additional manual ch 1 changes

Author: Jeffery Scott

doc/Makefile

@@ -3,7 +3,7 @@
 
 # You can set these variables from the command line.
 SPHINXOPTS    =
-SPHINXBUILD   = sphinx-build
+SPHINXBUILD   = /anaconda/bin/sphinx-build
 SPHINXPROJ    = MITgcm
 SOURCEDIR     = .
 BUILDDIR      = _build

doc/conf.py

@@ -92,7 +92,7 @@
 # number figures within section
 numfig_secnum_depth = 1
 
-math_number_all = True
+#math_number_all = True
 
 numfig_format = {'figure': 'Figure %s', 'table': 'Table %s', 'code-block': 'Listing %s', 'section': 'Section %s'}
 

doc/overview/atmosphere.rst

@@ -37,7 +37,7 @@ where
 
 In the above the ideal gas law, :math:`p=\rho RT`, has been expressed in
 terms of the Exner function :math:`\Pi (p)` given by :eq:`exner`
-(see also :ref:`atmos_appendix`)
+(see also :numref:`atmos_appendix`)
 
 .. math:: \Pi (p)=c_{p}(\frac{p}{p_{c}})^{\kappa }
    :label: exner
@@ -72,6 +72,6 @@ The boundary conditions at top and bottom are given by:
 Then the (hydrostatic form of) equations
 :eq:`horiz-mtm`-:eq:`humidity-salt` yields a consistent set of
 atmospheric equations which, for convenience, are written out in
-:math:`p-`\coordinates in :ref:`atmos_appendix` - see
+:math:`p-`\coordinates in :numref:`atmos_appendix` - see
 eqs. :eq:`atmos-prime`-:eq:`atmos-prime5`.
 

doc/overview/kinematic_bound.rst

@@ -26,7 +26,8 @@ surface’ in the resting fluid and :math:`\eta` is the departure from
 Horizontal
 ~~~~~~~~~~
 
-.. math:: \vec{\mathbf{v}}\cdot \vec{\mathbf{n}}=0  \label{eq:noflow}
+.. math:: \vec{\mathbf{v}}\cdot \vec{\mathbf{n}}=0
+   :label: noflow
 
 where :math:`\vec{\mathbf{n}}` is the normal to a solid boundary.
 

doc/overview/ocean.rst

@@ -46,6 +46,6 @@ where :math:`\eta` is the elevation of the free surface.
 
 Then equations :eq:`horiz-mtm`- :eq:`humidity-salt` yield a
 consistent set of oceanic equations which, for convenience, are written
-out in :math:`z-`\coordinates in :ref:`ocean_appendix` - see eqs. :eq:`eq-ocean-mom`
+out in :math:`z-`\coordinates in :numref:`ocean_appendix` - see eqs. :eq:`eq-ocean-mom`
 to :eq:`eq-ocean-salt`.
 

doc/overview/overview.rst

@@ -255,7 +255,7 @@ with :math:`\mathbf{\nabla }_{h}` operating in the horizontal and
 .. math:: \mathcal{Q}_{S}\mathcal{\ }\text{are forcing and dissipation of }S
 
 The :math:`\mathcal{F}^{\prime }s` and :math:`\mathcal{Q}^{\prime }s`
-are provided by ‘physics’ and forcing pac kages for atmosphere and ocean.
+are provided by ‘physics’ and forcing packages for atmosphere and ocean.
 These are described in later chapters.