Repository: combine-org/combine-notebooks (language: python)

Issue:
Disabling tests failing due to issue with sysbioapps.spdns.org
See https://github.com/combine-org/combine-notebooks/issues/26


Discussion / hints:

Fix patch:
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index be866a5..63affff 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -2,9 +2,9 @@ name: CI-CD
 
 on:
   push:
-    branches: [ master, development, experimental, test*, precommit, hello-world]
+    branches: [ main, development, experimental, test*, precommit, hello-world]
   pull_request:
-    branches: [ master, development, experimental, test*, precommit, hello-world]
+    branches: [ main, development, experimental, test*, precommit, hello-world]
 jobs:
 
   pre-commit:
diff --git a/.gitignore b/.gitignore
index f32bc85..09f8cf0 100644
--- a/.gitignore
+++ b/.gitignore
@@ -16,3 +16,5 @@ notebooks/.ipynb_checkpoints
 /notebooks/LEMS_example-single-izhikevich2007cell-sim.xml
 /notebooks/example-single-izhikevich2007cell-sim.v.dat
 /notebooks/hello_world_neuroml.nml
+/.coverage.*
+/build/
diff --git a/tox.ini b/tox.ini
index 1c1a864..0d692e7 100644
--- a/tox.ini
+++ b/tox.ini
@@ -21,18 +21,19 @@ deps=
 commands =
     pytest --nbmake {toxinidir}/notebooks/example_biopax.ipynb
     pytest --nbmake {toxinidir}/notebooks/example_cellml.ipynb
-    pytest --nbmake {toxinidir}/notebooks/example_sbgn.ipynb
     pytest --nbmake {toxinidir}/notebooks/example_sbml_antimony.ipynb
     pytest --nbmake {toxinidir}/notebooks/example_sbml_libsbml.ipynb
     pytest --nbmake {toxinidir}/notebooks/example_sbml_sbmlutils.ipynb
     pytest --nbmake {toxinidir}/notebooks/example_sedml.ipynb
-    pytest --nbmake {toxinidir}/notebooks/example_omex.ipynb
+    # Skipping; see https://github.com/combine-org/combine-notebooks/issues/26
+    #pytest --nbmake {toxinidir}/notebooks/example_sbgn.ipynb
+    #pytest --nbmake {toxinidir}/notebooks/example_omex.ipynb
+    #pytest --nbmake {toxinidir}/notebooks/sbgn.ipynb
+    #pytest --nbmake {toxinidir}/notebooks/omex.ipynb
     pytest --nbmake {toxinidir}/notebooks/cellml.ipynb
     pytest --nbmake {toxinidir}/notebooks/neuroml.ipynb
-    pytest --nbmake {toxinidir}/notebooks/sbgn.ipynb
     pytest --nbmake {toxinidir}/notebooks/sbml.ipynb
     pytest --nbmake {toxinidir}/notebooks/sedml.ipynb
-    pytest --nbmake {toxinidir}/notebooks/omex.ipynb
 
 [testenv:isort]
 skip_install = True


Test patch:
diff --git a/tests/examples/test_omex.py b/tests/examples/test_omex.py
index 9019bb4..fa8714d 100644
--- a/tests/examples/test_omex.py
+++ b/tests/examples/test_omex.py
@@ -1,10 +1,15 @@
 """Test OMEX functionality."""
 from pathlib import Path
 
+import pytest
+
 from combine_notebooks.combine_files import create_combine_files
 from combine_notebooks.examples.example_omex import create_omex
 
 
+@pytest.mark.skip(
+    reason="Failure to communicate with sysbioapps.spdns.org; see https://github.com/combine-org/combine-notebooks/issues/26"
+)
 def test_create_repressilator_omex(tmp_path: Path) -> None:
     """Test creation of COMBINE archive."""
     create_combine_files(tmp_path)
diff --git a/tests/examples/test_sbgn.py b/tests/examples/test_sbgn.py
index 5cec0c3..8657785 100644
--- a/tests/examples/test_sbgn.py
+++ b/tests/examples/test_sbgn.py
@@ -1,9 +1,14 @@
 """Test SBGN functionality."""
 from pathlib import Path
 
+import pytest
+
 from combine_notebooks.examples import example_sbgn
 
 
+@pytest.mark.skip(
+    reason="Failure to communicate with sysbioapps.spdns.org; see https://github.com/combine-org/combine-notebooks/issues/26"
+)
 def test_create_repressilator_libsbgn(tmp_path: Path) -> None:
     """Test creation of repressilator SBGN with libsbgn."""
     sbgn_path: Path = tmp_path / "test.xml"