Repository: biosimulators/Biosimulators_test_suite (language: python)

Issue:
Merge latest from dev
Mostly fixes for Python API changes from packages.


Discussion / hints:
Kudos, SonarCloud Quality Gate passed!&nbsp; &nbsp; [![Quality Gate passed](https://sonarsource.github.io/sonarcloud-github-static-resources/v2/checks/QualityGateBadge/passed-16px.png 'Quality Gate passed')](https://sonarcloud.io/dashboard?id=biosimulators_Biosimulators_test_suite&pullRequest=68)

[![Bug](https://sonarsource.github.io/sonarcloud-github-static-resources/v2/common/bug-16px.png 'Bug')](https://sonarcloud.io/project/issues?id=biosimulators_Biosimulators_test_suite&pullRequest=68&resolved=false&types=BUG) [![A](https://sonarsource.github.io/sonarcloud-github-static-resources/v2/checks/RatingBadge/A-16px.png 'A')](https://sonarcloud.io/project/issues?id=biosimulators_Biosimulators_test_suite&pullRequest=68&resolved=false&types=BUG) [0 Bugs](https://sonarcloud.io/project/issues?id=biosimulators_Biosimulators_test_suite&pullRequest=68&resolved=false&types=BUG)  
[![Vulnerability](https://sonarsource.github.io/sonarcloud-github-static-resources/v2/common/vulnerability-16px.png 'Vulnerability')](https://sonarcloud.io/project/issues?id=biosimulators_Biosimulators_test_suite&pullRequest=68&resolved=false&types=VULNERABILITY) [![A](https://sonarsource.github.io/sonarcloud-github-static-resources/v2/checks/RatingBadge/A-16px.png 'A')](https://sonarcloud.io/project/issues?id=biosimulators_Biosimulators_test_suite&pullRequest=68&resolved=false&types=VULNERABILITY) [0 Vulnerabilities](https://sonarcloud.io/project/issues?id=biosimulators_Biosimulators_test_suite&pullRequest=68&resolved=false&types=VULNERABILITY)  
[![Security Hotspot](https://sonarsource.github.io/sonarcloud-github-static-resources/v2/common/security_hotspot-16px.png 'Security Hotspot')](https://sonarcloud.io/project/security_hotspots?id=biosimulators_Biosimulators_test_suite&pullRequest=68&resolved=false&types=SECURITY_HOTSPOT) [![A](https://sonarsource.github.io/sonarcloud-github-static-resources/v2/checks/RatingBadge/A-16px.png 'A')](https://sonarcloud.io/project/security_hotspots?id=biosimulators_Biosimulators_test_suite&pullRequest=68&resolved=false&types=SECURITY_HOTSPOT) [0 Security Hotspots](https://sonarcloud.io/project/security_hotspots?id=biosimulators_Biosimulators_test_suite&pullRequest=68&resolved=false&types=SECURITY_HOTSPOT)  
[![Code Smell](https://sonarsource.github.io/sonarcloud-github-static-resources/v2/common/code_smell-16px.png 'Code Smell')](https://sonarcloud.io/project/issues?id=biosimulators_Biosimulators_test_suite&pullRequest=68&resolved=false&types=CODE_SMELL) [![A](https://sonarsource.github.io/sonarcloud-github-static-resources/v2/checks/RatingBadge/A-16px.png 'A')](https://sonarcloud.io/project/issues?id=biosimulators_Biosimulators_test_suite&pullRequest=68&resolved=false&types=CODE_SMELL) [0 Code Smells](https://sonarcloud.io/project/issues?id=biosimulators_Biosimulators_test_suite&pullRequest=68&resolved=false&types=CODE_SMELL)

[![No Coverage information](https://sonarsource.github.io/sonarcloud-github-static-resources/v2/checks/CoverageChart/NoCoverageInfo-16px.png 'No Coverage information')](https://sonarcloud.io/component_measures?id=biosimulators_Biosimulators_test_suite&pullRequest=68) No Coverage information  
[![0.0%](https://sonarsource.github.io/sonarcloud-github-static-resources/v2/checks/Duplications/3-16px.png '0.0%')](https://sonarcloud.io/component_measures?id=biosimulators_Biosimulators_test_suite&pullRequest=68&metric=new_duplicated_lines_density&view=list) [0.0% Duplication](https://sonarcloud.io/component_measures?id=biosimulators_Biosimulators_test_suite&pullRequest=68&metric=new_duplicated_lines_density&view=list)



Fix patch:
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index e9c8677..96c745c 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -49,10 +49,11 @@ 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 pip==23.0.0
+          python -m pip install pip==23.0.0
+          python -m pip --version
 
       - name: Install Java # for pyNeuroML
         uses: actions/setup-java@v2
diff --git a/docs/_static/documentation_options.js b/docs/_static/documentation_options.js
index 9da287c..78c3cf8 100644
--- a/docs/_static/documentation_options.js
+++ b/docs/_static/documentation_options.js
@@ -1,6 +1,6 @@
 var DOCUMENTATION_OPTIONS = {
     URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
-    VERSION: '0.1.86',
+    VERSION: '0.1.87',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',
diff --git a/docs/about.html b/docs/about.html
index c7577c5..5c6348e 100644
--- a/docs/about.html
+++ b/docs/about.html
@@ -9,7 +9,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.19: https://docutils.sourceforge.io/" />
 
-    <title>About the BioSimulators test suite &#8212; BioSimulators test suite 0.1.86 documentation</title>
+    <title>About the BioSimulators test suite &#8212; BioSimulators test suite 0.1.87 documentation</title>
   
   
   
diff --git a/docs/genindex.html b/docs/genindex.html
index 57d3f90..1699ccc 100644
--- a/docs/genindex.html
+++ b/docs/genindex.html
@@ -8,7 +8,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>Index &#8212; BioSimulators test suite 0.1.86 documentation</title>
+    <title>Index &#8212; BioSimulators test suite 0.1.87 documentation</title>
   
   
   
diff --git a/docs/index.html b/docs/index.html
index c910031..17d9273 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -9,7 +9,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.19: https://docutils.sourceforge.io/" />
 
-    <title>BioSimulators test suite documentation &#8212; BioSimulators test suite 0.1.86 documentation</title>
+    <title>BioSimulators test suite documentation &#8212; BioSimulators test suite 0.1.87 documentation</title>
   
   
   
diff --git a/docs/installation.html b/docs/installation.html
index aedb3be..b379c6c 100644
--- a/docs/installation.html
+++ b/docs/installation.html
@@ -9,7 +9,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.19: https://docutils.sourceforge.io/" />
 
-    <title>Installation instructions &#8212; BioSimulators test suite 0.1.86 documentation</title>
+    <title>Installation instructions &#8212; BioSimulators test suite 0.1.87 documentation</title>
   
   
   
diff --git a/docs/py-modindex.html b/docs/py-modindex.html
index ba1446d..f194779 100644
--- a/docs/py-modindex.html
+++ b/docs/py-modindex.html
@@ -8,7 +8,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>Python Module Index &#8212; BioSimulators test suite 0.1.86 documentation</title>
+    <title>Python Module Index &#8212; BioSimulators test suite 0.1.87 documentation</title>
   
   
   
diff --git a/docs/search.html b/docs/search.html
index 84ef28e..e02ce77 100644
--- a/docs/search.html
+++ b/docs/search.html
@@ -7,7 +7,7 @@
 
   <head>
     <meta charset="utf-8" />
-    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><title>Search - BioSimulators test suite 0.1.86 documentation</title>
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><title>Search - BioSimulators test suite 0.1.87 documentation</title>
   
   
   
diff --git a/docs/searchindex.js b/docs/searchindex.js
index 7007a42..5a56ba4 100644
--- a/docs/searchindex.js
+++ b/docs/searchindex.js
@@ -1,1 +1,1 @@
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method)": [[6, "biosimulators_test_suite.test_case.results_report.SimulatorGeneratesReportsOfSimulationResults.eval_outputs"]], "eval_outputs() (biosimulators_test_suite.test_case.sedml.simulatorproducesreportswithcuratednumberofdimensions method)": [[6, "biosimulators_test_suite.test_case.sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions.eval_outputs"]], "eval_outputs() (biosimulators_test_suite.test_case.sedml.simulatorsupportsmodelssimulationstasksdatageneratorsandreports method)": [[6, "biosimulators_test_suite.test_case.sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports.eval_outputs"]], "eval_outputs() (biosimulators_test_suite.test_case.sedml.simulatorsupportsmultiplereportsperseddocument method)": [[6, "biosimulators_test_suite.test_case.sedml.SimulatorSupportsMultipleReportsPerSedDocument.eval_outputs"]], "eval_outputs() (biosimulators_test_suite.test_case.sedml.simulatorsupportsmultipletasksperseddocument method)": [[6, "biosimulators_test_suite.test_case.sedml.SimulatorSupportsMultipleTasksPerSedDocument.eval_outputs"]], "exec_sedml_docs_in_archive() (biosimulators_test_suite.test_case.published_project.simulatorcanexecutepublishedproject method)": [[6, "biosimulators_test_suite.test_case.published_project.SimulatorCanExecutePublishedProject.exec_sedml_docs_in_archive"]], "expected_plots (biosimulators_test_suite.test_case.published_project.simulatorcanexecutepublishedproject attribute)": [[6, "biosimulators_test_suite.test_case.published_project.SimulatorCanExecutePublishedProject.expected_plots"]], "expected_reports (biosimulators_test_suite.test_case.published_project.simulatorcanexecutepublishedproject attribute)": [[6, "biosimulators_test_suite.test_case.published_project.SimulatorCanExecutePublishedProject.expected_reports"]], "filename (biosimulators_test_suite.test_case.published_project.simulatorcanexecutepublishedproject attribute)": [[6, "biosimulators_test_suite.test_case.published_project.SimulatorCanExecutePublishedProject.filename"]], "find_cases() (in module biosimulators_test_suite.test_case.published_project)": [[6, "biosimulators_test_suite.test_case.published_project.find_cases"]], "from_dict() (biosimulators_test_suite.test_case.published_project.simulatorcanexecutepublishedproject method)": [[6, "biosimulators_test_suite.test_case.published_project.SimulatorCanExecutePublishedProject.from_dict"]], "from_json() (biosimulators_test_suite.test_case.published_project.simulatorcanexecutepublishedproject method)": [[6, "biosimulators_test_suite.test_case.published_project.SimulatorCanExecutePublishedProject.from_json"]], "get_description() (biosimulators_test_suite.test_case.published_project.simulatorcanexecutepublishedproject method)": [[6, "biosimulators_test_suite.test_case.published_project.SimulatorCanExecutePublishedProject.get_description"]], "get_expected_reports() (biosimulators_test_suite.test_case.combine_archive.combinearchivetestcase method)": [[6, "biosimulators_test_suite.test_case.combine_archive.CombineArchiveTestCase.get_expected_reports"]], "id (biosimulators_test_suite.test_case.published_project.simulatorcanexecutepublishedproject attribute)": [[6, "biosimulators_test_suite.test_case.published_project.SimulatorCanExecutePublishedProject.id"]], "id (biosimulators_test_suite.test_case.published_project.syntheticcombinearchivetestcase attribute)": [[6, "biosimulators_test_suite.test_case.published_project.SyntheticCombineArchiveTestCase.id"]], "is_concrete() (biosimulators_test_suite.test_case.log.loggingtestcase method)": [[6, "biosimulators_test_suite.test_case.log.LoggingTestCase.is_concrete"]], "is_concrete() (biosimulators_test_suite.test_case.log.simulatorreportsthestatusoftheexecutionofcombinearchives method)": [[6, "biosimulators_test_suite.test_case.log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives.is_concrete"]], "is_concrete() (biosimulators_test_suite.test_case.log.simulatorreportsthestatusoftheexecutionofseddocuments method)": [[6, "biosimulators_test_suite.test_case.log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments.is_concrete"]], "is_concrete() (biosimulators_test_suite.test_case.log.simulatorreportsthestatusoftheexecutionofsedoutputs method)": [[6, "biosimulators_test_suite.test_case.log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs.is_concrete"]], "is_concrete() (biosimulators_test_suite.test_case.log.simulatorreportsthestatusoftheexecutionofsedtasks method)": [[6, "biosimulators_test_suite.test_case.log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks.is_concrete"]], "is_concrete() (biosimulators_test_suite.test_case.sedml.simulatorsupportsrepeatedtaskswithfunctionalrangevariables method)": [[6, "biosimulators_test_suite.test_case.sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables.is_concrete"]], "is_concrete() (biosimulators_test_suite.test_case.sedml.simulatorsupportsrepeatedtaskswithfunctionalranges method)": [[6, "biosimulators_test_suite.test_case.sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges.is_concrete"]], "is_concrete() (biosimulators_test_suite.test_case.sedml.simulatorsupportsrepeatedtaskswithlinearuniformranges method)": [[6, "biosimulators_test_suite.test_case.sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges.is_concrete"]], "is_concrete() (biosimulators_test_suite.test_case.sedml.simulatorsupportsrepeatedtaskswithlogarithmicuniformranges method)": [[6, "biosimulators_test_suite.test_case.sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges.is_concrete"]], "is_concrete() (biosimulators_test_suite.test_case.sedml.simulatorsupportsrepeatedtaskswithmultiplesubtasks method)": [[6, "biosimulators_test_suite.test_case.sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks.is_concrete"]], "is_concrete() (biosimulators_test_suite.test_case.sedml.simulatorsupportsrepeatedtaskswithnestedfunctionalranges method)": [[6, "biosimulators_test_suite.test_case.sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges.is_concrete"]], "is_concrete() (biosimulators_test_suite.test_case.sedml.simulatorsupportsrepeatedtaskswithnestedrepeatedtasks method)": [[6, "biosimulators_test_suite.test_case.sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks.is_concrete"]], "is_concrete() (biosimulators_test_suite.test_case.sedml.simulatorsupportsrepeatedtaskswithsubtasksofmixedtypes method)": [[6, "biosimulators_test_suite.test_case.sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes.is_concrete"]], "is_concrete() (biosimulators_test_suite.test_case.sedml.simulatorsupportsrepeatedtaskswithvectorranges method)": [[6, "biosimulators_test_suite.test_case.sedml.SimulatorSupportsRepeatedTasksWithVectorRanges.is_concrete"]], "is_curated_archive_suitable_for_building_synthetic_archive() (biosimulators_test_suite.test_case.published_project.syntheticcombinearchivetestcase method)": [[6, "biosimulators_test_suite.test_case.published_project.SyntheticCombineArchiveTestCase.is_curated_archive_suitable_for_building_synthetic_archive"]], "is_curated_sed_algorithm_suitable_for_building_synthetic_archive() (biosimulators_test_suite.test_case.published_project.syntheticcombinearchivetestcase method)": [[6, "biosimulators_test_suite.test_case.published_project.SyntheticCombineArchiveTestCase.is_curated_sed_algorithm_suitable_for_building_synthetic_archive"]], "is_curated_sed_algorithm_suitable_for_building_synthetic_archive() (biosimulators_test_suite.test_case.sedml.simulatorproducesreportswithcuratednumberofdimensions method)": [[6, "biosimulators_test_suite.test_case.sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions.is_curated_sed_algorithm_suitable_for_building_synthetic_archive"]], "is_curated_sed_algorithm_suitable_for_building_synthetic_archive() (biosimulators_test_suite.test_case.sedml.simulatorsupportsalgorithmparameters method)": [[6, "biosimulators_test_suite.test_case.sedml.SimulatorSupportsAlgorithmParameters.is_curated_sed_algorithm_suitable_for_building_synthetic_archive"]], "is_curated_sed_algorithm_suitable_for_building_synthetic_archive() (biosimulators_test_suite.test_case.sedml.simulatorsupportssubstitutingalgorithms method)": [[6, "biosimulators_test_suite.test_case.sedml.SimulatorSupportsSubstitutingAlgorithms.is_curated_sed_algorithm_suitable_for_building_synthetic_archive"]], "is_curated_sed_doc_suitable_for_building_synthetic_archive() (biosimulators_test_suite.test_case.published_project.syntheticcombinearchivetestcase method)": [[6, "biosimulators_test_suite.test_case.published_project.SyntheticCombineArchiveTestCase.is_curated_sed_doc_suitable_for_building_synthetic_archive"]], "is_curated_sed_model_suitable_for_building_synthetic_archive() (biosimulators_test_suite.test_case.published_project.syntheticcombinearchivetestcase method)": [[6, "biosimulators_test_suite.test_case.published_project.SyntheticCombineArchiveTestCase.is_curated_sed_model_suitable_for_building_synthetic_archive"]], "is_curated_sed_report_suitable_for_building_synthetic_archive() (biosimulators_test_suite.test_case.published_project.syntheticcombinearchivetestcase method)": [[6, "biosimulators_test_suite.test_case.published_project.SyntheticCombineArchiveTestCase.is_curated_sed_report_suitable_for_building_synthetic_archive"]], "is_curated_sed_simulation_suitable_for_building_synthetic_archive() (biosimulators_test_suite.test_case.published_project.syntheticcombinearchivetestcase method)": [[6, "biosimulators_test_suite.test_case.published_project.SyntheticCombineArchiveTestCase.is_curated_sed_simulation_suitable_for_building_synthetic_archive"]], "is_curated_sed_task_suitable_for_building_synthetic_archive() 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"biosimulators_test_suite.test_case.published_project.SimulatorCanExecutePublishedProject.name"]], "name (biosimulators_test_suite.test_case.published_project.syntheticcombinearchivetestcase attribute)": [[6, "biosimulators_test_suite.test_case.published_project.SyntheticCombineArchiveTestCase.name"]], "output_medium (biosimulators_test_suite.test_case.published_project.syntheticcombinearchivetestcase attribute)": [[6, "biosimulators_test_suite.test_case.published_project.SyntheticCombineArchiveTestCase.output_medium"]], "published_projects_test_cases (biosimulators_test_suite.test_case.published_project.syntheticcombinearchivetestcase attribute)": [[6, "biosimulators_test_suite.test_case.published_project.SyntheticCombineArchiveTestCase.published_projects_test_cases"]], "r_tol (biosimulators_test_suite.test_case.published_project.simulatorcanexecutepublishedproject attribute)": [[6, "biosimulators_test_suite.test_case.published_project.SimulatorCanExecutePublishedProject.r_tol"]], 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"biosimulators_test_suite.test_case.published_project.SimulatorCanExecutePublishedProject.task_requirements"]]}})
\ No newline at end of file
diff --git a/docs/tutorial.html b/docs/tutorial.html
index b65af2c..f6afc48 100644
--- a/docs/tutorial.html
+++ b/docs/tutorial.html
@@ -9,7 +9,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.19: https://docutils.sourceforge.io/" />
 
-    <title>Tutorial &#8212; BioSimulators test suite 0.1.86 documentation</title>
+    <title>Tutorial &#8212; BioSimulators test suite 0.1.87 documentation</title>
   
   
   


Test patch:
diff --git a/biosimulators_test_suite/_version.py b/biosimulators_test_suite/_version.py
index 95a0c62..81cb954 100644
--- a/biosimulators_test_suite/_version.py
+++ b/biosimulators_test_suite/_version.py
@@ -1,1 +1,1 @@
-__version__ = '0.1.87'
+__version__ = '0.1.88'
diff --git a/biosimulators_test_suite/test_case/sedml.py b/biosimulators_test_suite/test_case/sedml.py
index 975f140..0ec0c91 100644
--- a/biosimulators_test_suite/test_case/sedml.py
+++ b/biosimulators_test_suite/test_case/sedml.py
@@ -309,7 +309,9 @@ def build_synthetic_archives(self, specifications, curated_archive, curated_arch
                         new_value=value,
                     )
                 )
-
+            for mod in [model_1, model_2]:
+                for change in mod.changes:
+                    change.model = mod.id
             n_children = {}
             for child in node.getchildren():
                 _, _, _, child_target, _ = get_xml_node_namespace_tag_target(
@@ -448,6 +450,9 @@ def build_synthetic_archives(self, specifications, curated_archive, curated_arch
                         new_value=value,
                     )
                 )
+            for mod in [model_1, model_2]:
+                for change in mod.changes:
+                    change.model = mod.id
 
             n_children = {}
             for child in node.getchildren():
diff --git a/docs/source/biosimulators_test_suite.html b/docs/source/biosimulators_test_suite.html
index d26dffa..1f2b9b8 100644
--- a/docs/source/biosimulators_test_suite.html
+++ b/docs/source/biosimulators_test_suite.html
@@ -9,7 +9,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.19: https://docutils.sourceforge.io/" />
 
-    <title>biosimulators_test_suite package &#8212; BioSimulators test suite 0.1.86 documentation</title>
+    <title>biosimulators_test_suite package &#8212; BioSimulators test suite 0.1.87 documentation</title>
   
   
   
@@ -1339,7 +1339,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this
 <dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
 <dl class="py attribute">
 <dt class="sig sig-object py" id="biosimulators_test_suite.exec_cli.BaseController.Meta.arguments">
-<span class="sig-name descname"><span class="pre">arguments</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">[(['specifications'],</span> <span class="pre">{'type':</span> <span class="pre">&lt;class</span> <span class="pre">'str'&gt;,</span> <span class="pre">'help':</span> <span class="pre">'Path</span> <span class="pre">or</span> <span class="pre">URL</span> <span class="pre">to</span> <span class="pre">the</span> <span class="pre">specifications</span> <span class="pre">of</span> <span class="pre">the</span> <span class="pre">simulator'}),</span> <span class="pre">(['-c',</span> <span class="pre">'--test-case'],</span> <span class="pre">{'type':</span> <span class="pre">&lt;class</span> <span class="pre">'str'&gt;,</span> <span class="pre">'nargs':</span> <span class="pre">'+',</span> <span class="pre">'default':</span> <span class="pre">None,</span> <span class="pre">'dest':</span> <span class="pre">'case_ids',</span> <span class="pre">'help':</span> <span class="pre">&quot;Ids</span> <span class="pre">of</span> <span class="pre">test</span> <span class="pre">cases</span> <span class="pre">of</span> <span class="pre">evaluate</span> <span class="pre">(e.g.,</span> <span class="pre">'sedml.SimulatorSupportsModelAttributeChanges',</span> <span class="pre">'published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations')</span> <span class="pre">substrings</span> <span class="pre">of</span> <span class="pre">ids</span> <span class="pre">of</span> <span class="pre">test</span> <span class="pre">cases</span> <span class="pre">to</span> <span class="pre">evaluate</span> <span class="pre">(e.g.,</span> <span class="pre">'sedml.',</span> <span class="pre">'published_project.'</span> <span class="pre">to</span> <span class="pre">evaluate</span> <span class="pre">all</span> <span class="pre">SED-ML</span> <span class="pre">test</span> <span class="pre">cases</span> <span class="pre">or</span> <span class="pre">all</span> <span class="pre">test</span> <span class="pre">cases</span> <span class="pre">involving</span> <span class="pre">published</span> <span class="pre">projects).</span> <span class="pre">Default:</span> <span class="pre">evaluate</span> <span class="pre">all</span> <span class="pre">test</span> <span class="pre">cases&quot;}),</span> <span class="pre">(['--cli'],</span> <span class="pre">{'default':</span> <span class="pre">None,</span> <span class="pre">'help':</span> <span class="pre">'Command-line</span> <span class="pre">interface</span> <span class="pre">to</span> <span class="pre">use</span> <span class="pre">to</span> <span class="pre">execute</span> <span class="pre">the</span> <span class="pre">tests</span> <span class="pre">involving</span> <span class="pre">the</span> <span class="pre">simulation</span> <span class="pre">of</span> <span class="pre">COMBINE/OMEX</span> <span class="pre">archives</span> <span class="pre">rather</span> <span class="pre">than</span> <span class="pre">a</span> <span class="pre">Docker</span> <span class="pre">image'}),</span> <span class="pre">(['--synthetic-archives-dir'],</span> <span class="pre">{'default':</span> <span class="pre">None,</span> <span class="pre">'help':</span> <span class="pre">'Directory</span> <span class="pre">to</span> <span class="pre">save</span> <span class="pre">the</span> <span class="pre">synthetic</span> <span class="pre">COMBINE/OMEX</span> <span class="pre">archives</span> <span class="pre">generated</span> <span class="pre">by</span> <span class="pre">the</span> <span class="pre">test</span> <span class="pre">cases'}),</span> <span class="pre">(['--report'],</span> <span class="pre">{'default':</span> <span class="pre">None,</span> <span class="pre">'help':</span> <span class="pre">'Path</span> <span class="pre">to</span> <span class="pre">save</span> <span class="pre">a</span> <span class="pre">report</span> <span class="pre">of</span> <span class="pre">the</span> <span class="pre">results</span> <span class="pre">in</span> <span class="pre">JSON</span> <span class="pre">format'}),</span> <span class="pre">(['--verbose'],</span> <span class="pre">{'action':</span> <span class="pre">'store_true',</span> <span class="pre">'help':</span> <span class="pre">'If</span> <span class="pre">set,</span> <span class="pre">print</span> <span class="pre">the</span> <span class="pre">stdout</span> <span class="pre">and</span> <span class="pre">stderr</span> <span class="pre">of</span> <span class="pre">the</span> <span class="pre">execution</span> <span class="pre">of</span> <span class="pre">the</span> <span class="pre">tests</span> <span class="pre">in</span> <span class="pre">real</span> <span class="pre">time.'}),</span> <span class="pre">(['--work-dir'],</span> <span class="pre">{'default':</span> <span class="pre">None,</span> <span class="pre">'help':</span> <span class="pre">'Working</span> <span class="pre">directory</span> <span class="pre">for</span> <span class="pre">files</span> <span class="pre">for</span> <span class="pre">evaluating</span> <span class="pre">tests.</span> <span class="pre">This</span> <span class="pre">option</span> <span class="pre">enables</span> <span class="pre">intermediate</span> <span class="pre">files</span> <span class="pre">to</span> <span class="pre">be</span> <span class="pre">inspected</span> <span class="pre">rather</span> <span class="pre">than</span> <span class="pre">automatically</span> <span class="pre">cleaned</span> <span class="pre">up.'}),</span> <span class="pre">(['--do-not-validate-specs'],</span> <span class="pre">{'action':</span> <span class="pre">'store_true',</span> <span class="pre">'help':</span> <span class="pre">&quot;If</span> <span class="pre">set,</span> <span class="pre">don't</span> <span class="pre">validate</span> <span class="pre">the</span> <span class="pre">specifications</span> <span class="pre">of</span> <span class="pre">the</span> <span class="pre">simulator.&quot;}),</span> <span class="pre">(['--do-not-log-std-out-err'],</span> <span class="pre">{'action':</span> <span class="pre">'store_true',</span> <span class="pre">'help':</span> <span class="pre">&quot;If</span> <span class="pre">set,</span> <span class="pre">don't</span> <span class="pre">use</span> <span class="pre">capturer</span> <span class="pre">to</span> <span class="pre">collect</span> <span class="pre">stdout</span> <span class="pre">and</span> <span class="pre">stderr.&quot;}),</span> <span class="pre">(['--dry-run'],</span> <span class="pre">{'action':</span> <span class="pre">'store_true',</span> <span class="pre">'help':</span> <span class="pre">'If</span> <span class="pre">set,</span> <span class="pre">create</span> <span class="pre">synthetic</span> <span class="pre">archives,</span> <span class="pre">but</span> <span class="pre">do</span> <span class="pre">not</span> <span class="pre">use</span> <span class="pre">the</span> <span class="pre">simulator</span> <span class="pre">to</span> <span class="pre">execute</span> <span class="pre">them.'}),</span> <span class="pre">(['-v',</span> <span class="pre">'--version'],</span> <span class="pre">{'action':</span> <span class="pre">'version',</span> <span class="pre">'version':</span> <span class="pre">'0.1.86'})]</span></em><a class="reference external" href="https://github.com/biosimulators/Biosimulators_test_suite/blob/dev/biosimulators_test_suite/exec_cli.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#biosimulators_test_suite.exec_cli.BaseController.Meta.arguments" title="Permalink to this definition">#</a></dt>
+<span class="sig-name descname"><span class="pre">arguments</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">[(['specifications'],</span> <span class="pre">{'type':</span> <span class="pre">&lt;class</span> <span class="pre">'str'&gt;,</span> <span class="pre">'help':</span> <span class="pre">'Path</span> <span class="pre">or</span> <span class="pre">URL</span> <span class="pre">to</span> <span class="pre">the</span> <span class="pre">specifications</span> <span class="pre">of</span> <span class="pre">the</span> <span class="pre">simulator'}),</span> <span class="pre">(['-c',</span> <span class="pre">'--test-case'],</span> <span class="pre">{'type':</span> <span class="pre">&lt;class</span> <span class="pre">'str'&gt;,</span> <span class="pre">'nargs':</span> <span class="pre">'+',</span> <span class="pre">'default':</span> <span class="pre">None,</span> <span class="pre">'dest':</span> <span class="pre">'case_ids',</span> <span class="pre">'help':</span> <span class="pre">&quot;Ids</span> <span class="pre">of</span> <span class="pre">test</span> <span class="pre">cases</span> <span class="pre">of</span> <span class="pre">evaluate</span> <span class="pre">(e.g.,</span> <span class="pre">'sedml.SimulatorSupportsModelAttributeChanges',</span> <span class="pre">'published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations')</span> <span class="pre">substrings</span> <span class="pre">of</span> <span class="pre">ids</span> <span class="pre">of</span> <span class="pre">test</span> <span class="pre">cases</span> <span class="pre">to</span> <span class="pre">evaluate</span> <span class="pre">(e.g.,</span> <span class="pre">'sedml.',</span> <span class="pre">'published_project.'</span> <span class="pre">to</span> <span class="pre">evaluate</span> <span class="pre">all</span> <span class="pre">SED-ML</span> <span class="pre">test</span> <span class="pre">cases</span> <span class="pre">or</span> <span class="pre">all</span> <span class="pre">test</span> <span class="pre">cases</span> <span class="pre">involving</span> <span class="pre">published</span> <span class="pre">projects).</span> <span class="pre">Default:</span> <span class="pre">evaluate</span> <span class="pre">all</span> <span class="pre">test</span> <span class="pre">cases&quot;}),</span> <span class="pre">(['--cli'],</span> <span class="pre">{'default':</span> <span class="pre">None,</span> <span class="pre">'help':</span> <span class="pre">'Command-line</span> <span class="pre">interface</span> <span class="pre">to</span> <span class="pre">use</span> <span class="pre">to</span> <span class="pre">execute</span> <span class="pre">the</span> <span class="pre">tests</span> <span class="pre">involving</span> <span class="pre">the</span> <span class="pre">simulation</span> <span class="pre">of</span> <span class="pre">COMBINE/OMEX</span> <span class="pre">archives</span> <span class="pre">rather</span> <span class="pre">than</span> <span class="pre">a</span> <span class="pre">Docker</span> <span class="pre">image'}),</span> <span class="pre">(['--synthetic-archives-dir'],</span> <span class="pre">{'default':</span> <span class="pre">None,</span> <span class="pre">'help':</span> <span class="pre">'Directory</span> <span class="pre">to</span> <span class="pre">save</span> <span class="pre">the</span> <span class="pre">synthetic</span> <span class="pre">COMBINE/OMEX</span> <span class="pre">archives</span> <span class="pre">generated</span> <span class="pre">by</span> <span class="pre">the</span> <span class="pre">test</span> <span class="pre">cases'}),</span> <span class="pre">(['--report'],</span> <span class="pre">{'default':</span> <span class="pre">None,</span> <span class="pre">'help':</span> <span class="pre">'Path</span> <span class="pre">to</span> <span class="pre">save</span> <span class="pre">a</span> <span class="pre">report</span> <span class="pre">of</span> <span class="pre">the</span> <span class="pre">results</span> <span class="pre">in</span> <span class="pre">JSON</span> <span class="pre">format'}),</span> <span class="pre">(['--verbose'],</span> <span class="pre">{'action':</span> <span class="pre">'store_true',</span> <span class="pre">'help':</span> <span class="pre">'If</span> <span class="pre">set,</span> <span class="pre">print</span> <span class="pre">the</span> <span class="pre">stdout</span> <span class="pre">and</span> <span class="pre">stderr</span> <span class="pre">of</span> <span class="pre">the</span> <span class="pre">execution</span> <span class="pre">of</span> <span class="pre">the</span> <span class="pre">tests</span> <span class="pre">in</span> <span class="pre">real</span> <span class="pre">time.'}),</span> <span class="pre">(['--work-dir'],</span> <span class="pre">{'default':</span> <span class="pre">None,</span> <span class="pre">'help':</span> <span class="pre">'Working</span> <span class="pre">directory</span> <span class="pre">for</span> <span class="pre">files</span> <span class="pre">for</span> <span class="pre">evaluating</span> <span class="pre">tests.</span> <span class="pre">This</span> <span class="pre">option</span> <span class="pre">enables</span> <span class="pre">intermediate</span> <span class="pre">files</span> <span class="pre">to</span> <span class="pre">be</span> <span class="pre">inspected</span> <span class="pre">rather</span> <span class="pre">than</span> <span class="pre">automatically</span> <span class="pre">cleaned</span> <span class="pre">up.'}),</span> <span class="pre">(['--do-not-validate-specs'],</span> <span class="pre">{'action':</span> <span class="pre">'store_true',</span> <span class="pre">'help':</span> <span class="pre">&quot;If</span> <span class="pre">set,</span> <span class="pre">don't</span> <span class="pre">validate</span> <span class="pre">the</span> <span class="pre">specifications</span> <span class="pre">of</span> <span class="pre">the</span> <span class="pre">simulator.&quot;}),</span> <span class="pre">(['--do-not-log-std-out-err'],</span> <span class="pre">{'action':</span> <span class="pre">'store_true',</span> <span class="pre">'help':</span> <span class="pre">&quot;If</span> <span class="pre">set,</span> <span class="pre">don't</span> <span class="pre">use</span> <span class="pre">capturer</span> <span class="pre">to</span> <span class="pre">collect</span> <span class="pre">stdout</span> <span class="pre">and</span> <span class="pre">stderr.&quot;}),</span> <span class="pre">(['--dry-run'],</span> <span class="pre">{'action':</span> <span class="pre">'store_true',</span> <span class="pre">'help':</span> <span class="pre">'If</span> <span class="pre">set,</span> <span class="pre">create</span> <span class="pre">synthetic</span> <span class="pre">archives,</span> <span class="pre">but</span> <span class="pre">do</span> <span class="pre">not</span> <span class="pre">use</span> <span class="pre">the</span> <span class="pre">simulator</span> <span class="pre">to</span> <span class="pre">execute</span> <span class="pre">them.'}),</span> <span class="pre">(['-v',</span> <span class="pre">'--version'],</span> <span class="pre">{'action':</span> <span class="pre">'version',</span> <span class="pre">'version':</span> <span class="pre">'0.1.87'})]</span></em><a class="reference external" href="https://github.com/biosimulators/Biosimulators_test_suite/blob/dev/biosimulators_test_suite/exec_cli.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#biosimulators_test_suite.exec_cli.BaseController.Meta.arguments" title="Permalink to this definition">#</a></dt>
 <dd></dd></dl>
 
 <dl class="py attribute">
diff --git a/docs/source/biosimulators_test_suite.results.html b/docs/source/biosimulators_test_suite.results.html
index a9ed758..8d7d44c 100644
--- a/docs/source/biosimulators_test_suite.results.html
+++ b/docs/source/biosimulators_test_suite.results.html
@@ -9,7 +9,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.19: https://docutils.sourceforge.io/" />
 
-    <title>biosimulators_test_suite.results package &#8212; BioSimulators test suite 0.1.86 documentation</title>
+    <title>biosimulators_test_suite.results package &#8212; BioSimulators test suite 0.1.87 documentation</title>
   
   
   
@@ -504,7 +504,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this
 
 <dl class="py class">
 <dt class="sig sig-object py" id="biosimulators_test_suite.results.data_model.TestResultsReport">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">biosimulators_test_suite.results.data_model.</span></span><span class="sig-name descname"><span class="pre">TestResultsReport</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">test_suite_version</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'0.1.86'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">results</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">gh_issue</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">gh_action_run</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/biosimulators/Biosimulators_test_suite/blob/dev/biosimulators_test_suite/results/data_model.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#biosimulators_test_suite.results.data_model.TestResultsReport" title="Permalink to this definition">#</a></dt>
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">biosimulators_test_suite.results.data_model.</span></span><span class="sig-name descname"><span class="pre">TestResultsReport</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">test_suite_version</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'0.1.87'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">results</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">gh_issue</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">gh_action_run</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/biosimulators/Biosimulators_test_suite/blob/dev/biosimulators_test_suite/results/data_model.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#biosimulators_test_suite.results.data_model.TestResultsReport" title="Permalink to this definition">#</a></dt>
 <dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
 <p>A report of the results of executing the test suite with a simulation tool</p>
 <dl class="py attribute">
diff --git a/docs/source/biosimulators_test_suite.test_case.html b/docs/source/biosimulators_test_suite.test_case.html
index 45001f7..31ad6d1 100644
--- a/docs/source/biosimulators_test_suite.test_case.html
+++ b/docs/source/biosimulators_test_suite.test_case.html
@@ -9,7 +9,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.19: https://docutils.sourceforge.io/" />
 
-    <title>biosimulators_test_suite.test_case package &#8212; BioSimulators test suite 0.1.86 documentation</title>
+    <title>biosimulators_test_suite.test_case package &#8212; BioSimulators test suite 0.1.87 documentation</title>