8000 Adds documentation to pynxtools by domna · Pull Request #205 · FAIRmat-NFDI/pynxtools · GitHub
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Adds documentation to pynxtools 8000 #205

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Merged
merged 7 commits into from
Jan 15, 2024
Merged

Adds documentation to pynxtools #205

merged 7 commits into from
Jan 15, 2024

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domna
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@domna domna commented Jan 15, 2024

pynxtools shall be the place to host the pynxtools & nexus definitions combined documentation.
It should also be integrated in nomad at some point, maybe with the mkdocs-monorepo-plugin

This replaces FAIRmat-NFDI/nexus_definitions#75 and FAIRmat-NFDI/nexus_definitions#121

Todo:

  • CI/CD

@domna domna self-assigned this Jan 15, 2024
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domna commented Jan 15, 2024

@sherjeelshabih I will build ci/cd parts here and then we can merge and do the additional doc changes in a new PR. Good?

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coveralls commented Jan 15, 2024

Pull Request Test Coverage Report for Build 7531147355

  • 0 of 0 changed or added relevant lines in 0 files are covered.
  • No unchanged relevant lines lost coverage.
  • Overall coverage increased (+0.009%) to 44.55%

Totals Coverage Status
Change from base Build 7277681916: 0.009%
Covered Lines: 4864
Relevant Lines: 10918

💛 - Coveralls

@domna domna requested a review from sherjeelshabih January 15, 2024 12:56
@domna domna merged commit d5ea72a into master Jan 15, 2024
@domna domna deleted the documentation branch January 15, 2024 15:50

We use a Python tool to make converting our research data easier. This has a number of [readers](https://github.com/FAIRmat-NFDI/pynxtools/tree/master/pynxtools/dataconverter/readers) that support multiple file formats. You can browse the separate folders to find the reader that might work for you. A generic reader is the [JSON Map Reader](https://github.com/FAIRmat-NFDI/pynxtools/tree/master/pynxtools/dataconverter/readers/json_map).

We will use the [XPS Reader](https://github.com/FAIRmat-NFDI/pynxtools/tree/master/pynxtools/dataconverter/readers/xps) with Vamas (.vms) files as an example.
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Most probably this will change to
"We will use the XPS Reader with a file from SpecsLabProdigy file (.sle) as an example."

Need to update pynxtools and the example file first.

Comment on lines +51 to +52
- file1.vms
- otherfile.vms
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Suggested change
- file1.vms
- otherfile.vms
- main_data_file.sle
- metadata_file.slh
- eln_data_sle.yaml

Again, this cannot be changed now, it is just to get keep track of what needs to be changed later.


Next, you will run the conversion routine:
```console
dataconverter --reader xps
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dataconverter --reader xps
dataconverter --reader xps --nxdl NXmpes --input-file "main_data_file.sle" --input-file "metadata_file.slh" --input-file "eln_data_sle.yaml" --output "output.nxs"

Comment on lines +30 to +32
<img src="media/create-new-upload.gif" />

## Upload your NeXus file
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Shall we add other process where you upload your original file and choose the NeXusDataConverter?


Nomad also interprets and ```normalizes``` this data to make it interoperable with other corners of Material's research. To browse this ```normalized``` data you can browse the ```DATA``` tab. Here you see all the information Nomad has picked up and made available for search and comparison with synthesis, experimental, and computational materials data.

<img src="media/data-tab.gif" />
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Add GIF for browsing of instrument metadata once the example file is updated.

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