Integration nexus file

[RubelMozumder]

Summary by Sourcery

Implement Nexus file generation for XRD measurements.

PR #116 handled in #118 and #147.

[sourcery-ai]

Reviewer's Guide by Sourcery

This pull request integrates the nexus file generation into the XRD processing pipeline. It introduces functions to map NOMAD concepts to NeXus paths, populate datasets and attributes, and handle unit conversions. It also updates the _write_nx_file method to generate the nexus file using the populated data and a template based on the NXxrd_pan application definition.

Sequence diagram for NeXus file generation process

sequenceDiagram
    participant Archive as NOMAD Archive
    participant Writer as NX Writer
    participant Template as NeXus Template
    participant File as NeXus File

    Writer->>Template: generate_template_from_nxdl()
    Writer->>Archive: populate_nx_dataset_and_attribute()
    Archive-->>Writer: Return datasets and attributes
    Writer->>Template: Add datasets to template
    Writer->>Template: Add attributes to template
    Writer->>File: Write NeXus file using template
    Writer->>Archive: Update file references

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Class diagram for NeXus integration components

classDiagram
    class DatasetModel {
        +data: Any
        +internal_reference: Optional[bool]
        +archive_path: Optional[str]
    }

    class Writer {
        -_hdf5_datasets: dict
        -_hdf5_attributes: dict
        +_write_nx_file()
        +_write_hdf5_file()
        -_remove_nexus_annotations()
        -_set_hdf5_reference()
    }

    class Template {
        +dict data
        +dict optional
    }

    Writer --> DatasetModel : uses
    Writer --> Template : uses
    note for Writer "Handles NeXus file generation"
    note for DatasetModel "Stores dataset information"

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File-Level Changes

Change	Details	Files
Implementation of nexus file generation.	Added functions to map NOMAD archive data to NeXus datasets and attributes. Added functions to handle unit conversions for NeXus attributes. Added functions to create nexus groups and handle optional data. Implemented nexus file writing using pynxtools. Updated _write_nx_file to generate nexus file with archive data.	src/nomad_measurements/xrd/nx.py src/nomad_measurements/utils.py
Introduction of new dependencies and type annotations.	Added type annotations for improved code clarity. Introduced new dependencies like pint for unit handling and pydantic for data validation.	src/nomad_measurements/xrd/nx.py
Updated nexus dataset paths.	Added new paths to NEXUS_DATASET_PATHS to accommodate the new data being written to the nexus file.	src/nomad_measurements/xrd/nx.py

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[sourcery-ai]

Hey @RubelMozumder - I've reviewed your changes - here's some feedback:

Overall Comments:

• Remove the outdated TODO comments in _write_nx_file() since they have been implemented
• Consider adding more specific error messages when NeXus file generation fails to help with debugging

Here's what I looked at during the review

• 🟡 General issues: 3 issues found
• 🟢 Security: all looks good
• 🟢 Testing: all looks good
• 🟢 Complexity: all looks good
• 🟢 Documentation: all looks good

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[RubelMozumder]

This PR replaced by #150 .