sbmlutils - 0.9.0

Release notes for sbmlutils 0.9.0

We are pleased to release the next version of sbmlutils including the following changes:

Features

• bump pymetadata>=0.4.0 to switch to OLS4
• python 3.12 support (dropping python 3.9)
• pydantic fixes
• bugfixes
• updated sbml4humans
• libsbml-4.20.4
• improved ODE generation

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Published by github-actions[bot] over 1 year ago

sbmlutils - 0.8.7

Release notes for sbmlutils 0.8.7

We are pleased to release the next version of sbmlutils including the following changes:

Features

• bump python-libsbml>=5.20.2

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Published by github-actions[bot] over 2 years ago

sbmlutils - 0.8.6

Release notes for sbmlutils 0.8.6

We are pleased to release the next version of sbmlutils including the following changes:

Features

• fix #435, better unit support of sbml base units such as pascal or watt
• fix issue with registry: unexpected keyword argument 'deprecationOfflineDate'

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Published by github-actions[bot] over 2 years ago

sbmlutils - 0.8.5

Release notes for sbmlutils 0.8.5

We are pleased to release the next version of sbmlutils including the following changes:

Features

• fix #434, pydantic breaking changes
• minor fixes in type comparison
• bump pydantic version to >2.1 via pymetadata>=0.3.10

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Published by github-actions[bot] over 2 years ago

sbmlutils - 0.8.4

Release notes for sbmlutils 0.8.4

We are pleased to release the next version of sbmlutils including the following changes:

Features

• first version ODE report
• improvement: bump python-libsbml>=5.20.1
• updated development dependencies
• bugfix: logging flattening errors
• dropping python 3.8 support

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Published by github-actions[bot] over 2 years ago

sbmlutils - 0.8.3

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Published by github-actions[bot] over 2 years ago

sbmlutils - 0.8.2

Release notes for sbmlutils 0.8.2

We are pleased to release the next version of sbmlutils including the following changes:

Features

• first version ODE report
• improvement: bump python-libsbml>=5.20.1
• updated development dependencies
• bugfix: logging flattening errors
• dropping python 3.8 support

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Published by github-actions[bot] over 2 years ago

sbmlutils - 0.8.1

Release notes for sbmlutils 0.8.1

We are pleased to release the next version of sbmlutils including the following changes:

Features

• Fix #430, support for python 3.11

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Published by github-actions[bot] about 3 years ago

sbmlutils - 0.8.0

Release notes for sbmlutils 0.8.0

We are pleased to release the next version of sbmlutils including the following changes:

Features

• removed deprecated create_report
• Fix #409, support for AlgebraicRules
• Fix #333, full support of SBase information on rules: AssignmentRule, RateRule, AlgebraicRule.
• Fix #360, fixed CSS styling in SBML report
• Fix #414, better example for parameters and values in E-notation
• Fix #413, support for variable stoichiometries in reactions
• Fix #412, refactored equation handling
• removed deprecated write_model_to_sbml
• refactored validation options
• support for setting sid on InitialAssignment and Rules
• fixed issue with checking existing assignments and rules
• Fix #420, data structure for validation options. Support of general_consistency, identifier_consistency, mathml_consistency, units_consistency, sbo_consistency, overdetermined_model, modeling_practice
• Fix #418, simplified and clarified model creation options (backwards incompatibility!)
• Fix #422, improved handling of packages (backwards incompatibility!)
• Fix #411, support of antimony models
• Bump python-libsbml>=5.19.7, fixes for fbc support

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Published by github-actions[bot] about 3 years ago

sbmlutils - 0.7.6

Release notes for sbmlutils 0.7.6

We are pleased to release the next version of sbmlutils including the following changes:

Features

• update pymetadata to 0.3.0
• update depinfo>=2.0.0
• update python-libsbml>=5.19.5, security fixes
• logging helpers

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Published by github-actions[bot] over 3 years ago

sbmlutils - 0.7.5

Release notes for sbmlutils 0.7.5

We are pleased to release the next version of sbmlutils including the following changes:

Features

• Fix #400, better string formatting
• Fix #399, refactored test directory
• Fix #402, update pymetadata>=0.2.9
• Fix #401, fixing failing tests
• Fix #403, github twitter actions fixed

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Published by github-actions[bot] almost 4 years ago

sbmlutils - 0.7.4

Release notes for sbmlutils 0.7.4

We are pleased to release the next version of sbmlutils including the following changes:

Features

• Fix #400, better string formatting
• Fix #399, refactored test directory
• Fix #402, update pymetadata>=0.2.9
• Fix #401, fixing failing tests
• Fix #403, github twitter actions fixed

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Published by github-actions[bot] almost 4 years ago

sbmlutils - 0.7.3

Release notes for sbmlutils 0.7.3

We are pleased to release the next version of sbmlutils including the following changes:

Features

• Fix #400, better string formatting
• Fix #399, refactored test directory
• Fix #402, update pymetadata>=0.2.9
• Fix #401, fixing failing tests
• Fix #403, github twitter actions fixed

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Published by github-actions[bot] almost 4 years ago

sbmlutils - 0.7.2

Release notes for sbmlutils 0.7.2

We are pleased to release the next version of sbmlutils including the following changes:

Features

• support python 3.10, Fix #389

Fixes

• renamed master branch to main, Fix #395
• bugfix priority math on events, Fix #394
• drop libroadrunner dependency, Fix #396

Backwards compatibility

• moving interpolation functionality to sbmlsim

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Published by github-actions[bot] almost 4 years ago

sbmlutils - 0.7.1

Release notes for sbmlutils 0.6.6

We are pleased to release the next version of sbmlutils including the following changes:

Features

Fixes

• Fix #390, updated libsbml

Backwards compatibility

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Published by github-actions[bot] almost 4 years ago

sbmlutils - 0.7.0

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Published by github-actions[bot] almost 4 years ago

sbmlutils - 0.6.5

Release notes for sbmlutils 0.6.5

We are pleased to release the next version of sbmlutils including the following changes:

Features

• fixing libroadrunner to working version

Fixes

Backwards compatibility

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Published by github-actions[bot] about 4 years ago

sbmlutils - 0.6.4

Release notes for sbmlutils 0.6.4

We are pleased to release the next version of sbmlutils including the following changes:

Features

• updated dependencies
• updated biomodels test cases

Fixes

Backwards compatibility

• dropping python 3.7 support due to end of life

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Published by github-actions[bot] about 4 years ago

sbmlutils - 0.6.3

Release notes for sbmlutils 0.6.3

We are pleased to release the next version of sbmlutils including the following changes:

Features

• Fix #382, report tested against all curated biomodels
• support for omex compression (via pymetadata)

Fixes

• support avogadro unit in SBML reports
• Fix #381, fixing unit issue with local parameters

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Published by github-actions[bot] over 4 years ago

sbmlutils - 0.6.1

Release notes for sbmlutils 0.6.1

We are pleased to release the next version of sbmlutils including the following changes:

Features

Fixes

• Fix #372, selection box report OMEX
• Fix #374, order files alphabetically in OMEX tree
• Fix #367, search bar state fix
• Fix #370, bugfix table ids
• Fix #379, improved rendering checkbox
• Bugfix roadrunner times argument via dependency

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Published by github-actions[bot] over 4 years ago

sbmlutils - 0.6.0

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sbmlutils - 0.5.8

Release notes for sbmlutils 0.5.8

We are pleased to release the next version of sbmlutils including the following changes:

Features

• Cleanup and refactoring of report tables
• Cleanup of SBML inline model
• Fix #225 and Fix #227, OMEX support for sbml4humans

Fixes

• Fix #366, rendering navigation menu
• Fix #308, example url rendered correctly
• Fix #369, RateRule math displayed correctly
• Fix #368, cleanup of tables

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Published by github-actions[bot] over 4 years ago

sbmlutils - 0.5.7

Release notes for sbmlutils 0.5.7

Bugfix release.

Features

• Fix #361, resizable splitter in report (redesign)

Fixes

• Fix #359, simplified dependencies, testing on mac, fixed mac install
• Fix #355, improved rendering of units
• Fix #362, smaller units
• Fix #363, derivedUnits and link tags
• Fix #365, lower and upper flux bound rendered correctly
• Fix #346, conversion factor handled correctly
• Fix #364, better rendering of True/False symbols

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Published by github-actions[bot] over 4 years ago

sbmlutils - 0.5.6

Release notes for sbmlutils 0.5.6

Bugfix release.

Fixes

• Fix #356, NaNs handled correctly
• Fix #354, rendering rate rule prefix
• Fix #355, model examples distributed with sbml4humans
• Fix #342, correctly reporting packages for examples

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Published by github-actions[bot] over 4 years ago

sbmlutils - 0.5.5

Release notes for sbmlutils 0.5.5

Bugfix release.

Fixes

• Fix #350, additional validation of units on object creation
• Fix #349, better error message if UnitDefinitions are not created
• Fix #351, cleanup API & removal temp files
• Fix #348, correct handling of NaN and UTF-8 encoding
• Fix #336, fixed base unit definitions
• Fix #338, improved unit rendering and definition

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Published by github-actions[bot] over 4 years ago

sbmlutils - 0.5.4

Release notes for sbmlutils 0.5.4

Bugfix release.

Fixes

• Fix #340, improved document rendering
• Fix #343, better rendering badges.
• Fix #339, better rendering of model history
• Fix #344, table cleanup
• Fix #334, duplicate creators on model merging
• Fix #347, SBOTerms not set correctly
• Fix #341, improved logging with rich

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Published by github-actions[bot] over 4 years ago

sbmlutils - 0.5.3

Release notes for sbmlutils 0.5.3

Minor bugfix release.

Fixes

• fix zenodo integration and grant information

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Published by github-actions[bot] over 4 years ago

sbmlutils - 0.5.2

Release notes for sbmlutils 0.5.2

This is a major release improving the model builder. Main features are a much simpler unit definition and highly improved notes on all SBases.

New features

• first class model object
• improved unit handling for models using pint
• markdown notes
• zenodo metadata

Fixes

• fix slow enums (Fix #322)

Deprecated features

• old SBML report

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Published by github-actions[bot] over 4 years ago

sbmlutils - 0.5.0

Release notes for sbmlutils 0.5.0

New features

• new sbmlreport
• improved metadata handling
• cytoscape model visualization ## Fixes
• annotation fixes
• minor model fixes ## Deprecated features
• old SBML report

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Published by github-actions[bot] over 4 years ago

sbmlutils - 0.4.13

Release notes for sbmlutils 0.4.13

New features

• new sbmlreport prototype (alpha version) ## Fixes
• annotation fixes
• comp simplifications ## Deprecated features
• old SBML features

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Published by github-actions[bot] over 4 years ago

sbmlutils - 0.4.12

Release notes for sbmlutils 0.4.12

New features

Fixes

• fixed model merging ## Other
• added model merging example and updated documentation
• fixed failing model merging tests ## Deprecated features

Backwards incompatible changes

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Published by github-actions[bot] almost 5 years ago

sbmlutils - 0.4.11

Release notes for sbmlutils 0.4.11

New features

• add set of curated biomodels and test reports (#199)

Fixes

• Fix #224, units not set on AssignmentRules and RateRules
• Fix #208, fixed formulas with restricted symbols
• Bugfix recursive piecewise parsing in Mathml to Sympy

Other

• Removed old type annotations

Deprecated features

Backwards incompatible changes

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Published by github-actions[bot] almost 5 years ago

sbmlutils - 0.4.10

Release notes for sbmlutils 0.4.10

New features

• support simple generation of all SBML levels and versions #215
• complete mypy check and type annotions (many small bug fixes)
• support of uncertainties in HTML reports #133

Fixes

• added annotations and uncertainties to all core objects
• improved/consistent handling of compartment size and parameter value
• fixing mypy issues #192
• refactored information for SBML report
• CI for documentation #212
• allow empty equations in reactions (valid with SBML L3V2)
• first class support for comp:ReplacedBy elements
• bugfix litre vs liter and metre vs meter bug ## Other

Deprecated features

Backwards incompatible changes

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sbmlutils - 0.4.9

Release notes for sbmlutils 0.4.9

New features

Fixes

Other

Deprecated features

Backwards incompatible changes

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Published by github-actions[bot] about 5 years ago

sbmlutils - 0.4.8

Release notes for sbmlutils 0.4.8

New features

• API documentation
• improved examples

Fixes

• updated fstrings in reports #185
• fixed broken documentation links #179
• updated issue templates #180
• added type annotations and argument documentation in reports module #184
• flake8 fixes #198
• fix inline units in mathml rendering #201

Other

• sympy mathml formating and conversion #195

Deprecated features

• removed eventdata
• removed unsupported multi information

Backwards incompatible changes

• sbmlutils.templates moved to sbmlutils.examples.templates
• sbmlutils.modelcreator.creator moved to sbmlutils.creator

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Published by github-actions[bot] about 5 years ago

sbmlutils - 0.4.7

Release notes for sbmlutils 0.4.7

New features

Fixes

• update libroadrunner>=2.0.5 (bugfix logging)

Other

• updated contributing information
• templates for issues, questions, feature requests
• reporting of dependencies for debugging

Deprecated features

Backwards incompatible changes

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Published by github-actions[bot] about 5 years ago

sbmlutils - 0.4.6

Release notes for sbmlutils 0.4.6

• simplified model factory
• improved and simplified model examples
• support of distrib with comp (flattening)
• update to libsbml>=5.19.0
• update libroadrunner>=2.0.4
• bugfix #173, deprecated xlrd replaced with openpyxl
• improved test coverage to >70%
• dropping python 3.6 support

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sbmlutils - 0.4.5

Release notes for sbmlutils 0.4.5

• ensuring no diff on saving SBML
• examples for boundary condition and initial condition

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sbmlutils - 0.4.4

Release notes for sbmlutils 0.4.4

• fixed readthedocs build
• fixed code coverage reports
• fixed packaging of additional resources (#168)

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Published by github-actions[bot] over 5 years ago

sbmlutils - 0.4.3

Release notes for sbmlutils 0.4.2

• bugfix image in README
• updated and cleanup of documentation

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sbmlutils - 0.4.1

Release notes for sbmlutils 0.4.1

Highlights

New features

Fixes

• fixes coverage report

Deprecated features

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Published by github-actions[bot] over 5 years ago

sbmlutils - sbmlutils-v0.4.0: python utilities for SBML

Release notes for sbmlutils 0.4.0

Highlights

• switch from travis to github actions
• black code formating; isort import handling
• type annotations and documentations
• removed future imports and other legacy code
• refactored unittest to pytest
• cobra and optlang now optional
• cleanup of function signatures
• more comprehensive type annotations

New features

• python 3.8 support
• support and CI-CD for Mac-OS and Windows

Fixes

• fixed pep8 issues
• fixed compressed SBML loading

Deprecated features

• refactored DFBA to https://github.com/matthiaskoenig/dfba

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Published by matthiaskoenig over 5 years ago

sbmlutils - sbmlutils-v0.3.9: python utilities for SBML

• full support for distrib (distributions and uncertainty)

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Published by matthiaskoenig almost 6 years ago

sbmlutils - sbmlutils-v0.3.8: python utilities for SBML

Release notes

0.3.8

• python 3.7 support (dropping py3.5)
• model manipulation (merging of models)

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Published by matthiaskoenig about 6 years ago

sbmlutils - sbmlutils-v0.3.7: python utilities for SBML

0.3.7

• documentation updated
• additional annotation formats supported
• support of formula and charge on species
• fixed tests
• bug fixes

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Published by matthiaskoenig over 6 years ago

sbmlutils - sbmlutils-v0.3.6

• support for mass and charge
• refactored and simplified Reactions
• better port support
• exchange reaction template

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Published by matthiaskoenig over 6 years ago

sbmlutils - sbmlutils-v0.3.5

• bugfix missing files

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Published by matthiaskoenig over 6 years ago

sbmlutils - sbmlutils-v0.3.4

• improved annotation support (inline annotations, annotation by url)
• checking against MIRIAM collections and patterns

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Published by matthiaskoenig over 6 years ago

sbmlutils - sbmlutils-v0.3.3

Update cobrapy dependencies and bugfixes.

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Published by matthiaskoenig almost 7 years ago

sbmlutils - sbmlutils-v0.3.2

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Published by matthiaskoenig almost 7 years ago

sbmlutils - sbmlutils-v0.3.1

• libSBML 5.18.0
• first distrib support

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Published by matthiaskoenig almost 7 years ago

sbmlutils - sbmlutils-v0.3.0

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Published by matthiaskoenig almost 7 years ago

sbmlutils - v0.3.0-alpha.1

• better comp support
• layout support
• improved fbc report
• bug fixes
• dropping support for python2

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Published by matthiaskoenig almost 7 years ago

sbmlutils - sbmlutils-v0.2.0

• better comp support
• hasOnlySubstanceUnits in sbmlreport added
• initialAmounts and initialConcentrations supported in sbmlcreator
• bug fixes

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Published by matthiaskoenig over 7 years ago

sbmlutils - sbmlutils-v0.1.9

• update dependencies
• pip 10 fixes installer
• fixed unit tests
• bug fixes

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Published by matthiaskoenig over 7 years ago

sbmlutils - sbmlutils-v0.1.8 DFBA release

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Published by matthiaskoenig over 8 years ago

sbmlutils - v0.1.7a

• Cleanup of unnecessary files to reduce library size

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Published by matthiaskoenig over 8 years ago

sbmlutils - v0.1.6 Release

• update SBML reports (fbc & comp support)
• modelcreator fixes
• DFBA examples updated & annotated
• annotation fixes

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Published by matthiaskoenig over 8 years ago

sbmlutils - 0.1.5a2

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Published by matthiaskoenig almost 9 years ago

sbmlutils - 0.1.5a1

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Published by matthiaskoenig almost 9 years ago

sbmlutils - sbmlutils-0.1.4

• documentation update
• CI improvements
• pytest
• DFBA update & bug fixes
• DFBA examples (toy and diauxic growth)
• bug fixes

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Published by matthiaskoenig almost 9 years ago

sbmlutils - sbmlutils-0.1.3

• python 3 support
• clean travis build with pip
• DFBA implementation
• bugfixes & improvements

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Published by matthiaskoenig almost 9 years ago

sbmlutils - sbmlutils-0.1.2

• bug fixes
• unittests

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Published by matthiaskoenig over 9 years ago

sbmlutils - Testing & bug fixes

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Published by matthiaskoenig almost 10 years ago

sbmlutils - Initial release v0.1.0

Basic functionality of sbmlutils.

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Published by matthiaskoenig almost 10 years ago