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Metadata fbc3#1237

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akaviaLab wants to merge 122 commits intoopencobra:developencobra/cobrapy:develfrom akaviaLab:metadata_fbc3akaviaLab/cobrapy:metadata_fbc3Copy head branch name to clipboard

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Commits

Commits on Jun 4, 2020

• added annotation class

  Hemant27031999

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  782b645

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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

  matthiaskoenig

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• adding json example

  matthiaskoenig

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• fixed instance2

  Hemant27031999

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• work on cvterms

  matthiaskoenig

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Commits on Jun 18, 2020

• made backward compatible

  Hemant27031999

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• code review metadata

  matthiaskoenig

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Commits on Jun 21, 2020

• cleaned the metadata class by putting code in respective classes

  Hemant27031999

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Commits on Jun 23, 2020

• new annotation format supported for SBML to cobra model

  Hemant27031999

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Commits on Jun 24, 2020

• added io for json and other formats

  Hemant27031999

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Commits on Jun 25, 2020

• added tests for new annotation format

  Hemant27031999

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• updated history

  matthiaskoenig

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Commits on Jun 28, 2020

• fixing broken tests

  Hemant27031999

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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

  Hemant27031999

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Commits on Jul 1, 2020

• solved the problem of annotation copy

  Hemant27031999

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Commits on Jul 2, 2020

• new notes format

  Hemant27031999

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• code refactoring

  matthiaskoenig

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Commits on Jul 4, 2020

• modified history, keyvaluepair and notes

  Hemant27031999

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Commits on Jul 5, 2020

• modified tests and imports

  Hemant27031999

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Commits on Jul 6, 2020

• modified cvterm class

  Hemant27031999

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Commits on Jul 9, 2020

• small fixes

  matthiaskoenig

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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

  Hemant27031999

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• example test cases

  matthiaskoenig

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Commits on Jul 23, 2020

• added tests for UserDefinedConstraints

  Hemant27031999

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  efcf064

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• modified tests

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Commits on Jul 26, 2020

• small modifications

  Hemant27031999

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  d5dedc9

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• moved cobra directory to src directory

  Hemant27031999

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  f839755

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• solved conflicts

  Hemant27031999

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  9704a4b

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• fixed some tests

  Hemant27031999

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  211bf48

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• fixed conflicts and tests

  Hemant27031999

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Commits on Jul 27, 2020

• fixed tests

  Hemant27031999

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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

  Hemant27031999

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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

  Hemant27031999

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Commits on Aug 6, 2020

• modified json validation function

  Hemant27031999

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• removed python 2 support

  Hemant27031999

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• modified ids in json

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• code refactoring

  matthiaskoenig

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Commits on Aug 9, 2020

• reformatted code to python 3

  Hemant27031999

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Commits on Aug 15, 2020

• added datetime validation for py3.6

  Hemant27031999

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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

  matthiaskoenig

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• added .idea files

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• merged latest devel

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• refactored and cleanup of history

  matthiaskoenig

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• Intermediate refactoring, breaking changes

  matthiaskoenig

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  a6aefc5

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• refactored keyvaluepairs

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• cleanup of datetimes

  matthiaskoenig

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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

  Hemant27031999

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• added metadata.ipynb

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  c8b850a

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• fixed imports

  Hemant27031999

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• Merge branch 'devel' into metadata_fbc3_group

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• smaller fix to_dict usage

  matthiaskoenig

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Commits on Aug 28, 2020

• modified to_dict for cvterms

  Hemant27031999

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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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  uri.akavia

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  fbfb0e8

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• fixed most of the merging errors - most tests work

  

  uri.akavia

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• fixed test_annotation_format.py and deleted previous version

  

  uri.akavia

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• fixed SBML problems with merge

  

  uri.akavia

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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

  

  uri.akavia

  committed
  0237fae

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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

  

  uri.akavia

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• consistent schema_v2.json

  

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Commits on Jun 19, 2022

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

  

  uri.akavia

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• removed Notes as class

  

  uri.akavia

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• renamed constructors as requested

  

  uri.akavia

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• isort and black

  

  uri.akavia

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  166dc1b

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• isort error again

  

  uri.akavia

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• sorry, updating salmonella.xml broke test_delete.py

  

  uri.akavia

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• fix gitignore

  

  uri.akavia

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Commits on Jun 27, 2022

• documentation

  

  uri.akavia

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Commits on Jun 28, 2022

• incorporated changes from fixing mat PR

  

  uri.akavia

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• keyvaluepairs.py is documented

  

  uri.akavia

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Commits on Jun 30, 2022

• history.py is documented

  

  uri.akavia

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Commits on Jul 1, 2022

• black on reaction.py

  

  uri.akavia

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Commits on Jul 4, 2022

• removed notes.py and fixed some small bugs

  

  uri.akavia

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Commits on Jul 5, 2022

• creator is NamedTuple and has simpler api

  

  uri.akavia

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• replaced HistoryDateTime with standard datetime.datetime class

  

  uri.akavia

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• fix HistoryDateTime remaining

  

  uri.akavia

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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

  

  uri.akavia

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• Revert "minor bug in history.py"

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  uri.akavia

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• trying to fix 3.6 bug

  

  uri.akavia

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• trying to fix 3.6 bug again

  

  uri.akavia

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Commits on Jul 12, 2022

• some tidying of sbml.py

  

  uri.akavia

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• one query for CVTermList as requested

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  uri.akavia

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Commits on Jul 14, 2022

• better documentation

  

  uri.akavia

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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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  uri.akavia

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• reorganized metadata.py

  

  uri.akavia

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

  

  uri.akavia

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Commits on Jul 25, 2022

• finished documentation of metadata.py

  

  uri.akavia

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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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