Merge pull request #363 from incf-nidash/rm-big-comments

Pare down giant comment blocks that largely do what Git already does
incf-nidash · May 5, 2023 · 1472357 · 1472357
2 parents 411fb22 + 5c099f6
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diff --git a/src/nidm/experiment/Query.py b/src/nidm/experiment/Query.py
@@ -1,33 +1,5 @@
-# *****************************************************************************
-# *****************************************************************************
-#  nidm_query.py
-#  License: GPL
-# *****************************************************************************
-# *****************************************************************************
-# Date: 8-1-18                 Coded by: David Keator (dbkeator@gmail.com)
-# Filename: nidm_query.py
-#
-# Program description:  This program provides query functionality for NIDM-Experiment files
-#
-#
-# *****************************************************************************
-# Development environment: Python - PyCharm IDE
-#
-# *****************************************************************************
-# System requirements:  Python 3.X
-# Libraries: os, sys, rdflib, pandas, argparse, logging
-# *****************************************************************************
-# Start date: 8-1-18
-# Update history:
-# DATE            MODIFICATION				Who
-#
-#
-# *****************************************************************************
-# Programmer comments:
-#
-#
-# *****************************************************************************
-# *****************************************************************************
+"""This program provides query functionality for NIDM-Experiment files"""
+
 import functools
 import hashlib
 import json

diff --git a/src/nidm/experiment/tools/bidsmri2nidm.py b/src/nidm/experiment/tools/bidsmri2nidm.py
@@ -1,30 +1,8 @@
-# !/usr/bin/env python
-# *****************************************************************************
-# *****************************************************************************
-#   bidsmri2nidm.py
-#   License: Apache License, Version 2.0
-# *****************************************************************************
-# *****************************************************************************
-#  Date: 10-2-17                 Coded by: David Keator (dbkeator@gmail.com)
-#  Filename: bidsmri2nidm.py
-#
-#  Program description:  This program will convert a BIDS MRI dataset to a NIDM-Experiment
-#  RDF document.  It will parse phenotype information and simply store variables/values
-#  and link to the associated json data dictionary file.
-#
-# *****************************************************************************
-#  Development environment: Python - PyCharm IDE
-#
-# *****************************************************************************
-#  System requirements:  Python 3.X
-#  Libraries: pybids, numpy, matplotlib, pandas, scipy, math, dateutil, datetime,argparse,
-#  os,sys,getopt,csv
-# *****************************************************************************
-#  Programmer comments:
-#
-#
-# *****************************************************************************
-# *****************************************************************************
+"""
+This program will convert a BIDS MRI dataset to a NIDM-Experiment RDF document.
+It will parse phenotype information and simply store variables/values and link
+to the associated json data dictionary file.
+"""
 
 from argparse import ArgumentParser, RawTextHelpFormatter
 import csv

diff --git a/src/nidm/experiment/tools/csv2nidm.py b/src/nidm/experiment/tools/csv2nidm.py
@@ -1,33 +1,10 @@
-#!/usr/bin/env python
-# *****************************************************************************
-# *****************************************************************************
-#  csv2nidm.py
-#  License:Apache License, Version 2.0
-# *****************************************************************************
-# *****************************************************************************
-# Date: 01-19-18                 Coded by: David Keator (dbkeator@gmail.com)
-# Filename: csv2nidm.py
-#
-# Program description:  This program will load in a CSV file and iterate over the header
-# variable names performing an elastic search of https://scicrunch.org/ for NIDM-ReproNim
-# tagged terms that fuzzy match the variable names.  The user will then interactively pick
-# a term to associate with the variable name.  The resulting annotated CSV data will
-# then be written to a NIDM data file.
-#
-# *****************************************************************************
-# Development environment: Python - PyCharm IDE
-#
-# *****************************************************************************
-# System requirements:  Python 3.X
-# Libraries: pybids, numpy, matplotlib, pandas, scipy, math, dateutil, datetime,argparse,
-# os,sys,getopt,csv
-# *****************************************************************************
-# *****************************************************************************
-# Programmer comments:
-#
-#
-# *****************************************************************************
-# *****************************************************************************
+"""
+This program will load in a CSV file and iterate over the header variable names
+performing an elastic search of https://scicrunch.org/ for NIDM-ReproNim tagged
+terms that fuzzy match the variable names.  The user will then interactively
+pick a term to associate with the variable name.  The resulting annotated CSV
+data will then be written to a NIDM data file.
+"""
 
 from argparse import ArgumentParser
 from io import StringIO

diff --git a/src/nidm/experiment/tools/nidm2bids.py b/src/nidm/experiment/tools/nidm2bids.py
@@ -1,38 +1,11 @@
-#!/usr/bin/env python
-# *****************************************************************************
-# *****************************************************************************
-#  NIDM2BIDSMRI.py
-#  License: Apache License, Version 2.0
-# *****************************************************************************
-# *****************************************************************************
-# Date: 10-2-17                 Coded by: David Keator (dbkeator@gmail.com)
-# Filename: NIDM2BIDSMRI.py
-#
-# Program description:  This program will convert a NIDM-Experiment RDF document
-# to a BIDS dataset.  The program will query the NIDM-Experiment document for subjects,
-# MRI scans, and associated assessments saving the MRI data to disk in an organization
-# according to the BIDS specification, the demographics metadata to a participants.tsv
-# file, the project-level metadata to a dataset_description.json file, and the
-# assessments to *.tsv/*.json file pairs in a phenotypes directory.
-# *****************************************************************************
-# Development environment: Python - PyCharm IDE
-#
-# *****************************************************************************
-# System requirements:  Python 3.X
-# Libraries: pybids, numpy, matplotlib, pandas, scipy, math, dateutil, datetime,argparse,
-# os,sys,getopt,csv
-# *****************************************************************************
-# Start date: 10-2-17
-# Update history:
-# DATE            MODIFICATION				Who
-#
-#
-# *****************************************************************************
-# Programmer comments:
-#
-#
-# *****************************************************************************
-# *****************************************************************************
+"""
+This program will convert a NIDM-Experiment RDF document to a BIDS dataset.
+The program will query the NIDM-Experiment document for subjects, MRI scans,
+and associated assessments saving the MRI data to disk in an organization
+according to the BIDS specification, the demographics metadata to a
+participants.tsv file, the project-level metadata to a dataset_description.json
+file, and the assessments to *.tsv/*.json file pairs in a phenotypes directory.
+"""
 
 from argparse import ArgumentParser
 from io import StringIO

diff --git a/src/nidm/experiment/tools/nidm_concat.py b/src/nidm/experiment/tools/nidm_concat.py
@@ -1,34 +1,4 @@
-#!/usr/bin/env python
-# *****************************************************************************
-# *****************************************************************************
-#  nidm_utils.py
-#  License: Apache License, Version 2.0
-# *****************************************************************************
-# *****************************************************************************
-# Date: 11-28-18                 Coded by: David Keator (dbkeator@gmail.com)
-# Filename: nidm_utils.py
-#
-# Program description:  Tools for working with NIDM-Experiment files
-#
-# *****************************************************************************
-# Development environment: Python - PyCharm IDE
-#
-# *****************************************************************************
-# System requirements:  Python 3.X
-# Libraries: pybids, numpy, matplotlib, pandas, scipy, math, dateutil, datetime,argparse,
-# os,sys,getopt,csv
-# *****************************************************************************
-# Start date: 11-28-18
-# Update history:
-# DATE            MODIFICATION				Who
-#
-#
-# *****************************************************************************
-# Programmer comments:
-#
-#
-# *****************************************************************************
-# *****************************************************************************
+"""Tools for working with NIDM-Experiment files"""
 
 import click
 from nidm.experiment.Query import GetMergedGraph

diff --git a/src/nidm/experiment/tools/nidm_convert.py b/src/nidm/experiment/tools/nidm_convert.py
@@ -1,34 +1,4 @@
-#!/usr/bin/env python
-# *****************************************************************************
-# *****************************************************************************
-#  nidm_utils.py
-#  License: Apache License, Version 2.0
-# *****************************************************************************
-# *****************************************************************************
-# Date: 11-28-18                 Coded by: David Keator (dbkeator@gmail.com)
-# Filename: nidm_utils.py
-#
-# Program description:  Tools for working with NIDM-Experiment files
-#
-# *****************************************************************************
-# Development environment: Python - PyCharm IDE
-#
-# *****************************************************************************
-# System requirements:  Python 3.X
-# Libraries: pybids, numpy, matplotlib, pandas, scipy, math, dateutil, datetime,argparse,
-# os,sys,getopt,csv
-# *****************************************************************************
-# Start date: 11-28-18
-# Update history:
-# DATE            MODIFICATION				Who
-#
-#
-# *****************************************************************************
-# Programmer comments:
-#
-#
-# *****************************************************************************
-# *****************************************************************************
+""" Tools for working with NIDM-Experiment files """
 
 from os.path import basename, join, splitext
 import click

diff --git a/src/nidm/experiment/tools/nidm_linreg.py b/src/nidm/experiment/tools/nidm_linreg.py
@@ -1,35 +1,4 @@
-# coding=utf-8
-# !/usr/bin/env python
-# *****************************************************************************
-# *****************************************************************************
-#  nidm_linreg.py
-#  License: Apache License, Version 2.0
-# *****************************************************************************
-# *****************************************************************************
-# Date: 07-26-22                 Coded by: Ashmita Kumar (ashmita.kumar@gmail.com)
-# Filename: nidm_linreg.py
-#
-# Program description:  This program provides a tool to complete a linear regression on nidm files
-#
-#
-# *****************************************************************************
-# Development environment: Python - PyCharm IDE
-#
-# *****************************************************************************
-# System requirements:  Python 3.X
-# Libraries: os, sys, tempfile, pandas, click, nidm, csv, sklearn, numpy, statsmodel.api, patsy.contrasts
-# *****************************************************************************
-# Start date: 6-15-20
-# Update history:
-# DATE            MODIFICATION				Who
-#
-#
-# *****************************************************************************
-# Programmer comments:
-#
-#
-# *****************************************************************************
-# *****************************************************************************
+"""This program provides a tool to complete a linear regression on nidm files"""
 
 import csv
 import os

diff --git a/src/nidm/experiment/tools/nidm_merge.py b/src/nidm/experiment/tools/nidm_merge.py
@@ -1,34 +1,4 @@
-#!/usr/bin/env python
-# *****************************************************************************
-# *****************************************************************************
-#  nidm_utils.py
-#  License: Apache License, Version 2.0
-# *****************************************************************************
-# *****************************************************************************
-# Date: 11-28-18                 Coded by: David Keator (dbkeator@gmail.com)
-# Filename: nidm_utils.py
-#
-# Program description:  Tools for working with NIDM-Experiment files
-#
-# *****************************************************************************
-# Development environment: Python - PyCharm IDE
-#
-# *****************************************************************************
-# System requirements:  Python 3.X
-# Libraries: pybids, numpy, matplotlib, pandas, scipy, math, dateutil, datetime,argparse,
-# os,sys,getopt,csv
-# *****************************************************************************
-# Start date: 11-28-18
-# Update history:
-# DATE            MODIFICATION				Who
-#
-#
-# *****************************************************************************
-# Programmer comments:
-#
-#
-# *****************************************************************************
-# *****************************************************************************
+"""Tools for working with NIDM-Experiment files"""
 
 import click
 from rdflib import Graph, util

diff --git a/src/nidm/experiment/tools/nidm_query.py b/src/nidm/experiment/tools/nidm_query.py
@@ -1,34 +1,4 @@
-#!/usr/bin/env python
-# *****************************************************************************
-# *****************************************************************************
-#  nidm_query.py
-#  License: Apache License, Version 2.0
-# *****************************************************************************
-# *****************************************************************************
-# Date: 8-1-18                 Coded by: David Keator (dbkeator@gmail.com)
-# Filename: nidm_query.py
-#
-# Program description:  This program provides query functionality for NIDM-Experiment files
-#
-#
-# *****************************************************************************
-# Development environment: Python - PyCharm IDE
-#
-# *****************************************************************************
-# System requirements:  Python 3.X
-# Libraries: os, sys, rdflib, pandas, argparse, logging
-# *****************************************************************************
-# Start date: 8-1-18
-# Update history:
-# DATE            MODIFICATION				Who
-#
-#
-# *****************************************************************************
-# Programmer comments:
-#
-#
-# *****************************************************************************
-# *****************************************************************************
+"""This program provides query functionality for NIDM-Experiment files"""
 
 from json import dumps
 import os

diff --git a/src/nidm/experiment/tools/nidm_utils.py b/src/nidm/experiment/tools/nidm_utils.py
@@ -1,34 +1,4 @@
-#!/usr/bin/env python
-# *****************************************************************************
-# *****************************************************************************
-#  nidm_utils.py
-#  License: Apache License, Version 2.0
-# *****************************************************************************
-# *****************************************************************************
-# Date: 11-28-18                 Coded by: David Keator (dbkeator@gmail.com)
-# Filename: nidm_utils.py
-#
-# Program description:  Tools for working with NIDM-Experiment files
-#
-# *****************************************************************************
-# Development environment: Python - PyCharm IDE
-#
-# *****************************************************************************
-# System requirements:  Python 3.X
-# Libraries: pybids, numpy, matplotlib, pandas, scipy, math, dateutil, datetime,argparse,
-# os,sys,getopt,csv
-# *****************************************************************************
-# Start date: 11-28-18
-# Update history:
-# DATE            MODIFICATION				Who
-#
-#
-# *****************************************************************************
-# Programmer comments:
-#
-#
-# *****************************************************************************
-# *****************************************************************************
+""" Tools for working with NIDM-Experiment files """
 
 from argparse import ArgumentParser
 import os.path