Update version numbers and changelog.

SED-ML · Mar 14, 2024 · ba189f1 · ba189f1
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diff --git a/.github/workflows/BioPortal-submission.json b/.github/workflows/BioPortal-submission.json
@@ -1,9 +1,9 @@
 {
   "ontology": "https://data.bioontology.org/ontologies/KISAO",
-  "pullLocation": "https://raw.githubusercontent.com/SED-ML/KiSAO/2.32/kisao.owl",
+  "pullLocation": "https://raw.githubusercontent.com/SED-ML/KiSAO/2.34/kisao.owl",
   "hasOntologyLanguage": "OWL",
   "description": "The Kinetic Simulation Algorithm Ontology (KiSAO) is an ontology of algorithms for simulating and analyzing biological models, as well as the characteristics of these algorithms, their input parameters, and their outputs. In addition, KiSAO captures relationships among algorithms, their parameters, and their outputs.",
-  "version": "2.32",
+  "version": "2.34",
   "released": "2023-05-24T02:54:00-00:00",
   "status": "production",
   "homepage": "http://biomodels.net/kisao/",

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,13 @@
 # Changelog
 
+## 2.34 (OWL 2)
+- Added organizational 'DAE solver' (`KISAO_0000699`) for collecting solvers that can solve DAE problems.
+- Removed 'has characteristic' some 'differential-algebraic equation problem' from KINSOL and from 'method for solving a system of linear equations'.
+- The characteristics 'differential-algebraic equation problem' and ''ordinary differential equation problem' are no longer disjoint (and in fact the former are a complete subset of the latter).
+
+## 2.33 (OWL 2)
+- Reorganized the steady state algorithms: moved flux balance and steady state to 'general steady state method' (`KISAO_0000630`), and others to the 'steady state root-finding method' (`KISAO_0000407`)
+
 ## 2.32 (OWL 2)
 - Added algorithm concepts for eQuilibrator.
 - Added organizational 'ODE solver' (`KISAO_0000694`) for noting in SED-ML that some solver should be used, but which is not important.

diff --git a/kisao.owl b/kisao.owl
@@ -19,7 +19,7 @@
         <rdfs:label xml:lang="en">Kinetic Simulation Algorithm Ontology (KiSAO)</rdfs:label>
         <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://co.mbine.org/standards/kisao</rdfs:seeAlso>
         <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://identifiers.org/pubmed/22027554</rdfs:seeAlso>
-        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#decimal">2.32</owl:versionInfo>
+        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#decimal">2.34</owl:versionInfo>
         <skos:definition xml:lang="en">The Kinetic Simulation Algorithm Ontology (KiSAO) classifies algorithms available for the simulation and analysis of models in biology, and their characteristics and the parameters required for their use.</skos:definition>
     </owl:Ontology>
 

diff --git a/kisao_full.owl b/kisao_full.owl
@@ -19,7 +19,7 @@
         <rdfs:comment xml:lang="en">Kinetic Simulation Algorithm Ontology (full version, containing deprecated classes)</rdfs:comment>
         <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://co.mbine.org/standards/kisao</rdfs:seeAlso>
         <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://identifiers.org/pubmed/22027554</rdfs:seeAlso>
-        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#decimal">2.33</owl:versionInfo>
+        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#decimal">2.34</owl:versionInfo>
         <skos:definition xml:lang="en">The Kinetic Simulation Algorithm Ontology (KiSAO) classifies algorithms available for the simulation and analysis of models in biology, and their characteristics and the parameters required for their use.</skos:definition>
     </owl:Ontology>
 

diff --git a/libkisao/python/kisao/_version.py b/libkisao/python/kisao/_version.py
@@ -1 +1 @@
-__version__ = '2.33'
+__version__ = '2.34'
diff --git a/updating.md b/updating.md
@@ -0,0 +1,10 @@
+# What needs to be updated when making a new release
+
+Put new version into:
+* libkisao/python/kisao/_version.py
+* kisao.owl (i.e. <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#decimal">2.34</owl:versionInfo>)
+* kisao_full.owl (i.e. <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#decimal">2.34</owl:versionInfo>)
+* .github/workflows/BioPortal-submission.json
+
+Summarize changes in:
+* CHANGELOG.md