Develop Reference

Anaconda/Conda on OS X 11 -- Broken Jupyter Notebook with DEFAULT installation

I am running the latest Anaconda on OS X 11 and cannot for the life of me figure out how to get jupyter notebook to run. It ends in this error:
% jupyter notebook
Traceback (most recent call last):
File "/usr/local/opt/anaconda3/bin/jupyter-notebook", line 7, in <module>
from notebook.notebookapp import main
File "/usr/local/opt/anaconda3/lib/python3.7/site-packages/notebook/notebookapp.py", line 85, in <module>
from .services.contents.manager import ContentsManager
File "/usr/local/opt/anaconda3/lib/python3.7/site-packages/notebook/services/contents/manager.py", line 17, in <module>
from nbformat import sign, validate as validate_nb, ValidationError
File "/usr/local/opt/anaconda3/lib/python3.7/site-packages/nbformat/__init__.py", line 32, in <module>
from .validator import validate, ValidationError
File "/usr/local/opt/anaconda3/lib/python3.7/site-packages/nbformat/validator.py", line 12, in <module>
from .json_compat import get_current_validator, ValidationError
File "/usr/local/opt/anaconda3/lib/python3.7/site-packages/nbformat/json_compat.py", line 10, in <module>
import jsonschema
File "/usr/local/opt/anaconda3/lib/python3.7/site-packages/jsonschema/__init__.py", line 32, in <module>
from pkg_resources import get_distribution
ModuleNotFoundError: No module named 'pkg_resources'
I have tried fresh installs of both miniconda and anaconda without success. Nothing seems to work.
It baffles me that a default install of anaconda (no updates, no extra packages, nothing) is broken. Do these people even test their stuff?
Any solutions or suggestions? Thanks in advance!

Cannot import tensorflow in python3 and ImportError: This package should not be accessible on Python 3

I am trying to use tensorflow for research in my macbook. I use pip3 to install tensorflow in the system (not in virtual environment).
At first, I just want to verify tensorflow can be correctly imported via python3 in terminal. However, sometimes, I got the following problem when importing.
>>>import tensorflow as tf
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/Users/cyan/Library/Python/3.5/lib/python/site-packages/tensorflow/__init__.py", line 24, in <module>
from tensorflow.python import pywrap_tensorflow # pylint: disable=unused-import
File "/Users/cyan/Library/Python/3.5/lib/python/site-packages/tensorflow/python/__init__.py", line 47, in <module>
import numpy as np
File "/Library/Python/2.7/site-packages/numpy/__init__.py", line 142, in <module>
from . import add_newdocs
File "/Library/Python/2.7/site-packages/numpy/add_newdocs.py", line 13, in <module>
from numpy.lib import add_newdoc
File "/Library/Python/2.7/site-packages/numpy/lib/__init__.py", line 8, in <module>
from .type_check import *
File "/Library/Python/2.7/site-packages/numpy/lib/type_check.py", line 11, in <module>
import numpy.core.numeric as _nx
File "/Library/Python/2.7/site-packages/numpy/core/__init__.py", line 14, in <module>
from . import multiarray
ImportError: dlopen(/Library/Python/2.7/site-packages/numpy/core/multiarray.so, 2): Symbol not found: _PyBuffer_Type
Referenced from: /Library/Python/2.7/site-packages/numpy/core/multiarray.so
Expected in: flat namespace in /Library/Python/2.7/site-packages/numpy/core/multiarray.so
This error could only be solved if I ran the following code firstly before python3 execution
unset PYTHONPATH
If I didn't unset PYTHONPATH, I also found errors when checking the version of pip3 using
pip3 --version
The errors are shown as follows.
>> pip3 --version
Traceback (most recent call last):
File "/usr/local/bin/pip3", line 6, in <module>
from pip._internal import main
File "/Library/Python/2.7/site-packages/pip/_internal/__init__.py", line 19, in <module>
from pip._vendor.urllib3.exceptions import DependencyWarning
File "/Library/Python/2.7/site-packages/pip/_vendor/urllib3/__init__.py", line 8, in <module>
from .connectionpool import (
File "/Library/Python/2.7/site-packages/pip/_vendor/urllib3/connectionpool.py", line 11, in <module>
from .exceptions import (
File "/Library/Python/2.7/site-packages/pip/_vendor/urllib3/exceptions.py", line 2, in <module>
from .packages.six.moves.http_client import (
File "/Library/Python/2.7/site-packages/pip/_vendor/urllib3/packages/six.py", line 203, in load_module
mod = mod._resolve()
File "/Library/Python/2.7/site-packages/pip/_vendor/urllib3/packages/six.py", line 115, in _resolve
return _import_module(self.mod)
File "/Library/Python/2.7/site-packages/pip/_vendor/urllib3/packages/six.py", line 82, in _import_module
__import__(name)
File "/Library/Python/2.7/site-packages/http/__init__.py", line 7, in <module>
raise ImportError('This package should not be accessible on Python 3. '
ImportError: This package should not be accessible on Python 3. Either you are trying to run from the python-future src folder or your installation of python-future is corrupted.
I thought it was so inconvenient to unset PYTHONPATH every time, so is there any solutions for this problem? I also want to import tensorflow in other text editor, such as Sublime and Pycharm, so I was really not sure what to do next.

I tried the same scenario. It is working fine for me. In the first error it seems your python installation is messed up. If you are using python3 in terminal, it should not refer to 2.7 libraries.
Also I dont think you require unset PYTHONPATH everytime. First thing is you dont need to setup PYTHONPATH. It seems the installation got issue.
You using homebrew in mac to install packages. If not I will say use homebrew and it will work as charm. As it adds dependency properly.
Thanks,
Ashish

Launch of orange3

I tried to launch of Orange 3 on Anaconda. But launch have produced errors below.
Traceback (most recent call last):
File "C:\Users\tomo\Anaconda2\envs\orange3\Scripts\orange-canvas-script.py", line 6, in
from Orange.canvas.__main__ import main
File "C:\Users\tomo\Anaconda2\envs\orange3\lib\site-packages\Orange\canvas\__main__.py", line 30, in
from Orange.canvas.application.canvasmain import CanvasMainWindow
File "C:\Users\tomo\Anaconda2\envs\orange3\lib\site-packages\Orange\canvas\application\canvasmain.py", line 61, in
from .canvastooldock import CanvasToolDock, QuickCategoryToolbar, \
File "C:\Users\tomo\Anaconda2\envs\orange3\lib\site-packages\Orange\canvas\application\canvastooldock.py", line 25, in
from ..document.quickmenu import MenuPage
File "C:\Users\tomo\Anaconda2\envs\orange3\lib\site-packages\Orange\canvas\document\__init__.py", line 17, in
from .schemeedit import SchemeEditWidget
File "C:\Users\tomo\Anaconda2\envs\orange3\lib\site-packages\Orange\canvas\document\schemeedit.py", line 37, in
from .suggestions import Suggestions
File "C:\Users\tomo\Anaconda2\envs\orange3\lib\site-packages\Orange\canvas\document\suggestions.py", line 7, in
from .interactions import NewLinkAction
File "C:\Users\tomo\Anaconda2\envs\orange3\lib\site-packages\Orange\canvas\document\interactions.py", line 28, in
from ..canvas import items
File "C:\Users\tomo\Anaconda2\envs\orange3\lib\site-packages\Orange\canvas\canvas\items\__init__.py", line 9, in
from .annotationitem import TextAnnotation, ArrowAnnotation
File "C:\Users\tomo\Anaconda2\envs\orange3\lib\site-packages\Orange\canvas\canvas\items\annotationitem.py", line 7, in
import CommonMark
ModuleNotFoundError: No module named 'CommonMark'
Acutually I found these error on this web and tried to install the r-commonmark 1.4 but it does not work well now.
Please tell me how to deal with it.

CommonMark is a package that Orange used. It was renamed in the latest release what causes that imports do not work. The issue should be solved by installing newer Orange3 version3.16.0

jupyter lab is broken how can I fix it?

I can't figure out why jupyter-lab is not working. something is broken and don't know where. I have searched the web for this and can't find a solution. COuld you please help. Appreciate it.
E:\gitrepos>jupyter lab
`Traceback (most recent call last):
File "E:\anaconda3\Scripts\jupyter-lab-script.py", line 3, in <module>
import jupyterlab.labapp
File "E:\anaconda3\lib\site-packages\jupyterlab\labapp.py", line 7, in <module>
from notebook.notebookapp import NotebookApp, aliases, flags
File "C:\Users\Dario.Romero\AppData\Roaming\Python\Python35\site-packages\notebook\notebookapp.py", line 78, in <module>
from .services.kernels.kernelmanager import MappingKernelManager
File "C:\Users\Dario.Romero\AppData\Roaming\Python\Python35\site-packages\notebook\services\kernels\kernelmanager.py", line 19, in <module>
from jupyter_client.session import Session
File "E:\anaconda3\lib\site-packages\jupyter_client\session.py", line 61, in <module>
from jupyter_client.jsonutil import extract_dates, squash_dates, date_default
File "E:\anaconda3\lib\site-packages\jupyter_client\jsonutil.py", line 11, in <module>
from dateutil.parser import parse as _dateutil_parse
ImportError: No module named 'dateutil.parser'`

You need to install the dateutil library: https://pypi.python.org/pypi/python-dateutil/
(If you used a package manager, the dependencies for JupyterLab should already have been installed. If you didn't, then you will need to install the dependencies yourself.)

Python embedding, ImportError: cannot import name _remove_dead_weakref

I am trying to run some C++ code with embedded Python. Code was working completely fine a couple of weeks ago. The code still compiles, but I am now getting the error
Traceback (most recent call last):
File "./main.py", line 1, in <module>
import numpy as np
File "/usr/local/lib/python2.7/site-packages/numpy/__init__.py", line 142, in <module>
from . import add_newdocs
File "/usr/local/lib/python2.7/site-packages/numpy/add_newdocs.py", line 13, in <module>
from numpy.lib import add_newdoc
File "/usr/local/lib/python2.7/site-packages/numpy/lib/__init__.py", line 8, in <module>
from .type_check import *
File "/usr/local/lib/python2.7/site-packages/numpy/lib/type_check.py", line 11, in <module>
import numpy.core.numeric as _nx
File "/usr/local/lib/python2.7/site-packages/numpy/core/__init__.py", line 74, in <module>
from numpy.testing.nosetester import _numpy_tester
File "/usr/local/lib/python2.7/site-packages/numpy/testing/__init__.py", line 10, in <module>
from unittest import TestCase
File "/usr/local/opt/python/Frameworks/Python.framework/Versions/2.7/lib/python2.7/unittest/__init__.py", line 64, in <module>
from .main import TestProgram, main
File "/usr/local/opt/python/Frameworks/Python.framework/Versions/2.7/lib/python2.7/unittest/main.py", line 7, in <module>
from . import loader, runner
File "/usr/local/opt/python/Frameworks/Python.framework/Versions/2.7/lib/python2.7/unittest/runner.py", line 7, in <module>
from .signals import registerResult
File "/usr/local/opt/python/Frameworks/Python.framework/Versions/2.7/lib/python2.7/unittest/signals.py", line 2, in <module>
import weakref
File "/usr/local/opt/python/Frameworks/Python.framework/Versions/2.7/lib/python2.7/weakref.py", line 14, in <module>
from _weakref import (
ImportError: cannot import name _remove_dead_weakref
Since then the only change I have made is to install the macOS Supplemental Update and to upgrade Python from 2.7.13_1 to 2.7.14_2 (using Homebrew). I have changed the relevant linker flags in the makefile, i.e. those that appear when I type python-config --ldflags. I have also made sure that the Python I am using is definitely the Homebrew one by inserting export PATH="/usr/local/opt/python/libexec/bin:$PATH" into my .bash_profile as directed by Homebrew.
I am not sure whether this error is because of the Python update, the recent macOS Supplemental Update, or something else. Any idea what the problem could be?
Thanks

I had the same problem;
In python 2.7 the NumPy 1.8.0 was available,
Then I installed NumPy (again) using brew, and it wasn't available in my python (2.7) anymore. (Got the same error you got here)
So I did "brew unlink python && brew link python" to use python 3 (instead of 2) which NumPy 1.14 is available in it.
I guess the python 2.7 was not compatible with this recent version of NumPy.