diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 3031d99..090fef1 100644 --- 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 index 900abe3..ca2bb2c 100644 --- 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 index 13b7089..e6d0c4f 100644 --- 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 index 14be0e2..9018c41 100644 --- 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 index 4a51d23..ee55125 100644 --- 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 `_. +The BioSimulators test suite is a tool for validating that biosimulation software tools implement the `BioSimulators standards for biosimulation tools `_. The test suite is composed of two parts: diff --git a/docs-src/tutorial.rst b/docs-src/tutorial.rst index 214f740..fc69ff6 100644 --- 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 index a104841..38dc399 100644 --- 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 index 0cdaffc..ee19f03 100644 Binary files a/examples/bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ.omex and b/examples/bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ.omex differ diff --git a/examples/bngl/test-bngl.omex b/examples/bngl/test-bngl.omex index 5358362..4df1f1e 100644 Binary files a/examples/bngl/test-bngl.omex and b/examples/bngl/test-bngl.omex differ diff --git a/requirements.txt b/requirements.txt index 53617ea..38dbfbc 100644 --- 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 index 6ff4fcc..76f82cc 100644 --- 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 index bf632af..2d66083 100644 --- 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',