chore: update *requirements.txt

[edkerk]

Main improvements in this PR:

• chore:
  • update dependencies in *requirements.txt (note format change since pip-tools 5.5.0+)

I hereby confirm that I have:

• Tested my code with all requirements for running the model
• Selected devel as a target branch (top left drop-down menu)
• If needed, asked first in the Gitter chat room about this PR

[mihai-sysbio]

Neat!

[mihai-sysbio]

It seems a part of the validation fails likely because of memote requiring travis-encrypt which, in turn, requires pyyaml which clashes with ruamel.yaml like this https://stackoverflow.com/questions/9286637/pyyaml-error-attribute-error-no-attribute-load .
Should we keep this part of the validation if we know it will continue to fail for some time?

[edkerk]

@mihai-sysbio Skipping that step can indeed be sensible, is there a memote issue to track whether this is solved?

Meanwhile, would it not work to change line 38 of .github/workflows/yaml-validation.yml from:

        pip install -r requirements/ci-requirements.txt

to

        pip install cobra

?
As memote would probably run in another GH, where the ci-requirements.txt could still be used? Or if it should work in the same GH, then first check for valid YAML after pip install cobra, then run pip install -r requirements/ci-requirements.txt for running memote? All as a workaround, until this issue is solved at memote.

[mihai-sysbio]

Great idea @edkerk ! I'm not sure why it doesn't work though - from what I can see in the requirements cobra is relying on a single yaml library. Furthermore, when trying this locally I get the same error.

[mihai-sysbio]

@edkerk it looks like there is no problem with the dependencies after all, just unexpected indentation in the yml file. I've manually fixed that for now in bb81286 and the validation passed.

[edkerk]

A few tweaks in the yml, now directly generated with RAVEN after commit SysBioChalmers/RAVEN@99a4536

[mihai-sysbio]

A few tweaks in the yml, now directly generated with RAVEN after commit SysBioChalmers/RAVEN@99a4536

nice! imho this PR is ready to be merged