Spyder: Completion and linting in the editor for Python files will not work during current session, or stopped working.

[joseavegaa]

Issue Report Checklist

• [x] Searched the issues page for similar reports
• [x] Read the relevant sections of the Spyder Troubleshooting Guide and followed its advice
• [x] Reproduced the issue after updating with conda update spyder (or pip, if not using Anaconda)
• [ ] Could not reproduce inside jupyter qtconsole (if console-related)
• [x] Tried basic troubleshooting (if a bug/error)
  
  
  
  • [x] Restarted Spyder
  
  
  • [x] Reset preferences with spyder --reset
  
  
  • [x] Reinstalled the latest version of Anaconda
  
  
  • [x] Tried the other applicable steps from the Troubleshooting Guide
  
  
• [x] Completed the Problem Description, Steps to Reproduce and Version sections below

Problem Description

After a few seconds of opening Spyder, I get the message in the title of the issue. LSP Python is down. Linting and completion work for a few seconds when opening Spyder, then stopped and the pop up shows again. Same problem as the one describe on #11026. As requested there, I'm opening a new issue.

Steps taken that didn't help the issue

• Running conda update -all
• Reinstalled Anaconda.
• Running spyder --reset
• Unable to reproduce issue on Windows.

What steps reproduce the problem?

1. Open Spyder.
2. Wait a few seconds.
3. The pop-up shows again.

Versions

• Spyder version: 4.1.4
• Python version: 3.7.7
• Operating System name/version: macOS 10.15.6

Screenshots

[steff456]

Hi @joseavegaa,
Can you please create a new conda environment and run spyder from there? Maybe the conda update -all damaged something in your environment.

conda create -n test-env python=3.7
conda activate test-env
conda install spyder=4.1.4

Please let me know if that works

[algent-al]

I have this exact issue in Solus. Just updated to version 4.1.4. Using python version 3.7.7.

[mmfink]

Hello @steff456
I also have this issue on Windows 10 using spyder 4.1.4 and python 3.7.7

I followed your test-env suggestion and I can confirm that LSP Python works in spyder in the test-env. Of the common packages between the test-env and the environment where it doesn't work, these are the package version differences:

  | test-env | not working env
-- | -- | --
astroid | 2.4.2 | 2.3.3
lazy-object-proxy | 1.4.3 | 1.5.0
pylint | 2.5.3 | 2.4.4
wrapt | 1.11.2 | 1.12.1

I force installed pylint=2.5.3 in the not working env:

>conda install pylint=2.5.3

## Package Plan ##

  added / updated specs:
    - pylint=2.5.3

The following packages will be UPDATED:

  astroid                                      2.3.3-py37_0 --> 2.4.2-py37_0
  pylint                                       2.4.4-py37_0 --> 2.5.3-py37_0

The following packages will be DOWNGRADED:

  lazy-object-proxy                    1.5.0-py37he774522_0 --> 1.4.3-py37he774522_0
  wrapt                               1.12.1-py37he774522_1 --> 1.11.2-py37he774522_0

...which takes care of all the version discrepancies. Unfortunately, that didn't make any difference in the error when opening spyder.

Any further suggestions on how to troubleshoot this? While I can run spyder from the test-env, I'd rather run it from the other env where the other packages I need are.

[steff456]

@mmfink, can you please put in here the conda list result in the not working environment?

[mmfink]

@steff456 - its rather long:
Name | Version | Build Channel
-- | -- | --
_anaconda_depends | 2020.07 | py37_0
_ipyw_jlab_nb_ext_conf | 0.1.0 | py37_0
alabaster | 0.7.12 | py37_0
anaconda | custom | py37_1
anaconda-client | 1.7.2 | py37_0
anaconda-navigator | 1.9.12 | py37_0
anaconda-project | 0.8.4 | py_0
argh | 0.26.2 | py37_0
asn1crypto | 1.3.0 | py37_1
astroid | 2.4.2 | py37_0
astropy | 4.0.1.post1 | py37he774522_1
atomicwrites | 1.4.0 | py_0
attrs | 19.3.0 | py_0
autopep8 | 1.5.3 | py_0
babel | 2.8.0 | py_0
backcall | 0.2.0 | py_0
backports | 1 | py_2
backports.functools_lru_cache | 1.6.1 | py_0
backports.shutil_get_terminal_size | 1.0.0 | py37_2
backports.tempfile | 1 | py_1
backports.weakref | 1.0.post1 | py_1
bcrypt | 3.1.7 | py37he774522_1
beautifulsoup4 | 4.9.1 | py37_0
bitarray | 1.4.2 | py37he774522_0
bkcharts | 0.2 | py37_0
blas | 1 | mkl
bleach | 3.1.5 | py_0
blosc | 1.19.0 | h7bd577a_0
bokeh | 2.1.1 | py37_0
boto | 2.49.0 | py37_0
bottleneck | 1.3.2 | py37h2a96729_1
brotlipy | 0.7.0 | py37he774522_1000
bzip2 | 1.0.8 | he774522_0
ca-certificates | 2020.6.24 | 0
certifi | 2020.6.20 | py37_0
cffi | 1.14.0 | py37h7a1dbc1_0
cftime | 1.2.1 | py37h2a96729_0
chardet | 3.0.4 | py37_1003
click | 7.1.2 | py_0
cloudpickle | 1.5.0 | py_0
clyent | 1.2.2 | py37_1
colorama | 0.4.3 | py_0
comtypes | 1.1.7 | py37_1001
conda | 4.8.3 | py37_0
conda-build | 3.18.11 | py37_0
conda-env | 2.6.0 | 1
conda-package-handling | 1.6.1 | py37h62dcd97_0
conda-verify | 3.4.2 | py_1
console_shortcut | 0.1.1 | 4
contextlib2 | 0.6.0.post1 | py_0
cryptography | 2.9.2 | py37h7a1dbc1_0
curl | 7.67.0 | h2a8f88b_0
cycler | 0.10.0 | py37_0
cython | 0.29.21 | py37ha925a31_0
cytoolz | 0.10.1 | py37he774522_0
dask | 2.20.0 | py_0
dask-core | 2.20.0 | py_0
decorator | 4.4.2 | py_0
defusedxml | 0.6.0 | py_0
diff-match-patch | 20200713 | py_0
distributed | 2.20.0 | py37_0
docutils | 0.16 | py37_1
entrypoints | 0.3 | py37_0
et_xmlfile | 1.0.1 | py_1001
expat | 2.2.9 | h33f27b4_2
fastcache | 1.1.0 | py37he774522_0
filelock | 3.0.12 | py_0
flake8 | 3.8.3 | py_0
flask | 1.1.2 | py_0
freetype | 2.10.2 | hd328e21_0
freexl | 1.0.5 | hfa6e2cd_0
fsspec | 0.7.4 | py_0
future | 0.18.2 | py37_1
gdal | 2.3.3 | py37hdf43c64_0
geos | 3.7.1 | h33f27b4_0
get_terminal_size | 1.0.0 | h38e98db_0
gevent | 20.6.2 | py37he774522_0
glob2 | 0.7 | py_0
gmpy2 | 2.0.8 | py37h0964b28_3
greenlet | 0.4.16 | py37he774522_0
h5py | 2.10.0 | py37h5e291fa_0
hdf4 | 4.2.13 | h712560f_2
hdf5 | 1.10.4 | h7ebc959_0
heapdict | 1.0.1 | py_0
html5lib | 1.1 | py_0
icc_rt | 2019.0.0 | h0cc432a_1
icu | 58.2 | ha925a31_3
idna | 2.1 | py_0
imageio | 2.9.0 | py_0
imagesize | 1.2.0 | py_0
importlib-metadata | 1.7.0 | py37_0
importlib_metadata | 1.7.0 | 0
intel-openmp | 2020.1 | 216
intervaltree | 3.0.2 | py_1
ipykernel | 5.3.4 | py37h5ca1d4c_0
ipython | 7.16.1 | py37h5ca1d4c_0
ipython_genutils | 0.2.0 | py37_0
ipywidgets | 7.5.1 | py_0
isort | 4.3.21 | py37_0
itsdangerous | 1.1.0 | py37_0
jdcal | 1.4.1 | py_0
jedi | 0.17.1 | py37_0
jinja2 | 2.11.2 | py_0
joblib | 0.16.0 | py_0
jpeg | 9b | hb83a4c4_2
json5 | 0.9.5 | py_0
jsonschema | 3.2.0 | py37_1
jupyter | 1.0.0 | py37_7
jupyter_client | 6.1.6 | py_0
jupyter_console | 6.1.0 | py_0
jupyter_core | 4.6.3 | py37_0
jupyterlab | 2.1.5 | py_0
jupyterlab_server | 1.2.0 | py_0
kealib | 1.4.12 | h07cbb95_0
keyring | 21.2.1 | py37_0
kiwisolver | 1.2.0 | py37h74a9793_0
krb5 | 1.16.4 | hc04afaa_0
lazy-object-proxy | 1.4.3 | py37he774522_0
libarchive | 3.4.2 | h5e25573_0
libboost | 1.67.0 | hd9e427e_4
libcurl | 7.67.0 | h2a8f88b_0
libgdal | 2.3.3 | h10f50ba_0
libiconv | 1.15 | h1df5818_7
libkml | 1.3.0 | he5f2a48_4
liblief | 0.10.1 | ha925a31_0
libllvm9 | 9.0.1 | h21ff451_0
libnetcdf | 4.6.1 | h411e497_2
libpng | 1.6.37 | h2a8f88b_0
libpq | 11.2 | h3235a2c_0
libsodium | 1.0.18 | h62dcd97_0
libspatialindex | 1.9.3 | h33f27b4_0
libspatialite | 4.3.0a | hc36aec2_19
libssh2 | 1.9.0 | h7a1dbc1_1
libtiff | 4.1.0 | h56a325e_1
libxml2 | 2.9.10 | h464c3ec_1
libxslt | 1.1.34 | he774522_0
llvmlite | 0.33.0 | py37ha925a31_0
locket | 0.2.0 | py37_1
lxml | 4.5.2 | py37h1350720_0
lz4-c | 1.9.2 | h62dcd97_1
lzo | 2.1 | he774522_2
m2w64-gcc-libgfortran | 5.3.0 | 6
m2w64-gcc-libs | 5.3.0 | 7
m2w64-gcc-libs-core | 5.3.0 | 7
m2w64-gmp | 6.1.0 | 2
m2w64-libwinpthread-git | 5.0.0.4634.697f757 | 2
markupsafe | 1.1.1 | py37hfa6e2cd_1
matplotlib | 3.2.2 | 0
matplotlib-base | 3.2.2 | py37h64f37c6_0
mccabe | 0.6.1 | py37_1
menuinst | 1.4.16 | py37he774522_1
mistune | 0.8.4 | py37hfa6e2cd_1001
mkl | 2020.1 | 216
mkl-service | 2.3.0 | py37hb782905_0
mkl_fft | 1.1.0 | py37h45dec08_0
mkl_random | 1.1.1 | py37h47e9c7a_0
mock | 4.0.2 | py_0
more-itertools | 8.4.0 | py_0
mpc | 1.1.0 | h7edee0f_1
mpfr | 4.0.2 | h62dcd97_1
mpir | 3.0.0 | hec2e145_1
mpmath | 1.1.0 | py37_0
msgpack-python | 1.0.0 | py37h74a9793_1
msys2-conda-epoch | 20160418 | 1
multipledispatch | 0.6.0 | py37_0
navigator-updater | 0.2.1 | py37_0
nbconvert | 5.6.1 | py37_1
nbformat | 5.0.7 | py_0
netcdf4 | 1.4.2 | py37h812ae01_0
networkx | 2.4 | py_1
nltk | 3.5 | py_0
nose | 1.3.7 | py37_1004
notebook | 6.0.3 | py37_0
numba | 0.50.1 | py37h47e9c7a_0
numexpr | 2.7.1 | py37h25d0782_0
numpy | 1.19.1 | py37h5510c5b_0
numpy-base | 1.19.1 | py37ha3acd2a_0
numpydoc | 1.1.0 | py_0
olefile | 0.46 | py37_0
openpyxl | 3.0.4 | py_0
openssl | 1.1.1g | he774522_0
packaging | 20.4 | py_0
pandas | 1.0.5 | py37h47e9c7a_0
pandoc | 2.1 | 0
pandocfilters | 1.4.2 | py37_1
paramiko | 2.7.1 | py_0
parso | 0.7.0 | py_0
partd | 1.1.0 | py_0
path | 14.0.1 | py37_0
path.py | 12.0.2 | py_0
pathlib2 | 2.3.5 | py37_1
pathtools | 0.1.2 | py_1
patsy | 0.5.1 | py37_0
pcre | 8.44 | ha925a31_0
pep8 | 1.7.1 | py37_0
pexpect | 4.8.0 | py37_1
pickleshare | 0.7.5 | py37_1001
pillow | 7.2.0 | py37hcc1f983_0
pip | 20.1.1 | py37_1
pkginfo | 1.5.0.1 | py37_0
pluggy | 0.13.1 | py37_0
ply | 3.11 | py37_0
powershell_shortcut | 0.0.1 | 3
proj4 | 5.2.0 | ha925a31_1
prometheus_client | 0.8.0 | py_0
prompt-toolkit | 3.0.5 | py_0
prompt_toolkit | 3.0.5 | 0
psutil | 5.7.0 | py37he774522_0
py | 1.9.0 | py_0
py-lief | 0.10.1 | py37ha925a31_0
pycodestyle | 2.6.0 | py_0
pycosat | 0.6.3 | py37he774522_0
pycparser | 2.2 | py_2
pycrypto | 2.6.1 | py37he774522_10
pycurl | 7.43.0.5 | py37h7a1dbc1_0
pydocstyle | 5.0.2 | py_0
pyflakes | 2.2.0 | py_0
pygments | 2.6.1 | py_0
pylint | 2.5.3 | py37_0
pynacl | 1.4.0 | py37h62dcd97_1
pyodbc | 4.0.30 | py37ha925a31_0
pyopenssl | 19.1.0 | py_1
pyparsing | 2.4.7 | py_0
pyqt | 5.9.2 | py37h6538335_2
pyreadline | 2.1 | py37_1
pyrsistent | 0.16.0 | py37he774522_0
pysocks | 1.7.1 | py37_1
pytables | 3.6.1 | py37h1da0976_0
pytest | 5.4.3 | py37_0
python | 3.7.7 | h81c818b_4
python-dateutil | 2.8.1 | py_0
python-jsonrpc-server | 0.3.4 | py_1
python-language-server | 0.34.1 | py37_0
python-libarchive-c | 2.9 | py_0
pytz | 2020.1 | py_0
pywavelets | 1.1.1 | py37he774522_0
pywin32 | 227 | py37he774522_1
pywin32-ctypes | 0.2.0 | py37_1001
pywinpty | 0.5.7 | py37_0
pyyaml | 5.3.1 | py37he774522_1
pyzmq | 19.0.1 | py37ha925a31_1
qdarkstyle | 2.8.1 | py_0
qt | 5.9.7 | vc14h73c81de_0
qtawesome | 0.7.2 | py_0
qtconsole | 4.7.5 | py_0
qtpy | 1.9.0 | py_0
regex | 2020.6.8 | py37he774522_0
requests | 2.24.0 | py_0
rope | 0.17.0 | py_0
rtree | 0.9.4 | py37h21ff451_1
ruamel_yaml | 0.15.87 | py37he774522_1
scikit-image | 0.16.2 | py37h47e9c7a_0
scikit-learn | 0.23.1 | py37h25d0782_0
scipy | 1.5.0 | py37h9439919_0
seaborn | 0.10.1 | py_0
send2trash | 1.5.0 | py37_0
setuptools | 49.2.0 | py37_0
simplegeneric | 0.8.1 | py37_2
singledispatch | 3.4.0.3 | py37_0
sip | 4.19.8 | py37h6538335_0
six | 1.15.0 | py_0
snappy | 1.1.8 | h33f27b4_0
snowballstemmer | 2.0.0 | py_0
sortedcollections | 1.2.1 | py_0
sortedcontainers | 2.2.2 | py_0
soupsieve | 2.0.1 | py_0
sphinx | 3.1.2 | py_0
sphinxcontrib | 1 | py37_1
sphinxcontrib-applehelp | 1.0.2 | py_0
sphinxcontrib-devhelp | 1.0.2 | py_0
sphinxcontrib-htmlhelp | 1.0.3 | py_0
sphinxcontrib-jsmath | 1.0.1 | py_0
sphinxcontrib-qthelp | 1.0.3 | py_0
sphinxcontrib-serializinghtml | 1.1.4 | py_0
sphinxcontrib-websupport | 1.2.3 | py_0
spyder | 4.1.4 | py37_0
spyder-kernels | 1.9.2 | py37_0
sqlalchemy | 1.3.18 | py37he774522_0
sqlite | 3.32.3 | h2a8f88b_0
statsmodels | 0.11.1 | py37he774522_0
sympy | 1.6.1 | py37_0
tbb | 2020 | h74a9793_0
tblib | 1.6.0 | py_0
terminado | 0.8.3 | py37_0
testpath | 0.4.4 | py_0
threadpoolctl | 2.1.0 | pyh5ca1d4c_0
tk | 8.6.10 | he774522_0
toml | 0.10.1 | py_0
toolz | 0.10.0 | py_0
tornado | 6.0.4 | py37he774522_1
tqdm | 4.47.0 | py_0
traitlets | 4.3.3 | py37_0
typed-ast | 1.4.1 | py37he774522_0
typing_extensions | 3.7.4.2 | py_0
ujson | 1.35 | py37hfa6e2cd_0
unicodecsv | 0.14.1 | py37_0
urllib3 | 1.25.9 | py_0
vc | 14.1 | h0510ff6_4
vs2015_runtime | 14.16.27012 | hf0eaf9b_3
watchdog | 0.10.3 | py37_0
wcwidth | 0.2.5 | py_0
webencodings | 0.5.1 | py37_1
werkzeug | 1.0.1 | py_0
wheel | 0.34.2 | py37_0
widgetsnbextension | 3.5.1 | py37_0
win_inet_pton | 1.1.0 | py37_0
win_unicode_console | 0.5 | py37_0
wincertstore | 0.2 | py37_0
winpty | 0.4.3 | 4
wrapt | 1.11.2 | py37he774522_0
xerces-c | 3.2.2 | ha925a31_0
xlrd | 1.2.0 | py37_0
xlsxwriter | 1.2.9 | py_0
xlwings | 0.19.5 | py37_0
xlwt | 1.3.0 | py37_0
xmltodict | 0.12.0 | py_0
xz | 5.2.5 | h62dcd97_0
yaml | 0.2.5 | he774522_0
yapf | 0.30.0 | py_0
zeromq | 4.3.2 | ha925a31_2
zict | 2.0.0 | py_0
zipp | 3.1.0 | py_0
zlib | 1.2.11 | h62dcd97_4
zope | 1 | py37_1
zope.event | 4.4 | py37_0
zope.interface | 4.7.1 | py37he774522_0
zstd | 1.4.5 | h04227a9_0

[steff456]

Hi @mmfink, can you do me another favor? Please start spyder in debug mode with spyder --debug-info verbose and in the main menu go to Tools>LSP and upload the logs under that option here

[mmfink]

Here you go, @steff456
This is the text of the server_python.log file. The file clears all contents as soon as the error dialog asking if you want to restart appears, so I would only be uploading empty files to you. At least I get a few seconds to copy/paste the contents. :-)

Nothing appears in the transport_python.log

Traceback (most recent call last):
  File "C:\Python3\anaconda3\lib\runpy.py", line 193, in _run_module_as_main
    "__main__", mod_spec)
  File "C:\Python3\anaconda3\lib\runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "C:\Python3\anaconda3\lib\site-packages\pyls\__main__.py", line 12, in <module>
    from .python_ls import (PythonLanguageServer, start_io_lang_server,
  File "C:\Python3\anaconda3\lib\site-packages\pyls\python_ls.py", line 12, in <module>
    from . import lsp, _utils, uris
  File "C:\Python3\anaconda3\lib\site-packages\pyls\_utils.py", line 9, in <module>
    import jedi
  File "C:\Python3\anaconda3\lib\site-packages\jedi\__init__.py", line 32, in <module>
    from jedi.api import Script, Interpreter, set_debug_function, \
  File "C:\Python3\anaconda3\lib\site-packages\jedi\api\__init__.py", line 24, in <module>
    from jedi.api import classes
  File "C:\Python3\anaconda3\lib\site-packages\jedi\api\classes.py", line 24, in <module>
    from jedi.inference.utils import unite
  File "C:\Python3\anaconda3\lib\site-packages\jedi\inference\__init__.py", line 70, in <module>
    from jedi.inference import imports
  File "C:\Python3\anaconda3\lib\site-packages\jedi\inference\imports.py", line 24, in <module>
    from jedi.inference import sys_path
  File "C:\Python3\anaconda3\lib\site-packages\jedi\inference\sys_path.py", line 8, in <module>
    from jedi.common import traverse_parents
ImportError: bad magic number in 'jedi.common': b'\x03\xf3\r\n'

Also, these lines appear every second or so in the Anaconda console:

2020-08-06 11:46:52,738 [DEBUG] [spyder.plugins.completion.languageserver.client] -> LSP server for python is down!!
2020-08-06 11:46:52,738 [DEBUG] [spyder.plugins.completion.languageserver.client] -> Transport layer for python is down!!

[steff456]

It seems that there's a problem in the environment, so to fix it please go to User\Anaconda\envs\not-working-env\Lib\site-packages inside that folder please run in cmd DEL /Q /F /S "*.pyc"
After that the LSP should be working fine, please let me know if this fixes the issue

[mmfink]

Yes! Working now. Thanks so much!

[steff456]

@algent-al as you are working in Linux please go to the site-packages ~/anaconda3/envs/not-working-env/lib/python3.7/site-packages and inside the folder run find . -name \*.pyc -delete
That will also fix your environment :)

[algent-al]

Hi @steff456 I have updated spyder using Solus build tools and not by using environments and i have installed it system wide. I don't have anaconda folder. Just need to mention that I am not a spyder3 user, just trying this for curiosity.

[steff456]

@algent-al we recommend using anaconda for Spyder, if you are new to python I will highly recommend to you to start using conda as manager even if you are only using it for curiosity :)

[joseavegaa]

Hello @steff456.

I have run the command find ~/anaconda3/envs/not-working-env/lib/python3.7/site-packages -name "*.pyc" -delete, restarted Spyder, and still getting the error.

Following that, I have started Spyder with spyder --debug-info verbose and got the same output as @mmfink from server_python.log, but the last line is this one instead:

ImportError: cannot import name 'traverse_parents' from 'jedi.common' (/opt/anaconda3/lib/python3.7/site-packages/jedi/common/__init__.py)

Seems that the issue is with Python directly, as I tried import jedi from the Python Interpreter, and it failed with the same message. I'm trying to reinstall Anaconda (Python with it) completely and see if it works.

[steff456]

Hi @joseavegaa,
That sounds like a nice idea, please let me know if reinstalling Anaconda your problem is fixed

[joseavegaa]

@steff456 seems that the problem was resolved by a clean installation. Thanks.

[ccordoba12]

Closing this one because all people involved were able to solve their problems.

[algent-al]

@steff456 Solved this issue for Solus, with this spyder installed system wide.
I had some missing dependencies like:

• python-language-server
• python-jsonrpc-server
• python-ujson

spyder didn't report in "Help > Dependecies" that pyls (python-language-server) was missing.

[steff456]

@algent-al thanks for the follow-up response, we will be adding these dependencies into the report dialog in a future release so it will be easier for us to see installation problems related to the PyLS. I'm glad that you could solve your Spyder :)