Code

PyEnzyme v2.0.0#67

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JR-1991 wants to merge 80 commits intomainEnzymeML/PyEnzyme:mainfrom v2-migrationEnzymeML/PyEnzyme:v2-migrationCopy head branch name to clipboard

+26,639-16,569

Commits

Commits on Jun 22, 2024

• remove old workflows

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• fix spelling

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• remove unused code and artifacts

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• add migrated lib

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• migrate to pyproject

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• linting and testing workflows

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• update fixtures

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• ignore mac things

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• fix typos

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• update readme

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• add new tests

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• only lint pyenzyme and tests

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• add dev examples

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Commits on Jun 25, 2024

• use serialization_alias for ld fields

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• remove unused imports

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Commits on Jun 26, 2024

• added pyright and poetry

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• regenerated lib via gen.toml including celsius

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• replaced content with newly generated model

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• replaced mode, added celsius as unit

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• remove unused import

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• Merge pull request #68 from EnzymeML/add-celsius

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  JR-1991

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Commits on Aug 16, 2024

• updated pandas dependency version range

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• update dev examples

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• implement sbml omex parser

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• adjust serializer to model change

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• adjust and extend mappings to model changes

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• format strings in multiple lines

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• model update

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• utilities to parse RDF

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• remove redundant unit arg

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• export vital sbml functions

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• adjust to model changes

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• add parameter fetcher

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• refactor and extend to nested and multiple types

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• rename to prevent mutability issues

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• add pymetadata dep for OMEX support

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• update tests

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• remove unused imports

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• remove unused units

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Commits on Aug 19, 2024

• update dev example

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• attach readers and writers to model class

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• add parameters to enzmldoc

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• move params to root

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• adapt to parameter loc and cast str to float

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• adapt parameter change

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• cast to float

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• add utility to strip ld keys

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• update tests

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Commits on Aug 20, 2024

• add to_pandas to EnzymeMLDocument

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• data, time, time_unit in MeasurementData not mandatory anymore

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Commits on Aug 23, 2024

• - can not assume filenames

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• - init defaults to add missing attributes

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• - omex uses /tab-separated-values for tsv

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Commits on Sep 7, 2024

• update dev examples

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• add default imports

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• extract all files within omex

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• adapt parser and serializer to annotations

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• add support for legacy and new version

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• rename method and update docs

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• use float instead of int

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• add function to extract the namespaces

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• update tests

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• add pydantic-xml dep

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• add testing section

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• add container test

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• check fragments instead of complete uris

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• Merge branch 'pydantic-xml' into v2-migration

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• if multiplier is 1 set it to None

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• add run command

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  1e3bee5

Commits on Sep 8, 2024

• add vessel_id to Complex

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• update dev examples

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• extract compartment for Complex

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• update tests

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• remove unused import

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Commits on Sep 23, 2024

• add suite class

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Commits on Sep 24, 2024

• fix units not recognized

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• Return None if unit is None

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• set temp unit and value optional

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Commits on Sep 25, 2024

• fix unit ids not retrieved corectly

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• fix unit ids and remove validation error

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