Spyder notebook complains about missing file or directory: 'jupyter'

[ccordoba12]

@BjornFJohansson commented on Fri Jan 19 2018

This issue might be in the wrong place, but I sent i automatically from spyder.

Description

What steps will reproduce the problem?

1. conda install -c spyder-ide spyder-notebook
2. switch to notebook pane in spyder
3. right click and open an ipynb file on the file system (that file works with the jupyter notebook cmd)

What is the expected output? What do you see instead?

Please provide any additional information below

File "/home/bjorn/anaconda3/envs/bjorn36/lib/python3.6/site-packages/spyder_notebook/notebookplugin.py", line 412, in open_notebook
self.create_new_client(filename=filename)
File "/home/bjorn/anaconda3/envs/bjorn36/lib/python3.6/site-packages/spyder_notebook/notebookplugin.py", line 314, in create_new_client
server_info = nbopen(filename)
File "/home/bjorn/anaconda3/envs/bjorn36/lib/python3.6/site-packages/spyder_notebook/utils/nbopen.py", line 75, in nbopen
proc = subprocess.Popen(command, creationflags=creation_flag)
File "/home/bjorn/anaconda3/envs/bjorn36/lib/python3.6/subprocess.py", line 709, in init
restore_signals, start_new_session)
File "/home/bjorn/anaconda3/envs/bjorn36/lib/python3.6/subprocess.py", line 1344, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'jupyter': 'jupyter'

Version and main components

• Spyder Version: 3.2.6
• Python Version: 3.6.3
• Qt Versions: 5.6.2, PyQt5 5.6 on Linux

Dependencies

pyflakes >=0.6.0 :  1.6.0 (OK)
pycodestyle >=2.3:  2.3.1 (OK)
pygments >=2.0   :  2.2.0 (OK)
pandas >=0.13.1  :  0.20.3 (OK)
numpy >=1.7      :  1.13.3 (OK)
sphinx >=0.6.6   :  1.6.3 (OK)
rope >=0.9.4     :  0.10.5 (OK)
jedi >=0.9.0     :  0.10.2 (OK)
psutil >=0.3     :  5.4.0 (OK)
nbconvert >=4.0  :  5.3.1 (OK)
sympy >=0.7.3    :  1.1.1 (OK)
cython >=0.21    :  0.26.1 (OK)
qtconsole >=4.2.0:  4.3.1 (OK)
IPython >=4.0    :  6.2.1 (OK)
pylint >=0.25    :  1.7.4 (OK)

`(bjorn36) bjorn@bjorn-ThinkPad-T450s:~$ conda install -c spyder-ide spyder-notebook
Fetching package metadata .................
Solving package specifications: .

Package plan for installation in environment /home/bjorn/anaconda3/envs/bjorn36:

The following NEW packages will be INSTALLED:

spyder-notebook: 0.1.1-py36_0 spyder-ide

spyder-noteboo 100% |####################################################################################| Time: 0:00:00 105.01 kB/s
(bjorn36) bjorn@bjorn-ThinkPad-T450s:~$ `

`(bjorn36) bjorn@bjorn-ThinkPad-T450s:~$ conda info
Current conda install:

           platform : linux-64
      conda version : 4.3.30
   conda is private : False
  conda-env version : 4.3.30
conda-build version : 3.1.3
     python version : 3.6.3.final.0
   requests version : 2.18.4
   root environment : /home/bjorn/anaconda3  (writable)
default environment : /home/bjorn/anaconda3/envs/bjorn36
   envs directories : /home/bjorn/anaconda3/envs
                      /home/bjorn/.conda/envs
      package cache : /home/bjorn/anaconda3/pkgs
                      /home/bjorn/.conda/pkgs
       channel URLs : https://repo.continuum.io/pkgs/main/linux-64
                      https://repo.continuum.io/pkgs/main/noarch
                      https://repo.continuum.io/pkgs/free/linux-64
                      https://repo.continuum.io/pkgs/free/noarch
                      https://repo.continuum.io/pkgs/r/linux-64
                      https://repo.continuum.io/pkgs/r/noarch
                      https://repo.continuum.io/pkgs/pro/linux-64
                      https://repo.continuum.io/pkgs/pro/noarch
                      https://conda.anaconda.org/conda-forge/linux-64
                      https://conda.anaconda.org/conda-forge/noarch
                      https://conda.anaconda.org/BjornFJohansson/linux-64
                      https://conda.anaconda.org/BjornFJohansson/noarch
        config file : /home/bjorn/.condarc
         netrc file : None
       offline mode : False
         user-agent : conda/4.3.30 requests/2.18.4 CPython/3.6.3 Linux/4.13.0-26-generic debian/stretch/sid glibc/2.23    
            UID:GID : 1000:1000

(bjorn36) bjorn@bjorn-ThinkPad-T450s:~$ conda list

packages in environment at /home/bjorn/anaconda3/envs/bjorn36:

alabaster 0.7.10 py36h306e16b_0 defaults
anaconda custom py36hbbc8b67_0 defaults
anaconda-client 1.6.5 py36h19c0dcd_0 defaults
anaconda-navigator 1.6.9 py36h11ddaaa_0 defaults
anaconda-project 0.8.0 py36h29abdf5_0 defaults
appdirs 1.4.3 py36_0 defaults
asn1crypto 0.22.0 py36h265ca7c_1 defaults
astroid 1.5.3 py36hbdb9df2_0 defaults
astropy 2.0.2 py36ha51211e_4 defaults
attrs 17.3.0 py36h5ab58ff_0 defaults
autopep8 1.3.3 py_0 conda-forge
babel 2.5.0 py36h7d14adf_0 defaults
backports 1.0 py36hfa02d7e_1 defaults
backports.shutil_get_terminal_size 1.0.0 py36hfea85ff_2 defaults
beautifulsoup4 4.6.0 py36h49b8c8c_1 defaults
biopython 1.69 np113py36_0 defaults
bitarray 0.8.1 py36h5834eb8_0 defaults
bkcharts 0.2 py36h735825a_0 defaults
blaze 0.11.3 py36h4e06776_0 defaults
bleach 2.0.0 py36h688b259_0 defaults
bokeh 0.12.10 py36hbb0e44a_0 defaults
boto 2.48.0 py36h6e4cd66_1 defaults
bottleneck 1.2.1 py36haac1ea0_0 defaults
bzip2 1.0.6 h0376d23_1 defaults
ca-certificates 2017.08.26 h1d4fec5_0 defaults
cairo 1.14.10 haa5651f_5 defaults
certifi 2017.7.27.1 py36h8b7b77e_0 defaults
cffi 1.10.0 py36had8d393_1 defaults
chardet 3.0.4 py36h0f667ec_1 defaults
click 6.7 py36h5253387_0 defaults
cloudpickle 0.4.0 py36h30f8c20_0 defaults
clyent 1.2.2 py36h7e57e65_1 defaults
colorama 0.3.9 py36h489cec4_0 defaults
contextlib2 0.5.5 py36h6c84a62_0 defaults
coverage 4.4.2 py36hca7c4c5_0 defaults
cryptography 2.0.3 py36ha225213_1 defaults
curl 7.55.1 hcb0b314_2 defaults
cycler 0.10.0 py36h93f1223_0 defaults
cython 0.26.1 py36h21c49d0_0 defaults
cytoolz 0.8.2 py36h708bfd4_0 defaults
dask 0.15.3 py36hdc2c8aa_0 defaults
dask-core 0.15.3 py36h10e6167_0 defaults
datashape 0.5.4 py36h3ad6b5c_0 defaults
dbus 1.10.22 h3b5a359_0 defaults
decorator 4.1.2 py36hd076ac8_0 defaults
distributed 1.19.1 py36h25f3894_0 defaults
docutils 0.14 py36hb0f60f5_0 defaults
dropbox 8.5.0 py36h9ff2726_0 anaconda
entrypoints 0.2.3 py36h1aec115_2 defaults
et_xmlfile 1.0.1 py36hd6bccc3_0 defaults
expat 2.2.4 hc00ebd1_1 defaults
fastcache 1.0.2 py36h5b0c431_0 defaults
filelock 2.0.12 py36hacfa1f5_0 defaults
flask 0.12.2 py36hb24657c_0 defaults
flask-cors 3.0.3 py36h2d857d3_0 defaults
fontconfig 2.12.4 h88586e7_1 defaults
freetype 2.8 h52ed37b_0 defaults
get_terminal_size 1.0.0 haa9412d_0 defaults
gevent 1.2.2 py36h2fe25dc_0 defaults
glib 2.53.6 hc861d11_1 defaults
glob2 0.5 py36h2c1b292_1 defaults
gmp 6.1.2 hb3b607b_0 defaults
gmpy2 2.0.8 py36h55090d7_1 defaults
graphite2 1.3.10 hc526e54_0 defaults
greenlet 0.4.12 py36h2d503a6_0 defaults
gst-plugins-base 1.12.2 he3457e5_0 defaults
gstreamer 1.12.2 h4f93127_0 defaults
h5py 2.7.0 py36he81ebca_1 defaults
harfbuzz 1.5.0 h2545bd6_0 defaults
hdf5 1.10.1 hb0523eb_0 defaults
heapdict 1.0.0 py36h79797d7_0 defaults
html5lib 0.999999999 py36h2cfc398_0 defaults
hypothesis 3.38.5 py36h196a6cc_0 defaults
icu 58.2 h211956c_0 defaults
idna 2.6 py36h82fb2a8_1 defaults
imageio 2.2.0 py36he555465_0 defaults
imagesize 0.7.1 py36h52d8127_0 defaults
intel-openmp 2018.0.0 h15fc484_7 defaults
ipdb 0.10.3 py36_0 conda-forge
ipykernel 4.6.1 py36hbf841aa_0 defaults
ipython 6.2.1 py36h88c514a_1 defaults
ipython_genutils 0.2.0 py36hb52b0d5_0 defaults
ipywidgets 7.0.0 py36h7b55c3a_0 defaults
isort 4.2.15 py36had401c0_0 defaults
itsdangerous 0.24 py36h93cc618_1 defaults
jbig 2.1 hdba287a_0 defaults
jdcal 1.3 py36h4c697fb_0 defaults
jedi 0.10.2 py36h552def0_0 defaults
jinja2 2.9.6 py36h489bce4_1 defaults
jpeg 9b habf39ab_1 defaults
jsonschema 2.6.0 py36h006f8b5_0 defaults
jupyter 1.0.0 py36h9896ce5_0 defaults
jupyter_client 5.1.0 py36h614e9ea_0 defaults
jupyter_console 5.2.0 py36he59e554_1 defaults
jupyter_core 4.4.0 py36h7c827e3_0 defaults
jupyterlab 0.30.6 py36h2f9c1c0_0 defaults
jupyterlab_launcher 0.6.0 py36_0 defaults
lazy-object-proxy 1.3.1 py36h10fcdad_0 defaults
libedit 3.1 heed3624_0 defaults
libffi 3.2.1 h4deb6c0_3 defaults
libgcc 5.4.0 0 brown-data-science
libgcc-ng 7.2.0 h7cc24e2_2 defaults
libgfortran-ng 7.2.0 h9f7466a_2 defaults
libpng 1.6.32 hda9c8bc_2 defaults
libsodium 1.0.13 h31c71d8_2 defaults
libssh2 1.8.0 h8c220ad_2 defaults
libstdcxx-ng 7.2.0 h7a57d05_2 defaults
libtiff 4.0.8 h90200ff_9 defaults
libtool 2.4.6 hd50d1a6_0 defaults
libxcb 1.12 h84ff03f_3 defaults
libxml2 2.9.4 h6b072ca_5 defaults
libxslt 1.1.29 hcf9102b_5 defaults
llvmlite 0.20.0 py36_0 defaults
locket 0.2.0 py36h787c0ad_1 defaults
lxml 4.1.0 py36h5b66e50_0 defaults
lzo 2.10 h1bfc0ba_1 defaults
markupsafe 1.0 py36hd9260cd_1 defaults
matplotlib 2.1.0 py36hba5de38_0 defaults
mccabe 0.6.1 py36h5ad9710_1 defaults
mistune 0.7.4 py36hbab8784_0 defaults
mkl 2018.0.0 hb491cac_4 defaults
mkl-service 1.1.2 py36h17a0993_4 defaults
mpc 1.0.3 hf803216_4 defaults
mpfr 3.1.5 h12ff648_1 defaults
mpldatacursor 0.6.2 py36_1 BjornFJohansson
mpmath 0.19 py36h8cc018b_2 defaults
msgpack-python 0.4.8 py36hec4c5d1_0 defaults
multipledispatch 0.4.9 py36h41da3fb_0 defaults
navigator-updater 0.1.0 py36h14770f7_0 defaults
nbconvert 5.3.1 py36hb41ffb7_0 defaults
nbformat 4.4.0 py36h31c9010_0 defaults
nbval 0.7 py_0 conda-forge
ncurses 6.0 h06874d7_1 defaults
networkx 2.0 py36h7e96fb8_0 defaults
nltk 3.2.4 py36h1a0979f_0 defaults
nose 1.3.7 py36hcdf7029_2 defaults
notebook 5.2.2 py36h40a37e6_0 defaults
numba 0.35.0 np113py36_10 defaults
numexpr 2.6.2 py36hdd3393f_1 defaults
numpy 1.13.3 py36ha12f23b_0 defaults
numpydoc 0.7.0 py36h18f165f_0 defaults
odo 0.5.1 py36h90ed295_0 defaults
olefile 0.44 py36h79f9f78_0 defaults
openpyxl 2.4.8 py36h41dd2a8_1 defaults
openssl 1.0.2l h077ae2c_5 defaults
ordered-set 2.0.2 py36_0 conda-forge
p7zip 16.02 hcef1464_0 brown-data-science
packaging 16.8 py36ha668100_1 defaults
pandas 0.20.3 py36h842e28d_2 defaults
pandoc 1.19.2.1 hea2e7c5_1 defaults
pandocfilters 1.4.2 py36ha6701b7_1 defaults
pango 1.40.11 h8191d47_0 defaults
partd 0.3.8 py36h36fd896_0 defaults
patchelf 0.9 hf79760b_2 defaults
path.py 10.3.1 py36he0c6f6d_0 defaults
pathlib2 2.3.0 py36h49efa8e_0 defaults
patsy 0.4.1 py36ha3be15e_0 defaults
pcre 8.41 hc71a17e_0 defaults
pdfrw 0.4 py36heaf6461_0 BjornFJohansson
pep8 1.7.0 py36h26ade29_0 defaults
pexpect 4.2.1 py36h3b9d41b_0 defaults
pickleshare 0.7.4 py36h63277f8_0 defaults
pillow 4.2.1 py36h9119f52_0 defaults
pint 0.8.1 py36_0 conda-forge
pip 9.0.1 py36h8ec8b28_3 defaults
pixman 0.34.0 h83dc358_2 defaults
pkginfo 1.4.1 py36h215d178_1 defaults
pluggy 0.6.0 py36hb689045_0 defaults
ply 3.10 py36hed35086_0 defaults
prettytable 0.7.2 py36_1 conda-forge
prompt_toolkit 1.0.15 py36h17d85b1_0 defaults
psutil 5.4.0 py36h84c53db_0 defaults
ptyprocess 0.5.2 py36h69acd42_0 defaults
py 1.5.2 py36h29bf505_0 defaults
pycodestyle 2.3.1 py36hf609f19_0 defaults
pycosat 0.6.2 py36h1a0ea17_1 defaults
pycparser 2.18 py36hf9f622e_1 defaults
pycrypto 2.6.1 py36h6998063_1 defaults
pycurl 7.43.0 py36h5e72054_3 defaults
pyexcel-ezodf 0.3.4 py_0 conda-forge
pyfiglet 0.7.5 py36_0 conda-forge
pyflakes 1.6.0 py36h7bd6a15_0 defaults
pygments 2.2.0 py36h0d3125c_0 defaults
pylint 1.7.4 py36hb9d4533_0 defaults
pympler 0.5 py36h6b12e4d_0 defaults
pyodbc 4.0.17 py36h999153c_0 defaults
pyopenssl 17.2.0 py36h5cc804b_0 defaults
pyparsing 2.2.0 py36hee85983_1 defaults
pypdf2 1.26.0 py36_1 conda-forge
pyqt 5.6.0 py36h0386399_5 defaults
pysocks 1.6.7 py36hd97a5b1_1 defaults
pytables 3.4.2 py36h3b5282a_2 defaults
pytest 3.3.1 py36_0 conda-forge
pytest-cov 2.5.1 py36hd4733f3_0 defaults
pytest-mock 1.6.3 py36_1 conda-forge
pytest-runner 3.0 py36hd5415d6_0 defaults
python 3.6.3 hc9025b9_1 defaults
python-dateutil 2.6.1 py36h88d3b88_1 defaults
pytz 2017.2 py36hc2ccc2a_1 defaults
pywavelets 0.5.2 py36he602eb0_0 defaults
pyyaml 3.12 py36hafb9ca4_1 defaults
pyzmq 16.0.2 py36h3b0cf96_2 defaults
qt 5.6.2 h974d657_12 defaults
qtawesome 0.4.4 py36h609ed8c_0 defaults
qtconsole 4.3.1 py36h8f73b5b_0 defaults
qtpy 1.3.1 py36h3691cc8_0 defaults
readline 7.0 hac23ff0_3 defaults
reportlab 3.4.0 py36_0 defaults
requests 2.18.4 py36he2e5f8d_1 defaults
requests-mock 1.4.0 py36_0 BjornFJohansson
requests-toolbelt 0.8.0 py36_0 conda-forge
rope 0.10.5 py36h1f8c17e_0 defaults
ruamel_yaml 0.11.14 py36ha2fb22d_2 defaults
scikit-image 0.13.0 py36had3c07a_1 defaults
scikit-learn 0.19.1 py36h7aa7ec6_0 defaults
scipy 0.19.1 py36h9976243_3 defaults
seaborn 0.8.0 py36h197244f_0 defaults
setuptools 38.2.4 py36_0 conda-forge
simplegeneric 0.8.1 py36h2cb9092_0 defaults
singledispatch 3.4.0.3 py36h7a266c3_0 defaults
sip 4.18.1 py36h51ed4ed_2 defaults
six 1.11.0 py36h372c433_1 defaults
snowballstemmer 1.2.1 py36h6febd40_0 defaults
sortedcollections 0.5.3 py36h3c761f9_0 defaults
sortedcontainers 1.5.7 py36hdf89491_0 defaults
sphinx 1.6.3 py36he5f0bdb_0 defaults
sphinxcontrib 1.0 py36h6d0f590_1 defaults
sphinxcontrib-websupport 1.0.1 py36hb5cb234_1 defaults
spyder 3.2.6 py36_0 defaults
spyder-notebook 0.1.1 py36_0 spyder-ide
sqlalchemy 1.1.13 py36hfb5efd7_0 defaults
sqlite 3.20.1 h6d8b0f3_1 defaults
statsmodels 0.8.0 py36h8533d0b_0 defaults
sympy 1.1.1 py36hc6d1c1c_0 defaults
tblib 1.3.2 py36h34cf8b6_0 defaults
termcolor 1.1.0 py36_0 defaults
terminado 0.6 py36ha25a19f_0 defaults
testpath 0.3.1 py36h8cadb63_0 defaults
tk 8.6.7 h5979e9b_1 defaults
toolz 0.8.2 py36h81f2dff_0 defaults
tornado 4.5.2 py36h1283b2a_0 defaults
tqdm 4.19.4 py36ha5a5176_0 defaults
traitlets 4.3.2 py36h674d592_0 defaults
twine 1.9.1 py36_2 conda-forge
typing 3.6.2 py36h7da032a_0 defaults
unicodecsv 0.14.1 py36ha668878_0 defaults
unixodbc 2.3.4 hc36303a_1 defaults
urllib3 1.22 py36hbe7ace6_0 defaults
wcwidth 0.1.7 py36hdf4376a_0 defaults
webencodings 0.5.1 py36h800622e_1 defaults
werkzeug 0.12.2 py36hc703753_0 defaults
wheel 0.29.0 py36he7f4e38_1 defaults
widgetsnbextension 3.0.2 py36hd01bb71_1 defaults
wrapt 1.10.11 py36h28b7045_0 defaults
xlrd 1.1.0 py36h1db9f0c_1 defaults
xlsxwriter 1.0.2 py36h3de1aca_0 defaults
xlwt 1.3.0 py36h7b00a1f_0 defaults
xz 5.2.3 h2bcbf08_1 defaults
yaml 0.1.7 h96e3832_1 defaults
zeromq 4.2.2 hb0b69da_1 defaults
zict 0.1.3 py36h3a3bf81_0 defaults
zlib 1.2.11 hfbfcf68_1 defaults
zope 1.0 py36_0 defaults
zope.interface 4.4.3 py36h0ccbf34_0 defaults
(bjorn36) bjorn@bjorn-ThinkPad-T450s:~$
`

---

@ccordoba12 commented on Fri Jan 19 2018

Moving this one to the right repo.

[ccordoba12]

@BjornFJohansson, do you have write permissions on your /tmp directory?

[BjornFJohansson]

Yeas I think so:

`Python 3.6.3 |Anaconda custom (64-bit)| (default, Oct 13 2017, 12:02:49)
Type "copyright", "credits" or "license" for more information.

IPython 6.2.1 -- An enhanced Interactive Python.

Restarting kernel...

with open("/tmp/file_to_write", "w") as f:
f.write("mycontent")

with open("/tmp/file_to_write", "r") as f:
print(f.read())
mycontent

In [3]:`

[BjornFJohansson]

I managed to get it running:

[BjornFJohansson]

I did the following:

nbopen.py

    print("Starting new server")
    kernelspec = 'spyder.utils.ipython.kernelspec.SpyderKernelSpec'
    command = ['/home/bjorn/anaconda3/envs/bjorn36/bin/jupyter', 'notebook', '--no-browser',
               '--notebook-dir={}'.format(nbdir),
               '--NotebookApp.password=',
               "--KernelSpecManager.kernel_spec_class='{}'".format(
                       kernelspec)]

    if os.name == 'nt':
        creation_flag = 0x08000000  # CREATE_NO_WINDOW
    else:
        creation_flag = 0  # Default value

    if DEV:
        env = os.environ.copy()
        env["PYTHONPATH"] = osp.dirname(get_module_path('spyder'))
        proc = subprocess.Popen(command, creationflags=creation_flag,
                                env=env)
    else:
        proc = subprocess.Popen(command, creationflags=creation_flag)

I changed the first item in the commands list. This could perhaps be solved
if I used the shell=True flag in Popen.

I also have to have a server already running or else I get a time out.

[BjornFJohansson]

There are subtle differences between how Popen works on Win and Linux.

https://docs.python.org/3/library/subprocess.html#subprocess.Popen

[BjornFJohansson]

Meanwhile I updated to notebook 5.3.1 and the timeout does not happen, possibly since it starts much faster.