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Metadata FBC3#1440

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Commits on Jun 4, 2020

• added annotation class

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• made some modifications

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Commits on Jun 9, 2020

• made the complete metadata package

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Commits on Jun 10, 2020

• modified meta_data classes

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Commits on Jun 11, 2020

• modified classes to look exactly like dictionaries and lists

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• modified imports and incorporated SBO term in metadata

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Commits on Jun 13, 2020

• made the classed to inherit from MutableSequence and MutableMapping

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Commits on Jun 15, 2020

• adding backward compatibility

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• added instance

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• work on annotation structure

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• adding json example

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• fixed instance2

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• work on cvterms

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Commits on Jun 18, 2020

• made backward compatible

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• code review metadata

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Commits on Jun 21, 2020

• cleaned the metadata class by putting code in respective classes

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Commits on Jun 23, 2020

• new annotation format supported for SBML to cobra model

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Commits on Jun 24, 2020

• added io for json and other formats

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Commits on Jun 25, 2020

• added tests for new annotation format

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• updated history

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Commits on Jun 28, 2020

• fixing broken tests

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• commented a few methods

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Commits on Jun 29, 2020

• added equal method inisde metadata classes

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Commits on Jun 30, 2020

• modified directories paths

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• fixed imports and tox tests

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Commits on Jul 1, 2020

• solved the problem of annotation copy

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Commits on Jul 2, 2020

• new notes format

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• code refactoring

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Commits on Jul 4, 2020

• modified history, keyvaluepair and notes

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Commits on Jul 5, 2020

• modified tests and imports

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Commits on Jul 6, 2020

• modified cvterm class

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Commits on Jul 9, 2020

• small fixes

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Commits on Jul 12, 2020

• refactored a few names

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Commits on Jul 15, 2020

• modified notes documentation

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Commits on Jul 16, 2020

• added user defined constraint class

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• example test cases

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Commits on Jul 23, 2020

• added tests for UserDefinedConstraints

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• modified tests

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Commits on Jul 26, 2020

• small modifications

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• moved cobra directory to src directory

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• solved conflicts

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• fixed some tests

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• fixed conflicts and tests

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Commits on Jul 27, 2020

• fixed tests

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• added support of group to JSON

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Commits on Jul 28, 2020

• added support for optional ids in UserDefinedConstraint class

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Commits on Jul 30, 2020

• added test for json validation function

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• added json schema import requirement

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• added helper function for UserDefinedConstraint

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• added validate function for json models

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Commits on Aug 5, 2020

• added ast tree for parsing constraint expression

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Commits on Aug 6, 2020

• modified json validation function

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• removed python 2 support

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• modified ids in json

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• code refactoring

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Commits on Aug 9, 2020

• reformatted code to python 3

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Commits on Aug 15, 2020

• added datetime validation for py3.6

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• modified dict.py

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• modified xfail

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• removed .idea files

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• removed .idea

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Commits on Aug 16, 2020

• merged with devel

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• removed idea

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Commits on Aug 21, 2020

• modified notes string passing

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Commits on Aug 26, 2020

• modified notes return type

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• adding dependency for json validation

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• added .idea files

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• merged latest devel

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• refactored and cleanup of history

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• Intermediate refactoring, breaking changes

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• refactored keyvaluepairs

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• cleanup of datetimes

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• cleanup metadata

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• cleanup dict methods

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Commits on Aug 27, 2020

• added to_dict for CVTerm and fixed models

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• added metadata.ipynb

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• fixed imports

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• Merge branch 'devel' into metadata_fbc3_group

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• smaller fix to_dict usage

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Commits on Aug 28, 2020

• modified to_dict for cvterms

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• separated UserDefinedConstraint

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Commits on May 11, 2022

• Merge branch 'devel' into metadata_fbc3_group

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• fixed most of the merging errors - most tests work

  

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• fixed test_annotation_format.py and deleted previous version

  

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• fixed SBML problems with merge

  

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Commits on May 12, 2022

• fixed field names of creators

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Commits on Jun 16, 2022

• Merge branch 'devel' into metadata_fbc3

  

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• fixed data, e_coli_new_format.json, schema_v2.json and some code changes in history.py and test_sbml.py

  

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• consistent schema_v2.json

  

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Commits on Jun 19, 2022

• merged devel into #988 and updated it to current code

  

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• removed Notes as class

  

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• renamed constructors as requested

  

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• isort and black

  

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• isort error again

  

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• sorry, updating salmonella.xml broke test_delete.py

  

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• fix gitignore

  

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Commits on Jun 27, 2022

• documentation

  

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Commits on Jun 28, 2022

• incorporated changes from fixing mat PR

  

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• keyvaluepairs.py is documented

  

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Commits on Jun 30, 2022

• history.py is documented

  

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Commits on Jul 1, 2022

• black on reaction.py

  

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Commits on Jul 4, 2022

• removed notes.py and fixed some small bugs

  

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Commits on Jul 5, 2022

• creator is NamedTuple and has simpler api

  

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• replaced HistoryDateTime with standard datetime.datetime class

  

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• fix HistoryDateTime remaining

  

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• maybe will work better on Python 3.6

  

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Commits on Jul 6, 2022

• Merge remote-tracking branch 'upstream/devel' into metadata_fbc3

  

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Commits on Jul 8, 2022

• minor bug in history.py

  

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• Revert "minor bug in history.py"

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• trying to fix 3.6 bug

  

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• trying to fix 3.6 bug again

  

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Commits on Jul 12, 2022

• some tidying of sbml.py

  

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• one query for CVTermList as requested

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Commits on Jul 14, 2022

• better documentation

  

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Commits on Jul 20, 2022

• almost complete documentation for cvterm.py including CVTerm, CVTermList - need examples (TODO)

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Commits on Jul 21, 2022

• some clarification and fixes of cvterm.py

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• reorganized metadata.py

  

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• fixed some changes in tests and example JSON due to changes in code

  

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Commits on Jul 25, 2022

• finished documentation of metadata.py

  

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• moved annotation_xml to conftest.py

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Commits on Jul 26, 2022

• fix unification of CVTerms done by sbml

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• simplified custompairs.py

  

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Commits on Mar 28, 2025

• Merged devel branch (2bee3b9) into this branch. Fixed some type annotations and added comments. Fixed issues that came forward when running tox. Updated pickle files due to renaming of custompairs.py.

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• Fixed some URLs in docstrings. Converted the Creator class to represent names as a single value (supported in SBML Core 3 Level 2 using vCard4) (based on comments by cdiener in https://github.com/o…

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Commits on Mar 29, 2025

• Enabled changing the Metadata Qualifier names to more readable names. For now, renamed bqm_* to Modelling_* and bqb_* to Biological_*.

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Commits on Mar 31, 2025

• Updated the documentation to reflect the latest changes in the Metadata interface. Removed the Notes section, since that code was removed anyway.

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Commits on Apr 1, 2025

• Initial work on a more convenient and cobrapy-style interface to annotations.

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Commits on Apr 2, 2025

• Initial work to improve the handling of key-value pair annotations.

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• Partially fixed reading/writing sbml with the new annotation interface. Reintroduced __repr__ methods.

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Commits on Apr 3, 2025

• Re-implemented many of the annotation methods. New functions for flattening the annotation trees. Passes most annotation tests, except legacy annotation compatibility tests.

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Commits on Apr 10, 2025

• Moved old style annotations to SimplifiedAnnotationsInterface, accessible through object.annotations.simplified.

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Commits on Apr 11, 2025

• Pretty complete dict-like old-style annotation implementation.

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• Old-style annotations improvements

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• Changed the organization of old- and new-style annotations.

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Commits on Apr 14, 2025

• Fixed json loading and saving with the new annotation/metadata object structure.

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Commits on Apr 15, 2025

• Added some default qualifiers, mainly for manuscripts/books/patents, where Biological_is does not make sense.

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• Renamed cvterm and keyvaluepair files to standardized and custom files, corresponding to the new metadata type names.

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Commits on Apr 16, 2025

• Updated pickle files, json v2 schema.

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• Improved documentation, renamed CustomAnnotationList to CustomAnnotationStore.

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Commits on Apr 17, 2025

• Reorganized annotation interfaces, added docstrings.

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Commits on Apr 22, 2025

• Renamed Identifier -> Resource and MetaData -> Metadata.

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• Updated docstrings of annotation methods.

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• Improved documentation for standardized annotations.

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Commits on Apr 23, 2025

• Added docstrings, added strict mode to Resource, added StandardizedAnnotationList to serve as alternative to StandardizedAnnotationStore, but without ownership.

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• Added standardized annotation indexing by qualifier(s), added a QualifiersAlias enum to handle common sets of qualifiers.

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Commits on Apr 24, 2025

• Added the StandardizedAnnotationStore.resources_for method, which provides a powerful interface to select resources.

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• Better documentation for custom annotations and the legacy annotation interface.

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• Small fixes and increased test coverage for standardized annotations.

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• Improved test coverage of metadata-related methods.

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Commits on Apr 25, 2025

• Updated json schema v2 custom annotations.

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• Consolidate ownership/parent methods for annotations.

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• Cleanup, fixed spelling errors, small fixes.

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• Added extra methods/tests to make sure existing code I found on github keeps working.

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• Implemented saving CustomAnnotations/keyvaluepairs to SBML, added test cases, improved implementation. Almost all tests are still passing, except some that seem to be caused by lacking implementati…

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Commits on Apr 27, 2025

• Fixed issues with int/floating point charges (change in FBCv2->v3: fbc-20304). Only remaining failing test is missing implementation of saving nested annotations of KeyValuePairs (fbc-21502).

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Commits on Apr 30, 2025

• Fixed error when using python 3.8. I accidentally used a newer python feature.

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• Improved parsing of identifier.org URLS. Different cases (old style URLs and compact urls with integrated namespace) should all work correctly now. Changed Resource equality to namespace+identifier…

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Commits on May 1, 2025

• Improved Resource class, added convenience of directly using compact identifiers.org identifiers as URI. Added the appropriate tests for that. Made hashing method consistent with equality method.

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• Fixed test that failed due to new hashing logic.

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• Improved documentation, added some examples. Improved test coverage for standardized.py.

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Commits on May 5, 2025

• Performance improvements for metadata. Custom (deep)copy implementations to speed up copying of models.

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• Set libsbml version to 5.20.5, since this fixes cvterms nested in kvps not being written to SBML. Updated tests. Added xfail test for nested kvps.

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• The updated libsbml does not support python 3.8, so setup.cfg has been adapted accordingly and some tests are marked for skipping when run with python 3.8.

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• Small fixes and optimizations

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Commits on May 6, 2025

• Omitted calling deepcopy as much as possible, since it adds a lot of overhead. Metadata should not have any recurring (identical) objects, so those checks are not necessary.

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