Cellprofiler: "data" directory not included in distribution build

[AetherUnbound]

After setting up an appropriate conda environment as per the wiki guide (https://github.com/CellProfiler/CellProfiler/wiki/Conda-Installation), I was unable to install CellProfiler as "non-editable", or without the editable tag. I found that this is because the data directory is not being picked up by setup.py. I was able to confirm this by copying the directory. Here's the output from that experiment:

mattb@AI-Linux-mattb:~/misc$ git clone https://github.com/CellProfiler/CellProfiler.git
Cloning into 'CellProfiler'...
remote: Counting objects: 85844, done.
remote: Compressing objects: 100% (33/33), done.
remote: Total 85844 (delta 18), reused 26 (delta 11), pack-reused 85800
Receiving objects: 100% (85844/85844), 88.68 MiB | 54.25 MiB/s, done.
Resolving deltas: 100% (70471/70471), done.
Checking connectivity... done.
mattb@AI-Linux-mattb:~/misc$ cd CellProfiler/
mattb@AI-Linux-mattb:~/misc/CellProfiler$ cat ../cp_env.yml 
name: cp-env
# in order of priority: lowest (top) to highest (bottom)
# run: conda env create -f environment.yml
# run: conda env update -f environment.yml
# run: conda env remove -n cellprofiler
# in order of priority: lowest (top) to highest (bottom)
channels:
  - anaconda
  - goodman # mysql-python for mac
  - bioconda
  - cyclus # java-jdk for windows
  - conda-forge # libxml2 for windows
dependencies:
  - appdirs
  - cython
  - h5py
  - ipywidgets
  - javabridge
  - java-jdk
  - jupyter
  - libtiff
  - libxml2
  - libxslt
  - lxml
  - packaging
  - pillow
  - pip
  - python=2
  - pyzmq
  - mahotas
  - matplotlib!=2.1.0,>2.0.0
  - mysql-python
  - numpy
  - raven
  - requests
  - scikit-image
  - scikit-learn
  - scipy
  - sphinx
  - tifffile
  - wxpython
  - pip:
    - cellh5
    - centrosome
    - inflect
    - prokaryote
    - python-bioformats==1.3.1
mattb@AI-Linux-mattb:~/misc/CellProfiler$ conda env create -f ../cp_env.yml 
Using Anaconda API: https://api.anaconda.org
Fetching package metadata ...................
Solving package specifications: .
raven-6.3.0-py 100% |#####################################################################################################################################################################| Time: 0:00:00 510.59 kB/s
Collecting cellh5
Collecting centrosome
Collecting inflect
  Downloading https://artifactory.corp.alleninstitute.org/artifactory/api/pypi/pypi-virtual/packages/66/15/2d176749884cbeda0c92e0d09e1303ff53a973eb3c6bb2136803b9d962c9/inflect-0.2.5-py2.py3-none-any.whl (58kB)
    100% |████████████████████████████████| 61kB 3.6MB/s 
Collecting prokaryote
Collecting python-bioformats==1.3.1
Requirement already satisfied: lxml in /home/mattb/programs/anaconda2/envs/cp-env/lib/python2.7/site-packages (from cellh5)
Requirement already satisfied: matplotlib in /home/mattb/programs/anaconda2/envs/cp-env/lib/python2.7/site-packages (from cellh5)
Requirement already satisfied: scikit-learn in /home/mattb/programs/anaconda2/envs/cp-env/lib/python2.7/site-packages (from cellh5)
Requirement already satisfied: scipy in /home/mattb/programs/anaconda2/envs/cp-env/lib/python2.7/site-packages (from cellh5)
Requirement already satisfied: pandas in /home/mattb/programs/anaconda2/envs/cp-env/lib/python2.7/site-packages (from cellh5)
Collecting hmmlearn (from cellh5)
Requirement already satisfied: numpy in /home/mattb/programs/anaconda2/envs/cp-env/lib/python2.7/site-packages (from cellh5)
Requirement already satisfied: h5py in /home/mattb/programs/anaconda2/envs/cp-env/lib/python2.7/site-packages (from cellh5)
Requirement already satisfied: scikit-image in /home/mattb/programs/anaconda2/envs/cp-env/lib/python2.7/site-packages (from centrosome)
Requirement already satisfied: pillow in /home/mattb/programs/anaconda2/envs/cp-env/lib/python2.7/site-packages (from centrosome)
Collecting future (from python-bioformats==1.3.1)
Collecting javabridge>=1.0 (from python-bioformats==1.3.1)
Requirement already satisfied: six>=1.10 in /home/mattb/programs/anaconda2/envs/cp-env/lib/python2.7/site-packages (from matplotlib->cellh5)
Requirement already satisfied: python-dateutil in /home/mattb/programs/anaconda2/envs/cp-env/lib/python2.7/site-packages (from matplotlib->cellh5)
Requirement already satisfied: functools32 in /home/mattb/programs/anaconda2/envs/cp-env/lib/python2.7/site-packages (from matplotlib->cellh5)
Requirement already satisfied: subprocess32 in /home/mattb/programs/anaconda2/envs/cp-env/lib/python2.7/site-packages (from matplotlib->cellh5)
Requirement already satisfied: pytz in /home/mattb/programs/anaconda2/envs/cp-env/lib/python2.7/site-packages (from matplotlib->cellh5)
Requirement already satisfied: cycler>=0.10 in /home/mattb/programs/anaconda2/envs/cp-env/lib/python2.7/site-packages (from matplotlib->cellh5)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=1.5.6 in /home/mattb/programs/anaconda2/envs/cp-env/lib/python2.7/site-packages (from matplotlib->cellh5)
Requirement already satisfied: networkx>=1.8 in /home/mattb/programs/anaconda2/envs/cp-env/lib/python2.7/site-packages (from scikit-image->centrosome)
Requirement already satisfied: PyWavelets>=0.4.0 in /home/mattb/programs/anaconda2/envs/cp-env/lib/python2.7/site-packages (from scikit-image->centrosome)
Requirement already satisfied: olefile in /home/mattb/programs/anaconda2/envs/cp-env/lib/python2.7/site-packages (from pillow->centrosome)
Requirement already satisfied: decorator>=4.1.0 in /home/mattb/programs/anaconda2/envs/cp-env/lib/python2.7/site-packages (from networkx>=1.8->scikit-image->centrosome)
Installing collected packages: hmmlearn, cellh5, centrosome, inflect, prokaryote, future, javabridge, python-bioformats
  Found existing installation: javabridge 1.0.14-1-gdf84bf8
    Uninstalling javabridge-1.0.14-1-gdf84bf8:
      Successfully uninstalled javabridge-1.0.14-1-gdf84bf8
Successfully installed cellh5-1.3.0 centrosome-1.0.8 future-0.16.0 hmmlearn-0.2.0 inflect-0.2.5 javabridge-1.0.15 prokaryote-2.3.1 python-bioformats-1.3.1
#
# To activate this environment, use:
# > source activate cp-env
#
# To deactivate an active environment, use:
# > source deactivate
#

mattb@AI-Linux-mattb:~/misc/CellProfiler$ . activate cp-env
(cp-env) mattb@AI-Linux-mattb:~/misc/CellProfiler$ python setup.py bdist_wheel

Installed /home/mattb/misc/CellProfiler/.eggs/pytest-3.2.3-py2.7.egg
Searching for py>=1.4.33
Reading https://pypi.python.org/simple/py/
Downloading https://pypi.python.org/packages/68/35/58572278f1c097b403879c1e9369069633d1cbad5239b9057944bb764782/py-1.4.34.tar.gz#md5=d9c3d8f734b0819ff48e355d77bf1730
Best match: py 1.4.34
Processing py-1.4.34.tar.gz
Writing /tmp/easy_install-GrTn1b/py-1.4.34/setup.cfg
Running py-1.4.34/setup.py -q bdist_egg --dist-dir /tmp/easy_install-GrTn1b/py-1.4.34/egg-dist-tmp-N96FbU
warning: no previously-included files matching '*.pyc' found anywhere in distribution
creating /home/mattb/misc/CellProfiler/.eggs/py-1.4.34-py2.7.egg
Extracting py-1.4.34-py2.7.egg to /home/mattb/misc/CellProfiler/.eggs

Installed /home/mattb/misc/CellProfiler/.eggs/py-1.4.34-py2.7.egg
running bdist_wheel
running build
running build_py
creating build
creating build/lib
creating build/lib/cellprofiler
copying cellprofiler/module.py -> build/lib/cellprofiler
copying cellprofiler/measurement.py -> build/lib/cellprofiler
copying cellprofiler/workspace.py -> build/lib/cellprofiler
copying cellprofiler/setting.py -> build/lib/cellprofiler
copying cellprofiler/worker.py -> build/lib/cellprofiler
copying cellprofiler/image.py -> build/lib/cellprofiler
copying cellprofiler/analysis.py -> build/lib/cellprofiler
copying cellprofiler/object.py -> build/lib/cellprofiler
copying cellprofiler/__init__.py -> build/lib/cellprofiler
copying cellprofiler/knime_bridge.py -> build/lib/cellprofiler
copying cellprofiler/pipeline.py -> build/lib/cellprofiler
copying cellprofiler/__main__.py -> build/lib/cellprofiler
copying cellprofiler/grid.py -> build/lib/cellprofiler
copying cellprofiler/preferences.py -> build/lib/cellprofiler
creating build/lib/cellprofiler/icons
copying cellprofiler/icons/__init__.py -> build/lib/cellprofiler/icons
creating build/lib/cellprofiler/modules
copying cellprofiler/modules/measuretexture.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/measureobjectintensity.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/flagimage.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/gaussianfilter.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/medialaxis.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/invertforprinting.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/displaydataonimage.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/measurecolocalization.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/measureobjectsizeshape.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/imagemath.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/removeobjectsbysize.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/correctilluminationcalculate.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/graytocolor.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/erosion.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/measuregranularity.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/enhanceorsuppressfeatures.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/calculatestatistics.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/threshold.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/measureimagequality.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/relateobjects.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/measureobjectskeleton.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/splitormergeobjects.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/makeprojection.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/label.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/straightenworms.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/removeholes.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/overlayobjects.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/identifyobjectsmanually.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/resizeobjects.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/createbatchfiles.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/displayplatemap.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/identifyobjectsingrid.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/measureimageareaoccupied.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/identifydeadworms.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/measureimageskeleton.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/dilation.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/colortogray.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/resize.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/editobjectsmanually.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/closing.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/exporttodatabase.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/metadata.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/smooth.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/measureimageintensity.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/classifyobjects.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/flipandrotate.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/maskimage.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/__init__.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/namesandtypes.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/displaydensityplot.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/enhanceedges.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/matchtemplate.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/identifytertiaryobjects.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/identify.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/correctilluminationapply.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/exporttospreadsheet.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/savecroppedobjects.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/untangleworms.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/identifysecondaryobjects.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/rescaleintensity.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/align.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/morphologicalskeleton.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/reducenoise.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/convertimagetoobjects.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/unmixcolors.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/loadimages.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/convertobjectstoimage.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/watershed.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/labelimages.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/medianfilter.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/opening.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/measureobjectneighbors.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/injectimage.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/displayscatterplot.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/_help.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/loadsingleimage.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/measureimageoverlap.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/tile.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/definegrid.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/overlayoutlines.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/identifyprimaryobjects.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/measureobjectintensitydistribution.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/images.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/mergeoutputfiles.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/loaddata.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/trackobjects.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/crop.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/saveimages.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/groups.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/shrinktoobjectcenters.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/displayhistogram.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/filterobjects.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/morph.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/measureobjectoverlap.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/expandorshrinkobjects.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/maskobjects.py -> build/lib/cellprofiler/modules
copying cellprofiler/modules/calculatemath.py -> build/lib/cellprofiler/modules
creating build/lib/cellprofiler/gui
copying cellprofiler/gui/plateviewer.py -> build/lib/cellprofiler/gui
copying cellprofiler/gui/errordialog.py -> build/lib/cellprofiler/gui
copying cellprofiler/gui/pathlist.py -> build/lib/cellprofiler/gui
copying cellprofiler/gui/menu.py -> build/lib/cellprofiler/gui
copying cellprofiler/gui/workspace.py -> build/lib/cellprofiler/gui
copying cellprofiler/gui/cornerbuttonmixin.py -> build/lib/cellprofiler/gui
copying cellprofiler/gui/preferencesview.py -> build/lib/cellprofiler/gui
copying cellprofiler/gui/namesubscriber.py -> build/lib/cellprofiler/gui
copying cellprofiler/gui/treecheckboxdialog.py -> build/lib/cellprofiler/gui
copying cellprofiler/gui/cpframe.py -> build/lib/cellprofiler/gui
copying cellprofiler/gui/htmldialog.py -> build/lib/cellprofiler/gui
copying cellprofiler/gui/pipelinecontroller.py -> build/lib/cellprofiler/gui
copying cellprofiler/gui/addmoduleframe.py -> build/lib/cellprofiler/gui
copying cellprofiler/gui/pipelinelistview.py -> build/lib/cellprofiler/gui
copying cellprofiler/gui/welcome.py -> build/lib/cellprofiler/gui
copying cellprofiler/gui/__init__.py -> build/lib/cellprofiler/gui
copying cellprofiler/gui/parametersampleframe.py -> build/lib/cellprofiler/gui
copying cellprofiler/gui/preferencesdlg.py -> build/lib/cellprofiler/gui
copying cellprofiler/gui/app.py -> build/lib/cellprofiler/gui
copying cellprofiler/gui/imagesetctrl.py -> build/lib/cellprofiler/gui
copying cellprofiler/gui/omerologin.py -> build/lib/cellprofiler/gui
copying cellprofiler/gui/metadatactrl.py -> build/lib/cellprofiler/gui
copying cellprofiler/gui/moduleview.py -> build/lib/cellprofiler/gui
copying cellprofiler/gui/tools.py -> build/lib/cellprofiler/gui
copying cellprofiler/gui/pipeline.py -> build/lib/cellprofiler/gui
copying cellprofiler/gui/artist.py -> build/lib/cellprofiler/gui
copying cellprofiler/gui/datatoolframe.py -> build/lib/cellprofiler/gui
copying cellprofiler/gui/viewworkspace.py -> build/lib/cellprofiler/gui
copying cellprofiler/gui/figure.py -> build/lib/cellprofiler/gui
copying cellprofiler/gui/editobjectsdlg.py -> build/lib/cellprofiler/gui
copying cellprofiler/gui/runmultiplepipelinesdialog.py -> build/lib/cellprofiler/gui
copying cellprofiler/gui/regexp_editor.py -> build/lib/cellprofiler/gui
copying cellprofiler/gui/dialog.py -> build/lib/cellprofiler/gui
creating build/lib/cellprofiler/utilities
copying cellprofiler/utilities/utf16encode.py -> build/lib/cellprofiler/utilities
copying cellprofiler/utilities/cpjvm.py -> build/lib/cellprofiler/utilities
copying cellprofiler/utilities/__init__.py -> build/lib/cellprofiler/utilities
copying cellprofiler/utilities/zmqrequest.py -> build/lib/cellprofiler/utilities
copying cellprofiler/utilities/rules.py -> build/lib/cellprofiler/utilities
copying cellprofiler/utilities/hdf5_dict.py -> build/lib/cellprofiler/utilities
creating build/lib/cellprofiler/modules/plugins
copying cellprofiler/modules/plugins/imagetemplate.py -> build/lib/cellprofiler/modules/plugins
copying cellprofiler/modules/plugins/measurementtemplate.py -> build/lib/cellprofiler/modules/plugins
copying cellprofiler/modules/plugins/__init__.py -> build/lib/cellprofiler/modules/plugins
creating build/lib/cellprofiler/gui/help
copying cellprofiler/gui/help/menu.py -> build/lib/cellprofiler/gui/help
copying cellprofiler/gui/help/search.py -> build/lib/cellprofiler/gui/help
copying cellprofiler/gui/help/__init__.py -> build/lib/cellprofiler/gui/help
copying cellprofiler/gui/help/content.py -> build/lib/cellprofiler/gui/help
creating build/lib/cellprofiler/gui/html
copying cellprofiler/gui/html/utils.py -> build/lib/cellprofiler/gui/html
copying cellprofiler/gui/html/__init__.py -> build/lib/cellprofiler/gui/html
copying cellprofiler/gui/html/htmlwindow.py -> build/lib/cellprofiler/gui/html
installing to build/bdist.linux-x86_64/wheel
running install
running install_lib
creating build/bdist.linux-x86_64
creating build/bdist.linux-x86_64/wheel
creating build/bdist.linux-x86_64/wheel/cellprofiler
copying build/lib/cellprofiler/module.py -> build/bdist.linux-x86_64/wheel/cellprofiler
copying build/lib/cellprofiler/measurement.py -> build/bdist.linux-x86_64/wheel/cellprofiler
copying build/lib/cellprofiler/workspace.py -> build/bdist.linux-x86_64/wheel/cellprofiler
copying build/lib/cellprofiler/setting.py -> build/bdist.linux-x86_64/wheel/cellprofiler
copying build/lib/cellprofiler/worker.py -> build/bdist.linux-x86_64/wheel/cellprofiler
copying build/lib/cellprofiler/image.py -> build/bdist.linux-x86_64/wheel/cellprofiler
copying build/lib/cellprofiler/analysis.py -> build/bdist.linux-x86_64/wheel/cellprofiler
copying build/lib/cellprofiler/object.py -> build/bdist.linux-x86_64/wheel/cellprofiler
copying build/lib/cellprofiler/__init__.py -> build/bdist.linux-x86_64/wheel/cellprofiler
creating build/bdist.linux-x86_64/wheel/cellprofiler/icons
copying build/lib/cellprofiler/icons/__init__.py -> build/bdist.linux-x86_64/wheel/cellprofiler/icons
creating build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/measuretexture.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/measureobjectintensity.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/flagimage.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/gaussianfilter.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/medialaxis.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/invertforprinting.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/displaydataonimage.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/measurecolocalization.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/measureobjectsizeshape.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/imagemath.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/removeobjectsbysize.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/correctilluminationcalculate.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/graytocolor.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/erosion.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/measuregranularity.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/enhanceorsuppressfeatures.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/calculatestatistics.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/threshold.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/measureimagequality.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/relateobjects.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/measureobjectskeleton.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/splitormergeobjects.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
creating build/bdist.linux-x86_64/wheel/cellprofiler/modules/plugins
copying build/lib/cellprofiler/modules/plugins/imagetemplate.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules/plugins
copying build/lib/cellprofiler/modules/plugins/measurementtemplate.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules/plugins
copying build/lib/cellprofiler/modules/plugins/__init__.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules/plugins
copying build/lib/cellprofiler/modules/makeprojection.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/label.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/straightenworms.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/removeholes.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/overlayobjects.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/identifyobjectsmanually.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/resizeobjects.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/createbatchfiles.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/displayplatemap.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/identifyobjectsingrid.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/measureimageareaoccupied.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/identifydeadworms.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/measureimageskeleton.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/dilation.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/colortogray.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/resize.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/editobjectsmanually.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/closing.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/exporttodatabase.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/metadata.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/smooth.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/measureimageintensity.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/classifyobjects.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/flipandrotate.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/maskimage.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/__init__.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/namesandtypes.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/displaydensityplot.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/enhanceedges.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/matchtemplate.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/identifytertiaryobjects.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/identify.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/correctilluminationapply.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/exporttospreadsheet.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/savecroppedobjects.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/untangleworms.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/identifysecondaryobjects.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/rescaleintensity.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/align.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/morphologicalskeleton.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/reducenoise.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/convertimagetoobjects.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/unmixcolors.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/loadimages.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/convertobjectstoimage.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/watershed.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/labelimages.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/medianfilter.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/opening.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/measureobjectneighbors.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/injectimage.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/displayscatterplot.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/_help.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/loadsingleimage.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/measureimageoverlap.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/tile.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/definegrid.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/overlayoutlines.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/identifyprimaryobjects.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/measureobjectintensitydistribution.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/images.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/mergeoutputfiles.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/loaddata.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/trackobjects.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/crop.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/saveimages.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/groups.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/shrinktoobjectcenters.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/displayhistogram.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/filterobjects.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/morph.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/measureobjectoverlap.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/expandorshrinkobjects.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/maskobjects.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/modules/calculatemath.py -> build/bdist.linux-x86_64/wheel/cellprofiler/modules
copying build/lib/cellprofiler/knime_bridge.py -> build/bdist.linux-x86_64/wheel/cellprofiler
creating build/bdist.linux-x86_64/wheel/cellprofiler/gui
copying build/lib/cellprofiler/gui/plateviewer.py -> build/bdist.linux-x86_64/wheel/cellprofiler/gui
copying build/lib/cellprofiler/gui/errordialog.py -> build/bdist.linux-x86_64/wheel/cellprofiler/gui
copying build/lib/cellprofiler/gui/pathlist.py -> build/bdist.linux-x86_64/wheel/cellprofiler/gui
copying build/lib/cellprofiler/gui/menu.py -> build/bdist.linux-x86_64/wheel/cellprofiler/gui
copying build/lib/cellprofiler/gui/workspace.py -> build/bdist.linux-x86_64/wheel/cellprofiler/gui
copying build/lib/cellprofiler/gui/cornerbuttonmixin.py -> build/bdist.linux-x86_64/wheel/cellprofiler/gui
copying build/lib/cellprofiler/gui/preferencesview.py -> build/bdist.linux-x86_64/wheel/cellprofiler/gui
copying build/lib/cellprofiler/gui/namesubscriber.py -> build/bdist.linux-x86_64/wheel/cellprofiler/gui
copying build/lib/cellprofiler/gui/treecheckboxdialog.py -> build/bdist.linux-x86_64/wheel/cellprofiler/gui
creating build/bdist.linux-x86_64/wheel/cellprofiler/gui/help
copying build/lib/cellprofiler/gui/help/menu.py -> build/bdist.linux-x86_64/wheel/cellprofiler/gui/help
copying build/lib/cellprofiler/gui/help/search.py -> build/bdist.linux-x86_64/wheel/cellprofiler/gui/help
copying build/lib/cellprofiler/gui/help/__init__.py -> build/bdist.linux-x86_64/wheel/cellprofiler/gui/help
copying build/lib/cellprofiler/gui/help/content.py -> build/bdist.linux-x86_64/wheel/cellprofiler/gui/help
copying build/lib/cellprofiler/gui/cpframe.py -> build/bdist.linux-x86_64/wheel/cellprofiler/gui
copying build/lib/cellprofiler/gui/htmldialog.py -> build/bdist.linux-x86_64/wheel/cellprofiler/gui
copying build/lib/cellprofiler/gui/pipelinecontroller.py -> build/bdist.linux-x86_64/wheel/cellprofiler/gui
copying build/lib/cellprofiler/gui/addmoduleframe.py -> build/bdist.linux-x86_64/wheel/cellprofiler/gui
copying build/lib/cellprofiler/gui/pipelinelistview.py -> build/bdist.linux-x86_64/wheel/cellprofiler/gui
copying build/lib/cellprofiler/gui/welcome.py -> build/bdist.linux-x86_64/wheel/cellprofiler/gui
copying build/lib/cellprofiler/gui/__init__.py -> build/bdist.linux-x86_64/wheel/cellprofiler/gui
copying build/lib/cellprofiler/gui/parametersampleframe.py -> build/bdist.linux-x86_64/wheel/cellprofiler/gui
copying build/lib/cellprofiler/gui/preferencesdlg.py -> build/bdist.linux-x86_64/wheel/cellprofiler/gui
creating build/bdist.linux-x86_64/wheel/cellprofiler/gui/html
copying build/lib/cellprofiler/gui/html/utils.py -> build/bdist.linux-x86_64/wheel/cellprofiler/gui/html
copying build/lib/cellprofiler/gui/html/__init__.py -> build/bdist.linux-x86_64/wheel/cellprofiler/gui/html
copying build/lib/cellprofiler/gui/html/htmlwindow.py -> build/bdist.linux-x86_64/wheel/cellprofiler/gui/html
copying build/lib/cellprofiler/gui/app.py -> build/bdist.linux-x86_64/wheel/cellprofiler/gui
copying build/lib/cellprofiler/gui/imagesetctrl.py -> build/bdist.linux-x86_64/wheel/cellprofiler/gui
copying build/lib/cellprofiler/gui/omerologin.py -> build/bdist.linux-x86_64/wheel/cellprofiler/gui
copying build/lib/cellprofiler/gui/metadatactrl.py -> build/bdist.linux-x86_64/wheel/cellprofiler/gui
copying build/lib/cellprofiler/gui/moduleview.py -> build/bdist.linux-x86_64/wheel/cellprofiler/gui
copying build/lib/cellprofiler/gui/tools.py -> build/bdist.linux-x86_64/wheel/cellprofiler/gui
copying build/lib/cellprofiler/gui/pipeline.py -> build/bdist.linux-x86_64/wheel/cellprofiler/gui
copying build/lib/cellprofiler/gui/artist.py -> build/bdist.linux-x86_64/wheel/cellprofiler/gui
copying build/lib/cellprofiler/gui/datatoolframe.py -> build/bdist.linux-x86_64/wheel/cellprofiler/gui
copying build/lib/cellprofiler/gui/viewworkspace.py -> build/bdist.linux-x86_64/wheel/cellprofiler/gui
copying build/lib/cellprofiler/gui/figure.py -> build/bdist.linux-x86_64/wheel/cellprofiler/gui
copying build/lib/cellprofiler/gui/editobjectsdlg.py -> build/bdist.linux-x86_64/wheel/cellprofiler/gui
copying build/lib/cellprofiler/gui/runmultiplepipelinesdialog.py -> build/bdist.linux-x86_64/wheel/cellprofiler/gui
copying build/lib/cellprofiler/gui/regexp_editor.py -> build/bdist.linux-x86_64/wheel/cellprofiler/gui
copying build/lib/cellprofiler/gui/dialog.py -> build/bdist.linux-x86_64/wheel/cellprofiler/gui
copying build/lib/cellprofiler/pipeline.py -> build/bdist.linux-x86_64/wheel/cellprofiler
copying build/lib/cellprofiler/__main__.py -> build/bdist.linux-x86_64/wheel/cellprofiler
creating build/bdist.linux-x86_64/wheel/cellprofiler/utilities
copying build/lib/cellprofiler/utilities/utf16encode.py -> build/bdist.linux-x86_64/wheel/cellprofiler/utilities
copying build/lib/cellprofiler/utilities/cpjvm.py -> build/bdist.linux-x86_64/wheel/cellprofiler/utilities
copying build/lib/cellprofiler/utilities/__init__.py -> build/bdist.linux-x86_64/wheel/cellprofiler/utilities
copying build/lib/cellprofiler/utilities/zmqrequest.py -> build/bdist.linux-x86_64/wheel/cellprofiler/utilities
copying build/lib/cellprofiler/utilities/rules.py -> build/bdist.linux-x86_64/wheel/cellprofiler/utilities
copying build/lib/cellprofiler/utilities/hdf5_dict.py -> build/bdist.linux-x86_64/wheel/cellprofiler/utilities
copying build/lib/cellprofiler/grid.py -> build/bdist.linux-x86_64/wheel/cellprofiler
copying build/lib/cellprofiler/preferences.py -> build/bdist.linux-x86_64/wheel/cellprofiler
running install_egg_info
running egg_info
creating CellProfiler.egg-info
writing requirements to CellProfiler.egg-info/requires.txt
writing CellProfiler.egg-info/PKG-INFO
writing top-level names to CellProfiler.egg-info/top_level.txt
writing dependency_links to CellProfiler.egg-info/dependency_links.txt
writing entry points to CellProfiler.egg-info/entry_points.txt
writing manifest file 'CellProfiler.egg-info/SOURCES.txt'
reading manifest file 'CellProfiler.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'CellProfiler.egg-info/SOURCES.txt'
Copying CellProfiler.egg-info to build/bdist.linux-x86_64/wheel/CellProfiler-3.0.0-py2.7.egg-info
running install_scripts
creating build/bdist.linux-x86_64/wheel/CellProfiler-3.0.0.dist-info/WHEEL
(cp-env) mattb@AI-Linux-mattb:~/misc/CellProfiler$ pip install dist/CellProfiler-3.0.0-py2-none-any.whl 
Processing ./dist/CellProfiler-3.0.0-py2-none-any.whl
Requirement already satisfied: prokaryote==2.3.1 in /home/mattb/programs/anaconda2/envs/cp-env/lib/python2.7/site-packages (from CellProfiler==3.0.0)
Requirement already satisfied: scikit-image in /home/mattb/programs/anaconda2/envs/cp-env/lib/python2.7/site-packages (from CellProfiler==3.0.0)
Requirement already satisfied: numpy in /home/mattb/programs/anaconda2/envs/cp-env/lib/python2.7/site-packages (from CellProfiler==3.0.0)
Requirement already satisfied: javabridge in /home/mattb/programs/anaconda2/envs/cp-env/lib/python2.7/site-packages (from CellProfiler==3.0.0)
Requirement already satisfied: requests in /home/mattb/programs/anaconda2/envs/cp-env/lib/python2.7/site-packages (from CellProfiler==3.0.0)
Requirement already satisfied: python-bioformats==1.3.1 in /home/mattb/programs/anaconda2/envs/cp-env/lib/python2.7/site-packages (from CellProfiler==3.0.0)
Requirement already satisfied: inflect in /home/mattb/programs/anaconda2/envs/cp-env/lib/python2.7/site-packages (from CellProfiler==3.0.0)
Requirement already satisfied: scikit-learn in /home/mattb/programs/anaconda2/envs/cp-env/lib/python2.7/site-packages (from CellProfiler==3.0.0)
Requirement already satisfied: MySQL-python in /home/mattb/programs/anaconda2/envs/cp-env/lib/python2.7/site-packages (from CellProfiler==3.0.0)
Requirement already satisfied: docutils in /home/mattb/programs/anaconda2/envs/cp-env/lib/python2.7/site-packages (from CellProfiler==3.0.0)
Requirement already satisfied: scipy in /home/mattb/programs/anaconda2/envs/cp-env/lib/python2.7/site-packages (from CellProfiler==3.0.0)
Requirement already satisfied: centrosome in /home/mattb/programs/anaconda2/envs/cp-env/lib/python2.7/site-packages (from CellProfiler==3.0.0)
Requirement already satisfied: raven in /home/mattb/programs/anaconda2/envs/cp-env/lib/python2.7/site-packages (from CellProfiler==3.0.0)
Requirement already satisfied: matplotlib!=2.1.0,>=2.0.0 in /home/mattb/programs/anaconda2/envs/cp-env/lib/python2.7/site-packages (from CellProfiler==3.0.0)
Collecting pyzmq==15.3.0 (from CellProfiler==3.0.0)
  Downloading https://artifactory.corp.alleninstitute.org/artifactory/api/pypi/pypi-virtual/packages/06/a7/b577b788e59ae988c5aba322568341e28f4fde50289751a40d630f05413f/pyzmq-15.3.0-cp27-cp27mu-manylinux1_x86_64.whl (2.8MB)
    100% |████████████████████████████████| 2.8MB 586kB/s 
Collecting joblib (from CellProfiler==3.0.0)
  Downloading https://artifactory.corp.alleninstitute.org/artifactory/api/pypi/pypi-virtual/packages/4f/51/870b2ec270fc29c5d89f85353da420606a9cb39fba4747127e7c7d7eb25d/joblib-0.11-py2.py3-none-any.whl (176kB)
    100% |████████████████████████████████| 184kB 4.2MB/s 
Requirement already satisfied: mahotas in /home/mattb/programs/anaconda2/envs/cp-env/lib/python2.7/site-packages (from CellProfiler==3.0.0)
Requirement already satisfied: h5py in /home/mattb/programs/anaconda2/envs/cp-env/lib/python2.7/site-packages (from CellProfiler==3.0.0)
Requirement already satisfied: six>=1.7.3 in /home/mattb/programs/anaconda2/envs/cp-env/lib/python2.7/site-packages (from scikit-image->CellProfiler==3.0.0)
Requirement already satisfied: networkx>=1.8 in /home/mattb/programs/anaconda2/envs/cp-env/lib/python2.7/site-packages (from scikit-image->CellProfiler==3.0.0)
Requirement already satisfied: pillow>=2.1.0 in /home/mattb/programs/anaconda2/envs/cp-env/lib/python2.7/site-packages (from scikit-image->CellProfiler==3.0.0)
Requirement already satisfied: PyWavelets>=0.4.0 in /home/mattb/programs/anaconda2/envs/cp-env/lib/python2.7/site-packages (from scikit-image->CellProfiler==3.0.0)
Requirement already satisfied: chardet<3.1.0,>=3.0.2 in /home/mattb/programs/anaconda2/envs/cp-env/lib/python2.7/site-packages (from requests->CellProfiler==3.0.0)
Requirement already satisfied: idna<2.7,>=2.5 in /home/mattb/programs/anaconda2/envs/cp-env/lib/python2.7/site-packages (from requests->CellProfiler==3.0.0)
Requirement already satisfied: urllib3<1.23,>=1.21.1 in /home/mattb/programs/anaconda2/envs/cp-env/lib/python2.7/site-packages (from requests->CellProfiler==3.0.0)
Requirement already satisfied: certifi>=2017.4.17 in /home/mattb/programs/anaconda2/envs/cp-env/lib/python2.7/site-packages (from requests->CellProfiler==3.0.0)
Requirement already satisfied: future in /home/mattb/programs/anaconda2/envs/cp-env/lib/python2.7/site-packages (from python-bioformats==1.3.1->CellProfiler==3.0.0)
Requirement already satisfied: contextlib2 in /home/mattb/programs/anaconda2/envs/cp-env/lib/python2.7/site-packages (from raven->CellProfiler==3.0.0)
Requirement already satisfied: python-dateutil in /home/mattb/programs/anaconda2/envs/cp-env/lib/python2.7/site-packages (from matplotlib!=2.1.0,>=2.0.0->CellProfiler==3.0.0)
Requirement already satisfied: functools32 in /home/mattb/programs/anaconda2/envs/cp-env/lib/python2.7/site-packages (from matplotlib!=2.1.0,>=2.0.0->CellProfiler==3.0.0)
Requirement already satisfied: subprocess32 in /home/mattb/programs/anaconda2/envs/cp-env/lib/python2.7/site-packages (from matplotlib!=2.1.0,>=2.0.0->CellProfiler==3.0.0)
Requirement already satisfied: pytz in /home/mattb/programs/anaconda2/envs/cp-env/lib/python2.7/site-packages (from matplotlib!=2.1.0,>=2.0.0->CellProfiler==3.0.0)
Requirement already satisfied: cycler>=0.10 in /home/mattb/programs/anaconda2/envs/cp-env/lib/python2.7/site-packages (from matplotlib!=2.1.0,>=2.0.0->CellProfiler==3.0.0)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=1.5.6 in /home/mattb/programs/anaconda2/envs/cp-env/lib/python2.7/site-packages (from matplotlib!=2.1.0,>=2.0.0->CellProfiler==3.0.0)
Requirement already satisfied: decorator>=4.1.0 in /home/mattb/programs/anaconda2/envs/cp-env/lib/python2.7/site-packages (from networkx>=1.8->scikit-image->CellProfiler==3.0.0)
Requirement already satisfied: olefile in /home/mattb/programs/anaconda2/envs/cp-env/lib/python2.7/site-packages (from pillow>=2.1.0->scikit-image->CellProfiler==3.0.0)
Installing collected packages: pyzmq, joblib, CellProfiler
  Found existing installation: pyzmq 16.0.2
    Uninstalling pyzmq-16.0.2:
      Successfully uninstalled pyzmq-16.0.2
Successfully installed CellProfiler-3.0.0 joblib-0.11 pyzmq-15.3.0
(cp-env) mattb@AI-Linux-mattb:~/misc/CellProfiler$ cellprofiler
GLib-GIO-Message: Using the 'memory' GSettings backend.  Your settings will not be saved or shared with other applications.
Traceback (most recent call last):
  File "/home/mattb/programs/anaconda2/envs/cp-env/bin/cellprofiler", line 11, in <module>
    sys.exit(main())
  File "/home/mattb/programs/anaconda2/envs/cp-env/lib/python2.7/site-packages/cellprofiler/__main__.py", line 152, in main
    app = cellprofiler.gui.app.App(0, workspace_path=workspace_path, pipeline_path=pipeline_path)
  File "/home/mattb/programs/anaconda2/envs/cp-env/lib/python2.7/site-packages/cellprofiler/gui/app.py", line 55, in __init__
    super(App, self).__init__(*args, **kwargs)
  File "/home/mattb/programs/anaconda2/envs/cp-env/lib/python2.7/site-packages/wx-3.0-gtk2/wx/_core.py", line 8631, in __init__
    self._BootstrapApp()
  File "/home/mattb/programs/anaconda2/envs/cp-env/lib/python2.7/site-packages/wx-3.0-gtk2/wx/_core.py", line 8196, in _BootstrapApp
    return _core_.PyApp__BootstrapApp(*args, **kwargs)
  File "/home/mattb/programs/anaconda2/envs/cp-env/lib/python2.7/site-packages/cellprofiler/gui/app.py", line 58, in OnInit
    import cellprofiler.gui.cpframe
  File "/home/mattb/programs/anaconda2/envs/cp-env/lib/python2.7/site-packages/cellprofiler/gui/cpframe.py", line 7, in <module>
    import cellprofiler.gui.figure
  File "/home/mattb/programs/anaconda2/envs/cp-env/lib/python2.7/site-packages/cellprofiler/gui/figure.py", line 41, in <module>
    import cellprofiler.gui.help.content
  File "/home/mattb/programs/anaconda2/envs/cp-env/lib/python2.7/site-packages/cellprofiler/gui/help/content.py", line 88, in <module>
    ("Using The Display Window Menu Bar", read_content("display_menu_bar.rst")),
  File "/home/mattb/programs/anaconda2/envs/cp-env/lib/python2.7/site-packages/cellprofiler/gui/help/content.py", line 22, in read_content
    with open(resource_filename, "r") as f:
IOError: [Errno 2] No such file or directory: '/home/mattb/programs/anaconda2/envs/cp-env/lib/python2.7/site-packages/cellprofiler/data/help/display_menu_bar.rst'
^C
(cp-env) mattb@AI-Linux-mattb:~/misc/CellProfiler$ cp -r cellprofiler/data/ /home/mattb/programs/anaconda2/envs/cp-env/lib/python2.7/site-packages/cellprofiler/
(cp-env) mattb@AI-Linux-mattb:~/misc/CellProfiler$ cellprofiler
GLib-GIO-Message: Using the 'memory' GSettings backend.  Your settings will not be saved or shared with other applications.

(cellprofiler:28426): Gdk-WARNING **: gdk_window_set_icon_list: icons too large

(cellprofiler:28426): Gdk-WARNING **: gdk_window_set_icon_list: icons too large
Exiting the pipeline validation thread

_(CellProfiler launched properly this last time)_

Steps to reproduce:

1. Create a conda environment with the suggested environment file (slight modifications from the wiki suggestion due to the mismatch between the setup.py version numbers and the versions pulled by conda, I could potentially make that as a separate issue).
2. Install CellProfiler as a "non-editable" package, i.e. without the editable flag
3. Run cellprofiler (proceeds to fail with IO Error due to missing data directory

Steps to rectify:

1. Copy data from Github source into anaconda distribution location

[AetherUnbound]

I'm working on this in issues/3375 in my own fork.

[mcquin]

Create a conda environment with the suggested environment file (slight modifications from the wiki suggestion due to the mismatch between the setup.py version numbers and the versions pulled by conda, I could potentially make that as a separate issue).

If you don't mind sending us your environment.yml, we can get the wiki instructions upgraded. GitHub file upload or old fashioned copy & paste is fine.

[AetherUnbound]

I'll wait to update it for now, because I believe this fix should also allow CellProfiler to be added as the last pip install in the environment.yaml file. Ideally this would allow people to install CellProfiler with a single command.

[AetherUnbound]

Closed with #3380