From 09813a52662b0ff0e8e4b83c09cc99da860d3ca1 Mon Sep 17 00:00:00 2001
From: Nick Wogan <nicholaswogan@gmail.com>
Date: Thu, 26 Oct 2023 21:33:18 -0700
Subject: [PATCH] version. documentation

---
 CMakeLists.txt                             |  2 +-
 clima/cython/Radtran.pyx                   |  7 +++++++
 src/radtran/clima_radtran.f90              |  3 +++
 templates/runaway_greenhouse/settings.yaml | 12 ++++++------
 4 files changed, 17 insertions(+), 7 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 133f102..ffe5520 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -1,6 +1,6 @@
 cmake_minimum_required(VERSION "3.14")
 
-project(Clima LANGUAGES Fortran C VERSION "0.3.10")
+project(Clima LANGUAGES Fortran C VERSION "0.3.11")
 
 set(CMAKE_Fortran_MODULE_DIRECTORY "${CMAKE_BINARY_DIR}/modules")
 
diff --git a/clima/cython/Radtran.pyx b/clima/cython/Radtran.pyx
index 639e2fb..99482d6 100644
--- a/clima/cython/Radtran.pyx
+++ b/clima/cython/Radtran.pyx
@@ -27,6 +27,13 @@ cdef class Radtran:
     return T_skin
 
   def opacities2yaml(self):
+    """Returns a yaml string representing all opacities in the model.
+
+    Returns 
+    -------
+    str
+        string representing all opacities.
+    """
     cdef int out_len
     cdef void *out_cp
     rad_pxd.radtran_opacities2yaml_wrapper_1(&self._ptr, &out_len, &out_cp)
diff --git a/src/radtran/clima_radtran.f90 b/src/radtran/clima_radtran.f90
index 62405b3..083d125 100644
--- a/src/radtran/clima_radtran.f90
+++ b/src/radtran/clima_radtran.f90
@@ -419,6 +419,7 @@ subroutine Radtran_TOA_fluxes(self, T_surface, T, P, densities, dz, pdensities,
 
   end subroutine
 
+  !> The skin temperature
   function Radtran_skin_temperature(self, bond_albedo) result(T_skin)
     use clima_eqns, only: skin_temperature
     class(Radtran), target, intent(inout) :: self
@@ -436,6 +437,7 @@ function Radtran_skin_temperature(self, bond_albedo) result(T_skin)
     T_skin = skin_temperature(stellar_radiation, bond_albedo)
   end function
 
+  !> The equilibrium temperature
   function Radtran_equilibrium_temperature(self, bond_albedo) result(T_eq)
     use clima_eqns, only: equilibrium_temperature
     class(Radtran), target, intent(inout) :: self
@@ -453,6 +455,7 @@ function Radtran_equilibrium_temperature(self, bond_albedo) result(T_eq)
     T_eq = equilibrium_temperature(stellar_radiation, bond_albedo)
   end function
 
+  !> Returns a yaml string representing all opacities in the model.
   function Radtran_opacities2yaml(self) result(out)
     class(Radtran), target, intent(inout) :: self
     character(:), allocatable :: out
diff --git a/templates/runaway_greenhouse/settings.yaml b/templates/runaway_greenhouse/settings.yaml
index c2b6082..4876d9b 100644
--- a/templates/runaway_greenhouse/settings.yaml
+++ b/templates/runaway_greenhouse/settings.yaml
@@ -33,20 +33,20 @@ optical-properties:
     # Here you specify opacites. You can see avaliable opacities by looking in
     # `clima/data/` folder. `CIA`, `rayleigh`, `photolysis-xs` and `water-continuum`
     # are optional. If you omit these keys then these opacities will not be included.
-    # `k-distributions` is a required key for now.
+    # `k-distributions` is the only required key. For most keys you can optionally 
+    # do `k-distributions: true`, which will activate all possible opacities in that
+    # category.
     opacities:
-     # k-distributions
+      # k-distributions
       k-distributions: [H2O, CO2]
 
       # CIA opacities
       CIA: [CO2-CO2, N2-N2]
 
-      # Rayleigh scattering. You can optionally do
-      # rayleigh: true
-      # which activates all possible rayleigh species
+      # Rayleigh scattering.
       rayleigh: [H2O, CO2, N2]
 
-      # Potolysis cross sections. Specify true/false or a list of species
+      # Potolysis cross sections.
       photolysis-xs: false
 
       # MT_CKD H2O continuum.