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fix example #103

Merged
merged 4 commits into from
Dec 13, 2024
Merged

fix example #103

merged 4 commits into from
Dec 13, 2024

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lukaspie
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@lukaspie lukaspie commented Dec 13, 2024

Summary by Sourcery

Fix inconsistencies in the XPS ELN data schema by standardizing section names to lowercase and updating units for various quantities. Update documentation to reflect these changes and correct application definition references.

Bug Fixes:

  • Correct the schema name from 'XPS data schema' to 'XPS ELN data schema' in the YAML file.

Enhancements:

  • Standardize section and subsection names in the YAML schema to use lowercase, improving consistency.

Documentation:

  • Update the README to clarify the introduction and viewing of uploaded data, and correct the application definition link from NXmpes to NXxps.

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sourcery-ai bot commented Dec 13, 2024

Reviewer's Guide by Sourcery

This PR updates the XPS data schema and documentation to align with the NXxps application definition, improves naming conventions, adds proper units to quantities, and reorganizes the documentation structure. The changes primarily focus on schema refinements and documentation clarity.

Updated ER diagram for XPS ELN data schema

erDiagram
    XPS {
        STRING name
        STRING base_sections
        STRING m_annotations
    }
    XPS ||--o{ user : has
    user {
        STRING affiliation
        STRING orcid
    }
    XPS ||--o{ instrument : has
    instrument {
        STRING device_information
        STRING energy_resolution
        STRING source_xray
    }
    XPS ||--o{ sample : has
    sample {
        STRING substance
        FLOAT molecular_mass "g/mol"
    }
    sample ||--o{ history : has
    history {
        STRING sample_preparation
    }
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File-Level Changes

Change Details Files
Updated schema naming and base section references
  • Changed schema name from 'XPS data schema' to 'XPS ELN data schema'
  • Updated base section from NexusDataConverter to ElnYamlConverter
  • Standardized section naming to use lowercase
src/pynxtools_xps/nomad/examples/xps.scheme.archive.yaml
Added proper units to numerical quantities
  • Added joule unit to energy resolution
  • Added meter unit to beam distance
  • Added units for temperature, power, current, and pressure measurements
  • Added g/mol unit for molecular mass
src/pynxtools_xps/nomad/examples/xps.scheme.archive.yaml
Simplified schema structure by removing redundant sections
  • Removed Value_log subsection from pressure_gauge
  • Removed Current_log subsection from flood_gun
  • Moved molecular_mass from subsection to quantity
src/pynxtools_xps/nomad/examples/xps.scheme.archive.yaml
Updated documentation and references
  • Changed NXmpes references to NXxps
  • Reorganized README structure for better clarity
  • Updated contact information and documentation links
src/pynxtools_xps/nomad/examples/README.md
src/pynxtools_xps/nomad/entrypoints.py
File structure changes
  • Added new eln_conversion.archive.json and nexus_conversion.archive.json files
  • Removed Specs_conversion.archive.json
src/pynxtools_xps/nomad/examples/eln_conversion.archive.json
src/pynxtools_xps/nomad/examples/nexus_conversion.archive.json
src/pynxtools_xps/nomad/examples/Specs_conversion.archive.json

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Hey @lukaspie - I've reviewed your changes and they look great!

Here's what I looked at during the review
  • 🟡 General issues: 1 issue found
  • 🟢 Security: all looks good
  • 🟢 Testing: all looks good
  • 🟢 Complexity: all looks good
  • 🟢 Documentation: all looks good

Sourcery is free for open source - if you like our reviews please consider sharing them ✨
Help me be more useful! Please click 👍 or 👎 on each comment and I'll use the feedback to improve your reviews.


Below, you find an overview of your uploaded data.
Click on the `> /` button to get a list of your data or select **FILES** from the top menu of this upload.
Click on the `> /` button to get a list of your file or select **FILES** from the top menu of this upload.
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suggestion (typo): There appears to be a typo: 'list of your file' should be 'list of your files'

Suggested change
Click on the `> /` button to get a list of your file or select **FILES** from the top menu of this upload.
Click on the `> /` button to get a list of your files or select **FILES** from the top menu of this upload.

@lukaspie lukaspie merged commit aa65867 into main Dec 13, 2024
7 checks passed
@lukaspie lukaspie deleted the example-fix branch December 13, 2024 13:46
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