No-credential data download

.github/workflows/test-conda.yml

@@ -7,6 +7,8 @@ on:
       - '!documentation'
   schedule:  # once a day at midnight UTC
     - cron: '0 0 * * *'
+  pull_request: # requires approval for first-time contributors
+    types: [synchronize, opened, reopened, labeled]
   workflow_dispatch: # Manually trigger with 'Run workflow' button
 
 concurrency: # Replace Cancel Workflow Action
@@ -22,8 +24,6 @@ jobs:
     env:
       OS: ubuntu-latest
       PYTHON: '3.9'
-      UCSF_BOX_TOKEN: ${{ secrets.UCSF_BOX_TOKEN }} # for download and testing
-      UCSF_BOX_USER: ${{ secrets.UCSF_BOX_USER }}
     services:
       mysql:
         image: datajoint/mysql:8.0
@@ -57,23 +57,23 @@ jobs:
         pip install --quiet .[test]
     - name: Download data
       env:
-        BASEURL: ftps://ftp.box.com/trodes_to_nwb_test_data/
-        NWBFILE: minirec20230622.nwb # Relative to Base URL
-        VID_ONE: 20230622_sample_01_a1/20230622_sample_01_a1.1.h264
-        VID_TWO: 20230622_sample_02_a1/20230622_sample_02_a1.1.h264
+        BASEURL: https://ucsf.box.com/shared/static/
+        NWB_URL: k3sgql6z475oia848q1rgms4zdh4rkjn.nwb
+        VID1URL: ykep8ek4ogad20wz4p0vuyuqfo60cv3w.h264
+        VID2URL: d2jjk0y565ru75xqojio3hymmehzr5he.h264
+        NWBFILE: minirec20230622.nwb
+        VID_ONE: 20230622_minirec_01_s1.1.h264
+        VID_TWO: 20230622_minirec_02_s2.1.h264
         RAW_DIR: /home/runner/work/spyglass/spyglass/tests/_data/raw/
         VID_DIR: /home/runner/work/spyglass/spyglass/tests/_data/video/
       run: |
         mkdir -p $RAW_DIR $VID_DIR
-        wget_opts() { # Declare func with download options
-          wget \
-            --recursive --no-verbose --no-host-directories --no-directories \
-            --user "$UCSF_BOX_USER" --password "$UCSF_BOX_TOKEN" \
-            -P "$1" "$BASEURL""$2"
+        curl_opts() { # Declare func with download options
+          curl -L --output "$1""$2" "$BASEURL""$3"
         }
-        wget_opts $RAW_DIR $NWBFILE
-        wget_opts $VID_DIR $VID_ONE
-        wget_opts $VID_DIR $VID_TWO
+        curl_opts $RAW_DIR $NWBFILE $NWB_URL
+        curl_opts $VID_DIR $VID_ONE $VID1URL
+        curl_opts $VID_DIR $VID_TWO $VID2URL
     - name: Run tests
       run: |
-        pytest --no-docker --no-dlc
+        pytest --no-docker --no-dlc tests/

CHANGELOG.md

@@ -37,6 +37,7 @@ dj.FreeTable(dj.conn(), "common_session.session_group").drop()
     - Remove debug statement #1164
     - Add testing for python versions 3.9, 3.10, 3.11, 3.12 #1169
     - Initialize tables in pytests #1181
+    - Download test data without credentials, trigger on approved PRs #1180
 - Allow python \< 3.13 #1169
 - Remove numpy version restriction #1169
 - Merge table delete removes orphaned master entries #1164

environment.yml

@@ -9,7 +9,7 @@
 name: spyglass
 channels:
   - conda-forge
-  - defaults
+  # - defaults # deprecated
   - franklab
   - edeno
   # - pytorch # dlc-only

environment_dlc.yml

@@ -9,7 +9,7 @@
 name: spyglass-dlc
 channels:
   - conda-forge
-  - defaults
+  # - defaults # deprecated
   - franklab
   - edeno
   - pytorch   # dlc-only

src/spyglass/common/common_behav.py

@@ -197,7 +197,7 @@ def fetch1_dataframe(self):
             id_rp = [(n["id"], n["raw_position"]) for n in self.fetch_nwb()]
 
             if len(set(rp.interval for _, rp in id_rp)) > 1:
-                logger.warn("Loading DataFrame with multiple intervals.")
+                logger.warning("Loading DataFrame with multiple intervals.")
 
             df_list = [
                 pd.DataFrame(
@@ -395,7 +395,9 @@ def _no_transaction_make(self, key, verbose=True, skip_duplicates=False):
         )
 
         if videos is None:
-            logger.warn(f"No video data interface found in {nwb_file_name}\n")
+            logger.warning(
+                f"No video data interface found in {nwb_file_name}\n"
+            )
             return
         else:
             videos = videos.time_series

src/spyglass/common/common_device.py

@@ -88,7 +88,9 @@ def insert_from_nwbfile(cls, nwbf, config=None):
                 + f"{ndx_devices.keys()}"
             )
         else:
-            logger.warn("No conforming data acquisition device metadata found.")
+            logger.warning(
+                "No conforming data acquisition device metadata found."
+            )
 
     @classmethod
     def get_all_device_names(cls, nwbf, config) -> tuple:
@@ -305,7 +307,7 @@ def insert_from_nwbfile(cls, nwbf, config=None):
         if device_name_list:
             logger.info(f"Inserted camera devices {device_name_list}")
         else:
-            logger.warn("No conforming camera device metadata found.")
+            logger.warning("No conforming camera device metadata found.")
         return device_name_list
 
 
@@ -462,7 +464,7 @@ def insert_from_nwbfile(cls, nwbf, config=None):
         if all_probes_types:
             logger.info(f"Inserted probes {all_probes_types}")
         else:
-            logger.warn("No conforming probe metadata found.")
+            logger.warning("No conforming probe metadata found.")
 
         return all_probes_types
 
@@ -709,7 +711,7 @@ def create_from_nwbfile(
 
         query = ProbeType & {"probe_type": probe_type}
         if len(query) == 0:
-            logger.warn(
+            logger.warning(
                 f"No ProbeType found with probe_type '{probe_type}'. Aborting."
             )
             return
@@ -769,7 +771,7 @@ def create_from_nwbfile(
                     ]
 
         if not device_found:
-            logger.warn(
+            logger.warning(
                 "No electrodes in the NWB file were associated with a device "
                 + f"named '{nwb_device_name}'."
             )

src/spyglass/common/common_dio.py

@@ -38,7 +38,7 @@ def make(self, key):
             nwbf, "behavioral_events", pynwb.behavior.BehavioralEvents
         )
         if behav_events is None:
-            logger.warn(
+            logger.warning(
                 "No conforming behavioral events data interface found in "
                 + f"{nwb_file_name}\n"
             )

src/spyglass/common/common_session.py

@@ -152,7 +152,7 @@ def _add_data_acquisition_device_part(self, nwb_file_name, nwbf, config={}):
                 "data_acquisition_device_name": device_name
             }
             if len(query) == 0:
-                logger.warn(
+                logger.warning(
                     "Cannot link Session with DataAcquisitionDevice.\n"
                     + f"DataAcquisitionDevice does not exist: {device_name}"
                 )
@@ -180,7 +180,7 @@ def _add_experimenter_part(
             # ensure that the foreign key exists and do nothing if not
             query = LabMember & {"lab_member_name": name}
             if len(query) == 0:
-                logger.warn(
+                logger.warning(
                     "Cannot link Session with LabMember. "
                     + f"LabMember does not exist: {name}"
                 )

src/spyglass/common/common_subject.py

@@ -37,7 +37,7 @@ def insert_from_nwbfile(cls, nwbf: NWBFile, config: dict = None):
         """
         config = config or dict()
         if "Subject" not in config and nwbf.subject is None:
-            logger.warn("No subject metadata found.\n")
+            logger.warning("No subject metadata found.\n")
             return None
 
         conf = config["Subject"][0] if "Subject" in config else dict()

src/spyglass/common/common_task.py

@@ -33,7 +33,7 @@ def insert_from_nwbfile(cls, nwbf: pynwb.NWBFile):
         """
         tasks_mod = nwbf.processing.get("tasks")
         if tasks_mod is None:
-            logger.warn(f"No tasks processing module found in {nwbf}\n")
+            logger.warning(f"No tasks processing module found in {nwbf}\n")
             return
         for task in tasks_mod.data_interfaces.values():
             if cls.check_task_table(task):
@@ -136,7 +136,7 @@ def make(self, key):
         tasks_mod = nwbf.processing.get("tasks")
         config_tasks = config.get("Tasks", [])
         if tasks_mod is None and (not config_tasks):
-            logger.warn(
+            logger.warning(
                 f"No tasks processing module found in {nwbf} or config\n"
             )
             return
@@ -163,7 +163,7 @@ def make(self, key):
                         for camera_id in valid_camera_ids
                     ]
                 else:
-                    logger.warn(
+                    logger.warning(
                         f"No camera device found with ID {camera_ids} in NWB "
                         + f"file {nwbf}\n"
                     )
@@ -186,7 +186,7 @@ def make(self, key):
                         epoch, session_intervals
                     )
                     if target_interval is None:
-                        logger.warn("Skipping epoch.")
+                        logger.warning("Skipping epoch.")
                         continue
                     key["interval_list_name"] = target_interval
                     task_inserts.append(key.copy())
@@ -219,7 +219,7 @@ def make(self, key):
                     epoch, session_intervals
                 )
                 if target_interval is None:
-                    logger.warn("Skipping epoch.")
+                    logger.warning("Skipping epoch.")
                     continue
                 new_key["interval_list_name"] = target_interval
                 task_inserts.append(key.copy())

src/spyglass/common/prepopulate/prepopulate.py

@@ -57,7 +57,7 @@ def populate_from_yaml(yaml_path: str):
                 if k in table_cls.primary_key
             }
             if not primary_key_values:
-                logger.warn(
+                logger.warning(
                     f"Populate: No primary key provided in data {entry_dict} "
                     + f"for table {table_cls.__name__}"
                 )

src/spyglass/position/v1/dlc_utils_makevid.py

@@ -5,7 +5,6 @@
 import subprocess
 from concurrent.futures import ProcessPoolExecutor, TimeoutError, as_completed
 from pathlib import Path
-from typing import Tuple
 
 import matplotlib
 import matplotlib.pyplot as plt
@@ -190,10 +189,6 @@ def _set_frame_info(self):
 
         self.pad_len = len(str(self.n_frames))
 
-    def _set_input_stats(self, video_filename=None) -> Tuple[int, int]:
-        """Get the width and height of the video."""
-        logger.debug("Getting video stats with ffprobe")
-
     def _set_plot_bases(self):
         """Create the figure and axes for the video."""
         logger.debug("Setting plot bases")
@@ -309,15 +304,20 @@ def centroid_to_px(*idx):
             )
         )
 
-    def _set_orient_line(self, frame, pos_ind):
-        def orient_list(c):
-            return [c, c + 30 * np.cos(self.orientation_mean[pos_ind])]
+    def _get_orient_line(self, pos_ind):
+        orient = self.orientation_mean[pos_ind]
+        if isinstance(orient, np.ndarray):
+            orient = orient[0]  # Trodes passes orientation as a 1D array
 
-        if np.all(np.isnan(self.orientation_mean[pos_ind])):
-            self.orientation_line.set_data((np.NaN, np.NaN))
+        def orient_list(c, axis="x"):
+            func = np.cos if axis == "x" else np.sin
+            return [c, c + 30 * func(orient)]
+
+        if np.all(np.isnan(orient)):
+            return ([np.NaN], [np.NaN])
         else:
-            c0, c1 = self._get_centroid_data(pos_ind)
-            self.orientation_line.set_data(orient_list(c0), orient_list(c1))
+            x, y = self._get_centroid_data(pos_ind)
+            return (orient_list(x), orient_list(y, axis="y"))
 
     def _generate_single_frame(self, frame_ind):
         """Generate a single frame and save it as an image."""
@@ -364,7 +364,7 @@ def _generate_single_frame(self, frame_ind):
                 )
             )
         self.centroid_position_dot.set_offsets(dlc_centroid_data)
-        _ = self._set_orient_line(frame, pos_ind)
+        self.orientation_line.set_data(self._get_orient_line(pos_ind))
 
         time_delta = pd.Timedelta(
             pd.to_datetime(self.position_time[pos_ind] * 1e9, unit="ns")

src/spyglass/position/v1/position_trodes_position.py

@@ -344,9 +344,14 @@ def make(self, key):
         adj_df = _fix_col_names(raw_df)  # adjust 'xloc1' to 'xloc'
 
         limit = params.get("limit", None)
-        if limit or test_mode:
+
+        if limit and not test_mode:
             params["debug"] = True
             output_video_filename = Path(".") / f"TEST_VID_{limit}.mp4"
+        elif test_mode:
+            limit = 10
+
+        if limit:
             # pytest video data has mismatched shapes in some cases
             min_len = limit or min(len(adj_df), len(pos_df), len(video_time))
             adj_df = adj_df.head(min_len)
@@ -401,7 +406,7 @@ def make(self, key):
             **params,
         )
 
-        if limit:
+        if limit and not test_mode:
             return vid_maker
 
         self.insert1(dict(**key, has_video=True))

src/spyglass/spikesorting/utils.py

@@ -108,7 +108,7 @@ def get_group_by_shank(
             if omit_ref_electrode_group and (
                 str(e_group) == str(ref_elec_group)
             ):
-                logger.warn(
+                logger.warning(
                     f"Omitting electrode group {e_group} from sort groups "
                     + "because contains reference."
                 )
@@ -117,7 +117,7 @@ def get_group_by_shank(
 
             # omit unitrodes if indicated
             if omit_unitrode and len(shank_elect) == 1:
-                logger.warn(
+                logger.warning(
                     f"Omitting electrode group {e_group}, shank {shank} "
                     + "from sort groups because unitrode."
                 )

src/spyglass/spikesorting/v0/sortingview.py

@@ -72,7 +72,7 @@ def make(self, key: dict):
                 LabMember.LabMemberInfo & {"lab_member_name": team_member}
             ).fetch("google_user_name")
             if len(google_user_id) != 1:
-                logger.warn(
+                logger.warning(
                     f"Google user ID for {team_member} does not exist or more than one ID detected;\
                         permission not given to {team_member}, skipping..."
                 )

src/spyglass/spikesorting/v0/sortingview_helper_fn.py

@@ -136,7 +136,7 @@ def _generate_url(
     )
 
     if initial_curation is not None:
-        logger.warn("found initial curation")
+        logger.warning("found initial curation")
         sorting_curation_uri = kcl.store_json(initial_curation)
     else:
         sorting_curation_uri = None

src/spyglass/spikesorting/v0/spikesorting_artifact.py

@@ -263,7 +263,7 @@ def _get_artifact_times(
             [[valid_timestamps[0], valid_timestamps[-1]]]
         )
         artifact_times_empty = np.asarray([])
-        logger.warn("No artifacts detected.")
+        logger.warning("No artifacts detected.")
         return recording_interval, artifact_times_empty
 
     # convert indices to intervals

src/spyglass/spikesorting/v0/spikesorting_curation.py

@@ -266,7 +266,7 @@ def save_sorting_nwb(
         AnalysisNwbfile().add(key["nwb_file_name"], analysis_file_name)
 
         if object_ids == "":
-            logger.warn(
+            logger.warning(
                 "Sorting contains no units."
                 "Created an empty analysis nwb file anyway."
             )

src/spyglass/spikesorting/v1/artifact.py

@@ -98,7 +98,7 @@ def insert_selection(cls, key: dict):
         """
         query = cls & key
         if query:
-            logger.warn("Similar row(s) already inserted.")
+            logger.warning("Similar row(s) already inserted.")
             return query.fetch(as_dict=True)
         key["artifact_id"] = uuid.uuid4()
         cls.insert1(key, skip_duplicates=True)
@@ -290,7 +290,7 @@ def _get_artifact_times(
             [[valid_timestamps[0], valid_timestamps[-1]]]
         )
         artifact_times_empty = np.asarray([])
-        logger.warn("No artifacts detected.")
+        logger.warning("No artifacts detected.")
         return recording_interval, artifact_times_empty
 
     # convert indices to intervals

src/spyglass/spikesorting/v1/figurl_curation.py

@@ -51,7 +51,7 @@ def insert_selection(cls, key: dict):
         if "figurl_curation_id" in key:
             query = cls & {"figurl_curation_id": key["figurl_curation_id"]}
             if query:
-                logger.warn("Similar row(s) already inserted.")
+                logger.warning("Similar row(s) already inserted.")
                 return query.fetch(as_dict=True)
         key["figurl_curation_id"] = uuid.uuid4()
         cls.insert1(key, skip_duplicates=True)