Merge pull request #151 from kabilar/main

Patch issue with nullable attributes

Author: dimitri-yatsenko

.devcontainer/Dockerfile

@@ -22,7 +22,6 @@ RUN \
     pip install --no-cache-dir --upgrade black pip && \
     echo '. /etc/bash_completion' >> /home/vscode/.bashrc && \
     echo 'export PS1="\[\e[32;1m\]\u\[\e[m\]@\[\e[34;1m\]\H\[\e[m\]:\[\e[33;1m\]\w\[\e[m\]$ "' >> /home/vscode/.bashrc && \
-    # dircolors -b >> /home/vscode/.bashrc && \  # somehow fix colors
     apt-get clean
 
 COPY ./ /tmp/element-calcium-imaging/

CHANGELOG.md

@@ -3,6 +3,11 @@
 Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
 [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) convention.
 
+## [0.7.6] - 2023-06-30
+
++ Add - Null value for `package_version` in `imaging*` modules to patch bug
++ Update - `tutorial.ipynb` notebook to insert values for nullable attributes
+
 ## [0.7.5] - 2023-06-20
 
 + Update - Requirements
@@ -146,6 +151,7 @@ Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
 + Add - `scan` and `imaging` modules
 + Add - Readers for `ScanImage`, `ScanBox`, `Suite2p`, `CaImAn`
 
+[0.7.6]: https://github.com/datajoint/element-calcium-imaging/releases/tag/0.7.6
 [0.7.5]: https://github.com/datajoint/element-calcium-imaging/releases/tag/0.7.5
 [0.7.4]: https://github.com/datajoint/element-calcium-imaging/releases/tag/0.7.4
 [0.7.3]: https://github.com/datajoint/element-calcium-imaging/releases/tag/0.7.3

README.md

@@ -1,6 +1,6 @@
 [![PyPI version](https://badge.fury.io/py/element-calcium-imaging.svg)](http://badge.fury.io/py/element-calcium-imaging)
 
-# DataJoint Element - Functional Calcium Imaging
+# DataJoint Element for Functional Calcium Imaging
 
 DataJoint Element for functional calcium imaging with 
 [ScanImage](https://docs.scanimage.org/), 
@@ -13,7 +13,8 @@ and `Bruker Prairie View` acquisition software; and
 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. This repository also provides a tutorial environment and notebooks to learn the pipeline.
+combined with other Elements to assemble a fully functional pipeline. This repository 
+also provides a tutorial environment and notebooks to learn the pipeline.
 
 ## Experiment Flowchart
 
@@ -23,11 +24,13 @@ combined with other Elements to assemble a fully functional pipeline. This repos
 
 ![pipeline](https://raw.githubusercontent.com/datajoint/element-calcium-imaging/main/images/pipeline_imaging.svg)
 
-+ We have designed three variations of the pipeline to handle different use cases. Displayed above is the default `imaging` schema.  Details on all of the `imaging` schemas can be found in the [Data Pipeline](https://datajoint.com/docs/elements/element-calcium-imaging/latest/pipeline/) documentation page.
++ We have designed three variations of the pipeline to handle different use cases. 
+Displayed above is the default `imaging` schema.  Details on all of the `imaging` 
+schemas can be found in the [Data Pipeline](https://datajoint.com/docs/elements/
+element-calcium-imaging/latest/pipeline/) documentation page.
 
 ## Getting Started
 
-
 + Install from PyPI
 
      ```bash
@@ -40,7 +43,8 @@ combined with other Elements to assemble a fully functional pipeline. This repos
 
 ## Support
 
-+ If you need help getting started or run into any errors, please contact our team by email at [email protected].
++ If you need help getting started or run into any errors, please open a GitHub Issue 
+or contact our team by email at [email protected].
 
 ## Interactive Tutorial
 

element_calcium_imaging/imaging.py

@@ -528,7 +528,7 @@ def make(self, key):
         else:
             raise ValueError(f"Unknown task mode: {task_mode}")
 
-        self.insert1(key)
+        self.insert1({**key, "package_version": ""})
 
 
 @schema

element_calcium_imaging/imaging_no_curation.py

@@ -528,7 +528,7 @@ def make(self, key):
         else:
             raise ValueError(f"Unknown task mode: {task_mode}")
 
-        self.insert1(key)
+        self.insert1({**key, "package_version": ""})
 
 
 # -------------- Motion Correction --------------

element_calcium_imaging/imaging_preprocess.py

@@ -262,7 +262,7 @@ def make(self, key):
         else:
             raise ValueError(f"Unknown task mode: {task_mode}")
 
-        self.insert1(key)
+        self.insert1({**key, "package_version": ""})
 
 
 @schema
@@ -741,7 +741,7 @@ def make(self, key):
         else:
             raise ValueError(f"Unknown task mode: {task_mode}")
 
-        self.insert1(key)
+        self.insert1({**key, "package_version": ""})
 
 
 @schema

element_calcium_imaging/version.py

@@ -1,2 +1,2 @@
 """Package metadata."""
-__version__ = "0.7.5"
+__version__ = "0.7.6"