Merge pull request #182 from DimitriPapadopoulos/codespell

Fix typos not found by codespell

CHANGELOG.md

@@ -52,7 +52,7 @@ File IO
 
 Processing
 ----------
-* Add the util/xcpy.py module for interfacing nmrglue with Topspin (#103, #105)
+* Add the util/xcpy.py module for interfacing nmrglue with TopSpin (#103, #105)
 * Add additional options to the autops function (#108)
 * Improvements to the autops function (#124)
 

doc/source/reference/xcpy.rst

@@ -1,8 +1,8 @@
 nmrglue.misc.xcpy
 =================
 
-This module is intended for use with the Bruker Topspin software. 
-It runs external scripts via Jython (subprocess module) that ships with Topspin. 
+This module is intended for use with the Bruker TopSpin software. 
+It runs external scripts via Jython (subprocess module) that ships with TopSpin. 
 Currently, it allows only external CPython programs to run. By default, it passes
 the current folder, expno and procno to the external CPython program (if available).
 For an example of how this should look like in practice, see 
@@ -28,7 +28,7 @@ Installation
 ------------
 1. Copy (or symlink) this file to the following directory:
 <topspin_location>/exp/stan/nmr/py/user/
-2. If you now type 'xcpy' on the command line within Topspin,
+2. If you now type 'xcpy' on the command line within TopSpin,
 this documentation should pop up
 3. A configuration file needs to be written out so that xcpy
 knows the location of the CPython executable and a folder where

examples/bruker_write_pdata/write_2d.py

@@ -1,5 +1,5 @@
 """
-Writing 2D data processed with Nmrpipe back into Topspin format
+Writing 2D data processed with Nmrpipe back into TopSpin format
 
 """
 import os
@@ -15,7 +15,7 @@
 # read in data processed using TOPSPIN
 # this is required only to get access to the dictionary
 # as a reference starting point to write the data back out
-# in a way Topspin can read it
+# in a way TopSpin can read it
 tdic, _ = ng.bruker.read_pdata(os.path.join(DATA_DIR, 'pdata', '1'))
 
 # read in data processed using nmrpipe

nmrglue/fileio/bruker.py

@@ -1141,7 +1141,7 @@ def read_pdata(dir=".", bin_files=None, procs_files=None, read_procs=True,
     """
     Read processed Bruker files from a directory.
 
-    In Topspin and other programs this data is typically scaled by dividing by
+    In TopSpin and other programs this data is typically scaled by dividing by
     2 ** -NC_proc where NC_proc is defined in the procs file.  This scaling
     can be accomplished by setting the scale_data parameter to True.
 

nmrglue/util/misc.py

@@ -29,7 +29,7 @@ def pair_similar(dic1, data1, dic2, data2, verb=False, atol=ATOL, rtol=RTOL,
     verb : bool, optional
         Set True for verbose reporting.
     atol : float, optional
-        The absolute tolerant parameter to pass to numpy.allclose.
+        The absolute tolerance parameter to pass to numpy.allclose.
     rtol : float, optional
         The relative tolerance parameter to pass to numpy.allclose.
 
@@ -60,7 +60,7 @@ def isdatasimilar(data1, data2, verb=False, atol=ATOL, rtol=RTOL):
     verb : bool, optional
         Set True for verbose reporting.
     atol : float, optional
-        The absolute tolerant parameter to pass to numpy.allclose.
+        The absolute tolerance parameter to pass to numpy.allclose.
     rtol : float, optional
         The relative tolerance parameter to pass to numpy.allclose.
 

nmrglue/util/xcpy.py

@@ -9,7 +9,7 @@
 INSTALLATION
 1. Copy (or symlink) this file to the following directory:
 <topspin_location>/exp/stan/nmr/py/user/
-2. If you now type 'xcpy' on the command line within Topspin,
+2. If you now type 'xcpy' on the command line within TopSpin,
 this documentation should pop up
 3. A configuration file needs to be written out so that xcpy
 knows the location of the CPython executable and a folder where
@@ -19,7 +19,7 @@
 
 DESCRIPTION
 xcpy supports running external scripts via Jython (subprocess module)
-that ships with Topspin. Currently, it allows only external CPython
+that ships with TopSpin. Currently, it allows only external CPython
 programs to run. By default, it passes the current folder, expno and procno
 to the external CPython program (if available).
 
@@ -70,7 +70,7 @@
 def topspin_error():
     errmsg = """
     This file is meant to be executed
-    using Jython from within Topspin
+    using Jython from within TopSpin
     Please see the doctring for more
     details.
     """
@@ -80,11 +80,11 @@ def topspin_error():
 def check_jython():
     """
     Checks whether Jython is being used to run this script
-    from within Topspin
+    from within TopSpin
 
     """
     # some of the functions defined in the global namespace
-    # by Topspin which are also used by xcpy
+    # by TopSpin which are also used by xcpy
     topspin_inbuilts = ["MSG", "INPUT_DIALOG", "CURDATA"]
 
     g = globals().keys()
@@ -98,9 +98,9 @@ def check_jython():
 
 def topspin_location():
     """
-    Gets Topspin home directory. Also serves to check
+    Gets TopSpin home directory. Also serves to check
     whether the script is being executed from within
-    Topspin or externally.
+    TopSpin or externally.
 
     """
     try:
@@ -213,7 +213,7 @@ def exists(filename, raise_error=False):
 
 def current_data():
     """
-    Returns the current EXPNO and PROCNO open in Topspin,
+    Returns the current EXPNO and PROCNO open in TopSpin,
     if executed when a data folder is open
 
     """