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nomad-coe / nomad

NOMAD lets you manage and share your materials science data in a way that makes it truly useful to you, your group, and the community.
https://nomad-lab.eu
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Improve documentation for "how to run a parse" #86

Open nakib opened 1 year ago

nakib commented 1 year ago

I'm requesting improvement of the doc at http://nomad-lab.eu/prod/v1/staging/docs/apis/local_parsers.html

Details:

  1. The concept of a parser might not be familiar to the user, so a link to the doc describing it would help.
  2. A lot of the doc is about handling potential troubleshooting related to installing a dependency. This could be handled in a separate doc and be linked from here.
  3. Add a link to the normalization doc.
  4. Explain under what circumstances can the normalization step may be skipped?
  5. The python code should explain that the normalization step may be commented out for the case when normalization is not required.
hampusnasstrom commented 2 months ago

Hello, I followed tutorial 13 but executed the following command:

nomad parse tests/data/test_sintering.archive.yaml --show-archive > normalized.archive.json

the following error appears even though everything is configured correctly in my environment: ModuleNotFoundError: No module named 'sintering' You are accessing functionality that requires extra dependencies. Check the NOMAD documentation or install all extra dependencies: pip install nomad-lab[infrastructure,dev]

But these modules are well installed too.

@PauloGitHB this is probably not the best place to discuss this problem as this is not an issue concerning the parsing documentation. I would recommend to either ask on our Discord server: https://discord.gg/Gyzx3ukUw8 (recommended as I believe it's an issue with your environment and not a problem with NOMAD), or open a separate issue describing your problem, ideally with a link to a repository where you are working and a set of steps for how to reproduce your issue.

That being said, the error states that you don't have a module called 'sintering' which would either suggest that you have not installed the plugin you are developing in your environment or that said plugin doesn't include a module called 'sintering'.

PauloGitHB commented 2 months ago

Hello,

Sorry I saw the forum title too late but I have already deleted my comment.

Thank you for your help

Have a nice day

De : Hampus Näsström @.> Envoyé : jeudi 19 septembre 2024 15:12 À : nomad-coe/nomad @.> Cc : Paul Levasseur @.>; Mention @.> Objet : Re: [nomad-coe/nomad] Improve documentation for "how to run a parse" (Issue #86)

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Hello, I followed tutorial 13 but executed the following command:

nomad parse tests/data/test_sintering.archive.yaml --show-archive > normalized.archive.json

the following error appears even though everything is configured correctly in my environment: ModuleNotFoundError: No module named 'sintering' You are accessing functionality that requires extra dependencies. Check the NOMAD documentation or install all extra dependencies: pip install nomad-lab[infrastructure,dev]

But these modules are well installed too.

@PauloGitHBhttps://github.com/PauloGitHB this is probably not the best place to discuss this problem as this is not an issue concerning the parsing documentation. I would recommend to either ask on our Discord server: https://discord.gg/Gyzx3ukUw8 (recommended as I believe it's an issue with your environment and not a problem with NOMAD), or open a separate issue describing your problem, ideally with a link to a repository where you are working and a set of steps for how to reproduce your issue.

That being said, the error states that you don't have a module called 'sintering' which would either suggest that you have not installed the plugin you are developing in your environment or that said plugin doesn't include a module called 'sintering'.

— Reply to this email directly, view it on GitHubhttps://github.com/nomad-coe/nomad/issues/86#issuecomment-2360950181, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A6D3PVQSKHNQJRXII2GPDNLZXLETHAVCNFSM6AAAAABOPZFZLGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNRQHE2TAMJYGE. You are receiving this because you were mentioned.Message ID: @.***>