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Metadata fbc3 #1237

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Commits on Jun 4, 2020

  1. added annotation class

    @Hemant27031999
    Hemant27031999 committed Jun 4, 2020
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  2. made some modifications

    @Hemant27031999
    Hemant27031999 committed Jun 4, 2020
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Commits on Jun 9, 2020

  1. made the complete metadata package

    @Hemant27031999
    Hemant27031999 committed Jun 9, 2020
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Commits on Jun 10, 2020

  1. modified meta_data classes

    @Hemant27031999
    Hemant27031999 committed Jun 10, 2020
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Commits on Jun 11, 2020

  1. modified classes to look exactly like dictionaries and lists

    @Hemant27031999
    Hemant27031999 committed Jun 11, 2020
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  2. modified imports and incorporated SBO term in metadata

    @Hemant27031999
    Hemant27031999 committed Jun 11, 2020
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Commits on Jun 13, 2020

  1. made the classed to inherit from MutableSequence and MutableMapping

    @Hemant27031999
    Hemant27031999 committed Jun 13, 2020
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Commits on Jun 15, 2020

  1. adding backward compatibility

    @Hemant27031999
    Hemant27031999 committed Jun 15, 2020
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  2. added instance

    @Hemant27031999
    Hemant27031999 committed Jun 15, 2020
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  3. work on annotation structure

    @matthiaskoenig
    matthiaskoenig committed Jun 15, 2020
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  4. adding json example

    @matthiaskoenig
    matthiaskoenig committed Jun 15, 2020
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  5. fixed instance2

    @Hemant27031999
    Hemant27031999 committed Jun 15, 2020
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  6. work on cvterms

    @matthiaskoenig
    matthiaskoenig committed Jun 15, 2020
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Commits on Jun 18, 2020

  1. made backward compatible

    @Hemant27031999
    Hemant27031999 committed Jun 18, 2020
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  2. code review metadata

    @matthiaskoenig
    matthiaskoenig committed Jun 18, 2020
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Commits on Jun 21, 2020

  1. cleaned the metadata class by putting code in respective classes

    @Hemant27031999
    Hemant27031999 committed Jun 21, 2020
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Commits on Jun 23, 2020

  1. new annotation format supported for SBML to cobra model

    @Hemant27031999
    Hemant27031999 committed Jun 23, 2020
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Commits on Jun 24, 2020

  1. added io for json and other formats

    @Hemant27031999
    Hemant27031999 committed Jun 24, 2020
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Commits on Jun 25, 2020

  1. added tests for new annotation format

    @Hemant27031999
    Hemant27031999 committed Jun 25, 2020
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  2. updated history

    @matthiaskoenig
    matthiaskoenig committed Jun 25, 2020
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Commits on Jun 28, 2020

  1. fixing broken tests

    @Hemant27031999
    Hemant27031999 committed Jun 28, 2020
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  2. commented a few methods

    @Hemant27031999
    Hemant27031999 committed Jun 28, 2020
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Commits on Jun 29, 2020

  1. added equal method inisde metadata classes

    @Hemant27031999
    Hemant27031999 committed Jun 29, 2020
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Commits on Jun 30, 2020

  1. modified directories paths

    @Hemant27031999
    Hemant27031999 committed Jun 30, 2020
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  2. fixed imports and tox tests

    @Hemant27031999
    Hemant27031999 committed Jun 30, 2020
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Commits on Jul 1, 2020

  1. solved the problem of annotation copy

    @Hemant27031999
    Hemant27031999 committed Jul 1, 2020
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Commits on Jul 2, 2020

  1. new notes format

    @Hemant27031999
    Hemant27031999 committed Jul 2, 2020
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  2. code refactoring

    @matthiaskoenig
    matthiaskoenig committed Jul 2, 2020
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Commits on Jul 4, 2020

  1. modified history, keyvaluepair and notes

    @Hemant27031999
    Hemant27031999 committed Jul 4, 2020
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Commits on Jul 5, 2020

  1. modified tests and imports

    @Hemant27031999
    Hemant27031999 committed Jul 5, 2020
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Commits on Jul 6, 2020

  1. modified cvterm class

    @Hemant27031999
    Hemant27031999 committed Jul 6, 2020
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Commits on Jul 9, 2020

  1. small fixes

    @matthiaskoenig
    matthiaskoenig committed Jul 9, 2020
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Commits on Jul 12, 2020

  1. refactored a few names

    @Hemant27031999
    Hemant27031999 committed Jul 12, 2020
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Commits on Jul 15, 2020

  1. modified notes documentation

    @Hemant27031999
    Hemant27031999 committed Jul 15, 2020
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Commits on Jul 16, 2020

  1. added user defined constraint class

    @Hemant27031999
    Hemant27031999 committed Jul 16, 2020
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  2. example test cases

    @matthiaskoenig
    matthiaskoenig committed Jul 16, 2020
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Commits on Jul 23, 2020

  1. added tests for UserDefinedConstraints

    @Hemant27031999
    Hemant27031999 committed Jul 23, 2020
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  2. modified tests

    @Hemant27031999
    Hemant27031999 committed Jul 23, 2020
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Commits on Jul 26, 2020

  1. small modifications

    @Hemant27031999
    Hemant27031999 committed Jul 26, 2020
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  2. moved cobra directory to src directory

    @Hemant27031999
    Hemant27031999 committed Jul 26, 2020
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  3. solved conflicts

    @Hemant27031999
    Hemant27031999 committed Jul 26, 2020
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  4. fixed some tests

    @Hemant27031999
    Hemant27031999 committed Jul 26, 2020
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  5. fixed conflicts and tests

    @Hemant27031999
    Hemant27031999 committed Jul 26, 2020
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Commits on Jul 27, 2020

  1. fixed tests

    @Hemant27031999
    Hemant27031999 committed Jul 27, 2020
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  2. added support of group to JSON

    @Hemant27031999
    Hemant27031999 committed Jul 27, 2020
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Commits on Jul 28, 2020

  1. added support for optional ids in UserDefinedConstraint class

    @Hemant27031999
    Hemant27031999 committed Jul 28, 2020
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Commits on Jul 30, 2020

  1. added test for json validation function

    @Hemant27031999
    Hemant27031999 committed Jul 30, 2020
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  2. added json schema import requirement

    @Hemant27031999
    Hemant27031999 committed Jul 30, 2020
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  3. added helper function for UserDefinedConstraint

    @Hemant27031999
    Hemant27031999 committed Jul 30, 2020
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  4. added validate function for json models

    @Hemant27031999
    Hemant27031999 committed Jul 30, 2020
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Commits on Aug 5, 2020

  1. added ast tree for parsing constraint expression

    @Hemant27031999
    Hemant27031999 committed Aug 5, 2020
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Commits on Aug 6, 2020

  1. modified json validation function

    @Hemant27031999
    Hemant27031999 committed Aug 6, 2020
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  2. removed python 2 support

    @Hemant27031999
    Hemant27031999 committed Aug 6, 2020
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  3. modified ids in json

    @Hemant27031999
    Hemant27031999 committed Aug 6, 2020
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  4. code refactoring

    @matthiaskoenig
    matthiaskoenig committed Aug 6, 2020
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Commits on Aug 9, 2020

  1. reformatted code to python 3

    @Hemant27031999
    Hemant27031999 committed Aug 9, 2020
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Commits on Aug 15, 2020

  1. added datetime validation for py3.6

    @Hemant27031999
    Hemant27031999 committed Aug 15, 2020
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  2. modified dict.py

    @Hemant27031999
    Hemant27031999 committed Aug 15, 2020
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  3. modified xfail

    @Hemant27031999
    Hemant27031999 committed Aug 15, 2020
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  4. removed .idea files

    @Hemant27031999
    Hemant27031999 committed Aug 15, 2020
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  5. removed .idea

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Commits on Aug 16, 2020

  1. merged with devel

    @Hemant27031999
    Hemant27031999 committed Aug 16, 2020
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  2. removed idea

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    Hemant27031999 committed Aug 16, 2020
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Commits on Aug 21, 2020

  1. modified notes string passing

    @Hemant27031999
    Hemant27031999 committed Aug 21, 2020
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Commits on Aug 26, 2020

  1. modified notes return type

    @Hemant27031999
    Hemant27031999 committed Aug 26, 2020
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  2. adding dependency for json validation

    @matthiaskoenig
    matthiaskoenig committed Aug 26, 2020
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  3. added .idea files

    @matthiaskoenig
    matthiaskoenig committed Aug 26, 2020
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  4. merged latest devel

    @matthiaskoenig
    matthiaskoenig committed Aug 26, 2020
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  5. refactored and cleanup of history

    @matthiaskoenig
    matthiaskoenig committed Aug 26, 2020
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  6. Intermediate refactoring, breaking changes

    @matthiaskoenig
    matthiaskoenig committed Aug 26, 2020
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  7. refactored keyvaluepairs

    @matthiaskoenig
    matthiaskoenig committed Aug 26, 2020
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  8. cleanup of datetimes

    @matthiaskoenig
    matthiaskoenig committed Aug 26, 2020
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  9. cleanup metadata

    @matthiaskoenig
    matthiaskoenig committed Aug 26, 2020
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  10. cleanup dict methods

    @matthiaskoenig
    matthiaskoenig committed Aug 26, 2020
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Commits on Aug 27, 2020

  1. added to_dict for CVTerm and fixed models

    @Hemant27031999
    Hemant27031999 committed Aug 27, 2020
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  2. added metadata.ipynb

    @Hemant27031999
    Hemant27031999 committed Aug 27, 2020
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  3. fixed imports

    @Hemant27031999
    Hemant27031999 committed Aug 27, 2020
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  4. Merge branch 'devel' into metadata_fbc3_group

    @Hemant27031999
    Hemant27031999 authored Aug 27, 2020
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  5. smaller fix to_dict usage

    @matthiaskoenig
    matthiaskoenig committed Aug 27, 2020
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Commits on Aug 28, 2020

  1. modified to_dict for cvterms

    @Hemant27031999
    Hemant27031999 committed Aug 28, 2020
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  2. separated UserDefinedConstraint

    @Hemant27031999
    Hemant27031999 committed Aug 28, 2020
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Commits on May 11, 2022

  1. Merge branch 'devel' into metadata_fbc3_group 

    # Conflicts:
#	setup.cfg
#	src/cobra/core/__init__.py
#	src/cobra/core/formula.py
#	src/cobra/core/object.py
#	src/cobra/flux_analysis/variability.py
#	src/cobra/io/dict.py
#	src/cobra/io/json.py
#	src/cobra/io/sbml.py
#	src/cobra/manipulation/validate.py
#	src/cobra/sampling/achr.py
#	src/cobra/sampling/optgp.py
#	src/cobra/test/data/mini.pickle
#	src/cobra/test/data/salmonella.pickle
#	src/cobra/test/test_io/conftest.py
#	src/cobra/test/test_io/test_annotation_format.py
#	src/cobra/test/test_io/test_io_order.py
#	src/cobra/test/test_io/test_json.py
#	src/cobra/test/test_io/test_mat.py
#	src/cobra/test/test_io/test_pickle.py
#	src/cobra/test/test_io/test_yaml.py
#	src/cobra/test/test_manipulation.py
#	tests/test_io/test_notes.py
#	tests/test_io/test_sbml.py
    uri.akavia committed May 11, 2022
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  2. fixed most of the merging errors - most tests work

    uri.akavia committed May 11, 2022
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  3. fixed test_annotation_format.py and deleted previous version

    uri.akavia committed May 11, 2022
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  4. fixed SBML problems with merge

    uri.akavia committed May 11, 2022
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Commits on May 12, 2022

  1. fixed field names of creators 

    Some tidying of test_json.py
    uri.akavia committed May 12, 2022
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Commits on Jun 16, 2022

  1. Merge branch 'devel' into metadata_fbc3

    uri.akavia committed Jun 16, 2022
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  2. fixed data, e_coli_new_format.json, schema_v2.json and some code chan… 

    …ges in history.py and test_sbml.py
    uri.akavia committed Jun 16, 2022
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  3. consistent schema_v2.json

    uri.akavia committed Jun 16, 2022
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Commits on Jun 19, 2022

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

    uri.akavia committed Jun 19, 2022
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  2. removed Notes as class

    uri.akavia committed Jun 19, 2022
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  3. renamed constructors as requested

    uri.akavia committed Jun 19, 2022
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  4. isort and black

    uri.akavia committed Jun 19, 2022
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  5. isort error again

    uri.akavia committed Jun 19, 2022
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  6. sorry, updating salmonella.xml broke test_delete.py

    uri.akavia committed Jun 19, 2022
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  7. fix gitignore

    uri.akavia committed Jun 19, 2022
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Commits on Jun 27, 2022

  1. documentation

    uri.akavia committed Jun 27, 2022
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Commits on Jun 28, 2022

  1. incorporated changes from fixing mat PR

    uri.akavia committed Jun 28, 2022
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  2. keyvaluepairs.py is documented

    uri.akavia committed Jun 28, 2022
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Commits on Jun 30, 2022

  1. history.py is documented

    uri.akavia committed Jun 30, 2022
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Commits on Jul 1, 2022

  1. black on reaction.py

    uri.akavia committed Jul 1, 2022
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Commits on Jul 4, 2022

  1. removed notes.py and fixed some small bugs

    uri.akavia committed Jul 4, 2022
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Commits on Jul 5, 2022

  1. creator is NamedTuple and has simpler api

    uri.akavia committed Jul 5, 2022
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  2. replaced HistoryDateTime with standard datetime.datetime class

    uri.akavia committed Jul 5, 2022
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  3. fix HistoryDateTime remaining

    uri.akavia committed Jul 5, 2022
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  4. maybe will work better on Python 3.6

    uri.akavia committed Jul 5, 2022
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Commits on Jul 6, 2022

  1. Merge remote-tracking branch 'upstream/devel' into metadata_fbc3

    uri.akavia committed Jul 6, 2022
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Commits on Jul 8, 2022

  1. minor bug in history.py

    uri.akavia committed Jul 8, 2022
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  2. Revert "minor bug in history.py" 

    This reverts commit c95b8c6.
    uri.akavia committed Jul 8, 2022
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  3. trying to fix 3.6 bug

    uri.akavia committed Jul 8, 2022
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  4. trying to fix 3.6 bug again

    uri.akavia committed Jul 8, 2022
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Commits on Jul 12, 2022

  1. some tidying of sbml.py

    uri.akavia committed Jul 12, 2022
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  2. one query for CVTermList as requested 

    sbml document history is saved
added relevant tests
    uri.akavia committed Jul 12, 2022
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Commits on Jul 14, 2022

  1. better documentation

    uri.akavia committed Jul 14, 2022
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Commits on Jul 20, 2022

  1. almost complete documentation for cvterm.py including CVTerm, CVTermL… 

    …ist - need examples (TODO)

Qualifiers as string enum
CVTermList will output list of dicts, not a dict
update_pickles.py
minor renaming
changed sbml.py according to previous changes. cleaned up processing of history in sbml.py
changed test_metadata.py according to these changes
    uri.akavia committed Jul 20, 2022
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Commits on Jul 21, 2022

  1. some clarification and fixes of cvterm.py 

    improve equality of History object
some tidying of metadata.py and adding __eq__ function
added test_old_style_annotation to test_metadata.py
    uri.akavia committed Jul 21, 2022
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  2. reorganized metadata.py

    uri.akavia committed Jul 21, 2022
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  3. fixed some changes in tests and example JSON due to changes in code

    uri.akavia committed Jul 21, 2022
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Commits on Jul 25, 2022

  1. finished documentation of metadata.py

    uri.akavia committed Jul 25, 2022
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  2. moved annotation_xml to conftest.py 

    updated some data and tests
    uri.akavia committed Jul 25, 2022
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Commits on Jul 26, 2022

  1. fix unification of CVTerms done by sbml 

    Some minor modifications and comments on sbml and test_sbml.py
    uri.akavia committed Jul 26, 2022
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  2. simplified custompairs.py

    uri.akavia committed Jul 26, 2022
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