added instructions for forking submodules

docs/source/reference/git-submodules.rst

@@ -3,4 +3,74 @@
 Git submodules
 ==============
 
-todo
+
+Forking submodules
+------------------
+
+This sections describes updating git submodules to use your own forks. You can
+update submodule so that they use your forks at any time. It is recommended you
+only update the submodules that you need to, and that you leave submodules that
+you don't need to modify pointing to the GEOS-Chem repositories.
+
+The rest of this section assumes you are in the top-level of GCHPctm, i.e.,
+
+.. code-block:: console
+
+   $ cd GCHPctm   # navigate to top-level of GCHPctm
+
+First, identify the submodules that you need to modify. The :file:`.gitmodules`
+file has the paths and URLs to the submodules. You can see it with the following
+command
+
+.. code-block:: console
+
+   $ cat .gitmodules 
+   [submodule "src/MAPL"]
+      path = src/MAPL
+      url = https://github.com/sdeastham/MAPL
+   [submodule "src/GMAO_Shared"]
+      path = src/GMAO_Shared
+      url = https://github.com/geoschem/GMAO_Shared
+   [submodule "ESMA_cmake"]
+      path = ESMA_cmake
+      url = https://github.com/geoschem/ESMA_cmake
+   [submodule "src/gFTL-shared"]
+      path = src/gFTL-shared
+      url = https://github.com/geoschem/gFTL-shared.git
+   [submodule "src/FMS"]
+      path = src/FMS
+      url = https://github.com/geoschem/FMS.git
+   [submodule "src/GCHP_GridComp/FVdycoreCubed_GridComp"]
+      path = src/GCHP_GridComp/FVdycoreCubed_GridComp
+      url = https://github.com/sdeastham/FVdycoreCubed_GridComp.git
+   [submodule "src/GCHP_GridComp/GEOSChem_GridComp/geos-chem"]
+      path = src/GCHP_GridComp/GEOSChem_GridComp/geos-chem
+      url = https://github.com/sdeastham/geos-chem.git
+   [submodule "src/GCHP_GridComp/HEMCO_GridComp/HEMCO"]
+      path = src/GCHP_GridComp/HEMCO_GridComp/HEMCO
+      url = https://github.com/geoschem/HEMCO.git
+
+Once you know which submodules you need to update, fork each of them on GitHub.
+
+Once you have your own forks for the submodules that you are going to modify, update
+the submodule URLs in :file:`.gitmodules`
+
+.. code-block:: console
+
+   $ git config -f .gitmodules -e    # opens editor, update URLs for your forks
+
+Synchronize your submodules
+
+.. code-block:: console
+
+   $ git submodule sync 
+
+Add and commit the update to :file:`.gitmodules`.
+
+.. code-block:: console
+
+   $ git add .gitmodules
+   $ git commit -m "Updated submodules to use my own forks"
+
+Now, when you push to your GCHPctm fork, you should see the submodules point to your
+submodule forks.

docs/source/step-by-step/satellite-overpass.rst

@@ -29,6 +29,9 @@ NetCDF file with the following format
          latitude:units = "degrees_north" ;
    }
 
+.. important::
+   Longitudes must be between 0 and 360.
+
 To configure 1D output, you can add the following attributes to any collection in 
 :file:`HISTORY.rc`.
 
@@ -44,7 +47,9 @@ To configure 1D output, you can add the following attributes to any collection i
 
 
 .. note::  
-   1D output is only valid for instantaneous sampling.
+   1D output only works for instantaneous sampling.
+
+   The :literal:`frequency` attribute is ignored when :literal:`track_file` is used.
 
 
 Creating a satellite track file
@@ -107,7 +112,6 @@ the :file:`tropomi_overpass_c24.nc`.
 
      TROPOMI_NO2.template:       '%y4%m2%d2_%h2%n2z.nc4',
      TROPOMI_NO2.format:         'CFIO',
-     TROPOMI_NO2.frequency:      240000
      TROPOMI_NO2.duration:       240000
      TROPOMI_NO2.track_file:     tropomi_overpass_c24.nc
      TROPOMI_NO2.recycle_track:  1