pip install --no-deps [package] removes EVERYTHING from site-packages

jolespin commented 5 years ago

Environment

pip version: 19.2.3
Python version: 3.6
OS:

Description When I install my python package using pip it removes everything from site-packages. This happened off a fresh install of conda and pip.

I created this environment soothsayer_env and then cloned it into testing_env:

(testing_env) Joshs-MacBook-Pro:~ mu$ ls /Users/mu/anaconda3/envs/soothsayer_env/lib/python3.6/site-packages/
Bio                                   dateutil                              libpasteurize                         patsy-0.5.1.dist-info                 scikit_learn-0.21.3.dist-info
BioSQL                                decorator-4.4.0.dist-info             lockfile                              pexpect                               scipy
CacheControl-0.12.5-py2.7.egg-info    decorator.py                          lockfile-0.12.2-py2.7.egg-info        pexpect-4.7.0.dist-info               scipy-1.3.1.dist-info
Click-7.0-py2.7.egg-info              defusedxml                            lxml                                  pickleshare-0.7.5-py3.6.egg-info      seaborn
Cython                                defusedxml-0.6.0.dist-info            lxml-4.4.1-py3.6.egg-info             pickleshare.py                        seaborn-0.9.0.dist-info
Cython-0.29.13.dist-info              docopt-0.6.2.dist-info                markupsafe                            pip                                   send2trash
IPython                               docopt.py                             matplotlib                            pip-19.2.3-py3.6.egg-info             setuptools
Jinja2-2.10.1.dist-info               dot_parser.py                         matplotlib-3.1.1-py3.6-nspkg.pth      pkg_resources                         setuptools-41.2.0-py3.6.egg-info
MarkupSafe-1.1.1.dist-info            easy_install.py                       matplotlib-3.1.1.dist-info            pluggy                                sip.pyi
PIL                                   entrypoints-0.3.dist-info             matplotlib_venn                       pluggy-0.12.0.dist-info               sip.so
Pillow-6.1.0.dist-info                entrypoints.py                        matplotlib_venn-0.11.5-py2.7.egg-info prometheus_client                     sipconfig.py
PyHamcrest-1.9.0-py2.7.egg-info       et_xmlfile                            mistune-0.8.4.dist-info               prometheus_client-0.7.1.dist-info     sipdistutils.py
PyQt5                                 et_xmlfile-1.0.1.dist-info            mistune.py                            prompt_toolkit                        six-1.12.0-py3.6.egg-info
PyYAML-5.1.2-py3.6.egg-info           ete3                                  more_itertools                        prompt_toolkit-2.0.9.dist-info        six.py
Pygments-2.4.2.dist-info              ete3-3.1.1-py3.6.egg-info             more_itertools-7.2.0.dist-info        psutil                                skbio
README.md                             fastcluster-1.1.25-py3.6.egg-info     mpl_toolkits                          psutil-5.6.3.dist-info                sklearn
README.txt                            fastcluster.py                        msgpack                               ptyprocess                            soothsayer
SQLAlchemy-1.3.8.dist-info            future                                msgpack-0.6.2.dist-info               ptyprocess-0.6.0.dist-info            soothsayer-2019.8.dist-info
Send2Trash-1.5.0.dist-info            future-0.17.1-py3.6.egg-info          natsort                               pvectorc.cpython-36m-darwin.so        sqlalchemy
__pycache__                           gneiss                                natsort-6.0.0.dist-info               py                                    statsmodels
_fastcluster.cpython-36m-darwin.so    gneiss-0.4.5-py3.7.egg-info           nbconvert                             py-1.8.0.dist-info                    statsmodels-0.10.1.dist-info
_pyrsistent_version.py                hamcrest                              nbconvert-5.6.0.dist-info             pybids-0.9.4.dist-info                templateflow
_pytest                               hdmedians                             nbformat                              pydot-1.4.1.dist-info                 templateflow-0.4.1.dist-info
_yaml.cpython-36m-darwin.so           hdmedians-0.13.dist-info              nbformat-4.4.0.dist-info              pydot.py                              teneto
adjustText                            importlib_metadata                    networkx                              pygments                              teneto-0.4.5.dist-info
adjustText-0.7.3.dist-info            importlib_metadata-0.23.dist-info     networkx-2.3.dist-info                pygraphviz                            terminado
appnope                               ipykernel                             nibabel                               pygraphviz-1.5.dist-info              terminado-0.8.2.dist-info
appnope-0.1.0-py3.6.egg-info          ipykernel-5.1.2.dist-info             nibabel-2.5.1.dist-info               pylab.py                              ternary
astropy                               ipykernel_launcher.py                 nilearn                               pyparsing-2.4.2.dist-info             testpath
astropy-3.2.1-py3.6.egg-info          ipython-7.8.0.dist-info               nilearn-0.5.2.dist-info               pyparsing.py                          testpath-0.4.2.dist-info
atomicwrites                          ipython_genutils                      nisext                                pyrsistent                            tests
atomicwrites-1.3.0-py2.7.egg-info     ipython_genutils-0.2.0-py2.7.egg-info nose                                  pyrsistent-0.15.4.dist-info           tornado
attr                                  jdcal-1.4.1.dist-info                 nose-1.3.7-py3.6.egg-info             pytest-5.1.2-py3.6.egg-info           tornado-6.0.3.dist-info
attrs-19.1.0.dist-info                jdcal.py                              notebook                              pytest.py                             tqdm
backcall                              jedi                                  notebook-6.0.1.dist-info              pytest_arraydiff                      tqdm-4.36.1.dist-info
backcall-0.1.0.dist-info              jedi-0.15.1.dist-info                 num2words                             pytest_arraydiff-0.3.dist-info        traitlets
benchmarks                            jinja2                                num2words-0.5.10.dist-info            pytest_astropy-0.5.0.dist-info        traitlets-4.3.2-py3.6.egg-info
bids                                  joblib                                numpy                                 pytest_doctestplus                    tzlocal
bids_validator                        joblib-0.13.2-py2.7.egg-info          numpy-1.17.2.dist-info                pytest_doctestplus-0.4.0.dist-info    tzlocal-2.0.0.dist-info
bids_validator-1.2.4.dist-info        json5                                 olefile                               pytest_openfiles                      wcwidth
biom                                  json5-0.8.5.dist-info                 olefile-0.46-py2.7.egg-info           pytest_openfiles-0.4.0.dist-info      wcwidth-0.1.7-py2.7.egg-info
biom_format-2.1.7.dist-info           jsonschema                            openpyxl                              pytest_remotedata                     webencodings
biopython-1.74.dist-info              jsonschema-3.0.2.dist-info            openpyxl-2.6.3.dist-info              pytest_remotedata-0.3.1.dist-info     webencodings-0.5.1.dist-info
bleach                                jupyter.py                            packaging                             python_dateutil-2.8.0.dist-info       wheel
bleach-3.1.0.dist-info                jupyter_client                        packaging-19.2.dist-info              python_louvain-0.13.dist-info         wheel-0.33.6-py3.6.egg-info
bokeh                                 jupyter_client-5.3.3.dist-info        palettable                            python_ternary-1.0.6.dist-info        xarray
bokeh-1.3.4.dist-info                 jupyter_core                          palettable-3.3.0.dist-info            pytz                                  xarray-0.13.0.dist-info
cachecontrol                          jupyter_core-4.5.0.dist-info          pandas                                pytz-2019.2.dist-info                 yaml
certifi                               jupyterlab                            pandas-0.25.1.dist-info               pyximport                             zipp-0.6.0.dist-info
certifi-2016.09.26-py3.6.egg-info     jupyterlab-1.1.4.dist-info            pandocfilters-1.4.2.dist-info         pyzmq-18.1.0.dist-info                zipp.py
click                                 jupyterlab_server                     pandocfilters.py                      requests                              zmq
community                             jupyterlab_server-1.0.6.dist-info     parso                                 requests-2.12.5-py3.6.egg-info
cycler-0.10.0-py2.7.egg-info          kiwisolver-1.1.0.dist-info            parso-0.5.1.dist-info                 rpy2
cycler.py                             kiwisolver.cpython-36m-darwin.so      past                                  rpy2-2.9.4-py3.6.egg-info
cython.py                             libfuturize                           patsy                                 scikit_bio-0.5.5.dist-info

Now look at this:


(testing_env) Joshs-MacBook-Pro:~ mu$ ls /Users/mu/anaconda3/envs/testing_env/lib/python3.6/site-packages/
soothsayer                   soothsayer-2019.10.dist-info

Expected behavior Not to delete my modules

How to Reproduce I ran the following commands in separate instances with the same results:

pip install --no-deps git+https://github.com/jolespin/soothsayer

and locally:

pip install --no-deps ~/Google/Informatics/Algorithms/Packages/soothsayer/

My setup script hasn't changed. This has happened with pip before and I have no idea why it does this sometimes.

Here's my pip before it got deleted by pip:

pip 19.2.3 from /Users/mu/anaconda3/envs/soothsayer_env/lib/python3.6/site-packages/pip (python 3.6)

chrahunt commented 5 years ago

I think some details are missing for us to have a clear picture, please bear with me.

I created this environment soothsayer_env and then cloned it into testing_env

What is soothsayer_env, a virtualenv virtual environment, venv virtual environment, or conda environment (?)? What does it mean to "clone" it into testing_env? What commands would I run to recreate your setup?

and locally: pip install --no-deps ~/Google/Informatics/Algorithms/Packages/soothsayer/

Where does this directory come from? Does it have the same contents as git+https://github.com/jolespin/soothsayer?

My setup script hasn't changed.

Can you provide the setup script you're talking about?

Also, in the first command you're showing ls of /Users/mu/anaconda3/envs/soothsayer_env/lib/python3.6/site-packages/, but in the second command you're showing ls of /Users/mu/anaconda3/envs/testing_env/lib/python3.6/site-packages/ (soothsayer_env vs testing_env). Did testing_env previously contain all of the other packages or something else?

jolespin commented 5 years ago

Sorry about that. Those are huge details I left out.

soothsayer_env and testing_env are conda environments.

setup script: https://github.com/jolespin/soothsayer/blob/master/setup.py

import re, datetime
from setuptools import setup, find_packages

# Version
version = None
with open("./soothsayer/__init__.py", "r") as f:
    for line in f.readlines():
        line = line.strip()
        if line.startswith("__version__"):
            version = line.split("=")[-1].strip().strip('"')
assert version is not None, "Check version in soothsayer/__init__.py"

setup(name='soothsayer',
      version=version,
      description='High-level API for (bio-)informatics',
      url='https://github.com/jolespin/soothsayer',
      author='Josh L. Espinoza',
      author_email='jespinoz@jcvi.org',
      license='BSD-3',
      packages=find_packages(include=("*", "./*")),
      install_requires=[
    "matplotlib >= 2.2.2",
    "scipy >= 1.0",
    "scikit-learn >= 0.20.2",
    "numpy >= 1.13", #, < 1.14.0",
    'pandas >= 0.24.2',
    'networkx >= 2.0',
    'ete3 >= 3.0',
    'scikit-bio >= 0.5.1',
    "biopython >= 1.5",
    "xarray >= 0.10.3",
    "tqdm >=4.19",
    "openpyxl >= 2.5",
    "astropy >= 3.0",
    "rpy2 >= 2.9",
    "matplotlib_venn",
    "palettable >= 3.0.0",
    "adjustText",
    "tzlocal",
    "statsmodels >= 0.10.0", #https://github.com/statsmodels/statsmodels/issues/5899 May need to use this separately: pip install git+https://github.com/statsmodels/statsmodels.git@maintenance/0.10.x
    "teneto",

      ],
     include_package_data=True,
     scripts=['bin/clairvoyance.py', "bin/run_soothsayer.py"],

)

You can recreate my situation by doing this:

wget https://github.com/jolespin/soothsayer/blob/master/install/soothsayer_py36_v2019.08.osx.yml

conda env create --name soothsayer_env --file soothsayer_py36_v2019.08.osx.yml

conda create --name testing_env --clone soothsayer_env

Yes, testing_env used to contain everything from soothsayer_env prior to updating my soothsayer package.

Any help would be greatly appreciated. Thank's for taking a look at this!

jolespin commented 5 years ago

I just tried downgrading to 19.2.3-py36_0 --> 18.0-py36_1001 and still got the error.

I've install my package using the following and it worked: python setup.py install

jolespin commented 5 years ago

Here's my reproduction:

Remove broken environment and clone original environment

``` (base) Joshs-MacBook-Pro:~ mu$ conda env remove --name testing_env; conda create --name testing_env --clone soothsayer_env; conda activate testing_env Remove all packages in environment /Users/mu/anaconda3/envs/testing_env: Source: /Users/mu/anaconda3/envs/soothsayer_env Destination: /Users/mu/anaconda3/envs/testing_env Packages: 325 Files: 11124 Preparing transaction: done Verifying transaction: done Executing transaction: done # # To activate this environment, use # # $ conda activate testing_env # # To deactivate an active environment, use # # $ conda deactivate ```

Show site-packages directory

``` (testing_env) Joshs-MacBook-Pro:~ mu$ ls /Users/mu/anaconda3/envs/testing_env/lib/python3.6/site-packages/ Bio ete3 nibabel pytest_openfiles BioSQL ete3-3.1.1-py3.6.egg-info nibabel-2.5.1.dist-info pytest_openfiles-0.4.0.dist-info CacheControl-0.12.5-py2.7.egg-info fastcluster-1.1.25-py3.6.egg-info nilearn pytest_remotedata Click-7.0-py2.7.egg-info fastcluster.py nilearn-0.5.2.dist-info pytest_remotedata-0.3.1.dist-info Cython future nisext python_dateutil-2.8.0.dist-info Cython-0.29.13.dist-info future-0.17.1-py3.6.egg-info nose python_louvain-0.13.dist-info IPython gneiss nose-1.3.7-py3.6.egg-info python_ternary-1.0.6.dist-info Jinja2-2.10.1.dist-info gneiss-0.4.5-py3.7.egg-info notebook pytz MarkupSafe-1.1.1.dist-info hamcrest notebook-6.0.1.dist-info pytz-2019.2.dist-info PIL hdmedians num2words pyximport Pillow-6.1.0.dist-info hdmedians-0.13.dist-info num2words-0.5.10.dist-info pyzmq-18.1.0.dist-info PyHamcrest-1.9.0-py2.7.egg-info importlib_metadata numpy requests PyQt5 importlib_metadata-0.23.dist-info numpy-1.17.2.dist-info requests-2.12.5-py3.6.egg-info PyYAML-5.1.2-py3.6.egg-info ipykernel olefile rpy2 Pygments-2.4.2.dist-info ipykernel-5.1.2.dist-info olefile-0.46-py2.7.egg-info rpy2-2.9.4-py3.6.egg-info README.md ipykernel_launcher.py openpyxl scikit_bio-0.5.5.dist-info README.txt ipython-7.8.0.dist-info openpyxl-2.6.3.dist-info scikit_learn-0.21.3.dist-info SQLAlchemy-1.3.8.dist-info ipython_genutils packaging scipy Send2Trash-1.5.0.dist-info ipython_genutils-0.2.0-py2.7.egg-info packaging-19.2.dist-info scipy-1.3.1.dist-info __pycache__ jdcal-1.4.1.dist-info palettable seaborn _fastcluster.cpython-36m-darwin.so jdcal.py palettable-3.3.0.dist-info seaborn-0.9.0.dist-info _pyrsistent_version.py jedi pandas send2trash _pytest jedi-0.15.1.dist-info pandas-0.25.1.dist-info setuptools _yaml.cpython-36m-darwin.so jinja2 pandocfilters-1.4.2.dist-info setuptools-41.2.0-py3.6.egg-info adjustText joblib pandocfilters.py sip.pyi adjustText-0.7.3.dist-info joblib-0.13.2-py2.7.egg-info parso sip.so appnope json5 parso-0.5.1.dist-info sipconfig.py appnope-0.1.0-py3.6.egg-info json5-0.8.5.dist-info past sipdistutils.py astropy jsonschema patsy six-1.12.0-py3.6.egg-info astropy-3.2.1-py3.6.egg-info jsonschema-3.0.2.dist-info patsy-0.5.1.dist-info six.py atomicwrites jupyter.py pexpect skbio atomicwrites-1.3.0-py2.7.egg-info jupyter_client pexpect-4.7.0.dist-info sklearn attr jupyter_client-5.3.3.dist-info pickleshare-0.7.5-py3.6.egg-info soothsayer attrs-19.1.0.dist-info jupyter_core pickleshare.py soothsayer-2019.8.dist-info backcall jupyter_core-4.5.0.dist-info pip sqlalchemy backcall-0.1.0.dist-info jupyterlab pip-19.2.3-py3.6.egg-info statsmodels benchmarks jupyterlab-1.1.4.dist-info pkg_resources statsmodels-0.10.1.dist-info bids jupyterlab_server pluggy templateflow bids_validator jupyterlab_server-1.0.6.dist-info pluggy-0.12.0.dist-info templateflow-0.4.1.dist-info bids_validator-1.2.4.dist-info kiwisolver-1.1.0.dist-info prometheus_client teneto biom kiwisolver.cpython-36m-darwin.so prometheus_client-0.7.1.dist-info teneto-0.4.5.dist-info biom_format-2.1.7.dist-info libfuturize prompt_toolkit terminado biopython-1.74.dist-info libpasteurize prompt_toolkit-2.0.9.dist-info terminado-0.8.2.dist-info bleach lockfile psutil ternary bleach-3.1.0.dist-info lockfile-0.12.2-py2.7.egg-info psutil-5.6.3.dist-info testpath bokeh lxml ptyprocess testpath-0.4.2.dist-info bokeh-1.3.4.dist-info lxml-4.4.1-py3.6.egg-info ptyprocess-0.6.0.dist-info tests cachecontrol markupsafe pvectorc.cpython-36m-darwin.so tornado certifi matplotlib py tornado-6.0.3.dist-info certifi-2016.09.26-py3.6.egg-info matplotlib-3.1.1-py3.6-nspkg.pth py-1.8.0.dist-info tqdm click matplotlib-3.1.1.dist-info pybids-0.9.4.dist-info tqdm-4.36.1.dist-info community matplotlib_venn pydot-1.4.1.dist-info traitlets cycler-0.10.0-py2.7.egg-info matplotlib_venn-0.11.5-py2.7.egg-info pydot.py traitlets-4.3.2-py3.6.egg-info cycler.py mistune-0.8.4.dist-info pygments tzlocal cython.py mistune.py pygraphviz tzlocal-2.0.0.dist-info dateutil more_itertools pygraphviz-1.5.dist-info wcwidth decorator-4.4.0.dist-info more_itertools-7.2.0.dist-info pylab.py wcwidth-0.1.7-py2.7.egg-info decorator.py mpl_toolkits pyparsing-2.4.2.dist-info webencodings defusedxml msgpack pyparsing.py webencodings-0.5.1.dist-info defusedxml-0.6.0.dist-info msgpack-0.6.2.dist-info pyrsistent wheel docopt-0.6.2.dist-info natsort pyrsistent-0.15.4.dist-info wheel-0.33.6-py3.6.egg-info docopt.py natsort-6.0.0.dist-info pytest-5.1.2-py3.6.egg-info xarray dot_parser.py nbconvert pytest.py xarray-0.13.0.dist-info easy_install.py nbconvert-5.6.0.dist-info pytest_arraydiff yaml entrypoints-0.3.dist-info nbformat pytest_arraydiff-0.3.dist-info zipp-0.6.0.dist-info entrypoints.py nbformat-4.4.0.dist-info pytest_astropy-0.5.0.dist-info zipp.py et_xmlfile networkx pytest_doctestplus zmq et_xmlfile-1.0.1.dist-info networkx-2.3.dist-info pytest_doctestplus-0.4.0.dist-info ```

Install package from GitHub with all verbosity flags

``` (testing_env) Joshs-MacBook-Pro:~ mu$ pip install git+https://github.com/jolespin/soothsayer -v -v -v Created temporary directory: /private/var/folders/b0/30gxwqd95x995btmclwt4wjm0000gn/T/pip-ephem-wheel-cache-w_w6_t48 Created temporary directory: /private/var/folders/b0/30gxwqd95x995btmclwt4wjm0000gn/T/pip-req-tracker-hblkn_n3 Created requirements tracker '/private/var/folders/b0/30gxwqd95x995btmclwt4wjm0000gn/T/pip-req-tracker-hblkn_n3' Created temporary directory: /private/var/folders/b0/30gxwqd95x995btmclwt4wjm0000gn/T/pip-install-rjpzqwh1 Collecting git+https://github.com/jolespin/soothsayer Created temporary directory: /private/var/folders/b0/30gxwqd95x995btmclwt4wjm0000gn/T/pip-req-build-b_qclz48 Cloning https://github.com/jolespin/soothsayer to /private/var/folders/b0/30gxwqd95x995btmclwt4wjm0000gn/T/pip-req-build-b_qclz48 Running command git clone -q https://github.com/jolespin/soothsayer /private/var/folders/b0/30gxwqd95x995btmclwt4wjm0000gn/T/pip-req-build-b_qclz48 Added git+https://github.com/jolespin/soothsayer to build tracker '/private/var/folders/b0/30gxwqd95x995btmclwt4wjm0000gn/T/pip-req-tracker-hblkn_n3' Running setup.py (path:/private/var/folders/b0/30gxwqd95x995btmclwt4wjm0000gn/T/pip-req-build-b_qclz48/setup.py) egg_info for package from git+https://github.com/jolespin/soothsayer Running command python setup.py egg_info running egg_info creating pip-egg-info/soothsayer.egg-info writing pip-egg-info/soothsayer.egg-info/PKG-INFO writing dependency_links to pip-egg-info/soothsayer.egg-info/dependency_links.txt writing requirements to pip-egg-info/soothsayer.egg-info/requires.txt writing top-level names to pip-egg-info/soothsayer.egg-info/top_level.txt writing manifest file 'pip-egg-info/soothsayer.egg-info/SOURCES.txt' reading manifest file 'pip-egg-info/soothsayer.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching '*' under directory 'examples' warning: no files found matching '*.py' under directory 'soothsayer/io/data_type/' warning: no files found matching '*.py' under directory 'soothsayer/tests/data/' warning: no previously-included files matching '*.py[cod]' found anywhere in distribution warning: no previously-included files matching '__pycache__' found anywhere in distribution writing manifest file 'pip-egg-info/soothsayer.egg-info/SOURCES.txt' Source in /private/var/folders/b0/30gxwqd95x995btmclwt4wjm0000gn/T/pip-req-build-b_qclz48 has version 2019.10, which satisfies requirement soothsayer==2019.10 from git+https://github.com/jolespin/soothsayer Removed soothsayer==2019.10 from git+https://github.com/jolespin/soothsayer from build tracker '/private/var/folders/b0/30gxwqd95x995btmclwt4wjm0000gn/T/pip-req-tracker-hblkn_n3' Requirement already satisfied: matplotlib>=2.2.2 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from soothsayer==2019.10) (3.1.1) Requirement already satisfied: scipy>=1.0 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from soothsayer==2019.10) (1.3.1) Requirement already satisfied: scikit-learn>=0.20.2 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from soothsayer==2019.10) (0.21.3) Requirement already satisfied: numpy>=1.13 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from soothsayer==2019.10) (1.17.2) Requirement already satisfied: pandas>=0.24.2 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from soothsayer==2019.10) (0.25.1) Requirement already satisfied: networkx>=2.0 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from soothsayer==2019.10) (2.3) Requirement already satisfied: ete3>=3.0 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from soothsayer==2019.10) (3.1.1) Requirement already satisfied: scikit-bio>=0.5.1 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from soothsayer==2019.10) (0.5.5) Requirement already satisfied: biopython>=1.5 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from soothsayer==2019.10) (1.74) Requirement already satisfied: xarray>=0.10.3 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from soothsayer==2019.10) (0.13.0) Requirement already satisfied: tqdm>=4.19 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from soothsayer==2019.10) (4.36.1) Requirement already satisfied: openpyxl>=2.5 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from soothsayer==2019.10) (2.6.3) Requirement already satisfied: astropy>=3.0 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from soothsayer==2019.10) (3.2.1) Requirement already satisfied: rpy2>=2.9 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from soothsayer==2019.10) (2.9.4) Requirement already satisfied: matplotlib_venn in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from soothsayer==2019.10) (0.11.5) Requirement already satisfied: palettable>=3.0.0 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from soothsayer==2019.10) (3.3.0) Requirement already satisfied: adjustText in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from soothsayer==2019.10) (0.7.3) Requirement already satisfied: tzlocal in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from soothsayer==2019.10) (2.0.0) Requirement already satisfied: statsmodels>=0.10.0 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from soothsayer==2019.10) (0.10.1) Requirement already satisfied: teneto in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from soothsayer==2019.10) (0.4.5) Requirement already satisfied: cycler>=0.10 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from matplotlib>=2.2.2->soothsayer==2019.10) (0.10.0) Requirement already satisfied: python-dateutil>=2.1 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from matplotlib>=2.2.2->soothsayer==2019.10) (2.8.0) Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from matplotlib>=2.2.2->soothsayer==2019.10) (2.4.2) Requirement already satisfied: kiwisolver>=1.0.1 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from matplotlib>=2.2.2->soothsayer==2019.10) (1.1.0) Requirement already satisfied: joblib>=0.11 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from scikit-learn>=0.20.2->soothsayer==2019.10) (0.13.2) Requirement already satisfied: pytz>=2017.2 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from pandas>=0.24.2->soothsayer==2019.10) (2019.2) Requirement already satisfied: decorator>=4.3.0 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from networkx>=2.0->soothsayer==2019.10) (4.4.0) Requirement already satisfied: lockfile>=0.10.2 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from scikit-bio>=0.5.1->soothsayer==2019.10) (0.12.2) Requirement already satisfied: CacheControl>=0.11.5 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from scikit-bio>=0.5.1->soothsayer==2019.10) (0.12.5) Requirement already satisfied: hdmedians>=0.13 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from scikit-bio>=0.5.1->soothsayer==2019.10) (0.13) Requirement already satisfied: IPython>=3.2.0 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from scikit-bio>=0.5.1->soothsayer==2019.10) (7.8.0) Requirement already satisfied: natsort>=4.0.3 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from scikit-bio>=0.5.1->soothsayer==2019.10) (6.0.0) Requirement already satisfied: et-xmlfile in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from openpyxl>=2.5->soothsayer==2019.10) (1.0.1) Requirement already satisfied: jdcal in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from openpyxl>=2.5->soothsayer==2019.10) (1.4.1) Requirement already satisfied: six in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from rpy2>=2.9->soothsayer==2019.10) (1.12.0) Requirement already satisfied: jinja2 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from rpy2>=2.9->soothsayer==2019.10) (2.10.1) Requirement already satisfied: patsy>=0.4.0 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from statsmodels>=0.10.0->soothsayer==2019.10) (0.5.1) Requirement already satisfied: pybids>=0.7.1 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from teneto->soothsayer==2019.10) (0.9.4) Requirement already satisfied: nilearn>=0.4.0 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from teneto->soothsayer==2019.10) (0.5.2) Requirement already satisfied: python-louvain>=0.13 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from teneto->soothsayer==2019.10) (0.13) Requirement already satisfied: templateflow>=0.3 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from teneto->soothsayer==2019.10) (0.4.1) Requirement already satisfied: setuptools in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from kiwisolver>=1.0.1->matplotlib>=2.2.2->soothsayer==2019.10) (41.2.0) Requirement already satisfied: requests in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from CacheControl>=0.11.5->scikit-bio>=0.5.1->soothsayer==2019.10) (2.12.5) Requirement already satisfied: msgpack in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from CacheControl>=0.11.5->scikit-bio>=0.5.1->soothsayer==2019.10) (0.6.2) Requirement already satisfied: Cython>=0.23 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from hdmedians>=0.13->scikit-bio>=0.5.1->soothsayer==2019.10) (0.29.13) Requirement already satisfied: jedi>=0.10 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from IPython>=3.2.0->scikit-bio>=0.5.1->soothsayer==2019.10) (0.15.1) Requirement already satisfied: pexpect; sys_platform != "win32" in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from IPython>=3.2.0->scikit-bio>=0.5.1->soothsayer==2019.10) (4.7.0) Requirement already satisfied: appnope; sys_platform == "darwin" in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from IPython>=3.2.0->scikit-bio>=0.5.1->soothsayer==2019.10) (0.1.0) Requirement already satisfied: pickleshare in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from IPython>=3.2.0->scikit-bio>=0.5.1->soothsayer==2019.10) (0.7.5) Requirement already satisfied: traitlets>=4.2 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from IPython>=3.2.0->scikit-bio>=0.5.1->soothsayer==2019.10) (4.3.2) Requirement already satisfied: pygments in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from IPython>=3.2.0->scikit-bio>=0.5.1->soothsayer==2019.10) (2.4.2) Requirement already satisfied: prompt-toolkit<2.1.0,>=2.0.0 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from IPython>=3.2.0->scikit-bio>=0.5.1->soothsayer==2019.10) (2.0.9) Requirement already satisfied: backcall in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from IPython>=3.2.0->scikit-bio>=0.5.1->soothsayer==2019.10) (0.1.0) Requirement already satisfied: MarkupSafe>=0.23 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from jinja2->rpy2>=2.9->soothsayer==2019.10) (1.1.1) Requirement already satisfied: bids-validator in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from pybids>=0.7.1->teneto->soothsayer==2019.10) (1.2.4) Requirement already satisfied: sqlalchemy in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from pybids>=0.7.1->teneto->soothsayer==2019.10) (1.3.8) Requirement already satisfied: num2words in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from pybids>=0.7.1->teneto->soothsayer==2019.10) (0.5.10) Requirement already satisfied: nibabel>=2.1 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from pybids>=0.7.1->teneto->soothsayer==2019.10) (2.5.1) Requirement already satisfied: parso>=0.5.0 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from jedi>=0.10->IPython>=3.2.0->scikit-bio>=0.5.1->soothsayer==2019.10) (0.5.1) Requirement already satisfied: ptyprocess>=0.5 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from pexpect; sys_platform != "win32"->IPython>=3.2.0->scikit-bio>=0.5.1->soothsayer==2019.10) (0.6.0) Requirement already satisfied: ipython_genutils in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from traitlets>=4.2->IPython>=3.2.0->scikit-bio>=0.5.1->soothsayer==2019.10) (0.2.0) Requirement already satisfied: wcwidth in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from prompt-toolkit<2.1.0,>=2.0.0->IPython>=3.2.0->scikit-bio>=0.5.1->soothsayer==2019.10) (0.1.7) Requirement already satisfied: docopt>=0.6.2 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from num2words->pybids>=0.7.1->teneto->soothsayer==2019.10) (0.6.2) Building wheels for collected packages: soothsayer Created temporary directory: /private/var/folders/b0/30gxwqd95x995btmclwt4wjm0000gn/T/pip-wheel-_0l0slq1 Building wheel for soothsayer (setup.py) ... Destination directory: /private/var/folders/b0/30gxwqd95x995btmclwt4wjm0000gn/T/pip-wheel-_0l0slq1 Running command /Users/mu/anaconda3/envs/testing_env/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/b0/30gxwqd95x995btmclwt4wjm0000gn/T/pip-req-build-b_qclz48/setup.py'"'"'; __file__='"'"'/private/var/folders/b0/30gxwqd95x995btmclwt4wjm0000gn/T/pip-req-build-b_qclz48/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /private/var/folders/b0/30gxwqd95x995btmclwt4wjm0000gn/T/pip-wheel-_0l0slq1 --python-tag cp36 running bdist_wheel running build running build_py creating build creating build/lib creating build/lib/soothsayer copying soothsayer/__init__.py -> build/lib/soothsayer creating build/lib/soothsayer/statistics copying soothsayer/statistics/__init__.py -> build/lib/soothsayer/statistics copying soothsayer/statistics/statistics.py -> build/lib/soothsayer/statistics creating build/lib/soothsayer/classification copying soothsayer/classification/classification.py -> build/lib/soothsayer/classification copying soothsayer/classification/__init__.py -> build/lib/soothsayer/classification creating build/lib/soothsayer/tree copying soothsayer/tree/tree.py -> build/lib/soothsayer/tree copying soothsayer/tree/__init__.py -> build/lib/soothsayer/tree creating build/lib/soothsayer/feature_extraction copying soothsayer/feature_extraction/__init__.py -> build/lib/soothsayer/feature_extraction copying soothsayer/feature_extraction/feature_extraction.py -> build/lib/soothsayer/feature_extraction creating build/lib/soothsayer/core copying soothsayer/core/__init__.py -> build/lib/soothsayer/core copying soothsayer/core/core.py -> build/lib/soothsayer/core creating build/lib/soothsayer/ordination copying soothsayer/ordination/ordination.py -> build/lib/soothsayer/ordination copying soothsayer/ordination/__init__.py -> build/lib/soothsayer/ordination creating build/lib/soothsayer/hierarchy copying soothsayer/hierarchy/__init__.py -> build/lib/soothsayer/hierarchy copying soothsayer/hierarchy/hierarchy.py -> build/lib/soothsayer/hierarchy creating build/lib/soothsayer/microbiome copying soothsayer/microbiome/__init__.py -> build/lib/soothsayer/microbiome copying soothsayer/microbiome/microbiome.py -> build/lib/soothsayer/microbiome creating build/lib/soothsayer/io copying soothsayer/io/io.py -> build/lib/soothsayer/io copying soothsayer/io/__init__.py -> build/lib/soothsayer/io creating build/lib/soothsayer/utils copying soothsayer/utils/__init__.py -> build/lib/soothsayer/utils copying soothsayer/utils/utils.py -> build/lib/soothsayer/utils creating build/lib/soothsayer/symmetry copying soothsayer/symmetry/symmetry.py -> build/lib/soothsayer/symmetry copying soothsayer/symmetry/__init__.py -> build/lib/soothsayer/symmetry creating build/lib/soothsayer/networks copying soothsayer/networks/__init__.py -> build/lib/soothsayer/networks copying soothsayer/networks/networks.py -> build/lib/soothsayer/networks creating build/lib/soothsayer/r_wrappers copying soothsayer/r_wrappers/__init__.py -> build/lib/soothsayer/r_wrappers copying soothsayer/r_wrappers/r_wrappers.py -> build/lib/soothsayer/r_wrappers creating build/lib/soothsayer/transmute copying soothsayer/transmute/conversion.py -> build/lib/soothsayer/transmute copying soothsayer/transmute/__init__.py -> build/lib/soothsayer/transmute copying soothsayer/transmute/transmute.py -> build/lib/soothsayer/transmute copying soothsayer/transmute/normalization.py -> build/lib/soothsayer/transmute creating build/lib/soothsayer/db copying soothsayer/db/db.py -> build/lib/soothsayer/db copying soothsayer/db/__init__.py -> build/lib/soothsayer/db creating build/lib/soothsayer/visuals copying soothsayer/visuals/__init__.py -> build/lib/soothsayer/visuals copying soothsayer/visuals/visuals.py -> build/lib/soothsayer/visuals creating build/lib/soothsayer/regression copying soothsayer/regression/regression.py -> build/lib/soothsayer/regression copying soothsayer/regression/__init__.py -> build/lib/soothsayer/regression creating build/lib/soothsayer/io/tables copying soothsayer/io/tables/__init__.py -> build/lib/soothsayer/io/tables copying soothsayer/io/tables/tables.py -> build/lib/soothsayer/io/tables creating build/lib/soothsayer/io/web copying soothsayer/io/web/web.py -> build/lib/soothsayer/io/web copying soothsayer/io/web/__init__.py -> build/lib/soothsayer/io/web creating build/lib/soothsayer/io/objects copying soothsayer/io/objects/__init__.py -> build/lib/soothsayer/io/objects copying soothsayer/io/objects/objects.py -> build/lib/soothsayer/io/objects creating build/lib/soothsayer/io/text copying soothsayer/io/text/__init__.py -> build/lib/soothsayer/io/text copying soothsayer/io/text/text.py -> build/lib/soothsayer/io/text creating build/lib/soothsayer/io/bioinformatics copying soothsayer/io/bioinformatics/bioinformatics.py -> build/lib/soothsayer/io/bioinformatics copying soothsayer/io/bioinformatics/__init__.py -> build/lib/soothsayer/io/bioinformatics running egg_info creating soothsayer.egg-info writing soothsayer.egg-info/PKG-INFO writing dependency_links to soothsayer.egg-info/dependency_links.txt writing requirements to soothsayer.egg-info/requires.txt writing top-level names to soothsayer.egg-info/top_level.txt writing manifest file 'soothsayer.egg-info/SOURCES.txt' reading manifest file 'soothsayer.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching '*' under directory 'examples' warning: no files found matching '*.py' under directory 'soothsayer/io/data_type/' warning: no files found matching '*.py' under directory 'soothsayer/tests/data/' warning: no previously-included files matching '*.py[cod]' found anywhere in distribution warning: no previously-included files matching '__pycache__' found anywhere in distribution writing manifest file 'soothsayer.egg-info/SOURCES.txt' creating build/lib/soothsayer/feature_extraction/algorithms copying soothsayer/feature_extraction/algorithms/clairvoyant.py -> build/lib/soothsayer/feature_extraction/algorithms creating build/lib/soothsayer/r_wrappers/packages copying soothsayer/r_wrappers/packages/WGCNA.py -> build/lib/soothsayer/r_wrappers/packages copying soothsayer/r_wrappers/packages/dynamicTreeCut.py -> build/lib/soothsayer/r_wrappers/packages copying soothsayer/r_wrappers/packages/edgeR.py -> build/lib/soothsayer/r_wrappers/packages copying soothsayer/r_wrappers/packages/metagenomeSeq.py -> build/lib/soothsayer/r_wrappers/packages copying soothsayer/r_wrappers/packages/philr.py -> build/lib/soothsayer/r_wrappers/packages copying soothsayer/db/kegg-module.pbz2 -> build/lib/soothsayer/db copying soothsayer/db/pfam.pbz2 -> build/lib/soothsayer/db copying soothsayer/db/tigrfam.pbz2 -> build/lib/soothsayer/db running build_scripts creating build/scripts-3.6 copying and adjusting bin/clairvoyance.py -> build/scripts-3.6 copying and adjusting bin/run_soothsayer.py -> build/scripts-3.6 changing mode of build/scripts-3.6/clairvoyance.py from 644 to 755 changing mode of build/scripts-3.6/run_soothsayer.py from 644 to 755 installing to build/bdist.macosx-10.9-x86_64/wheel running install running install_lib creating build/bdist.macosx-10.9-x86_64 creating build/bdist.macosx-10.9-x86_64/wheel creating build/bdist.macosx-10.9-x86_64/wheel/soothsayer creating build/bdist.macosx-10.9-x86_64/wheel/soothsayer/statistics copying build/lib/soothsayer/statistics/__init__.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/statistics copying build/lib/soothsayer/statistics/statistics.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/statistics creating build/bdist.macosx-10.9-x86_64/wheel/soothsayer/classification copying build/lib/soothsayer/classification/classification.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/classification copying build/lib/soothsayer/classification/__init__.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/classification creating build/bdist.macosx-10.9-x86_64/wheel/soothsayer/tree copying build/lib/soothsayer/tree/tree.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/tree copying build/lib/soothsayer/tree/__init__.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/tree creating build/bdist.macosx-10.9-x86_64/wheel/soothsayer/feature_extraction creating build/bdist.macosx-10.9-x86_64/wheel/soothsayer/feature_extraction/algorithms copying build/lib/soothsayer/feature_extraction/algorithms/clairvoyant.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/feature_extraction/algorithms copying build/lib/soothsayer/feature_extraction/__init__.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/feature_extraction copying build/lib/soothsayer/feature_extraction/feature_extraction.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/feature_extraction creating build/bdist.macosx-10.9-x86_64/wheel/soothsayer/core copying build/lib/soothsayer/core/__init__.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/core copying build/lib/soothsayer/core/core.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/core creating build/bdist.macosx-10.9-x86_64/wheel/soothsayer/ordination copying build/lib/soothsayer/ordination/ordination.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/ordination copying build/lib/soothsayer/ordination/__init__.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/ordination creating build/bdist.macosx-10.9-x86_64/wheel/soothsayer/hierarchy copying build/lib/soothsayer/hierarchy/__init__.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/hierarchy copying build/lib/soothsayer/hierarchy/hierarchy.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/hierarchy creating build/bdist.macosx-10.9-x86_64/wheel/soothsayer/microbiome copying build/lib/soothsayer/microbiome/__init__.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/microbiome copying build/lib/soothsayer/microbiome/microbiome.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/microbiome creating build/bdist.macosx-10.9-x86_64/wheel/soothsayer/io creating build/bdist.macosx-10.9-x86_64/wheel/soothsayer/io/tables copying build/lib/soothsayer/io/tables/__init__.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/io/tables copying build/lib/soothsayer/io/tables/tables.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/io/tables creating build/bdist.macosx-10.9-x86_64/wheel/soothsayer/io/web copying build/lib/soothsayer/io/web/web.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/io/web copying build/lib/soothsayer/io/web/__init__.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/io/web copying build/lib/soothsayer/io/io.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/io copying build/lib/soothsayer/io/__init__.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/io creating build/bdist.macosx-10.9-x86_64/wheel/soothsayer/io/objects copying build/lib/soothsayer/io/objects/__init__.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/io/objects copying build/lib/soothsayer/io/objects/objects.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/io/objects creating build/bdist.macosx-10.9-x86_64/wheel/soothsayer/io/text copying build/lib/soothsayer/io/text/__init__.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/io/text copying build/lib/soothsayer/io/text/text.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/io/text creating build/bdist.macosx-10.9-x86_64/wheel/soothsayer/io/bioinformatics copying build/lib/soothsayer/io/bioinformatics/bioinformatics.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/io/bioinformatics copying build/lib/soothsayer/io/bioinformatics/__init__.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/io/bioinformatics copying build/lib/soothsayer/__init__.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer creating build/bdist.macosx-10.9-x86_64/wheel/soothsayer/utils copying build/lib/soothsayer/utils/__init__.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/utils copying build/lib/soothsayer/utils/utils.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/utils creating build/bdist.macosx-10.9-x86_64/wheel/soothsayer/symmetry copying build/lib/soothsayer/symmetry/symmetry.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/symmetry copying build/lib/soothsayer/symmetry/__init__.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/symmetry creating build/bdist.macosx-10.9-x86_64/wheel/soothsayer/networks copying build/lib/soothsayer/networks/__init__.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/networks copying build/lib/soothsayer/networks/networks.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/networks creating build/bdist.macosx-10.9-x86_64/wheel/soothsayer/r_wrappers copying build/lib/soothsayer/r_wrappers/__init__.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/r_wrappers creating build/bdist.macosx-10.9-x86_64/wheel/soothsayer/r_wrappers/packages copying build/lib/soothsayer/r_wrappers/packages/philr.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/r_wrappers/packages copying build/lib/soothsayer/r_wrappers/packages/edgeR.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/r_wrappers/packages copying build/lib/soothsayer/r_wrappers/packages/WGCNA.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/r_wrappers/packages copying build/lib/soothsayer/r_wrappers/packages/metagenomeSeq.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/r_wrappers/packages copying build/lib/soothsayer/r_wrappers/packages/dynamicTreeCut.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/r_wrappers/packages copying build/lib/soothsayer/r_wrappers/r_wrappers.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/r_wrappers creating build/bdist.macosx-10.9-x86_64/wheel/soothsayer/transmute copying build/lib/soothsayer/transmute/conversion.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/transmute copying build/lib/soothsayer/transmute/__init__.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/transmute copying build/lib/soothsayer/transmute/transmute.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/transmute copying build/lib/soothsayer/transmute/normalization.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/transmute creating build/bdist.macosx-10.9-x86_64/wheel/soothsayer/db copying build/lib/soothsayer/db/db.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/db copying build/lib/soothsayer/db/__init__.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/db copying build/lib/soothsayer/db/kegg-module.pbz2 -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/db copying build/lib/soothsayer/db/tigrfam.pbz2 -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/db copying build/lib/soothsayer/db/pfam.pbz2 -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/db creating build/bdist.macosx-10.9-x86_64/wheel/soothsayer/visuals copying build/lib/soothsayer/visuals/__init__.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/visuals copying build/lib/soothsayer/visuals/visuals.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/visuals creating build/bdist.macosx-10.9-x86_64/wheel/soothsayer/regression copying build/lib/soothsayer/regression/regression.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/regression copying build/lib/soothsayer/regression/__init__.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/regression running install_egg_info Copying soothsayer.egg-info to build/bdist.macosx-10.9-x86_64/wheel/soothsayer-2019.10-py3.6.egg-info running install_scripts creating build/bdist.macosx-10.9-x86_64/wheel/soothsayer-2019.10.data creating build/bdist.macosx-10.9-x86_64/wheel/soothsayer-2019.10.data/scripts copying build/scripts-3.6/run_soothsayer.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer-2019.10.data/scripts copying build/scripts-3.6/clairvoyance.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer-2019.10.data/scripts changing mode of build/bdist.macosx-10.9-x86_64/wheel/soothsayer-2019.10.data/scripts/run_soothsayer.py to 755 changing mode of build/bdist.macosx-10.9-x86_64/wheel/soothsayer-2019.10.data/scripts/clairvoyance.py to 755 creating build/bdist.macosx-10.9-x86_64/wheel/soothsayer-2019.10.dist-info/WHEEL creating '/private/var/folders/b0/30gxwqd95x995btmclwt4wjm0000gn/T/pip-wheel-_0l0slq1/soothsayer-2019.10-cp36-none-any.whl' and adding 'build/bdist.macosx-10.9-x86_64/wheel' to it adding 'soothsayer/__init__.py' adding 'soothsayer/classification/__init__.py' adding 'soothsayer/classification/classification.py' adding 'soothsayer/core/__init__.py' adding 'soothsayer/core/core.py' adding 'soothsayer/db/__init__.py' adding 'soothsayer/db/db.py' adding 'soothsayer/db/kegg-module.pbz2' adding 'soothsayer/db/pfam.pbz2' adding 'soothsayer/db/tigrfam.pbz2' adding 'soothsayer/feature_extraction/__init__.py' adding 'soothsayer/feature_extraction/feature_extraction.py' adding 'soothsayer/feature_extraction/algorithms/clairvoyant.py' adding 'soothsayer/hierarchy/__init__.py' adding 'soothsayer/hierarchy/hierarchy.py' adding 'soothsayer/io/__init__.py' adding 'soothsayer/io/io.py' adding 'soothsayer/io/bioinformatics/__init__.py' adding 'soothsayer/io/bioinformatics/bioinformatics.py' adding 'soothsayer/io/objects/__init__.py' adding 'soothsayer/io/objects/objects.py' adding 'soothsayer/io/tables/__init__.py' adding 'soothsayer/io/tables/tables.py' adding 'soothsayer/io/text/__init__.py' adding 'soothsayer/io/text/text.py' adding 'soothsayer/io/web/__init__.py' adding 'soothsayer/io/web/web.py' adding 'soothsayer/microbiome/__init__.py' adding 'soothsayer/microbiome/microbiome.py' adding 'soothsayer/networks/__init__.py' adding 'soothsayer/networks/networks.py' adding 'soothsayer/ordination/__init__.py' adding 'soothsayer/ordination/ordination.py' adding 'soothsayer/r_wrappers/__init__.py' adding 'soothsayer/r_wrappers/r_wrappers.py' adding 'soothsayer/r_wrappers/packages/WGCNA.py' adding 'soothsayer/r_wrappers/packages/dynamicTreeCut.py' adding 'soothsayer/r_wrappers/packages/edgeR.py' adding 'soothsayer/r_wrappers/packages/metagenomeSeq.py' adding 'soothsayer/r_wrappers/packages/philr.py' adding 'soothsayer/regression/__init__.py' adding 'soothsayer/regression/regression.py' adding 'soothsayer/statistics/__init__.py' adding 'soothsayer/statistics/statistics.py' adding 'soothsayer/symmetry/__init__.py' adding 'soothsayer/symmetry/symmetry.py' adding 'soothsayer/transmute/__init__.py' adding 'soothsayer/transmute/conversion.py' adding 'soothsayer/transmute/normalization.py' adding 'soothsayer/transmute/transmute.py' adding 'soothsayer/tree/__init__.py' adding 'soothsayer/tree/tree.py' adding 'soothsayer/utils/__init__.py' adding 'soothsayer/utils/utils.py' adding 'soothsayer/visuals/__init__.py' adding 'soothsayer/visuals/visuals.py' adding 'soothsayer-2019.10.data/scripts/clairvoyance.py' adding 'soothsayer-2019.10.data/scripts/run_soothsayer.py' adding 'soothsayer-2019.10.dist-info/METADATA' adding 'soothsayer-2019.10.dist-info/WHEEL' adding 'soothsayer-2019.10.dist-info/top_level.txt' adding 'soothsayer-2019.10.dist-info/RECORD' removing build/bdist.macosx-10.9-x86_64/wheel done Created wheel for soothsayer: filename=soothsayer-2019.10-cp36-none-any.whl size=391520 sha256=fb660813e4ce2b7bb4cc68a356d5782225e0becf41d51f97f3b3573f11416e0b Stored in directory: /private/var/folders/b0/30gxwqd95x995btmclwt4wjm0000gn/T/pip-ephem-wheel-cache-w_w6_t48/wheels/cc/44/4b/5076913cf12db0fd41327ab919f8f0b1a82a173227df5f4c64 Removing source in /private/var/folders/b0/30gxwqd95x995btmclwt4wjm0000gn/T/pip-req-build-b_qclz48 Successfully built soothsayer Installing collected packages: soothsayer Found existing installation: soothsayer 2019.8 Uninstalling soothsayer-2019.8: Created temporary directory: /Users/mu/anaconda3/envs/testing_env/bin/~_pycache__ Removing file or directory /Users/mu/anaconda3/envs/testing_env/bin/__pycache__/ Created temporary directory: /private/var/folders/b0/30gxwqd95x995btmclwt4wjm0000gn/T/pip-uninstall-j_k5os38 Removing file or directory /Users/mu/anaconda3/envs/testing_env/bin/clairvoyance.py Removing file or directory /Users/mu/anaconda3/envs/testing_env/bin/run_soothsayer.py Created temporary directory: /Users/mu/anaconda3/envs/testing_env/lib/python3.6/~ite-packages Removing file or directory /Users/mu/anaconda3/envs/testing_env/lib/python3.6/site-packages/ Successfully uninstalled soothsayer-2019.8 Successfully installed soothsayer-2019.10 Cleaning up... Removed build tracker '/private/var/folders/b0/30gxwqd95x995btmclwt4wjm0000gn/T/pip-req-tracker-hblkn_n3' ```

Show site-packages is empty

``` (testing_env) Joshs-MacBook-Pro:~ mu$ ls /Users/mu/anaconda3/envs/testing_env/lib/python3.6/site-packages/ soothsayer soothsayer-2019.10.dist-info ```

jolespin commented 5 years ago

If I delete the package files in site-packages first, and then install, then it works?

``` (testing_env) Joshs-MacBook-Pro:~ mu$ conda activate testing_env (testing_env) Joshs-MacBook-Pro:~ mu$ ls /Users/mu/anaconda3/envs/testing_env/lib/python3.6/site-packages/ Bio dateutil libpasteurize patsy-0.5.1.dist-info scikit_learn-0.21.3.dist-info BioSQL decorator-4.4.0.dist-info lockfile pexpect scipy CacheControl-0.12.5-py2.7.egg-info decorator.py lockfile-0.12.2-py2.7.egg-info pexpect-4.7.0.dist-info scipy-1.3.1.dist-info Click-7.0-py2.7.egg-info defusedxml lxml pickleshare-0.7.5-py3.6.egg-info seaborn Cython defusedxml-0.6.0.dist-info lxml-4.4.1-py3.6.egg-info pickleshare.py seaborn-0.9.0.dist-info Cython-0.29.13.dist-info docopt-0.6.2.dist-info markupsafe pip send2trash IPython docopt.py matplotlib pip-19.2.3-py3.6.egg-info setuptools Jinja2-2.10.1.dist-info dot_parser.py matplotlib-3.1.1-py3.6-nspkg.pth pkg_resources setuptools-41.2.0-py3.6.egg-info MarkupSafe-1.1.1.dist-info easy_install.py matplotlib-3.1.1.dist-info pluggy sip.pyi PIL entrypoints-0.3.dist-info matplotlib_venn pluggy-0.12.0.dist-info sip.so Pillow-6.1.0.dist-info entrypoints.py matplotlib_venn-0.11.5-py2.7.egg-info prometheus_client sipconfig.py PyHamcrest-1.9.0-py2.7.egg-info et_xmlfile mistune-0.8.4.dist-info prometheus_client-0.7.1.dist-info sipdistutils.py PyQt5 et_xmlfile-1.0.1.dist-info mistune.py prompt_toolkit six-1.12.0-py3.6.egg-info PyYAML-5.1.2-py3.6.egg-info ete3 more_itertools prompt_toolkit-2.0.9.dist-info six.py Pygments-2.4.2.dist-info ete3-3.1.1-py3.6.egg-info more_itertools-7.2.0.dist-info psutil skbio README.md fastcluster-1.1.25-py3.6.egg-info mpl_toolkits psutil-5.6.3.dist-info sklearn README.txt fastcluster.py msgpack ptyprocess soothsayer SQLAlchemy-1.3.8.dist-info future msgpack-0.6.2.dist-info ptyprocess-0.6.0.dist-info soothsayer-2019.8.dist-info Send2Trash-1.5.0.dist-info future-0.17.1-py3.6.egg-info natsort pvectorc.cpython-36m-darwin.so sqlalchemy __pycache__ gneiss natsort-6.0.0.dist-info py statsmodels _fastcluster.cpython-36m-darwin.so gneiss-0.4.5-py3.7.egg-info nbconvert py-1.8.0.dist-info statsmodels-0.10.1.dist-info _pyrsistent_version.py hamcrest nbconvert-5.6.0.dist-info pybids-0.9.4.dist-info templateflow _pytest hdmedians nbformat pydot-1.4.1.dist-info templateflow-0.4.1.dist-info _yaml.cpython-36m-darwin.so hdmedians-0.13.dist-info nbformat-4.4.0.dist-info pydot.py teneto adjustText importlib_metadata networkx pygments teneto-0.4.5.dist-info adjustText-0.7.3.dist-info importlib_metadata-0.23.dist-info networkx-2.3.dist-info pygraphviz terminado appnope ipykernel nibabel pygraphviz-1.5.dist-info terminado-0.8.2.dist-info appnope-0.1.0-py3.6.egg-info ipykernel-5.1.2.dist-info nibabel-2.5.1.dist-info pylab.py ternary astropy ipykernel_launcher.py nilearn pyparsing-2.4.2.dist-info testpath astropy-3.2.1-py3.6.egg-info ipython-7.8.0.dist-info nilearn-0.5.2.dist-info pyparsing.py testpath-0.4.2.dist-info atomicwrites ipython_genutils nisext pyrsistent tests atomicwrites-1.3.0-py2.7.egg-info ipython_genutils-0.2.0-py2.7.egg-info nose pyrsistent-0.15.4.dist-info tornado attr jdcal-1.4.1.dist-info nose-1.3.7-py3.6.egg-info pytest-5.1.2-py3.6.egg-info tornado-6.0.3.dist-info attrs-19.1.0.dist-info jdcal.py notebook pytest.py tqdm backcall jedi notebook-6.0.1.dist-info pytest_arraydiff tqdm-4.36.1.dist-info backcall-0.1.0.dist-info jedi-0.15.1.dist-info num2words pytest_arraydiff-0.3.dist-info traitlets benchmarks jinja2 num2words-0.5.10.dist-info pytest_astropy-0.5.0.dist-info traitlets-4.3.2-py3.6.egg-info bids joblib numpy pytest_doctestplus tzlocal bids_validator joblib-0.13.2-py2.7.egg-info numpy-1.17.2.dist-info pytest_doctestplus-0.4.0.dist-info tzlocal-2.0.0.dist-info bids_validator-1.2.4.dist-info json5 olefile pytest_openfiles wcwidth biom json5-0.8.5.dist-info olefile-0.46-py2.7.egg-info pytest_openfiles-0.4.0.dist-info wcwidth-0.1.7-py2.7.egg-info biom_format-2.1.7.dist-info jsonschema openpyxl pytest_remotedata webencodings biopython-1.74.dist-info jsonschema-3.0.2.dist-info openpyxl-2.6.3.dist-info pytest_remotedata-0.3.1.dist-info webencodings-0.5.1.dist-info bleach jupyter.py packaging python_dateutil-2.8.0.dist-info wheel bleach-3.1.0.dist-info jupyter_client packaging-19.2.dist-info python_louvain-0.13.dist-info wheel-0.33.6-py3.6.egg-info bokeh jupyter_client-5.3.3.dist-info palettable python_ternary-1.0.6.dist-info xarray bokeh-1.3.4.dist-info jupyter_core palettable-3.3.0.dist-info pytz xarray-0.13.0.dist-info cachecontrol jupyter_core-4.5.0.dist-info pandas pytz-2019.2.dist-info yaml certifi jupyterlab pandas-0.25.1.dist-info pyximport zipp-0.6.0.dist-info certifi-2016.09.26-py3.6.egg-info jupyterlab-1.1.4.dist-info pandocfilters-1.4.2.dist-info pyzmq-18.1.0.dist-info zipp.py click jupyterlab_server pandocfilters.py requests zmq community jupyterlab_server-1.0.6.dist-info parso requests-2.12.5-py3.6.egg-info cycler-0.10.0-py2.7.egg-info kiwisolver-1.1.0.dist-info parso-0.5.1.dist-info rpy2 cycler.py kiwisolver.cpython-36m-darwin.so past rpy2-2.9.4-py3.6.egg-info cython.py libfuturize patsy scikit_bio-0.5.5.dist-info (testing_env) Joshs-MacBook-Pro:~ mu$ rm -r /Users/mu/anaconda3/envs/testing_env/lib/python3.6/site-packages/soothsaye*; pip install git+https://github.com/jolespin/soothsayer -v -v -v Created temporary directory: /private/var/folders/b0/30gxwqd95x995btmclwt4wjm0000gn/T/pip-ephem-wheel-cache-s2v21yva Created temporary directory: /private/var/folders/b0/30gxwqd95x995btmclwt4wjm0000gn/T/pip-req-tracker-z4ukfjbr Created requirements tracker '/private/var/folders/b0/30gxwqd95x995btmclwt4wjm0000gn/T/pip-req-tracker-z4ukfjbr' Created temporary directory: /private/var/folders/b0/30gxwqd95x995btmclwt4wjm0000gn/T/pip-install-6akdamck Collecting git+https://github.com/jolespin/soothsayer Created temporary directory: /private/var/folders/b0/30gxwqd95x995btmclwt4wjm0000gn/T/pip-req-build-31burof5 Cloning https://github.com/jolespin/soothsayer to /private/var/folders/b0/30gxwqd95x995btmclwt4wjm0000gn/T/pip-req-build-31burof5 Running command git clone -q https://github.com/jolespin/soothsayer /private/var/folders/b0/30gxwqd95x995btmclwt4wjm0000gn/T/pip-req-build-31burof5 Added git+https://github.com/jolespin/soothsayer to build tracker '/private/var/folders/b0/30gxwqd95x995btmclwt4wjm0000gn/T/pip-req-tracker-z4ukfjbr' Running setup.py (path:/private/var/folders/b0/30gxwqd95x995btmclwt4wjm0000gn/T/pip-req-build-31burof5/setup.py) egg_info for package from git+https://github.com/jolespin/soothsayer Running command python setup.py egg_info running egg_info creating pip-egg-info/soothsayer.egg-info writing pip-egg-info/soothsayer.egg-info/PKG-INFO writing dependency_links to pip-egg-info/soothsayer.egg-info/dependency_links.txt writing requirements to pip-egg-info/soothsayer.egg-info/requires.txt writing top-level names to pip-egg-info/soothsayer.egg-info/top_level.txt writing manifest file 'pip-egg-info/soothsayer.egg-info/SOURCES.txt' reading manifest file 'pip-egg-info/soothsayer.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching '*' under directory 'examples' warning: no files found matching '*.py' under directory 'soothsayer/io/data_type/' warning: no files found matching '*.py' under directory 'soothsayer/tests/data/' warning: no previously-included files matching '*.py[cod]' found anywhere in distribution warning: no previously-included files matching '__pycache__' found anywhere in distribution writing manifest file 'pip-egg-info/soothsayer.egg-info/SOURCES.txt' Source in /private/var/folders/b0/30gxwqd95x995btmclwt4wjm0000gn/T/pip-req-build-31burof5 has version 2019.10, which satisfies requirement soothsayer==2019.10 from git+https://github.com/jolespin/soothsayer Removed soothsayer==2019.10 from git+https://github.com/jolespin/soothsayer from build tracker '/private/var/folders/b0/30gxwqd95x995btmclwt4wjm0000gn/T/pip-req-tracker-z4ukfjbr' Requirement already satisfied: matplotlib>=2.2.2 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from soothsayer==2019.10) (3.1.1) Requirement already satisfied: scipy>=1.0 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from soothsayer==2019.10) (1.3.1) Requirement already satisfied: scikit-learn>=0.20.2 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from soothsayer==2019.10) (0.21.3) Requirement already satisfied: numpy>=1.13 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from soothsayer==2019.10) (1.17.2) Requirement already satisfied: pandas>=0.24.2 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from soothsayer==2019.10) (0.25.1) Requirement already satisfied: networkx>=2.0 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from soothsayer==2019.10) (2.3) Requirement already satisfied: ete3>=3.0 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from soothsayer==2019.10) (3.1.1) Requirement already satisfied: scikit-bio>=0.5.1 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from soothsayer==2019.10) (0.5.5) Requirement already satisfied: biopython>=1.5 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from soothsayer==2019.10) (1.74) Requirement already satisfied: xarray>=0.10.3 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from soothsayer==2019.10) (0.13.0) Requirement already satisfied: tqdm>=4.19 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from soothsayer==2019.10) (4.36.1) Requirement already satisfied: openpyxl>=2.5 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from soothsayer==2019.10) (2.6.3) Requirement already satisfied: astropy>=3.0 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from soothsayer==2019.10) (3.2.1) Requirement already satisfied: rpy2>=2.9 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from soothsayer==2019.10) (2.9.4) Requirement already satisfied: matplotlib_venn in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from soothsayer==2019.10) (0.11.5) Requirement already satisfied: palettable>=3.0.0 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from soothsayer==2019.10) (3.3.0) Requirement already satisfied: adjustText in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from soothsayer==2019.10) (0.7.3) Requirement already satisfied: tzlocal in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from soothsayer==2019.10) (2.0.0) Requirement already satisfied: statsmodels>=0.10.0 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from soothsayer==2019.10) (0.10.1) Requirement already satisfied: teneto in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from soothsayer==2019.10) (0.4.5) Requirement already satisfied: python-dateutil>=2.1 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from matplotlib>=2.2.2->soothsayer==2019.10) (2.8.0) Requirement already satisfied: cycler>=0.10 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from matplotlib>=2.2.2->soothsayer==2019.10) (0.10.0) Requirement already satisfied: kiwisolver>=1.0.1 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from matplotlib>=2.2.2->soothsayer==2019.10) (1.1.0) Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from matplotlib>=2.2.2->soothsayer==2019.10) (2.4.2) Requirement already satisfied: joblib>=0.11 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from scikit-learn>=0.20.2->soothsayer==2019.10) (0.13.2) Requirement already satisfied: pytz>=2017.2 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from pandas>=0.24.2->soothsayer==2019.10) (2019.2) Requirement already satisfied: decorator>=4.3.0 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from networkx>=2.0->soothsayer==2019.10) (4.4.0) Requirement already satisfied: lockfile>=0.10.2 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from scikit-bio>=0.5.1->soothsayer==2019.10) (0.12.2) Requirement already satisfied: natsort>=4.0.3 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from scikit-bio>=0.5.1->soothsayer==2019.10) (6.0.0) Requirement already satisfied: CacheControl>=0.11.5 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from scikit-bio>=0.5.1->soothsayer==2019.10) (0.12.5) Requirement already satisfied: IPython>=3.2.0 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from scikit-bio>=0.5.1->soothsayer==2019.10) (7.8.0) Requirement already satisfied: hdmedians>=0.13 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from scikit-bio>=0.5.1->soothsayer==2019.10) (0.13) Requirement already satisfied: et-xmlfile in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from openpyxl>=2.5->soothsayer==2019.10) (1.0.1) Requirement already satisfied: jdcal in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from openpyxl>=2.5->soothsayer==2019.10) (1.4.1) Requirement already satisfied: six in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from rpy2>=2.9->soothsayer==2019.10) (1.12.0) Requirement already satisfied: jinja2 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from rpy2>=2.9->soothsayer==2019.10) (2.10.1) Requirement already satisfied: patsy>=0.4.0 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from statsmodels>=0.10.0->soothsayer==2019.10) (0.5.1) Requirement already satisfied: templateflow>=0.3 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from teneto->soothsayer==2019.10) (0.4.1) Requirement already satisfied: nilearn>=0.4.0 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from teneto->soothsayer==2019.10) (0.5.2) Requirement already satisfied: python-louvain>=0.13 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from teneto->soothsayer==2019.10) (0.13) Requirement already satisfied: pybids>=0.7.1 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from teneto->soothsayer==2019.10) (0.9.4) Requirement already satisfied: setuptools in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from kiwisolver>=1.0.1->matplotlib>=2.2.2->soothsayer==2019.10) (41.2.0) Requirement already satisfied: requests in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from CacheControl>=0.11.5->scikit-bio>=0.5.1->soothsayer==2019.10) (2.12.5) Requirement already satisfied: msgpack in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from CacheControl>=0.11.5->scikit-bio>=0.5.1->soothsayer==2019.10) (0.6.2) Requirement already satisfied: appnope; sys_platform == "darwin" in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from IPython>=3.2.0->scikit-bio>=0.5.1->soothsayer==2019.10) (0.1.0) Requirement already satisfied: pexpect; sys_platform != "win32" in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from IPython>=3.2.0->scikit-bio>=0.5.1->soothsayer==2019.10) (4.7.0) Requirement already satisfied: backcall in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from IPython>=3.2.0->scikit-bio>=0.5.1->soothsayer==2019.10) (0.1.0) Requirement already satisfied: jedi>=0.10 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from IPython>=3.2.0->scikit-bio>=0.5.1->soothsayer==2019.10) (0.15.1) Requirement already satisfied: pickleshare in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from IPython>=3.2.0->scikit-bio>=0.5.1->soothsayer==2019.10) (0.7.5) Requirement already satisfied: prompt-toolkit<2.1.0,>=2.0.0 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from IPython>=3.2.0->scikit-bio>=0.5.1->soothsayer==2019.10) (2.0.9) Requirement already satisfied: pygments in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from IPython>=3.2.0->scikit-bio>=0.5.1->soothsayer==2019.10) (2.4.2) Requirement already satisfied: traitlets>=4.2 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from IPython>=3.2.0->scikit-bio>=0.5.1->soothsayer==2019.10) (4.3.2) Requirement already satisfied: Cython>=0.23 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from hdmedians>=0.13->scikit-bio>=0.5.1->soothsayer==2019.10) (0.29.13) Requirement already satisfied: MarkupSafe>=0.23 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from jinja2->rpy2>=2.9->soothsayer==2019.10) (1.1.1) Requirement already satisfied: nibabel>=2.0.2 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from nilearn>=0.4.0->teneto->soothsayer==2019.10) (2.5.1) Requirement already satisfied: bids-validator in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from pybids>=0.7.1->teneto->soothsayer==2019.10) (1.2.4) Requirement already satisfied: num2words in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from pybids>=0.7.1->teneto->soothsayer==2019.10) (0.5.10) Requirement already satisfied: sqlalchemy in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from pybids>=0.7.1->teneto->soothsayer==2019.10) (1.3.8) Requirement already satisfied: ptyprocess>=0.5 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from pexpect; sys_platform != "win32"->IPython>=3.2.0->scikit-bio>=0.5.1->soothsayer==2019.10) (0.6.0) Requirement already satisfied: parso>=0.5.0 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from jedi>=0.10->IPython>=3.2.0->scikit-bio>=0.5.1->soothsayer==2019.10) (0.5.1) Requirement already satisfied: wcwidth in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from prompt-toolkit<2.1.0,>=2.0.0->IPython>=3.2.0->scikit-bio>=0.5.1->soothsayer==2019.10) (0.1.7) Requirement already satisfied: ipython_genutils in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from traitlets>=4.2->IPython>=3.2.0->scikit-bio>=0.5.1->soothsayer==2019.10) (0.2.0) Requirement already satisfied: docopt>=0.6.2 in ./anaconda3/envs/testing_env/lib/python3.6/site-packages (from num2words->pybids>=0.7.1->teneto->soothsayer==2019.10) (0.6.2) Building wheels for collected packages: soothsayer Created temporary directory: /private/var/folders/b0/30gxwqd95x995btmclwt4wjm0000gn/T/pip-wheel-l501uu_3 Building wheel for soothsayer (setup.py) ... Destination directory: /private/var/folders/b0/30gxwqd95x995btmclwt4wjm0000gn/T/pip-wheel-l501uu_3 Running command /Users/mu/anaconda3/envs/testing_env/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/b0/30gxwqd95x995btmclwt4wjm0000gn/T/pip-req-build-31burof5/setup.py'"'"'; __file__='"'"'/private/var/folders/b0/30gxwqd95x995btmclwt4wjm0000gn/T/pip-req-build-31burof5/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /private/var/folders/b0/30gxwqd95x995btmclwt4wjm0000gn/T/pip-wheel-l501uu_3 --python-tag cp36 running bdist_wheel running build running build_py creating build creating build/lib creating build/lib/soothsayer copying soothsayer/__init__.py -> build/lib/soothsayer creating build/lib/soothsayer/statistics copying soothsayer/statistics/__init__.py -> build/lib/soothsayer/statistics copying soothsayer/statistics/statistics.py -> build/lib/soothsayer/statistics creating build/lib/soothsayer/classification copying soothsayer/classification/classification.py -> build/lib/soothsayer/classification copying soothsayer/classification/__init__.py -> build/lib/soothsayer/classification creating build/lib/soothsayer/tree copying soothsayer/tree/tree.py -> build/lib/soothsayer/tree copying soothsayer/tree/__init__.py -> build/lib/soothsayer/tree creating build/lib/soothsayer/feature_extraction copying soothsayer/feature_extraction/__init__.py -> build/lib/soothsayer/feature_extraction copying soothsayer/feature_extraction/feature_extraction.py -> build/lib/soothsayer/feature_extraction creating build/lib/soothsayer/core copying soothsayer/core/__init__.py -> build/lib/soothsayer/core copying soothsayer/core/core.py -> build/lib/soothsayer/core creating build/lib/soothsayer/ordination copying soothsayer/ordination/ordination.py -> build/lib/soothsayer/ordination copying soothsayer/ordination/__init__.py -> build/lib/soothsayer/ordination creating build/lib/soothsayer/hierarchy copying soothsayer/hierarchy/__init__.py -> build/lib/soothsayer/hierarchy copying soothsayer/hierarchy/hierarchy.py -> build/lib/soothsayer/hierarchy creating build/lib/soothsayer/microbiome copying soothsayer/microbiome/__init__.py -> build/lib/soothsayer/microbiome copying soothsayer/microbiome/microbiome.py -> build/lib/soothsayer/microbiome creating build/lib/soothsayer/io copying soothsayer/io/io.py -> build/lib/soothsayer/io copying soothsayer/io/__init__.py -> build/lib/soothsayer/io creating build/lib/soothsayer/utils copying soothsayer/utils/__init__.py -> build/lib/soothsayer/utils copying soothsayer/utils/utils.py -> build/lib/soothsayer/utils creating build/lib/soothsayer/symmetry copying soothsayer/symmetry/symmetry.py -> build/lib/soothsayer/symmetry copying soothsayer/symmetry/__init__.py -> build/lib/soothsayer/symmetry creating build/lib/soothsayer/networks copying soothsayer/networks/__init__.py -> build/lib/soothsayer/networks copying soothsayer/networks/networks.py -> build/lib/soothsayer/networks creating build/lib/soothsayer/r_wrappers copying soothsayer/r_wrappers/__init__.py -> build/lib/soothsayer/r_wrappers copying soothsayer/r_wrappers/r_wrappers.py -> build/lib/soothsayer/r_wrappers creating build/lib/soothsayer/transmute copying soothsayer/transmute/conversion.py -> build/lib/soothsayer/transmute copying soothsayer/transmute/__init__.py -> build/lib/soothsayer/transmute copying soothsayer/transmute/transmute.py -> build/lib/soothsayer/transmute copying soothsayer/transmute/normalization.py -> build/lib/soothsayer/transmute creating build/lib/soothsayer/db copying soothsayer/db/db.py -> build/lib/soothsayer/db copying soothsayer/db/__init__.py -> build/lib/soothsayer/db creating build/lib/soothsayer/visuals copying soothsayer/visuals/__init__.py -> build/lib/soothsayer/visuals copying soothsayer/visuals/visuals.py -> build/lib/soothsayer/visuals creating build/lib/soothsayer/regression copying soothsayer/regression/regression.py -> build/lib/soothsayer/regression copying soothsayer/regression/__init__.py -> build/lib/soothsayer/regression creating build/lib/soothsayer/io/tables copying soothsayer/io/tables/__init__.py -> build/lib/soothsayer/io/tables copying soothsayer/io/tables/tables.py -> build/lib/soothsayer/io/tables creating build/lib/soothsayer/io/web copying soothsayer/io/web/web.py -> build/lib/soothsayer/io/web copying soothsayer/io/web/__init__.py -> build/lib/soothsayer/io/web creating build/lib/soothsayer/io/objects copying soothsayer/io/objects/__init__.py -> build/lib/soothsayer/io/objects copying soothsayer/io/objects/objects.py -> build/lib/soothsayer/io/objects creating build/lib/soothsayer/io/text copying soothsayer/io/text/__init__.py -> build/lib/soothsayer/io/text copying soothsayer/io/text/text.py -> build/lib/soothsayer/io/text creating build/lib/soothsayer/io/bioinformatics copying soothsayer/io/bioinformatics/bioinformatics.py -> build/lib/soothsayer/io/bioinformatics copying soothsayer/io/bioinformatics/__init__.py -> build/lib/soothsayer/io/bioinformatics running egg_info creating soothsayer.egg-info writing soothsayer.egg-info/PKG-INFO writing dependency_links to soothsayer.egg-info/dependency_links.txt writing requirements to soothsayer.egg-info/requires.txt writing top-level names to soothsayer.egg-info/top_level.txt writing manifest file 'soothsayer.egg-info/SOURCES.txt' reading manifest file 'soothsayer.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching '*' under directory 'examples' warning: no files found matching '*.py' under directory 'soothsayer/io/data_type/' warning: no files found matching '*.py' under directory 'soothsayer/tests/data/' warning: no previously-included files matching '*.py[cod]' found anywhere in distribution warning: no previously-included files matching '__pycache__' found anywhere in distribution writing manifest file 'soothsayer.egg-info/SOURCES.txt' creating build/lib/soothsayer/feature_extraction/algorithms copying soothsayer/feature_extraction/algorithms/clairvoyant.py -> build/lib/soothsayer/feature_extraction/algorithms creating build/lib/soothsayer/r_wrappers/packages copying soothsayer/r_wrappers/packages/WGCNA.py -> build/lib/soothsayer/r_wrappers/packages copying soothsayer/r_wrappers/packages/dynamicTreeCut.py -> build/lib/soothsayer/r_wrappers/packages copying soothsayer/r_wrappers/packages/edgeR.py -> build/lib/soothsayer/r_wrappers/packages copying soothsayer/r_wrappers/packages/metagenomeSeq.py -> build/lib/soothsayer/r_wrappers/packages copying soothsayer/r_wrappers/packages/philr.py -> build/lib/soothsayer/r_wrappers/packages copying soothsayer/db/kegg-module.pbz2 -> build/lib/soothsayer/db copying soothsayer/db/pfam.pbz2 -> build/lib/soothsayer/db copying soothsayer/db/tigrfam.pbz2 -> build/lib/soothsayer/db running build_scripts creating build/scripts-3.6 copying and adjusting bin/clairvoyance.py -> build/scripts-3.6 copying and adjusting bin/run_soothsayer.py -> build/scripts-3.6 changing mode of build/scripts-3.6/clairvoyance.py from 644 to 755 changing mode of build/scripts-3.6/run_soothsayer.py from 644 to 755 installing to build/bdist.macosx-10.9-x86_64/wheel running install running install_lib creating build/bdist.macosx-10.9-x86_64 creating build/bdist.macosx-10.9-x86_64/wheel creating build/bdist.macosx-10.9-x86_64/wheel/soothsayer creating build/bdist.macosx-10.9-x86_64/wheel/soothsayer/statistics copying build/lib/soothsayer/statistics/__init__.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/statistics copying build/lib/soothsayer/statistics/statistics.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/statistics creating build/bdist.macosx-10.9-x86_64/wheel/soothsayer/classification copying build/lib/soothsayer/classification/classification.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/classification copying build/lib/soothsayer/classification/__init__.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/classification creating build/bdist.macosx-10.9-x86_64/wheel/soothsayer/tree copying build/lib/soothsayer/tree/tree.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/tree copying build/lib/soothsayer/tree/__init__.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/tree creating build/bdist.macosx-10.9-x86_64/wheel/soothsayer/feature_extraction creating build/bdist.macosx-10.9-x86_64/wheel/soothsayer/feature_extraction/algorithms copying build/lib/soothsayer/feature_extraction/algorithms/clairvoyant.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/feature_extraction/algorithms copying build/lib/soothsayer/feature_extraction/__init__.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/feature_extraction copying build/lib/soothsayer/feature_extraction/feature_extraction.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/feature_extraction creating build/bdist.macosx-10.9-x86_64/wheel/soothsayer/core copying build/lib/soothsayer/core/__init__.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/core copying build/lib/soothsayer/core/core.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/core creating build/bdist.macosx-10.9-x86_64/wheel/soothsayer/ordination copying build/lib/soothsayer/ordination/ordination.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/ordination copying build/lib/soothsayer/ordination/__init__.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/ordination creating build/bdist.macosx-10.9-x86_64/wheel/soothsayer/hierarchy copying build/lib/soothsayer/hierarchy/__init__.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/hierarchy copying build/lib/soothsayer/hierarchy/hierarchy.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/hierarchy creating build/bdist.macosx-10.9-x86_64/wheel/soothsayer/microbiome copying build/lib/soothsayer/microbiome/__init__.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/microbiome copying build/lib/soothsayer/microbiome/microbiome.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/microbiome creating build/bdist.macosx-10.9-x86_64/wheel/soothsayer/io creating build/bdist.macosx-10.9-x86_64/wheel/soothsayer/io/tables copying build/lib/soothsayer/io/tables/__init__.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/io/tables copying build/lib/soothsayer/io/tables/tables.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/io/tables creating build/bdist.macosx-10.9-x86_64/wheel/soothsayer/io/web copying build/lib/soothsayer/io/web/web.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/io/web copying build/lib/soothsayer/io/web/__init__.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/io/web copying build/lib/soothsayer/io/io.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/io copying build/lib/soothsayer/io/__init__.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/io creating build/bdist.macosx-10.9-x86_64/wheel/soothsayer/io/objects copying build/lib/soothsayer/io/objects/__init__.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/io/objects copying build/lib/soothsayer/io/objects/objects.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/io/objects creating build/bdist.macosx-10.9-x86_64/wheel/soothsayer/io/text copying build/lib/soothsayer/io/text/__init__.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/io/text copying build/lib/soothsayer/io/text/text.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/io/text creating build/bdist.macosx-10.9-x86_64/wheel/soothsayer/io/bioinformatics copying build/lib/soothsayer/io/bioinformatics/bioinformatics.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/io/bioinformatics copying build/lib/soothsayer/io/bioinformatics/__init__.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/io/bioinformatics copying build/lib/soothsayer/__init__.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer creating build/bdist.macosx-10.9-x86_64/wheel/soothsayer/utils copying build/lib/soothsayer/utils/__init__.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/utils copying build/lib/soothsayer/utils/utils.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/utils creating build/bdist.macosx-10.9-x86_64/wheel/soothsayer/symmetry copying build/lib/soothsayer/symmetry/symmetry.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/symmetry copying build/lib/soothsayer/symmetry/__init__.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/symmetry creating build/bdist.macosx-10.9-x86_64/wheel/soothsayer/networks copying build/lib/soothsayer/networks/__init__.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/networks copying build/lib/soothsayer/networks/networks.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/networks creating build/bdist.macosx-10.9-x86_64/wheel/soothsayer/r_wrappers copying build/lib/soothsayer/r_wrappers/__init__.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/r_wrappers creating build/bdist.macosx-10.9-x86_64/wheel/soothsayer/r_wrappers/packages copying build/lib/soothsayer/r_wrappers/packages/philr.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/r_wrappers/packages copying build/lib/soothsayer/r_wrappers/packages/edgeR.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/r_wrappers/packages copying build/lib/soothsayer/r_wrappers/packages/WGCNA.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/r_wrappers/packages copying build/lib/soothsayer/r_wrappers/packages/metagenomeSeq.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/r_wrappers/packages copying build/lib/soothsayer/r_wrappers/packages/dynamicTreeCut.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/r_wrappers/packages copying build/lib/soothsayer/r_wrappers/r_wrappers.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/r_wrappers creating build/bdist.macosx-10.9-x86_64/wheel/soothsayer/transmute copying build/lib/soothsayer/transmute/conversion.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/transmute copying build/lib/soothsayer/transmute/__init__.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/transmute copying build/lib/soothsayer/transmute/transmute.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/transmute copying build/lib/soothsayer/transmute/normalization.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/transmute creating build/bdist.macosx-10.9-x86_64/wheel/soothsayer/db copying build/lib/soothsayer/db/db.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/db copying build/lib/soothsayer/db/__init__.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/db copying build/lib/soothsayer/db/kegg-module.pbz2 -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/db copying build/lib/soothsayer/db/tigrfam.pbz2 -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/db copying build/lib/soothsayer/db/pfam.pbz2 -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/db creating build/bdist.macosx-10.9-x86_64/wheel/soothsayer/visuals copying build/lib/soothsayer/visuals/__init__.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/visuals copying build/lib/soothsayer/visuals/visuals.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/visuals creating build/bdist.macosx-10.9-x86_64/wheel/soothsayer/regression copying build/lib/soothsayer/regression/regression.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/regression copying build/lib/soothsayer/regression/__init__.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer/regression running install_egg_info Copying soothsayer.egg-info to build/bdist.macosx-10.9-x86_64/wheel/soothsayer-2019.10-py3.6.egg-info running install_scripts creating build/bdist.macosx-10.9-x86_64/wheel/soothsayer-2019.10.data creating build/bdist.macosx-10.9-x86_64/wheel/soothsayer-2019.10.data/scripts copying build/scripts-3.6/run_soothsayer.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer-2019.10.data/scripts copying build/scripts-3.6/clairvoyance.py -> build/bdist.macosx-10.9-x86_64/wheel/soothsayer-2019.10.data/scripts changing mode of build/bdist.macosx-10.9-x86_64/wheel/soothsayer-2019.10.data/scripts/run_soothsayer.py to 755 changing mode of build/bdist.macosx-10.9-x86_64/wheel/soothsayer-2019.10.data/scripts/clairvoyance.py to 755 creating build/bdist.macosx-10.9-x86_64/wheel/soothsayer-2019.10.dist-info/WHEEL creating '/private/var/folders/b0/30gxwqd95x995btmclwt4wjm0000gn/T/pip-wheel-l501uu_3/soothsayer-2019.10-cp36-none-any.whl' and adding 'build/bdist.macosx-10.9-x86_64/wheel' to it adding 'soothsayer/__init__.py' adding 'soothsayer/classification/__init__.py' adding 'soothsayer/classification/classification.py' adding 'soothsayer/core/__init__.py' adding 'soothsayer/core/core.py' adding 'soothsayer/db/__init__.py' adding 'soothsayer/db/db.py' adding 'soothsayer/db/kegg-module.pbz2' adding 'soothsayer/db/pfam.pbz2' adding 'soothsayer/db/tigrfam.pbz2' adding 'soothsayer/feature_extraction/__init__.py' adding 'soothsayer/feature_extraction/feature_extraction.py' adding 'soothsayer/feature_extraction/algorithms/clairvoyant.py' adding 'soothsayer/hierarchy/__init__.py' adding 'soothsayer/hierarchy/hierarchy.py' adding 'soothsayer/io/__init__.py' adding 'soothsayer/io/io.py' adding 'soothsayer/io/bioinformatics/__init__.py' adding 'soothsayer/io/bioinformatics/bioinformatics.py' adding 'soothsayer/io/objects/__init__.py' adding 'soothsayer/io/objects/objects.py' adding 'soothsayer/io/tables/__init__.py' adding 'soothsayer/io/tables/tables.py' adding 'soothsayer/io/text/__init__.py' adding 'soothsayer/io/text/text.py' adding 'soothsayer/io/web/__init__.py' adding 'soothsayer/io/web/web.py' adding 'soothsayer/microbiome/__init__.py' adding 'soothsayer/microbiome/microbiome.py' adding 'soothsayer/networks/__init__.py' adding 'soothsayer/networks/networks.py' adding 'soothsayer/ordination/__init__.py' adding 'soothsayer/ordination/ordination.py' adding 'soothsayer/r_wrappers/__init__.py' adding 'soothsayer/r_wrappers/r_wrappers.py' adding 'soothsayer/r_wrappers/packages/WGCNA.py' adding 'soothsayer/r_wrappers/packages/dynamicTreeCut.py' adding 'soothsayer/r_wrappers/packages/edgeR.py' adding 'soothsayer/r_wrappers/packages/metagenomeSeq.py' adding 'soothsayer/r_wrappers/packages/philr.py' adding 'soothsayer/regression/__init__.py' adding 'soothsayer/regression/regression.py' adding 'soothsayer/statistics/__init__.py' adding 'soothsayer/statistics/statistics.py' adding 'soothsayer/symmetry/__init__.py' adding 'soothsayer/symmetry/symmetry.py' adding 'soothsayer/transmute/__init__.py' adding 'soothsayer/transmute/conversion.py' adding 'soothsayer/transmute/normalization.py' adding 'soothsayer/transmute/transmute.py' adding 'soothsayer/tree/__init__.py' adding 'soothsayer/tree/tree.py' adding 'soothsayer/utils/__init__.py' adding 'soothsayer/utils/utils.py' adding 'soothsayer/visuals/__init__.py' adding 'soothsayer/visuals/visuals.py' adding 'soothsayer-2019.10.data/scripts/clairvoyance.py' adding 'soothsayer-2019.10.data/scripts/run_soothsayer.py' adding 'soothsayer-2019.10.dist-info/METADATA' adding 'soothsayer-2019.10.dist-info/WHEEL' adding 'soothsayer-2019.10.dist-info/top_level.txt' adding 'soothsayer-2019.10.dist-info/RECORD' removing build/bdist.macosx-10.9-x86_64/wheel done Created wheel for soothsayer: filename=soothsayer-2019.10-cp36-none-any.whl size=391520 sha256=f26048a2ff8ca895e57633a3181393b9aea8a606adba8de187a6f7f2b3638cb7 Stored in directory: /private/var/folders/b0/30gxwqd95x995btmclwt4wjm0000gn/T/pip-ephem-wheel-cache-s2v21yva/wheels/cc/44/4b/5076913cf12db0fd41327ab919f8f0b1a82a173227df5f4c64 Removing source in /private/var/folders/b0/30gxwqd95x995btmclwt4wjm0000gn/T/pip-req-build-31burof5 Successfully built soothsayer Installing collected packages: soothsayer Successfully installed soothsayer-2019.10 Cleaning up... Removed build tracker '/private/var/folders/b0/30gxwqd95x995btmclwt4wjm0000gn/T/pip-req-tracker-z4ukfjbr' (testing_env) Joshs-MacBook-Pro:~ mu$ ls /Users/mu/anaconda3/envs/testing_env/lib/python3.6/site-packages/ Bio dateutil libpasteurize patsy-0.5.1.dist-info scikit_learn-0.21.3.dist-info BioSQL decorator-4.4.0.dist-info lockfile pexpect scipy CacheControl-0.12.5-py2.7.egg-info decorator.py lockfile-0.12.2-py2.7.egg-info pexpect-4.7.0.dist-info scipy-1.3.1.dist-info Click-7.0-py2.7.egg-info defusedxml lxml pickleshare-0.7.5-py3.6.egg-info seaborn Cython defusedxml-0.6.0.dist-info lxml-4.4.1-py3.6.egg-info pickleshare.py seaborn-0.9.0.dist-info Cython-0.29.13.dist-info docopt-0.6.2.dist-info markupsafe pip send2trash IPython docopt.py matplotlib pip-19.2.3-py3.6.egg-info setuptools Jinja2-2.10.1.dist-info dot_parser.py matplotlib-3.1.1-py3.6-nspkg.pth pkg_resources setuptools-41.2.0-py3.6.egg-info MarkupSafe-1.1.1.dist-info easy_install.py matplotlib-3.1.1.dist-info pluggy sip.pyi PIL entrypoints-0.3.dist-info matplotlib_venn pluggy-0.12.0.dist-info sip.so Pillow-6.1.0.dist-info entrypoints.py matplotlib_venn-0.11.5-py2.7.egg-info prometheus_client sipconfig.py PyHamcrest-1.9.0-py2.7.egg-info et_xmlfile mistune-0.8.4.dist-info prometheus_client-0.7.1.dist-info sipdistutils.py PyQt5 et_xmlfile-1.0.1.dist-info mistune.py prompt_toolkit six-1.12.0-py3.6.egg-info PyYAML-5.1.2-py3.6.egg-info ete3 more_itertools prompt_toolkit-2.0.9.dist-info six.py Pygments-2.4.2.dist-info ete3-3.1.1-py3.6.egg-info more_itertools-7.2.0.dist-info psutil skbio README.md fastcluster-1.1.25-py3.6.egg-info mpl_toolkits psutil-5.6.3.dist-info sklearn README.txt fastcluster.py msgpack ptyprocess soothsayer SQLAlchemy-1.3.8.dist-info future msgpack-0.6.2.dist-info ptyprocess-0.6.0.dist-info soothsayer-2019.10.dist-info Send2Trash-1.5.0.dist-info future-0.17.1-py3.6.egg-info natsort pvectorc.cpython-36m-darwin.so sqlalchemy __pycache__ gneiss natsort-6.0.0.dist-info py statsmodels _fastcluster.cpython-36m-darwin.so gneiss-0.4.5-py3.7.egg-info nbconvert py-1.8.0.dist-info statsmodels-0.10.1.dist-info _pyrsistent_version.py hamcrest nbconvert-5.6.0.dist-info pybids-0.9.4.dist-info templateflow _pytest hdmedians nbformat pydot-1.4.1.dist-info templateflow-0.4.1.dist-info _yaml.cpython-36m-darwin.so hdmedians-0.13.dist-info nbformat-4.4.0.dist-info pydot.py teneto adjustText importlib_metadata networkx pygments teneto-0.4.5.dist-info adjustText-0.7.3.dist-info importlib_metadata-0.23.dist-info networkx-2.3.dist-info pygraphviz terminado appnope ipykernel nibabel pygraphviz-1.5.dist-info terminado-0.8.2.dist-info appnope-0.1.0-py3.6.egg-info ipykernel-5.1.2.dist-info nibabel-2.5.1.dist-info pylab.py ternary astropy ipykernel_launcher.py nilearn pyparsing-2.4.2.dist-info testpath astropy-3.2.1-py3.6.egg-info ipython-7.8.0.dist-info nilearn-0.5.2.dist-info pyparsing.py testpath-0.4.2.dist-info atomicwrites ipython_genutils nisext pyrsistent tests atomicwrites-1.3.0-py2.7.egg-info ipython_genutils-0.2.0-py2.7.egg-info nose pyrsistent-0.15.4.dist-info tornado attr jdcal-1.4.1.dist-info nose-1.3.7-py3.6.egg-info pytest-5.1.2-py3.6.egg-info tornado-6.0.3.dist-info attrs-19.1.0.dist-info jdcal.py notebook pytest.py tqdm backcall jedi notebook-6.0.1.dist-info pytest_arraydiff tqdm-4.36.1.dist-info backcall-0.1.0.dist-info jedi-0.15.1.dist-info num2words pytest_arraydiff-0.3.dist-info traitlets benchmarks jinja2 num2words-0.5.10.dist-info pytest_astropy-0.5.0.dist-info traitlets-4.3.2-py3.6.egg-info bids joblib numpy pytest_doctestplus tzlocal bids_validator joblib-0.13.2-py2.7.egg-info numpy-1.17.2.dist-info pytest_doctestplus-0.4.0.dist-info tzlocal-2.0.0.dist-info bids_validator-1.2.4.dist-info json5 olefile pytest_openfiles wcwidth biom json5-0.8.5.dist-info olefile-0.46-py2.7.egg-info pytest_openfiles-0.4.0.dist-info wcwidth-0.1.7-py2.7.egg-info biom_format-2.1.7.dist-info jsonschema openpyxl pytest_remotedata webencodings biopython-1.74.dist-info jsonschema-3.0.2.dist-info openpyxl-2.6.3.dist-info pytest_remotedata-0.3.1.dist-info webencodings-0.5.1.dist-info bleach jupyter.py packaging python_dateutil-2.8.0.dist-info wheel bleach-3.1.0.dist-info jupyter_client packaging-19.2.dist-info python_louvain-0.13.dist-info wheel-0.33.6-py3.6.egg-info bokeh jupyter_client-5.3.3.dist-info palettable python_ternary-1.0.6.dist-info xarray bokeh-1.3.4.dist-info jupyter_core palettable-3.3.0.dist-info pytz xarray-0.13.0.dist-info cachecontrol jupyter_core-4.5.0.dist-info pandas pytz-2019.2.dist-info yaml certifi jupyterlab pandas-0.25.1.dist-info pyximport zipp-0.6.0.dist-info certifi-2016.09.26-py3.6.egg-info jupyterlab-1.1.4.dist-info pandocfilters-1.4.2.dist-info pyzmq-18.1.0.dist-info zipp.py click jupyterlab_server pandocfilters.py requests zmq community jupyterlab_server-1.0.6.dist-info parso requests-2.12.5-py3.6.egg-info cycler-0.10.0-py2.7.egg-info kiwisolver-1.1.0.dist-info parso-0.5.1.dist-info rpy2 cycler.py kiwisolver.cpython-36m-darwin.so past rpy2-2.9.4-py3.6.egg-info cython.py libfuturize patsy scikit_bio-0.5.5.dist-info ```

jolespin commented 4 years ago

Do you have any insight on why this could be happening?

nicktimko commented 4 years ago

Is your original environment broken in some subtle way? Can you try to come up with the minimal set of commands to cause this problem in a fresh machine (e.g. Docker container)?

If I do something like docker run --rm -it python:slim /bin/bash and run:

python3 -m venv /venv
/venv/bin/pip3 install numpy
ls /venv/lib/python3.8/site-packages/  # numpy is here.

apt update; apt install -y git
/venv/bin/pip3 install --no-deps git+https://github.com/jolespin/soothsayer
ls /venv/lib/python3.8/site-packages/  # numpy and soothsayer are both here.

no-response[bot] commented 4 years ago

This issue has been automatically closed because there has been no response to our request for more information from the original author. With only the information that is currently in the issue, we don't have enough information to take action. Please reach out if you have or find the answers we need so that we can investigate further.

pypa / pip

pip install --no-deps [package] removes EVERYTHING from site-packages #7170