ERROR: Package 'itaxotools-pygblocks' requires a different Python: 3.10.12 not in '<4,>=3.11'

[morfogeno]

Tried to install Concantenator with the command "pip install . -f packages.html" but unsuccessful as the new pygblocks depends on Phyton 3.11. I run Pop!_OS 22.04 LTS". New to python, saw it is cumbersome and somewhat dangerous to upgrade in linux. Have to set a environment. Could be possible to installl without pigblocks, since I don't intend to mask sites

[morfogeno]

edit: I have Windows 7 in virtualbox but can't install Phyton 3.11 on this OS

[StefanPatman]

Hello, thanks for posting. This was an oversight in the readme, which I just updated.

Please try installing from the win7-compat branch, which supports Python versions older than 3.11:

git clone https://github.com/iTaxoTools/ConcatenatorGui.git -b win7-compat
cd ConcatenatorGui
pip install . -f packages.html

I will not be maintaining these branches in the future, but they are up to date with the main branch so far.

While verifying that this still works, I noticed that MAFFTpy may occasionally fail to install with an error message similar to ERROR: Failed building wheel for mafftpy. If you encounter this error, please try re-running the pip install . -f packages.html command, for me it simply worked on the second try after the initial failure.

I hope this helps!

[morfogeno]

Thank you for your solicitude and rapid response, Stefan. First, I have to learn how to delete what was already isntalled which was by command rm -rf .git "ConcatanatorGui. While reading tutorials, I tried the "git pull" commands and saw branches. Then I tried to install first (before the Win7 you directed) branch v0.3.1 beacause I thought you were recommending Win7 branch so I could install in my Win7 virtual box. But I rather prefer on linux. Didn't work (required older versions (3.6). Then I remove the folder again and tried Win7 but then appeared the error:

File "/tmp/pip-build-env-h3t3j_gh/overlay/local/lib/python3.10/dist-packages/setuptools/py33compat.py", line 55, in unescape = getattr(html, 'unescape', html_parser.HTMLParser().unescape) AttributeError: 'HTMLParser' object has no attribute 'unescape'

I am stuck. Thanks

[StefanPatman]

It might be simpler for you to download the Windows 7 executable and run it in your virtualbox (or even with wine under Linux): https://github.com/iTaxoTools/ConcatenatorGui/releases/tag/v0.3.1

I just verified that the win7-compat branch still works for Python 3.8.6 under Ubuntu 22.04.3. I see no reason why it wouldn't for the respective Pop!_OS. The branch name is a bit misleading, but the main reason to support older versions of Python is for building Windows 7 executables. Installing a more recent version of Python should be the recommended course of action for most Linux users. The error you quoted seems to be a problem with setuptools, not Concatenator, so I cannot help much with that.

I'm not sure if you need to worry about uninstalling Concatenator; from what you described it never installed successfully. The commands from my previous quote should still theoretically work. You may confirm this by using pip list and checking if concatenator is included. Simply deleting the downloaded files using your file manager should be enough.

Perhaps it would help if you used pipenv to create an isolated environment to run the program:

pip install pipenv

git clone https://github.com/iTaxoTools/ConcatenatorGui.git -b win7-compat
cd ConcatenatorGui

pipenv shell

pip install . -f packages.html
concatenator-gui

exit

Then run concatenator using pipenv run concatenator-gui from inside the folder in the future.

I recommend looking into pyenv and pipenv/venv for setting up Python on your system.

Unfortunately, there are no plans to create executables nor wheel distributables for Concatenator on Linux. The only way to use the program on Linux is to install from source. Hopefully the information above is enough to help with that.