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205 changes: 205 additions & 0 deletions .metadata/nomad_plugin_metadata.auto.yaml
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id: pynxtools-em
metadata_schema_version: 1.0.0
name: pynxtools-em
description: pynxtools-em is a pynxtools reader plugin for electron microscopy (EM)
data.
license: LICENSE
upstream_repository: https://github.com/FAIRmat-NFDI/pynxtools-em
documentation: https://fairmat-nfdi.github.io/pynxtools-em/
homepage: https://github.com/FAIRmat-NFDI/pynxtools-em
issue_tracker: https://github.com/FAIRmat-NFDI/pynxtools-em/issues
authors:
- name: "Markus K\xFChbach"
- name: Sherjeel Shabih
- name: Sandor Brockhauser
- name: Erdmann Spiecker
- name: Heiko B. Weber
- name: Christoph Koch
- name: Claudia Draxl
entry_points:
- id: nomad.plugin:em_example_upload_entry_point
entry_point_group: nomad.plugin
entry_point_name: em_example_upload_entry_point
python_object: pynxtools_em.nomad.example_uploads:em_example_upload_entry_point
capability_type: example_upload
capabilities:
- id: em_example_upload_entry_point
capability_type: example_upload
title: em_example_upload_entry_point
summary: "\n This example presents the capabilities of the NOMAD platform\
\ to store and standardize electron microscopy data.\n It shows the generation\
\ of a NeXus file according to the\n [`NXem`](https://fairmat-nfdi.github.io/nexus_definitions/classes/applications/NXem.html#nxem)\n\
\ application definition.\n The example contains a small SEM dataset\
\ to get started and keep the size of your\n NOMAD installation small.\
\ Ones started, we recommend to change the respective input file in the NOMAD\
\ Oasis\n ELN to run the example with your own datasets.\n "
schema_dependencies:
- dependency_type: python_package
package_name: pynxtools
version_range: '>=0.12.0'
optional: false
purpose: runtime
- dependency_type: python_package
package_name: hyperspy
version_range: '>=1.7.6'
optional: false
purpose: runtime
- dependency_type: python_package
package_name: rosettasciio
version_range: ''
optional: false
purpose: runtime
- dependency_type: python_package
package_name: kikuchipy
version_range: ''
optional: false
purpose: runtime
- dependency_type: python_package
package_name: pyxem
version_range: ''
optional: false
purpose: runtime
- dependency_type: python_package
package_name: nionswift
version_range: ''
optional: false
purpose: runtime
- dependency_type: python_package
package_name: flatdict
version_range: ==4.0.0
optional: false
purpose: runtime
- dependency_type: python_package
package_name: xmltodict
version_range: ''
optional: false
purpose: runtime
- dependency_type: python_package
package_name: xraydb
version_range: ''
optional: false
purpose: runtime
- dependency_type: python_package
package_name: tzlocal
version_range: ''
optional: false
purpose: runtime
- dependency_type: python_package
package_name: mypy
version_range: ''
optional: true
purpose: optional
- dependency_type: python_package
package_name: ruff
version_range: '>=0.14.0'
optional: true
purpose: optional
- dependency_type: python_package
package_name: pytest
version_range: ''
optional: true
purpose: optional
- dependency_type: python_package
package_name: pytest-cov
version_range: ''
optional: true
purpose: optional
- dependency_type: python_package
package_name: pytest-timeout
version_range: ''
optional: true
purpose: optional
- dependency_type: python_package
package_name: structlog
version_range: ''
optional: true
purpose: optional
- dependency_type: python_package
package_name: types-pyyaml
version_range: ''
optional: true
purpose: optional
- dependency_type: python_package
package_name: types-pytz
version_range: ''
optional: true
purpose: optional
- dependency_type: python_package
package_name: types-requests
version_range: ''
optional: true
purpose: optional
- dependency_type: python_package
package_name: pre-commit
version_range: ''
optional: true
purpose: optional
- dependency_type: python_package
package_name: mkdocs
version_range: ''
optional: true
purpose: optional
- dependency_type: python_package
package_name: mkdocs-material
version_range: ''
optional: true
purpose: optional
- dependency_type: python_package
package_name: mkdocs-material-extensions
version_range: ''
optional: true
purpose: optional
- dependency_type: python_package
package_name: mkdocs-macros-plugin
version_range: ''
optional: true
purpose: optional
- dependency_type: python_package
package_name: pymdown-extensions
version_range: ''
optional: true
purpose: optional
- dependency_type: python_package
package_name: mkdocs-click
version_range: ''
optional: true
purpose: optional
- dependency_type: python_package
package_name: nomad-lab
version_range: '[infrastructure]>=1.3.17'
optional: true
purpose: optional
- dependency_type: python_package
package_name: jupyter
version_range: ''
optional: true
purpose: optional
- dependency_type: python_package
package_name: jupyterlab
version_range: ''
optional: true
purpose: optional
- dependency_type: python_package
package_name: jupyterlab_h5web
version_range: ''
optional: true
purpose: optional
metadata_provenance:
- source: pyproject
extraction_method: deterministic
generated_at: '2026-03-19T15:05:50.731960+00:00'
generator_version: 0.1.0
- source: plugin_entry_points
extraction_method: deterministic
generated_at: '2026-03-19T15:05:50.731996+00:00'
generator_version: 0.1.0
- source: citation_cff
extraction_method: deterministic
generated_at: '2026-03-19T15:05:50.732010+00:00'
generator_version: 0.1.0
stars: 3
owner: FAIRmat-NFDI
owner_type: Organization
created: '2024-03-18T17:41:58Z'
last_updated: '2026-02-11T15:06:16Z'
archived: false
84 changes: 84 additions & 0 deletions .metadata/nomad_plugin_metadata.manual.yaml
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# Maintainer-owned metadata overrides and manual additions.
# This file is never machine-overwritten after creation.
# Use null/empty values as placeholders; only non-empty values override auto output.
# list[str] domain/topic tags (e.g. "simulations", "spectroscopy")
subject:
- measurements
- microscopy
- electron-microscopy
- nexus
- data-standardization
# enum {alpha, beta, stable, archived}
maturity: beta
# str, e.g. "main"
repository_default_branch: main

# Deployment flags.
deployment:
# boolean
on_central: true
# boolean
on_example_oasis: null
# boolean
on_pypi: true
# str (PyPI package name)
pypi_package: pynxtools-em

# Suggested usages for registry filtering/discovery.
suggested_usages:
-
# str (stable ID slug), e.g. "parse-xrd-patterns"
id: standardize-em-data-to-nxem
# str
title: Standardize EM data to NXem
# str (what user wants to do), e.g. "Import and parse raw files"
user_intent: Convert and structure electron microscopy data according to NXem
# enum {simulations, measurements, synthesis, cross-domain, workflow, infrastructure}
domain_category: measurements
# str, e.g. "XRD", "DFT"
technique: electron-microscopy
# str, e.g. "beginner", "expert"
audience: intermediate
# enum {alpha, beta, stable, archived}
maturity: beta
# list[str]
tags: [em, tem, sem, nexus, nxem]
-
# str (stable ID slug), e.g. "parse-xrd-patterns"
id: test-em-workflow-with-example-upload
# str
title: Test NOMAD EM workflow with example upload
# str (what user wants to do), e.g. "Import and parse raw files"
user_intent: Use the bundled EM example upload to validate NOMAD processing and mapping
# enum {simulations, measurements, synthesis, cross-domain, workflow, infrastructure}
domain_category: workflow
# str, e.g. "XRD", "DFT"
technique: example-upload
# str, e.g. "beginner", "expert"
audience: beginner
# enum {alpha, beta, stable, archived}
maturity: beta
# list[str]
tags: [example-upload, onboarding, em]

# Optional file format metadata enrichments.
file_format_support:
-
# str (stable ID), e.g. "csv"
id: null
# str display label, e.g. ".csv"
label: null
# str capability reference (links to capabilities[].id), e.g. "vasp_parser"
capability_id: null
# str producer/code family for ambiguous extensions, e.g. "vasp", "quantumespresso"
producer: null
# list[str] extensions including dot, e.g. [".csv", ".txt"]
extensions: []
# list[str], e.g. ["text/csv"]
mime_types: []
# str, e.g. "CIF", "NeXus"
standard: null
# str, instrument or context label
instrument_context: null
# str free text notes
notes: null
4 changes: 4 additions & 0 deletions .metadata/plugin-metadata.override-report.yaml
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summary:
overridden_field_count: 0
manual_precedence: true
overridden_fields: []
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