ignore R/rpy2 tests on windows CI

conda/meta.yaml

@@ -20,8 +20,7 @@ build:
   noarch: python
   preserve_egg_dir: True
   number: 0
-  string: py{{ PY_VER }}
-  script: {{PYTHON}} -m pip install . -vv
+  script: {{PYTHON}} -m pip install --no-deps  --no-build-isolation . -vv
 
 requirements:
   build:
@@ -37,7 +36,7 @@ requirements:
 
 test:
   requires:
-    {% for dep in deps + conda_deps + test_deps %}
+    {% for dep in test_deps %}
     - {{ dep }}
     {% endfor %}
   imports:

pyproject.toml

@@ -32,8 +32,8 @@ dynamic = ["readme","version"]
 dependencies = [
     "numpy",
     "scipy",
-    "matplotlib-base",
     "pandas",
+    "rpy2"
 ]
 
 [project.optional-dependencies]
@@ -60,7 +60,7 @@ dependencies = [
     "openalea.plantgl",
     "openalea.caribu",
     "openalea.astk",
-    "rpy2"
+    "matplotlib-base"
 ]
 [tool.setuptools.dynamic]
 readme = {file = ["README.md"]}

test/__init__.py

@@ -0,0 +1 @@
+# Needed to make conftest.py visible

test/conftest.py

@@ -0,0 +1,14 @@
+import pytest
+
+try:
+    # test if R's stats package loads correctly
+    import rpy2.robjects as ro
+    ro.r("na.omit")  # will error on broken R
+    R_OK = True
+except Exception:
+    R_OK = False
+
+pytest_r_skip = pytest.mark.skipif(
+    not R_OK,
+    reason="Skipping R/rpy2 tests on this platform due to broken R/rpy2 installation"
+)

test/test_AdelWheat.py

@@ -1,9 +1,9 @@
 from openalea.adel.astk_interface import AdelWheat
 from openalea.astk.Weather import sample_weather
+from .conftest import pytest_r_skip
 
 
-
-
+@pytest_r_skip
 def test_adelwheat():
     seq, weather = sample_weather()
     seq = seq.tz_localize(tz='Europe/Paris')

test/test_Adel_Maxwell_plante11.py

@@ -5,7 +5,10 @@
 from openalea.adel.AdelR import devCsv, setAdel, RunAdel, genGeoLeaf, genGeoAxe, \
     csvAsDict
 
+from .conftest import pytest_r_skip
 
+
+@pytest_r_skip
 def test_organ_length():
     dir = str(pathlib.Path(__file__).parent.resolve() / "data" / "test_Adel_Maxwell_plante11/Maxwell_")
     sufix = "_plante11.csv"

test/test_adelwheat_dynamic.py

@@ -1,8 +1,9 @@
 """Test use cases of adel/fspm wheat coupling"""
-
 from openalea.adel.adelwheat_dynamic import AdelWheatDyn
+from .conftest import pytest_r_skip
 
 
+@pytest_r_skip
 def test_add_metamer():
     # create a plant with 3 metamers
     adel = AdelWheatDyn(seed=1234)

test/test_astk_interface.py

@@ -1,5 +1,7 @@
 from openalea.adel.astk_interface import AdelWheat
+from .conftest import pytest_r_skip
 
+pytestmark = pytest_r_skip
 
 def test_static():
     nplants = 1

test/test_data_samples.py

@@ -1,6 +1,8 @@
 from openalea.adel.data_samples import *
+from .conftest import pytest_r_skip
 
 
+@pytest_r_skip
 def test_leaf_db():
     db = leaves_db()
     sr = srdb()
@@ -12,6 +14,7 @@ def test_leaf_db():
     assert leaves is not None
 
 
+@pytest_r_skip
 def test_devT():
     dev = devT()
     assert dev is not None