Merge pull request #5 from djarecka/mnt/no_fsl

adding FSL check for tests that run the task

Author: effigies

pydra/tasks/fsl/preprocess/tests/test_run_applywarp.py

@@ -3,6 +3,9 @@
 from ..applywarp import ApplyWarp
 
 
+@pytest.mark.xfail(
+    "FSLDIR" not in os.environ, reason="no FSL found", raises=FileNotFoundError
+)
 @pytest.mark.parametrize(
     "inputs, outputs", [({"ref_file": 'f"{in_file}"'}, ["out_file"])]
 )

pydra/tasks/fsl/preprocess/tests/test_run_bet.py

@@ -3,6 +3,9 @@
 from ..bet import BET
 
 
+@pytest.mark.xfail(
+    "FSLDIR" not in os.environ, reason="no FSL found", raises=FileNotFoundError
+)
 @pytest.mark.parametrize(
     "inputs, outputs",
     [

pydra/tasks/fsl/preprocess/tests/test_run_fast.py

@@ -3,6 +3,9 @@
 from ..fast import FAST
 
 
+@pytest.mark.xfail(
+    "FSLDIR" not in os.environ, reason="no FSL found", raises=FileNotFoundError
+)
 @pytest.mark.parametrize("inputs, outputs", [])
 def test_FAST(test_data, inputs, outputs):
     in_file = Path(test_data) / "test.nii.gz"

pydra/tasks/fsl/preprocess/tests/test_run_first.py

@@ -3,6 +3,9 @@
 from ..first import FIRST
 
 
+@pytest.mark.xfail(
+    "FSLDIR" not in os.environ, reason="no FSL found", raises=FileNotFoundError
+)
 @pytest.mark.parametrize("inputs, outputs", [])
 def test_FIRST(test_data, inputs, outputs):
     in_file = Path(test_data) / "test.nii.gz"

pydra/tasks/fsl/preprocess/tests/test_run_flirt.py

@@ -3,6 +3,9 @@
 from ..flirt import FLIRT
 
 
+@pytest.mark.xfail(
+    "FSLDIR" not in os.environ, reason="no FSL found", raises=FileNotFoundError
+)
 @pytest.mark.parametrize("inputs, outputs", [])
 def test_FLIRT(test_data, inputs, outputs):
     in_file = Path(test_data) / "test.nii.gz"

pydra/tasks/fsl/preprocess/tests/test_run_fnirt.py

@@ -3,6 +3,9 @@
 from ..fnirt import FNIRT
 
 
+@pytest.mark.xfail(
+    "FSLDIR" not in os.environ, reason="no FSL found", raises=FileNotFoundError
+)
 @pytest.mark.parametrize(
     "inputs, outputs",
     [

pydra/tasks/fsl/preprocess/tests/test_run_mcflirt.py

@@ -3,6 +3,9 @@
 from ..mcflirt import MCFLIRT
 
 
+@pytest.mark.xfail(
+    "FSLDIR" not in os.environ, reason="no FSL found", raises=FileNotFoundError
+)
 @pytest.mark.parametrize("inputs, outputs", [(None, ["out_file"])])
 def test_MCFLIRT(test_data, inputs, outputs):
     in_file = Path(test_data) / "test.nii.gz"

pydra/tasks/fsl/preprocess/tests/test_run_prelude.py

@@ -3,6 +3,9 @@
 from ..prelude import PRELUDE
 
 
+@pytest.mark.xfail(
+    "FSLDIR" not in os.environ, reason="no FSL found", raises=FileNotFoundError
+)
 @pytest.mark.parametrize("inputs, outputs", [])
 def test_PRELUDE(test_data, inputs, outputs):
     in_file = Path(test_data) / "test.nii.gz"

pydra/tasks/fsl/preprocess/tests/test_run_slicetimer.py

@@ -3,6 +3,9 @@
 from ..slicetimer import SliceTimer
 
 
+@pytest.mark.xfail(
+    "FSLDIR" not in os.environ, reason="no FSL found", raises=FileNotFoundError
+)
 @pytest.mark.parametrize(
     "inputs, outputs",
     [({"ref_file": 'f"{in_file}"'}, ["out_file", "slice_time_corrected_file"])],

pydra/tasks/fsl/preprocess/tests/test_run_susan.py

@@ -3,6 +3,9 @@
 from ..susan import SUSAN
 
 
+@pytest.mark.xfail(
+    "FSLDIR" not in os.environ, reason="no FSL found", raises=FileNotFoundError
+)
 @pytest.mark.parametrize(
     "inputs, outputs",
     [({"brightness_threshold": 0.01, "fwhm": 2}, ["out_file", "smoothed_file"])],