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Testing issue upon installation

See original GitHub issue

I tried fresh installation on OSX, following the doc (stable release 1.0), and obtained the following issue when running axondeepseg_test:

julien-macbook:~ $ virtualenv ads_venv_test
New python executable in /Users/julien/ads_venv_test/bin/python
Installing setuptools, pip, wheel...done.
julien-macbook:~ $ source ads_venv_test/bin/activate
(ads_venv_test) julien-macbook:~ $ pip install axondeepseg
Collecting axondeepseg
  Downloading https://files.pythonhosted.org/packages/74/0c/aeac1e632f4823252e3660fdf44f06c1d0ec64310c41da9b1ec6188dacbe/AxonDeepSeg-1.0-py2.py3-none-any.whl (14.9MB)
    100% |████████████████████████████████| 15.0MB 1.5MB/s 
Collecting scikit-learn>=0.18.1 (from axondeepseg)
  Using cached https://files.pythonhosted.org/packages/22/47/dfc1c815a75afc940789df0e125d55cf9e1eceaf589d89f285f9df575235/scikit_learn-0.19.2-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Collecting scipy>=0.19 (from axondeepseg)
  Using cached https://files.pythonhosted.org/packages/d1/d6/3eac96ffcf7cbeb37ed72982cf3fdd3138472cb04ab32cdce1f444d765f2/scipy-1.1.0-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Collecting pytest-cov==2.5.1 (from axondeepseg)
  Using cached https://files.pythonhosted.org/packages/30/7d/7f6a78ae44a1248ee28cc777586c18b28a1df903470e5d34a6e25712b8aa/pytest_cov-2.5.1-py2.py3-none-any.whl
Collecting pillow>=3.4.2 (from axondeepseg)
  Using cached https://files.pythonhosted.org/packages/a8/56/0f2427d8df966e002fbb748d8537d8f037321b762997a6f05d24cb7334d7/Pillow-5.2.0-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Collecting scikit-image>=0.12.3 (from axondeepseg)
  Using cached https://files.pythonhosted.org/packages/14/6c/67d8aeeeae8cb0a6117bcaee35ccead489e085859b404d3cf2c37066ec78/scikit_image-0.14.0-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Collecting pandas>=0.19.2 (from axondeepseg)
  Using cached https://files.pythonhosted.org/packages/58/9a/f571a032f5f2bf5b8a5d63ce079428c5423299853ed2d8d96626f441801d/pandas-0.23.3-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Collecting mpld3>=0.3 (from axondeepseg)
Collecting tabulate>=0.7.7 (from axondeepseg)
Collecting tqdm>=4.14.0 (from axondeepseg)
  Downloading https://files.pythonhosted.org/packages/7d/e6/19dfaff08fcbee7f3453e5b537e65a8364f1945f921a36d08be1e2ff3475/tqdm-4.24.0-py2.py3-none-any.whl (43kB)
    100% |████████████████████████████████| 51kB 11.6MB/s 
Collecting pytest==3.5.0 (from axondeepseg)
  Using cached https://files.pythonhosted.org/packages/ed/96/271c93f75212c06e2a7ec3e2fa8a9c90acee0a4838dc05bf379ea09aae31/pytest-3.5.0-py2.py3-none-any.whl
Collecting tensorflow>=1.3.0 (from axondeepseg)
  Using cached https://files.pythonhosted.org/packages/80/e0/f480d4b60136f8b16250de150abf425a1099d914d36d33bf568b91a10275/tensorflow-1.9.0-cp27-cp27m-macosx_10_11_x86_64.whl
Collecting prettytable>=0.7.2 (from axondeepseg)
Collecting matplotlib>=1.5.3 (from axondeepseg)
  Using cached https://files.pythonhosted.org/packages/61/38/d70e8bf77d5cb27d5f3595edd0b3978825063feadd023786d2591e393e6e/matplotlib-2.2.2-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Collecting numpy>=1.12.0 (from axondeepseg)
  Downloading https://files.pythonhosted.org/packages/3c/bf/e36756c562f7386be78c6942f0a8a647ee4eb374cdf219bece7054832b14/numpy-1.15.0-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (24.5MB)
    100% |████████████████████████████████| 24.5MB 1.3MB/s 
Collecting imageio>=2.2.0 (from axondeepseg)
  Using cached https://files.pythonhosted.org/packages/a7/1d/33c8686072148b3b0fcc12a2e0857dd8316b8ae20a0fa66c8d6a6d01c05c/imageio-2.3.0-py2.py3-none-any.whl
Collecting raven==6.8.0 (from axondeepseg)
  Using cached https://files.pythonhosted.org/packages/21/14/a06bcd2aa519bb659f5cf9e0b8c29158155cea7f6ce6e947d06967642df6/raven-6.8.0-py2.py3-none-any.whl
Collecting coverage>=3.7.1 (from pytest-cov==2.5.1->axondeepseg)
  Using cached https://files.pythonhosted.org/packages/8a/27/68ca17e26df117a993dec8f590929670f96a976de56d52e6b6c939156013/coverage-4.5.1-cp27-cp27m-macosx_10_12_x86_64.whl
Collecting PyWavelets>=0.4.0 (from scikit-image>=0.12.3->axondeepseg)
  Using cached https://files.pythonhosted.org/packages/da/2a/dd1b00eb1835e0f8d6f8b8f024fb77183cf1fe1d6910d95d48394cd80740/PyWavelets-0.5.2-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Collecting cloudpickle>=0.2.1 (from scikit-image>=0.12.3->axondeepseg)
  Using cached https://files.pythonhosted.org/packages/e7/bf/60ae7ec1e8c6742d2abbb6819c39a48ee796793bcdb7e1d5e41a3e379ddd/cloudpickle-0.5.3-py2.py3-none-any.whl
Collecting networkx>=1.8 (from scikit-image>=0.12.3->axondeepseg)
Collecting dask[array]>=0.9.0 (from scikit-image>=0.12.3->axondeepseg)
  Using cached https://files.pythonhosted.org/packages/91/52/427541141707ac533a6dcafa3bff7ff8b57ded3c9ea84d6ec014d15fbbff/dask-0.18.2-py2.py3-none-any.whl
Collecting six>=1.10.0 (from scikit-image>=0.12.3->axondeepseg)
  Using cached https://files.pythonhosted.org/packages/67/4b/141a581104b1f6397bfa78ac9d43d8ad29a7ca43ea90a2d863fe3056e86a/six-1.11.0-py2.py3-none-any.whl
Collecting python-dateutil>=2.5.0 (from pandas>=0.19.2->axondeepseg)
  Using cached https://files.pythonhosted.org/packages/cf/f5/af2b09c957ace60dcfac112b669c45c8c97e32f94aa8b56da4c6d1682825/python_dateutil-2.7.3-py2.py3-none-any.whl
Collecting pytz>=2011k (from pandas>=0.19.2->axondeepseg)
  Using cached https://files.pythonhosted.org/packages/30/4e/27c34b62430286c6d59177a0842ed90dc789ce5d1ed740887653b898779a/pytz-2018.5-py2.py3-none-any.whl
Collecting pluggy<0.7,>=0.5 (from pytest==3.5.0->axondeepseg)
  Using cached https://files.pythonhosted.org/packages/82/05/43e3947125a2137cba4746135c75934ceed1863f27e050fc560052104a71/pluggy-0.6.0-py2-none-any.whl
Collecting more-itertools>=4.0.0 (from pytest==3.5.0->axondeepseg)
  Downloading https://files.pythonhosted.org/packages/fb/d3/77f337876600747ae307ea775ff264c5304a691941cd347382c7932c60ad/more_itertools-4.3.0-py2-none-any.whl (48kB)
    100% |████████████████████████████████| 51kB 10.0MB/s 
Collecting py>=1.5.0 (from pytest==3.5.0->axondeepseg)
  Using cached https://files.pythonhosted.org/packages/f3/bd/83369ff2dee18f22f27d16b78dd651e8939825af5f8b0b83c38729069962/py-1.5.4-py2.py3-none-any.whl
Collecting attrs>=17.4.0 (from pytest==3.5.0->axondeepseg)
  Using cached https://files.pythonhosted.org/packages/41/59/cedf87e91ed541be7957c501a92102f9cc6363c623a7666d69d51c78ac5b/attrs-18.1.0-py2.py3-none-any.whl
Collecting funcsigs; python_version < "3.0" (from pytest==3.5.0->axondeepseg)
  Using cached https://files.pythonhosted.org/packages/69/cb/f5be453359271714c01b9bd06126eaf2e368f1fddfff30818754b5ac2328/funcsigs-1.0.2-py2.py3-none-any.whl
Requirement already satisfied: setuptools in ./ads_venv_test/lib/python2.7/site-packages (from pytest==3.5.0->axondeepseg) (40.0.0)
Collecting mock>=2.0.0 (from tensorflow>=1.3.0->axondeepseg)
  Using cached https://files.pythonhosted.org/packages/e6/35/f187bdf23be87092bd0f1200d43d23076cee4d0dec109f195173fd3ebc79/mock-2.0.0-py2.py3-none-any.whl
Collecting termcolor>=1.1.0 (from tensorflow>=1.3.0->axondeepseg)
Collecting astor>=0.6.0 (from tensorflow>=1.3.0->axondeepseg)
  Using cached https://files.pythonhosted.org/packages/35/6b/11530768cac581a12952a2aad00e1526b89d242d0b9f59534ef6e6a1752f/astor-0.7.1-py2.py3-none-any.whl
Collecting backports.weakref>=1.0rc1 (from tensorflow>=1.3.0->axondeepseg)
  Using cached https://files.pythonhosted.org/packages/88/ec/f598b633c3d5ffe267aaada57d961c94fdfa183c5c3ebda2b6d151943db6/backports.weakref-1.0.post1-py2.py3-none-any.whl
Collecting tensorboard<1.10.0,>=1.9.0 (from tensorflow>=1.3.0->axondeepseg)
  Using cached https://files.pythonhosted.org/packages/d5/98/e2e9d5afbc86cef0b2dd0f4ab791519b9bd305ea207e1e5c2f9a9f2f6da6/tensorboard-1.9.0-py2-none-any.whl
Collecting gast>=0.2.0 (from tensorflow>=1.3.0->axondeepseg)
Collecting grpcio>=1.8.6 (from tensorflow>=1.3.0->axondeepseg)
  Using cached https://files.pythonhosted.org/packages/66/89/4a90caabd51c17686cbb48a9bbe8c592c4be929c0d2542d2ffde76b0d671/grpcio-1.13.0-cp27-cp27m-macosx_10_12_x86_64.whl
Requirement already satisfied: wheel in ./ads_venv_test/lib/python2.7/site-packages (from tensorflow>=1.3.0->axondeepseg) (0.31.1)
Collecting enum34>=1.1.6 (from tensorflow>=1.3.0->axondeepseg)
  Using cached https://files.pythonhosted.org/packages/c5/db/e56e6b4bbac7c4a06de1c50de6fe1ef3810018ae11732a50f15f62c7d050/enum34-1.1.6-py2-none-any.whl
Collecting absl-py>=0.1.6 (from tensorflow>=1.3.0->axondeepseg)
  Downloading https://files.pythonhosted.org/packages/96/5d/18feb90462c8edaae71305716c7e8bac479fc9dface63221f808a6b95880/absl-py-0.3.0.tar.gz (84kB)
    100% |████████████████████████████████| 92kB 10.8MB/s 
Collecting protobuf>=3.4.0 (from tensorflow>=1.3.0->axondeepseg)
  Using cached https://files.pythonhosted.org/packages/4f/56/a21f2d077ceae7fd521c0ed31fb8bb1c7f13ffbb09bf7dd27de6cf6bad08/protobuf-3.6.0-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Collecting kiwisolver>=1.0.1 (from matplotlib>=1.5.3->axondeepseg)
  Using cached https://files.pythonhosted.org/packages/79/d8/94633718f3f77dcb638687a77ba199325a1cb158d2d4b00c9dc17f2b5c72/kiwisolver-1.0.1-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Collecting cycler>=0.10 (from matplotlib>=1.5.3->axondeepseg)
  Using cached https://files.pythonhosted.org/packages/f7/d2/e07d3ebb2bd7af696440ce7e754c59dd546ffe1bbe732c8ab68b9c834e61/cycler-0.10.0-py2.py3-none-any.whl
Collecting subprocess32 (from matplotlib>=1.5.3->axondeepseg)
  Using cached https://files.pythonhosted.org/packages/fa/60/b50459f291cae6bc1d0ff711b75e5130684fd3949370fdba78f6c57c1903/subprocess32-3.5.2-cp27-cp27m-macosx_10_6_intel.whl
Collecting backports.functools-lru-cache (from matplotlib>=1.5.3->axondeepseg)
  Using cached https://files.pythonhosted.org/packages/03/8e/2424c0e65c4a066e28f539364deee49b6451f8fcd4f718fefa50cc3dcf48/backports.functools_lru_cache-1.5-py2.py3-none-any.whl
Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 (from matplotlib>=1.5.3->axondeepseg)
  Using cached https://files.pythonhosted.org/packages/6a/8a/718fd7d3458f9fab8e67186b00abdd345b639976bc7fb3ae722e1b026a50/pyparsing-2.2.0-py2.py3-none-any.whl
Collecting contextlib2; python_version < "3.2" (from raven==6.8.0->axondeepseg)
  Using cached https://files.pythonhosted.org/packages/a2/71/8273a7eeed0aff6a854237ab5453bc9aa67deb49df4832801c21f0ff3782/contextlib2-0.5.5-py2.py3-none-any.whl
Collecting decorator>=4.1.0 (from networkx>=1.8->scikit-image>=0.12.3->axondeepseg)
  Using cached https://files.pythonhosted.org/packages/bc/bb/a24838832ba35baf52f32ab1a49b906b5f82fb7c76b2f6a7e35e140bac30/decorator-4.3.0-py2.py3-none-any.whl
Collecting toolz>=0.7.3; extra == "array" (from dask[array]>=0.9.0->scikit-image>=0.12.3->axondeepseg)
Collecting pbr>=0.11 (from mock>=2.0.0->tensorflow>=1.3.0->axondeepseg)
  Downloading https://files.pythonhosted.org/packages/69/1c/98cba002ed975a91a0294863d9c774cc0ebe38e05bbb65e83314550b1677/pbr-4.2.0-py2.py3-none-any.whl (100kB)
    100% |████████████████████████████████| 102kB 11.8MB/s 
Collecting futures>=3.1.1; python_version < "3" (from tensorboard<1.10.0,>=1.9.0->tensorflow>=1.3.0->axondeepseg)
  Using cached https://files.pythonhosted.org/packages/2d/99/b2c4e9d5a30f6471e410a146232b4118e697fa3ffc06d6a65efde84debd0/futures-3.2.0-py2-none-any.whl
Collecting werkzeug>=0.11.10 (from tensorboard<1.10.0,>=1.9.0->tensorflow>=1.3.0->axondeepseg)
  Using cached https://files.pythonhosted.org/packages/20/c4/12e3e56473e52375aa29c4764e70d1b8f3efa6682bef8d0aae04fe335243/Werkzeug-0.14.1-py2.py3-none-any.whl
Collecting markdown>=2.6.8 (from tensorboard<1.10.0,>=1.9.0->tensorflow>=1.3.0->axondeepseg)
  Using cached https://files.pythonhosted.org/packages/6d/7d/488b90f470b96531a3f5788cf12a93332f543dbab13c423a5e7ce96a0493/Markdown-2.6.11-py2.py3-none-any.whl
Building wheels for collected packages: absl-py
  Running setup.py bdist_wheel for absl-py ... done
  Stored in directory: /Users/julien/Library/Caches/pip/wheels/4c/16/ef/e36a23f2432e9220f8845f94e2c3abd39e7d9d1cd458d3159d
Successfully built absl-py
tensorflow 1.9.0 has requirement setuptools<=39.1.0, but you'll have setuptools 40.0.0 which is incompatible.
Installing collected packages: scikit-learn, numpy, scipy, pluggy, six, more-itertools, py, attrs, funcsigs, pytest, coverage, pytest-cov, pillow, PyWavelets, kiwisolver, cycler, subprocess32, pytz, backports.functools-lru-cache, pyparsing, python-dateutil, matplotlib, cloudpickle, decorator, networkx, toolz, dask, scikit-image, pandas, mpld3, tabulate, tqdm, pbr, mock, termcolor, astor, backports.weakref, futures, werkzeug, markdown, protobuf, tensorboard, gast, enum34, grpcio, absl-py, tensorflow, prettytable, imageio, contextlib2, raven, axondeepseg
Successfully installed PyWavelets-0.5.2 absl-py-0.3.0 astor-0.7.1 attrs-18.1.0 axondeepseg-1.0 backports.functools-lru-cache-1.5 backports.weakref-1.0.post1 cloudpickle-0.5.3 contextlib2-0.5.5 coverage-4.5.1 cycler-0.10.0 dask-0.18.2 decorator-4.3.0 enum34-1.1.6 funcsigs-1.0.2 futures-3.2.0 gast-0.2.0 grpcio-1.13.0 imageio-2.3.0 kiwisolver-1.0.1 markdown-2.6.11 matplotlib-2.2.2 mock-2.0.0 more-itertools-4.3.0 mpld3-0.3 networkx-2.1 numpy-1.15.0 pandas-0.23.3 pbr-4.2.0 pillow-5.2.0 pluggy-0.6.0 prettytable-0.7.2 protobuf-3.6.0 py-1.5.4 pyparsing-2.2.0 pytest-3.5.0 pytest-cov-2.5.1 python-dateutil-2.7.3 pytz-2018.5 raven-6.8.0 scikit-image-0.14.0 scikit-learn-0.19.2 scipy-1.1.0 six-1.11.0 subprocess32-3.5.2 tabulate-0.8.2 tensorboard-1.9.0 tensorflow-1.9.0 termcolor-1.1.0 toolz-0.9.0 tqdm-4.24.0 werkzeug-0.14.1
(ads_venv_test) julien-macbook:~ $ pip install https://storage.googleapis.com/tensorflow/mac/cpu/tensorflow-1.3.0-py2-none-any.whl
Collecting tensorflow==1.3.0 from https://storage.googleapis.com/tensorflow/mac/cpu/tensorflow-1.3.0-py2-none-any.whl
  Using cached https://storage.googleapis.com/tensorflow/mac/cpu/tensorflow-1.3.0-py2-none-any.whl
Requirement already satisfied: numpy>=1.11.0 in ./ads_venv_test/lib/python2.7/site-packages (from tensorflow==1.3.0) (1.15.0)
Requirement already satisfied: mock>=2.0.0 in ./ads_venv_test/lib/python2.7/site-packages (from tensorflow==1.3.0) (2.0.0)
Collecting tensorflow-tensorboard<0.2.0,>=0.1.0 (from tensorflow==1.3.0)
  Using cached https://files.pythonhosted.org/packages/fb/34/14c23665a725c73932891e09b8f017a53aad545c9d5019d2817102dc5d9b/tensorflow_tensorboard-0.1.8-py2-none-any.whl
Requirement already satisfied: wheel in ./ads_venv_test/lib/python2.7/site-packages (from tensorflow==1.3.0) (0.31.1)
Requirement already satisfied: backports.weakref>=1.0rc1 in ./ads_venv_test/lib/python2.7/site-packages (from tensorflow==1.3.0) (1.0.post1)
Requirement already satisfied: protobuf>=3.3.0 in ./ads_venv_test/lib/python2.7/site-packages (from tensorflow==1.3.0) (3.6.0)
Requirement already satisfied: six>=1.10.0 in ./ads_venv_test/lib/python2.7/site-packages (from tensorflow==1.3.0) (1.11.0)
Requirement already satisfied: pbr>=0.11 in ./ads_venv_test/lib/python2.7/site-packages (from mock>=2.0.0->tensorflow==1.3.0) (4.2.0)
Requirement already satisfied: funcsigs>=1; python_version < "3.3" in ./ads_venv_test/lib/python2.7/site-packages (from mock>=2.0.0->tensorflow==1.3.0) (1.0.2)
Requirement already satisfied: markdown>=2.6.8 in ./ads_venv_test/lib/python2.7/site-packages (from tensorflow-tensorboard<0.2.0,>=0.1.0->tensorflow==1.3.0) (2.6.11)
Collecting bleach==1.5.0 (from tensorflow-tensorboard<0.2.0,>=0.1.0->tensorflow==1.3.0)
  Using cached https://files.pythonhosted.org/packages/33/70/86c5fec937ea4964184d4d6c4f0b9551564f821e1c3575907639036d9b90/bleach-1.5.0-py2.py3-none-any.whl
Requirement already satisfied: werkzeug>=0.11.10 in ./ads_venv_test/lib/python2.7/site-packages (from tensorflow-tensorboard<0.2.0,>=0.1.0->tensorflow==1.3.0) (0.14.1)
Collecting html5lib==0.9999999 (from tensorflow-tensorboard<0.2.0,>=0.1.0->tensorflow==1.3.0)
Requirement already satisfied: setuptools in ./ads_venv_test/lib/python2.7/site-packages (from protobuf>=3.3.0->tensorflow==1.3.0) (40.0.0)
Installing collected packages: html5lib, bleach, tensorflow-tensorboard, tensorflow
  Found existing installation: tensorflow 1.9.0
    Uninstalling tensorflow-1.9.0:
      Successfully uninstalled tensorflow-1.9.0
Successfully installed bleach-1.5.0 html5lib-0.9999999 tensorflow-1.3.0 tensorflow-tensorboard-0.1.8
(ads_venv_test) julien-macbook:~ $ axondeepseg_test
/Users/julien/ads_venv_test/lib/python2.7/site-packages/scipy/linalg/basic.py:17: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._solve_toeplitz import levinson
/Users/julien/ads_venv_test/lib/python2.7/site-packages/scipy/linalg/__init__.py:207: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._decomp_update import *
/Users/julien/ads_venv_test/lib/python2.7/site-packages/scipy/sparse/lil.py:19: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from . import _csparsetools
/Users/julien/ads_venv_test/lib/python2.7/site-packages/scipy/sparse/csgraph/__init__.py:165: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._shortest_path import shortest_path, floyd_warshall, dijkstra,\
/Users/julien/ads_venv_test/lib/python2.7/site-packages/scipy/sparse/csgraph/_validation.py:5: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._tools import csgraph_to_dense, csgraph_from_dense,\
/Users/julien/ads_venv_test/lib/python2.7/site-packages/scipy/sparse/csgraph/__init__.py:167: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._traversal import breadth_first_order, depth_first_order, \
/Users/julien/ads_venv_test/lib/python2.7/site-packages/scipy/sparse/csgraph/__init__.py:169: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._min_spanning_tree import minimum_spanning_tree
/Users/julien/ads_venv_test/lib/python2.7/site-packages/scipy/sparse/csgraph/__init__.py:170: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._reordering import reverse_cuthill_mckee, maximum_bipartite_matching, \
/Users/julien/ads_venv_test/lib/python2.7/site-packages/scipy/special/__init__.py:640: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._ufuncs import *
/Users/julien/ads_venv_test/lib/python2.7/site-packages/scipy/special/_ellip_harm.py:7: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._ellip_harm_2 import _ellipsoid, _ellipsoid_norm
/Users/julien/ads_venv_test/lib/python2.7/site-packages/scipy/interpolate/_bsplines.py:10: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from . import _bspl
/Users/julien/ads_venv_test/lib/python2.7/site-packages/scipy/spatial/__init__.py:95: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from .ckdtree import *
/Users/julien/ads_venv_test/lib/python2.7/site-packages/scipy/spatial/__init__.py:96: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from .qhull import *
/Users/julien/ads_venv_test/lib/python2.7/site-packages/scipy/spatial/_spherical_voronoi.py:18: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from . import _voronoi
/Users/julien/ads_venv_test/lib/python2.7/site-packages/scipy/spatial/distance.py:122: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from . import _hausdorff
/Users/julien/ads_venv_test/lib/python2.7/site-packages/scipy/ndimage/measurements.py:36: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from . import _ni_label
/Users/julien/ads_venv_test/lib/python2.7/site-packages/scipy/signal/_max_len_seq.py:8: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._max_len_seq_inner import _max_len_seq_inner
/Users/julien/ads_venv_test/lib/python2.7/site-packages/scipy/signal/_upfirdn.py:36: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._upfirdn_apply import _output_len, _apply
/Users/julien/ads_venv_test/lib/python2.7/site-packages/scipy/optimize/_trlib/__init__.py:1: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._trlib import TRLIBQuadraticSubproblem
/Users/julien/ads_venv_test/lib/python2.7/site-packages/scipy/optimize/_numdiff.py:10: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._group_columns import group_dense, group_sparse
/Users/julien/ads_venv_test/lib/python2.7/site-packages/scipy/signal/spectral.py:10: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._spectral import _lombscargle
/Users/julien/ads_venv_test/lib/python2.7/site-packages/scipy/stats/_continuous_distns.py:18: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from . import _stats
/Users/julien/ads_venv_test/lib/python2.7/site-packages/scipy/signal/_peak_finding.py:13: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._peak_finding_utils import (_argmaxima1d, _select_by_peak_distance,
/Users/julien/ads_venv_test/lib/python2.7/site-packages/pandas/_libs/__init__.py:4: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from .tslib import iNaT, NaT, Timestamp, Timedelta, OutOfBoundsDatetime
/Users/julien/ads_venv_test/lib/python2.7/site-packages/pandas/__init__.py:26: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from pandas._libs import (hashtable as _hashtable,
/Users/julien/ads_venv_test/lib/python2.7/site-packages/pandas/core/dtypes/common.py:6: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from pandas._libs import algos, lib
/Users/julien/ads_venv_test/lib/python2.7/site-packages/pandas/core/util/hashing.py:7: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from pandas._libs import hashing, tslib
/Users/julien/ads_venv_test/lib/python2.7/site-packages/pandas/core/indexes/base.py:7: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from pandas._libs import (lib, index as libindex, tslib as libts,
/Users/julien/ads_venv_test/lib/python2.7/site-packages/pandas/tseries/offsets.py:21: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  import pandas._libs.tslibs.offsets as liboffsets
/Users/julien/ads_venv_test/lib/python2.7/site-packages/pandas/core/ops.py:16: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from pandas._libs import algos as libalgos, ops as libops
/Users/julien/ads_venv_test/lib/python2.7/site-packages/pandas/core/indexes/interval.py:32: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from pandas._libs.interval import (
/Users/julien/ads_venv_test/lib/python2.7/site-packages/pandas/core/internals.py:14: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from pandas._libs import internals as libinternals
/Users/julien/ads_venv_test/lib/python2.7/site-packages/pandas/core/sparse/array.py:33: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  import pandas._libs.sparse as splib
/Users/julien/ads_venv_test/lib/python2.7/site-packages/pandas/core/window.py:36: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  import pandas._libs.window as _window
/Users/julien/ads_venv_test/lib/python2.7/site-packages/pandas/core/groupby/groupby.py:68: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from pandas._libs import (lib, reduction,
/Users/julien/ads_venv_test/lib/python2.7/site-packages/pandas/core/reshape/reshape.py:30: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from pandas._libs import algos as _algos, reshape as _reshape
/Users/julien/ads_venv_test/lib/python2.7/site-packages/pandas/io/parsers.py:45: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  import pandas._libs.parsers as parsers
/Users/julien/ads_venv_test/lib/python2.7/site-packages/pandas/io/pytables.py:50: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from pandas._libs import algos, lib, writers as libwriters
/Users/julien/ads_venv_test/lib/python2.7/site-packages/pywt/__init__.py:16: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._extensions._pywt import *
/Users/julien/ads_venv_test/lib/python2.7/site-packages/pywt/_swt.py:1: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._extensions._swt import swt_max_level, swt as _swt, swt_axis as _swt_axis
Traceback (most recent call last):
  File "/Users/julien/ads_venv_test/bin/axondeepseg_test", line 7, in <module>
    from AxonDeepSeg.integrity_test import integrity_test
  File "/Users/julien/ads_venv_test/lib/python2.7/site-packages/AxonDeepSeg/integrity_test.py", line 9, in <module>
    from AxonDeepSeg.testing.segmentation_scoring import *
  File "/Users/julien/ads_venv_test/lib/python2.7/site-packages/AxonDeepSeg/testing/segmentation_scoring.py", line 11, in <module>
    import matplotlib.pyplot as plt
  File "/Users/julien/ads_venv_test/lib/python2.7/site-packages/matplotlib/pyplot.py", line 115, in <module>
    _backend_mod, new_figure_manager, draw_if_interactive, _show = pylab_setup()
  File "/Users/julien/ads_venv_test/lib/python2.7/site-packages/matplotlib/backends/__init__.py", line 62, in pylab_setup
    [backend_name], 0)
  File "/Users/julien/ads_venv_test/lib/python2.7/site-packages/matplotlib/backends/backend_macosx.py", line 17, in <module>
    from matplotlib.backends import _macosx
RuntimeError: Python is not installed as a framework. The Mac OS X backend will not be able to function correctly if Python is not installed as a framework. See the Python documentation for more information on installing Python as a framework on Mac OS X. Please either reinstall Python as a framework, or try one of the other backends. If you are using (Ana)Conda please install python.app and replace the use of 'python' with 'pythonw'. See 'Working with Matplotlib on OSX' in the Matplotlib FAQ for more information.

And when running axondeepseg i get the following:

(ads_venv_test) julien-macbook:~ $ axondeepseg
/Users/julien/ads_venv_test/lib/python2.7/site-packages/scipy/linalg/basic.py:17: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._solve_toeplitz import levinson
/Users/julien/ads_venv_test/lib/python2.7/site-packages/scipy/linalg/__init__.py:207: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._decomp_update import *
/Users/julien/ads_venv_test/lib/python2.7/site-packages/scipy/special/__init__.py:640: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._ufuncs import *
/Users/julien/ads_venv_test/lib/python2.7/site-packages/scipy/special/_ellip_harm.py:7: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._ellip_harm_2 import _ellipsoid, _ellipsoid_norm
/Users/julien/ads_venv_test/lib/python2.7/site-packages/scipy/interpolate/_bsplines.py:10: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from . import _bspl
/Users/julien/ads_venv_test/lib/python2.7/site-packages/scipy/sparse/lil.py:19: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from . import _csparsetools
/Users/julien/ads_venv_test/lib/python2.7/site-packages/scipy/sparse/csgraph/__init__.py:165: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._shortest_path import shortest_path, floyd_warshall, dijkstra,\
/Users/julien/ads_venv_test/lib/python2.7/site-packages/scipy/sparse/csgraph/_validation.py:5: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._tools import csgraph_to_dense, csgraph_from_dense,\
/Users/julien/ads_venv_test/lib/python2.7/site-packages/scipy/sparse/csgraph/__init__.py:167: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._traversal import breadth_first_order, depth_first_order, \
/Users/julien/ads_venv_test/lib/python2.7/site-packages/scipy/sparse/csgraph/__init__.py:169: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._min_spanning_tree import minimum_spanning_tree
/Users/julien/ads_venv_test/lib/python2.7/site-packages/scipy/sparse/csgraph/__init__.py:170: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._reordering import reverse_cuthill_mckee, maximum_bipartite_matching, \
/Users/julien/ads_venv_test/lib/python2.7/site-packages/scipy/spatial/__init__.py:95: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from .ckdtree import *
/Users/julien/ads_venv_test/lib/python2.7/site-packages/scipy/spatial/__init__.py:96: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from .qhull import *
/Users/julien/ads_venv_test/lib/python2.7/site-packages/scipy/spatial/_spherical_voronoi.py:18: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from . import _voronoi
/Users/julien/ads_venv_test/lib/python2.7/site-packages/scipy/spatial/distance.py:122: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from . import _hausdorff
/Users/julien/ads_venv_test/lib/python2.7/site-packages/scipy/ndimage/measurements.py:36: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from . import _ni_label
/Users/julien/ads_venv_test/lib/python2.7/site-packages/scipy/signal/_max_len_seq.py:8: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._max_len_seq_inner import _max_len_seq_inner
/Users/julien/ads_venv_test/lib/python2.7/site-packages/scipy/signal/_upfirdn.py:36: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._upfirdn_apply import _output_len, _apply
/Users/julien/ads_venv_test/lib/python2.7/site-packages/scipy/optimize/_trlib/__init__.py:1: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._trlib import TRLIBQuadraticSubproblem
/Users/julien/ads_venv_test/lib/python2.7/site-packages/scipy/optimize/_numdiff.py:10: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._group_columns import group_dense, group_sparse
/Users/julien/ads_venv_test/lib/python2.7/site-packages/scipy/signal/spectral.py:10: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._spectral import _lombscargle
/Users/julien/ads_venv_test/lib/python2.7/site-packages/scipy/stats/_continuous_distns.py:18: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from . import _stats
/Users/julien/ads_venv_test/lib/python2.7/site-packages/scipy/signal/_peak_finding.py:13: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._peak_finding_utils import (_argmaxima1d, _select_by_peak_distance,
/Users/julien/ads_venv_test/lib/python2.7/site-packages/pandas/_libs/__init__.py:4: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from .tslib import iNaT, NaT, Timestamp, Timedelta, OutOfBoundsDatetime
/Users/julien/ads_venv_test/lib/python2.7/site-packages/pandas/__init__.py:26: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from pandas._libs import (hashtable as _hashtable,
/Users/julien/ads_venv_test/lib/python2.7/site-packages/pandas/core/dtypes/common.py:6: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from pandas._libs import algos, lib
/Users/julien/ads_venv_test/lib/python2.7/site-packages/pandas/core/util/hashing.py:7: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from pandas._libs import hashing, tslib
/Users/julien/ads_venv_test/lib/python2.7/site-packages/pandas/core/indexes/base.py:7: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from pandas._libs import (lib, index as libindex, tslib as libts,
/Users/julien/ads_venv_test/lib/python2.7/site-packages/pandas/tseries/offsets.py:21: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  import pandas._libs.tslibs.offsets as liboffsets
/Users/julien/ads_venv_test/lib/python2.7/site-packages/pandas/core/ops.py:16: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from pandas._libs import algos as libalgos, ops as libops
/Users/julien/ads_venv_test/lib/python2.7/site-packages/pandas/core/indexes/interval.py:32: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from pandas._libs.interval import (
/Users/julien/ads_venv_test/lib/python2.7/site-packages/pandas/core/internals.py:14: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from pandas._libs import internals as libinternals
/Users/julien/ads_venv_test/lib/python2.7/site-packages/pandas/core/sparse/array.py:33: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  import pandas._libs.sparse as splib
/Users/julien/ads_venv_test/lib/python2.7/site-packages/pandas/core/window.py:36: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  import pandas._libs.window as _window
/Users/julien/ads_venv_test/lib/python2.7/site-packages/pandas/core/groupby/groupby.py:68: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from pandas._libs import (lib, reduction,
/Users/julien/ads_venv_test/lib/python2.7/site-packages/pandas/core/reshape/reshape.py:30: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from pandas._libs import algos as _algos, reshape as _reshape
/Users/julien/ads_venv_test/lib/python2.7/site-packages/pandas/io/parsers.py:45: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  import pandas._libs.parsers as parsers
/Users/julien/ads_venv_test/lib/python2.7/site-packages/pandas/io/pytables.py:50: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from pandas._libs import algos, lib, writers as libwriters
/Users/julien/ads_venv_test/lib/python2.7/site-packages/pywt/__init__.py:16: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._extensions._pywt import *
/Users/julien/ads_venv_test/lib/python2.7/site-packages/pywt/_swt.py:1: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._extensions._swt import swt_max_level, swt as _swt, swt_axis as _swt_axis
AxonDeepSeg v.1.0
usage: axondeepseg [-h] -t {SEM,TEM} -i IMGPATH [IMGPATH ...] [-m MODEL]
                   [-s SIZEPIXEL] [-v {0,1,2,3}] [-o OVERLAP]
axondeepseg: error: argument -t/--type is required
(ads_venv_test) julien-macbook:~ $

Issue Analytics

  • State:closed
  • Created 5 years ago
  • Comments:6 (6 by maintainers)

github_iconTop GitHub Comments

1reaction
mathieuboudreaucommented, Aug 2, 2018

Ya I just noticed this too – I think it’s because we have a requirement for numpy greater to a certain version and not equal to one, and they just recently (July 23rd) upgraded to 1.15 (hence we did as well).

A lot of people seem to be annoyed by this warning: https://github.com/numpy/numpy/issues/11628

I think we might be able to resolve it by setting the numpy==14.5 or lower in the requirements file for now until they release a version with a fix.

0reactions
jcohenadadcommented, Aug 2, 2018

testing pass, but i keep having these weird RuntimeWarning from numpy

julien-macbook:~ $ which python
/usr/local/bin/python
julien-macbook:~ $ python
Python 2.7.15 (default, Jul 10 2018, 12:11:41) 
[GCC 4.2.1 Compatible Apple LLVM 9.1.0 (clang-902.0.39.2)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> quit()
julien-macbook:~ $ virtualenv --version
15.1.0
julien-macbook:~ $ virtualenv venv_ads1.1dev0
New python executable in /Users/julien/venv_ads1.1dev0/bin/python
Installing setuptools, pip, wheel...done.
julien-macbook:~ $ source venv_ads1.1dev0/bin/activate
(venv_ads1.1dev0) julien-macbook:~ $ pip install --pre axondeepseg==1.1dev0
Collecting axondeepseg==1.1dev0
  Downloading https://files.pythonhosted.org/packages/81/33/75c6b530f965738f789ed20036cac0b9f8e6972730f7f5f3fe7cbdb1f7a6/AxonDeepSeg-1.1.dev0-py2.py3-none-any.whl (14.9MB)
    100% |████████████████████████████████| 15.0MB 1.8MB/s 
Collecting scikit-learn>=0.18.1 (from axondeepseg==1.1dev0)
  Using cached https://files.pythonhosted.org/packages/22/47/dfc1c815a75afc940789df0e125d55cf9e1eceaf589d89f285f9df575235/scikit_learn-0.19.2-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Collecting scipy>=0.19 (from axondeepseg==1.1dev0)
  Using cached https://files.pythonhosted.org/packages/d1/d6/3eac96ffcf7cbeb37ed72982cf3fdd3138472cb04ab32cdce1f444d765f2/scipy-1.1.0-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Collecting pytest-cov==2.5.1 (from axondeepseg==1.1dev0)
  Using cached https://files.pythonhosted.org/packages/30/7d/7f6a78ae44a1248ee28cc777586c18b28a1df903470e5d34a6e25712b8aa/pytest_cov-2.5.1-py2.py3-none-any.whl
Collecting pillow>=3.4.2 (from axondeepseg==1.1dev0)
  Using cached https://files.pythonhosted.org/packages/a8/56/0f2427d8df966e002fbb748d8537d8f037321b762997a6f05d24cb7334d7/Pillow-5.2.0-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Collecting scikit-image>=0.12.3 (from axondeepseg==1.1dev0)
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Collecting pandas>=0.19.2 (from axondeepseg==1.1dev0)
  Using cached https://files.pythonhosted.org/packages/58/9a/f571a032f5f2bf5b8a5d63ce079428c5423299853ed2d8d96626f441801d/pandas-0.23.3-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Collecting mpld3>=0.3 (from axondeepseg==1.1dev0)
Collecting tabulate>=0.7.7 (from axondeepseg==1.1dev0)
Collecting tqdm>=4.14.0 (from axondeepseg==1.1dev0)
  Using cached https://files.pythonhosted.org/packages/7d/e6/19dfaff08fcbee7f3453e5b537e65a8364f1945f921a36d08be1e2ff3475/tqdm-4.24.0-py2.py3-none-any.whl
Collecting pytest==3.5.0 (from axondeepseg==1.1dev0)
  Using cached https://files.pythonhosted.org/packages/ed/96/271c93f75212c06e2a7ec3e2fa8a9c90acee0a4838dc05bf379ea09aae31/pytest-3.5.0-py2.py3-none-any.whl
Collecting tensorflow>=1.3.0 (from axondeepseg==1.1dev0)
  Downloading https://files.pythonhosted.org/packages/9b/cc/e537b7b3e29f128c0237e1be5242affd24c89eec03cbb8ded154f5eb9b80/tensorflow-1.10.0rc1-cp27-cp27m-macosx_10_11_x86_64.whl (55.5MB)
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Collecting prettytable>=0.7.2 (from axondeepseg==1.1dev0)
Collecting matplotlib>=1.5.3 (from axondeepseg==1.1dev0)
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Collecting numpy>=1.12.0 (from axondeepseg==1.1dev0)
  Using cached https://files.pythonhosted.org/packages/3c/bf/e36756c562f7386be78c6942f0a8a647ee4eb374cdf219bece7054832b14/numpy-1.15.0-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Collecting imageio>=2.2.0 (from axondeepseg==1.1dev0)
  Using cached https://files.pythonhosted.org/packages/a7/1d/33c8686072148b3b0fcc12a2e0857dd8316b8ae20a0fa66c8d6a6d01c05c/imageio-2.3.0-py2.py3-none-any.whl
Collecting raven==6.8.0 (from axondeepseg==1.1dev0)
  Using cached https://files.pythonhosted.org/packages/21/14/a06bcd2aa519bb659f5cf9e0b8c29158155cea7f6ce6e947d06967642df6/raven-6.8.0-py2.py3-none-any.whl
Collecting coverage>=3.7.1 (from pytest-cov==2.5.1->axondeepseg==1.1dev0)
  Downloading https://files.pythonhosted.org/packages/07/00/ad73e3029fda1ebb42a780219ca675866edc5714e52fdd45fbf5ea6f65fa/coverage-5.0a1-cp27-cp27m-macosx_10_13_intel.whl (183kB)
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Collecting PyWavelets>=0.4.0 (from scikit-image>=0.12.3->axondeepseg==1.1dev0)
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Collecting cloudpickle>=0.2.1 (from scikit-image>=0.12.3->axondeepseg==1.1dev0)
  Using cached https://files.pythonhosted.org/packages/e7/bf/60ae7ec1e8c6742d2abbb6819c39a48ee796793bcdb7e1d5e41a3e379ddd/cloudpickle-0.5.3-py2.py3-none-any.whl
Collecting networkx>=1.8 (from scikit-image>=0.12.3->axondeepseg==1.1dev0)
Collecting dask[array]>=0.9.0 (from scikit-image>=0.12.3->axondeepseg==1.1dev0)
  Using cached https://files.pythonhosted.org/packages/91/52/427541141707ac533a6dcafa3bff7ff8b57ded3c9ea84d6ec014d15fbbff/dask-0.18.2-py2.py3-none-any.whl
Collecting six>=1.10.0 (from scikit-image>=0.12.3->axondeepseg==1.1dev0)
  Using cached https://files.pythonhosted.org/packages/67/4b/141a581104b1f6397bfa78ac9d43d8ad29a7ca43ea90a2d863fe3056e86a/six-1.11.0-py2.py3-none-any.whl
Collecting python-dateutil>=2.5.0 (from pandas>=0.19.2->axondeepseg==1.1dev0)
  Using cached https://files.pythonhosted.org/packages/cf/f5/af2b09c957ace60dcfac112b669c45c8c97e32f94aa8b56da4c6d1682825/python_dateutil-2.7.3-py2.py3-none-any.whl
Collecting pytz>=2011k (from pandas>=0.19.2->axondeepseg==1.1dev0)
  Using cached https://files.pythonhosted.org/packages/30/4e/27c34b62430286c6d59177a0842ed90dc789ce5d1ed740887653b898779a/pytz-2018.5-py2.py3-none-any.whl
Collecting pluggy<0.7,>=0.5 (from pytest==3.5.0->axondeepseg==1.1dev0)
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Collecting more-itertools>=4.0.0 (from pytest==3.5.0->axondeepseg==1.1dev0)
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Collecting py>=1.5.0 (from pytest==3.5.0->axondeepseg==1.1dev0)
  Using cached https://files.pythonhosted.org/packages/f3/bd/83369ff2dee18f22f27d16b78dd651e8939825af5f8b0b83c38729069962/py-1.5.4-py2.py3-none-any.whl
Collecting attrs>=17.4.0 (from pytest==3.5.0->axondeepseg==1.1dev0)
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Collecting funcsigs; python_version < "3.0" (from pytest==3.5.0->axondeepseg==1.1dev0)
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Requirement already satisfied: setuptools in ./venv_ads1.1dev0/lib/python2.7/site-packages (from pytest==3.5.0->axondeepseg==1.1dev0) (40.0.0)
Collecting protobuf>=3.6.0 (from tensorflow>=1.3.0->axondeepseg==1.1dev0)
  Using cached https://files.pythonhosted.org/packages/4f/56/a21f2d077ceae7fd521c0ed31fb8bb1c7f13ffbb09bf7dd27de6cf6bad08/protobuf-3.6.0-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Requirement already satisfied: wheel in ./venv_ads1.1dev0/lib/python2.7/site-packages (from tensorflow>=1.3.0->axondeepseg==1.1dev0) (0.31.1)
Collecting astor>=0.6.0 (from tensorflow>=1.3.0->axondeepseg==1.1dev0)
  Using cached https://files.pythonhosted.org/packages/35/6b/11530768cac581a12952a2aad00e1526b89d242d0b9f59534ef6e6a1752f/astor-0.7.1-py2.py3-none-any.whl
Collecting backports.weakref>=1.0rc1 (from tensorflow>=1.3.0->axondeepseg==1.1dev0)
  Using cached https://files.pythonhosted.org/packages/88/ec/f598b633c3d5ffe267aaada57d961c94fdfa183c5c3ebda2b6d151943db6/backports.weakref-1.0.post1-py2.py3-none-any.whl
Collecting termcolor>=1.1.0 (from tensorflow>=1.3.0->axondeepseg==1.1dev0)
Collecting gast>=0.2.0 (from tensorflow>=1.3.0->axondeepseg==1.1dev0)
Collecting grpcio>=1.8.6 (from tensorflow>=1.3.0->axondeepseg==1.1dev0)
  Downloading https://files.pythonhosted.org/packages/7e/a4/97dccf32d851e0b078c2c38749387195d4356bd59e8aabe6614d899d3b60/grpcio-1.14.0rc2-cp27-cp27m-macosx_10_12_x86_64.whl (1.7MB)
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Collecting absl-py>=0.1.6 (from tensorflow>=1.3.0->axondeepseg==1.1dev0)
Collecting enum34>=1.1.6 (from tensorflow>=1.3.0->axondeepseg==1.1dev0)
  Using cached https://files.pythonhosted.org/packages/c5/db/e56e6b4bbac7c4a06de1c50de6fe1ef3810018ae11732a50f15f62c7d050/enum34-1.1.6-py2-none-any.whl
Collecting tensorboard<1.11.0,>=1.10.0 (from tensorflow>=1.3.0->axondeepseg==1.1dev0)
  Downloading https://files.pythonhosted.org/packages/e0/11/8ac6a52179a290a249f80cb6e157f1bb1f87a7e44dba8a0869701d8076cb/tensorboard-1.10.0-py2-none-any.whl (3.3MB)
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Collecting mock>=2.0.0 (from tensorflow>=1.3.0->axondeepseg==1.1dev0)
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Collecting kiwisolver>=1.0.1 (from matplotlib>=1.5.3->axondeepseg==1.1dev0)
  Using cached https://files.pythonhosted.org/packages/79/d8/94633718f3f77dcb638687a77ba199325a1cb158d2d4b00c9dc17f2b5c72/kiwisolver-1.0.1-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Collecting cycler>=0.10 (from matplotlib>=1.5.3->axondeepseg==1.1dev0)
  Using cached https://files.pythonhosted.org/packages/f7/d2/e07d3ebb2bd7af696440ce7e754c59dd546ffe1bbe732c8ab68b9c834e61/cycler-0.10.0-py2.py3-none-any.whl
Collecting subprocess32 (from matplotlib>=1.5.3->axondeepseg==1.1dev0)
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Collecting backports.functools-lru-cache (from matplotlib>=1.5.3->axondeepseg==1.1dev0)
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Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 (from matplotlib>=1.5.3->axondeepseg==1.1dev0)
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Collecting contextlib2; python_version < "3.2" (from raven==6.8.0->axondeepseg==1.1dev0)
  Using cached https://files.pythonhosted.org/packages/a2/71/8273a7eeed0aff6a854237ab5453bc9aa67deb49df4832801c21f0ff3782/contextlib2-0.5.5-py2.py3-none-any.whl
Collecting decorator>=4.1.0 (from networkx>=1.8->scikit-image>=0.12.3->axondeepseg==1.1dev0)
  Using cached https://files.pythonhosted.org/packages/bc/bb/a24838832ba35baf52f32ab1a49b906b5f82fb7c76b2f6a7e35e140bac30/decorator-4.3.0-py2.py3-none-any.whl
Collecting toolz>=0.7.3; extra == "array" (from dask[array]>=0.9.0->scikit-image>=0.12.3->axondeepseg==1.1dev0)
Collecting futures>=2.2.0 (from grpcio>=1.8.6->tensorflow>=1.3.0->axondeepseg==1.1dev0)
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Collecting werkzeug>=0.11.10 (from tensorboard<1.11.0,>=1.10.0->tensorflow>=1.3.0->axondeepseg==1.1dev0)
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Collecting markdown>=2.6.8 (from tensorboard<1.11.0,>=1.10.0->tensorflow>=1.3.0->axondeepseg==1.1dev0)
  Using cached https://files.pythonhosted.org/packages/6d/7d/488b90f470b96531a3f5788cf12a93332f543dbab13c423a5e7ce96a0493/Markdown-2.6.11-py2.py3-none-any.whl
Collecting pbr>=0.11 (from mock>=2.0.0->tensorflow>=1.3.0->axondeepseg==1.1dev0)
  Using cached https://files.pythonhosted.org/packages/69/1c/98cba002ed975a91a0294863d9c774cc0ebe38e05bbb65e83314550b1677/pbr-4.2.0-py2.py3-none-any.whl
tensorflow 1.10.0rc1 has requirement numpy<=1.14.5,>=1.13.3, but you'll have numpy 1.15.0 which is incompatible.
tensorflow 1.10.0rc1 has requirement setuptools<=39.1.0, but you'll have setuptools 40.0.0 which is incompatible.
Installing collected packages: scikit-learn, numpy, scipy, pluggy, six, more-itertools, py, attrs, funcsigs, pytest, coverage, pytest-cov, pillow, PyWavelets, kiwisolver, cycler, subprocess32, pytz, backports.functools-lru-cache, pyparsing, python-dateutil, matplotlib, cloudpickle, decorator, networkx, toolz, dask, scikit-image, pandas, mpld3, tabulate, tqdm, protobuf, astor, backports.weakref, termcolor, gast, enum34, futures, grpcio, absl-py, werkzeug, markdown, tensorboard, pbr, mock, tensorflow, prettytable, imageio, contextlib2, raven, axondeepseg
Successfully installed PyWavelets-0.5.2 absl-py-0.3.0 astor-0.7.1 attrs-18.1.0 axondeepseg-1.1.dev0 backports.functools-lru-cache-1.5 backports.weakref-1.0.post1 cloudpickle-0.5.3 contextlib2-0.5.5 coverage-5.0a1 cycler-0.10.0 dask-0.18.2 decorator-4.3.0 enum34-1.1.6 funcsigs-1.0.2 futures-3.2.0 gast-0.2.0 grpcio-1.14.0rc2 imageio-2.3.0 kiwisolver-1.0.1 markdown-2.6.11 matplotlib-2.2.2 mock-2.0.0 more-itertools-4.3.0 mpld3-0.3 networkx-2.1 numpy-1.15.0 pandas-0.23.3 pbr-4.2.0 pillow-5.2.0 pluggy-0.6.0 prettytable-0.7.2 protobuf-3.6.0 py-1.5.4 pyparsing-2.2.0 pytest-3.5.0 pytest-cov-2.5.1 python-dateutil-2.7.3 pytz-2018.5 raven-6.8.0 scikit-image-0.14.0 scikit-learn-0.19.2 scipy-1.1.0 six-1.11.0 subprocess32-3.5.2 tabulate-0.8.2 tensorboard-1.10.0 tensorflow-1.10.0rc1 termcolor-1.1.0 toolz-0.9.0 tqdm-4.24.0 werkzeug-0.14.1
(venv_ads1.1dev0) julien-macbook:~ $ pip install https://storage.googleapis.com/tensorflow/mac/cpu/tensorflow-1.3.0-py2-none-any.whl
Collecting tensorflow==1.3.0 from https://storage.googleapis.com/tensorflow/mac/cpu/tensorflow-1.3.0-py2-none-any.whl
  Using cached https://storage.googleapis.com/tensorflow/mac/cpu/tensorflow-1.3.0-py2-none-any.whl
Requirement already satisfied: numpy>=1.11.0 in ./venv_ads1.1dev0/lib/python2.7/site-packages (from tensorflow==1.3.0) (1.15.0)
Requirement already satisfied: mock>=2.0.0 in ./venv_ads1.1dev0/lib/python2.7/site-packages (from tensorflow==1.3.0) (2.0.0)
Collecting tensorflow-tensorboard<0.2.0,>=0.1.0 (from tensorflow==1.3.0)
  Using cached https://files.pythonhosted.org/packages/fb/34/14c23665a725c73932891e09b8f017a53aad545c9d5019d2817102dc5d9b/tensorflow_tensorboard-0.1.8-py2-none-any.whl
Requirement already satisfied: wheel in ./venv_ads1.1dev0/lib/python2.7/site-packages (from tensorflow==1.3.0) (0.31.1)
Requirement already satisfied: backports.weakref>=1.0rc1 in ./venv_ads1.1dev0/lib/python2.7/site-packages (from tensorflow==1.3.0) (1.0.post1)
Requirement already satisfied: protobuf>=3.3.0 in ./venv_ads1.1dev0/lib/python2.7/site-packages (from tensorflow==1.3.0) (3.6.0)
Requirement already satisfied: six>=1.10.0 in ./venv_ads1.1dev0/lib/python2.7/site-packages (from tensorflow==1.3.0) (1.11.0)
Requirement already satisfied: pbr>=0.11 in ./venv_ads1.1dev0/lib/python2.7/site-packages (from mock>=2.0.0->tensorflow==1.3.0) (4.2.0)
Requirement already satisfied: funcsigs>=1; python_version < "3.3" in ./venv_ads1.1dev0/lib/python2.7/site-packages (from mock>=2.0.0->tensorflow==1.3.0) (1.0.2)
Requirement already satisfied: markdown>=2.6.8 in ./venv_ads1.1dev0/lib/python2.7/site-packages (from tensorflow-tensorboard<0.2.0,>=0.1.0->tensorflow==1.3.0) (2.6.11)
Collecting bleach==1.5.0 (from tensorflow-tensorboard<0.2.0,>=0.1.0->tensorflow==1.3.0)
  Using cached https://files.pythonhosted.org/packages/33/70/86c5fec937ea4964184d4d6c4f0b9551564f821e1c3575907639036d9b90/bleach-1.5.0-py2.py3-none-any.whl
Requirement already satisfied: werkzeug>=0.11.10 in ./venv_ads1.1dev0/lib/python2.7/site-packages (from tensorflow-tensorboard<0.2.0,>=0.1.0->tensorflow==1.3.0) (0.14.1)
Collecting html5lib==0.9999999 (from tensorflow-tensorboard<0.2.0,>=0.1.0->tensorflow==1.3.0)
Requirement already satisfied: setuptools in ./venv_ads1.1dev0/lib/python2.7/site-packages (from protobuf>=3.3.0->tensorflow==1.3.0) (40.0.0)
Installing collected packages: html5lib, bleach, tensorflow-tensorboard, tensorflow
  Found existing installation: tensorflow 1.10.0rc1
    Uninstalling tensorflow-1.10.0rc1:
      Successfully uninstalled tensorflow-1.10.0rc1
Successfully installed bleach-1.5.0 html5lib-0.9999999 tensorflow-1.3.0 tensorflow-tensorboard-0.1.8



(venv_ads1.1dev0) julien-macbook:~ $ axondeepseg_test
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/scipy/linalg/basic.py:17: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._solve_toeplitz import levinson
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/scipy/linalg/__init__.py:207: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._decomp_update import *
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/scipy/sparse/lil.py:19: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from . import _csparsetools
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/scipy/sparse/csgraph/__init__.py:165: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._shortest_path import shortest_path, floyd_warshall, dijkstra,\
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/scipy/sparse/csgraph/_validation.py:5: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._tools import csgraph_to_dense, csgraph_from_dense,\
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/scipy/sparse/csgraph/__init__.py:167: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._traversal import breadth_first_order, depth_first_order, \
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/scipy/sparse/csgraph/__init__.py:169: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._min_spanning_tree import minimum_spanning_tree
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/scipy/sparse/csgraph/__init__.py:170: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._reordering import reverse_cuthill_mckee, maximum_bipartite_matching, \
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/scipy/special/__init__.py:640: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._ufuncs import *
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/scipy/special/_ellip_harm.py:7: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._ellip_harm_2 import _ellipsoid, _ellipsoid_norm
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/scipy/interpolate/_bsplines.py:10: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from . import _bspl
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/scipy/spatial/__init__.py:95: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from .ckdtree import *
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/scipy/spatial/__init__.py:96: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from .qhull import *
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/scipy/spatial/_spherical_voronoi.py:18: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from . import _voronoi
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/scipy/spatial/distance.py:122: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from . import _hausdorff
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/scipy/ndimage/measurements.py:36: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from . import _ni_label
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/scipy/signal/_max_len_seq.py:8: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._max_len_seq_inner import _max_len_seq_inner
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/scipy/signal/_upfirdn.py:36: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._upfirdn_apply import _output_len, _apply
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/scipy/optimize/_trlib/__init__.py:1: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._trlib import TRLIBQuadraticSubproblem
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/scipy/optimize/_numdiff.py:10: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._group_columns import group_dense, group_sparse
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/scipy/signal/spectral.py:10: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._spectral import _lombscargle
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/scipy/stats/_continuous_distns.py:18: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from . import _stats
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/scipy/signal/_peak_finding.py:13: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._peak_finding_utils import (_argmaxima1d, _select_by_peak_distance,
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/pandas/_libs/__init__.py:4: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from .tslib import iNaT, NaT, Timestamp, Timedelta, OutOfBoundsDatetime
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/pandas/__init__.py:26: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from pandas._libs import (hashtable as _hashtable,
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/pandas/core/dtypes/common.py:6: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from pandas._libs import algos, lib
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/pandas/core/util/hashing.py:7: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from pandas._libs import hashing, tslib
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/pandas/core/indexes/base.py:7: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from pandas._libs import (lib, index as libindex, tslib as libts,
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/pandas/tseries/offsets.py:21: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  import pandas._libs.tslibs.offsets as liboffsets
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/pandas/core/ops.py:16: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from pandas._libs import algos as libalgos, ops as libops
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/pandas/core/indexes/interval.py:32: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from pandas._libs.interval import (
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/pandas/core/internals.py:14: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from pandas._libs import internals as libinternals
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/pandas/core/sparse/array.py:33: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  import pandas._libs.sparse as splib
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/pandas/core/window.py:36: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  import pandas._libs.window as _window
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/pandas/core/groupby/groupby.py:68: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from pandas._libs import (lib, reduction,
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/pandas/core/reshape/reshape.py:30: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from pandas._libs import algos as _algos, reshape as _reshape
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/pandas/io/parsers.py:45: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  import pandas._libs.parsers as parsers
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/pandas/io/pytables.py:50: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from pandas._libs import algos, lib, writers as libwriters
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/pywt/__init__.py:16: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._extensions._pywt import *
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/pywt/_swt.py:1: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._extensions._swt import swt_max_level, swt as _swt, swt_axis as _swt_axis
Reading test configuration file.
Computing the segmentation of axon and myelin on test image.
Loading acquisitions ...
Rescaling acquisitions to the target resolution ...
Graph construction ...
Beginning inference ...
processing patch 1 of 6
processing patch 2 of 6
processing patch 3 of 6
processing patch 4 of 6
processing patch 5 of 6
processing patch 6 of 6
WARNING:root:Lossy conversion from int64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.
WARNING:root:Lossy conversion from int64 to uint8. Range [0, 1]. Convert image to uint8 prior to saving to suppress this warning.
Generating axon and myelin segmentation masks and saving.
* * * Integrity test passed. AxonDeepSeg is correctly installed. * * * 


(venv_ads1.1dev0) julien-macbook:~ $ axondeepseg
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/scipy/linalg/basic.py:17: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._solve_toeplitz import levinson
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/scipy/linalg/__init__.py:207: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._decomp_update import *
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/scipy/special/__init__.py:640: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._ufuncs import *
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/scipy/special/_ellip_harm.py:7: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._ellip_harm_2 import _ellipsoid, _ellipsoid_norm
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/scipy/interpolate/_bsplines.py:10: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from . import _bspl
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/scipy/sparse/lil.py:19: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from . import _csparsetools
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/scipy/sparse/csgraph/__init__.py:165: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._shortest_path import shortest_path, floyd_warshall, dijkstra,\
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/scipy/sparse/csgraph/_validation.py:5: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._tools import csgraph_to_dense, csgraph_from_dense,\
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/scipy/sparse/csgraph/__init__.py:167: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._traversal import breadth_first_order, depth_first_order, \
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/scipy/sparse/csgraph/__init__.py:169: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._min_spanning_tree import minimum_spanning_tree
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/scipy/sparse/csgraph/__init__.py:170: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._reordering import reverse_cuthill_mckee, maximum_bipartite_matching, \
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/scipy/spatial/__init__.py:95: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from .ckdtree import *
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/scipy/spatial/__init__.py:96: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from .qhull import *
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/scipy/spatial/_spherical_voronoi.py:18: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from . import _voronoi
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/scipy/spatial/distance.py:122: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from . import _hausdorff
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/scipy/ndimage/measurements.py:36: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from . import _ni_label
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/scipy/signal/_max_len_seq.py:8: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._max_len_seq_inner import _max_len_seq_inner
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/scipy/signal/_upfirdn.py:36: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._upfirdn_apply import _output_len, _apply
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/scipy/optimize/_trlib/__init__.py:1: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._trlib import TRLIBQuadraticSubproblem
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/scipy/optimize/_numdiff.py:10: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._group_columns import group_dense, group_sparse
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/scipy/signal/spectral.py:10: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._spectral import _lombscargle
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/scipy/stats/_continuous_distns.py:18: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from . import _stats
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/scipy/signal/_peak_finding.py:13: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._peak_finding_utils import (_argmaxima1d, _select_by_peak_distance,
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/pandas/_libs/__init__.py:4: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from .tslib import iNaT, NaT, Timestamp, Timedelta, OutOfBoundsDatetime
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/pandas/__init__.py:26: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from pandas._libs import (hashtable as _hashtable,
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/pandas/core/dtypes/common.py:6: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from pandas._libs import algos, lib
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/pandas/core/util/hashing.py:7: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from pandas._libs import hashing, tslib
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/pandas/core/indexes/base.py:7: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from pandas._libs import (lib, index as libindex, tslib as libts,
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/pandas/tseries/offsets.py:21: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  import pandas._libs.tslibs.offsets as liboffsets
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/pandas/core/ops.py:16: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from pandas._libs import algos as libalgos, ops as libops
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/pandas/core/indexes/interval.py:32: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from pandas._libs.interval import (
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/pandas/core/internals.py:14: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from pandas._libs import internals as libinternals
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/pandas/core/sparse/array.py:33: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  import pandas._libs.sparse as splib
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/pandas/core/window.py:36: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  import pandas._libs.window as _window
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/pandas/core/groupby/groupby.py:68: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from pandas._libs import (lib, reduction,
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/pandas/core/reshape/reshape.py:30: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from pandas._libs import algos as _algos, reshape as _reshape
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/pandas/io/parsers.py:45: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  import pandas._libs.parsers as parsers
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/pandas/io/pytables.py:50: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from pandas._libs import algos, lib, writers as libwriters
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/pywt/__init__.py:16: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._extensions._pywt import *
/Users/julien/venv_ads1.1dev0/lib/python2.7/site-packages/pywt/_swt.py:1: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._extensions._swt import swt_max_level, swt as _swt, swt_axis as _swt_axis
AxonDeepSeg v.1.1dev
usage: axondeepseg [-h] -t {SEM,TEM} -i IMGPATH [IMGPATH ...] [-m MODEL]
                   [-s SIZEPIXEL] [-v {0,1,2,3}] [-o OVERLAP]
axondeepseg: error: argument -t/--type is required
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Potential issue with gold standards (or fifty shades of myelin)

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Patch extraction bug, or unclear functionality?