68 create entry from api creates entries without m def

[ka-sarthak]

• m_to_dict adds the m_def by default when the EntryData section is wrapped with EntryArchive, and this is supplied to create_entry_from_api. If a standalone EntryData section is supplied instead, with_root_def=True needs to be specified in m_to_dict.
• Fixed a bug where the save method used entry_name instead of mainfile.

[Copilot]

Pull Request Overview

This PR ensures that entries created from the API correctly include the m_def information when a standalone EntryData section is supplied and fixes a bug in the save method where the wrong file attribute was used.

• Updated m_to_dict call to use with_root_def=True for standalone EntryData cases
• Fixed a bug in the save method by switching from entry_name to mainfile

Reviewed Changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated no comments.

File	Description
src/nomad_analysis/utils.py	Updates the m_to_dict call to include m_def using with_root_def for standalone EntryData.
src/nomad_analysis/jupyter/schema.py	Fixes the file name parameter by using mainfile instead of entry_name.

Comments suppressed due to low confidence (2)

src/nomad_analysis/utils.py:200

• Consider adding unit tests to verify that m_to_dict correctly adds the m_def field when with_root_def is True for standalone EntryData cases.

            'data': section.m_to_dict(with_root_def=True),

src/nomad_analysis/jupyter/schema.py:493

• Consider adding tests to verify that the save method correctly uses the mainfile attribute to set the file name, ensuring the bug fix is maintained.

            file_name=self.m_parent.metadata.mainfile,