docs/changes/latest.inc

@@ -35,6 +35,8 @@ Enhancements
 - Add :class:`junifer.markers.EdgeCentricFCParcels` and :class:`junifer.markers.EdgeCentricFCSpheres`
   (:gh:`64` by `Leonard Sasse`_).
 
+- Change HCP datagrabber tests to decrease CI running time (:gh:`155` by `Fede Raimondo`_).
+
 Bugs
 ~~~~
 

junifer/datagrabber/hcp.py

@@ -142,7 +142,11 @@ class HCP1200(PatternDataGrabber):
             The list of elements in the dataset.
 
         """
-        subjects = [x.name for x in self.datadir.iterdir() if x.is_dir()]
+        subjects = [
+            x.name
+            for x in self.datadir.iterdir()
+            if x.is_dir() and not x.name.startswith(".")
+        ]
         elems = []
         for subject, task, phase_encoding in product(
             subjects, self.tasks, self.phase_encodings

junifer/datagrabber/tests/test_hcp.py

@@ -3,17 +3,31 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Optional
+from typing import Optional, Iterable
 
 import pytest
 
-from junifer.datagrabber.hcp import DataladHCP1200
+from junifer.datagrabber.hcp import DataladHCP1200, HCP1200
 from junifer.utils import configure_logging
 
 
 URI = "https://gin.g-node.org/juaml/datalad-example-hcp1200"
 
 
+@pytest.fixture(scope="module")
+def hcpdg() -> Iterable[DataladHCP1200]:
+    """Return a HCP1200 datagrabber."""
+    dg = DataladHCP1200()
+    # Set URI to Gin
+    dg.uri = URI
+    # Set correct root directory
+    dg._rootdir = "."
+    with dg:
+        for t_elem in dg.get_elements():
+            dg[t_elem]
+        yield dg
+
+
 @pytest.mark.parametrize(
     "tasks, phase_encodings, expected_path_name",
     [
@@ -38,15 +52,19 @@ URI = "https://gin.g-node.org/juaml/datalad-example-hcp1200"
         ("MOTOR", "RL", "tfMRI_MOTOR_RL_hp2000_clean.nii.gz"),
     ],
 )
-def test_dataladhcp1200_datagrabber(
+def test_hcp1200_datagrabber(
+    hcpdg: DataladHCP1200,
     tasks: Optional[str],
     phase_encodings: Optional[str],
     expected_path_name: str,
 ) -> None:
-    """Test datalad HCP1200 datagrabber.
+    """Test HCP1200 datagrabber.
 
     Parameters
     ----------
+    hcpdg : DataladHCP1200
+        The Datalad version of the datagrabber with the first subject
+        already cloned.
     tasks : str
         The parametrized tasks.
     phase_encodings : str
@@ -56,35 +74,31 @@ def test_dataladhcp1200_datagrabber(
 
     """
     configure_logging(level="DEBUG")
-    dg = DataladHCP1200(
+    dg = HCP1200(
+        datadir=hcpdg.datadir,
         tasks=tasks,
         phase_encodings=phase_encodings,
     )
-    # Set URI to Gin
+    # Get all elements
-    dg.uri = URI
+    all_elements = dg.get_elements()
-    # Set correct root directory
+    # Get test element
-    dg._rootdir = "."
+    test_element = all_elements[0]
-    with dg:
+    # Get test element data
-        # Get all elements
+    out = dg[test_element]
-        all_elements = dg.get_elements()
+    # Asserts data type
-        # Get test element
+    assert "BOLD" in out
-        test_element = all_elements[0]
+    # Assert data file name
-        # Get test element data
+    assert out["BOLD"]["path"].name == expected_path_name
-        out = dg[test_element]
+    # Assert data file path exists
-        # Asserts data type
+    assert out["BOLD"]["path"].exists()
-        assert "BOLD" in out
+    # Assert data file path is a file
-        # Assert data file name
+    assert out["BOLD"]["path"].is_file()
-        assert out["BOLD"]["path"].name == expected_path_name
+    # Assert metadata
-        # Assert data file path exists
+    assert "meta" in out["BOLD"]
-        assert out["BOLD"]["path"].exists()
+    meta = out["BOLD"]["meta"]
-        # Assert data file path is a file
+    assert "element" in meta
-        assert out["BOLD"]["path"].is_file()
+    assert "subject" in meta["element"]
-        # Assert metadata
+    assert test_element[0] == meta["element"]["subject"]
-        assert "meta" in out["BOLD"]
-        meta = out["BOLD"]["meta"]
-        assert "element" in meta
-        assert "subject" in meta["element"]
-        assert test_element[0] == meta["element"]["subject"]
 
 
 @pytest.mark.parametrize(
@@ -110,14 +124,18 @@ def test_dataladhcp1200_datagrabber(
         ("MOTOR", "RL"),
     ],
 )
-def test_dataladhcp1200_datagrabber_single_access(
+def test_hcp1200_datagrabber_single_access(
+    hcpdg: DataladHCP1200,
     tasks: Optional[str],
     phase_encodings: Optional[str],
 ) -> None:
-    """Test datalad HCP1200 datagrabber single access.
+    """Test HCP1200 datagrabber single access.
 
     Parameters
     ----------
+    hcpdg : DataladHCP1200
+        The Datalad version of the datagrabber with the first subject
+        already cloned.
     tasks : str
         The parametrized tasks.
     phase_encodings : str
@@ -125,14 +143,11 @@ def test_dataladhcp1200_datagrabber_single_access(
 
     """
     configure_logging(level="DEBUG")
-    dg = DataladHCP1200(
+    dg = HCP1200(
+        datadir=hcpdg.datadir,
         tasks=tasks,
         phase_encodings=phase_encodings,
     )
-    # Set URI to Gin
-    dg.uri = URI
-    # Set correct root directory
-    dg._rootdir = "."
     with dg:
         # Get all elements
         all_elements = dg.get_elements()
@@ -149,14 +164,18 @@ def test_dataladhcp1200_datagrabber_single_access(
         (["REST1", "REST2"], None),
     ],
 )
-def test_dataladhcp1200_datagrabber_multi_access(
+def test_hcp1200_datagrabber_multi_access(
+    hcpdg: DataladHCP1200,
     tasks: Optional[str],
     phase_encodings: Optional[str],
 ) -> None:
-    """Test datalad HCP1200 datagrabber multiple access.
+    """Test HCP1200 datagrabber multiple access.
 
     Parameters
     ----------
+    hcpdg : DataladHCP1200
+        The Datalad version of the datagrabber with the first subject
+        already cloned.
     tasks : str
         The parametrized tasks.
     phase_encodings : str
@@ -164,14 +183,11 @@ def test_dataladhcp1200_datagrabber_multi_access(
 
     """
     configure_logging(level="DEBUG")
-    dg = DataladHCP1200(
+    dg = HCP1200(
-        tasks=["REST1", "REST2"],
+        datadir=hcpdg.datadir,
-        phase_encodings=["LR", "RL"],
+        tasks=tasks,
+        phase_encodings=phase_encodings,
     )
-    # Set URI to Gin
-    dg.uri = URI
-    # Set correct root directory
-    dg._rootdir = "."
     with dg:
         # Get all elements
         all_elements = dg.get_elements()
@@ -181,17 +197,23 @@ def test_dataladhcp1200_datagrabber_multi_access(
             assert element[2] in ["LR", "RL"]
 
 
-def test_dataladhcp1200_datagrabber_multi_access_task_simple() -> None:
+def test_hcp1200_datagrabber_multi_access_task_simple(
-    """Test datalad HCP1200 datagrabber simple multiple access for task."""
+    hcpdg: DataladHCP1200,
+) -> None:
+    """Test HCP1200 datagrabber simple multiple access for task.
+
+    Parameters
+    ----------
+    hcpdg : DataladHCP1200
+        The Datalad version of the datagrabber with the first subject
+        already cloned.
+    """
     configure_logging(level="DEBUG")
-    dg = DataladHCP1200(
+    dg = HCP1200(
+        datadir=hcpdg.datadir,
         tasks="REST1",
         phase_encodings=["LR", "RL"],
     )
-    # Set URI to Gin
-    dg.uri = URI
-    # Set correct root directory
-    dg._rootdir = "."
     with dg:
         # Get all elements
         all_elements = dg.get_elements()
@@ -201,17 +223,23 @@ def test_dataladhcp1200_datagrabber_multi_access_task_simple() -> None:
             assert element[2] in ["LR", "RL"]
 
 
-def test_dataladhcp1200_datagrabber_multi_access_phase_simple() -> None:
+def test_hcp1200_datagrabber_multi_access_phase_simple(
-    """Test datalad HCP1200 datagrabber simple multiple access for phase."""
+    hcpdg: DataladHCP1200,
+) -> None:
+    """Test HCP1200 datagrabber simple multiple access for phase.
+
+    Parameters
+    ----------
+    hcpdg : DataladHCP1200
+        The Datalad version of the datagrabber with the first subject
+        already cloned.
+    """
     configure_logging(level="DEBUG")
-    dg = DataladHCP1200(
+    dg = HCP1200(
+        datadir=hcpdg.datadir,
         tasks=["REST1", "REST2"],
         phase_encodings="LR",
     )
-    # Set URI to Gin
-    dg.uri = URI
-    # Set correct root directory
-    dg._rootdir = "."
     with dg:
         # Get all elements
         all_elements = dg.get_elements()
@@ -230,11 +258,11 @@ def test_dataladhcp1200_datagrabber_multi_access_phase_simple() -> None:
         (["FOO", "BAR"], "LR"),
     ],
 )
-def test_dataladhcp1200_datagrabber_incorrect_access_task(
+def test_hcp1200_datagrabber_incorrect_access_task(
     tasks: Optional[str],
     phase_encodings: Optional[str],
 ) -> None:
-    """Test datalad HCP1200 datagrabber incorrect access for task.
+    """Test HCP1200 datagrabber incorrect access for task.
 
     Parameters
     ----------
@@ -246,7 +274,8 @@ def test_dataladhcp1200_datagrabber_incorrect_access_task(
     """
     configure_logging(level="DEBUG")
     with pytest.raises(ValueError, match="not a valid HCP-YA fMRI task input"):
-        _ = DataladHCP1200(
+        _ = HCP1200(
+            datadir=".",
             tasks=tasks,
             phase_encodings=phase_encodings,
         )
@@ -261,11 +290,11 @@ def test_dataladhcp1200_datagrabber_incorrect_access_task(
         (["REST1", "REST2"], "BAR"),
     ],
 )
-def test_dataladhcp1200_datagrabber_incorrect_access_phase(
+def test_hcp1200_datagrabber_incorrect_access_phase(
     tasks: Optional[str],
     phase_encodings: Optional[str],
 ) -> None:
-    """Test datalad HCP1200 datagrabber incorrect access for phase.
+    """Test HCP1200 datagrabber incorrect access for phase.
 
     Parameters
     ----------
@@ -277,7 +306,41 @@ def test_dataladhcp1200_datagrabber_incorrect_access_phase(
     """
     configure_logging(level="DEBUG")
     with pytest.raises(ValueError, match="not a valid HCP-YA phase encoding"):
-        _ = DataladHCP1200(
+        _ = HCP1200(
+            datadir=".",
             tasks=tasks,
             phase_encodings=phase_encodings,
         )
+
+
+def test_hcp1200_datagrabber_elements(
+    hcpdg: DataladHCP1200,
+) -> None:
+    """Test HCP1200 datagrabber elements.
+
+    Parameters
+    ----------
+    hcpdg : DataladHCP1200
+        The Datalad version of the datagrabber with the first subject
+        already cloned.
+    """
+    configure_logging(level="DEBUG")
+    dg = HCP1200(
+        datadir=hcpdg.datadir,
+        tasks="REST1",
+        phase_encodings="LR",
+    )
+    with dg:
+        # Get all elements
+        expected_subjects = [
+            f"sub-{x:02d}" for x in range(1, 10)
+        ]
+        found_subjects = []
+        all_elements = dg.get_elements()
+        # Check only specified task and phase encoding are found
+        for element in all_elements:
+            found_subjects.append(element[0])
+            assert element[1] == "REST1"
+            assert element[2] in ["LR", "RL"]
+
+        assert set(found_subjects) == set(expected_subjects)