Adding nexus in ref

[RubelMozumder]

Implement Nexus file generation for XRD measurements.

PR #116 handled in #118 and #150.

[sourcery-ai]

Reviewer's Guide by Sourcery

This pull request implements NeXus support for XRD measurements. It introduces a new schema for storing NeXus references and populates it during normalization. Additionally, it includes functions to traverse archive data, map archive data to NeXus, and write NeXus files.

Sequence diagram for NeXus file generation process

sequenceDiagram
    participant Archive
    participant HDF5Handler
    participant Template
    participant Writer

    Archive->>HDF5Handler: write_nx_file()
    HDF5Handler->>Template: generate_template_from_nxdl()
    HDF5Handler->>HDF5Handler: populate_nx_dataset_and_attribute()
    loop For each dataset
        HDF5Handler->>Template: Add dataset to template
    end
    loop For each attribute
        HDF5Handler->>Template: Add attribute to template
    end
    HDF5Handler->>Writer: write(template)
    Writer-->>HDF5Handler: Return success
    HDF5Handler->>Archive: Update reference

Loading

Class diagram for NeXus implementation

classDiagram
    class ELNXRayDiffraction {
        +nexus_results: ArchiveSection
        +normalize(archive, logger)
        +get_read_write_functions()
    }

    class HDF5Handler {
        +write_nx_file()
        -_write_hdf5_file()
        -_remove_nexus_annotations()
    }

    class DatasetModel {
        +data: Any
    }

    ELNXRayDiffraction --> HDF5Handler
    HDF5Handler --> DatasetModel

    note for ELNXRayDiffraction "Added nexus_results field"
    note for HDF5Handler "Implemented NeXus file generation"

Loading

File-Level Changes

Change	Details	Files
Added support for NeXus in the XRD schema and data processing.	Introduced a new nexus_results field in the ELNXRayDiffraction schema to store references to NeXus entries. Added functions to traverse the archive data structure and map archive data to the corresponding NeXus datasets and attributes. Implemented a write_nx_file method in the HDF5Handler class to generate NeXus files. Included functions to populate NeXus datasets and attributes from the archive data. Added logic to populate the nexus_results field during normalization if a NeXus file exists and ends with '.nxs'.	src/nomad_measurements/xrd/schema.py src/nomad_measurements/xrd/nx.py src/nomad_measurements/utils.py

---

Tips and commands

Interacting with Sourcery

• Trigger a new review: Comment @sourcery-ai review on the pull request.
• Continue discussions: Reply directly to Sourcery's review comments.
• Generate a GitHub issue from a review comment: Ask Sourcery to create an
  issue from a review comment by replying to it.
• Generate a pull request title: Write @sourcery-ai anywhere in the pull
  request title to generate a title at any time.
• Generate a pull request summary: Write @sourcery-ai summary anywhere in
  the pull request body to generate a PR summary at any time. You can also use
  this command to specify where the summary should be inserted.

Customizing Your Experience

Access your dashboard to:

• Enable or disable review features such as the Sourcery-generated pull request
  summary, the reviewer's guide, and others.
• Change the review language.
• Add, remove or edit custom review instructions.
• Adjust other review settings.

Getting Help

• Contact our support team for questions or feedback.
• Visit our documentation for detailed guides and information.
• Keep in touch with the Sourcery team by following us on X/Twitter, LinkedIn or GitHub.

[sourcery-ai]

Hey @RubelMozumder - 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 ✨

• X
• Mastodon
• LinkedIn
• Facebook

_{Help me be more useful! Please click 👍 or 👎 on each comment and I'll use the feedback to improve your reviews.}

[sourcery-ai]

issue (bug_risk): Error handling could mask original exception when cleanup fails

Consider handling file deletion errors separately to preserve the original exception context and ensure proper cleanup.

[ka-sarthak]

Looks great!