Frequently asked questions and bug reports

Bug reports

To report a problem with sett or if you have a question that is not covered in the present documentation please open an issue on our public gitlab repo https://gitlab.com/biomedit/sett/-/issues

Frequently asked questions

Warning “Config: Unexpected keys: …” at startup

Problem: when invoking sett or sett-cli, a warning appears:
```
Config: Unexpected keys: ...
```
Solution:
- via GUI: Visit Settings and press 💾 Save to config file.
- Via terminal: Edit your config.json (see sett configuration file) and remove the line defining the unexpected variable.

Nothing happens when running sett-gui (Windows)

Problem: when staring sett-gui in the terminal, nothing happens and the application does not start. In principle, this happens mostly on windows machines (on Linux/MacOS, error messages should be displayed in the terminal).
Solution: this generally indicates that an error occurred while the sett-gui application was launched. On Windows machines, this can be tricky to debug since the actual error is not displayed in the terminal. However, this problem often stems from a missing dependency, and you should therefore make sure that:
- GnuPG is installed on your machine - see here.
- sett was installed with all its python dependencies (this should in principle be the case if sett was installed using pip).
If this does not resolve the issue, you can try to manually start sett-gui in an interactive python3 session and see what the error message is:
1. Start a python3 session on your machine.
2. Run the following 2 commands, and see which error you get:
```
from sett.gui.__main__ import run
run()
```

Error “No module named ‘PySide2’” on sett startup (Linux / MacOS)

Problem: when starting sett, the following error is displayed in the terminal: ModuleNotFoundError: No module named 'PySide2'. In addition, the following error (or something similar) might also be shown: ImportError: libOpenGL.so.0: cannot open shared object file: No such file or directory or the same error but with libGLX.so.0 or libEGL.so.1 instead of libOpenGL.so.0.
Solution: depending on the operating system you are using, this error can have multiple causes.
- If using a recent operating system that fully supports PySide6 If your operating system is reasonably recent and supports PySide6, then the underlying problem is not the lack of PySide2, but most likely the fact that PySide6 is not correctly installed or is missing a dependency.
  
  To fix the issue, please verify that:
  - PySide6 is installed on your system: pip list will list all installed Python packages.
  - The openGL library is installed on your system. OpenGL is an operating system library (not a Python module!) required by PySide6. However, this library is not always automatically installed when PySide6 is installed, and must in some cases be installed manually.
    
    Here are commands for popular Linux distributions:
    - Linux Ubuntu or Debian: apt install libopengl0 libegl1
    - Linux Fedora: dnf install libglvnd-opengl libglvnd-glx libglvnd-egl
- If using an older operating system that does not support PySide6 If you are using an older operating system (e.g. CentOS 7), then it is possible that PySide6 is not supported. In this case, sett must be run in so-called “legacy” mode, which requires PySide2 to be present on your system.
  
  To fix the issue, please verify that:
  - PySide2 is installed on your system.
  - The “legacy” version of sett is installed on your system. The sett legacy version can be installed with: pip install sett[legacy].

sett generates SHA-1 keys

Problem: you are using sett and notice that it generates SHA-1 keys. This is a problem because SHA-1 is considered insecure and should NOT be used anymore.
Solution: to generate non-SHA-1 keys, you must use GnuPG command line executable. There is currently no option in sett to enforce the generation of non-SHA-1 keys. It is possible to generate non-SHA-1 keys by using following options (see this thread as well): --cert-digest-algo SHA256 --s2k-digest-algo SHA256. Instead of SHA256, select your preferred digest algorithm and/or one which is supported by your version of GnuPG, and compatible with other systems.

For more information on key management using GnuPG command line executable, kindly refer to PGP key management with sett.