Merge pull request #36 from CBroz1/main

JaerongA · web-flow · commit fdd6bd7fcf56 · 2023-01-20T10:10:38.000-06:00
Minor NWB fix, markdown lint, spell check, precommit fixes
diff --git a/.markdownlint.yaml b/.markdownlint.yaml
@@ -3,13 +3,13 @@
 # https://github.com/DavidAnson/markdownlint/blob/main/doc/Rules.md
 MD009: false # permit trailing spaces
 MD007: false # List indenting - permit 4 spaces
-MD013: 
+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: 
+    allowed_elements:
         - "br"
 MD034: false # Permit bare URLs
 MD031: false # Spacing w/code blocks. Conflicts with `??? Note` and code tab styling
diff --git a/.pre-commit-config.yaml b/.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
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,15 +1,17 @@
 # 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.
 
 ## [0.1.5] - Unreleased
 
-- Added - `surgery` schema
-- Added - mkdocs documentation
+- Add - `surgery` schema
+- Add - mkdocs documentation
+- Update - string typing for NWB export of Species
 
 ## [0.1.4] - 2022-08-30
 
-- Added - "subject_nickname" into Subject table
+- Add - "subject_nickname" into Subject table
 - Update - rework "SubjectCull" table
 
 ## [0.1.3] - 2022-07-06
@@ -18,27 +20,27 @@ Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
 
 ## [0.1.2] - 2022-06-27
 
-- Added - Code of Conduct
+- Add - Code of Conduct
 - Update - pull subject from parent directory in nwb export
 - Update - for genotyping.BreedingPair part tables, projection from Subject
   - genotyping.BreedingPair.Mother, change attribute to 'mother'
   - genotyping.BreedingPair.Father, change attribute to 'father'
 
 ## [0.1.1] - 2022-05-10
 
-- Added - NWB export
+- Add - NWB export
 - Update - Shorten subject primary key to varchar(8)
-- Added - Adopt black formatting into code base
+- Add - Adopt black formatting into code base
 
 ## [0.1.0b0] - 2021-05-07
 
 - Update - First beta release
 
 ## [0.1.0a1] - 2021-05-03
 
-- Added - GitHub Action release process
-- Added - `subject` schema
-- Added - `genotyping` schema
+- Add - GitHub Action release process
+- Add - `subject` schema
+- Add - `genotyping` schema
 
 [0.1.5]: https://github.com/datajoint/element-animal/releases/tag/0.1.5
 [0.1.4]: https://github.com/datajoint/element-animal/releases/tag/0.1.4
diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md
@@ -1,4 +1,3 @@
-
 # Contributor Covenant Code of Conduct
 
 ## Our Pledge
diff --git a/CONTRIBUTING.md b/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.
diff --git a/README.md b/README.md
@@ -4,7 +4,7 @@ DataJoint Element for storing animal meta data, genotype, and surgery informatio
 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. 
+to assemble a fully functional pipeline.
 
 Installation and usage instructions can be found at the [Element documentation](https://datajoint.com/docs/elements/element-animal).
 
diff --git a/cspell.json b/cspell.json
@@ -0,0 +1,53 @@
+// 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",
+        "dorso",
+        "dura",
+        "Ecker",
+        "electophysiology",
+        "elif",
+        "Ephys",
+        "genotyping",
+        "Genotyping",
+        "Hoenselaar",
+        "IACUC",
+        "inlinehilite",
+        "linenums",
+        "mkdocs",
+        "mkdocstrings",
+        "opto",
+        "pymdownx",
+        "Reimer",
+        "Roboto",
+        "RRID",
+        "Rxiv",
+        "Sabatini",
+        "Sasaki",
+        "Shen",
+        "Siapas",
+        "Sinz",
+        "Sitonic",
+        "Tolias",
+        "Yatsenko",
+        "Zuckerman",
+        "zygosity",
+        "Zygosity"
+    ]
+}
diff --git a/docs/mkdocs.yaml b/docs/mkdocs.yaml
@@ -16,7 +16,7 @@ nav:
 # Markdown in mkdocs
 # 01. Redering concatenates across single line breaks. This means...
 #     A. We have to be careful to add extra line breaks around paragraphs,
-#        including between the end of a pgf and the beginnign of bullets.
+#        including between the end of a pgf and the beginning of bullets.
 #     B. We can use hard wrapping to make github reviews easier to read.
 #        VSCode Rewrap extension offers a keyboard shortcut for hard wrap
 #        at the ruler, but don't add breaks in [multiword links](example.com)
@@ -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
diff --git a/docs/src/citation.md b/docs/src/citation.md
@@ -5,19 +5,19 @@ 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
+    - 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 ([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
+    - 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 Animal 
-    (version {{ PATCH_VERSION }})
+    - DataJoint Elements ([RRID:SCR_021894](https://scicrunch.org/resolver/SCR_021894)) -
+      Element Animal (version {{ PATCH_VERSION }})
diff --git a/docs/src/concepts.md b/docs/src/concepts.md
@@ -18,7 +18,7 @@ Additionally, we interviewed these teams to understand their experiment workflow
 associated tools, and interfaces. These teams include:
 
 - [International Brain Laboratory](https://github.com/int-brain-lab/IBL-pipeline)
-- BrainCoGs (Princeton Neuroscience Institute) 
+- BrainCoGs (Princeton Neuroscience Institute)
   ([Python](https://github.com/BrainCOGS/U19-pipeline_python) / [MATLAB](https://github.com/BrainCOGS/U19-pipeline-matlab))
 - [MoC3 (Columbia Zuckerman Institute) + Costa Lab (private repository) + Hillman Lab](https://github.com/ZuckermanBrain/datajoint-hillman)
 - [Sabatini Lab](https://github.com/bernardosabatinilab/sabatini-datajoint-pipeline)
diff --git a/docs/src/index.md b/docs/src/index.md
@@ -8,16 +8,16 @@ to assemble a fully functional pipeline.
 
 + `element-animal` features a DataJoint pipeline design for subject and genotyping management.
 
-+ `element-animal` is not a complete workflow by itself, but rather a modular design of
-tables and dependencies.
++ `element-animal` is not a complete workflow by itself, but rather a modular design
+  of tables and dependencies.
 
 + `element-animal` can be flexibly attached to any DataJoint workflow.
 
-Visit the [Concepts page](./concepts.md) for more information on
-colony management and Element Animal.  To get started with building your data 
-pipeline visit the [Tutorials page](./tutorials.md).
+Visit the [Concepts page](./concepts.md) for more information on colony management and
+Element Animal. To get started with building your data pipeline visit the
+[Tutorials page](./tutorials.md).
 
-![Subect schema diagram](https://raw.githubusercontent.com/datajoint/element-animal/main/images/subject_diagram.svg)
+![Subject schema diagram](https://raw.githubusercontent.com/datajoint/element-animal/main/images/subject_diagram.svg)
 
 ![Genotyping schema diagram](https://raw.githubusercontent.com/datajoint/element-animal/main/images/genotyping_diagram.svg)
 
diff --git a/element_animal/export/__init__.py b/element_animal/export/__init__.py
@@ -1 +1,3 @@
 from .nwb import subject_to_nwb
+
+__all__ = ["subject_to_nwb"]
diff --git a/element_animal/export/nwb.py b/element_animal/export/nwb.py
@@ -1,5 +1,6 @@
-from datetime import datetime
 import json
+from datetime import datetime
+
 import pynwb
 
 from .. import subject
@@ -28,7 +29,7 @@ def subject_to_nwb(session_key: dict):
             datetime.strptime("00:00:00", "%H:%M:%S").time(),
         ),
         description=json.dumps(subject_info, default=str),
-        species=(subject.Line & subject_query).fetch("species"),
+        species=str((subject.Line & subject_query).fetch("species")),
         genotype=" x ".join(
             (subject.Line.Allele * subject.Subject.Line & subject_query).fetch("allele")
         ),
diff --git a/element_animal/genotyping.py b/element_animal/genotyping.py
@@ -1,8 +1,9 @@
-import datajoint as dj
 import importlib
 import inspect
-from . import subject
 
+import datajoint as dj
+
+from . import subject
 
 schema = dj.schema()
 
@@ -41,7 +42,7 @@ def activate(
     assert inspect.ismodule(
         linking_module
     ), "The argument 'linking_module' must be a module's name or a module"
-    
+
     global _linking_module
     _linking_module = linking_module
 
diff --git a/element_animal/subject.py b/element_animal/subject.py
@@ -1,7 +1,7 @@
-import datajoint as dj
 import importlib
 import inspect
 
+import datajoint as dj
 
 schema = dj.schema()
 
@@ -100,7 +100,7 @@ class Source(dj.Part):
         -> master
         ---
         -> Source
-        source_identifier=''  : varchar(255) 
+        source_identifier=''  : varchar(255)
         source_url=''         : varchar(255) # link to the line information
         expression_data_url='': varchar(255) # link to the expression pattern from Allen institute brain atlas
         """
diff --git a/element_animal/surgery.py b/element_animal/surgery.py
@@ -1,6 +1,8 @@
-import datajoint as dj
 import importlib
 import inspect
+
+import datajoint as dj
+
 from . import subject
 
 schema = dj.Schema()
@@ -121,7 +123,7 @@ class ImplantationType(dj.Lookup):
     contents = (
         ("ephys", "electophysiology"),
         ("fiber", "fiber photometry"),
-        ("opto", "optogenetic pertubation"),
+        ("opto", "optogenetic perturbation"),
     )
 
 
diff --git a/setup.py b/setup.py
@@ -1,7 +1,8 @@
 #!/usr/bin/env python
-from setuptools import setup, find_packages
 from os import path
 
+from setuptools import find_packages, setup
+
 pkg_name = next(p for p in find_packages() if "." not in p)
 here = path.abspath(path.dirname(__file__))
 
@@ -16,7 +17,7 @@
 
 setup(
     name=pkg_name.replace("_", "-"),
-    version=__version__,
+    version=__version__,  # noqa: F821
     description="DataJoint Element for Animal Management",
     long_description=long_description,
     long_description_content_type="text/markdown",

Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,3 @@`
`1`		`-`
`2`	`1`	`# Contributor Covenant Code of Conduct`
`3`	`2`
`4`	`3`	`## Our Pledge`