Merge pull request #165 from kabilar/patch

Patch issue with nullable attributes

.github/workflows/release.yaml

@@ -0,0 +1,27 @@
+name: Release
+on:
+  workflow_dispatch:
+jobs:
+  make_github_release:
+    uses: datajoint/.github/.github/workflows/make_github_release.yaml@main
+  pypi_release:
+    needs: make_github_release
+    uses: datajoint/.github/.github/workflows/pypi_release.yaml@main
+    secrets:
+      TWINE_USERNAME: ${{secrets.TWINE_USERNAME}}
+      TWINE_PASSWORD: ${{secrets.TWINE_PASSWORD}}
+    with:
+      UPLOAD_URL: ${{needs.make_github_release.outputs.release_upload_url}}
+  mkdocs_release:
+    uses: datajoint/.github/.github/workflows/mkdocs_release.yaml@main
+    permissions: 
+      contents: write
+  # devcontainer-build:
+  #   uses: datajoint/.github/.github/workflows/devcontainer-build.yaml@main
+  # devcontainer-publish:
+  #   needs: 
+  #     - devcontainer-build
+  #   uses: datajoint/.github/.github/workflows/devcontainer-publish.yaml@main
+  #   secrets:
+  #     DOCKERHUB_USERNAME: ${{secrets.DOCKERHUB_USERNAME}}
+  #     DOCKERHUB_TOKEN: ${{secrets.DOCKERHUB_TOKEN_FOR_ELEMENTS}}

.github/workflows/test.yaml

@@ -0,0 +1,34 @@
+name: Test
+on:
+  push:
+  pull_request:
+  workflow_dispatch:
+jobs:
+  # devcontainer-build:
+  #   uses: datajoint/.github/.github/workflows/devcontainer-build.yaml@main
+  tests:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        py_ver: ["3.9", "3.10"]
+        mysql_ver: ["8.0", "5.7"]
+        include:
+          - py_ver: "3.8"
+            mysql_ver: "5.7"
+          - py_ver: "3.7"
+            mysql_ver: "5.7"
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{matrix.py_ver}}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{matrix.py_ver}}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install flake8 "black[jupyter]"
+      - name: Run style tests
+        run: |
+          python_version=${{matrix.py_ver}}
+          black element_array_ephys --check --verbose --target-version py${python_version//.}
+

CHANGELOG.md

@@ -3,9 +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.
 
-## [Unreleased] - 2023-06-23
+## [0.2.11] - 2023-06-29
 
 + Update - Improve kilosort triggering routine - better logging, remove temporary files, robust resumable processing
++ Add - Null value for `package_version` to patch bug
++ Update - GitHub Actions workflows
++ Update - README instructions
 
 ## [0.2.10] - 2023-05-26
 

README.md

@@ -1,12 +1,40 @@
-# DataJoint Element - Array Electrophysiology Element
+[![PyPI version](https://badge.fury.io/py/element-array-ephys.svg)](http://badge.fury.io/py/element-array-ephys)
 
-DataJoint Element for extracellular array electrophysiology. DataJoint Elements
-collectively standardize and automate data collection and analysis for neuroscience
-experiments.  Each Element is a modular pipeline for data storage and processing with
-corresponding database tables that can be combined with other Elements to assemble a
-fully functional pipeline.
+# DataJoint Element for Extracellular Electrophysiology
 
-![diagram](https://raw.githubusercontent.com/datajoint/element-array-ephys/main/images/diagram_flowchart.svg)
+DataJoint Element for extracellular array electrophysiology that processes data 
+acquired with a polytrode probe
+(e.g. [Neuropixels](https://www.neuropixels.org), Neuralynx) using the
+[SpikeGLX](https://github.com/billkarsh/SpikeGLX) or
+[OpenEphys](https://open-ephys.org/gui) acquisition software and 
+[MATLAB-based Kilosort](https://github.com/MouseLand/Kilosort) or [python-based
+Kilosort](https://github.com/MouseLand/pykilosort) spike sorting software. DataJoint 
+Elements collectively standardize and automate data collection and analysis for 
+neuroscience experiments. Each Element is a modular pipeline for data storage and 
+processing with corresponding database tables that can be combined with other Elements 
+to assemble a fully functional pipeline.
 
-Installation and usage instructions can be found at the
-[Element documentation](https://datajoint.com/docs/elements/element-array-ephys).
+## Experiment flowchart
+
+![flowchart](https://raw.githubusercontent.com/datajoint/element-array-ephys/main/images/diagram_flowchart.svg)
+
+## Data Pipeline Diagram
+
+![datajoint](https://raw.githubusercontent.com/datajoint/element-array-ephys/main/images/attached_array_ephys_element_acute.svg)
+
+
+## Getting Started
+
++ Install from PyPI
+
+     ```bash
+     pip install element-array-ephys
+     ```
+
++ [Interactive tutorial on GitHub Codespaces](https://github.com/datajoint/workflow-array-ephys#interactive-tutorial)
+
++ [Documentation](https://datajoint.com/docs/elements/element-array-ephys)
+
+## Support
+
++ If you need help getting started or run into any errors, please contact our team by email at [email protected].

element_array_ephys/ephys_acute.py

@@ -910,7 +910,7 @@ def make(self, key):
             raise ValueError(f"Unknown task mode: {task_mode}")
 
         creation_time, _, _ = kilosort.extract_clustering_info(kilosort_dir)
-        self.insert1({**key, "clustering_time": creation_time})
+        self.insert1({**key, "clustering_time": creation_time, "package_version": ""})
 
 
 @schema

element_array_ephys/ephys_chronic.py

@@ -839,7 +839,7 @@ def make(self, key):
             raise ValueError(f"Unknown task mode: {task_mode}")
 
         creation_time, _, _ = kilosort.extract_clustering_info(kilosort_dir)
-        self.insert1({**key, "clustering_time": creation_time})
+        self.insert1({**key, "clustering_time": creation_time, "package_version": ""})
 
 
 @schema

element_array_ephys/ephys_no_curation.py

@@ -916,7 +916,7 @@ def make(self, key):
             raise ValueError(f"Unknown task mode: {task_mode}")
 
         creation_time, _, _ = kilosort.extract_clustering_info(kilosort_dir)
-        self.insert1({**key, "clustering_time": creation_time})
+        self.insert1({**key, "clustering_time": creation_time, "package_version": ""})
 
 
 @schema