JlibSEDML 2.2.3
This is JlibSEDML 2.2.3 released April 2016, compatible with SEDML Level 1 Version 2
New features
- This release has improved support for level 1 version 2 - it will now validate
level 1 version 2 documents against the XML schema.
2.2.2 - January 2016
This is a maintenance release with no new functionality, but some orthogonal improvements:
- System out calls replaced with slf4j logging, for better integration with your logging
library
- Javadoc improvements - all 100 Javadoc errors fixed.
- updated library dependencies.
- Replaced Ant build with Gradle build.
Notes from previous releases:
2.2.1 - May 2014
- More methods added to RepeatedTask
- implemented support for logarithmic UniformRange
- validation for jdom 1.1.3 compatibility
- cleaning up some obsolete test classes, and more.
2.2.0 released Apr 2014. New features include:
Implementation of the Dec 3, 2013 final version of the Simulation Experiment Description Markup Language (SED-ML) :
Level 1 Version 2
This is JlibSEDML 2.1.0 released Jun 2013. New features include:
Implementation of the draft of the Simulation Experiment Description Markup Language (SED-ML) :
Level 1 Version 2
This is JlibSEDML 2.0.1 released April 2012. New features include:
1) Improved XPath prefix mapping to support XPath prefixes generated by the SED-ED editor.
To ensure prefixes can be resolved to an XML namespace, SED generates a prefix from a namespace,
converting '/' character to _. jlibsedml can now match these prefixes to the namespaces
from which they were derived.
2 )Added XML convenience functions
3) Convenience methods in SEDML objects
a) To add datagenerators easily
b) to get maths from DG.
(Needs Javadoc ).
This is JlibSEDML 2.0.0 released March 2012, and has major
incompatible API changes from the version 1.x series.
The main change is a renaming of the packages into the org.jlibsedml namespace.
This was necessary in order to create a unique namespace for jlibsedml that can
be coordinated with the website URL www.jlibsedml.org, and to distance this project
from the official www.sed-ml.org namespace. The new package name
also enables the deployment of the library to the Maven central repository,
which was not possible before.
Clearly the package renaming will break all current code using version 1 of jlibsedml.
This current release, 2.0.0 contains no new functionality from 1.2.0, so updating
is entirely optional, but all new development to support new levels of
SED-ML will be performed in the org.jlibsedml namespace.
From this point on we don't expect the package names to change anymore!
jlibsedml 1.2.0 - New functionality & bugfixes since 1.1.4:
------------------------------------------
- Setter methods added for most attributes of core SED-ML elements. These methods
were purposely omitted up till now in order to keep objects immutable once created. However,
this makes modifying objects rather awkward, so they are added now.
- The XPath prefix reg-exp that identifies prefixes has been enhanced to cope with a wider
range of prefixes.
- Addition of a pom.xml file for incorporation of jlibsedml into a Maven build.
- Improvements to the SED-ML-to-HTML stylesheet, to display names in preference to IDs.
- Addition of Schematron schema elements for enhanced validation of SED-ML documents.
Anticipated breaking API changes
-------------------------------
None expected.
This is JlibSEDML 1.1.4 released November 2011, and is a bugfix / minor functional change release for
SEDML level 1 version 1.
New functionality & bugfixes since 1.1.3:
------------------------------------------
Addition of an XSLT stylesheet, sedml2html.xsl, converting SED-ML to HTML
New functionality & bugfixes since 1.1.2:
------------------------------------------
Addition of visitor pattern to navigate the SEDML object structure.
New functionality & bugfixes since 1.1.1:
------------------------------------------
1. Added a Biomodels model retriever class, org.jlibsedml.modelsupport.BioModelsModelsRetriever, which can obtain Biomodels SBML files from a
Miriam URN of the form urn:miriam:biomodels.db:BIOMD0000000XXX.xml
2. Fixed some validation bugs, which hid some SED-ML errors when validating against the schema.
3. Top level MathML elements ( i.e., 'math' elements ) are now in MathML namespace, not SED-ML namespace
as they have been, erroneously.
4. A new version of JMathML ( version 2.1 ) is now bundled with jlibsedml, with several bugfixes.
Breaking API changes:
---------------------
None expected.
New functionality & bugfixes since 1.1.0:
------------------------------------------
1. Made constructor for NewXML public. This was an oversight in 1.0.0.(Tracker 3286903)
2. Added public accessor for all Kisao terms.
3. Provided a publicly accessible collection of supported model terms (Tracker 3288178 )
4. SimulationsValidator bug fixed which caused NPE if the simulation is invalid.
5. Changes and outputs are now written in schema order (rather than the order they were added to
the SEDML model). Tracker 3296093
6. Tracker 3295947 - a bug which caused NewXML to have the XML to be added to the model be
in the SED-ML namespace is fixed so that it is now added in the empty namespace.
7. The ModelResolver class is now public API to allow Model 'source' attributes to be resolved
independently of the execution framework ( tracker 3300133).
8. Annotations can now be read in properly for all SED-ML elements (tracker 3287552).
Breaking API changes:
--------------------
None expected.
Please send bug-reports, suggestions and comments to the jlibsedml tracker at
http://sourceforge.net/tracker/?group_id=323585
Thanks,
Richard Adams
University of Edinburgh
April 2012
