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CHANGELOG.md

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Changelog

Observes Semantic Versioning standard and Keep a Changelog convention.

[0.9.5] - 2024-03-22

  • Add - pytest
  • Fix - minor bugfix in tests
  • Update - clean up notebook
  • Update - Elements installed directly from GitHub instead of PyPI
  • Update - Black formatting tests

[0.9.4] - 2024-02-05

  • Fix - bugfix ingesting field xyz for mesoscan (multiROI) from ScanImage
  • Update - make output_dir if not exist for task_mode="trigger"

0.9.3 - 2024-01-29

  • Update - DataJoint Elements to install from GitHub instead of PyPI
  • Fix - element-interface required during package installation
  • Fix - apply formatting with black across the repository

0.9.2 - 2024-01-10

  • Fix - Imports and attribute values in notebooks to resolve DataJoint errors

0.9.1 - 2023-12-19

  • Update - Tutorial notebook
  • Fix - minor fixes in setup.py and README

0.9.0 - 2023-10-13

  • Add - Export to NWB and upload to DANDI

0.8.1 - 2023-08-31

  • Fix - Rename get_image_files to get_calcium_imaging_files where missed

0.8.0 - 2023-08-08

  • Update - Rename get_image_files to get_calcium_imaging_files, and update arguments
  • Update - Remove CaImAn installation from the Dev Container due to memory limits of a free GitHub Codespace account
  • Update - Installation instructions

0.7.9 - 2023-07-27

  • Update - GitHub Actions to run every Monday at 8am
  • Update - Dev Container to install CaImAn and rename Docker image
  • Update - extras_require to increment element-interface version
  • Update - extras_require to include caiman, sbxreader, and scanreader

0.7.8 - 2023-07-27

  • Update - import statement for prairie_view_loader in scan.py

0.7.7 - 2023-07-13

  • Add - Environment variables for the Python version in the Dev Container
  • Add - Versions for the VS Code extensions in the Dev Container

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

0.7.4 - 2023-06-19

  • Add - Dev Container Docker image ID
  • Update - Remove .devcontainer/local/
  • Update - Move docker compose up command from devcontainer.json to README

0.7.3 - 2023-06-09

  • Fix - Output of cells within the tutorial notebook

0.7.2 - 2023-06-08

  • Update - tutorial notebook

0.7.1 - 2023-06-07

  • Fix - Docs to render notebooks
  • Fix - get_imaging_root_data_dir function

0.7.0 - 2023-06-06

  • Update - Merge workflow-calcium-imaging into element-calcium-imaging PR #135
  • Add - extras_require feature to setup.py
  • Add - GitHub Actions that call reusable workflows in the datajoint/.github repository
  • Update - Replace get_nd2_files, etc. functions with get_image_files function
  • Add - tutorial_pipeline.py script for notebooks to import and activate schemas
  • Update - Replace reference.Equipment with lab.Device table
  • Update - Remove demo_prepare.ipynb
  • Update - Rename demo_run.ipynb to demo.ipynb
  • Update - __init__.py to use environment variables (if available) in place of dj.config['custom'] values

0.6.2 - 2023-05-22

  • Add - CaImAn, Suite2p, and EXTRACT citations

0.6.1 - 2023-05-15

  • Update - Docs

0.6.0 - 2023-05-15

  • Add - Quality metrics
  • Update - Docs and readme

0.5.7 - 2023-05-11

  • Fix - .ipynb dark mode output for all notebooks.
  • Fix - Remove GOOGLE_ANALYTICS_KEY from u24_element_release_call.yml.

0.5.6 - 2023-04-28

  • Fix - .ipynb output in tutorials is not visible in dark mode.
  • Fix - typos in docstrings.

0.5.5 - 2023-04-06

  • Update - Bump element-interface requirement to 0.5.1.

0.5.4 - 2023-03-08

  • Add - Requirement for ipywidgets
  • Update - Docker Compose file for docs release

0.5.3 - 2023-02-23

  • Add - spelling, markdown, and pre-commit config files
  • Add - Notebook rendering to docs

0.5.2 - 2023-01-11

  • Bugfix - fix errors in ingesting single-plane PrairieView scans into ScanInfo
  • Add - Optional installation of caiman and suite2p through pip

0.5.1 - 2022-12-15

  • Add - Imports for prairieview loader

0.5.0 - 2022-12-14

  • Add - Cell extraction with EXTRACT package

0.4.2 - 2022-11-02

  • Bugfix - Add plotting package to the requirements to generate the figures
  • Add - Scan date parser from nd2 files

0.4.1 - 2022-10-28

  • Update - Bump version to trigger PyPI release to revert updates from incorrect tag

0.4.0 - 2022-10-28

  • Add - New schema imaging_report to compute and store figures from results
  • Add - Widget to display figures

0.3.0 - 2022-10-07

  • Add - Reader for Bruker PrairieView acquisition system

0.2.2 - 2022-09-28

  • Update - Minor table explanation edits
  • Update - Query simplifications
  • Update - Minor code refactoring

0.2.1 - 2022-09-12

  • Bugfix - fix errors in auto generating new ProcessingTask

0.2.0 - 2022-07-01

  • Add - Imaging module (imaging_preprocess.py) for pre-processing steps

0.1.0 - 2022-06-29

  • Add - Support for element-interface
  • Add - Trigger Suite2p and CaImAn
  • Add - Imaging module for no curation
  • Add - Support for Nikon acquisition system
  • Add - scan_datetime and scan_duration attributes
  • Add - Estimate for scan duration
  • Add - Citation section to README
  • Update - Move background file to elements.datajoint.org
  • Add - Adopt black formatting into code base

0.1.0b0 - 2021-05-07

  • Update - First beta release

0.1.0a4 - 2021-05-07

  • Update - Add workaround to handle DataJoint 0.13.* issue #914

0.1.0a3 - 2021-05-03

  • Add - GitHub Action release process
  • Add - scan and imaging modules
  • Add - Readers for ScanImage, ScanBox, Suite2p, CaImAn