dj-sciops · ttngu207 · Dec 10, 2025 · Mar 4, 2025 · May 19, 2025 · May 19, 2025
diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile
@@ -1,10 +1,13 @@
-FROM python:3.9-slim@sha256:5f0192a4f58a6ce99f732fe05e3b3d00f12ae62e183886bca3ebe3d202686c7f
+ARG PY_VER=3.11
+ARG DISTRO=bullseye
+FROM mcr.microsoft.com/devcontainers/python:${PY_VER}-${DISTRO}
 
-ENV PATH /usr/local/bin:$PATH
-ENV PYTHON_VERSION 3.9.17
+# Avoid warnings by switching to noninteractive
+ENV DEBIAN_FRONTEND=noninteractive
+
+USER root
 
 RUN \
-    adduser --system --disabled-password --shell /bin/bash vscode && \
     # install docker
     apt-get update && \
     apt-get install ca-certificates curl gnupg lsb-release -y && \
@@ -45,4 +48,5 @@ ENV EPHYS_ROOT_DATA_DIR /workspaces/element-array-ephys/example_data
 ENV DATABASE_PREFIX neuro_
 
 USER vscode
-CMD bash -c "sudo rm /var/run/docker.pid; sudo dockerd"
+
+CMD bash -c "sudo rm /var/run/docker.pid; sudo dockerd"
diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
@@ -22,8 +22,8 @@
 		},
 		"vscode": {
 			"extensions": [
-				"ms-python.python@2023.8.0",
-				"ms-toolsai.jupyter@2023.3.1201040234"
+				"ms-python.python@2025.6.1",
+				"ms-toolsai.jupyter@2025.4.1"
 			]
 		}
 	}

diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml
@@ -1,5 +1,5 @@
 blank_issues_enabled: false
 contact_links:
   - name: DataJoint Contribution Guideline
-    url: https://docs.datajoint.org/python/community/02-Contribute.html
+    url: https://docs.datajoint.com/about/contribute/
     about: Please make sure to review the DataJoint Contribution Guidelines
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,20 @@
 Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
  [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) convention.
 
+## [0.4.5] - 2025-09-17
+
++ Fix - Rename `env.yml` to `conda_env.yml` for consistency with other projects
++ Update - Passing tests by blackifying previous updates
+
+## [0.4.4] - 2025-06-06
+
++ Update - Update params in test/tutorial
++ Fix - Moved KiloSort's template_features  to additional_files 
+
+## [0.4.3] - 2025-06-03
+
++ Update - Use `Spikeinterface` official released versions (instead of install directly from source)
+
 ## [0.4.2] - 2025-03-25
 
 + Fix - Add key_source to `ProbeLevelReport` to filter for 'good' quality units

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -1,5 +1,5 @@
 # Contribution Guidelines
 
 This project follows the
-[DataJoint Contribution Guidelines](https://datajoint.com/docs/about/contribute/).
+[DataJoint Contribution Guidelines](https://docs.datajoint.com/about/contribute/).
 Please reference the link for more full details.
diff --git a/README.md b/README.md
@@ -44,7 +44,7 @@ environment and notebooks to learn the pipeline.
 + [Interactive tutorial on GitHub
   Codespaces](https://github.com/datajoint/element-array-ephys#interactive-tutorial)
 
-+ [Documentation](https://datajoint.com/docs/elements/element-array-ephys)
++ [Documentation](https://docs.datajoint.com/elements/element-array-ephys/)
 
 ## Support
 

diff --git a/env.yml → conda_env.yml b/env.yml → conda_env.yml
diff --git a/docs/mkdocs.yaml b/docs/mkdocs.yaml
@@ -1,7 +1,7 @@
 --- # ---------------------- PROJECT SPECIFIC ---------------------------
 
 site_name: DataJoint Documentation
-site_url: http://localhost/docs/elements/element-array-ephys
+site_url: https://docs.datajoint.com/elements/element-array-ephys/
 repo_url: https://github.com/datajoint/element-array-ephys
 repo_name: datajoint/element-array-ephys
 nav:

diff --git a/docs/src/.overrides/partials/nav.html b/docs/src/.overrides/partials/nav.html
@@ -7,15 +7,14 @@
 {% endif %}
 <nav class="{{ class }}" aria-label="{{ lang.t('nav.title') }}" data-md-level="0">
     <label class="md-nav__title" for="__drawer">
-        <a href="{{ config.extra.homepage | d(nav.homepage.url, true) | url }}"
-            title="{{ config.site_name | e }}" class="md-nav__button md-logo"
-            aria-label="{{ config.site_name }}" data-md-component="logo">
+        <a href="{{ config.extra.homepage | d(nav.homepage.url, true) | url }}" title="{{ config.site_name | e }}"
+            class="md-nav__button md-logo" aria-label="{{ config.site_name }}" data-md-component="logo">
             {% include "partials/logo.html" %}
         </a>
         {#-
         Add DataJoint home link to navigation header, otherwise unchanged
         -#}
-        <a href="https://datajoint.com/docs/elements/" title="DataJoint Elements">
+        <a href="https://docs.datajoint.com/elements/" title="DataJoint Elements">
             ⬅ Home
         </a>
     </label>

diff --git a/docs/src/concepts.md b/docs/src/concepts.md
@@ -103,15 +103,15 @@ is a table within the Element or a table connected to the Element.
 
 ![diagram](https://raw.githubusercontent.com/datajoint/element-array-ephys/main/images/attached_array_ephys_element_acute.svg)
 
-### `subject` schema ([API docs](https://datajoint.com/docs/elements/element-animal/api/element_animal/subject))
+### `subject` schema ([API docs](https://docs.datajoint.com/elements/element-animal/0.1/api/element_animal/subject/))
 
 Although not required, most choose to connect the `Session` table to a `Subject` table.
 
 | Table | Description |
 | --- | --- |
 | Subject | A table containing basic information of the research subject. |
 
-### `session` schema ([API docs](https://datajoint.com/docs/elements/element-session/api/element_session/session_with_datetime))
+### `session` schema ([API docs](https://docs.datajoint.com/elements/element-session/))
 
 | Table | Description |
 | --- | --- |

diff --git a/docs/src/tutorials/index.md b/docs/src/tutorials/index.md
@@ -11,7 +11,7 @@ all the necessary dependencies and sample data to run the tutorials.
 
 Installation of the Element requires an integrated development environment and database.
 Instructions to setup each of the components can be found on the
-[User Instructions](https://datajoint.com/docs/elements/user-guide/) page. The example
+[User Instructions](https://docs.datajoint.com/elements/user-guide/) page. The example
 tutorial uses several Elements (Lab, Animal, Session, Event, and Electrophysiology) to construct
 a complete pipeline, and is able to ingest experimental metadata and run model training
 and inference.

diff --git a/element_array_ephys/ephys.py b/element_array_ephys/ephys.py
@@ -4,7 +4,7 @@
 import pathlib
 import re
 from decimal import Decimal
-
+from typing import Any, Dict, List, Tuple
 import datajoint as dj
 import numpy as np
 import pandas as pd
@@ -293,14 +293,28 @@ class EphysFile(dj.Part):
         file_path: varchar(255)  # filepath relative to root data directory
         """
 
-    def make(self, key):
-        """Populates table with electrophysiology recording information."""
+    def make_fetch(self, key: dict) -> Tuple[pathlib.Path, str, List[str], List[str]]:
+        """Fetch required data from database for processing."""
         session_dir = find_full_path(
             get_ephys_root_data_dir(), get_session_directory(key)
         )
         inserted_probe_serial_number = (ProbeInsertion * probe.Probe & key).fetch1(
             "probe"
         )
+        supported_probe_types = list(probe.ProbeType.fetch("probe_type"))
+        supported_acq_software = list(AcquisitionSoftware.fetch("acq_software"))
+
+        return session_dir, inserted_probe_serial_number, supported_probe_types, supported_acq_software
+
+    def make_compute(
+        self,
+        key: dict,
+        session_dir: pathlib.Path,
+        inserted_probe_serial_number: str,
+        supported_probe_types: List[str],
+        supported_acq_software: List[str],
+    ) -> Tuple[Dict[str, Any], List[Dict[str, Any]], Dict[str, Any], List[Dict[str, Any]], List[Dict[str, Any]]]:
+        """Populates table with electrophysiology recording information."""
 
         # Search session dir and determine acquisition software
         for ephys_pattern, ephys_acq_type in (
@@ -317,13 +331,11 @@ def make(self, key):
                 "Neither SpikeGLX nor Open Ephys recording files found"
             )
 
-        if acq_software not in AcquisitionSoftware.fetch("acq_software"):
+        if acq_software not in supported_acq_software:
             raise NotImplementedError(
                 f"Processing ephys files from acquisition software of type {acq_software} is not yet implemented."
             )
 
-        supported_probe_types = probe.ProbeType.fetch("probe_type")
-
         if acq_software == "SpikeGLX":
             for meta_filepath in ephys_meta_filepaths:
                 spikeglx_meta = spikeglx.SpikeGLXMeta(meta_filepath)
@@ -483,6 +495,18 @@ def make(self, key):
                 f"Processing ephys files from acquisition software of type {acq_software} is not yet implemented."
             )
 
+        return econfig_entry, econfig_electrodes, ephys_recording_entry, ephys_file_entries, ephys_channel_entries
+
+    def make_insert(
+        self,
+        key: dict,
+        econfig_entry: Dict[str, Any],
+        econfig_electrodes: List[Dict[str, Any]],
+        ephys_recording_entry: Dict[str, Any],
+        ephys_file_entries: List[Dict[str, Any]],
+        ephys_channel_entries: List[Dict[str, Any]],
+    ) -> None:
+        """Insert computed data into database tables."""
         # Insert into probe.ElectrodeConfig (recording configuration)
         if not probe.ElectrodeConfig & {
             "electrode_config_hash": econfig_entry["electrode_config_hash"]

diff --git a/element_array_ephys/ephys_report.py b/element_array_ephys/ephys_report.py
@@ -8,7 +8,7 @@
 import datajoint as dj
 from element_interface.utils import dict_to_uuid
 
-from . import probe, ephys
+from . import ephys, probe
 
 schema = dj.schema()
 
@@ -50,7 +50,7 @@ class ProbeLevelReport(dj.Computed):
     ---
     drift_map_plot: attach
     """
-    
+
     @property
     def key_source(self):
         return ephys.CuratedClustering & (

diff --git a/element_array_ephys/readers/kilosort.py b/element_array_ephys/readers/kilosort.py
@@ -5,7 +5,7 @@
 import numpy as np
 import re
 import logging
-from .utils import convert_to_number
+from element_array_ephys.readers.utils import convert_to_number
 
 log = logging.getLogger(__name__)
 
@@ -21,12 +21,7 @@ class Kilosort:
         "similar_templates.npy",
         "spike_templates.npy",
         "spike_times.npy",
-        "template_features.npy",
-        "template_feature_ind.npy",
         "templates.npy",
-        "templates_ind.npy",
-        "whitening_mat.npy",
-        "whitening_mat_inv.npy",
         "spike_clusters.npy",
     ]
 
@@ -35,6 +30,11 @@ class Kilosort:
         "spike_times_sec_adj.npy",
         "cluster_groups.csv",
         "cluster_KSLabel.tsv",
+        "template_features.npy",
+        "template_feature_ind.npy",
+        "templates_ind.npy",
+        "whitening_mat.npy",
+        "whitening_mat_inv.npy",
     ]
 
     kilosort_files = _kilosort_core_files + _kilosort_additional_files
@@ -47,7 +47,7 @@ def __init__(self, kilosort_dir):
 
         self.validate()
 
-        params_filepath = kilosort_dir / "params.py"
+        params_filepath = self._kilosort_dir / "params.py"
         self._info = {
             "time_created": datetime.fromtimestamp(params_filepath.stat().st_ctime),
             "time_modified": datetime.fromtimestamp(params_filepath.stat().st_mtime),

diff --git a/element_array_ephys/readers/spikeglx.py b/element_array_ephys/readers/spikeglx.py
@@ -281,7 +281,7 @@ def __init__(self, meta_filepath):
         elif probe_model == 24:
             self.probe_model = "neuropixels 2.0 - MS"
         else:
-            self.probe_model = str(probe_model)
+            self.probe_model = self.probe_PN
 
         # Get recording time
         self.recording_time = datetime.strptime(

diff --git a/element_array_ephys/version.py b/element_array_ephys/version.py
@@ -1,3 +1,3 @@
 """Package metadata."""
 
-__version__ = "0.4.2"
+__version__ = "0.4.6"