Merge branch 'develop' into 663-add-inorganic-phosphorus-pools

docs/source/_toc.yaml

@@ -214,6 +214,7 @@ subtrees:
 
   - caption: Reference
     entries:
+      - file: glossary
       - file: bibliography
       - file: genindex
       - file: modindex

docs/source/conf.py

@@ -100,6 +100,7 @@
     "sphinx_rtd_theme",
     "sphinx_external_toc",
     "sphinx_design",
+    "hoverxref.extension",
 ]
 autodoc_default_flags = ["members"]
 autosummary_generate = True
@@ -245,3 +246,8 @@ class MyReferenceStyle(AuthorYearReferenceStyle):
 html_sidebars = {
     "**": ["logo-text.html", "globaltoc.html", "localtoc.html", "searchbox.html"]
 }
+
+# Configure hoverxref
+hoverxref_roles = ["term"]
+
+hoverxref_role_types = {"term": "tooltip"}

docs/source/glossary.md

@@ -0,0 +1,36 @@
+---
+jupyter:
+  jupytext:
+    cell_metadata_filter: all,-trusted
+    main_language: python
+    notebook_metadata_filter: settings,mystnb,language_info
+    text_representation:
+      extension: .md
+      format_name: markdown
+      format_version: '1.3'
+      jupytext_version: 1.16.6
+---
+
+# Glossary
+
+```{glossary}
+
+POM
+  Particulate Organic Matter. A form of organic matter that derives from the
+  decomposition and fragmentation of litter and other necromass. Generally, these
+  particulates are still in a state where the tissue they orginated from can be
+  determined. This chemical complexity makes this a form of protected carbon, however this
+  is generally only a signifcant store of protected carbon in heavily waterlogged soils.
+
+MAOM
+  Mineral Associated Organic Matter. This is organic matter which has formed a strong
+  association with soil minerals. This association impedes breakdown, making this a form
+  of protected carbon.
+
+LMWC
+  Low Molecular Weight Carbon. These are organic molecules that are simple and soluble,
+  i.e. molecules that do not require further transformation to be transportable across
+  cell membranes. Thus, the avaliablity of this type of organic matter strongly determines
+  microbial growth rates.
+
+```

docs/source/virtual_ecosystem/theory/soil/soil_theory.md

@@ -90,14 +90,14 @@ very slowly (order of years to decades) and so in most soils it is the main form
 
 Microbial biomass accounts for a small fraction of total soil carbon. However, microbes
 are key drivers of soil carbon cycling, with significant flows of carbon through the
-microbial biomass pool. Microbes assist in the formation of LMWC by excreting enzymes
-that breakdown POM. They then utilise LMWC to form biomass. Microbial waste products and
-necromass either break down into LMWC, or form mineral associations. In addition,
-microbial respiration is one of the major sources of carbon loss to the system. This
-pool turns over rapidly (order of days) and only represents a very small fraction of
-total soil carbon. However, it is very important to track because many soil processes
-are driven by microbes, and so depend either implicitly or explicitly on the size of
-this pool.
+microbial biomass pool. Microbes assist in the formation of {term}`LMWC` by excreting
+enzymes that breakdown {term}`POM`. They then utilise LMWC to form biomass. Microbial
+waste products and necromass either break down into LMWC, or form mineral associations.
+In addition, microbial respiration is one of the major sources of carbon loss to the
+system. This pool turns over rapidly (order of days) and only represents a very small
+fraction of total soil carbon. However, it is very important to track because many soil
+processes are driven by microbes, and so depend either implicitly or explicitly on the
+size of this pool.
 
 ## Nitrogen pools