Merge branch 'datajoint:main' into main

Author: kushalbakshi

.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

README.md

@@ -26,17 +26,18 @@ The easiest way to learn about DataJoint Elements is to use the tutorial noteboo
 
 Here are some options that provide a great experience:
 
-- **Cloud-based IDE**: (*recommended*)
+- Cloud-based Development Environment: (*recommended*)
   - Launch using [GitHub Codespaces](https://github.com/features/codespaces) using the `+` option which will `Create codespace on main` in the codebase repository on your fork with default options. For more control, see the `...` where you may create `New with options...`.
   - Build time for a codespace is **~7m**. This is done infrequently and cached for convenience.
   - Start time for a codespace is **~30s**. This will pull the built codespace from cache when you need it.
   - *Tip*: Each month, GitHub renews a [free-tier](https://docs.github.com/en/billing/managing-billing-for-github-codespaces/about-billing-for-github-codespaces#monthly-included-storage-and-core-hours-for-personal-accounts) quota of compute and storage. Typically we run into the storage limits before anything else since Codespaces consume storage while stopped. It is best to delete Codespaces when not actively in use and recreate when needed. We'll soon be creating prebuilds to avoid larger build times. Once any portion of your quota is reached, you will need to wait for it to be reset at the end of your cycle or add billing info to your GitHub account to handle overages.
   - *Tip*: GitHub auto names the codespace but you can rename the codespace so that it is easier to identify later.
-- **Local IDE**:
-  - Ensure you have [Git](https://git-scm.com/book/en/v2/Getting-Started-Installing-Git)
-  - Ensure you have [Docker](https://docs.docker.com/get-docker/)
-  - Ensure you have [VSCode](https://code.visualstudio.com/)
-  - Install the [Dev Containers extension](https://marketplace.visualstudio.com/items?itemName=ms-vscode-remote.remote-containers)
+- Local Development Environment:
+  - Note: On Windows, running the tutorial notebook with the example data in a Dev Container is not currently possible due to a s3fs mounting issue.  Please use the `Cloud-based Development Environment` option above.
+  - Install [Git](https://git-scm.com/book/en/v2/Getting-Started-Installing-Git)
+  - Install [Docker](https://docs.docker.com/get-docker/)
+  - Install [VSCode](https://code.visualstudio.com/)
+  - Install the VSCode [Dev Containers extension](https://marketplace.visualstudio.com/items?itemName=ms-vscode-remote.remote-containers)
   - `git clone` the codebase repository and open it in VSCode
   - Use the `Dev Containers extension` to `Reopen in Container` (More info in the `Getting started` included with the extension)
 

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": {