Apply suggestions from code review

Co-authored-by: Kabilar Gunalan <[email protected]>

Author: CBroz1

CHANGELOG.md

@@ -3,7 +3,7 @@
 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] - 2022-12-12
-+ Add - "project" schema for project/study/experiment related tables
++ Add - `project` schema for project/study/experiment related tables
 
 ## [0.1.2] - 2022-10-17
 + Update - CICD for triggering PyPI release

element_lab/lab.py

@@ -29,9 +29,9 @@ class Organization(dj.Manual):
 
     Attributes:
         organization ( varchar(24) ): Abbreviated organization name.
-        organization_name ( varchar(255) ): Full organization name.
-        organization_address ( varchar(512) ): Address of the organization.
-        organization_comment ( varchar(1024) ): Additional notes on the organization.
+        org_name ( varchar(255) ): Full organization name.
+        org_address ( varchar(512), optional ): Address of the organization.
+        org_comment ( varchar(1024), optional ): Additional notes on the organization.
     """
 
     definition = """# Top-level list of all organizations involved in any of the projects
@@ -59,7 +59,7 @@ class Lab(dj.Lookup):
     lab             : varchar(24)    # Abbreviated lab name
     ---
     lab_name        : varchar(255)   # Full lab name
-    address         : varchar(255)
+    address         : varchar(255)    # Physical lab address
     time_zone       : varchar(64)    # 'UTC±X' format or timezone, e.g., America/New_York
     """
 
@@ -107,17 +107,17 @@ class User(dj.Lookup):
 
     Attributes:
         user ( varchar(32) ): User name.
-        user_email ( varchar(128) ): User email address.
-        user_cellphone ( varchar(32) ): User cellphone number.
-        user_fullname ( varchar(64) ): User full name
+        user_email ( varchar(128), optional ): User email address.
+        user_cellphone ( varchar(32), optional ): User cellphone number.
+        user_fullname ( varchar(64), optional ): User full name
     """
 
     definition = """# Table for storing user information.
     user                : varchar(32)  # username, short identifier
     ---
     user_email=''       : varchar(128)
     user_cellphone=''   : varchar(32)
-    user_fullname=''    : varchar(64)  # full name used to uniquely ID an individual
+    user_fullname=''    : varchar(64)  # Full name used to uniquely identify an individual
     """
 
 
@@ -154,15 +154,15 @@ class ProtocolType(dj.Lookup):
 
 @schema
 class Protocol(dj.Lookup):
-    """Protocol approved by some institutions like IACUC, IRB, or experimental protocol.
+    """Protocol approved by institutions (e.g. IACUC, IRB), or experimental protocol.
 
     Attributes:
         protocol ( varchar(36) ): Protocol identifier.
         ProtocolType (foreign key): ProtocolType key.
-        protocol_description( varchar(255) ): Optional. Description of the protocol.
+        protocol_description( varchar(255), optional ): Description of the protocol.
     """
 
-    definition = """# Protocol approved by some institutions like IACUC, IRB, or experimental protocol
+    definition = """# Protocol approved by institutions (e.g. IACUC, IRB), or experimental protocol.
     protocol                : varchar(36)   # Protocol identifier.
     ---
     -> ProtocolType

element_lab/project.py

@@ -18,13 +18,13 @@ def activate(
     """
     activate(schema_name, create_schema=True, create_tables=True, linking_module=None)
         :param schema_name: schema name on the database server to activate the
-                            `lab` element
+                            `project` module
         :param create_schema: when True (default), create schema in the
                               database if it does not yet exist.
         :param create_tables: when True (default), create tables in the
                               database if they do not yet exist.
         :param linking_module: a module (or name) containing the required
-                            dependencies to activate the `event` element:
+                            dependencies to activate the `project` module.
         Upstream tables:
             + Lab: table defining general lab information
             + User: table defining user/personnel/experimenter associated with Project.
@@ -33,7 +33,8 @@ def activate(
     if isinstance(linking_module, str):
         linking_module = importlib.import_module(linking_module)
     assert inspect.ismodule(linking_module), (
-        "The argument 'linking_module' must" + " be a module or module name"
+        "The argument 'linking_module' must be a module or module name"
+
     )
 
     global _linking_module
@@ -55,13 +56,13 @@ class Project(dj.Manual):
         project ( varchar(24) ): Abbreviated project name
         project_title ( varchar(1024) ): Full project title and/or description
         project_start_date (date): The start of the project
-        project_end_date (date, nullable): The end date of the project
+        project_end_date (date, optional): The end date of the project
         project_comment ( varchar(1024), optional): additional notes on the project
     """
 
     definition = """# Top-level grouping of studies and experiments
-    ---
     project               : varchar(24)   # abbreviated project name
+    ---
     project_title         : varchar(1024) # full project title and/or description
     project_start_date    : date          # the start of the project
     project_end_date=NULL : date          # the end date of the project
@@ -86,15 +87,15 @@ class ProjectPersonnel(dj.Manual):
 
 @schema
 class ProjectKeywords(dj.Manual):
-    """Project keywords, exported dataset meta info
+    """Project keywords. If the dataset is exported, this metadata is saved within the NWB file.
 
     Attributes:
         Project (foreign key): Project key
         keyword ( varchar(32) ): Keywords describing the project
     """
 
     definition = """
-    # Project keywords, exported dataset meta info
+    # Project keywords. If the dataset is exported, this metadata is saved within the NWB file.
     -> Project
     keyword: varchar(32) # Keywords describing the project
     """
@@ -113,21 +114,20 @@ class ProjectPublication(dj.Manual):
     # Project's resulting publications
     -> Project
     publication: varchar(255)  # Publication name or citation
-
     """
 
 
 @schema
 class ProjectSourceCode(dj.Manual):
-    """URL to source code for replication
+    """Web address of source code
 
     Attributes:
         Project (foreign key): Project key
         repository_url ( varchar(255) ): Link to code repository
         repository_name ( varchar(32), optional): Name of code repository
     """
 
-    definition = """# URL to source code for replication
+    definition = """# Web address of source code
     -> Project
     repository_url     : varchar(255)  # Link to code repository
 
@@ -143,8 +143,7 @@ class Study(dj.Manual):
     Attributes:
         Project (foreign key): Project key
         study ( varchar(24) ): Abbreviated study name, e.g., 'Aim 1'
-        study_name ( varchar(128) ): Full study name, e.g., 'perceptual response tasks',
-            or 'Aim 1'
+        study_name ( varchar(128) ): Full study name, e.g., 'perceptual response tasks'
         study_description ( varchar(1024), optional): Description of study goals,
             objectives, and/or methods
     """
@@ -173,7 +172,7 @@ class Protocol(dj.Part):
 
 @schema
 class Experiment(dj.Manual):
-    """Experimental tasks/protocols and their associated lab and study
+    """Experimental tasks and their associated lab, study, and protocol
 
     Attributes:
         experiment ( varchar(24) ): Abbreviated experiment name
@@ -185,7 +184,7 @@ class Experiment(dj.Manual):
         Protocol (foreign key, optional): Protocol key
     """
 
-    definition = """# Experimental tasks/protocols and their associated lab and study
+    definition = """# Experimental tasks and their associated lab, study, and protocol
     experiment                : varchar(24)   # Abbreviated experiment name
     ---
     experiment_name=''        : varchar(128)  # Experiment full name or identifier