insert reading of default optimade_config.json in example run script run.sh

[rartino]

This tiny fix resolves a stumbling block for new users trying out optimade-python-tools.

Without this fix, someone downloading optimade-python-tools and executing ./run.sh to try it out gets a server that otherwise works, but reports a 501 internal server error upon accessing the /structures endpoint without a a clear error description pointing the user what to do. Enabling debug mode explains that the error is a pydantic validation error due to missing chemical formula fields.

The issue is that the test data in optimade/server/data/test_structures.json absolutely needs the aliases mapping set up in the config file distributed with optimade-python-tools in /optimade_config.json. Hence, it is not possible to start a demo server without also reading that config file.

While one could consider other solutions (e.g., changing the default config hardcoded inside the python files), I think it is the expected behavior that the default example run script uses the included example config file, so that edits in that file are reflected by the running server.

[codecov]

Codecov Report

Merging #627 (184f685) into master (f5e7b57) will not change coverage.
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@@           Coverage Diff           @@
##           master     #627   +/-   ##
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  Coverage   93.27%   93.27%           
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  Files          60       60           
  Lines        3256     3256           
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  Hits         3037     3037           
  Misses        219      219           

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validator	66.89% <ø> (ø)

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[ml-evs]

Thanks for this @rartino! I just have a minor tweak to only use the demo value if the env var hasn't been set so that run.sh can still be used generally.

Please let us know if you run into any other problems!

[rartino]

It may be an idea to document somewhere, perhaps in a comment in run.sh and/or in a comment in server/config.py and/or in one of the readme files that any config setting can be overriden by an environment variable named OPTIMADE_<config setting>. I had to dig pretty far until I realized how that feature works since it is provided automatically by uvicorn and the env_prefix = "optimade_" in config.py.

(On the other hand, the most crucial config setting to override is the one that points to the config file to read, which is now at least explicitly demonstrated in run.sh)

[ml-evs]

It may be an idea to document somewhere, perhaps in a comment in run.sh and/or in a comment in server/config.py and/or in one of the readme files that any config setting can be overriden by an environment variable named OPTIMADE_<config setting>. I had to dig pretty far until I realized how that feature works since it is provided automatically by uvicorn and the env_prefix = "optimade_" in config.py.

(On the other hand, the most crucial config setting to override is the one that points to the config file to read, which is now at least explicitly demonstrated in run.sh)

We have this section in our documentation (https://www.optimade.org/optimade-python-tools/configuration/#environment-variables) but perhaps it would be nice to link to it in the script itself, I agree the distinction between uvicorn flags/OPTIMADE options is a bit confusing.

A docs overhaul is bubbling up to the top of my priorities for this package...

[CasperWA]

A docs overhaul is bubbling up to the top of my priorities for this package...

Yeah, an overhaul/update and some PR for it.

[CasperWA]

Looks good, this. Thanks @rartino !

[rartino]

We have this section in our documentation (https://www.optimade.org/optimade-python-tools/configuration/#environment-variables) but perhaps it would be nice to link to it in the script itself, I agree the distinction between uvicorn flags/OPTIMADE options is a bit confusing.

Ah, thanks, I had indeed missed this. In fact, I had missed that there was a pre-rendered version of the full docs at https://www.optimade.org/optimade-python-tools/, (but I see I could have picked up the configuration info from reading `docs/configuration.md".)

Perhaps in the overhaul of the docs once could consider a slightly more prominent link to https://www.optimade.org/optimade-python-tools/ in the README.md to help direct those who glances over it, e.g. as:

# Documentation 

Full documentation is available at the [optimade-python-tools website.](https://www.optimade.org/optimade-python-tools/)

(But I see how this link gets a bit weird if you want the first page of the website to be rendered from the README.md, hmm...)

[CasperWA]

This works for me, but I'll let @ml-evs get the final say (and merge rights) on this.
Thanks @rartino 👍

[ml-evs]

Thanks again @rartino, this is really helpful.

I just added a link to the config docs in the fallback print out so hopefully that is clearer too.