Merge branch 'dev' into deploy

biosimulators · Jan 6, 2021 · 994352c · 994352c
2 parents 6f84a4a + 3cdbd3a
commit 994352c
Show file tree

Hide file tree

Showing 12 changed files with 13 additions and 13 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -65,8 +65,8 @@ jobs:
         run: python -m pip install .[tests]
 
       - name: Run the tests
-        env:
-          BIOSIMULATORS_API_ENDPOINT: https://api.biosimulators.dev/ # TODO: change to biosimulators.org
+        # env:
+        #   BIOSIMULATORS_API_ENDPOINT: https://api.biosimulators.dev/ # uncomment to run tests using the dev deployment
         run: python -m pytest tests/ --cov=./biosimulators_test_suite --cov-report=xml
 
       - name: Upload the coverage report to Codecov

diff --git a/README.md b/README.md
@@ -5,7 +5,7 @@
 
 # BioSimulators test suite
 
-The BioSimulators test suite is a tool for validating that biosimulation software tools implement the [BioSimulators standards for biosimulation tools](https://biosimulators.org/standards). 
+The BioSimulators test suite is a tool for validating that biosimulation software tools implement the [BioSimulators standards for biosimulation tools](https://biosimulators.org/standards).
 
 The test suite is composed of two parts:
 

diff --git a/biosimulators_test_suite/_version.py b/biosimulators_test_suite/_version.py
@@ -1 +1 @@
-__version__ = '0.1.11'
+__version__ = '0.1.12'
diff --git a/biosimulators_test_suite/test_case/cli.py b/biosimulators_test_suite/test_case/cli.py
@@ -138,7 +138,7 @@ def eval(self, specifications):
         result = subprocess.run(['docker', 'run', '--tty', '--rm', image_url, '-v'],
                                 stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
         log = result.stdout.decode() if result.stdout else ''
-        supported = re.match(r'\d+\.\d+', log)
+        supported = re.search(r'\d+\.\d+', log)
         if not supported:
             warnings.warn(('Command-line interface should support the `-v` option for displaying version information inline.\n\n'
                            'The command-line interface displayed the following when executed with `-v`:\n\n  {}'
@@ -148,7 +148,7 @@ def eval(self, specifications):
         result = subprocess.run(['docker', 'run', '--tty', '--rm', image_url, '--version'],
                                 stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
         log = result.stdout.decode() if result.stdout else ''
-        supported = re.match(r'\d+\.\d+', log)
+        supported = re.search(r'\d+\.\d+', log)
         if not supported:
             warnings.warn(('Command-line interface should support the `--version` option for displaying version information inline.\n\n'
                            'The command-line interface displayed the following when executed with `--version`:\n\n  {}'

diff --git a/docs-src/index.rst b/docs-src/index.rst
@@ -1,7 +1,7 @@
 BioSimulators test suite documentation
 ===========================================
 
-The BioSimulators test suite is a tool for validating that biosimulation software tools implement the `BioSimulators standards for biosimulation tools <https://biosimulators.org/standards>`_. 
+The BioSimulators test suite is a tool for validating that biosimulation software tools implement the `BioSimulators standards for biosimulation tools <https://biosimulators.org/standards>`_.
 
 The test suite is composed of two parts:
 

diff --git a/docs-src/tutorial.rst b/docs-src/tutorial.rst
@@ -37,7 +37,7 @@ Please follow these steps to use the GitHub API to programmatically submit issue
 #. Create a GitHub account
 #. Create a token for your GitHub account with the scope ``public_repo``
 #. Execute HTTP POST requests to create issues. The body of the issue should be a JSON-encoded dictionary as illustrated below. The dictionary should have the following keys:
-  
+
   * ``labels``: Its value should be equal to ``["Validate/submit simulator"]``.
   * ``title``: A descriptive title for your issue such as ``Submit tellurium 2.1.6``.
   * ``body``: A YAML-encoded description of your simulator as outlined above.

diff --git a/examples/README.md b/examples/README.md
@@ -60,7 +60,7 @@ Below is information about the compatibility of a selection of archives.
 | [`Edelstein-Biol-Cybern....omex`](https://github.com/biosimulators/Biosimulators_test_suite/raw/dev/examples/sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation.omex) | non-spatial continuous ([0000293](https://www.ebi.ac.uk/ols/ontologies/sbo/terms?iri=http%3A%2F%2Fbiomodels.net%2FSBO%2FSBO_0000293)) | LSODA ([0000088](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000088))           | SBML ([format_2585](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585))     | [PySCeS](https://biosimulators.org/simulators/pysces)                 |
 | [`Escherichia....omex`](https://github.com/biosimulators/Biosimulators_test_suite/raw/dev/examples/sbml-fbc/Escherichia-coli-core-metabolism.omex) | flux balance ([0000624](https://www.ebi.ac.uk/ols/ontologies/sbo/terms?iri=http%3A%2F%2Fbiomodels.net%2FSBO%2FSBO_0000624)) | FBA ([0000437](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000437))           | SBML ([format_2585](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585))     | [COBRApy](https://biosimulators.org/simulators/cobrapy)                 |
 | [`Parmar-BMC-Syst-Biol....omex`](https://github.com/biosimulators/Biosimulators_test_suite/raw/dev/examples/sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution.omex) | non-spatial continuous ([0000293](https://www.ebi.ac.uk/ols/ontologies/sbo/terms?iri=http%3A%2F%2Fbiomodels.net%2FSBO%2FSBO_0000293)) | CVODE ([0000019](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019))           | SBML ([format_2585](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585))     | [PySCeS](https://biosimulators.org/simulators/pysces), [tellurium](https://biosimulators.org/simulators/tellurium), [VCell](https://biosimulators.org/simulators/vcell)                 |
-| [`Szymanska-J-Theor-Biol....omex`](https://github.com/biosimulators/Biosimulators_test_suite/raw/dev/examples/sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis.omex) | non-spatial continuous ([0000293](https://www.ebi.ac.uk/ols/ontologies/sbo/terms?iri=http%3A%2F%2Fbiomodels.net%2FSBO%2FSBO_0000293)) | CVODES ([0000496](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000496))           | SBML ([format_2585](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585))     | [AMICI](https://biosimulators.org/simulators/amici)     
+| [`Szymanska-J-Theor-Biol....omex`](https://github.com/biosimulators/Biosimulators_test_suite/raw/dev/examples/sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis.omex) | non-spatial continuous ([0000293](https://www.ebi.ac.uk/ols/ontologies/sbo/terms?iri=http%3A%2F%2Fbiomodels.net%2FSBO%2FSBO_0000293)) | CVODES ([0000496](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000496))           | SBML ([format_2585](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585))     | [AMICI](https://biosimulators.org/simulators/amici)
 | [`test-bngl.omex`](https://github.com/biosimulators/Biosimulators_test_suite/raw/dev/examples/bngl/test-bngl.omex) | non-spatial continuous ([0000293](https://www.ebi.ac.uk/ols/ontologies/sbo/terms?iri=http%3A%2F%2Fbiomodels.net%2FSBO%2FSBO_0000293)) | CVODE ([0000019](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019))           | BNGL ([format_3972](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3972))     | [BioNetGen](https://biosimulators.org/simulators/bionetgen)  |
 | [`Tomida-EMBO-J....omex`](https://github.com/biosimulators/Biosimulators_test_suite/raw/dev/examples/sbml-core/Tomida-EMBO-J-2003-NFAT-translocation.omex) | non-spatial continuous ([0000293](https://www.ebi.ac.uk/ols/ontologies/sbo/terms?iri=http%3A%2F%2Fbiomodels.net%2FSBO%2FSBO_0000293)) | LSODA/LSODAR ([0000560](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000560))           | SBML ([format_2585](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585))     | [COPASI](https://biosimulators.org/simulators/copasi)                  |
 | [`Varusai-Sci-Rep....omex`](https://github.com/biosimulators/Biosimulators_test_suite/raw/dev/examples/sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML.omex) | non-spatial continuous ([0000293](https://www.ebi.ac.uk/ols/ontologies/sbo/terms?iri=http%3A%2F%2Fbiomodels.net%2FSBO%2FSBO_0000293)) | LSODA/LSODAR ([0000560](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000560))           | SBML ([format_2585](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585))     | [COPASI](https://biosimulators.org/simulators/copasi)                  |

diff --git a/examples/bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ.omex b/examples/bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ.omex
diff --git a/examples/bngl/test-bngl.omex b/examples/bngl/test-bngl.omex
diff --git a/requirements.txt b/requirements.txt
@@ -1,4 +1,4 @@
-biosimulators_utils[docker] >= 0.1.29
+biosimulators_utils[docker] >= 0.1.31
 capturer
 cement
 docker

diff --git a/tests/fixtures/COPASI.specs.json b/tests/fixtures/COPASI.specs.json
@@ -1515,8 +1515,8 @@
   "interfaceTypes": ["web service", "desktop application", "library", "command-line application", "BioSimulators Docker image"],
   "supportedOperatingSystemTypes": ["Linux", "Mac OS", "Windows"],
   "supportedProgrammingLanguages": [
-    {"namespace": "Linguist", "id": "Python"}, 
-    {"namespace": "Linguist", "id": "C#"}, 
+    {"namespace": "Linguist", "id": "Python"},
+    {"namespace": "Linguist", "id": "C#"},
     {"namespace": "Linguist", "id": "Java"}
   ],
   "funding": [],

diff --git a/tests/test_exec_gh_action.py b/tests/test_exec_gh_action.py
@@ -210,7 +210,7 @@ def test_push_image(self):
             action = exec_gh_action.ValidateCommitSimulatorGitHubAction()
 
         specs = {
-            'id': 'Tellurium',
+            'id': 'tellurium',
             'version': '2.1.6',
             'image': {
                 'url': 'ghcr.io/biosimulators/biosimulators_tellurium/tellurium:2.1.6',