Cleanup commit

biosimulators · Nov 15, 2024 · 7a84f35 · 7a84f35
1 parent 8aa3780
commit 7a84f35
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Showing 19 changed files with 482 additions and 1,364 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -141,7 +141,7 @@ jobs:
 
       - name: Compile the documentation
         run: |
-          poetry run sphinx-apidoc . setup.py --output-dir docs-src/source --force --module-first --no-toc
+          poetry run sphinx-apidoc . pyproject.toml --output-dir docs-src/source --force --module-first --no-toc
           mkdir -p docs-src/_static
           poetry run sphinx-build docs-src docs
 
@@ -180,7 +180,7 @@ jobs:
 
       - name: Compile the documentation
         run: |
-          poetry run sphinx-apidoc . setup.py --output-dir docs-src/source --force --module-first --no-toc
+          poetry run sphinx-apidoc . pyproject.toml --output-dir docs-src/source --force --module-first --no-toc
           mkdir -p docs-src/_static
           poetry run sphinx-build docs-src docs
 

diff --git a/biosimulators_test_suite/test_case/published_project.py b/biosimulators_test_suite/test_case/published_project.py
@@ -504,7 +504,8 @@ class SyntheticCombineArchiveTestCase(TestCase):
     EXEC_WITH_SINGULARITY = False
     REPORT_ERROR_AS_SKIP = False
 
-    def __init__(self, id=None, name=None, description=None, output_medium=OutputMedium.console, published_projects_test_cases=None):
+    def __init__(self, id=None, name=None, description=None,
+                 output_medium=OutputMedium.console, published_projects_test_cases=None):
         """
         Args:
             id (:obj:`str`, optional): id
@@ -514,7 +515,8 @@ def __init__(self, id=None, name=None, description=None, output_medium=OutputMed
             published_projects_test_cases (:obj:`list` of :obj:`SimulatorCanExecutePublishedProject`, optional):
                 curated COMBINE/OMEX archives that can be used to generate example archives for testing
         """
-        super(SyntheticCombineArchiveTestCase, self).__init__(id=id, name=name, description=description, output_medium=output_medium)
+        super(SyntheticCombineArchiveTestCase, self).__init__(id=id, name=name, description=description,
+                                                              output_medium=output_medium)
         self.published_projects_test_cases = published_projects_test_cases or []
         self._published_projects_test_case = None
 
@@ -570,6 +572,7 @@ def _eval(self, specifications, working_dirname, synthetic_archives_dir=None, dr
 
         # read curated archives and find one that is suitable for testing
         suitable_curated_archive = False
+        raise RuntimeError("--" + str([str(case.filename) for case in self.published_projects_test_cases]) + "--")
         for published_projects_test_case in self.published_projects_test_cases:
             self._published_projects_test_case = published_projects_test_case
 
@@ -604,7 +607,8 @@ def _eval(self, specifications, working_dirname, synthetic_archives_dir=None, dr
             shutil.rmtree(shared_archive_dir)
 
         if not suitable_curated_archive:
-            raise SkippedTestCaseException('No curated COMBINE/OMEX archives are available to generate archives for testing')
+            raise SkippedTestCaseException('No curated COMBINE/OMEX archives are available to '
+                                           f'generate archives for testing.\n[{self.published_projects_test_cases}]')
 
         expected_results_of_synthetic_archives = self.build_synthetic_archives(
             specifications, curated_archive, shared_archive_dir, curated_sed_docs)

diff --git a/docs-src/_static/biosimulators-logo.svg b/docs-src/_static/biosimulators-logo.svg
diff --git a/docs-src/_static/css/biosimulators.css b/docs-src/_static/css/biosimulators.css
diff --git a/docs-src/source/biosimulators_test_suite.rst b/docs-src/source/biosimulators_test_suite.rst
@@ -66,18 +66,18 @@ biosimulators\_test\_suite.exec\_gh\_action module
    :undoc-members:
    :show-inheritance:
 
-biosimulators\_test\_suite.utils module
----------------------------------------
+biosimulators\_test\_suite.test\_warnings module
+------------------------------------------------
 
-.. automodule:: biosimulators_test_suite.utils
+.. automodule:: biosimulators_test_suite.test_warnings
    :members:
    :undoc-members:
    :show-inheritance:
 
-biosimulators\_test\_suite.warnings module
-------------------------------------------
+biosimulators\_test\_suite.utils module
+---------------------------------------
 
-.. automodule:: biosimulators_test_suite.warnings
+.. automodule:: biosimulators_test_suite.utils
    :members:
    :undoc-members:
    :show-inheritance:
diff --git a/docs-src/source/setup.rst b/docs-src/source/setup.rst
@@ -0,0 +1,7 @@
+setup module
+============
+
+.. automodule:: setup
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/about.html b/docs/about.html
@@ -119,14 +119,8 @@
 
 
 
-
-
-
-
-
-    <img src="_static/biosimulators-logo.svg" class="logo__image only-light" alt="BioSimulators test suite 0.2 documentation - Home"/>
-    <script>document.write(`<img src="_static/biosimulators-logo.svg" class="logo__image only-dark" alt="BioSimulators test suite 0.2 documentation - Home"/>`);</script>
 
+    <p class="title logo__title">BioSimulators test suite 0.2 documentation</p>
 
 </a></div>
 

diff --git a/docs/genindex.html b/docs/genindex.html
@@ -116,14 +116,8 @@
 
 
 
-
-
-
-
-
-    <img src="_static/biosimulators-logo.svg" class="logo__image only-light" alt="BioSimulators test suite 0.2 documentation - Home"/>
-    <script>document.write(`<img src="_static/biosimulators-logo.svg" class="logo__image only-dark" alt="BioSimulators test suite 0.2 documentation - Home"/>`);</script>
 
+    <p class="title logo__title">BioSimulators test suite 0.2 documentation</p>
 
 </a></div>
 

diff --git a/docs/index.html b/docs/index.html
@@ -118,14 +118,8 @@
 
 
 
-
-
-
-
-
-    <img src="_static/biosimulators-logo.svg" class="logo__image only-light" alt="BioSimulators test suite 0.2 documentation - Home"/>
-    <script>document.write(`<img src="_static/biosimulators-logo.svg" class="logo__image only-dark" alt="BioSimulators test suite 0.2 documentation - Home"/>`);</script>
 
+    <p class="title logo__title">BioSimulators test suite 0.2 documentation</p>
 
 </a></div>
 

diff --git a/docs/installation.html b/docs/installation.html
@@ -119,14 +119,8 @@
 
 
 
-
-
-
-
-
-    <img src="_static/biosimulators-logo.svg" class="logo__image only-light" alt="BioSimulators test suite 0.2 documentation - Home"/>
-    <script>document.write(`<img src="_static/biosimulators-logo.svg" class="logo__image only-dark" alt="BioSimulators test suite 0.2 documentation - Home"/>`);</script>
 
+    <p class="title logo__title">BioSimulators test suite 0.2 documentation</p>
 
 </a></div>
 

diff --git a/docs/py-modindex.html b/docs/py-modindex.html
@@ -119,14 +119,8 @@
 
 
 
-
-
-
-
-
-    <img src="_static/biosimulators-logo.svg" class="logo__image only-light" alt="BioSimulators test suite 0.2 documentation - Home"/>
-    <script>document.write(`<img src="_static/biosimulators-logo.svg" class="logo__image only-dark" alt="BioSimulators test suite 0.2 documentation - Home"/>`);</script>
 
+    <p class="title logo__title">BioSimulators test suite 0.2 documentation</p>
 
 </a></div>
 

diff --git a/docs/search.html b/docs/search.html
@@ -118,14 +118,8 @@
 
 
 
-
-
-
-
-
-    <img src="_static/biosimulators-logo.svg" class="logo__image only-light" alt="BioSimulators test suite 0.2 documentation - Home"/>
-    <script>document.write(`<img src="_static/biosimulators-logo.svg" class="logo__image only-dark" alt="BioSimulators test suite 0.2 documentation - Home"/>`);</script>
 
+    <p class="title logo__title">BioSimulators test suite 0.2 documentation</p>
 
 </a></div>
 

diff --git a/docs/searchindex.js b/docs/searchindex.js
diff --git a/docs/source/biosimulators_test_suite.html b/docs/source/biosimulators_test_suite.html
@@ -119,14 +119,8 @@
 
 
 
-
-
-
-
-
-    <img src="../_static/biosimulators-logo.svg" class="logo__image only-light" alt="BioSimulators test suite 0.2 documentation - Home"/>
-    <script>document.write(`<img src="../_static/biosimulators-logo.svg" class="logo__image only-dark" alt="BioSimulators test suite 0.2 documentation - Home"/>`);</script>
 
+    <p class="title logo__title">BioSimulators test suite 0.2 documentation</p>
 
 </a></div>
 

diff --git a/docs/source/biosimulators_test_suite.results.html b/docs/source/biosimulators_test_suite.results.html
@@ -119,14 +119,8 @@
 
 
 
-
-
-
-
-
-    <img src="../_static/biosimulators-logo.svg" class="logo__image only-light" alt="BioSimulators test suite 0.2 documentation - Home"/>
-    <script>document.write(`<img src="../_static/biosimulators-logo.svg" class="logo__image only-dark" alt="BioSimulators test suite 0.2 documentation - Home"/>`);</script>
 
+    <p class="title logo__title">BioSimulators test suite 0.2 documentation</p>
 
 </a></div>
 

diff --git a/docs/source/biosimulators_test_suite.test_case.html b/docs/source/biosimulators_test_suite.test_case.html
@@ -119,14 +119,8 @@
 
 
 
-
-
-
-
-
-    <img src="../_static/biosimulators-logo.svg" class="logo__image only-light" alt="BioSimulators test suite 0.2 documentation - Home"/>
-    <script>document.write(`<img src="../_static/biosimulators-logo.svg" class="logo__image only-dark" alt="BioSimulators test suite 0.2 documentation - Home"/>`);</script>
 
+    <p class="title logo__title">BioSimulators test suite 0.2 documentation</p>
 
 </a></div>