Switch of stderr and stdout

[smoretti]

Hi Iakov
Hope everything is fine for you.

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We have started using godon for the next Selectome release.

It looks stderr and stdout are reversed: iteration information goes to stdout, and more useful information goes to stderr.

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Also for branch site model and H1, could you add in the output for each tested branch/node:

• omega0
• omega2a and omega2b
• p0, p1 & p2a+p2b proportions
• kappa value

Best

[Iakov Davydov]

Hi @smoretti , great to hear from you!

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Regarding stderr & stdout. I probably never though about this for too long Is there any guidelines/convention/reasoning why one should be stdout and other stderr?

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Speaking about value export, I would strongly suggest using JSON export instead of parsing stdout/stderr, which could be unstable (or even change from stderr to stdout ). As far as I remember all of those parameters (perhaps transformed) are exported via JSON. Is something missing? It should be very easy to extract values from JSON using jq, python or perl.

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Best,

Iakov

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[smoretti]

Thanks Iakov, the JSON output looks to contain everything we need.

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About stderr/stdout: I guess all useful information should go to stdout, i.e. branch and hypothese tested, maximum likelihood, …

Stderr should contain errors and warnings.

But what about less useful information like iteration status? Maybe in stderr also

[Iakov Davydov]

reverse stdout and stderr, fixes #1

Hopefully, no one is relying on stdout/stderr output. The correct way is to rely on JSON or trajectory outputs.

→ <<cset 8be085bace73>>

[Iakov Davydov]

Hi @smoretti , it should be fixed now in master.

Could you please test if it works for you?

[smoretti]

It works perfectly for us.
Thanks