Merge dev into mpbn

.github/workflows/BioPortal-submission.json

@@ -1,10 +1,10 @@
 {
   "ontology": "https://data.bioontology.org/ontologies/KISAO",
-  "pullLocation": "https://raw.githubusercontent.com/SED-ML/KiSAO/2.14/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": "2.14",
-  "released": "2021-04-29T02:54:00-00:00",
+  "version": "2.34",
+  "released": "2023-05-24T02:54:00-00:00",
   "status": "production",
   "homepage": "http://biomodels.net/kisao/",
   "documentation": "http://biomodels.net/kisao/",

.github/workflows/ci.yml

@@ -31,8 +31,8 @@ jobs:
 
       - name: Install pip and setuptools
         run: |
-          python -m pip install --upgrade pip
-          python -m pip install --upgrade setuptools
+          python -m pip install --upgrade pip==23.0.0
+          python -m pip install --upgrade pip==23.0.0
 
       - name: Install the Python KiSAO package
         working-directory: libkisao/python
@@ -104,7 +104,7 @@ jobs:
         run: |
           mainBranch=$(git symbolic-ref refs/remotes/origin/HEAD | cut -d '/' -f 4)
           mainBranchHeadRevision=$(git rev-parse refs/remotes/origin/${mainBranch})
-          echo "::set-output name=mainBranchHeadRevision::$mainBranchHeadRevision"
+          echo "mainBranchHeadRevision=$mainBranchHeadRevision" >> $GITHUB_OUTPUT
 
   determineIfReleaseNeeded:
     name: Determine if the package should be released
@@ -127,13 +127,17 @@ jobs:
           release="0"
 
           if [[ "${{ github.ref }}" =~ ^refs/tags/ ]]; then
+            echo "First check passed"
             tag_hash=$(git rev-parse "${{ github.ref }}")
+            echo "tag_hash: $tag_hash"
             if [ "$tag_hash" == "${{ needs.getMainBranchHeadRevision.outputs.mainBranchHeadRevision }}" ]; then
+              echo "Second check passed"
               release="1"
             fi
           fi
 
-          echo "::set-output name=release::$release"
+          echo "release=$release" >> $GITHUB_OUTPUT
+          echo "release=$release"
 
   commitCompiledDocumentation:
     name: Commit and push compiled documentation to GitHub
@@ -148,8 +152,8 @@ jobs:
         uses: actions/checkout@master
         with:
           fetch-depth: 1
-          ref: dev
-          token: ${{ secrets.ADMIN_GITHUB_TOKEN }}
+#          ref: dev
+#          token: ${{ secrets.ADMIN_GITHUB_TOKEN }}
 
       # Install the requirements for the tests
       - name: Install Python
@@ -167,8 +171,8 @@ jobs:
 
       - name: Install pip and setuptools
         run: |
-          python -m pip install --upgrade pip
-          python -m pip install --upgrade setuptools
+          python -m pip install --upgrade pip==23.0.0
+          python -m pip install --upgrade pip==23.0.0
 
       - name: Install the Python KiSAO package
         working-directory: libkisao/python
@@ -220,7 +224,7 @@ jobs:
           else
             docsChanged=0
           fi
-          echo "::set-output name=docsChanged::$docsChanged"
+          echo "docsChanged=$docsChanged" >> $GITHUB_OUTPUT
 
       - name: Push the compiled documentation
         if: startsWith(github.ref, 'refs/tags/') && steps.commit-docs.outputs.docsChanged == '1'
@@ -240,8 +244,9 @@ jobs:
       - name: Checkout repo
         uses: actions/checkout@master
         with:
-          ref: dev
-          token: ${{ secrets.ADMIN_GITHUB_TOKEN }}
+          fetch-depth: 1
+#          ref: dev
+#          token: ${{ secrets.ADMIN_GITHUB_TOKEN }}
 
       - name: Merge dev branch into deploy branch
         uses: devmasx/[email protected]
@@ -256,7 +261,7 @@ jobs:
           TAG: ${{ github.ref }}
         run: |
           version="${TAG/refs\/tags\//}"
-          echo "::set-output name=version::$version"
+          echo "version=$version" >> $GITHUB_OUTPUT
 
       - name: Create GitHub release
         uses: "marvinpinto/action-automatic-releases@latest"
@@ -337,10 +342,10 @@ jobs:
           restore-keys: |
             ${{ runner.os }}-pip-
 
-      - name: Install pip and setuptools
+      - name: Install pip
         run: |
-          python -m pip install --upgrade pip
-          python -m pip install --upgrade setuptools
+          python -m pip install --upgrade pip==23.0.0
+          python -m pip install --upgrade pip==23.0.0
 
       # Create PyPI release
       - name: Create PyPI release
@@ -352,12 +357,8 @@ jobs:
           # Install pandoc
           sudo apt-get update -y
           sudo apt-get install -y --no-install-recommends wget
-
-          wget https://github.com/jgm/pandoc/releases -O /tmp/pandocVersions.html
-          urlPart=`grep "\.deb" /tmp/pandocVersions.html | head -n 1 | cut -d'/' -f2-7 | cut -d'"' -f1`
-          wget "https://github.com/$urlPart" -O /tmp/pandoc.deb
+          wget "https://github.com/jgm/pandoc/releases/download/3.1.3/pandoc-3.1.3-1-amd64.deb" -O /tmp/pandoc.deb         
           sudo dpkg -i /tmp/pandoc.deb
-          rm /tmp/pandocVersions.html
           rm /tmp/pandoc.deb
 
           # Copy OWL file and LICENSE so it can be bundled into the Python package

CHANGELOG.md

@@ -1,8 +1,25 @@
 # Changelog
 
-## 2.31 (OWL 2)
+## 2.35 (OWL 2)
 - Added algorithms and characteristics for attractor methods in mpbn
 
+## 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.
+- Added 'parameters for' (`KISAO_0000695`) to indicate that the children parameters of this term are applied when the parent general term is implented as the more-specific value of this term.
+
+## 2.31 (OWL 2)
+- Added concepts for Metabolic Pathway Analysis
+- Added top-level algorithm concept for network optimization methods and nested the Metabolic Pathway Analysis methods, flux balance methods, and resource balance analysis under this
+
 ## 2.30 (OWL 2)
 - Added and unified aggregation functions for SED-ML L1V4
   - maximum ignoring NaN (`KISAO_0000828`)