Add sample SLEAP data containing mixed (user/predicted) labels (#85)

* Update poses registry * Update tests to use reusable SLEAP file fixture * Configure sphinx gallery to rerun examples
neuroinformatics-unit · Nov 14, 2023 · 73858ad · 73858ad
1 parent e5ccc83
commit 73858ad
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Showing 4 changed files with 24 additions and 14 deletions.
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -94,6 +94,7 @@
     "examples_dirs": ["../../examples"],
     "filename_pattern": "/*.py",  # which files to execute before inclusion
     "gallery_dirs": ["examples"],  # output directory
+    "run_stale_examples": True,  # re-run examples on each build
 }
 
 # -- Options for HTML output -------------------------------------------------
@@ -133,7 +134,7 @@
 # so a file named "default.css" will overwrite the builtin "default.css".
 # html_static_path = ['_static']
 
-# The linkcheck builder will skip verifying that anchors exist when checking 
+# The linkcheck builder will skip verifying that anchors exist when checking
 # these URLs
 linkcheck_anchors_ignore_for_url = [
     "https://gin.g-node.org/G-Node/Info/wiki/",

diff --git a/movement/datasets.py b/movement/datasets.py
@@ -36,6 +36,8 @@
         "SLEAP_two-mice_social-interaction.predictions.slp": "45881affde9704c045e70b8d4b3f6bbb8d9bd8ef9f4cdea6d173cfe35857549b",  # noqa: E501
         "SLEAP_three-mice_Aeon_proofread.analysis.h5": "82ebd281c406a61536092863bc51d1a5c7c10316275119f7daf01c1ff33eac2a",  # noqa: E501
         "SLEAP_three-mice_Aeon_proofread.predictions.slp": "7b7436a52dfd5f4d80d7c66919ad1a1732e5435fe33faf9011ec5f7b7074e788",  # noqa: E501
+        "SLEAP_three-mice_Aeon_mixed-labels.analysis.h5": "899651ec027eb8fd6181246f89142ad1c0a40f14394fc8144d44ea093c0e137d",  # noqa: E501
+        "SLEAP_three-mice_Aeon_mixed-labels.predictions.slp": "6d3f2c5446e9c12aabf28d5a9470835736b0419dcefebba89c305114f83b82d1",  # noqa: E501
     },
 )
 

diff --git a/tests/conftest.py b/tests/conftest.py
@@ -26,6 +26,8 @@ def pytest_configure():
             "SLEAP_single-mouse_EPM.predictions.slp",
             "SLEAP_three-mice_Aeon_proofread.analysis.h5",
             "SLEAP_three-mice_Aeon_proofread.predictions.slp",
+            "SLEAP_three-mice_Aeon_mixed-labels.analysis.h5",
+            "SLEAP_three-mice_Aeon_mixed-labels.predictions.slp",
         ]
     }
 
@@ -167,6 +169,21 @@ def dlc_style_df():
     return pd.read_hdf(pytest.POSE_DATA.get("DLC_single-wasp.predictions.h5"))
 
 
+@pytest.fixture(
+    params=[
+        "SLEAP_single-mouse_EPM.analysis.h5",
+        "SLEAP_single-mouse_EPM.predictions.slp",
+        "SLEAP_three-mice_Aeon_proofread.analysis.h5",
+        "SLEAP_three-mice_Aeon_proofread.predictions.slp",
+        "SLEAP_three-mice_Aeon_mixed-labels.analysis.h5",
+        "SLEAP_three-mice_Aeon_mixed-labels.predictions.slp",
+    ]
+)
+def sleap_file(request):
+    """Return the file path for a SLEAP .h5 or .slp file."""
+    return pytest.POSE_DATA.get(request.param)
+
+
 @pytest.fixture
 def valid_tracks_array():
     """Return a function that generate different kinds

diff --git a/tests/test_unit/test_load_poses.py b/tests/test_unit/test_load_poses.py
@@ -42,21 +42,11 @@ def assert_dataset(
         )
         assert dataset.fps is None
 
-    @pytest.mark.parametrize(
-        "file_name",
-        [
-            "SLEAP_single-mouse_EPM.analysis.h5",
-            "SLEAP_single-mouse_EPM.predictions.slp",
-            "SLEAP_three-mice_Aeon_proofread.analysis.h5",
-            "SLEAP_three-mice_Aeon_proofread.predictions.slp",
-        ],
-    )
-    def test_load_from_slp_file(self, file_name):
+    def test_load_from_slp_file(self, sleap_file):
         """Test that loading pose tracks from valid SLEAP files
         returns a proper Dataset."""
-        file_path = POSE_DATA.get(file_name)
-        ds = load_poses.from_sleap_file(file_path)
-        self.assert_dataset(ds, file_path, "SLEAP")
+        ds = load_poses.from_sleap_file(sleap_file)
+        self.assert_dataset(ds, sleap_file, "SLEAP")
 
     @pytest.mark.parametrize(
         "file_name",