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Variable explorer not working due to incompatibility between Numpy 2 and 1 #22842

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9 of 10 tasks
ingo-m opened this issue Nov 4, 2024 · 5 comments
Open
9 of 10 tasks

Variable explorer not working due to incompatibility between Numpy 2 and 1 #22842

ingo-m opened this issue Nov 4, 2024 · 5 comments
Labels
component:Variable Explorer type:Bug
Milestone
v6.1.0

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@ingo-m
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ingo-m commented Nov 4, 2024 •
edited
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Issue Report Checklist

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

Problem Description

For years, I always installed spyder directly into conda envs, no problem. However, since I switched to Ubuntu 24 (with wayland) that does not work anymore (see #22219).

So instead, I installed the spyder deb package (currently spyder 5.5.1):

sudo apt-get install spyder

I also installed numpy & pandas in the system python env (not sure whether this was necessary):

sudo apt-get install python3-numpy python3-pandas python3-ipython

But now I cannot inspect objects (such as numpy arrays and pandas dataframes) from the variable explorer anymore ("Spyder was unable to retrieve the value of this variable from the console.").

More specifically, I can inspect numpy arrays and dataframes from the variable explorer when using spyder's default python interpreter (presumably system python), but not when using a conda env.

Now that's not ideal, because obviously for interactive python development I need to use my project's conda env with all relevant packages, not system python.

I'm aware of #22784 and that there might be a mismatch between system python and the conda env, but the question is how to solve this?

Is there any way to get the variable explorer to work after installing spyder as a deb package (which, again, is the only way to get spyder to work under Ubuntu 24 & wayland AFAIK)?

Versions

This is from the "About Spyder" menu (referring to system python):

  • Spyder version: 5.5.1 (pip)
  • Python version: 3.12.3 64-bit
  • Qt version: 5.15.13
  • PyQt5 version: 5.15.10
  • Operating System: Linux-6.8.0-48-generic-x86_64-with-glibc2.39

Ubuntu 24.04.1 LTS

My conda env is using python 3.12.7

Conda env packages (spyder python interpreter is configured to use this env) 
# Name                	Version               	Build  Channel
_libgcc_mutex         	0.1             	conda_forge	conda-forge
_openmp_mutex         	4.5                   	2_gnu	conda-forge
aiohappyeyeballs      	2.4.3                	pypi_0	pypi
aiohttp               	3.10.10              	pypi_0	pypi
aiosignal             	1.3.1                	pypi_0	pypi
altair                	5.4.1                	pypi_0	pypi
anyio                 	4.6.2.post1          	pypi_0	pypi
asttokens             	2.4.1                	pypi_0	pypi
asyncpg               	0.30.0               	pypi_0	pypi
attrs                 	24.2.0               	pypi_0	pypi
authlib               	1.3.2                	pypi_0	pypi
blinker               	1.8.2                	pypi_0	pypi
blosc2                	2.7.1                	pypi_0	pypi
boto3                 	1.35.54              	pypi_0	pypi
botocore              	1.35.54              	pypi_0	pypi
bzip2                 	1.0.8            	h4bc722e_7	conda-forge
ca-certificates       	2024.8.30        	hbcca054_0	conda-forge
cachetools            	5.5.0                	pypi_0	pypi
certifi               	2024.8.30      	pyhd8ed1ab_0	conda-forge
cffi                  	1.17.1               	pypi_0	pypi
charset-normalizer    	3.4.0                	pypi_0	pypi
click                 	8.1.7                	pypi_0	pypi
cloudpickle           	3.1.0                	pypi_0	pypi
comm                  	0.2.2                	pypi_0	pypi
contourpy             	1.3.0                	pypi_0	pypi
cryptography          	43.0.3               	pypi_0	pypi
cycler                	0.12.1               	pypi_0	pypi
debugpy               	1.8.7                	pypi_0	pypi
decorator             	5.1.1                	pypi_0	pypi
diffusers             	0.31.0               	pypi_0	pypi
distlib               	0.3.9          	pyhd8ed1ab_0	conda-forge
distro                	1.9.0                	pypi_0	pypi
dnspython             	2.7.0                	pypi_0	pypi
executing             	2.1.0                	pypi_0	pypi
fastapi               	0.115.4              	pypi_0	pypi
filelock              	3.16.1         	pyhd8ed1ab_0	conda-forge
flatbuffers           	24.3.25              	pypi_0	pypi
fonttools             	4.54.1               	pypi_0	pypi
frozenlist            	1.5.0                	pypi_0	pypi
fsspec                	2024.10.0            	pypi_0	pypi
geoip2                	4.8.0                	pypi_0	pypi
gitdb                 	4.0.11               	pypi_0	pypi
gitpython             	3.1.43               	pypi_0	pypi
google-api-core       	2.22.0               	pypi_0	pypi
google-api-python-client  2.151.0              	pypi_0	pypi
google-auth           	2.35.0               	pypi_0	pypi
google-auth-httplib2  	0.2.0                	pypi_0	pypi
google-search-results 	2.4.2                	pypi_0	pypi
googleapis-common-protos  1.65.0               	pypi_0	pypi
greenlet              	3.1.1                	pypi_0	pypi
h11                   	0.14.0               	pypi_0	pypi
html2image            	2.0.5                	pypi_0	pypi
httpcore              	1.0.6                	pypi_0	pypi
httplib2              	0.22.0               	pypi_0	pypi
httpx                 	0.27.2               	pypi_0	pypi
huggingface-hub       	0.26.2               	pypi_0	pypi
idna                  	3.10                 	pypi_0	pypi
imageio               	2.36.0               	pypi_0	pypi
importlib-metadata    	8.5.0                	pypi_0	pypi
ipykernel             	6.29.5               	pypi_0	pypi
ipython               	8.29.0               	pypi_0	pypi
jedi                  	0.19.1               	pypi_0	pypi
jinja2                	3.1.4                	pypi_0	pypi
jiter                 	0.7.0                	pypi_0	pypi
jmespath              	1.0.1                	pypi_0	pypi
joblib                	1.4.2                	pypi_0	pypi
jsonschema            	4.23.0               	pypi_0	pypi
jsonschema-specifications 2024.10.1            	pypi_0	pypi
jupyter-client        	8.6.3                	pypi_0	pypi
jupyter-core          	5.7.2                	pypi_0	pypi
kiwisolver            	1.4.7                	pypi_0	pypi
ld_impl_linux-64      	2.43             	h712a8e2_2	conda-forge
libexpat              	2.6.3            	h5888daf_0	conda-forge
libffi                	3.4.2            	h7f98852_5	conda-forge
libgcc                	14.2.0           	h77fa898_1	conda-forge
libgcc-ng             	14.2.0           	h69a702a_1	conda-forge
libgomp               	14.2.0           	h77fa898_1	conda-forge
libnsl                	2.0.1            	hd590300_0	conda-forge
libsqlite             	3.47.0           	hadc24fc_1	conda-forge
libuuid               	2.38.1           	h0b41bf4_0	conda-forge
libxcrypt             	4.4.36           	hd590300_1	conda-forge
libzlib               	1.3.1            	hb9d3cd8_2	conda-forge
mangum                	0.19.0               	pypi_0	pypi
markdown-it-py        	3.0.0                	pypi_0	pypi
markupsafe            	3.0.2                	pypi_0	pypi
matplotlib            	3.9.2                	pypi_0	pypi
matplotlib-inline     	0.1.7                	pypi_0	pypi
maxminddb             	2.6.2                	pypi_0	pypi
mdurl                 	0.1.2                	pypi_0	pypi
mpmath                	1.3.0                	pypi_0	pypi
msgpack               	1.1.0                	pypi_0	pypi
multidict             	6.1.0                	pypi_0	pypi
narwhals              	1.13.1               	pypi_0	pypi
ncurses               	6.5              	he02047a_1	conda-forge
ndindex               	1.9.2                	pypi_0	pypi
nest-asyncio          	1.6.0                	pypi_0	pypi
networkx              	3.4.2                	pypi_0	pypi
numexpr               	2.10.1               	pypi_0	pypi
numpy                 	2.1.3                	pypi_0	pypi
nvidia-cublas-cu12    	12.4.5.8             	pypi_0	pypi
nvidia-cuda-cupti-cu12	12.4.127             	pypi_0	pypi
nvidia-cuda-nvrtc-cu12	12.4.127             	pypi_0	pypi
nvidia-cuda-runtime-cu12  12.4.127             	pypi_0	pypi
nvidia-cudnn-cu12     	9.1.0.70             	pypi_0	pypi
nvidia-cufft-cu12     	11.2.1.3             	pypi_0	pypi
nvidia-curand-cu12    	10.3.5.147           	pypi_0	pypi
nvidia-cusolver-cu12  	11.6.1.9             	pypi_0	pypi
nvidia-cusparse-cu12  	12.3.1.170           	pypi_0	pypi
nvidia-nccl-cu12      	2.21.5               	pypi_0	pypi
nvidia-nvjitlink-cu12 	12.4.127             	pypi_0	pypi
nvidia-nvtx-cu12      	12.4.127             	pypi_0	pypi
ollama                	0.3.3                	pypi_0	pypi
openai                	1.53.0               	pypi_0	pypi
openssl               	3.3.2            	hb9d3cd8_0	conda-forge
packaging             	24.1           	pyhd8ed1ab_0	conda-forge
pandas                	2.2.3                	pypi_0	pypi
parso                 	0.8.4                	pypi_0	pypi
pexpect               	4.9.0                	pypi_0	pypi
pillow                	10.4.0               	pypi_0	pypi
pip                   	24.3.1         	pyh8b19718_0	conda-forge
pipenv                	2024.3.1       	pyhd8ed1ab_0	conda-forge
platformdirs          	4.3.6          	pyhd8ed1ab_0	conda-forge
plotly                	5.24.1               	pypi_0	pypi
prompt-toolkit        	3.0.48               	pypi_0	pypi
propcache             	0.2.0                	pypi_0	pypi
proto-plus            	1.25.0               	pypi_0	pypi
protobuf              	5.28.3               	pypi_0	pypi
psutil                	6.1.0                	pypi_0	pypi
psycopg2-binary       	2.9.10               	pypi_0	pypi
ptyprocess            	0.7.0                	pypi_0	pypi
pure-eval             	0.2.3                	pypi_0	pypi
py-cpuinfo            	9.0.0                	pypi_0	pypi
pyarrow               	18.0.0               	pypi_0	pypi
pyasn1                	0.6.1                	pypi_0	pypi
pyasn1-modules        	0.4.1                	pypi_0	pypi
pycparser             	2.22                 	pypi_0	pypi
pydantic              	1.10.18              	pypi_0	pypi
pydeck                	0.9.1                	pypi_0	pypi
pygments              	2.18.0               	pypi_0	pypi
pygtail               	0.14.0               	pypi_0	pypi
pymongo               	4.10.1               	pypi_0	pypi
pyparsing             	3.2.0                	pypi_0	pypi
python                	3.12.7      	hc5c86c4_0_cpython	conda-forge
python-dateutil       	2.9.0.post0          	pypi_0	pypi
python-dotenv         	1.0.1                	pypi_0	pypi
pytz                  	2024.2               	pypi_0	pypi
pyyaml                	6.0.2                	pypi_0	pypi
pyzmq                 	26.2.0               	pypi_0	pypi
readline              	8.2              	h8228510_1	conda-forge
redis                 	5.2.0                	pypi_0	pypi
referencing           	0.35.1               	pypi_0	pypi
regex                 	2024.9.11            	pypi_0	pypi
requests              	2.32.3               	pypi_0	pypi
requests-file         	2.1.0                	pypi_0	pypi
rich                  	13.9.4               	pypi_0	pypi
rpds-py               	0.20.1               	pypi_0	pypi
rq                    	2.0.0                	pypi_0	pypi
rsa                   	4.9                  	pypi_0	pypi
ruff                  	0.7.2                	pypi_0	pypi
s3transfer            	0.10.3               	pypi_0	pypi
safetensors           	0.4.5                	pypi_0	pypi
scikit-learn          	1.5.2                	pypi_0	pypi
scipy                 	1.14.1               	pypi_0	pypi
seaborn               	0.13.2               	pypi_0	pypi
sentence-transformers 	3.2.1                	pypi_0	pypi
setuptools            	75.3.0         	pyhd8ed1ab_0	conda-forge
six                   	1.16.0               	pypi_0	pypi
smmap                 	5.0.1                	pypi_0	pypi
sniffio               	1.3.1                	pypi_0	pypi
spyder-kernels        	2.5.0                	pypi_0	pypi
sqlalchemy            	2.0.36               	pypi_0	pypi
stack-data            	0.6.3                	pypi_0	pypi
starlette             	0.41.2               	pypi_0	pypi
streamlit             	1.39.0               	pypi_0	pypi
stripe                	11.2.0               	pypi_0	pypi
sympy                 	1.13.1               	pypi_0	pypi
tables                	3.10.1               	pypi_0	pypi
tenacity              	9.0.0                	pypi_0	pypi
threadpoolctl         	3.5.0                	pypi_0	pypi
tiktoken              	0.8.0                	pypi_0	pypi
tilemapbase           	0.4.7                	pypi_0	pypi
tk                    	8.6.13      	noxft_h4845f30_101	conda-forge
tldextract            	5.1.2                	pypi_0	pypi
tokenizers            	0.20.1               	pypi_0	pypi
toml                  	0.10.2               	pypi_0	pypi
torch                 	2.5.1                	pypi_0	pypi
tornado               	6.4.1                	pypi_0	pypi
tqdm                  	4.66.6               	pypi_0	pypi
traitlets             	5.14.3               	pypi_0	pypi
transformers          	4.46.1               	pypi_0	pypi
triton                	3.1.0                	pypi_0	pypi
typing-extensions     	4.12.2               	pypi_0	pypi
tzdata                	2024.2               	pypi_0	pypi
tzlocal               	5.2                  	pypi_0	pypi
uritemplate           	4.1.1                	pypi_0	pypi
urllib3               	2.2.3                	pypi_0	pypi
uvicorn               	0.32.0               	pypi_0	pypi
virtualenv            	20.27.1        	pyhd8ed1ab_0	conda-forge
watchdog              	5.0.3                	pypi_0	pypi
wcwidth               	0.2.13               	pypi_0	pypi
webdriver-manager     	4.0.2                	pypi_0	pypi
websocket-client      	1.8.0                	pypi_0	pypi
wheel                 	0.44.0         	pyhd8ed1ab_0	conda-forge
wurlitzer             	3.1.1                	pypi_0	pypi
xz                    	5.2.6            	h166bdaf_0	conda-forge
yarl                  	1.17.1               	pypi_0	pypi
zipp                  	3.20.2               	pypi_0	pypi

Dependencies

Spyder dependencies 
# Mandatory:
atomicwrites >=1.2.0             :  1.4.1 (OK)
chardet >=2.0.0                  :  5.2.0 (OK)
cloudpickle >=0.5.0              :  3.0.0 (OK)
cookiecutter >=1.6.0             :  2.6.0 (OK)
diff_match_patch >=20181111      :  20230430 (OK)
intervaltree >=3.0.2             :  3.0.2 (OK)
IPython >=8.13.0,<9.0.0,!=8.17.1 :  8.20.0 (OK)
jedi >=0.17.2,<0.20.0            :  0.19.1 (OK)
jellyfish >=0.7                  :  0.10.0 (OK)
jsonschema >=3.2.0               :  4.10.3 (OK)
keyring >=17.0.0                 :  24.3.1 (OK)
nbconvert >=4.0                  :  6.5.3 (OK)
numpydoc >=0.6.0                 :  1.6.0 (OK)
parso >=0.7.0,<0.9.0             :  0.8.3 (OK)
pexpect >=4.4.0                  :  4.9.0 (OK)
pickleshare >=0.4                :  0.7.5 (OK)
psutil >=5.3                     :  5.9.8 (OK)
pygments >=2.0                   :  2.17.2 (OK)
pylint >=2.5.0,<3.1              :  3.0.3 (OK)
pylint_venv >=3.0.2              :  3.0.2 (OK)
pyls_spyder >=0.4.0              :  0.4.0 (OK)
pylsp >=1.10.0,<1.11.0           :  1.10.0 (OK)
pylsp_black >=2.0.0,<3.0.0       :  2.0.0 (OK)
qdarkstyle >=3.2.0,<3.3.0        :  3.2.3 (OK)
qstylizer >=0.2.2                :  0.2.2 (OK)
qtawesome >=1.2.1                :  1.2.3 (OK)
qtconsole >=5.5.1,<5.6.0         :  5.5.1 (OK)
qtpy >=2.1.0                     :  2.4.1 (OK)
rtree >=0.9.7                    :  1.2.0 (OK)
setuptools >=49.6.0              :  68.1.2 (OK)
sphinx >=0.6.6                   :  7.2.6 (OK)
spyder_kernels >=2.5.0,<2.6.0    :  2.5.0 (OK)
textdistance >=4.2.0             :  4.6.0 (OK)
three_merge >=0.1.1              :  0.1.1 (OK)
watchdog >=0.10.3                :  3.0.0 (OK)
xdg >=0.26                       :  0.28 (OK)
zmq >=22.1.0                     :  24.0.1 (OK)

# Optional:
cython >=0.21                    :  None (NOK)
matplotlib >=3.0.0               :  3.6.3 (OK)
numpy >=1.7                      :  1.26.4 (OK)
pandas >=1.1.1                   :  2.1.4 (OK)
scipy >=0.17.0                   :  1.11.4 (OK)
sympy >=0.7.3                    :  1.12 (OK)
@ingo-m
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ingo-m commented Nov 4, 2024

PS: I can get the Spyder variable explorer to work when pinning the versions of numpy, pandas, scipy, and matplotlib in the conda env to the exact same versions as the Spyder dependencies. But these versions are fairly old, and cause dependency conflicts if I'm trying to include any additional packages in my conda env.

@ccordoba12
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Hey @ingo-m, this is basically a duplicate of issue #22784, so I'm going to close it in favor of that one.

You also found the cause of this problem:

PS: I can get the Spyder variable explorer to work when pinning the versions of numpy, pandas, scipy, and matplotlib in the conda env to the exact same versions as the Spyder dependencies.

This means your distro packages depend on Numpy 1 but you had Numpy 2 installed in your conda env. Since the two versions don't produce compatible objects, it's not possible to use the Variable Explorer to visualize arrays or dataframes with it.

@ccordoba12 ccordoba12 closed this as not planned Won't fix, can't repro, duplicate, stale Nov 4, 2024
@ccordoba12
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Sorry, this was actually not a duplicate of #22784, but now you know the cause and why what you did worked.

We'll try to provide a better error message for this in a later release.

@ccordoba12 ccordoba12 reopened this Nov 4, 2024
@ccordoba12 ccordoba12 changed the title Variable explorer not working, Spyder deb package, Ubuntu 24 Variable explorer not working due to incompatibility between Numpy 2 and 1 Nov 4, 2024
@ccordoba12 ccordoba12 added this to the v6.1.0 milestone Nov 4, 2024
@ingo-m
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ingo-m commented Nov 5, 2024

Ok thanks.

If there's nothing more that can be done about it at the moment I don't mind if you close the issue, I just thought it makes sense to document the issue here for others & future reference.

The root cause of my problem is that I can't get spyder to work in a conda env on Ubuntu 24 (which uses wayland). Installing spyder as a deb package is only a workaround, which in turn causes the problem with the variable explorer.

@ccordoba12
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The root cause of my problem is that I can't get spyder to work in a conda env on Ubuntu 24 (which uses wayland).

Well, you can also install Xorg with apt and use a Xorg session instead. That way you'll be able to use conda instead of the distro package, which is always going to be outdated.

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