Start cleaning up documentation.

Cargo.toml

@@ -18,6 +18,7 @@ strum_macros = "0.26"
 regex = "1.10.3"
 biodivine-xml-doc = "0.3.0"
 sbml-macros = { path = "sbml-macros" }
+embed-doc-image = "0.1.4"
 
 [dev-dependencies]
 sbml-test-suite = { path = "sbml-test-suite" }

README.md

@@ -90,7 +90,7 @@ fn main() {
    let compartment_id = compartments.get(0).id().get();
    let s = Species::new(model.document(), &species_id, &compartment_id);
    let species_name = "MySpecies".to_string();
-   s.name().set(Some(&species_name));
+   s.name().set_some(&species_name);
 
    // Then, add it to the current list of species.
    species.push(s);

src/constants/element.rs

@@ -120,13 +120,13 @@ pub const ALLOWED_CHILDREN: Map<&str, &[&str]> = phf_map! {
     "listOfUnitDefinitions" => extended_sbase_children!("unitDefinition"),
     "unitDefinition" => extended_sbase_children!("listOfUnits"),
     "listOfUnits" => extended_sbase_children!("unit"),
-    "unit" => extended_sbase_children!(),
+    "unit" => ALLOWED_SBASE_CHILDREN,
     "listOfCompartments" => extended_sbase_children!("compartment"),
-    "compartment" => extended_sbase_children!(),
+    "compartment" => ALLOWED_SBASE_CHILDREN,
     "listOfSpecies" => extended_sbase_children!("species"),
-    "species" => extended_sbase_children!(),
+    "species" => ALLOWED_SBASE_CHILDREN,
     "listOfParameters" => extended_sbase_children!("parameter"),
-    "parameter" => extended_sbase_children!(),
+    "parameter" => ALLOWED_SBASE_CHILDREN,
     "listOfInitialAssignments" => extended_sbase_children!("initialAssignment"),
     "initialAssignment" => extended_sbase_children!("math"),
     "listOfRules" => extended_sbase_children!("algebraicRule", "assignmentRule", "rateRule"),
@@ -139,12 +139,12 @@ pub const ALLOWED_CHILDREN: Map<&str, &[&str]> = phf_map! {
     "reaction" => extended_sbase_children!("listOfReactants", "listOfProducts", "listOfModifiers", "kineticLaw"),
     "listOfReactants" => extended_sbase_children!("speciesReference"),
     "listOfProducts" => extended_sbase_children!("speciesReference"),
-    "speciesReference" => extended_sbase_children!(),
+    "speciesReference" => ALLOWED_SBASE_CHILDREN,
     "listOfModifiers" => extended_sbase_children!("modifierSpeciesReference"),
-    "modifierSpeciesReference" => extended_sbase_children!(),
+    "modifierSpeciesReference" => ALLOWED_SBASE_CHILDREN,
     "kineticLaw" => extended_sbase_children!("math", "listOfLocalParameters"),
     "listOfLocalParameters" => extended_sbase_children!("localParameter"),
-    "localParameter" => extended_sbase_children!(),
+    "localParameter" => ALLOWED_SBASE_CHILDREN,
     "listOfEvents" => extended_sbase_children!("event"),
     "event" => extended_sbase_children!("trigger", "priority", "delay", "listOfEventAssignments"),
     "trigger" => extended_sbase_children!("math"),
@@ -299,30 +299,37 @@ pub const MATHML_BINARY_OPERATORS: &[&str] = &[
     "outerproduct",
 ];
 
-// source: https://www.w3.org/TR/MathML2/chapter4.html#contm.funopqual
-pub const MATHML_NARY_OPERATORS: &[&str] = &[
-    "plus",
-    "times",
-    "max",
-    "min",
-    "gcd",
-    "lcm",
-    "mean",
-    "sdev",
-    "variance",
-    "median",
-    "mode",
-    "union",
-    "intersect",
-    "cartesianproduct",
-    "selector",
-    "and",
-    "or",
-    "xor",
-    "eq",
-    "neq",
-    "leq",
-    "lt",
-    "geq",
-    "gt",
-];
+/*
+
+   This is currently unused, but will become relevant once we start implementing
+   the MathML abstraction.
+
+   // source: https://www.w3.org/TR/MathML2/chapter4.html#contm.funopqual
+   pub const MATHML_NARY_OPERATORS: &[&str] = &[
+       "plus",
+       "times",
+       "max",
+       "min",
+       "gcd",
+       "lcm",
+       "mean",
+       "sdev",
+       "variance",
+       "median",
+       "mode",
+       "union",
+       "intersect",
+       "cartesianproduct",
+       "selector",
+       "and",
+       "or",
+       "xor",
+       "eq",
+       "neq",
+       "leq",
+       "lt",
+       "geq",
+       "gt",
+   ];
+
+*/

src/constants/mod.rs

@@ -1,3 +1,3 @@
-pub mod document;
-pub mod element;
-pub mod namespaces;
+pub(crate) mod document;
+pub(crate) mod element;
+pub(crate) mod namespaces;

src/constants/namespaces.rs

@@ -12,16 +12,19 @@ pub const URL_HTML: &str = "http://www.w3.org/1999/xhtml";
 pub const URL_MATHML: &str = "http://www.w3.org/1998/Math/MathML";
 
 /// The URL of the "default" empty namespace.
+#[cfg(test)]
 pub const URL_EMPTY: &str = "";
 
 /// The "core" SBML namespace. Default prefix for this namespace is empty.
 pub const NS_SBML_CORE: Namespace = ("", URL_SBML_CORE);
 
 /// The "core" HTML namespace. Default prefix for this namespace is empty.
+#[cfg(test)]
 pub const NS_HTML: Namespace = ("", URL_HTML);
 
 /// The MathML namespace. Default prefix for this namespace is empty.
 pub const NS_MATHML: (&str, &str) = ("", URL_MATHML);
 
 /// The "default" empty namespace. Default prefix for this namespace is empty.
+#[cfg(test)]
 pub const NS_EMPTY: (&str, &str) = ("", URL_EMPTY);