Typos found by codespell

Add a codespell section in setup.cfg in the process.

doc/source/devel/index.rst

@@ -1,8 +1,8 @@
 .. _development-guide:
 
-==================
-Developement Guide
-==================
+=================
+Development Guide
+=================
 
 This guide provides instructions for setting up an environment for developing
 nmrglue and an overview of the project layout and contribution process.
@@ -96,7 +96,7 @@ Unpack this archive in the ``examples`` directory.  Run the
 ``make_links.sh`` shell script to make symbolic links to the test data which
 reused in a number of example.  On operating systems which do not support
 symbolic links (Windows), the data in the test data directory will need to be 
-copied by hand into the appropiate locations.  
+copied by hand into the appropriate locations.  
 
 
 Project Layout
@@ -132,7 +132,7 @@ Suggestions
 When working with the nmrglue source code please consider the following when
 preparing patches.  
 
-* Coding Style : The nmrglue source code trys to follow the 
+* Coding Style : The nmrglue source code tries to follow the 
   `PEP8 <http://www.python.org/dev/peps/pep-0008/>`_ style guide.  Consider 
   using a tool, such as `pep8 <http://pypi.python.org/pypi/pep8>`__ or 
   `pylint <https://pylint.org/>`_ to check your Python code against 
@@ -181,7 +181,7 @@ In addition, the location of the the test data sets must be specified in the
 In order to run all nmrglue unit tests, the tests data sets must be 
 downloaded, unpacked, and the all conversions scripts contained in the
 archive must be run.  Many of these scripts require additional NMR software 
-(NMRPipe, etc), see the ``README`` file in the test data achive for additional 
+(NMRPipe, etc), see the ``README`` file in the test data archive for additional 
 details.  A subset of the full test suite can be run without installing any 
 additional software.
 

doc/source/examples/apod_viewer_1win.rst

@@ -12,7 +12,7 @@ In this application users can examine graphically the apodization windows
 produced by the various window functions supported by NMRPipe.  In this example
 the canvas in which the apodization windows are drawn and the location to input
 the apodization parameter are contained in the same window.  The
-:ref:`apod_viewer_2win` example has the canvas and input area in seperate
+:ref:`apod_viewer_2win` example has the canvas and input area in separate
 windows.   
 
 [:download:`source code <../../../examples/sample_applications/apod_viewer_1win.py>`]

doc/source/examples/apod_viewer_2win.rst

@@ -11,7 +11,7 @@ additional python modules like
 In this application users can examine graphically the apodization windows 
 produced by the various window functions supported by NMRPipe.  In this example
 the canvas in which the apodization windows are drawn and the location to input
-the apodization parameter are contained in two seperate same window.  The
+the apodization parameter are contained in two separate same window.  The
 :ref:`apod_viewer_1win` example has the canvas and input area in a single 
 window.   
 

doc/source/examples/integrate_1d.rst

@@ -5,8 +5,8 @@ integration example: integrate_1d
 
 This example shows how to use nmrglue to integrate a 1D NMRPipe spectra.  The
 script reads in ppm peak limits from ``limits.in`` and takes a simple 
-summation integral of each peak using the spectra contained in ``1d_data.ft``.  The integration values are writting to ``area.out`` and a plot is make showing
-the integration limits and values overlayed on the spectra to ``plot.png``.
+summation integral of each peak using the spectra contained in ``1d_data.ft``.  The integration values are writing to ``area.out`` and a plot is make showing
+the integration limits and values overlaid on the spectra to ``plot.png``.
 
 The data used in this example is available for 
 `download. <https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/nmrglue/example_integrate_1d.zip>`_

doc/source/examples/integrate_2d.rst

@@ -6,7 +6,7 @@ integration example: integrate_2d
 This example shows how to use nmrglue to integrate a 2D NMRPipe spectra.  The
 script reads in point limits from ``limits.in`` and takes a simple 
 summation integral of all points in each box described.  The integrated 
-volumes are writting to ``volumes.out``.  For a method to graphically examine
+volumes are writing to ``volumes.out``.  For a method to graphically examine
 these limits see :ref:`plot_2d_boxes`.  Similarly to check the peak 
 assignments see :ref:`plot_2d_assignments`.
 

doc/source/reference/bruker.rst

@@ -11,7 +11,7 @@ User Information
 User Functions
 ^^^^^^^^^^^^^^
 
-These are functions which are targetted for users of nmrglue.
+These are functions which are targeted for users of nmrglue.
 
 .. autosummary::
     :toctree: generated/
@@ -38,8 +38,8 @@ These are functions which are targetted for users of nmrglue.
 
 
 
-Developer Infomation
---------------------
+Developer Information
+---------------------
 
 .. include:: ../../../nmrglue/fileio/bruker.py
     :start-line: 11

doc/source/reference/convert.rst

@@ -11,7 +11,7 @@ User Information
 User Classes
 ^^^^^^^^^^^^
 
-This class is targetted for users of nmrglue.
+This class is targeted for users of nmrglue.
 
 .. autoclass:: converter
     :members:

doc/source/reference/nmrml.rst

@@ -18,8 +18,8 @@ User Functions
 
     read
 
-Developer Infomation
---------------------
+Developer Information
+---------------------
 
 Developer Functions
 ^^^^^^^^^^^^^^^^^^^

doc/source/reference/rnmrtk.rst

@@ -27,8 +27,8 @@ User Functions
     create_dic
 
 
-Developer Infomation
---------------------
+Developer Information
+---------------------
 
 Developer Functions
 ^^^^^^^^^^^^^^^^^^^

doc/source/reference/simpson.rst

@@ -24,8 +24,8 @@ User Functions
     read_raw_bin_2d
     read_binary
 
-Developer Infomation
---------------------
+Developer Information
+---------------------
 
 Developer Functions
 ^^^^^^^^^^^^^^^^^^^

doc/source/reference/tecmag.rst

@@ -18,8 +18,8 @@ User Functions
     guess_udic
 
 
-Developer Infomation
---------------------
+Developer Information
+---------------------
 
 .. include:: ../../../nmrglue/fileio/tecmag.py
     :start-line: 4

doc/source/reference/varian.rst

@@ -32,8 +32,8 @@ User Functions
     create_dic
 
 
-Developer Infomation
---------------------
+Developer Information
+---------------------
 
 .. include:: ../../../nmrglue/fileio/varian.py
     :start-line: 8

doc/source/tutorial.rst

@@ -313,7 +313,7 @@ reference your data in more common NMR units nmrglue provides the
     >>> uc1 = ng.pipe.make_uc(dic,data,dim=1)
 
 We now have unit conversion objects for both axes in the 2D spectrum.  We can
-use these objects to determined the nearest point for a given unit:
+use these objects to determine the nearest point for a given unit:
 
     >>> uc0("100.0 ppm")
     1397

examples/bruker_processed_1d/dig_filter_remove.py

@@ -24,7 +24,7 @@
 pipe_precorr_frq = ng.pipe.read('pre.ft')[1][::-1]
 pipe_precorr_frq = ng.proc_autophase.autops(pipe_precorr_frq, 'peak_minima')
 
-#---data processed using NMRPipe (post-procesing)
+#---data processed using NMRPipe (post-processing)
 pipe_postcorr_frq = ng.pipe.read('post.ft')[1][::-1]
 pipe_postcorr_frq = ng.proc_autophase.autops(pipe_postcorr_frq, 'acme') 
 

examples/coadd/coadd_1d_pipe/coadd_1d.py

@@ -8,7 +8,7 @@
 flist = glob.glob("test*.fid")
 flist.sort()
 
-# initilize the new data
+# initialize the new data
 dic, data = ng.pipe.read(flist[0])
 coadd_data = np.zeros_like(data)
 coadd_dic = dict(dic)

examples/coadd/coadd_2d_pipe/coadd_2d.py

@@ -8,7 +8,7 @@
 flist = glob.glob("test*.fid")
 flist.sort()
 
-# initilize the new data
+# initialize the new data
 dic, data = ng.pipe.read(flist[0])
 coadd_data = np.zeros_like(data)
 coadd_dic = dict(dic)

examples/coadd/coadd_pseudo3d_pipe/coadd_pseudo3d.py

@@ -16,7 +16,7 @@
 # loop over the files
 for base_fname in flist:
 
-    # initilize the new data
+    # initialize the new data
     dic, data = ng.pipe.read(base_fname)
     coadd_data = np.zeros_like(data)
     coadd_dic = dict(dic)

examples/convert/agilent2pipe_2d/agilent2pipe_2d.py

@@ -17,7 +17,7 @@
 udic[1]['car']      = 55.0 * 125.691; udic[0]['car']      = 120.0 * 50.648
 udic[1]['label']    = '13C'         ; udic[0]['label']    = '15N'    
 
-# create the converter object and initilize with Agilent data
+# create the converter object and initialize with Agilent data
 C = ng.convert.converter()
 C.from_varian(dic, data, udic)
 

examples/convert/agilent2pipe_2d_tppi/agilent2pipe_2d_tppi.py

@@ -17,7 +17,7 @@
 u[1]['car']      = 101.274 * 125.681    ; u[0]['car']      = 101.274 * 125.681
 u[1]['label']    = 'C13x'               ; u[0]['label']    = 'C13y'           
 
-# create the converter object and initilize with Agilent data
+# create the converter object and initialize with Agilent data
 C = ng.convert.converter()
 C.from_varian(dic, data, u)
 

examples/convert/agilent2pipe_3d/agilent2pipe_3d.py

@@ -37,7 +37,7 @@
 udic[0]['label']    = 'CA'
 
 
-# create the converter object and initilize with Agilent data
+# create the converter object and initialize with Agilent data
 C = ng.convert.converter()
 C.from_varian(dic, data, udic)
 

examples/convert/bruker2pipe_1d/bruker2pipe_1d.py

@@ -15,7 +15,7 @@
 udic[0]['car']      = 4.773 * 600.133
 udic[0]['label']    = '1H'
 
-# create the converter object and initilize with Bruker data
+# create the converter object and initialize with Bruker data
 C = ng.convert.converter()
 C.from_bruker(dic, data, udic)
 

examples/convert/bruker2pipe_2d/bruker2pipe_2d.py

@@ -17,7 +17,7 @@
 u[1]['car']      = 4.773 * 800.134  ;  u[0]['car']      = 58.742 * 201.204
 u[1]['label']    = '1H'             ;  u[0]['label']    = '13C'            
 
-# create the converter object and initilize with Bruker data
+# create the converter object and initialize with Bruker data
 C = ng.convert.converter()
 C.from_bruker(dic, data, u)
 

examples/convert/bruker2pipe_3d/bruker2pipe_3d.py

@@ -37,7 +37,7 @@
 udic[0]['label']    = '13C'
 
 
-# create the converter object and initilize with Bruker data
+# create the converter object and initialize with Bruker data
 C = ng.convert.converter()
 C.from_bruker(dic, data, udic)
 

examples/convert/pipe2sparky_2d/pipe2sparky_2d.py

@@ -8,7 +8,7 @@
 # Set the spectral parameters 
 udic = ng.pipe.guess_udic(dic, data)
 
-# create the converter object and initilize with NMRPipe data
+# create the converter object and initialize with NMRPipe data
 C = ng.convert.converter()
 C.from_pipe(dic, data, udic)
 

examples/convert/pipe2sparky_3d/pipe2sparky_3d.py

@@ -9,7 +9,7 @@
 # Set the spectral parameters 
 udic = ng.pipe.guess_udic(dic, data)
 
-# create the converter object and initilize with NMRPipe data
+# create the converter object and initialize with NMRPipe data
 C = ng.convert.converter()
 C.from_pipe(dic, data, udic)
 

examples/fitting_data/t1_measurements/extract_trajs.py

@@ -1,5 +1,5 @@
 #! /usr/bin/env python
-# Scipt to extract trajectories from a series a 2D spectrum.
+# Script to extract trajectories from a series a 2D spectrum.
 
 import nmrglue as ng
 import numpy as np

examples/fitting_data/t1_measurements/xy_s3e.com

@@ -5,7 +5,7 @@
 # By: Jonathan Helmus ([email protected])
 
 # data must be converted to nmrpipe data with twice the number of points
-# in the indirect dimention using var2pipe and the A/B S3E block the intermost
+# in the indirect dimension using var2pipe and the A/B S3E block the intermost
 # array
 
 # var2pipe sign alternates the Y vectors for States so we have:

examples/integration/integrate_1d/integrate_1d.py

@@ -1,5 +1,5 @@
 #! /usr/bin/env python
-# Example scipt to show integration of a 1D spectrum
+# Example script to show integration of a 1D spectrum
 
 import nmrglue as ng
 import numpy as np
@@ -12,7 +12,7 @@
 # read in the integration limits
 peak_list = np.recfromtxt("limits.in")
 
-# determind the ppm scale
+# determine the ppm scale
 uc = ng.pipe.make_uc(dic, data)
 ppm_scale = uc.ppm_scale()
 

examples/jbnmr_examples/make_jbnmr_zip_files.com

@@ -32,7 +32,7 @@ s4_2d_plotting/test.ft2
 mv jbnmr_s4_2d_plotting.zip ./zip_files/.
 
 
-# Listing S5 seperate interleaved
+# Listing S5 separate interleaved
 zip jbnmr_s5_seperate_interleaved.zip               \
 s5_seperate_interleaved/seperate.py                 \
 s5_seperate_interleaved/README.rst                  \
@@ -44,7 +44,7 @@ s5_seperate_interleaved/arrayed_data.fid/fid
 
 mv jbnmr_s5_seperate_interleaved.zip ./zip_files/.
 
-# Listing S6 seperate inner_phase
+# Listing S6 separate inner_phase
 zip jbnmr_s6_seperate_inner_phase.zip               \
 s6_seperate_inner_phase/seperate.py                 \
 s6_seperate_inner_phase/README.rst                  \

examples/jbnmr_examples/s11_strip_plots/README.rst

@@ -11,7 +11,7 @@ this example a three 3D solid state NMR spectra are visualized as strip plots.
 Instructions
 ------------
 
-Process each of the three 3D spectra by decending into the appopiate directory
+Process each of the three 3D spectra by descending into the appopiate directory
 and executing the `fid.com` followed by the `xy.com` NMRPipe scripts.
 
 

examples/jbnmr_examples/s12-s15_relaxation_analysis/README.rst

@@ -6,7 +6,7 @@ Introduction
 
 This example is taken from Listing S12 - S15 in the 2013 JBNMR nmrglue paper.
 In this example a series of 3D NMRPipe files containing relaxation trajectories
-for a solid state NMR experment and analyzed.  
+for a solid state NMR experiment and analyzed.  
 
 
 

examples/jbnmr_examples/s12-s15_relaxation_analysis/fit_exp.py

@@ -28,7 +28,7 @@ def residuals(p, y, x):
     peak = filename[:3]
     print "Fitting Peak:", peak
 
-    # fit the trajectory using contrainted least squares optimization
+    # fit the trajectory using constrained least squares optimization
     trajectory = np.loadtxt(filename)
     x, ier = leastsqbound(residuals, x0, bounds=bounds, 
                             args=(trajectory, relaxation_times))

examples/jbnmr_examples/s5_seperate_interleaved/README.rst

@@ -1,16 +1,16 @@
-Seperated interleaved example
+Separated interleaved example
 =============================
 
 Introduction
 ------------
 
 This example is taken from Listing S5 in the 2013 JBNMR nmrglue paper.  In
-this example a pseudo-3D NMRPipe data set is seperated into 2D data sets using
+this example a pseudo-3D NMRPipe data set is separated into 2D data sets using
 the script `seperate.py`. 
 
 
 Instructions
 ------------
 
-Execute `python seperate.py` to seperate the pseudo-3D data set into 2D data
+Execute `python seperate.py` to separate the pseudo-3D data set into 2D data
 sets.  Six directories with names `techo_XXXX.fid` will be created.

examples/jbnmr_examples/s6_seperate_inner_phase/README.rst

@@ -1,16 +1,16 @@
-Seperated inner phase example
+Separated inner phase example
 =============================
 
 Introduction
 ------------
 
 This example is taken from Listing S6 in the 2013 JBNMR nmrglue paper.  In
-this example a pseudo-3D NMRPipe data set is seperated into 2D data sets using
+this example a pseudo-3D NMRPipe data set is separated into 2D data sets using
 the script `seperate.py` where there is an innermost quadrature phase loop. 
 
 
 Instructions
 ------------
 
-Execute `python seperate.py` to seperate the pseudo-3D data set into 2D data
+Execute `python seperate.py` to separate the pseudo-3D data set into 2D data
 sets.  Ten directories with names `nredor_XX.fid` will be created.