Merge pull request #162 from ESCOMP/fische/doc_links

Fix broken links in documentation.

doc/source/cesm_configurations.rst

@@ -12,9 +12,9 @@ a science and technical perspective. CESM supports numerous
 <http://www.cesm.ucar.edu/models/cesm2/cesm/compsets.html>`_.  In
 addition, each model component has input options to configure specific
 `model settings
-<http://www.cesm.ucar.edu/models/cesm2/component_xml/index.html>`_
+<http://www.cesm.ucar.edu/models/cesm2/settings/current>`_
 and `parameterizations
-<http://www.cesm.ucar.edu/models/cesm2/component_namelists/index.html>`_.
+<http://www.cesm.ucar.edu/models/cesm2/settings/current>`_.
 
 
 CESM2 Components
@@ -35,7 +35,7 @@ and an external system processing component
 - external system processing (esp) 
 
 In addition CESM2 is accompanied by a `driver/coupler (cpl7)
-<http://esmci.github.io/cime/driver_cpl/index.html>`_ that coordinates
+<http://esmci.github.io/cime/versions/master/html/driver_cpl/index.html>`_ that coordinates
 the time evolution of geophysical components and periodically permits
 the components to exchange data.  Each component is represented in one
 of several modes: "active," "data," "dead," or "stub" that permits the
@@ -73,32 +73,32 @@ The CESM2 components can be summarized as follows:
    :widths: 12, 10, 10, 10, 60
 
    "atmosphere","atm","cam", "active","The `Community Atmosphere Model (CAM) <http://www.cesm.ucar.edu/models/cesm2/atmosphere/>`_ is a global atmospheric general circulation model developed from the NCAR CCM3."                                                                                                                                      
-   "atmosphere","atm","datm", "data", "The `data atmosphere <http://esmci.github.io/cime/data_models/data-atm.html>`_ component is a pure data component that reads in atmospheric forcing data"
+   "atmosphere","atm","datm", "data", "The `data atmosphere <http://esmci.github.io/cime/versions/master/html/data_models/data-atm.html>`_ component is a pure data component that reads in atmospheric forcing data"
    "atmosphere","atm", "xatm", "dead", "Used only for testing the driver/coupler"
    "atmosphere","atm", "satm", "stub", "Used only to satisy the interface requirements"
    "land", "lnd", "clm", "active", "The `Community Land Model (CLM) <http://www.cesm.ucar.edu/models/cesm2/land/>`_ is the result of a collaborative project between scientists in the Terrestrial Sciences Section of the Climate and Global Dynamics Division (CGD) at NCAR and the CESM Land Model Working Group. Other principal working groups that also contribute to the CLM are Biogeochemistry, Paleoclimate, and Climate Change and Assessment."
-   "land", "lnd", "dlnd", "data", "The `data land component <http://esmci.github.io/cime/data_models/data-lnd.html>`_ is a purely data-land component (reading in coupler history data for atm/land fluxes and land albedos produced by a previous run, or snow surface mass balance fields) or both."
+   "land", "lnd", "dlnd", "data", "The `data land component <http://esmci.github.io/cime/versions/master/html/data_models/data-lnd.html>`_ is a purely data-land component (reading in coupler history data for atm/land fluxes and land albedos produced by a previous run, or snow surface mass balance fields) or both."
    "land", "lnd", "xlnd", "dead", "Used only for testing the driver/coupler"
    "land", "lnd", "slnd", "stub", "Used only to satisy the interface requirements"
    "river", "rof", "rtm", "active", "The `river transport model (RTM) <http://www.cesm.ucar.edu/models/cesm2/river/>`_ was previously part of CLM and was developed to route total runoff from the land surface model to either the active ocean or marginal seas which enables the hydrologic cycle to be closed (Branstetter 2001, Branstetter and Famiglietti 1999). This is needed to model ocean convection and circulation, which is affected by freshwater input."
    "river", "rof", "mosart", "active", "`MOdel for Scale Adaptive River Transport (MOSART) <http://www.cesm.ucar.edu/models/cesm2/river/>`_ , a new large-scale river routing model. MOSART improves the magnitude and timing of river flow simulations."
-   "river", "rof", "drof", "data", "The `data runoff model <http://esmci.github.io/cime/data_models/data-river.html>`_ was previously part of the data land model and functions as a purely data-runoff model (reading in runoff data)."
+   "river", "rof", "drof", "data", "The `data runoff model <http://esmci.github.io/cime/versions/master/html/data_models/data-river.html>`_ was previously part of the data land model and functions as a purely data-runoff model (reading in runoff data)."
    "river", "rof", "xrof", "dead", "Used only for testing the driver/coupler"
    "river", "rof", "srof", "stub", "Used only to satisy the interface requirements"
    "ocean", "ocn", "pop", "active", "The ocean model is an extension of the `Parallel Ocean Program (POP) <http://www.cesm.ucar.edu/models/cesm2/ocean/>`_ Version 2 from Los Alamos National Laboratory (LANL)."
-   "ocean", "ocn", "docn", "data", "The `data ocean <http://esmci.github.io/cime/data_models/data-ocean.html>`_ component has two distinct modes of operation. It can run as a pure data model, reading ocean SSTs (normally climatological) from input datasets, interpolating in space and time, and then passing these to the coupler. Alternatively, docn can compute updated SSTs based on a slab ocean model where bottom ocean heat flux convergence and boundary layer depths are read in and used with the atmosphere/ocean and ice/ocean fluxes obtained from the coupler."
+   "ocean", "ocn", "docn", "data", "The `data ocean <http://esmci.github.io/cime/versions/master/html/data_models/data-ocean.html>`_ component has two distinct modes of operation. It can run as a pure data model, reading ocean SSTs (normally climatological) from input datasets, interpolating in space and time, and then passing these to the coupler. Alternatively, docn can compute updated SSTs based on a slab ocean model where bottom ocean heat flux convergence and boundary layer depths are read in and used with the atmosphere/ocean and ice/ocean fluxes obtained from the coupler."
    "ocean", "ocn", "xocn", "dead"
    "ocean", "ocn", "socn", "stub"
    "sea-ice", "ice", "cice", "active", "The `sea-ice component (CICE) <http://www.cesm.ucar.edu/models/cesm2/sea-ice/>`_ is an extension of the Los Alamos National Laboratory (LANL) sea-ice model and was developed though collaboration within the CESM Polar Climate Working Group (PCWG). In CESM, CICE can run as a fully prognostic component or in prescribed mode where ice coverage (normally climatological) is read in."
-   "sea-ice", "ice", "dice", "data", "The `data ice <http://esmci.github.io/cime/data_models/data-seaice.html>`_ component is a partially prognostic model. The model reads in ice coverage and receives atmospheric forcing from the coupler, and then it calculates the ice/atmosphere and ice/ocean fluxes. The data ice component acts very similarly to CICE running in prescribed mode."
+   "sea-ice", "ice", "dice", "data", "The `data ice <http://esmci.github.io/cime/versions/master/html/data_models/data-seaice.html>`_ component is a partially prognostic model. The model reads in ice coverage and receives atmospheric forcing from the coupler, and then it calculates the ice/atmosphere and ice/ocean fluxes. The data ice component acts very similarly to CICE running in prescribed mode."
    "sea-ice", "ice", "xice", "dead", "Used only for testing the driver/coupler"
    "sea-ice", "ice", "sice", "stub"
    "land-ice", "glc", "cism", "active", The `CISM component <http://www.cesm.ucar.edu/models/cesm2/land-ice/>`_ is an extension of the Glimmer ice sheet model.                                                                                                                                                                                        
    "land-ice", "glc", "sglc", "stub", "Used only to satisy the interface requirements"
    "ocean-wave", "wav", "wav", "ww3","The `ww3 <http://www.cesm.ucar.edu/models/cesm2/wave/>`_ component adds prognostic ocean waves to the system" 
    "ocean-wave", "wav", "xwav", "dead", "Used only for testing the driver/coupler"
    "ocean-wave", "wav", "swav", "stub", "Used only to satisy the interface requirements"
-   "coupler", "cpl", "cpl", "active", "The `CESM coupler <http://esmci.github.io/cime/driver_cpl/index.html>`_ was built primarily through a collaboration of the NCAR CESM Software Engineering Group and the Argonne National Laboratory (ANL). The MCT coupling library provides much of the infrastructure."
+   "coupler", "cpl", "cpl", "active", "The `CESM coupler <http://esmci.github.io/cime/versions/master/html/driver_cpl/index.html>`_ was built primarily through a collaboration of the NCAR CESM Software Engineering Group and the Argonne National Laboratory (ANL). The MCT coupling library provides much of the infrastructure."
 
 
 CESM2 Component Sets
@@ -181,7 +181,7 @@ files to fill in information required for the target platform. This
 functionality is handy in accelerating the porting process and quickly
 getting a case running on a new platform. For more information on
 porting, see the `CIME porting guide
-<http://esmci.github.io/cime/users_guide/porting-cime.html>`_.  The
+<http://esmci.github.io/cime/versions/master/html/users_guide/porting-cime.html>`_.  The
 list of available machines are documented in `CESM supported machines
 <http://www.cesm.ucar.edu/models/cesm2/cesm/machines.html>`_.
 Running **query_config** with the ``--machines`` option will also show
@@ -204,7 +204,7 @@ These control runs should be scientifically reproducible on the
 original platform or other platforms. Bit-for-bit reproducibility
 cannot be guaranteed due to variations in compiler or system
 versions. Users should carry out their own `port validations
-<http://esmci.github.io/cime/users_guide/porting-cime.html#validating-your-port>`_
+<http://esmci.github.io/cime/versions/master/html/users_guide/porting-cime.html#validating-your-port>`_
 on any platform prior to doing scientific runs or scientific analysis
 and documentation.
 

doc/source/downloading_cesm.rst

@@ -16,7 +16,7 @@ software.  You will need access to the command line clients, ``git``
 (v1.8 or greater) and ``svn`` (v1.8 or greater but less than v1.11).  
 Currently, our Subversion server
 software is at version 1.8.17. For more information or to download
-open source tools, visit `Subversion <http://subversion.tigris.org/>`_
+open source tools, visit `Subversion <http://subversion.apache.org/>`_
 and `git downloads <https://git-scm.com/downloads>`_.
 
 With valid git and svn clients installed on the machine where CESM will be

doc/source/introduction.rst

@@ -66,7 +66,7 @@ into the Earth's past, present, and future climate states.
 CESM can be run on a number of different `hardware platforms
 <http://www.cesm.ucar.edu/models/cesm2/cesm/machines.html>`__, and
 has a relatively flexible design with respect to `processor layout
-<http://esmci.github.io/cime/users_guide/pes-threads.html>`__
+<http://esmci.github.io/cime/versions/master/html/users_guide/pes-threads.html>`__
 of components.
 
 The CESM project is a cooperative effort among U.S. climate
@@ -113,7 +113,7 @@ installing and running CESM2.
 
 -  `pnetcdf 1.7.0 is required and 1.8.1 is optional but recommended <http://trac.mcs.anl.gov/projects/parallel-netcdf/>`_
 
--  `Trilinos <http://trilinos.gov/>`_ may be required for certain configurations 
+-  `Trilinos <https://trilinos.github.io/>`_ may be required for certain configurations 
 
 -  `LAPACK <http://www.netlib.org/lapack/>`_ and `BLAS <http://www.netlib.org/blas/>`_
 

doc/source/quickstart.rst

@@ -7,15 +7,15 @@
 The following quick start guide is for versions of CESM2 that have
 already been ported to the local target machine. CESM2 is built on the
 CIME (Common Infrastructure for Modeling Earth) framework.
-Please refer to the `CIME Porting Documentation <http://esmci.github.io/cime/users_guide/porting-cime.html>`_ if CIME has not
+Please refer to the `CIME Porting Documentation <http://esmci.github.io/cime/versions/master/html/users_guide/porting-cime.html>`_ if CIME has not
 yet been ported to the target machine. 
 
 If you are new to CESM2, please consider reading the
 `CIME Case Control System Part 1: Basic Usage guide <https://esmci.github.io/cime/index.html>`_ first.
 
 This is the procedure for quickly setting up and running a CESM2 case.
 
-Download CESM2 (see `Downloading CESM2 <downloading_cesm.html>`_).
+Download CESM2 (see `Downloading CESM2 <downloading_cesm.rst>`_).
 
 Select a component set, and a resolution for your case.  Details of available
 component sets and resolutions are available from the `query_config`_ tool located
@@ -152,7 +152,7 @@ now are:
       ./xmlquery STOP_OPTION,STOP_N
 
    These default settings can be useful in `troubleshooting
-   <http://esmci.github.io/cime/users_guide/troubleshooting.html>`_ runtime problems
+   <http://esmci.github.io/cime/versions/master/html/users_guide/troubleshooting.html>`_ runtime problems
    before submitting for a longer time, but will not allow the model to run long enough to
    produce monthly history climatology files. In order to produce history files, increase
    the run length to a month or longer:
@@ -225,8 +225,7 @@ comma separated names and no spaces):
 
 
 .. _CIME: http://esmci.github.io/cime
-.. _porting: http://esmci.github.io/cime/users_guide/porting-cime
-.. _query_config: http://esmci.github.io/cime/users_guide/introduction-and-overview.html#discovering-available-cases-with-query-config
-.. _create_newcase: http://esmci.github.io/cime/users_guide/create-a-case.html
-.. _xmlchange: http://esmci.github.io/cime/Tools_user/xmlchange.html
-.. _case.setup: http://esmci.github.io/cime/users_guide/setting-up-a-case.html
+.. _query_config: http://esmci.github.io/cime/versions/master/html/users_guide/introduction-and-overview.html#discovering-available-cases-with-query-config
+.. _create_newcase: http://esmci.github.io/cime/versions/master/html/users_guide/create-a-case.html
+.. _xmlchange: http://esmci.github.io/cime/versions/master/html/Tools_user/xmlchange.html
+.. _case.setup: http://esmci.github.io/cime/versions/master/html/users_guide/setting-up-a-case.html