Problems running SlicerJupyter on MacOS

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1

I was trying to get the app working by following the instructions here: GitHub - Slicer/SlicerJupyter: Extension for 3D Slicer that allows the application to be used from Jupyter notebook

I started the Jupyter Server from within the app:

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image2880×1800 283 KB

I installed node.js, moved both node and npm files from /usr/local/bin to Slicer.app/contents/MacOS where the “Slicer” executable is located (when I click the file it opens 3DSlicer).

I ran pip_install(‘jupyterlab’) in the python console but got the error “name ‘pip_install’ is not defined”. I can access pip through my terminal but these commands still fail:

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image2880×1800 744 KB

Last login: Tue Dec 15 22:07:32 on ttys000
jon@Jonathans-MBP ~ % python3
Python 3.9.0 (v3.9.0:9cf6752276, Oct 5 2020, 11:29:23)
[Clang 6.0 (clang-600.0.57)] on darwin
Type “help”, “copyright”, “credits” or “license” for more information.
pip_install(‘jupyterlab’)
Traceback (most recent call last):
File “”, line 1, in
NameError: name ‘pip_install’ is not defined

2

Do you only have problems with JupyterLab? Does classic Jupyter work well if you click “Start Jupyter server” button (server starts correctly and Jupyter GUI starts in your web browser)?

pip_install('jupyterlab') command must be run from Slicer’s Python console (Ctrl-3). To use SlicerJupyter, you don’t even need to have Python installed on your computer.

3

Thanks for clarifying about the slicer’s python console. This fails at the
slicer.util._executePythonModule command, here’s the logs:

Python 3.6.7 (default, Sep 30 2020, 16:04:14) 
[GCC 4.2.1 Compatible Apple LLVM 10.0.0 (clang-1000.11.45.5)] on darwin
>>> 
Collecting pillow
  Using cached Pillow-8.0.1-cp36-cp36m-macosx_10_10_x86_64.whl (2.2 MB)
Installing collected packages: pillow
  Attempting uninstall: pillow
    Found existing installation: Pillow 8.0.1
    Uninstalling Pillow-8.0.1:
      Successfully uninstalled Pillow-8.0.1
Successfully installed pillow-8.0.1
WARNING: You are using pip version 20.1.1; however, version 20.3.3 is available.
You should consider upgrading via the '/Applications/Slicer.app/Contents/bin/./python-real -m pip install --upgrade pip' command.
Collecting jupyter
  Using cached jupyter-1.0.0-py2.py3-none-any.whl (2.7 kB)
Collecting ipywidgets
  Using cached ipywidgets-7.5.1-py2.py3-none-any.whl (121 kB)
Collecting pandas
  Using cached pandas-1.1.5-cp36-cp36m-macosx_10_9_x86_64.whl (10.2 MB)
Collecting ipyevents
  Using cached ipyevents-0.8.1-py2.py3-none-any.whl (150 kB)
Collecting ipycanvas
  Using cached ipycanvas-0.7.0-py2.py3-none-any.whl (247 kB)
Collecting nbconvert
  Using cached nbconvert-6.0.7-py3-none-any.whl (552 kB)
Collecting jupyter-console
  Using cached jupyter_console-6.2.0-py3-none-any.whl (22 kB)
Collecting qtconsoleCollecting traitlets>=4.3.1
  Using cached traitlets-4.3.3-py2.py3-none-any.whl (75 kB)
Collecting nbformat>=4.2.0
  Using cached nbformat-5.0.8-py3-none-any.whl (172 kB)
Collecting ipython>=4.0.0; python_version >= "3.3"
  Using cached ipython-7.16.1-py3-none-any.whl (785 kB)
Collecting widgetsnbextension~=3.5.0
  Using cached widgetsnbextension-3.5.1-py2.py3-none-any.whl (2.2 MB)
Collecting python-dateutil>=2.7.3
  Using cached python_dateutil-2.8.1-py2.py3-none-any.whl (227 kB)
Requirement already satisfied: numpy>=1.15.4 in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from pandas) (1.19.1)
Collecting pytz>=2017.2
  Using cached pytz-2020.4-py2.py3-none-any.whl (509 kB)
Collecting orjson
  Using cached orjson-3.4.6-cp36-cp36m-macosx_10_7_x86_64.whl (231 kB)
Requirement already satisfied: pillow>=6.0 in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from ipycanvas) (8.0.1)
Collecting defusedxml
  Using cached defusedxml-0.6.0-py2.py3-none-any.whl (23 kB)
Collecting jinja2>=2.4
  Using cached Jinja2-2.11.2-py2.py3-none-any.whl (125 kB)
Collecting jupyterlab-pygments
  Using cached jupyterlab_pygments-0.1.2-py2.py3-none-any.whl (4.6 kB)
Processing /Users/jon/Library/Caches/pip/wheels/12/12/89/fe63ac4d6ee6440daab4db77b78c63f7f192b700f844b6639f/pandocfilters-1.4.3-py3-none-any.whl
Collecting testpath
  Using cached testpath-0.4.4-py2.py3-none-any.whl (163 kB)
Collecting jupyter-core
  Using cached jupyter_core-4.7.0-py3-none-any.whl (82 kB)
Collecting nbclient<0.6.0,>=0.5.0
  Using cached nbclient-0.5.1-py3-none-any.whl (65 kB)
Requirement already satisfied: pygments>=2.4.1 in ./Slicer.app/Contents/Extensions-29402/SlicerJupyter/lib/python3.6/site-packages (from nbconvert->jupyter) (2.4.1)
Collecting entrypoints>=0.2.2
  Using cached entrypoints-0.3-py2.py3-none-any.whl (11 kB)
Collecting mistune<2,>=0.8.1
  Using cached mistune-0.8.4-py2.py3-none-any.whl (16 kB)
Collecting bleach
  Using cached bleach-3.2.1-py2.py3-none-any.whl (145 kB)
Collecting jupyter-client
  Using cached jupyter_client-6.1.7-py3-none-any.whl (108 kB)
Collecting prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0
  Using cached prompt_toolkit-3.0.8-py3-none-any.whl (355 kB)
Collecting qtpy
  Using cached QtPy-1.9.0-py2.py3-none-any.whl (54 kB)
Collecting ipython-genutils
  Using cached ipython_genutils-0.2.0-py2.py3-none-any.whl (26 kB)
Collecting pyzmq>=17.1
  Using cached pyzmq-20.0.0-cp36-cp36m-macosx_10_9_intel.whl (1.4 MB)
Collecting tornado>=4.2
  Using cached tornado-6.1-cp36-cp36m-macosx_10_9_x86_64.whl (416 kB)
Collecting appnope; platform_system == "Darwin"
  Using cached appnope-0.1.2-py2.py3-none-any.whl (4.3 kB)
Collecting terminado>=0.8.3
  Using cached terminado-0.9.1-py3-none-any.whl (13 kB)
Collecting Send2Trash
  Using cached Send2Trash-1.5.0-py3-none-any.whl (12 kB)
Collecting prometheus-client
  Using cached prometheus_client-0.9.0-py2.py3-none-any.whl (53 kB)
Collecting argon2-cffi
  Using cached argon2-cffi-20.1.0.tar.gz (1.8 MB)
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: finished with status 'done'
    Preparing wheel metadata: started
    Preparing wheel metadata: finished with status 'done'
Collecting decorator
  Using cached decorator-4.4.2-py2.py3-none-any.whl (9.2 kB)
Requirement already satisfied: six in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from traitlets>=4.3.1->ipywidgets) (1.15.0)
Collecting jsonschema!=2.5.0,>=2.4
  Using cached jsonschema-3.2.0-py2.py3-none-any.whl (56 kB)
Collecting backcall
  Using cached backcall-0.2.0-py2.py3-none-any.whl (11 kB)
Collecting pexpect; sys_platform != "win32"
  Using cached pexpect-4.8.0-py2.py3-none-any.whl (59 kB)
Requirement already satisfied: jedi>=0.10 in ./Slicer.app/Contents/Extensions-29402/SlicerJupyter/lib/python3.6/site-packages (from ipython>=4.0.0; python_version >= "3.3"->ipywidgets) (0.17.0)
Collecting pickleshare
  Using cached pickleshare-0.7.5-py2.py3-none-any.whl (6.9 kB)
Requirement already satisfied: setuptools>=18.5 in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from ipython>=4.0.0; python_version >= "3.3"->ipywidgets) (49.2.0)
Collecting MarkupSafe>=0.23
  Using cached MarkupSafe-1.1.1-cp36-cp36m-macosx_10_6_intel.whl (18 kB)
Collecting async-generator
  Using cached async_generator-1.10-py3-none-any.whl (18 kB)
Collecting nest-asyncio
  Using cached nest_asyncio-1.4.3-py3-none-any.whl (5.3 kB)
Requirement already satisfied: packaging in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from bleach->nbconvert->jupyter) (20.4)
Collecting webencodings
  Using cached webencodings-0.5.1-py2.py3-none-any.whl (11 kB)
Collecting wcwidth
  Using cached wcwidth-0.2.5-py2.py3-none-any.whl (30 kB)
Collecting ptyprocess; os_name != "nt"
  Using cached ptyprocess-0.6.0-py2.py3-none-any.whl (39 kB)
Collecting cffi>=1.0.0
  Using cached cffi-1.14.4-cp36-cp36m-macosx_10_9_x86_64.whl (176 kB)
Collecting attrs>=17.4.0
  Using cached attrs-20.3.0-py2.py3-none-any.whl (49 kB)
Processing /Users/jon/Library/Caches/pip/wheels/34/13/19/294da8e11bce7e563afee51251b9fa878185e14f4b5caf00cb/pyrsistent-0.17.3-cp36-cp36m-macosx_10_13_x86_64.whl
Collecting importlib-metadata; python_version < "3.8"
  Using cached importlib_metadata-3.3.0-py3-none-any.whl (10 kB)
Requirement already satisfied: parso>=0.7.0 in ./Slicer.app/Contents/Extensions-29402/SlicerJupyter/lib/python3.6/site-packages (from jedi>=0.10->ipython>=4.0.0; python_version >= "3.3"->ipywidgets) (0.7.1)
Requirement already satisfied: pyparsing>=2.0.2 in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from packaging->bleach->nbconvert->jupyter) (2.4.7)
Collecting pycparser
  Using cached pycparser-2.20-py2.py3-none-any.whl (112 kB)
Collecting zipp>=0.5
  Using cached zipp-3.4.0-py3-none-any.whl (5.2 kB)
Collecting typing-extensions>=3.6.4; python_version < "3.8"
  Using cached typing_extensions-3.7.4.3-py3-none-any.whl (22 kB)
Building wheels for collected packages: argon2-cffi
  Building wheel for argon2-cffi (PEP 517): started
  Building wheel for argon2-cffi (PEP 517): finished with status 'error'
  ERROR: Command errored out with exit status 1:
   command: /Applications/Slicer.app/Contents/bin/./python-real /Applications/Slicer.app/Contents/lib/Python/lib/python3.6/site-packages/pip/_vendor/pep517/_in_process.py build_wheel /var/folders/gk/xk6mdq_d7m7db3_6d4_6sg5w0000gn/T/tmpj7paas7y
       cwd: /private/var/folders/gk/xk6mdq_d7m7db3_6d4_6sg5w0000gn/T/pip-install-j5wn1lco/argon2-cffi
  Complete output (29 lines):
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build/lib.macosx-10.13-x86_64-3.6
  creating build/lib.macosx-10.13-x86_64-3.6/argon2
  copying src/argon2/__init__.py -> build/lib.macosx-10.13-x86_64-3.6/argon2
  copying src/argon2/low_level.py -> build/lib.macosx-10.13-x86_64-3.6/argon2
  copying src/argon2/_ffi_build.py -> build/lib.macosx-10.13-x86_64-3.6/argon2
  copying src/argon2/_password_hasher.py -> build/lib.macosx-10.13-x86_64-3.6/argon2
  copying src/argon2/exceptions.py -> build/lib.macosx-10.13-x86_64-3.6/argon2
  copying src/argon2/_legacy.py -> build/lib.macosx-10.13-x86_64-3.6/argon2
  copying src/argon2/__main__.py -> build/lib.macosx-10.13-x86_64-3.6/argon2
  copying src/argon2/_utils.py -> build/lib.macosx-10.13-x86_64-3.6/argon2
  running build_clib
  building 'argon2' library
  creating build/temp.macosx-10.13-x86_64-3.6
  creating build/temp.macosx-10.13-x86_64-3.6/extras
  creating build/temp.macosx-10.13-x86_64-3.6/extras/libargon2
  creating build/temp.macosx-10.13-x86_64-3.6/extras/libargon2/src
  creating build/temp.macosx-10.13-x86_64-3.6/extras/libargon2/src/blake2
  /usr/bin/clang -pthread -Wall -g -fPIC -msse2 -Iextras/libargon2/src/../include -Iextras/libargon2/src/blake2 -c extras/libargon2/src/argon2.c -o build/temp.macosx-10.13-x86_64-3.6/extras/libargon2/src/argon2.o
  /usr/bin/clang -pthread -Wall -g -fPIC -msse2 -Iextras/libargon2/src/../include -Iextras/libargon2/src/blake2 -c extras/libargon2/src/blake2/blake2b.c -o build/temp.macosx-10.13-x86_64-3.6/extras/libargon2/src/blake2/blake2b.o
  /usr/bin/clang -pthread -Wall -g -fPIC -msse2 -Iextras/libargon2/src/../include -Iextras/libargon2/src/blake2 -c extras/libargon2/src/core.c -o build/temp.macosx-10.13-x86_64-3.6/extras/libargon2/src/core.o
  /usr/bin/clang -pthread -Wall -g -fPIC -msse2 -Iextras/libargon2/src/../include -Iextras/libargon2/src/blake2 -c extras/libargon2/src/encoding.c -o build/temp.macosx-10.13-x86_64-3.6/extras/libargon2/src/encoding.o
  /usr/bin/clang -pthread -Wall -g -fPIC -msse2 -Iextras/libargon2/src/../include -Iextras/libargon2/src/blake2 -c extras/libargon2/src/opt.c -o build/temp.macosx-10.13-x86_64-3.6/extras/libargon2/src/opt.o
  /usr/bin/clang -pthread -Wall -g -fPIC -msse2 -Iextras/libargon2/src/../include -Iextras/libargon2/src/blake2 -c extras/libargon2/src/thread.c -o build/temp.macosx-10.13-x86_64-3.6/extras/libargon2/src/thread.o
  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ar rc build/temp.macosx-10.13-x86_64-3.6/libargon2.a build/temp.macosx-10.13-x86_64-3.6/extras/libargon2/src/argon2.o build/temp.macosx-10.13-x86_64-3.6/extras/libargon2/src/blake2/blake2b.o build/temp.macosx-10.13-x86_64-3.6/extras/libargon2/src/core.o build/temp.macosx-10.13-x86_64-3.6/extras/libargon2/src/encoding.o build/temp.macosx-10.13-x86_64-3.6/extras/libargon2/src/opt.o build/temp.macosx-10.13-x86_64-3.6/extras/libargon2/src/thread.o
  error: command '/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ar' failed with exit status 1
  ----------------------------------------
  ERROR: Failed building wheel for argon2-cffi
Failed to build argon2-cffi
ERROR: Could not build wheels for argon2-cffi which use PEP 517 and cannot be installed directly
WARNING: You are using pip version 20.1.1; however, version 20.3.3 is available.
You should consider upgrading via the '/Applications/Slicer.app/Contents/bin/./python-real -m pip install --upgrade pip' command.
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/Applications/Slicer.app/Contents/Extensions-29402/SlicerJupyter/lib/Slicer-4.11/qt-scripted-modules/JupyterNotebooks.py", line 53, in installRequiredPackages
    slicer.util.pip_install("jupyter ipywidgets pandas ipyevents ipycanvas --no-warn-script-location")
  File "/Applications/Slicer.app/Contents/bin/Python/slicer/util.py", line 2569, in pip_install
    _executePythonModule('pip', args)
  File "/Applications/Slicer.app/Contents/bin/Python/slicer/util.py", line 2545, in _executePythonModule
    logProcessOutput(proc)
  File "/Applications/Slicer.app/Contents/bin/Python/slicer/util.py", line 2517, in logProcessOutput
    raise CalledProcessError(retcode, proc.args, output=proc.stdout, stderr=proc.stderr)
subprocess.CalledProcessError: Command '['/Applications/Slicer.app/Contents/bin/../bin/PythonSlicer', '-m', 'pip', 'install', 'jupyter', 'ipywidgets', 'pandas', 'ipyevents', 'ipycanvas', '--no-warn-script-location']' returned non-zero exit status 1.

  Using cached qtconsole-5.0.1-py3-none-any.whl (118 kB)
Collecting ipykernel
  Using cached ipykernel-5.4.2-py3-none-any.whl (119 kB)
Collecting notebook
  Using cached notebook-6.1.5-py3-none-any.whl (9.5 MB)
>>> pip_install('jupyterlab')
Collecting jupyterlab  Using cached jupyterlab-2.2.9-py3-none-any.whl (7.9 MB)
Collecting jupyterlab-server<2.0,>=1.1.5
  Using cached jupyterlab_server-1.2.0-py3-none-any.whl (29 kB)
Collecting jinja2>=2.10
  Using cached Jinja2-2.11.2-py2.py3-none-any.whl (125 kB)
Collecting notebook>=4.3.1
  Using cached notebook-6.1.5-py3-none-any.whl (9.5 MB)
Collecting tornado!=6.0.0,!=6.0.1,!=6.0.2
  Using cached tornado-6.1-cp36-cp36m-macosx_10_9_x86_64.whl (416 kB)
Collecting jsonschema>=3.0.1
  Using cached jsonschema-3.2.0-py2.py3-none-any.whl (56 kB)
Collecting json5
  Using cached json5-0.9.5-py2.py3-none-any.whl (17 kB)
Requirement already satisfied: requests in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from jupyterlab-server<2.0,>=1.1.5->jupyterlab) (2.24.0)
Collecting MarkupSafe>=0.23
  Using cached MarkupSafe-1.1.1-cp36-cp36m-macosx_10_6_intel.whl (18 kB)
Collecting jupyter-core>=4.6.1
  Using cached jupyter_core-4.7.0-py3-none-any.whl (82 kB)
Collecting traitlets>=4.2.1
  Using cached traitlets-4.3.3-py2.py3-none-any.whl (75 kB)
Collecting jupyter-client>=5.3.4
  Using cached jupyter_client-6.1.7-py3-none-any.whl (108 kB)
Collecting ipython-genutils
  Using cached ipython_genutils-0.2.0-py2.py3-none-any.whl (26 kB)
Collecting pyzmq>=17
  Using cached pyzmq-20.0.0-cp36-cp36m-macosx_10_9_intel.whl (1.4 MB)
Collecting nbconvert
  Using cached nbconvert-6.0.7-py3-none-any.whl (552 kB)
Collecting Send2Trash
  Using cached Send2Trash-1.5.0-py3-none-any.whl (12 kB)
Collecting prometheus-client
  Using cached prometheus_client-0.9.0-py2.py3-none-any.whl (53 kB)
Collecting terminado>=0.8.3
  Using cached terminado-0.9.1-py3-none-any.whl (13 kB)
Collecting argon2-cffi
  Using cached argon2-cffi-20.1.0.tar.gz (1.8 MB)
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: finished with status 'done'
    Preparing wheel metadata: started
    Preparing wheel metadata: finished with status 'done'
Collecting nbformat
  Using cached nbformat-5.0.8-py3-none-any.whl (172 kB)
Collecting ipykernel
  Using cached ipykernel-5.4.2-py3-none-any.whl (119 kB)
Processing /Users/jon/Library/Caches/pip/wheels/34/13/19/294da8e11bce7e563afee51251b9fa878185e14f4b5caf00cb/pyrsistent-0.17.3-cp36-cp36m-macosx_10_13_x86_64.whl
Requirement already satisfied: six>=1.11.0 in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from jsonschema>=3.0.1->jupyterlab-server<2.0,>=1.1.5->jupyterlab) (1.15.0)
Collecting attrs>=17.4.0
  Using cached attrs-20.3.0-py2.py3-none-any.whl (49 kB)
Requirement already satisfied: setuptools in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from jsonschema>=3.0.1->jupyterlab-server<2.0,>=1.1.5->jupyterlab) (49.2.0)
Collecting importlib-metadata; python_version < "3.8"
  Using cached importlib_metadata-3.3.0-py3-none-any.whl (10 kB)
Requirement already satisfied: certifi>=2017.4.17 in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from requests->jupyterlab-server<2.0,>=1.1.5->jupyterlab) (2020.6.20)
Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from requests->jupyterlab-server<2.0,>=1.1.5->jupyterlab) (1.25.10)
Requirement already satisfied: chardet<4,>=3.0.2 in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from requests->jupyterlab-server<2.0,>=1.1.5->jupyterlab) (3.0.4)
Requirement already satisfied: idna<3,>=2.5 in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from requests->jupyterlab-server<2.0,>=1.1.5->jupyterlab) (2.10)
Collecting decorator
  Using cached decorator-4.4.2-py2.py3-none-any.whl (9.2 kB)
Collecting python-dateutil>=2.1
  Using cached python_dateutil-2.8.1-py2.py3-none-any.whl (227 kB)
Processing /Users/jon/Library/Caches/pip/wheels/12/12/89/fe63ac4d6ee6440daab4db77b78c63f7f192b700f844b6639f/pandocfilters-1.4.3-py3-none-any.whl
Collecting defusedxml
  Using cached defusedxml-0.6.0-py2.py3-none-any.whl (23 kB)
Requirement already satisfied: pygments>=2.4.1 in ./Slicer.app/Contents/Extensions-29402/SlicerJupyter/lib/python3.6/site-packages (from nbconvert->notebook>=4.3.1->jupyterlab) (2.4.1)
Collecting testpath
  Using cached testpath-0.4.4-py2.py3-none-any.whl (163 kB)
Collecting mistune<2,>=0.8.1
  Using cached mistune-0.8.4-py2.py3-none-any.whl (16 kB)
Collecting entrypoints>=0.2.2
  Using cached entrypoints-0.3-py2.py3-none-any.whl (11 kB)
Collecting jupyterlab-pygments
  Using cached jupyterlab_pygments-0.1.2-py2.py3-none-any.whl (4.6 kB)
Collecting nbclient<0.6.0,>=0.5.0
  Using cached nbclient-0.5.1-py3-none-any.whl (65 kB)
Collecting bleach
  Using cached bleach-3.2.1-py2.py3-none-any.whl (145 kB)
Collecting ptyprocess; os_name != "nt"
  Using cached ptyprocess-0.6.0-py2.py3-none-any.whl (39 kB)
Collecting cffi>=1.0.0
  Using cached cffi-1.14.4-cp36-cp36m-macosx_10_9_x86_64.whl (176 kB)
Collecting appnope; platform_system == "Darwin"
  Using cached appnope-0.1.2-py2.py3-none-any.whl (4.3 kB)
Collecting ipython>=5.0.0
  Using cached ipython-7.16.1-py3-none-any.whl (785 kB)
Collecting typing-extensions>=3.6.4; python_version < "3.8"
  Using cached typing_extensions-3.7.4.3-py3-none-any.whl (22 kB)
Collecting zipp>=0.5
  Using cached zipp-3.4.0-py3-none-any.whl (5.2 kB)
Collecting nest-asyncio
  Using cached nest_asyncio-1.4.3-py3-none-any.whl (5.3 kB)
Collecting async-generator
  Using cached async_generator-1.10-py3-none-any.whl (18 kB)
Collecting webencodings
  Using cached webencodings-0.5.1-py2.py3-none-any.whl (11 kB)
Requirement already satisfied: packaging in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from bleach->nbconvert->notebook>=4.3.1->jupyterlab) (20.4)
Collecting pycparser
  Using cached pycparser-2.20-py2.py3-none-any.whl (112 kB)
Collecting backcall
  Using cached backcall-0.2.0-py2.py3-none-any.whl (11 kB)
Requirement already satisfied: jedi>=0.10 in ./Slicer.app/Contents/Extensions-29402/SlicerJupyter/lib/python3.6/site-packages (from ipython>=5.0.0->ipykernel->notebook>=4.3.1->jupyterlab) (0.17.0)
Collecting pexpect; sys_platform != "win32"
  Using cached pexpect-4.8.0-py2.py3-none-any.whl (59 kB)
Collecting pickleshare
  Using cached pickleshare-0.7.5-py2.py3-none-any.whl (6.9 kB)
Collecting prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0
  Using cached prompt_toolkit-3.0.8-py3-none-any.whl (355 kB)
Requirement already satisfied: pyparsing>=2.0.2 in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from packaging->bleach->nbconvert->notebook>=4.3.1->jupyterlab) (2.4.7)
Requirement already satisfied: parso>=0.7.0 in ./Slicer.app/Contents/Extensions-29402/SlicerJupyter/lib/python3.6/site-packages (from jedi>=0.10->ipython>=5.0.0->ipykernel->notebook>=4.3.1->jupyterlab) (0.7.1)
Collecting wcwidth
  Using cached wcwidth-0.2.5-py2.py3-none-any.whl (30 kB)
Building wheels for collected packages: argon2-cffi
  Building wheel for argon2-cffi (PEP 517): started
  Building wheel for argon2-cffi (PEP 517): finished with status 'error'
  ERROR: Command errored out with exit status 1:
   command: /Applications/Slicer.app/Contents/bin/./python-real /Applications/Slicer.app/Contents/lib/Python/lib/python3.6/site-packages/pip/_vendor/pep517/_in_process.py build_wheel /var/folders/gk/xk6mdq_d7m7db3_6d4_6sg5w0000gn/T/tmpkye11kzt
       cwd: /private/var/folders/gk/xk6mdq_d7m7db3_6d4_6sg5w0000gn/T/pip-install-efqdzjlq/argon2-cffi
  Complete output (29 lines):
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build/lib.macosx-10.13-x86_64-3.6
  creating build/lib.macosx-10.13-x86_64-3.6/argon2
  copying src/argon2/__init__.py -> build/lib.macosx-10.13-x86_64-3.6/argon2
  copying src/argon2/low_level.py -> build/lib.macosx-10.13-x86_64-3.6/argon2
  copying src/argon2/_ffi_build.py -> build/lib.macosx-10.13-x86_64-3.6/argon2

  copying src/argon2/_password_hasher.py -> build/lib.macosx-10.13-x86_64-3.6/argon2
  copying src/argon2/exceptions.py -> build/lib.macosx-10.13-x86_64-3.6/argon2
  copying src/argon2/_legacy.py -> build/lib.macosx-10.13-x86_64-3.6/argon2
  copying src/argon2/__main__.py -> build/lib.macosx-10.13-x86_64-3.6/argon2
  copying src/argon2/_utils.py -> build/lib.macosx-10.13-x86_64-3.6/argon2
  running build_clib
  building 'argon2' library
  creating build/temp.macosx-10.13-x86_64-3.6
  creating build/temp.macosx-10.13-x86_64-3.6/extras
  creating build/temp.macosx-10.13-x86_64-3.6/extras/libargon2
  creating build/temp.macosx-10.13-x86_64-3.6/extras/libargon2/src
  creating build/temp.macosx-10.13-x86_64-3.6/extras/libargon2/src/blake2
  /usr/bin/clang -pthread -Wall -g -fPIC -msse2 -Iextras/libargon2/src/../include -Iextras/libargon2/src/blake2 -c extras/libargon2/src/argon2.c -o build/temp.macosx-10.13-x86_64-3.6/extras/libargon2/src/argon2.o
  /usr/bin/clang -pthread -Wall -g -fPIC -msse2 -Iextras/libargon2/src/../include -Iextras/libargon2/src/blake2 -c extras/libargon2/src/blake2/blake2b.c -o build/temp.macosx-10.13-x86_64-3.6/extras/libargon2/src/blake2/blake2b.o
  /usr/bin/clang -pthread -Wall -g -fPIC -msse2 -Iextras/libargon2/src/../include -Iextras/libargon2/src/blake2 -c extras/libargon2/src/core.c -o build/temp.macosx-10.13-x86_64-3.6/extras/libargon2/src/core.o
  /usr/bin/clang -pthread -Wall -g -fPIC -msse2 -Iextras/libargon2/src/../include -Iextras/libargon2/src/blake2 -c extras/libargon2/src/encoding.c -o build/temp.macosx-10.13-x86_64-3.6/extras/libargon2/src/encoding.o
  /usr/bin/clang -pthread -Wall -g -fPIC -msse2 -Iextras/libargon2/src/../include -Iextras/libargon2/src/blake2 -c extras/libargon2/src/opt.c -o build/temp.macosx-10.13-x86_64-3.6/extras/libargon2/src/opt.o
  /usr/bin/clang -pthread -Wall -g -fPIC -msse2 -Iextras/libargon2/src/../include -Iextras/libargon2/src/blake2 -c extras/libargon2/src/thread.c -o build/temp.macosx-10.13-x86_64-3.6/extras/libargon2/src/thread.o
  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ar rc build/temp.macosx-10.13-x86_64-3.6/libargon2.a build/temp.macosx-10.13-x86_64-3.6/extras/libargon2/src/argon2.o build/temp.macosx-10.13-x86_64-3.6/extras/libargon2/src/blake2/blake2b.o build/temp.macosx-10.13-x86_64-3.6/extras/libargon2/src/core.o build/temp.macosx-10.13-x86_64-3.6/extras/libargon2/src/encoding.o build/temp.macosx-10.13-x86_64-3.6/extras/libargon2/src/opt.o build/temp.macosx-10.13-x86_64-3.6/extras/libargon2/src/thread.o
  error: command '/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ar' failed with exit status 1
  ----------------------------------------
  ERROR: Failed building wheel for argon2-cffi
Failed to build argon2-cffi
ERROR: Could not build wheels for argon2-cffi which use PEP 517 and cannot be installed directly
WARNING: You are using pip version 20.1.1; however, version 20.3.3 is available.
You should consider upgrading via the '/Applications/Slicer.app/Contents/bin/./python-real -m pip install --upgrade pip' command.
Traceback (most recent call last):
  File "<console>", line 1, in <module>
  File "/Applications/Slicer.app/Contents/bin/Python/slicer/util.py", line 2569, in pip_install
    _executePythonModule('pip', args)
  File "/Applications/Slicer.app/Contents/bin/Python/slicer/util.py", line 2545, in _executePythonModule
    logProcessOutput(proc)
  File "/Applications/Slicer.app/Contents/bin/Python/slicer/util.py", line 2517, in logProcessOutput
    raise CalledProcessError(retcode, proc.args, output=proc.stdout, stderr=proc.stderr)
subprocess.CalledProcessError: Command '['/Applications/Slicer.app/Contents/bin/../bin/PythonSlicer', '-m', 'pip', 'install', 'jupyterlab']' returned non-zero exit status 1.
>>> 
>>> slicer.util._executePythonModule('jupyter',['labextension','install','@jupyter-widgets/jupyterlab-manager','ipycanvas','ipyevents'])
/Applications/Slicer.app/Contents/bin/./python-real: No module named jupyter
Traceback (most recent call last):
  File "<console>", line 1, in <module>
  File "/Applications/Slicer.app/Contents/bin/Python/slicer/util.py", line 2545, in _executePythonModule
    logProcessOutput(proc)
  File "/Applications/Slicer.app/Contents/bin/Python/slicer/util.py", line 2517, in logProcessOutput
    raise CalledProcessError(retcode, proc.args, output=proc.stdout, stderr=proc.stderr)
subprocess.CalledProcessError: Command '['/Applications/Slicer.app/Contents/bin/../bin/PythonSlicer', '-m', 'jupyter', 'labextension', 'install', '@jupyter-widgets/jupyterlab-manager', 'ipycanvas', 'ipyevents']' returned non-zero exit status 1.
4

I also tried to upgrade pip as per the log output but that didn’t work either

jon@Jonathans-MBP ~ % /Applications/Slicer.app/Contents/bin/./python-real -m pip install --upgrade pip
Could not find platform independent libraries <prefix>
Could not find platform dependent libraries <exec_prefix>
Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>]
Fatal Python error: Py_Initialize: unable to load the file system codec
ModuleNotFoundError: No module named 'encodings'

Current thread 0x000000011a8a6dc0 (most recent call first):
zsh: abort      /Applications/Slicer.app/Contents/bin/./python-real -m pip install --upgrade 
jon@Jonathans-MBP ~ %
5

You got the error because Jupyter server uses argon2-cffi package, which does not have wheels for macOS for Python-3.6.7. I’ve updated SlicerJupyter to bundle this package with the extension, so it is not necessary to build it during installation. Please try it again tomorrow (uninstall and install SlicerJupyter).

Updating pip is not necessary (but if you do that then probably it does not cause any problem either).

You got the error when you executed python-real because the virtual python environment was not set up. Instead of running python-real directly, you can use PythonSlicer executable, which sets up the virtual python environment and launches python-real.

1 Like
6

Solved! I reinstalled and it launched right into the localhost webpage for Jupyter notebook. I was also able to update pip by calling PythonSlicer instead of python-real. Perhaps this warrants an update of the warning output?

image
image2880×1800 329 KB

Collecting pillow

Using cached Pillow-8.0.1-cp36-cp36m-macosx_10_10_x86_64.whl (2.2 MB)

Installing collected packages: pillow

Attempting uninstall: pillow

Found existing installation: Pillow 8.0.1

Uninstalling Pillow-8.0.1:

Successfully uninstalled Pillow-8.0.1

Successfully installed pillow-8.0.1

WARNING: You are using pip version 20.1.1; however, version 20.3.3 is available.

You should consider upgrading via the ‘/Applications/Slicer.app/Contents/bin/./python-real -m pip install --upgrade pip’ command.

Collecting jupyter

Using cached jupyter-1.0.0-py2.py3-none-any.whl (2.7 kB)

Collecting ipywidgets

Using cached ipywidgets-7.5.1-py2.py3-none-any.whl (121 kB)

Collecting pandas

Using cached pandas-1.1.5-cp36-cp36m-macosx_10_9_x86_64.whl (10.2 MB)

Collecting ipyevents

Using cached ipyevents-0.8.1-py2.py3-none-any.whl (150 kB)

Collecting ipycanvas

Downloading ipycanvas-0.8.0-py2.py3-none-any.whl (257 kB)

Collecting notebook

Using cached notebook-6.1.5-py3-none-any.whl (9.5 MB)

Collecting ipykernel

Using cached ipykernel-5.4.2-py3-none-any.whl (119 kB)

Collecting jupyter-console

Using cached jupyter_console-6.2.0-py3-none-any.whl (22 kB)

Collecting nbconvert

Using cached nbconvert-6.0.7-py3-none-any.whl (552 kB)

Collecting qtconsole

Using cached qtconsole-5.0.1-py3-none-any.whl (118 kB)

Collecting nbformat>=4.2.0

Using cached nbformat-5.0.8-py3-none-any.whl (172 kB)

Collecting traitlets>=4.3.1

Using cached traitlets-4.3.3-py2.py3-none-any.whl (75 kB)

Collecting ipython>=4.0.0; python_version >= “3.3”

Using cached ipython-7.16.1-py3-none-any.whl (785 kB)

Collecting widgetsnbextension~=3.5.0

Using cached widgetsnbextension-3.5.1-py2.py3-none-any.whl (2.2 MB)

Requirement already satisfied: numpy>=1.15.4 in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from pandas) (1.19.1)

Collecting pytz>=2017.2

Using cached pytz-2020.4-py2.py3-none-any.whl (509 kB)

Collecting python-dateutil>=2.7.3

Using cached python_dateutil-2.8.1-py2.py3-none-any.whl (227 kB)

Collecting orjson

Using cached orjson-3.4.6-cp36-cp36m-macosx_10_7_x86_64.whl (231 kB)

Requirement already satisfied: pillow>=6.0 in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from ipycanvas) (8.0.1)

Collecting Send2Trash

Using cached Send2Trash-1.5.0-py3-none-any.whl (12 kB)

Collecting terminado>=0.8.3

Using cached terminado-0.9.1-py3-none-any.whl (13 kB)

Collecting pyzmq>=17

Using cached pyzmq-20.0.0-cp36-cp36m-macosx_10_9_intel.whl (1.4 MB)

Collecting jupyter-client>=5.3.4

Using cached jupyter_client-6.1.7-py3-none-any.whl (108 kB)

Requirement already satisfied: argon2-cffi in ./Slicer.app/Contents/Extensions-29402/SlicerJupyter/lib/python3.6/site-packages (from notebook->jupyter) (20.1.0)

Collecting tornado>=5.0

Using cached tornado-6.1-cp36-cp36m-macosx_10_9_x86_64.whl (416 kB)

Collecting ipython-genutils

Using cached ipython_genutils-0.2.0-py2.py3-none-any.whl (26 kB)

Collecting prometheus-client

Using cached prometheus_client-0.9.0-py2.py3-none-any.whl (53 kB)

Collecting jinja2

Using cached Jinja2-2.11.2-py2.py3-none-any.whl (125 kB)

Collecting jupyter-core>=4.6.1

Using cached jupyter_core-4.7.0-py3-none-any.whl (82 kB)

Collecting appnope; platform_system == “Darwin”

Using cached appnope-0.1.2-py2.py3-none-any.whl (4.3 kB)

Collecting prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0

Using cached prompt_toolkit-3.0.8-py3-none-any.whl (355 kB)

Requirement already satisfied: pygments in ./Slicer.app/Contents/Extensions-29402/SlicerJupyter/lib/python3.6/site-packages (from jupyter-console->jupyter) (2.4.1)

Processing /Users/jon/Library/Caches/pip/wheels/12/12/89/fe63ac4d6ee6440daab4db77b78c63f7f192b700f844b6639f/pandocfilters-1.4.3-py3-none-any.whl

Collecting nbclient<0.6.0,>=0.5.0

Using cached nbclient-0.5.1-py3-none-any.whl (65 kB)

Collecting testpath

Using cached testpath-0.4.4-py2.py3-none-any.whl (163 kB)

Collecting jupyterlab-pygments

Using cached jupyterlab_pygments-0.1.2-py2.py3-none-any.whl (4.6 kB)

Collecting defusedxml

Using cached defusedxml-0.6.0-py2.py3-none-any.whl (23 kB)

Collecting entrypoints>=0.2.2

Using cached entrypoints-0.3-py2.py3-none-any.whl (11 kB)

Collecting bleach

Using cached bleach-3.2.1-py2.py3-none-any.whl (145 kB)

Collecting mistune<2,>=0.8.1

Using cached mistune-0.8.4-py2.py3-none-any.whl (16 kB)

Collecting qtpy

Using cached QtPy-1.9.0-py2.py3-none-any.whl (54 kB)

Collecting jsonschema!=2.5.0,>=2.4

Using cached jsonschema-3.2.0-py2.py3-none-any.whl (56 kB)

Collecting decorator

Using cached decorator-4.4.2-py2.py3-none-any.whl (9.2 kB)

Requirement already satisfied: six in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from traitlets>=4.3.1->ipywidgets) (1.15.0)

Collecting pexpect; sys_platform != “win32”

Using cached pexpect-4.8.0-py2.py3-none-any.whl (59 kB)

Collecting pickleshare

Using cached pickleshare-0.7.5-py2.py3-none-any.whl (6.9 kB)

Collecting backcall

Using cached backcall-0.2.0-py2.py3-none-any.whl (11 kB)

Requirement already satisfied: jedi>=0.10 in ./Slicer.app/Contents/Extensions-29402/SlicerJupyter/lib/python3.6/site-packages (from ipython>=4.0.0; python_version >= “3.3”->ipywidgets) (0.17.0)

Requirement already satisfied: setuptools>=18.5 in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from ipython>=4.0.0; python_version >= “3.3”->ipywidgets) (49.2.0)

Collecting ptyprocess; os_name != “nt”

Using cached ptyprocess-0.6.0-py2.py3-none-any.whl (39 kB)

Requirement already satisfied: cffi>=1.0.0 in ./Slicer.app/Contents/Extensions-29402/SlicerJupyter/lib/python3.6/site-packages (from argon2-cffi->notebook->jupyter) (1.14.4)

Collecting MarkupSafe>=0.23

Using cached MarkupSafe-1.1.1-cp36-cp36m-macosx_10_6_intel.whl (18 kB)

Collecting wcwidth

Using cached wcwidth-0.2.5-py2.py3-none-any.whl (30 kB)

Collecting nest-asyncio

Using cached nest_asyncio-1.4.3-py3-none-any.whl (5.3 kB)

Collecting async-generator

Using cached async_generator-1.10-py3-none-any.whl (18 kB)

Requirement already satisfied: packaging in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from bleach->nbconvert->jupyter) (20.4)

Collecting webencodings

Using cached webencodings-0.5.1-py2.py3-none-any.whl (11 kB)

Collecting attrs>=17.4.0

Using cached attrs-20.3.0-py2.py3-none-any.whl (49 kB)

Collecting importlib-metadata; python_version < “3.8”

Using cached importlib_metadata-3.3.0-py3-none-any.whl (10 kB)

Processing /Users/jon/Library/Caches/pip/wheels/34/13/19/294da8e11bce7e563afee51251b9fa878185e14f4b5caf00cb/pyrsistent-0.17.3-cp36-cp36m-macosx_10_13_x86_64.whl

Requirement already satisfied: parso>=0.7.0 in ./Slicer.app/Contents/Extensions-29402/SlicerJupyter/lib/python3.6/site-packages (from jedi>=0.10->ipython>=4.0.0; python_version >= “3.3”->ipywidgets) (0.7.1)

Requirement already satisfied: pycparser in ./Slicer.app/Contents/Extensions-29402/SlicerJupyter/lib/python3.6/site-packages (from cffi>=1.0.0->argon2-cffi->notebook->jupyter) (2.20)

Requirement already satisfied: pyparsing>=2.0.2 in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from packaging->bleach->nbconvert->jupyter) (2.4.7)

Collecting zipp>=0.5

Using cached zipp-3.4.0-py3-none-any.whl (5.2 kB)

Collecting typing-extensions>=3.6.4; python_version < “3.8”

Using cached typing_extensions-3.7.4.3-py3-none-any.whl (22 kB)

Installing collected packages: Send2Trash, ptyprocess, tornado, terminado, pyzmq, python-dateutil, decorator, ipython-genutils, traitlets, jupyter-core, jupyter-client, appnope, wcwidth, prompt-toolkit, pexpect, pickleshare, backcall, ipython, ipykernel, pandocfilters, attrs, zipp, typing-extensions, importlib-metadata, pyrsistent, jsonschema, nbformat, nest-asyncio, async-generator, nbclient, testpath, jupyterlab-pygments, defusedxml, MarkupSafe, jinja2, entrypoints, webencodings, bleach, mistune, nbconvert, prometheus-client, notebook, jupyter-console, widgetsnbextension, ipywidgets, qtpy, qtconsole, jupyter, pytz, pandas, ipyevents, orjson, ipycanvas

Successfully installed MarkupSafe-1.1.1 Send2Trash-1.5.0 appnope-0.1.2 async-generator-1.10 attrs-20.3.0 backcall-0.2.0 bleach-3.2.1 decorator-4.4.2 defusedxml-0.6.0 entrypoints-0.3 importlib-metadata-3.3.0 ipycanvas-0.8.0 ipyevents-0.8.1 ipykernel-5.4.2 ipython-7.16.1 ipython-genutils-0.2.0 ipywidgets-7.5.1 jinja2-2.11.2 jsonschema-3.2.0 jupyter-1.0.0 jupyter-client-6.1.7 jupyter-console-6.2.0 jupyter-core-4.7.0 jupyterlab-pygments-0.1.2 mistune-0.8.4 nbclient-0.5.1 nbconvert-6.0.7 nbformat-5.0.8 nest-asyncio-1.4.3 notebook-6.1.5 orjson-3.4.6 pandas-1.1.5 pandocfilters-1.4.3 pexpect-4.8.0 pickleshare-0.7.5 prometheus-client-0.9.0 prompt-toolkit-3.0.8 ptyprocess-0.6.0 pyrsistent-0.17.3 python-dateutil-2.8.1 pytz-2020.4 pyzmq-20.0.0 qtconsole-5.0.1 qtpy-1.9.0 terminado-0.9.1 testpath-0.4.4 tornado-6.1 traitlets-4.3.3 typing-extensions-3.7.4.3 wcwidth-0.2.5 webencodings-0.5.1 widgetsnbextension-3.5.1 zipp-3.4.0

WARNING: You are using pip version 20.1.1; however, version 20.3.3 is available.

You should consider upgrading via the ‘/Applications/Slicer.app/Contents/bin/./python-real -m pip install --upgrade pip’ command.

Enabling notebook extension jupyter-js-widgets/extension…

  • Validating: e[32mOKe[0m

Enabling notebook extension ipyevents/extension…

  • Validating: e[32mOKe[0m

Installed kernelspec slicer-4.11 in /Users/jon/Library/Jupyter/kernels/slicer-4.11

pip_install(‘jupyterlab’)

Collecting jupyterlab Using cached jupyterlab-2.2.9-py3-none-any.whl (7.9 MB)

Collecting jupyterlab-server<2.0,>=1.1.5

Using cached jupyterlab_server-1.2.0-py3-none-any.whl (29 kB)

Requirement already satisfied: tornado!=6.0.0,!=6.0.1,!=6.0.2 in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from jupyterlab) (6.1)

Requirement already satisfied: jinja2>=2.10 in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from jupyterlab) (2.11.2)

Requirement already satisfied: notebook>=4.3.1 in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from jupyterlab) (6.1.5)

Requirement already satisfied: jsonschema>=3.0.1 in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from jupyterlab-server<2.0,>=1.1.5->jupyterlab) (3.2.0)

Collecting json5

Using cached json5-0.9.5-py2.py3-none-any.whl (17 kB)

Requirement already satisfied: requests in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from jupyterlab-server<2.0,>=1.1.5->jupyterlab) (2.24.0)

Requirement already satisfied: MarkupSafe>=0.23 in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from jinja2>=2.10->jupyterlab) (1.1.1)

Requirement already satisfied: nbformat in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from notebook>=4.3.1->jupyterlab) (5.0.8)

Requirement already satisfied: pyzmq>=17 in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from notebook>=4.3.1->jupyterlab) (20.0.0)

Requirement already satisfied: ipython-genutils in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from notebook>=4.3.1->jupyterlab) (0.2.0)

Requirement already satisfied: nbconvert in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from notebook>=4.3.1->jupyterlab) (6.0.7)

Requirement already satisfied: ipykernel in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from notebook>=4.3.1->jupyterlab) (5.4.2)

Requirement already satisfied: jupyter-client>=5.3.4 in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from notebook>=4.3.1->jupyterlab) (6.1.7)

Requirement already satisfied: Send2Trash in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from notebook>=4.3.1->jupyterlab) (1.5.0)

Requirement already satisfied: argon2-cffi in ./Slicer.app/Contents/Extensions-29402/SlicerJupyter/lib/python3.6/site-packages (from notebook>=4.3.1->jupyterlab) (20.1.0)

Requirement already satisfied: prometheus-client in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from notebook>=4.3.1->jupyterlab) (0.9.0)

Requirement already satisfied: terminado>=0.8.3 in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from notebook>=4.3.1->jupyterlab) (0.9.1)

Requirement already satisfied: traitlets>=4.2.1 in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from notebook>=4.3.1->jupyterlab) (4.3.3)

Requirement already satisfied: jupyter-core>=4.6.1 in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from notebook>=4.3.1->jupyterlab) (4.7.0)

Requirement already satisfied: pyrsistent>=0.14.0 in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from jsonschema>=3.0.1->jupyterlab-server<2.0,>=1.1.5->jupyterlab) (0.17.3)

Requirement already satisfied: six>=1.11.0 in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from jsonschema>=3.0.1->jupyterlab-server<2.0,>=1.1.5->jupyterlab) (1.15.0)

Requirement already satisfied: importlib-metadata; python_version < “3.8” in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from jsonschema>=3.0.1->jupyterlab-server<2.0,>=1.1.5->jupyterlab) (3.3.0)

Requirement already satisfied: setuptools in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from jsonschema>=3.0.1->jupyterlab-server<2.0,>=1.1.5->jupyterlab) (49.2.0)

Requirement already satisfied: attrs>=17.4.0 in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from jsonschema>=3.0.1->jupyterlab-server<2.0,>=1.1.5->jupyterlab) (20.3.0)

Requirement already satisfied: certifi>=2017.4.17 in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from requests->jupyterlab-server<2.0,>=1.1.5->jupyterlab) (2020.6.20)

Requirement already satisfied: chardet<4,>=3.0.2 in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from requests->jupyterlab-server<2.0,>=1.1.5->jupyterlab) (3.0.4)

Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from requests->jupyterlab-server<2.0,>=1.1.5->jupyterlab) (1.25.10)

Requirement already satisfied: idna<3,>=2.5 in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from requests->jupyterlab-server<2.0,>=1.1.5->jupyterlab) (2.10)

Requirement already satisfied: bleach in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from nbconvert->notebook>=4.3.1->jupyterlab) (3.2.1)

Requirement already satisfied: pandocfilters>=1.4.1 in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from nbconvert->notebook>=4.3.1->jupyterlab) (1.4.3)

Requirement already satisfied: mistune<2,>=0.8.1 in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from nbconvert->notebook>=4.3.1->jupyterlab) (0.8.4)

Requirement already satisfied: jupyterlab-pygments in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from nbconvert->notebook>=4.3.1->jupyterlab) (0.1.2)

Requirement already satisfied: pygments>=2.4.1 in ./Slicer.app/Contents/Extensions-29402/SlicerJupyter/lib/python3.6/site-packages (from nbconvert->notebook>=4.3.1->jupyterlab) (2.4.1)

Requirement already satisfied: entrypoints>=0.2.2 in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from nbconvert->notebook>=4.3.1->jupyterlab) (0.3)

Requirement already satisfied: defusedxml in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from nbconvert->notebook>=4.3.1->jupyterlab) (0.6.0)

Requirement already satisfied: nbclient<0.6.0,>=0.5.0 in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from nbconvert->notebook>=4.3.1->jupyterlab) (0.5.1)

Requirement already satisfied: testpath in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from nbconvert->notebook>=4.3.1->jupyterlab) (0.4.4)

Requirement already satisfied: appnope; platform_system == “Darwin” in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from ipykernel->notebook>=4.3.1->jupyterlab) (0.1.2)

Requirement already satisfied: ipython>=5.0.0 in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from ipykernel->notebook>=4.3.1->jupyterlab) (7.16.1)

Requirement already satisfied: python-dateutil>=2.1 in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from jupyter-client>=5.3.4->notebook>=4.3.1->jupyterlab) (2.8.1)

Requirement already satisfied: cffi>=1.0.0 in ./Slicer.app/Contents/Extensions-29402/SlicerJupyter/lib/python3.6/site-packages (from argon2-cffi->notebook>=4.3.1->jupyterlab) (1.14.4)

Requirement already satisfied: ptyprocess; os_name != “nt” in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from terminado>=0.8.3->notebook>=4.3.1->jupyterlab) (0.6.0)

Requirement already satisfied: decorator in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from traitlets>=4.2.1->notebook>=4.3.1->jupyterlab) (4.4.2)

Requirement already satisfied: typing-extensions>=3.6.4; python_version < “3.8” in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from importlib-metadata; python_version < “3.8”->jsonschema>=3.0.1->jupyterlab-server<2.0,>=1.1.5->jupyterlab) (3.7.4.3)

Requirement already satisfied: zipp>=0.5 in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from importlib-metadata; python_version < “3.8”->jsonschema>=3.0.1->jupyterlab-server<2.0,>=1.1.5->jupyterlab) (3.4.0)

Requirement already satisfied: packaging in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from bleach->nbconvert->notebook>=4.3.1->jupyterlab) (20.4)

Requirement already satisfied: webencodings in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from bleach->nbconvert->notebook>=4.3.1->jupyterlab) (0.5.1)

Requirement already satisfied: async-generator in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from nbclient<0.6.0,>=0.5.0->nbconvert->notebook>=4.3.1->jupyterlab) (1.10)

Requirement already satisfied: nest-asyncio in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from nbclient<0.6.0,>=0.5.0->nbconvert->notebook>=4.3.1->jupyterlab) (1.4.3)

Requirement already satisfied: backcall in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from ipython>=5.0.0->ipykernel->notebook>=4.3.1->jupyterlab) (0.2.0)

Requirement already satisfied: pexpect; sys_platform != “win32” in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from ipython>=5.0.0->ipykernel->notebook>=4.3.1->jupyterlab) (4.8.0)

Requirement already satisfied: jedi>=0.10 in ./Slicer.app/Contents/Extensions-29402/SlicerJupyter/lib/python3.6/site-packages (from ipython>=5.0.0->ipykernel->notebook>=4.3.1->jupyterlab) (0.17.0)

Requirement already satisfied: pickleshare in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from ipython>=5.0.0->ipykernel->notebook>=4.3.1->jupyterlab) (0.7.5)

Requirement already satisfied: prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0 in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from ipython>=5.0.0->ipykernel->notebook>=4.3.1->jupyterlab) (3.0.8)

Requirement already satisfied: pycparser in ./Slicer.app/Contents/Extensions-29402/SlicerJupyter/lib/python3.6/site-packages (from cffi>=1.0.0->argon2-cffi->notebook>=4.3.1->jupyterlab) (2.20)

Requirement already satisfied: pyparsing>=2.0.2 in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from packaging->bleach->nbconvert->notebook>=4.3.1->jupyterlab) (2.4.7)

Requirement already satisfied: parso>=0.7.0 in ./Slicer.app/Contents/Extensions-29402/SlicerJupyter/lib/python3.6/site-packages (from jedi>=0.10->ipython>=5.0.0->ipykernel->notebook>=4.3.1->jupyterlab) (0.7.1)

Requirement already satisfied: wcwidth in ./Slicer.app/Contents/lib/Python/lib/python3.6/site-packages (from prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0->ipython>=5.0.0->ipykernel->notebook>=4.3.1->jupyterlab) (0.2.5)

Installing collected packages: json5, jupyterlab-server, jupyterlab

WARNING: The script pyjson5 is installed in ‘/Applications/Slicer.app/Contents/lib/Python/bin’ which is not on PATH.

Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.

WARNING: The scripts jlpm, jupyter-lab, jupyter-labextension and jupyter-labhub are installed in ‘/Applications/Slicer.app/Contents/lib/Python/bin’ which is not on PATH.

Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.

Successfully installed json5-0.9.5 jupyterlab-2.2.9 jupyterlab-server-1.2.0

WARNING: You are using pip version 20.1.1; however, version 20.3.3 is available.

You should consider upgrading via the ‘/Applications/Slicer.app/Contents/bin/./python-real -m pip install --upgrade pip’ command.

jon@Jonathans-MBP ~ % /Applications/Slicer.app/Contents/bin/./PythonSlicer -m pip install --upgrade pip
Collecting pip
Downloading pip-20.3.3-py2.py3-none-any.whl (1.5 MB)
|████████████████████████████████| 1.5 MB 3.5 MB/s
Installing collected packages: pip
Attempting uninstall: pip
Found existing installation: pip 20.1.1
Uninstalling pip-20.1.1:
Successfully uninstalled pip-20.1.1
WARNING: The scripts pip, pip3 and pip3.6 are installed in ‘/Applications/Slicer.app/Contents/lib/Python/bin’ which is not on PATH.
Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
Successfully installed pip-20.3.3

7

Thanks for the feedback. It’s good to know that the fix worked. I’ve added some notes on the warnings to the module documentation.