Uploaded a working version of pygmt on colab

[andrebelem]

This version is 100% functional in colab with PyGMT version v0.5.0, Python 3.7.13 (default, Apr 24 2022) and GMT lib version 6.5.0.

[seisman]

This version is 100% functional in colab with PyGMT version v0.5.0, Python 3.7.13 (default, Apr 24 2022) and GMT lib version 6.5.0.

As I understand it, Google Colab only provides Python 3.7, but PyGMT requires Python>=3.8 since v0.6.0. Do you know any way to install newer Python versions in Google Colab? I've tried many times but failed.

[andrebelem]

Every time I tried to change Python version, some problem happened. However, installing GMT as I did, and then pip install pygmt, works perfectly.

Maybe we should write a "Warning" that even though PyGMT requires Python>=3.8, it works fine with 3.7 as long as it doesn't conflict with some internal requirement. As far as I could test with simple things (maps, figures, XY, etc) it works perfectly and without restrictions.

[weiji14]

Related issues at googlecolab/colabtools#1422 and googlecolab/colabtools#2165. No timeline as to when Google Colab will use Python 3.8+ though :/

Did any of you manage to try the solutions at https://stackoverflow.com/questions/60775160/install-python-3-8-kernel-in-google-colaboratory?

[andrebelem]

Hello @weiji14
The solution I found was to install GMT "along" with the default Python 3.7 from colab and it works! In fact, in my classes I use COLAB with students and I have been doing exercises with PyGMT. So far there are no conflicts. The only downside is the installation time of 6-8 minutes.

But again - GMT/PyGMT over Python 3.7 COLAB works perfectly with the recipe I gave.

Maybe, instead of trying to go through this Branch that requires Python 3.8, we can create a parallel one for anyone who wants to use PyGMT via COLAB. I don't know how many people fit into this, but for example, in my classes it's much more practical for students to use COLAB in the teaching lab.

[andrebelem]

trying to understand what in the validator was wrong. I believe it is not patch related.

[weiji14]

Looks like Google Colab finally updated to Python 3.8 in googlecolab/colabtools#3246 🎉 Shall we revive this Pull Request?

[weiji14]

I tried running this code block:

!wget --quiet https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh
!chmod +x Mambaforge-Linux-x86_64.sh
!bash ./Mambaforge-Linux-x86_64.sh -bfp /usr/local
!mamba install -q -y --prefix /usr/local python=3.8 pygmt

import sys
import os
sys.path.append("/usr/local/lib/python3.8/site-packages")
os.environ["GMT_LIBRARY_PATH"]="/usr/local/lib"

But am getting an error like so on import pygmt:

GMTCLibNotFoundError: Error loading GMT shared library at '/usr/local/lib/libgmt.so'.
/usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.30' not found (required by /usr/local/lib/./libgdal.so.32)
Error loading GMT shared library at 'libgmt.so'.
libgmt.so: cannot open shared object file: No such file or directory

I had a look at https://stackoverflow.com/questions/23244418/set-ld-library-path-before-importing-in-python which suggested setting LD_LIBRARY_PATH but that didn't work. Also tried symlinking following https://askubuntu.com/questions/1418016/glibcxx-3-4-30-not-found-in-conda-environment but that failed too. Need to try something else.

[joa-quim]

I know this one. GCC12 broke compatibility of libstdc++ and conda uses GCC12 to build GMT. So if GMT is called from some program (very likely Python) built with and older version of GCC that error occurs.

[seisman]

Superseded by #45.