Merge pull request #42 from CBroz1/main

Add NWB support for project schema, pre-commit and markdownlint

Author: kabilar

.gitignore

@@ -106,6 +106,7 @@ ENV/
 # datajoint
 dj_local_conf.json
 dj_local_conf_old.json
+temp*
 
 # emacs
 **/*~

.markdownlint.yaml

@@ -0,0 +1,16 @@
+# 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:
+        - "br"
+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

@@ -1,23 +1,31 @@
 # 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.
+
+## [0.2.0] - 2022-01-20
 
-## [0.2.0] - 2022-12-12
 + Add - `project` schema for project/study/experiment related tables
++ Add - pre-commit and markdown lint checks
 
 ## [0.1.2] - 2022-10-17
+
 + Update - CICD for triggering PyPI release
 
 ## [0.1.1] - 2022-05-10
+
 + Add - Adopted black formatting into code base
 
 ## [0.1.0b1] - 2022-01-28
+
 + Add - Functions to generate dictionaries for NWB export.
 
 ## [0.1.0b0] - 2021-05-07
+
 + Add - First beta release
 
 ## [0.1.0a1] - 2021-04-30
+
 + Add - GitHub Action release process
 + Add - `lab` schema
 

CODE_OF_CONDUCT.md

@@ -1,4 +1,3 @@
-
 # Contributor Covenant Code of Conduct
 
 ## Our Pledge

CONTRIBUTING.md

@@ -1,2 +1,5 @@
 # Contribution Guidelines
-This project follows the [DataJoint Contribution Guidelines](https://docs.datajoint.io/python/community/02-Contribute.html). Please reference the link for more full details.
+
+This project follows the
+[DataJoint Contribution Guidelines](https://datajoint.com/docs/community/contribute/).
+Please reference the link for more full details.

README.md

@@ -1,47 +1,9 @@
 # DataJoint Element - Lab
 
-DataJoint Element for lab metadata. 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 lab metadata. 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.
 
-+ `element-lab` features a DataJoint pipeline design for lab related information, such as Lab, User, Project, Protocol, Source.
-
-+ `element-lab` is not a complete workflow by itself, but rather a modular design of tables and dependencies. 
-
-+ `element-lab` can be flexibly attached to any DataJoint workflow.
-
-+ See the [Element Lab documentation](https://elements.datajoint.org/description/lab/) for the background information and development timeline.
-
-+ For more information on the DataJoint Elements project, please visit https://elements.datajoint.org.  This work is supported by the National Institutes of Health.
-
-## Element architecture
-
-![element lab diagram](images/lab_diagram.svg)
-
-## Installation
-```
-pip install element-lab
-```
-
-If you already have an older version of ***element-lab*** installed using `pip`, upgrade with
-```
-pip install --upgrade element-lab
-```
-
-## Element usage
-
-+ `element-lab` is not a complete workflow by itself, but rather a modular design of tables and dependencies that can be flexibly attached to any DataJoint workflow.
-
-+ See the [workflow-calcium-imaging](https://github.com/datajoint/workflow-calcium-imaging) and [workflow-array-ephys](https://github.com/datajoint/workflow-array-ephys) repositories for example usages of `element-lab`.
-
-## Citation
-
-+ If your work uses DataJoint and DataJoint Elements, please cite the respective Research Resource Identifiers (RRIDs) and manuscripts.
-
-+ DataJoint for Python or MATLAB
-    + Yatsenko D, Reimer J, Ecker AS, Walker EY, Sinz F, Berens P, Hoenselaar A, Cotton RJ, Siapas AS, Tolias AS. DataJoint: managing big scientific data using MATLAB or Python. bioRxiv. 2015 Jan 1:031658. doi: https://doi.org/10.1101/031658
-
-    + DataJoint ([RRID:SCR_014543](https://scicrunch.org/resolver/SCR_014543)) - DataJoint for `<Select Python or MATLAB>` (version `<Enter version number>`)
-
-+ DataJoint Elements
-    + Yatsenko D, Nguyen T, Shen S, Gunalan K, Turner CA, Guzman R, Sasaki M, Sitonic D, Reimer J, Walker EY, Tolias AS. DataJoint Elements: Data Workflows for Neurophysiology. bioRxiv. 2021 Jan 1. doi: https://doi.org/10.1101/2021.03.30.437358
-
-    + DataJoint Elements ([RRID:SCR_021894](https://scicrunch.org/resolver/SCR_021894)) - Element Lab (version `<Enter version number>`)
+Installation and usage instructions can be found at the
+[Element documentation](https://datajoint.com/docs/elements/element-lab).

cspell.json

@@ -0,0 +1,44 @@
+// cSpell Settings
+//https://github.com/streetsidesoftware/vscode-spell-checker
+{
+    "version": "0.2", // Version of the setting file.  Always 0.2
+    "language": "en", // language - current active spelling language
+    "enabledLanguageIds": [
+        "markdown", "yaml", "python"
+    ],
+    // flagWords - list of words to be always considered incorrect
+    // This is useful for offensive words and common spelling errors.
+    // For example "hte" should be "the"
+    "flagWords": [],
+    "allowCompoundWords": true,
+    "ignorePaths": [
+        "./element_array_ephys.egg-info/*",
+        "./images/*"
+    ],
+    "words": [
+        "Berens",
+        "CICD",
+        "Ecker",
+        "elif",
+        "Ephys",
+        "Hoenselaar",
+        "IACUC",
+        "inlinehilite",
+        "linenums",
+        "mkdocs",
+        "mkdocstrings",
+        "pymdownx",
+        "Reimer",
+        "Roboto",
+        "RRID",
+        "Rxiv",
+        "Sasaki",
+        "Shen",
+        "Siapas",
+        "Sinz",
+        "Sitonic",
+        "Tolias",
+        "Yatsenko",
+        "Zuckerman"
+    ]
+}

docs/mkdocs.yaml

@@ -43,7 +43,7 @@ nav:
 #     HOST_UID=$(id -u) docker compose -f docs/docker-compose.yaml up --build
 #     ```
 # 02. Site analytics depend on a local environment variable GOOGLE_ANALYTICS_KEY
-#     You can find this in LastPass or declare with any string to suprress errors
+#     You can find this in LastPass or declare with any string to suppress errors
 # 03. The API section will pull docstrings.
 #     A. Follow google styleguide e.g.,
 #        https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html
@@ -126,6 +126,7 @@ markdown_extensions:
       linenums: true
   - pymdownx.inlinehilite
   - pymdownx.snippets
+  - footnotes
 
 extra:
   PATCH_VERSION: !ENV PATCH_VERSION

docs/src/citation.md

@@ -1,14 +1,12 @@
 
 # Citation
 
-If your work uses DataJoint and DataJoint Elements, please cite the respective Research Resource Identifiers (RRIDs) and manuscripts.
+If your work uses this Element, please cite the following manuscript and Research
+Resource Identifier (RRID).
 
-+ DataJoint for Python or MATLAB
-    +  Yatsenko D, Reimer J, Ecker AS, Walker EY, Sinz F, Berens P, Hoenselaar A, Cotton RJ, Siapas AS, Tolias AS. DataJoint: managing big scientific data using MATLAB or Python. bioRxiv. 2015 Jan 1:031658. doi: https://doi.org/10.1101/031658
++ Yatsenko D, Nguyen T, Shen S, Gunalan K, Turner CA, Guzman R, Sasaki M, Sitonic D,
+  Reimer J, Walker EY, Tolias AS. DataJoint Elements: Data Workflows for
+  Neurophysiology. bioRxiv. 2021 Jan 1. doi: https://doi.org/10.1101/2021.03.30.437358
 
-    + DataJoint ([RRID:SCR_014543](https://scicrunch.org/resolver/SCR_014543)) - DataJoint for `<Select Python or MATLAB>` (version `<Enter version number>`)
-
-+ DataJoint Elements
-    + Yatsenko D, Nguyen T, Shen S, Gunalan K, Turner CA, Guzman R, Sasaki M, Sitonic D, Reimer J, Walker EY, Tolias AS. DataJoint Elements: Data Workflows for Neurophysiology. bioRxiv. 2021 Jan 1. doi: https://doi.org/10.1101/2021.03.30.437358
-
-    + DataJoint Elements ([RRID:SCR_021894](https://scicrunch.org/resolver/SCR_021894)) - Element Lab (version {{ PATCH_VERSION }})
++ DataJoint Elements ([RRID:SCR_021894](https://scicrunch.org/resolver/SCR_021894)) -
+  Element Lab (version {{ PATCH_VERSION }})