Add Z drift metrics to imaging_no_curation

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,39 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: 'bug'
+assignees: ''
+
+---
+
+## Bug Report
+
+### Description
+
+A clear and concise description of what is the overall operation that is intended to be
+performed that resulted in an error.
+
+### Reproducibility
+Include:
+- OS (WIN | MACOS | Linux)
+- DataJoint Element Version
+- MySQL Version
+- MySQL Deployment Strategy (local-native | local-docker | remote)
+- Minimum number of steps to reliably reproduce the issue
+- Complete error stack as a result of evaluating the above steps
+
+### Expected Behavior
+A clear and concise description of what you expected to happen.
+
+### Screenshots
+If applicable, add screenshots to help explain your problem.
+
+### Additional Research and Context
+Add any additional research or context that was conducted in creating this report.
+
+For example:
+- Related GitHub issues and PR's either within this repository or in other relevant
+  repositories.
+- Specific links to specific lines or a focus within source code.
+- Relevant summary of Maintainers development meetings, milestones, projects, etc.

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,5 @@
+blank_issues_enabled: false
+contact_links:
+  - name: DataJoint Contribution Guideline
+    url: https://datajoint.com/docs/community/contribute/
+    about: Please make sure to review the DataJoint Contribution Guidelines

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,57 @@
+---
+name: Feature request
+about: Suggest an idea for a new feature
+title: ''
+labels: 'enhancement'
+assignees: ''
+
+---
+
+## Feature Request
+
+### Problem
+
+A clear and concise description how this idea has manifested and the context. Elaborate
+on the need for this feature and/or what could be improved. Ex. I'm always frustrated
+when [...]
+
+### Requirements
+
+A clear and concise description of the requirements to satisfy the new feature. Detail
+what you expect from a successful implementation of the feature. Ex. When using this
+feature, it should [...]
+
+### Justification
+
+Provide the key benefits in making this a supported feature. Ex. Adding support for this
+feature would ensure [...]
+
+### Alternative Considerations
+
+Do you currently have a work-around for this? Provide any alternative solutions or
+features you've considered.
+
+### Related Errors
+Add any errors as a direct result of not exposing this feature.
+
+Please include steps to reproduce provided errors as follows:
+- OS (WIN | MACOS | Linux)
+- DataJoint Element Version
+- MySQL Version
+- MySQL Deployment Strategy (local-native | local-docker | remote)
+- Minimum number of steps to reliably reproduce the issue
+- Complete error stack as a result of evaluating the above steps
+
+### Screenshots
+If applicable, add screenshots to help explain your feature.
+
+### Additional Research and Context
+Add any additional research or context that was conducted in creating this feature request.
+
+For example:
+- Related GitHub issues and PR's either within this repository or in other relevant
+  repositories.
+- Specific links to specific lines or a focus within source code.
+- Relevant summary of Maintainers development meetings, milestones, projects, etc.
+- Any additional supplemental web references or links that would further justify this
+  feature request.

.gitignore

@@ -109,11 +109,13 @@ ENV/
 dj_local_conf.json
 dj_local_conf_old.json
 workflow_calcium_imaging/
+temp*
 
 # docs
 /docs/site
+/docs/src/tutorials/*ipynb
 
 # emacs
 **/*~
 **/#*#
-**/.#*
+**/.#*

.markdownlint.yaml

@@ -0,0 +1,17 @@
+# Markdown Linter configuration for docs
+# https://github.com/DavidAnson/markdownlint
+# https://github.com/DavidAnson/markdownlint/blob/main/doc/Rules.md
+MD009: false # permit trailing spaces
+MD007: false # List indenting - permit 4 spaces
+MD013:
+    line_length: "88" # Line length limits
+    tables: false # disable for tables
+    headings: false # disable for headings
+MD030: false # Number of spaces after a list
+MD033: # HTML elements allowed
+    allowed_elements:
+        - "figure"
+        - "figcaption"
+MD034: false # Permit bare URLs
+MD031: false # Spacing w/code blocks. Conflicts with `??? Note` and code tab styling
+MD046: false # Spacing w/code blocks. Conflicts with `??? Note` and code tab styling

.pre-commit-config.yaml

@@ -0,0 +1,58 @@
+default_stages: [commit, push]
+exclude: (^.github/|^docs/|^images/)
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-added-large-files # prevent giant files from being committed
+      - id: requirements-txt-fixer
+      - id: mixed-line-ending
+        args: ["--fix=lf"]
+        description: Forces to replace line ending by the UNIX 'lf' character.
+
+  # black
+  - repo: https://github.com/psf/black
+    rev: 22.12.0
+    hooks:
+      - id: black
+      - id: black-jupyter
+        args:
+          - --line-length=88
+
+  # isort
+  - repo: https://github.com/pycqa/isort
+    rev: 5.11.2
+    hooks:
+      - id: isort
+        args: ["--profile", "black"]
+        description: Sorts imports in an alphabetical order
+
+  # flake8
+  - repo: https://github.com/pycqa/flake8
+    rev: 4.0.1
+    hooks:
+      - id: flake8
+        args: # arguments to configure flake8
+          # making isort line length compatible with black
+          - "--max-line-length=88"
+          - "--max-complexity=18"
+          - "--select=B,C,E,F,W,T4,B9"
+
+          # these are errors that will be ignored by flake8
+          # https://www.flake8rules.com/rules/{code}.html
+          - "--ignore=E203,E501,W503,W605,E402"
+          # E203 - Colons should not have any space before them.
+          #        Needed for list indexing
+          # E501 - Line lengths are recommended to be no greater than 79 characters.
+          #        Needed as we conform to 88
+          # W503 - Line breaks should occur after the binary operator.
+          #        Needed because not compatible with black
+          # W605 - a backslash-character pair that is not a valid escape sequence now
+          #        generates a DeprecationWarning. This will eventually become a SyntaxError.
+          #        Needed because we use \d as an escape sequence
+          # E402 - Place module level import at the top.
+          #        Needed to prevent circular import error

CHANGELOG.md

@@ -1,19 +1,56 @@
 # Changelog
 
-Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) convention.
+Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
+[Keep a Changelog](https://keepachangelog.com/en/1.0.0/) convention.
+
+## [0.5.6] - 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
@@ -56,6 +93,13 @@ 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`
 
+[0.5.6]: https://github.com/datajoint/element-calcium-imaging/releases/tag/0.5.6
+[0.5.5]: https://github.com/datajoint/element-calcium-imaging/releases/tag/0.5.5
+[0.5.4]: https://github.com/datajoint/element-calcium-imaging/releases/tag/0.5.4
+[0.5.3]: https://github.com/datajoint/element-calcium-imaging/releases/tag/0.5.3
+[0.5.2]: https://github.com/datajoint/element-calcium-imaging/releases/tag/0.5.2
+[0.5.1]: https://github.com/datajoint/element-calcium-imaging/releases/tag/0.5.1
+[0.5.0]: https://github.com/datajoint/element-calcium-imaging/releases/tag/0.5.0
 [0.4.2]: https://github.com/datajoint/element-calcium-imaging/releases/tag/0.4.2
 [0.4.1]: https://github.com/datajoint/element-calcium-imaging/releases/tag/0.4.1
 [0.4.0]: https://github.com/datajoint/element-calcium-imaging/releases/tag/0.4.0