Merge pull request #97 from JaerongA/qc

Add a notebook for visualizing qc metrics

.devcontainer/Dockerfile

@@ -25,11 +25,14 @@ RUN \
     # dircolors -b >> /home/vscode/.bashrc && \  # somehow fix colors
     apt-get clean
 COPY ./requirements.txt /tmp/
+COPY ./requirements_dev.txt /tmp/
 RUN \
     # workflow dependencies
     apt-get install gcc ffmpeg libsm6 libxext6 -y && \
     pip install --no-cache-dir -r /tmp/requirements.txt && \
+    pip install --no-cache-dir -r /tmp/requirements_dev.txt && \
     rm /tmp/requirements.txt && \
+    rm /tmp/requirements_dev.txt && \
     apt-get clean
 
 ENV DJ_HOST fakeservices.datajoint.io

.devcontainer/devcontainer.json

@@ -1,6 +1,6 @@
 // For format details, see https://aka.ms/devcontainer.json.
 {
-	"name": "Remote Demo",
+	"name": "Demo with remote data",
 	"dockerComposeFile": "docker-compose.yaml",
 	"service": "app",
 	"workspaceFolder": "/workspaces/${localWorkspaceFolderBasename}",

.devcontainer/local/devcontainer.json

@@ -1,6 +1,6 @@
 // For format details, see https://aka.ms/devcontainer.json.
 {
-	"name": "Local Demo",
+	"name": "Demo with local data",
 	"dockerComposeFile": "docker-compose.yaml",
 	"service": "app",
 	"workspaceFolder": "/workspaces/${localWorkspaceFolderBasename}",

.gitignore

@@ -109,4 +109,5 @@ docker-compose.yml
 # temporary figures
 temp_ephys_figures/
 
-example_data
+example_data
+*.code-workspace

CHANGELOG.md

@@ -3,6 +3,12 @@
 Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
 [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) convention.
 
+## [0.3.2] - 2023-04-14
+
++ Add - `quality_metrics.ipynb` for visualizing quality metrics.
++ Add - Documentation for attributes in `ephys.QualityMetrics.Waveform`.
++ Update - pytest for `ephys.QualityMetrics.populate`.
+
 ## [0.3.1] - 2023-04-12
 
 + Add - pytest for new `QCmetric` tables.
@@ -87,6 +93,7 @@ Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
 
 + Add - Version
 
+[0.3.2]: https://github.com/datajoint/workflow-array-ephys/releases/tag/0.3.2
 [0.3.1]: https://github.com/datajoint/workflow-array-ephys/releases/tag/0.3.1
 [0.3.0]: https://github.com/datajoint/workflow-array-ephys/releases/tag/0.3.0
 [0.2.6]: https://github.com/datajoint/workflow-array-ephys/releases/tag/0.2.6

notebooks/demo_prepare.ipynb

@@ -140,7 +140,7 @@
     "        insertion_number=1,\n",
     "        paramset_idx=1,\n",
     "        task_mode='load', # load or trigger\n",
-    "        clustering_output_dir=\"subject5/session1/probe_1/ks2.1_01\"\n",
+    "        clustering_output_dir=\"subject5/session1/probe_1/kilosort2-5_1\"\n",
     "    )\n",
     ")\n",
     "\n",
@@ -204,13 +204,6 @@
     "\n",
     "# drop_databases(databases=['analysis', 'trial', 'event', 'ephys_report', 'ephys', 'probe', 'session', 'subject', 'project', 'lab'])\n"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {
@@ -229,7 +222,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.2"
+   "version": "3.9.16"
   },
   "orig_nbformat": 4,
   "vscode": {