Code

Adds multi format reader#250

Code

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domna merged 73 commits intomasterFAIRmat-NFDI/pynxtools:masterfrom multi-format-readerFAIRmat-NFDI/pynxtools:multi-format-readerCopy head branch name to clipboardAug 12, 2024

+611-34

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Commits on Aug 12, 2024

• Adds multi format reader

  

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• Adds standard parsings

  

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• Add json config parsing

  

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• Use default factory for list

  

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• Only resolve asterisk from same level

  

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• Remove residual testing code

  

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• Adds eln callback and config argument

  

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• Adds list parsing for special prefixes

  

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• Add **kwargs to example reader

  

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• Add nomad .pylintrc

  

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• modified: pynxtools/dataconverter/readers/multi/reader.py

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• Provide entry names and use __post_init__ for dataclass

  

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• Silence mypy false positive

  

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• Add ? notation for dependent keys

  

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• Ruff formatting

  

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• Remove pylintrc

  

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• Move reader to src dir

  

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• Adds processing order and optional groups removal

  

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• Move reader into src and delete old location

  

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• Fixes from testing

  

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• Adapt tests to definition overwrite message

  

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• Adapt get_data_dims

  

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• update defs once again

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• temporarily use feature branches in plugin tests

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• switch to plugin main branches again

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• Add docs for rules in NeXus

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• Git reset in publish workflow

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• fetch submodules, git reset before build

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• add workflow to simulate publishing

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• Add git status after build

  

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• Run diff

  

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• Remove publish test

  

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• Remove unused import

  

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• Add post_processing step

  

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• Write to new dict in json parsing, otherwise we always create an entry named entry

  

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• Copy values to new dict if no magic keyword is present

  

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• Resolve links from written data

  

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• add fix for missing keys in dict again (from c1ecb70)

  

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• Ruff format

  

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• Remove optional groups in the main loop

  

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• Call data dims when entry name is present

  

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• parse config before postprocess

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• modify docs

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• Pass keys to json callbacks

  

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• Replace ENTRY instead of ENTRY[entry] in config dict

  

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• Update prefix:value notation

  

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• Correctly remove ! dependent keys

  

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• Allow lists of possible values in config file

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• simplify static typing

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• Fix removal of missing groups

  

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• simplify code, make docstrings more elaborate

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• Configure handler for root logger

  

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• Init config_dict

  

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• pass parent key to parse_yml (#391)

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• Update default value for parent_key in FlattenSettings

  

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• Readd link flattening to flatten_json

  

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• Fix the config dict sorting

  

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• Use single pynxtools logger which does not propagate

  

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• Capture log calls from non-propagating loggers

  

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• Add create_link_dict parameter for flatten_json

  

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• propagate create_link_dict parameter

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• set create_link_dict to False for MultiFormatReader

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• re-add logger propagation

  

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• Adapt logging and don't parse objects if they are none

  

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• strip ! prefix before parsing lists

  

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• Remove unecessary checks for ! notation

  

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• make removed groups an info again

  

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• enhance docs of ParseJsonCallbacks

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• pop suppress_warning from kwargs

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• Remove caplog overwrite for non-root logger tests

  

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• custom logging formatting

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• make highlighted logger levels a constant

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• update nexus-version

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