing_env) jespinozlt-osx:~ jespinoz$ jupyter lab [I 12:40:07.777 LabApp] The port 8888 is already in use, trying another port. [I 12:40:07.787 LabApp] JupyterLab extension loaded from /Users/jespinoz/anaconda3/envs/soothsayer_testing_env/lib/python3.6/site-packages/jupyterlab [I 12:40:07.787 LabApp] JupyterLab application directory is /Users/jespinoz/anaconda3/envs/soothsayer_testing_env/share/jupyter/lab [I 12:40:07.790 LabApp] Serving notebooks from local directory: /Users/jespinoz [I 12:40:07.790 LabApp] The Jupyter Notebook is running at: [I 12:40:07.790 LabApp] http://localhost:8889/?token=bd72929cee66c75d4c99fc9d9d2a09a878b47c2dd5ccde86 [I 12:40:07.790 LabApp] or http://127.0.0.1:8889/?token=bd72929cee66c75d4c99fc9d9d2a09a878b47c2dd5ccde86 [I 12:40:07.790 LabApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation). [C 12:40:07.799 LabApp] To access the notebook, open this file in a browser: file:///Users/jespinoz/Library/Jupyter/runtime/nbserver-36956-open.html Or copy and paste one of these URLs: http://localhost:8889/?token=bd72929cee66c75d4c99fc9d9d2a09a878b47c2dd5ccde86 or http://127.0.0.1:8889/?token=bd72929cee66c75d4c99fc9d9d2a09a878b47c2dd5ccde86 [I 12:40:10.342 LabApp] 301 GET /lab/workspaces/auto-w/?reset&token=bd72929cee66c75d4c99fc9d9d2a09a878b47c2dd5ccde86&clone (::1) 1.35ms [I 12:40:11.515 LabApp] Build is up to date [I 12:40:14.081 LabApp] Build is up to date [I 12:40:16.655 LabApp] Kernel started: 89e34e14-0e36-46fb-beee-dc2bcc525daf [I 12:40:27.081 LabApp] Saving file at /Untitled.ipynb [W 12:41:16.667 LabApp] Timeout waiting for kernel_info reply from 89e34e14-0e36-46fb-beee-dc2bcc525daf ```

image

It gets stuck trying to just print 0

jolespin commented 4 years ago

Do you see any part of the installation process that could break jupyter? Ipython still works in the terminal. Could it be a pyqt thing?

jbednar commented 4 years ago

It looks like the environment differences are:

cloudpickle               1.2.2
colorcet                  2.0.2
dask                      2.4.0
datashader                0.7.0
datashape                 0.5.2
distributed               2.4.0
fsspec                    0.5.1
heapdict                  1.0.1
imageio                   2.5.0
llvmlite                  0.29.0
locket                    0.2.0
multipledispatch          0.6.0
numba                     0.45.1
param                     1.9.1
partd                     1.0.0
pyct                      0.4.6
pywavelets                1.0.3
scikit-image              0.15.0
sortedcontainers          2.1.0
tblib                     1.4.0
testpath                  0.3.1 -> 0.4.2
toolz                     0.10.0
zict                      1.0.0

I.e., testpath is upgraded, but the rest are additional new packages added as dependencies. Looking through that list, I don't see anything that should have anything to do with Jupyter. You could try installing each package one at a time to narrow it down, but it seems like a mystery to me!

philippjfr commented 4 years ago

testpath seems like the most likely candidate since it's a jupyter thing.

jbednar commented 4 years ago

And it's the only one changing versions! From the name I didn't see that it's Jupyter related, but sure, try downgrading that in the Datashader envt or upgrading it in the fresh envt, and see if it changes the status of either one.

jolespin commented 4 years ago

Thanks you guys. Found the culprit. I installed one by one from the bottom up (definitely should have went from the top down but w/e haha): 

(soothsayer_testing_env) jespinozlt-osx:~ jespinoz$ pip install distributed==2.4.0
Collecting distributed==2.4.0
  Using cached https://files.pythonhosted.org/packages/28/b4/a3fd1be0026fcea8cf3e963bff7ba098dd2e2ff52dd6a709481ec78e587c/distributed-2.4.0-py3-none-any.whl
Requirement already satisfied: psutil>=5.0 in ./anaconda3/envs/soothsayer_testing_env/lib/python3.6/site-packages (from distributed==2.4.0) (5.6.3)
Requirement already satisfied: pyyaml in ./anaconda3/envs/soothsayer_testing_env/lib/python3.6/site-packages (from distributed==2.4.0) (5.1.2)
Requirement already satisfied: tornado>=5 in ./anaconda3/envs/soothsayer_testing_env/lib/python3.6/site-packages (from distributed==2.4.0) (6.0.3)
Requirement already satisfied: msgpack in ./anaconda3/envs/soothsayer_testing_env/lib/python3.6/site-packages (from distributed==2.4.0) (0.6.2)
Requirement already satisfied: click>=6.6 in ./anaconda3/envs/soothsayer_testing_env/lib/python3.6/site-packages (from distributed==2.4.0) (7.0)
Requirement already satisfied: zict>=0.1.3 in ./anaconda3/envs/soothsayer_testing_env/lib/python3.6/site-packages (from distributed==2.4.0) (1.0.0)
Requirement already satisfied: tblib in ./anaconda3/envs/soothsayer_testing_env/lib/python3.6/site-packages (from distributed==2.4.0) (1.4.0)
Collecting dask>=2 (from distributed==2.4.0)
  Using cached https://files.pythonhosted.org/packages/19/39/5f782ac9cfc00cd7d2eae10e72e1bff2f0b396ec31961257acda55e0ef36/dask-2.4.0-py3-none-any.whl
Requirement already satisfied: toolz>=0.7.4 in ./anaconda3/envs/soothsayer_testing_env/lib/python3.6/site-packages (from distributed==2.4.0) (0.10.0)
Collecting cloudpickle>=0.2.2 (from distributed==2.4.0)
  Using cached https://files.pythonhosted.org/packages/c1/49/334e279caa3231255725c8e860fa93e72083567625573421db8875846c14/cloudpickle-1.2.2-py2.py3-none-any.whl
Requirement already satisfied: sortedcontainers!=2.0.0,!=2.0.1 in ./anaconda3/envs/soothsayer_testing_env/lib/python3.6/site-packages (from distributed==2.4.0) (2.1.0)
Requirement already satisfied: heapdict in ./anaconda3/envs/soothsayer_testing_env/lib/python3.6/site-packages (from zict>=0.1.3->distributed==2.4.0) (1.0.1)
Installing collected packages: dask, cloudpickle, distributed
Successfully installed cloudpickle-1.2.2 dask-2.4.0 distributed-2.4.0
(soothsayer_testing_env) jespinozlt-osx:~ jespinoz$ jupyter lab
[I 12:16:56.212 LabApp] The port 8888 is already in use, trying another port.
[I 12:16:56.213 LabApp] The port 8889 is already in use, trying another port.
[I 12:16:56.214 LabApp] The port 8890 is already in use, trying another port.
[I 12:16:56.223 LabApp] JupyterLab extension loaded from /Users/jespinoz/anaconda3/envs/soothsayer_testing_env/lib/python3.6/site-packages/jupyterlab
[I 12:16:56.223 LabApp] JupyterLab application directory is /Users/jespinoz/anaconda3/envs/soothsayer_testing_env/share/jupyter/lab
[I 12:16:56.226 LabApp] Serving notebooks from local directory: /Users/jespinoz
[I 12:16:56.226 LabApp] The Jupyter Notebook is running at:
[I 12:16:56.226 LabApp] http://localhost:8891/?token=6b18623f4eb35b56949dea2f7184ab11ab454b67e1c9227c
[I 12:16:56.226 LabApp]  or http://127.0.0.1:8891/?token=6b18623f4eb35b56949dea2f7184ab11ab454b67e1c9227c
[I 12:16:56.226 LabApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[C 12:16:56.233 LabApp]

    To access the notebook, open this file in a browser:
        file:///Users/jespinoz/Library/Jupyter/runtime/nbserver-10092-open.html
    Or copy and paste one of these URLs:
        http://localhost:8891/?token=6b18623f4eb35b56949dea2f7184ab11ab454b67e1c9227c
     or http://127.0.0.1:8891/?token=6b18623f4eb35b56949dea2f7184ab11ab454b67e1c9227c
[I 12:16:59.295 LabApp] Build is up to date
[I 12:16:59.908 LabApp] Kernel started: 3d30f858-1deb-4079-83e2-c9b5460c1611
[W 12:17:59.922 LabApp] Timeout waiting for kernel_info reply from 3d30f858-1deb-4079-83e2-c9b5460c1611
[I 12:18:59.872 LabApp] Saving file at /Untitled.ipynb

It's one of these: dask, cloudpickle, distributed

jolespin commented 4 years ago

Uninstalling distributed fixes jupyter!

How dependent is datashader on distributed?

jolespin commented 4 years ago

FYI: I think an additional dependency that wasn't installed was datashape. I uninstalled distributed then pip install datashader --no-deps.

Tried to run this code: http://datashader.org/user_guide/7_Networks.html

import math
import numpy as np
import pandas as pd

import datashader as ds
import datashader.transfer_functions as tf
from datashader.layout import random_layout, circular_layout, forceatlas2_layout
from datashader.bundling import connect_edges, hammer_bundle

from itertools import chain
jbednar commented 4 years ago

I don't think datashader itself imports distributed. It's used with Dask, but Datashader may well work fine without it as long as you only provide Pandas dataframes, not Dask ones.

ppwadhwa commented 3 years ago

Closing as it looks like its taken care of. Please re-open if there is a remaining issue.