how to fix import pygimli error libcholmod.so.3 on Mybinder

[stefanazzz]

Problem description

When trying to run from my Github repository using MyBinder,
import pygimli gives the following error:

"libcholmod.so.3: cannot open shared object file: No such file or directory (...)"

This can be fixed by adding python=3.8 to the yml environment file (see file below)

Your environment

from environment.yml file on github:

channels:
  - conda-forge
  - gimli
  - defaults
dependencies:
  - python=3.8          <-- add this line to make "import pygimli" work correctly
  - pygimli>=1.1.0

Notes

I suppose that 1.1.0 is compatible only with 3.8 not more recent versions. Note that pygimli >=1.5.0 shows the same problem when compiled with the current (May 2024) default mybinder python 3.11.x. I tried a few combinations but so far only 1.1.0 and 3.8 seem to work on mybinder.

[halbmy]

Can you try using pip install pygimli instead?

[stefanazzz]

Yes Thomas, I will try that too and let you know

…

On Mon, 20 May 2024 at 22:12, Thomas Günther ***@***.***> wrote: Can you try using pip install pygimli instead? — Reply to this email directly, view it on GitHub <#722 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AKX4DUTOFK64XKTP6QXQMITZDJRKNAVCNFSM6AAAAABH745DUGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMRRGIYTKMJXGU> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[ruboerner]

Is #721 (comment) probably related?

[stefanazzz]

yes, using pip in the environment.yml file also works (rather than downgrading to python 3.8): channels: - conda-forge - gimli - defaults dependencies: - pip: - pygimli

…

On Mon, May 20, 2024 at 10:12 PM Thomas Günther ***@***.***> wrote: Can you try using pip install pygimli instead? — Reply to this email directly, view it on GitHub <#722 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AKX4DUTOFK64XKTP6QXQMITZDJRKNAVCNFSM6AAAAABH745DUGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMRRGIYTKMJXGU> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[stefanazzz]

to reply to Ralph-Uwe, possibly related, but I would not know how to implement the symbolic links on github/mybinder

…

On Thu, May 23, 2024 at 7:42 AM Ralph-Uwe Börner ***@***.***> wrote: Is #721 (comment) <#721 (comment)> probably related? — Reply to this email directly, view it on GitHub <#722 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AKX4DUUJ7TLDDIYSZ2R6CQ3ZDWFTTAVCNFSM6AAAAABH745DUGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMRWGM2DMNBYGM> . You are receiving this because you authored the thread.Message ID: ***@***.***>