FAIRmat-NFDI / pynxtools

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• update-documentation-for-undocumented
• 121-code-for-handling-dicts-in-writer-should-be-improved
• 163-write-nxroot-attributes
• 165-merging-of-multiple-files
• 194-xps-slh-metadata-reader
• 196-import-problems-in-dev-install-when-in-parent-directory
• 198-github-issue-template-form-needs-to-be-fixed
• 206-xps-reader-nxmpes-update
• 208-logger-level
• 222-c-flag-not-working-in-read-nexus
• 223-add-a-get-required-flag-to-the-converter
• 224-xps-sub-reader-for-phi-versaprobe-data
• 232-bug-link-broken-in-converting-data-to-nexus-tutorial
• 241-pluginise-xps-reader
• 255-adding-default-attribute-to-immediate-child-group
• 261-add-a-skip-verification-flag-skip-verify-to-dataconverter
• 293-duplicate-reader-in-nomad
• 300-switch-to-src-layout
• 325-bug-update-help-of-dataconverter-in-that-no-longer-existent-names-of-readers-should-be-removed
• 397-bug-converter-failing-with-is-invalid-appdef-although-file-not-found-is-culprit
• 398-add-documentation-pages-for-multi-format-reader
• 403-improvement-add-nx-doc-string-as-attribute
• 405-move-readme-content-to-documentation
• 467-allow-kwargs-in-readertest
• 485-optional-results-material
• 511-use-new-fairmat-nomad-plugin-logo
• 521-add-support-for-formulas-in-multiformat-reader
• 563-bug-converter-does-not-warn-if-variadic-concept-name-is-invalid
• 583-update-chemical_formula-normalization
• 593-bug-dataconverter-validation-very-slow-for-large-arrays
• 599-undescriptive-error-message
• 599-undescriptive-error-message-cleanup
• 606-unconventional-function-naming
• 617-unpin-pint
• 643-bug-raise-error-if-there-are-two-variadic-concepts-with-the-same-name
• 644-bug-validation-fails-with-key-error-if-link-cannot-be-resolved
• 666-bug-validation-of-open-enumerations-does-not-search-for-custom-attribute
• 690-code-added-in-531-is-not-needed-anymore
• 716-spellchecking-should-include-the-source-code-as-well
• 84-update-and-add-test-for-hdfdict
• AddDoiUrl
• Bug_Attributes_Of_Nonexisting_Fields
• Bug_Validation_Error_When_Passing_Zero
• ConsiderIdentifier
• FixErrorIfUnitInPintQuantity
• FixOrOperandError
• Fix_nexus_parsers
• Fix_nomad_dependency
• HoodDefinition
• Hotfix
• KIT_xps
• ModificationForMetainfo
• RefixReference
• RetryToPublish
• SPM_file_parser
• STM_version_1
• SerialiseTest
• Stop_Overwritting_entry_type
• TemplateFromNxTree
• XPS_SLE_reader
• XRDPlugin
• XRD_reader_integretion
• XRD_use_ase
• XRDuseCase
• acknowledge-funding
• activate_ellipsometry_plugin_test
• activate_spm_raman
• add-definition-automatically
• add-ellips-plugin
• add-mkdocs-click
• add-nexus-version-file
• add-objects-to-transmission
• add-pynxtools-xps-to-extras
• add-stm-extra
• add-url-to-auto-definition
• add-warnings-test
• add_bool_to_nxcharornumber
• add_datetime_as_min_all_start_times
• add_default_plot
• add_more_tests
• add_raman_as_plugin
• add_warning_if_handle_function_is_ill_defined
• adds-test-group-optionality
• align-docs-with-nomad
• allow-multiple-branches-in-plugin-tests
• allow_wildcard_definition_in_reader_test
• apm-em-plugins-nxdefs-tracking
• apm-em-sprint14-p2
• apm-moved-to-pynxtools-apm
• apm_app
• apm_norm
• appdef-graph
• appdef-graph-tests
• author-lists
• automatic-versioning
• avoid-name-conflict
• base-class-inheritance
• basiceln_filename
• beam_path_demo_examples
• bring_back_nexus_defs
• build-artifacts
• bump-ruff
• bump-ruff-in-precommit
• bump_ruff_version
• bypass_v06
• cache-build-path
• cff_nxt_release
• check-nomad-requirements
• citation
• citation-for-v081
• citation-update
• cmmngr-patch-2
• compresssion-checks
• concept-name-for-nonvariadic
• connecting_to_base_sections
• constrain-plugin-versions
• control_entry_type
• convert_binary_strings
• convert_binary_strings_enhanced
• convert_int_to_float
• dataconverter-append
• definitions-script
• deprecate_ellipsometry_reader
• do-not-propagate-logger-in-testing
• docs-for-cli-api
• docs-plugin-howto-fix
• documentation
• drop-python38
• ellips_mock
• ellipsometry-add-aoi-scan-axis
• eln-mapper-nexus-tree
• em_refactoring
• enable-pynx-mpes-plugin-test
• entry_as_task
• entry_type
• entry_type2
• entrypoints-plugins
• example_update
• export
• extend_nx_type
• extra-for-all-plugins
• file-arguments
• fix-all-names-of-readers
• fix-axes-retrieval
• fix-build
• fix-coveralls
• fix-duplicate-print
• fix-enumeration-check
• fix-importlib-dependency
• fix-indentation-in-docs
• fix-inherited-child-retrieval
• fix-link-in-docs
• fix-logging-console
• fix-metainfo-tests
• fix-mpes-data-indices
• fix-mpes-reader-asterisk
• fix-naming-convention-adding
• fix-nexus-parsing
• fix-nomad-entrypoints
• fix-nomad-interface
• fix-required-under-optional
• fix-requirements-workflow
• fix-transmission-det-ranges
• fix-tutorial-links
• fix-type-hints
• fix-version-retrieval
• fix_attribute_enum_check
• fix_chemical_formula
• fix_clickopt_configfile_default
• fix_coverage
• fix_example
• fix_for_nexus_app_after_pynxtool_update
• fix_issue_670
• fix_linting
• fix_list_enums
• fix_minfo_domain
• fix_nexus_memory_leak
• fix_short_notation
• fix_validation_and_add_more_tests
• fix_validation_verify_nexus_install
• fixes-metainfo-generation-for-appdef-extended-basesection
• fixes_uint_posint_plus_dbg_hint
• fixing-template-and-path-issue
• full-checkout-for-publish
• full_visit
• generic_test_for_reader_plg
• generic_test_in_ci_cd
• get-method-template
• git-reset-in-build-step
• git-reset-in-publish-workflow
• hdf-based-validation
• hot_fix_pynxtools
• improves-dataconverter-writer-error
• include_raman_reader
• inheritance-chain-fixes
• inheritance-fix
• integrate-pynxtools-igor
• is_mock_argument
• joss_paper
• joss_paper_dataconverter_edit
• json_map_parsing
• jumpToReference_EmApmCgMs_2nd
• map-to-basesections
• map-to-basesections-reorganized
• map-to-basesections-reorganized_2
• master
• metainfo-pkg
• migration_changes
• mkdocs-dependencies
• mmov_em_apm_announcement
• move-buildwrapper-in-package
• move-nomad-examples-to-plugin
• move-nomad-examples-to-plugin_extend
• mpes-automate-data-indices
• mpes-reader-update
• mpesworkshop_167_new
• multi-format-reader
• newVersionSPM
• newer-python-support
• nexus-refactor
• nexus-rules-in-docs
• nexus_validation_tutorial
• nexus_validation_tutorial_try2
• no-log-error-for-missing-concepts
• no_inner_sections
• nomad-app
• nomad-compatibility
• nomad-hotfix
• nomad-logging-in-testing
• nomad-plugin
• nomad-release-check
• nx_char_type
• offset-units
• ontology-service
• open_enums_in_nomad
• optional-link-in-multireader
• optionality_check_in_nyam2nxdl
• package-title-in-Citation
• pin-ruff-0.3.4
• pint-units
• pluginise-mpes-reader
• plugins-in-docs
• prepare-v0.11.1
• prepare_next_release
• prepare_v0.12.0
• py310-as-standard
• py312
• pynxtools-release-0.10.2
• pytest-9
• python-312-in-dev
• python-version
• quick-fix
• quick-fix-mpes
• raise-lower-plugin-versions
• read-nexus-axis-fix
• read-nexus-log-level
• readme-updates
• reduce-dependencies
• refactor-xps-reader
• remove-dangling-xps-folder
• remove-nyaml2nxdl
• remove-obsolete-flags
• remove-pr-coveralls-message
• remove-pydantic
• remove-rii-converter
• remove-setuptools
• remove-transmission-and-hall
• remove-unneeded-doc-script
• remove_XRD
• rename-plugin-extra
• rename-to-pynxtools
• repease10_8
• replace_BasicEln
• reserved-prefixes-suffixes
• reset-plugin-branches
• restructure-docs
• revert-136-STM_version_1
• revert-263-update-ase-dep-in-pyproject
• revert-365-add_raman_as_plugin
• revert-528-ruff
• revert-675
• rm-dev-requirements
• rm-uv
• ruff
• search_app_for_NXsensor_scan_and_inhereting_classes
• self-closing-option
• sibling-inheritance
• simplify-attr-setter
• small-fixes
• small-test-fixes
• small-updates-to-multi-reader
• sort-readers
• spm_nxdef_deps
• str-output-in-read-nexus
• support-extends-in-nexus-tree
• support-npv2
• tester
• transmission-add-metadata-fields
• typo-and-url-fixes
• typos
• units-in-manifest
• units-registry-update
• update-ase-dep-in-pyproject
• update-citation
• update-definitions
• update-defs
• update-defs-and-related-tools
• update-defs-and-target
• update-defs-optical
• update-defs-readd-mpes-bc
• update-manifest
• update-markus-north
• update-nomad-link-in-cicd
• update-north-markus
• update-readme-with-correct-extra
• update-ruff
• update-ruff-settings
• update-units
• update-workflows
• update_SPM
• update_XRD_app_def
• update_and_release
• update_appdef-reference
• update_for_nexus_app_remove_userID_fix_column_sampleID
• update_req
• update_spm
• upgrade-numpy-and-ruff
• use-config-fs-tmp
• use-log-files-in-tests
• use-nxscan-for-eln-test
• useRoot
• uv-compile-and-install
• uv-env-in-publish-cicd
• v0.11.0
• validation-docs
• verification
• writer-variable-attrs
• xps-fixes
• xps-vms-reader

Merge c360bf6f1 into debd5cb82