From 5c8e1d45e274a6866a2ad245e2d8cd3301da0269 Mon Sep 17 00:00:00 2001
From: singlesp <sps253@cornell.edu>
Date: Thu, 16 Jan 2025 15:15:34 -0500
Subject: [PATCH 1/5] docstring

---
 cubids/__about__.py | 21 ++++++++++++++++++++-
 1 file changed, 20 insertions(+), 1 deletion(-)

diff --git a/cubids/__about__.py b/cubids/__about__.py
index d4341aebe..bb727e533 100644
--- a/cubids/__about__.py
+++ b/cubids/__about__.py
@@ -1,6 +1,25 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
-"""Base module variables."""
+"""Base module variables for CuBIDS.
+
+This module defines the base variables for the CuBIDS package, including version,
+package name, copyright, credits, and URLs.
+
+Attributes
+----------
+__version__ : str
+    The version of the CuBIDS package.
+__packagename__ : str
+    The name of the CuBIDS package.
+__copyright__ : str
+    The copyright information for the CuBIDS package.
+__credits__ : str
+    The credits for the CuBIDS package.
+__url__ : str
+    The URL for the CuBIDS package repository.
+DOWNLOAD_URL : str
+    The URL to download the CuBIDS package.
+"""
 try:
     from cubids._version import __version__
 except ImportError:

From 3d4f05ed13f349f0688b0c8fd15a53a3ae4b5407 Mon Sep 17 00:00:00 2001
From: singlesp <sps253@cornell.edu>
Date: Thu, 16 Jan 2025 15:17:19 -0500
Subject: [PATCH 2/5] docstring

---
 cubids/__init__.py | 35 ++++++++++++++++++++++++++++++++++-
 1 file changed, 34 insertions(+), 1 deletion(-)

diff --git a/cubids/__init__.py b/cubids/__init__.py
index ff9b1d3d5..92fffc3fa 100644
--- a/cubids/__init__.py
+++ b/cubids/__init__.py
@@ -1,4 +1,37 @@
-"""Top-level package for CuBIDS."""
+"""Top-level package for CuBIDS.
+
+This module initializes the CuBIDS package and imports its main submodules and attributes.
+
+Submodules
+----------
+cli : module
+    Command-line interface for CuBIDS.
+config : module
+    Configuration utilities for CuBIDS.
+constants : module
+    Constants used throughout the CuBIDS package.
+cubids : module
+    Core functionalities of the CuBIDS package.
+metadata_merge : module
+    Utilities for merging metadata in CuBIDS.
+utils : module
+    Utility functions for CuBIDS.
+validator : module
+    Validation utilities for CuBIDS.
+workflows : module
+    Workflows for CuBIDS operations.
+
+Attributes
+----------
+__version__ : str
+    The version of the CuBIDS package.
+__packagename__ : str
+    The name of the CuBIDS package.
+__copyright__ : str
+    The copyright information for the CuBIDS package.
+__credits__ : str
+    The credits for the CuBIDS package.
+"""
 
 from cubids import (
     cli,

From 86483d494806e3a0dd53201d67413b10c3b4657a Mon Sep 17 00:00:00 2001
From: singlesp <sps253@cornell.edu>
Date: Thu, 16 Jan 2025 15:33:50 -0500
Subject: [PATCH 3/5] docstring

---
 cubids/constants.py | 20 +++++++++++++-------
 1 file changed, 13 insertions(+), 7 deletions(-)

diff --git a/cubids/constants.py b/cubids/constants.py
index dfbc2072b..466d00428 100644
--- a/cubids/constants.py
+++ b/cubids/constants.py
@@ -1,14 +1,20 @@
-"""Constants for CuBIDS."""
+"""Constants for CuBIDS.
 
-# Names of identifier variables.
-# Used to place EntitySet and ParamGroup at the beginning of a dataframe,
-# but both are hardcoded in the relevant function.
+This module defines various constants used throughout the CuBIDS package.
+
+Attributes
+----------
+ID_VARS : set of str
+    Names of identifier variables. Used to place EntitySet and ParamGroup at
+    the beginning of a dataframe but both are hardcoded in the relevant function.
+NON_KEY_ENTITIES : set of str
+    Entities that should not be used to group parameter sets.
+IMAGING_PARAMS : set of str
+    List of metadata fields merged in `metadata_merge.py`.
+"""
 ID_VARS = set(["EntitySet", "ParamGroup", "FilePath"])
-# Entities that should not be used to group parameter sets
 NON_KEY_ENTITIES = set(["subject", "session", "extension"])
 # Multi-dimensional keys SliceTiming  XXX: what is this line about?
-# List of metadata fields and parameters (calculated by CuBIDS)
-# Not sure what this specific list is used for.
 IMAGING_PARAMS = set(
     [
         "ParallelReductionFactorInPlane",

From 6be61cdcb2d16e8ae24ac66522ac378e1e4573e3 Mon Sep 17 00:00:00 2001
From: singlesp <sps253@cornell.edu>
Date: Thu, 16 Jan 2025 15:36:02 -0500
Subject: [PATCH 4/5] module docstring

---
 cubids/utils.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/cubids/utils.py b/cubids/utils.py
index 09c02e349..c4cdb457f 100644
--- a/cubids/utils.py
+++ b/cubids/utils.py
@@ -1,4 +1,7 @@
-"""Miscellaneous utility functions for CuBIDS."""
+"""Miscellaneous utility functions for CuBIDS.
+
+This module provides various utility functions used throughout the CuBIDS package.
+"""
 
 import re
 from pathlib import Path

From 414ef92961c20ea553c0fec5f6bcf399fe7744cf Mon Sep 17 00:00:00 2001
From: singlesp <sps253@cornell.edu>
Date: Thu, 16 Jan 2025 15:40:39 -0500
Subject: [PATCH 5/5] black

---
 cubids/constants.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/cubids/constants.py b/cubids/constants.py
index 466d00428..54fdf451e 100644
--- a/cubids/constants.py
+++ b/cubids/constants.py
@@ -12,6 +12,7 @@
 IMAGING_PARAMS : set of str
     List of metadata fields merged in `metadata_merge.py`.
 """
+
 ID_VARS = set(["EntitySet", "ParamGroup", "FilePath"])
 NON_KEY_ENTITIES = set(["subject", "session", "extension"])
 # Multi-dimensional keys SliceTiming  XXX: what is this line about?