Spyder Kernels, anaconda and Python 3.9

Question

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Edit - pip uninstall not working

pip uninstall primer3
WARNING: Ignoring invalid distribution -umpy (c:\anaconda3\lib\site-packages)
WARNING: Ignoring invalid distribution -umexpr (c:\anaconda3\lib\site-packages)
WARNING: Ignoring invalid distribution -iopython (c:\anaconda3\lib\site-packages)
WARNING: Ignoring invalid distribution -illow (c:\anaconda3\lib\site-packages)
WARNING: Ignoring invalid distribution -cipy (c:\anaconda3\lib\site-packages)
WARNING: Ignoring invalid distribution -umpy (c:\anaconda3\lib\site-packages)
WARNING: Ignoring invalid distribution -umexpr (c:\anaconda3\lib\site-packages)
WARNING: Ignoring invalid distribution -iopython (c:\anaconda3\lib\site-packages)
WARNING: Ignoring invalid distribution -illow (c:\anaconda3\lib\site-packages)
WARNING: Ignoring invalid distribution -cipy (c:\anaconda3\lib\site-packages)
WARNING: Skipping primer3 as it is not installed.

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I am looking to use some software that requires Python v>=3.9. I downloaded it as described here via default options to C:\Users\u03132tk\AppData\Local\Programs\Python\Python39\python.exe.

My IDE is Spyder, originally installed at C:\ANACONDA3\Lib\site-packages\spyder. The original shortcut I clicked, C:\ProgramData\Microsoft\Windows\Start Menu\Programs\Anaconda3 (64-bit)\Spyder.lnk, executed these files:

C:\ANACONDA3\pythonw.exe 
C:\ANACONDA3\cwp.py 
C:\ANACONDA3 
C:\ANACONDA3\pythonw.exe 
C:\ANACONDA3\Scripts\spyder-script.py

As it was not the default interpreter for my Spyder version, I then downloaded Spyder version 5 via windows installer in the hope that it would use Python version 3.9 (it uses 3.8 :( ). Spyder v5 is installed at C:\Program Files\Spyder, and the shortcut I use to open it (C:\ProgramData\Microsoft\Windows\Start Menu\Programs\Spyder.lnk) executes these files:

C:\Program Files\Spyder\Python\pythonw.exe 
C:\Program Files\Spyder\Spyder.launch.pyw

After reading around I found out how to change the Python interpreter. My current problem is this error in the console:

The Python environment or installation whose interpreter is located at
    C:\Users\u03132tk\AppData\Local\Programs\Python\Python39\python.exe
doesn't have the spyder‑kernels module or the right version of it installed (>= 2.4.0 and < 2.5.0). Without this module is not possible for Spyder to create a console for you.

You can install it by activating your environment first (if necessary) and then running in a system terminal:
    conda install spyder-kernels=2.4
or
    pip install spyder-kernels==2.4.*

I did the pip option and it seemed to go OK, apart from these errors (the full output is given under 'text dump'):

ERROR: spyder 4.1.5 requires pyqt5<5.13; python_version >= "3", which is not installed.
ERROR: spyder 4.1.5 requires pyqtwebengine<5.13; python_version >= "3", which is not installed.
ERROR: spyder 4.1.5 has requirement spyder-kernels<1.10.0,>=1.9.4, but you'll have spyder-kernels 2.4.3 which is incompatible.
ERROR: ipykernel 6.16.2 has requirement traitlets>=5.1.0, but you'll have traitlets 4.3.2 which is incompatible.

Given that spyder-kernels-2.4.3 seemed to download OK, I thought it might be fine, but I get the same console error after restarting spyder. I have tried setting the preferred interpreter to C:\Users\u03132tk\AppData\Local\Programs\Python\Python39\python.exe, and I also tried copying the Python39 directory into C:\Program Files\Spyder and setting the preferred interpreter to C:\Program Files\Spyder\Python39\python.exe - neither worked.

I am not sure of best practices with this kind of thing at all - could the issue be that I have two Spyder versions? I have folders that seem to indicate the spyder kernels installed OK for both the old (C:\ANACONDA3\Lib\site-packages\spyder_kernels-2.4.3.dist-info, C:\ANACONDA3\Lib\site-packages\spyder_kernels) and new (C:\Program Files\Spyder\pkgs\spyder_kernels-2.4.3.dist-info, C:\Program Files\Spyder\pkgs\spyder_kernels) spyder versions.

Also, if my latest install of Spyder is outside the Anaconda ecosystem, will that make it harder to use packages (or can I just Pip install them as needed still)?

When I leave python and venture into my actual computer I am a complete amateur, so any help would be much appreciated!

Thanks, Tim

Text dump:

C:\Users\u03132tk>pip install spyder-kernels==2.4.*
Collecting spyder-kernels==2.4.*
  Downloading https://files.pythonhosted.org/packages/d8/63/2b2202362cca689c38f5a63268596f6fff14bdfb4a539103e4073b7064b0/spyder_kernels-2.4.3-py2.py3-none-any.whl (98kB)
     |████████████████████████████████| 102kB 6.4MB/s
Collecting pyzmq>=22.1.0; python_version >= "3" (from spyder-kernels==2.4.*)
  Downloading https://files.pythonhosted.org/packages/40/dd/1fe1f11eb03d177a141188c80d1134f64146db3c5cecbcf4054817a2f8af/pyzmq-25.0.2-cp37-cp37m-win_amd64.whl (1.2MB)
     |████████████████████████████████| 1.2MB ...
Collecting jupyter-client<9,>=7.4.9; python_version >= "3" (from spyder-kernels==2.4.*)
  Downloading https://files.pythonhosted.org/packages/fd/a7/ef3b7c8b9d6730a21febdd0809084e4cea6d2a7e43892436adecdd0acbd4/jupyter_client-7.4.9-py3-none-any.whl (133kB)
     |████████████████████████████████| 143kB 6.4MB/s
Collecting ipykernel<7,>=6.16.1; python_version >= "3" (from spyder-kernels==2.4.*)
  Downloading https://files.pythonhosted.org/packages/95/46/505364588f6145f5edd29c1506b1964dd397a668c49f8bb42deffb6a0168/ipykernel-6.16.2-py3-none-any.whl (138kB)
     |████████████████████████████████| 143kB ...
Requirement already satisfied: cloudpickle in c:\anaconda3\lib\site-packages (from spyder-kernels==2.4.*) (1.2.1)
Collecting ipython!=8.10.0,!=8.8.0,!=8.9.0,<9,>=7.31.1; python_version >= "3" (from spyder-kernels==2.4.*)
  Downloading https://files.pythonhosted.org/packages/7c/6a/1f1365f4bf9fcb349fcaa5b61edfcefa721aa13ff37c5631296b12fab8e5/ipython-7.34.0-py3-none-any.whl (793kB)
     |████████████████████████████████| 798kB 6.4MB/s
Requirement already satisfied: traitlets in c:\anaconda3\lib\site-packages (from jupyter-client<9,>=7.4.9; python_version >= "3"->spyder-kernels==2.4.*) (4.3.2)
Collecting jupyter-core>=4.9.2 (from jupyter-client<9,>=7.4.9; python_version >= "3"->spyder-kernels==2.4.*)
  Downloading https://files.pythonhosted.org/packages/02/8f/0e0ad6804c0a021a27410ec997626a7a955c20916454d0205f16eb83de4b/jupyter_core-4.12.0-py3-none-any.whl (89kB)
     |████████████████████████████████| 92kB 5.8MB/s
Collecting python-dateutil>=2.8.2 (from jupyter-client<9,>=7.4.9; python_version >= "3"->spyder-kernels==2.4.*)
  Downloading https://files.pythonhosted.org/packages/36/7a/87837f39d0296e723bb9b62bbb257d0355c7f6128853c78955f57342a56d/python_dateutil-2.8.2-py2.py3-none-any.whl (247kB)
     |████████████████████████████████| 256kB ...
Requirement already satisfied: entrypoints in c:\anaconda3\lib\site-packages (from jupyter-client<9,>=7.4.9; python_version >= "3"->spyder-kernels==2.4.*) (0.3)
Collecting tornado>=6.2 (from jupyter-client<9,>=7.4.9; python_version >= "3"->spyder-kernels==2.4.*)
  Downloading https://files.pythonhosted.org/packages/f3/9e/225a41452f2d9418d89be5e32cf824c84fe1e639d350d6e8d49db5b7f73a/tornado-6.2.tar.gz (504kB)
     |████████████████████████████████| 512kB 6.4MB/s
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
    Preparing wheel metadata ... done
Collecting nest-asyncio>=1.5.4 (from jupyter-client<9,>=7.4.9; python_version >= "3"->spyder-kernels==2.4.*)
  Downloading https://files.pythonhosted.org/packages/e9/1a/6dd9ec31cfdb34cef8fea0055b593ee779a6f63c8e8038ad90d71b7f53c0/nest_asyncio-1.5.6-py3-none-any.whl
Requirement already satisfied: packaging in c:\anaconda3\lib\site-packages (from ipykernel<7,>=6.16.1; python_version >= "3"->spyder-kernels==2.4.*) (19.0)
Collecting matplotlib-inline>=0.1 (from ipykernel<7,>=6.16.1; python_version >= "3"->spyder-kernels==2.4.*)
  Downloading https://files.pythonhosted.org/packages/f2/51/c34d7a1d528efaae3d8ddb18ef45a41f284eacf9e514523b191b7d0872cc/matplotlib_inline-0.1.6-py3-none-any.whl
Collecting debugpy>=1.0 (from ipykernel<7,>=6.16.1; python_version >= "3"->spyder-kernels==2.4.*)
  Downloading https://files.pythonhosted.org/packages/af/7e/61738aba4da0de74e797ca71013977ebd8d35f58b18e674da045efb30487/debugpy-1.6.7-cp37-cp37m-win_amd64.whl (4.8MB)
     |████████████████████████████████| 4.8MB 6.8MB/s
Requirement already satisfied: psutil in c:\anaconda3\lib\site-packages (from ipykernel<7,>=6.16.1; python_version >= "3"->spyder-kernels==2.4.*) (5.6.3)
Requirement already satisfied: backcall in c:\anaconda3\lib\site-packages (from ipython!=8.10.0,!=8.8.0,!=8.9.0,<9,>=7.31.1; python_version >= "3"->spyder-kernels==2.4.*) (0.1.0)
Requirement already satisfied: pickleshare in c:\anaconda3\lib\site-packages (from ipython!=8.10.0,!=8.8.0,!=8.9.0,<9,>=7.31.1; python_version >= "3"->spyder-kernels==2.4.*) (0.7.5)
Requirement already satisfied: setuptools>=18.5 in c:\anaconda3\lib\site-packages (from ipython!=8.10.0,!=8.8.0,!=8.9.0,<9,>=7.31.1; python_version >= "3"->spyder-kernels==2.4.*) (41.0.1)
Requirement already satisfied: jedi>=0.16 in c:\anaconda3\lib\site-packages (from ipython!=8.10.0,!=8.8.0,!=8.9.0,<9,>=7.31.1; python_version >= "3"->spyder-kernels==2.4.*) (0.17.1)
Requirement already satisfied: decorator in c:\anaconda3\lib\site-packages (from ipython!=8.10.0,!=8.8.0,!=8.9.0,<9,>=7.31.1; python_version >= "3"->spyder-kernels==2.4.*) (4.4.0)
Requirement already satisfied: pygments in c:\anaconda3\lib\site-packages (from ipython!=8.10.0,!=8.8.0,!=8.9.0,<9,>=7.31.1; python_version >= "3"->spyder-kernels==2.4.*) (2.4.2)
Requirement already satisfied: colorama; sys_platform == "win32" in c:\anaconda3\lib\site-packages (from ipython!=8.10.0,!=8.8.0,!=8.9.0,<9,>=7.31.1; python_version >= "3"->spyder-kernels==2.4.*) (0.4.1)
Requirement already satisfied: prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0 in c:\anaconda3\lib\site-packages (from ipython!=8.10.0,!=8.8.0,!=8.9.0,<9,>=7.31.1; python_version >= "3"->spyder-kernels==2.4.*) (2.0.9)
Requirement already satisfied: ipython-genutils in c:\anaconda3\lib\site-packages (from traitlets->jupyter-client<9,>=7.4.9; python_version >= "3"->spyder-kernels==2.4.*) (0.2.0)
Requirement already satisfied: six in c:\anaconda3\lib\site-packages (from traitlets->jupyter-client<9,>=7.4.9; python_version >= "3"->spyder-kernels==2.4.*) (1.12.0)
Requirement already satisfied: pywin32>=1.0; sys_platform == "win32" and platform_python_implementation != "PyPy" in c:\anaconda3\lib\site-packages (from jupyter-core>=4.9.2->jupyter-client<9,>=7.4.9; python_version >= "3"->spyder-kernels==2.4.*) (223)
Requirement already satisfied: pyparsing>=2.0.2 in c:\anaconda3\lib\site-packages (from packaging->ipykernel<7,>=6.16.1; python_version >= "3"->spyder-kernels==2.4.*) (2.4.0)
Requirement already satisfied: parso<0.8.0,>=0.7.0 in c:\anaconda3\lib\site-packages (from jedi>=0.16->ipython!=8.10.0,!=8.8.0,!=8.9.0,<9,>=7.31.1; python_version >= "3"->spyder-kernels==2.4.*) (0.7.0)
Requirement already satisfied: wcwidth in c:\anaconda3\lib\site-packages (from prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0->ipython!=8.10.0,!=8.8.0,!=8.9.0,<9,>=7.31.1; python_version >= "3"->spyder-kernels==2.4.*) (0.1.7)
Building wheels for collected packages: tornado
  Building wheel for tornado (PEP 517) ... done
  Stored in directory: C:\Users\u03132tk\AppData\Local\pip\Cache\wheels\4c\e2\a2\2a4d8b655b5018edd788430e998bfb2e15a2b7876dbee210e6
Successfully built tornado
ERROR: spyder 4.1.5 requires pyqt5<5.13; python_version >= "3", which is not installed.
ERROR: spyder 4.1.5 requires pyqtwebengine<5.13; python_version >= "3", which is not installed.
ERROR: spyder 4.1.5 has requirement spyder-kernels<1.10.0,>=1.9.4, but you'll have spyder-kernels 2.4.3 which is incompatible.
ERROR: ipykernel 6.16.2 has requirement traitlets>=5.1.0, but you'll have traitlets 4.3.2 which is incompatible.
Installing collected packages: pyzmq, jupyter-core, python-dateutil, tornado, nest-asyncio, jupyter-client, matplotlib-inline, debugpy, ipython, ipykernel, spyder-kernels
  Found existing installation: pyzmq 18.0.0
    Uninstalling pyzmq-18.0.0:
      Successfully uninstalled pyzmq-18.0.0
  Found existing installation: jupyter-core 4.6.3
    Uninstalling jupyter-core-4.6.3:
      Successfully uninstalled jupyter-core-4.6.3
  Found existing installation: python-dateutil 2.8.0
    Uninstalling python-dateutil-2.8.0:
      Successfully uninstalled python-dateutil-2.8.0
  Found existing installation: tornado 6.0.3
    Uninstalling tornado-6.0.3:
      Successfully uninstalled tornado-6.0.3
  Found existing installation: jupyter-client 6.1.7
    Uninstalling jupyter-client-6.1.7:
      Successfully uninstalled jupyter-client-6.1.7
  Found existing installation: ipython 7.6.1
    Uninstalling ipython-7.6.1:
      Successfully uninstalled ipython-7.6.1
  Found existing installation: ipykernel 5.3.4
    Uninstalling ipykernel-5.3.4:
      Successfully uninstalled ipykernel-5.3.4
  Found existing installation: spyder-kernels 1.9.4
    Uninstalling spyder-kernels-1.9.4:
      Successfully uninstalled spyder-kernels-1.9.4
Successfully installed debugpy-1.6.7 ipykernel-6.16.2 ipython-7.34.0 jupyter-client-7.4.9 jupyter-core-4.12.0 matplotlib-inline-0.1.6 nest-asyncio-1.5.6 python-dateutil-2.8.2 pyzmq-25.0.2 spyder-kernels-2.4.3 tornado-6.2

`C:\ProgramData\Microsoft\Windows\Start Menu\Programs\Anaconda3 (64-bit)\Spyder.lnk` - that's... a shortcut. It does nothing other than point to an actual file located somewhere else. It tells us exactly nothing. — matszwecja, May 23 '23 at 11:32
thanks for the comment - I went digging and got the correct paths (and learned a bit about my directory structure!). I gave the filepath targets of the shortcuts in case it helps. — Tim Kirkwood, May 23 '23 at 12:22

score 1 · Accepted Answer · answered May 24 '23 at 06:12

1

You created a very big headache for yourself. You now have three python installations and two spyder installations.

First, clean the mess:

Uninstall C:\Users\u03132tk\AppData\Local\Programs\Python\Python39 completely
Uninstall C:\Program Files\Spyder

Then, lets start at the original setup, you have spyder installed as part of anaconda and the requirement that you had was

I am looking to use some software that requires Python v>=3.9.

Here, you should just create a conda virtual environment, install a spyder kernel to it and then select that environment as interpreter in spyder. This command will create a new environment with python 3.9, run it in your anaconda prompt:

conda create -n py39 python=3.9 spyder-kernels pip #list all packages that your new environment should have

When you want to use this environment, simply write conda activate py39 in your anaconda prompt. After this, all conda/pip install commands will install to this specific environment, without modifying your base environment and you can install the software that you wanted here.

answered May 24 '23 at 06:12

FlyingTeller

17,638
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Hello, thank you for your answer. I will delete the packages as you suggest, but have since tried to update everything using conda, as described here - https://stackoverflow.com/q/76320554/11357695. Have I made the headache worse? – Tim Kirkwood May 24 '23 at 06:18
1

In general, you should be able to update your python version in your anaconda base environment without any issue. it is, however generally recommended to install as little as possible into your base environemnt, especially with pip. For your other issue, I would suggest that first you try to repair your base, maybe `pip uninstall primer3` and `pip install primer3` to make sure you get a correct setup for your new python version. – FlyingTeller May 24 '23 at 06:27
Thank you for the advice, I wish I had learned about venvs a while ago! Unfortunately pip uninstall doesnt seem to be working (pip is at C:\ANACONDA3\Lib\site-packages\pip) – Tim Kirkwood May 24 '23 at 06:36
I just saw that it should probably be `pip uninstall primer3-py`, ahve you used that? – FlyingTeller May 24 '23 at 06:38
just noticed that the distpackage is called `primer3-py`. Does `pip uninstall primer3-py` work? – FlyingTeller May 24 '23 at 06:42
IT WORKED! many thanks, this is not a good time for all my code to break so this is a relief - I assume I can just do this for all packages I want to use (numpy etc)? Also if post the comment to the linked question I can accept it – Tim Kirkwood May 24 '23 at 06:51
1

Great! Make sure that you only do this with `pip` packages. most probably are conda managed – FlyingTeller May 24 '23 at 07:24

Spyder Kernels, anaconda and Python 3.9

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