fix text issues across files

source/cfgs.rst

@@ -206,7 +206,7 @@ This configuration uses the three components
 
 - |OCE|, the ocean dynamical core
 - |ICE|, the thermodynamic-dynamic sea ice model.
-- |MBG|, passive tracer transport module and PISCES BGC model :cite:`aumont.ethé.ea_GMD15`
+- |TOP|, passive tracer transport module and PISCES BGC model :cite:`aumont.ethé.ea_GMD15`
 
 All components share the same grid.
 The model is forced with CORE-II normal year atmospheric forcing and

source/contrib.rst

@@ -12,11 +12,11 @@ Contributing
 Sending feedbacks and getting answers
 =====================================
 
-  Sending feedbacks is a useful way to contribute to NEMO efficency and reliability. Before doing so,please check
+Sending feedbacks is a useful way to contribute to NEMO efficency and reliability. Before doing so,please check
 on NEMO develoment platform in wiki, tickets, forum and online documentation so as 
 on :NEMO Discourse group:`https://nemo-ocean.discourse.group` if the subject has already been discussed. 
 You can either contribute to an existing discussion, or
-  Create an entry for the discussion online in Discourse, according to your needs
+Create an entry for the discussion online in Discourse, according to your needs
 
 Please follow the guidelines and try to be as specific as possible in the description.
 

source/da.rst

@@ -16,7 +16,7 @@ The assimilation interface to NEMO is split into three modules.
   (based on the assimilation increments).
 - ``TAM`` the tangent linear and adjoint model.
 
-Please see :doc:`NEMO reference manual <cite.html>` for more details including
+Please see :doc:`NEMO reference manual <cite>` for more details including
 information about the input file formats and the namelist settings.
 
 Observation and model comparison (``OBS``)

source/global.rst

@@ -6,6 +6,7 @@
 .. role:: green
 .. role:: grey
 .. role:: greysup(sup)
+.. role:: pisces
 
 .. inline code snippets
 
@@ -27,8 +28,9 @@
 .. |OCE|      replace::  :blue:`NEMO-OCE`
 .. |NEMO-ICE| replace::  :grey:`NEMO-SI`\ :greysup:`3`  :grey:`(Sea Ice)`
 .. |ICE|      replace::  :grey:`NEMO-SI`\ :greysup:`3`
-.. |NEMO-MBG| replace:: :green:`NEMO-TOP/PISCES (Tracers)`
-.. |MBG|      replace:: :green:`NEMO-TOP/PISCES`
+.. |NEMO-TOP| replace:: :green:`NEMO-TOP (Oceanic Tracers)`
+.. |TOP|      replace:: :green:`NEMO-TOP`
+.. |NEMO-PISCES| replace:: :pisces:`NEMO-PISCES`
 
 .. External links
 

source/index.rst

@@ -26,7 +26,7 @@ NEMO User Guide
    :glob:
    :titlesonly:
 
-   unpub/*
+#   unpub/*
 
 .. Only displayed with 'make drafthtml'
 

source/install.rst

-*******************
+********************
 Essential components
-*******************
+********************
 
 .. todo::
 

source/migration.rst

@@ -5,7 +5,7 @@ Migrating from 4.0.x to 4.2.x
 .. |nbsp| unicode:: 0xA0 .. non-breaking space
 
 Modification of input and output files
-=====
+======================================
 
 Up to NEMO version 4.0.x (inclusive), if the domain configuration includes one of the
 possible periodicity conditions (East-West (EW), North-South (SN) or North-Pole (NP)
@@ -148,7 +148,7 @@ Here is an example on how to create global attributes with the command ncatted:
 
 
 Speed up associated with reduced memory requirements
-=====
+====================================================
  
 In order to reduce the memory footprint in NEMO 4.2, an additional way of dealing with vertical scale factors has been implemented using cpp keys (``key_linssh``, ``key_qco``). These keys allow a reduction of the memory footprint by removing 26 x 3D arrays at the cost of 10 x 2D arrays. In tests without I/O, this implementation allows a speed up of 7 to 15% depending on the average memory load among processors.
 
@@ -197,7 +197,7 @@ For ice-shelf simulations, a ``key_isf`` cpp key is needed in addition to ``key_
 
 
 Shallow Water 
-=====
+=============
 
 The SWE (Shallow Water Equation) module (./src/SWE) is a demonstrator for shallow water equations newly included in NEMO v4.2. This module is an early demonstrator for the changes to the time-stepping scheme that are planned for the next release. It contains suitable shallow water time stepping routines for both Modified Leap Frog (stpmlf.F90) and Runge Kutta 3rd order (stprk3.F90) time schemes. Note that in the MLF case, the ``key_qco`` compilation pre-processing key is needed. RK3 requires both ``key_qco`` and either ``key_RK3`` or ``key_RK3all`` compilation pre-processing keys. RK3 time-stepping is a 3 stage algorithm: 1st and 2nd stages build estimates of intermediate fields, the 3rd stage integrates the model from n to n+1 using the intermediate estimates. With ``key_RK3all``, all the stages are integrated with the full suite of ocean dynamics including advection, vorticity, lateral diffusion, pressure gradient, and forcing. Instead, with ``key_RK3``, lateral diffusion and forcing are removed from stages 1 and 2. 
 

source/zooms.rst

@@ -2,10 +2,6 @@
 Embedded zooms
 **************
 
-.. todo::
-
-
-
 .. contents::
    :local: