add magres datatype #17423
add magres datatype #17423
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Transfered the metadata parsing using the ASE IO library to an abstract class "AtomicStructFile"
Earlier parent class was Text but was changed to GenericMol file for XYZ and Extended XYZ files
Also removed set_peek() method from extxyz due to functionality being present in AtomicStructFile abstract class.
Changed DatasetProtocol file_name attribute to be compatible with galaxy v23.1
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@Neonbluestoplight Hi, thanks for the contribution. New datatypes should generally target the dev version of Galaxy I think -- so could you please retarget your PR? |
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@martenson from https://github.com/galaxyproject/galaxy/blob/dev/doc/source/project/organization.rst#handling-pull-requests
The question is if this is too much of a refactoring. @Neonbluestoplight do you need it in 23.1? |
| @@ -771,6 +771,7 @@ | |||
| <datatype extension="cif" type="galaxy.datatypes.molecules:CIF" display_in_upload="true"/> | |||
| <datatype extension="xyz" type="galaxy.datatypes.molecules:XYZ" display_in_upload="true"/> | |||
| <datatype extension="extxyz" type="galaxy.datatypes.molecules:ExtendedXYZ" display_in_upload="true"/> | |||
| <datatype extension="magres" type="galaxy.datatypes.molecules:Magres" display_in_upload="true"/> | |||
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Hi both - I advised @Neonbluestoplight to target 23.1 based on the guidelines which Bjoern linked (we've always targetted the latest tagged release branch in the past when adding Datatypes). We didn't notice the repeated code that could be refactored until later on.
We don't need this desperately, as it's for an emerging use case we're looking to support in the future. Is there a anticipated release date for 23.2?
Didn't know these were possible xml tags, we can try adding this for all our datatypes as well (since I'm pretty sure they don't have them either). |
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@patrick-austin 23.2 went out on the 30th of January. I think that would be a better target, but dev is also alright, as 24.0 will likely go out in two months or so. If there is no current need for having this in 23.1 I would recommend not merging it there. |
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I'm sorry, but I'm afraid it's too late for 23.2. This can make it into 24.0. As per @martenson, you'll need to retarget this PR for dev. |
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Ah that's the source of confusion then - we were looking at https://github.com/galaxyproject/galaxy/releases where the latest release is 23.1.4 back on January 6th (and I only just got an email advertising the features of 23.2 last night via the mailing list). I can see that 23.2 does appear in https://github.com/galaxyproject/galaxy/tags though - I suppose tags are still in use but GitHub "releases" aren't accurate (anymore)? |
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@patrick-austin @Neonbluestoplight Correction: it is not too late since this is a datatype addition. Sorry for the confusion - my mistake! So yes, please target the |
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I guess this can be closed in favour of #17453 ? |
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Yes, I was about to close this right now. Thank you |
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I added the latest release to https://github.com/galaxyproject/galaxy/releases -- sorry for the confusion @Neonbluestoplight |
Added support for Ab initio Nuclear Magnetic Resonance file format (Magres). These are needed for Nuclear Magnetic Resonance (materials science) use cases. Also moved ASE metadata output functionality to its own class (AtomicStructFile) for easier addition of future datatypes that make use of ASE for metadata.
See:
https://www.ccpnc.ac.uk/docs/magres
cc @patrick-austin
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