fix errors

conf.py

@@ -15,7 +15,6 @@
 import sys
 import os
 import shlex
-import shlex
 
 sys.path.append(os.path.abspath('./_ext'))
 
@@ -37,10 +36,12 @@
     'sphinx.ext.mathjax',
     'sphinxcontrib.bibtex',
     'edit_on_github',
-    'purpose',
-    'example',
+    # 'purpose',
+    # 'example',
 ]
 
+bibtex_bibfiles = ['reference.bib']
+
 # Number figures
 numfig = True
 
@@ -68,9 +69,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '2.0'
+version = '1.0'
 # The full version, including alpha/beta/rc tags.
-release = '2.0'
+release = '1.0'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

content/files/weight.rst

@@ -3,7 +3,7 @@
 Weights file
 ============
 
-This file supplies the user-based weights that acts upon the model objective function. Each set of weights correspond to the functions (e.g., :math:`w_x`) within the :ref:`model objective function <mof>`. For ease, the weights in geographic coordinates are provided by the user. The following is the file structure is for the weights file:
+This file supplies the user-based weights that acts upon the model objective function. Each set of weights correspond to the functions (e.g., :math:`w_x`) within the model objective function. For ease, the weights in geographic coordinates are provided by the user. The following is the file structure is for the weights file:
 
 
 .. figure:: ../../images/weightsInp.png

content/programs/mviinv.rst

@@ -99,7 +99,7 @@ The parameters within the control file are:
 
 - ``remGamma``: This is a number that places (de-)emphasis on the remenant magnetization components (and extra scaling of **S,T** compents versus **P**). If ``null`` is chosen, the trade-off between induced and remanent components are 0.5. The higher the number, the stronger the inversion will try to recover an induced model.
 
-- ``SMOOTH_MOD``: This option was not available in previous versions of the code and can be used to define the reference model in and out of the derivative terms. The options are: ``SMOOTH_MOD_DIF`` (reference model is defined in the derivative terms) and ``SMOOTH_MOD`` (reference model is defined in only the smallest term). See equation :eq:`mof` for details.
+- ``SMOOTH_MOD``: This option was not available in previous versions of the code and can be used to define the reference model in and out of the derivative terms. The options are: ``SMOOTH_MOD_DIF`` (reference model is defined in the derivative terms) and ``SMOOTH_MOD`` (reference model is defined in only the smallest term).
 
 - ``w1.dat``: Name of the :ref:`weights file <weightsFile>` containing weighting matrices for the *P* component. If ``null`` is entered, default values of unity are used.
 

content/programs/mvisen.rst

@@ -41,8 +41,6 @@ The input parameters for the control file are:
 
      ``itol=2``: the user defines the threshold level and ``eps`` is the threshold to be used. If ``null`` is entered on this line, a default relative reconstruction error of 0.05 (e.g. 5%) is used and the relative threshold level is calculated (i.e., ``itol=1`` , ``eps=0.05``).
 
-     **NOTE** The detailed explanation of threshold level and reconstruction error can be found in the :ref:`wavelet section <waveletSection>` of this manual.
-
 
 Example of input file
 ~~~~~~~~~~~~~~~~~~~~~

content/programs/pfweight.rst

@@ -38,8 +38,8 @@ The input parameters for the control file are:
      | =2 for distance weighting.
 
 - ``alpha``, ``znot``: Parameters defining the depth weighting function: 
-     | When ``iwt=1``, ``alpha`` and ``znot`` are used as :math:`\alpha` and :math:`z_0` to define the :ref:`depth weighting <depthWeight>`
-     | When ``iwt=2``, ``alpha`` and ``znot`` are used as :math:`\alpha` and :math:`(R_o)` to define the :ref:`distance weighting <distWeight>`
+     | When ``iwt=1``, ``alpha`` and ``znot`` are used as :math:`\alpha` and :math:`z_0` to define the depth weighting <depthWeight>
+     | When ``iwt=2``, ``alpha`` and ``znot`` are used as :math:`\alpha` and :math:`(R_o)` to define the distance weighting <distWeight>
      | **NOTE 1**: If ``null`` is entered on this line (line 6), then the program sets ``alpha=3`` and calculates the value of :math:`z_o` based upon the mesh and data location. This is true for ``iwt=1`` or ``iwt=2``
      | **NOTE 2**: For most inversions, setting this input line to ``null`` is recommended. The option for inputing :math:`\alpha` and :math:`z_o` is provided for experienced users who would like to investigate the effect of the generalized depth weighting for special purposes. The value of :math:`\alpha` should normally be close to 3.0. Smaller values of give rise to weaker weighting as distance increases from the observation locations.
 
@@ -54,4 +54,4 @@ Example of input file
 Output files
 ------------
 
-The program outputs ``x_weight.txt``. A file in the format, which contains weights for each cell, based on :ref:`depth weighting <depthWeight>` (x = "depth") or :ref:`distance weighting <distWeight>`  (x = "distance"). A log file ``pfweight.log`` is also written.
+The program outputs ``x_weight.txt``. A file in the format, which contains weights for each cell, based on depth weighting (x = "depth") or distance weighting (x = "distance"). A log file ``pfweight.log`` is also written.

reference.bib

@@ -422,7 +422,7 @@ @Article{DavisLi11
   Author                   = {K Davis and Y Li},
   Journal                  = {Geophysical Journal International},
   Year                     = {2011},
-  Pages                    = {157-–166},
+  Pages                    = {157-�166},
   Volume                   = {185}
 }
 
@@ -431,7 +431,7 @@ @InProceedings{DavisLi10b
   Author                   = {K Davis and Y Li},
   Booktitle                = {Expanded Abstracts},
   Year                     = {2010},
-  Pages                    = {1172-–1177},
+  Pages                    = {1172-�1177},
   Publisher                = {{80th Annual Internat. Mtg. Soc. Expl. Geophys.}},
   Volume                   = {29}
 }
@@ -1482,7 +1482,7 @@ @Article{PaineHaederle01
   Author                   = {J Paine and M Haederle and M Flis},
   Journal                  = {Exploration Geophysics},
   Year                     = {2001},
-  Pages                    = {238-–242},
+  Pages                    = {238-�242},
   Volume                   = {32},
 
   Issue                    = {3 \& 4}
@@ -1788,7 +1788,7 @@ @Article{SmithWessel90
 }
 
 @TechReport{OGS04,
-  Title                    = {{Ontario airborne geophysical surveys, magnetic data, Central Abitibi Destor - Porcupine – Pipestone Faults Area}},
+  Title                    = {{Ontario airborne geophysical surveys, magnetic data, Central Abitibi Destor - Porcupine � Pipestone Faults Area}},
   Author                   = {Ontario~Geologic~Survey},
   Institution              = {Ontario Geological Survey},
   Year                     = {2004},
@@ -1889,7 +1889,7 @@ @Book{Vacquier51
 }
 
 @Article{vanStaal03,
-  Title                    = {{Geology and Tectonic History of the Bathurst Supergroup, Bathurst Mining Camp, and Its Relationship to Coeval Rocks in Southwestern New Brunswick and Adjacent Maine – A Synthesis}},
+  Title                    = {{Geology and Tectonic History of the Bathurst Supergroup, Bathurst Mining Camp, and Its Relationship to Coeval Rocks in Southwestern New Brunswick and Adjacent Maine � A Synthesis}},
   Author                   = {C R {Van Staal}},
   Journal                  = {{Econimic Geology, Monograph 11}},
   Year                     = {2003},
@@ -2059,7 +2059,7 @@ @Article{Zhdanov04
   Author                   = {M. S. Zhdanov and R. G. Ellis and S. Mukherjee},
   Journal                  = {Geophysics},
   Year                     = {2004},
-  Pages                    = {925–937},
+  Pages                    = {925--937},
   Volume                   = {69},
 
   Owner                    = {kdavis},

references.rst

@@ -4,6 +4,4 @@ References
 ==========
 
  .. bibliography:: reference.bib
-    :cited:
-    :style: alpha
-    :encoding: latex+latin
+    :all: