WIP: Subpackage coverage 72%

pyproject.toml

@@ -79,6 +79,7 @@ test = [
     "pre-commit",     # linting
     "pytest",         # unit testing
     "pytest-cov",     # code coverage
+    "pytest-xvfb",    # for headless testing of Qt
 ]
 docs = [
     "hatch",                 # Get version from env
@@ -120,12 +121,12 @@ ignore-words-list = 'nevers'
 [tool.pytest.ini_options]
 minversion = "7.0"
 addopts = [
-    "-sv",
-    "--sw", # stepwise: resume with next test after failure
-    "--pdb", # drop into debugger on failure
+    # "-sv", # verbose output
+    # "--sw", # stepwise: resume with next test after failure
+    # "--pdb", # drop into debugger on failure
     "-p no:warnings",
-    "--no-teardown", # don't teardown the database after tests
-    "--quiet-spy",                  # don't show logging from spyglass
+    # "--no-teardown", # don't teardown the database after tests
+    # "--quiet-spy",                  # don't show logging from spyglass
     "--show-capture=no",
     "--pdbcls=IPython.terminal.debugger:TerminalPdb", # use ipython debugger
     "--cov=spyglass",
@@ -134,6 +135,12 @@ addopts = [
 ]
 testpaths = ["tests"]
 log_level = "INFO"
+env = [
+    "QT_QPA_PLATFORM = offscreen", # QT fails headless without this
+    # "DISPLAY = :0", # QT fails headless without this
+    "TF_ENABLE_ONEDNN_OPTS = 0", # TF disable approx calcs
+    "TF_CPP_MIN_LOG_LEVEL = 2", # Disable TF warnings
+]
 
 [tool.coverage.run]
 source = ["*/src/spyglass/*"]

src/spyglass/decoding/v0/dj_decoder_conversion.py

@@ -26,6 +26,21 @@
         ObservationModel,
     )
 except ImportError as e:
+    (
+        Identity,
+        RandomWalk,
+        RandomWalkDirection1,
+        RandomWalkDirection2,
+        Uniform,
+        DiagonalDiscrete,
+        RandomDiscrete,
+        UniformDiscrete,
+        UserDefinedDiscrete,
+        Environment,
+        UniformInitialConditions,
+        UniformOneEnvironmentInitialConditions,
+        ObservationModel,
+    ) = [None] * 13
     logger.warning(e)
 from track_linearization import make_track_graph
 

src/spyglass/position/v1/dlc_utils.py

@@ -385,7 +385,17 @@ def infer_output_dir(key, makedir=True):
     """
     # TODO: add check to make sure interval_list_name refers to a single epoch
     # Or make key include epoch in and of itself instead of interval_list_name
-    nwb_file_name = key["nwb_file_name"].split("_.")[0]
+
+    file_name = key.get("nwb_file_name")
+    dlc_model_name = key.get("dlc_model_name")
+    epoch = key.get("epoch")
+
+    if not all([file_name, dlc_model_name, epoch]):
+        raise ValueError(
+            "Key must contain 'nwb_file_name', 'dlc_model_name', and 'epoch'"
+        )
+
+    nwb_file_name = file_name.split("_.")[0]
     output_dir = pathlib.Path(dlc_output_dir) / pathlib.Path(
         f"{nwb_file_name}/{nwb_file_name}_{key['epoch']:02}"
         f"_model_" + key["dlc_model_name"].replace(" ", "-")
@@ -1021,7 +1031,10 @@ def make_video(
         video.release()
         out.release()
         print("destroying cv2 windows")
-        cv2.destroyAllWindows()
+        try:
+            cv2.destroyAllWindows()
+        except cv2.error:  # if cv is already closed or does not have func
+            pass
         print("finished making video with opencv")
         return
 

src/spyglass/position/v1/position_dlc_pose_estimation.py

@@ -35,7 +35,7 @@ class DLCPoseEstimationSelection(SpyglassMixin, dj.Manual):
     """
 
     @classmethod
-    def get_video_crop(cls, video_path):
+    def get_video_crop(cls, video_path, crop_input=None):
         """
         Queries the user to determine the cropping parameters for a given video
 
@@ -61,9 +61,13 @@ def get_video_crop(cls, video_path):
         ax.set_yticks(np.arange(ylims[0], ylims[-1], -50))
         ax.grid(visible=True, color="white", lw=0.5, alpha=0.5)
         display(fig)
-        crop_input = input(
-            "Please enter the crop parameters for your video in format xmin, xmax, ymin, ymax, or 'none'\n"
-        )
+
+        if crop_input is None:
+            crop_input = input(
+                "Please enter the crop parameters for your video in format "
+                + "xmin, xmax, ymin, ymax, or 'none'\n"
+            )
+
         plt.close()
         if crop_input.lower() == "none":
             return None

src/spyglass/position/v1/position_dlc_selection.py

@@ -304,6 +304,8 @@ class DLCPosVideo(SpyglassMixin, dj.Computed):
     ---
     """
 
+    # TODO: Shoultn't this keep track of the video file it creates?
+
     def make(self, key):
         from tqdm import tqdm as tqdm
 
@@ -432,3 +434,4 @@ def make(self, key):
             crop=crop,
             **params["video_params"],
         )
+        self.insert1(key)

src/spyglass/position/v1/position_dlc_training.py

@@ -108,7 +108,7 @@ class DLCModelTrainingSelection(SpyglassMixin, dj.Manual):
     """
 
     def insert1(self, key, **kwargs):
-        training_id = key["training_id"]
+        training_id = key.get("training_id")
         if training_id is None:
             training_id = (
                 dj.U().aggr(self & key, n="max(training_id)").fetch1("n") or 0

tests/README.md

@@ -1,13 +1,27 @@
 # PyTests
 
+## Environment
+
+To facilitate headless testing of various Qt-based tools as well as Tensorflow,
+`pyproject.toml` includes some environment variables associated with the
+display. These are...
+
+- `QT_QPA_PLATFORM`: Set to `offscreen` to prevent the need for a display.
+- `TF_ENABLE_ONEDNN_OPTS`: Set to `1` to enable Tensorflow optimizations.
+- `TF_CPP_MIN_LOG_LEVEL`: Set to `2` to suppress Tensorflow warnings.
+
+<!-- - `DISPLAY`: Set to `:0` to prevent the need for a display. -->
+
+## Options
+
 This directory is contains files for testing the code. Simply by running
 `pytest` from the root directory, all tests will be run with default parameters
 specified in `pyproject.toml`. Notable optional parameters include...
 
 - Coverage items. The coverage report indicates what percentage of the code was
     included in tests.
 
-    - `--cov=spyglatss`: Which package should be described in the coverage report
+    - `--cov=spyglass`: Which package should be described in the coverage report
     - `--cov-report term-missing`: Include lines of items missing in coverage
 
 - Verbosity.

tests/common/test_behav.py

@@ -79,11 +79,6 @@ def test_populate_state_script(common, pop_state_script):
     ), "StateScript populate unexpected effect"
 
 
-@pytest.fixture(scope="session")
-def video_keys(common):
-    return common.VideoFile().fetch(as_dict=True)
-
-
 @pytest.mark.usefixtures("skipif_noextras")
 def test_videofile_update_entries(common, video_keys):
     """Test update entries"""

tests/conftest.py

@@ -388,6 +388,14 @@ def populate_exception():
     yield PopulateException
 
 
+# -------------------------- FIXTURES, COMMON TABLES --------------------------
+
+
+@pytest.fixture(scope="session")
+def video_keys(common):
+    return common.VideoFile().fetch(as_dict=True)
+
+
 # ------------------------- FIXTURES, POSITION TABLES -------------------------
 
 
@@ -428,7 +436,7 @@ def trodes_params(trodes_params_table, teardown):
             },
         },
     }
-    trodes_params_table.get_default()
+    _ = trodes_params_table.get_default()
     trodes_params_table.insert(
         [v for k, v in paramsets.items()], skip_duplicates=True
     )
@@ -778,10 +786,16 @@ def dlc_project_tbl(sgp):
     yield sgp.v1.DLCProject()
 
 
+@pytest.fixture(scope="session")
+def dlc_project_name():
+    yield "pytest_proj"
+
+
 @pytest.fixture(scope="session")
 def insert_project(
     verbose_context,
     teardown,
+    dlc_project_name,
     dlc_project_tbl,
     common,
     bodyparts,
@@ -791,7 +805,7 @@ def insert_project(
     common.LabTeam.insert1({"team_name": team_name}, skip_duplicates=True)
     with verbose_context:
         project_key = dlc_project_tbl.insert_new_project(
-            project_name="pytest_proj",
+            project_name=dlc_project_name,
             bodyparts=bodyparts,
             lab_team=team_name,
             frames_per_video=100,
@@ -858,8 +872,14 @@ def extract_frames(
         )
     vid_name = list(dlc_config["video_sets"].keys())[0].split("/")[-1]
     label_dir = project_dir / "labeled-data" / vid_name.split(".")[0]
+
     yield label_dir
 
+    for file in label_dir.glob("*png"):
+        if file.stem in ["img000", "img001"]:
+            continue
+        file.unlink()
+
 
 @pytest.fixture(scope="session")
 def labeled_vid_dir(extract_frames):
@@ -889,22 +909,30 @@ def add_training_files(dlc_project_tbl, project_key, fix_downloaded):
 
 
 @pytest.fixture(scope="session")
-def training_params_key(verbose_context, sgp, project_key):
-    training_params_name = "pytest"
+def dlc_training_params(sgp):
+    params_tbl = sgp.v1.DLCModelTrainingParams()
+    params_name = "pytest"
+    yield params_tbl, params_name
+
+
+@pytest.fixture(scope="session")
+def training_params_key(verbose_context, sgp, project_key, dlc_training_params):
+    params_tbl, params_name = dlc_training_params
     with verbose_context:
-        sgp.v1.DLCModelTrainingParams.insert_new_params(
-            paramset_name=training_params_name,
+        params_tbl.insert_new_params(
+            paramset_name=params_name,
             params={
                 "trainingsetindex": 0,
                 "shuffle": 1,
                 "gputouse": None,
                 "TFGPUinference": False,
                 "net_type": "resnet_50",
                 "augmenter_type": "imgaug",
+                "video_sets": "test skipping param",
             },
             skip_duplicates=True,
         )
-    yield {"dlc_training_params_name": training_params_name}
+    yield {"dlc_training_params_name": params_name}
 
 
 @pytest.fixture(scope="session")
@@ -913,7 +941,6 @@ def model_train_key(sgp, project_key, training_params_key):
     model_train_key = {
         **project_key,
         **training_params_key,
-        "training_id": 0,
     }
     sgp.v1.DLCModelTrainingSelection().insert1(
         {
@@ -974,19 +1001,17 @@ def pose_estimation_key(sgp, mini_copy_name, populate_model, model_key):
 
 @pytest.fixture(scope="session")
 def populate_pose_estimation(sgp, pose_estimation_key):
-    pose_est_tbl = sgp.v1.DLCPoseEstimation
-    if pose_est_tbl & pose_estimation_key:
-        yield
-    else:
+    pose_est_tbl = sgp.v1.DLCPoseEstimation()
+    if len(pose_est_tbl & pose_estimation_key) < 1:
         pose_est_tbl.populate(pose_estimation_key)
-        yield
+    yield pose_est_tbl
 
 
 @pytest.fixture(scope="session")
 def si_params_name(sgp, populate_pose_estimation):
     params_name = "low_bar"
     params_tbl = sgp.v1.DLCSmoothInterpParams
-    # if len(params_tbl & {"dlc_si_params_name": params_name}) == 0:
+    # if len(params_tbl & {"dlc_si_params_name": params_name}) < 1:
     if True:  # TODO: remove before merge
         nan_params = params_tbl.get_nan_params()
         nan_params["dlc_si_params_name"] = params_name
@@ -995,6 +1020,9 @@ def si_params_name(sgp, populate_pose_estimation):
                 "likelihood_thresh": 0.4,
                 "max_cm_between_pts": 100,
                 "num_inds_to_span": 50,
+                # Smoothing and Interpolation added later - must check
+                "smoothing_params": {"smoothing_duration": 0.05},
+                "interp_params": {"max_cm_to_interp": 100},
             }
         )
         params_tbl.insert1(nan_params, skip_duplicates=True)

tests/position/conftest.py

@@ -11,15 +11,6 @@
     58, 61, 69, 72, 97-100, 104, 149-161, 232-235, 239-241, 246, 259, 280,
     293-305, 310-316, 328-341, 356-373, 395, 404, 480, 487-488, 530, 548-561,
     594-601, 611-612, 641-657, 682-736, 762-772, 787, 809-1286
-
-TODO: tests for
-pose_estimat   51-71, 102, 115, 256, 345-366
-position.py    53, 99, 114, 119, 197-198, 205-219, 349, 353-355, 360, 382, 385, 407, 443-466
-project.py     45-54, 128-205, 250-255, 259, 278-303, 316, 347, 361-413, 425, 457, 476-479, 486-489, 514-555, 582, 596
-selection.py   213, 282, 308-417
-training.py    55, 67-73, 85-87, 113, 143-144, 161, 207-210
-es_position.py 67, 282-283, 361-362, 496, 502-503
-
 """
 
 from itertools import product as iter_prodect
@@ -33,7 +24,7 @@
 def dlc_video_params(sgp):
     sgp.v1.DLCPosVideoParams.insert_default()
     params_key = {"dlc_pos_video_params_name": "five_percent"}
-    sgp.v1.DLCPosVideoSelection.insert1(
+    sgp.v1.DLCPosVideoParams.insert1(
         {
             **params_key,
             "params": {
@@ -47,7 +38,7 @@ def dlc_video_params(sgp):
 
 
 @pytest.fixture(scope="session")
-def dlc_video_selection(sgp, dlc_key, dlc_video_params):
+def dlc_video_selection(sgp, dlc_key, dlc_video_params, populate_dlc):
     s_key = {**dlc_key, **dlc_video_params}
     sgp.v1.DLCPosVideoSelection.insert1(s_key, skip_duplicates=True)
     yield dlc_key
@@ -56,7 +47,7 @@ def dlc_video_selection(sgp, dlc_key, dlc_video_params):
 @pytest.fixture(scope="session")
 def populate_dlc_video(sgp, dlc_video_selection):
     sgp.v1.DLCPosVideo.populate(dlc_video_selection)
-    yield
+    yield sgp.v1.DLCPosVideo()
 
 
 @pytest.fixture(scope="session")
@@ -95,4 +86,4 @@ def increment_count():
         count[0] += 1
         return count[0]
 
-    return df.map(lambda x: increment_count() if x == 1 else x)
+    return df.applymap(lambda x: increment_count() if x == 1 else x)