Fix upper bound

Cargo.toml

@@ -22,7 +22,7 @@ rustdoc-args = [ "--html-in-header", "./src/docs-header.html" ]
 [dependencies]
 quick-xml = { version = "0.23.0-alpha3", features = ["serialize"] }
 serde = { version = "1.0", features = [ "derive" ] }
-pyo3 = { version = "0.14.1", optional = true }
+pyo3 = { version = "0.22.3", optional = true }
 itertools = "0.10"
 
 [features]

pyproject.toml

@@ -3,7 +3,7 @@ name = "rust_sbml"
 version = "0.6.1"
 description = "Python Bindings to rust_sbml"
 readme = "README.md"
-requires-python = ">=3.6"
+requires-python = ">=3.7"
 keywords = ["parser", "sbml", "science", "bioinformatics"]
 authors = [
   {email = "[email protected]"},
@@ -17,7 +17,6 @@ classifiers = [
     "License :: OSI Approved :: MIT License",
     "Operating System :: POSIX :: Linux",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.6",
     "Programming Language :: Python :: 3.7",
     "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",

src/annotation/mod.rs

@@ -5,7 +5,7 @@ use itertools::Itertools;
 use serde::{Deserialize, Serialize};
 use std::{collections::HashMap, convert::From};
 
-#[derive(Debug, Deserialize, Serialize, PartialEq, Eq, Clone)]
+#[derive(Debug, Deserialize, Serialize, PartialEq, Clone)]
 #[serde(rename_all = "camelCase")]
 pub struct Annotation {
     #[serde(rename = "$unflatten=rdf:RDF")]

src/base_types.rs

@@ -234,7 +234,7 @@ pub struct KineticLaw {
 /// use rust_sbml::Reaction;
 ///
 /// let reactions: Reaction = from_str(
-/// "<reaction id='J1' reversible='false' fbc:lowerFluxBound='-20'>
+/// "<reaction id='J1' reversible='false' fbc:lowerFluxBound='this_lower_bound' fbc:upperFluxBound='this_upper_bound'>
 ///         <listOfReactants>
 ///             <speciesReference species='X0' stoichiometry='2' constant='true'/>
 /// </listOfReactants>
@@ -258,6 +258,8 @@ pub struct KineticLaw {
 ///     .species_references
 ///     .iter()
 ///     .any(|specref| specref.species == "X0"));
+/// assert_eq!(reactions.lower_bound, Some(String::from("this_lower_bound")));
+/// assert_eq!(reactions.upper_bound, Some(String::from("this_upper_bound")));
 /// ```
 #[cfg_attr(feature = "default", pyclass)]
 #[derive(Debug, Deserialize, Serialize, PartialEq, Clone, Default)]
@@ -275,7 +277,7 @@ pub struct Reaction {
     pub kinetic_law: Option<KineticLaw>,
     #[serde(rename = "fbc:lowerFluxBound")]
     pub lower_bound: Option<String>,
-    #[serde(rename = "fbc:lowerUpperBound")]
+    #[serde(rename = "fbc:upperFluxBound")]
     pub upper_bound: Option<String>,
     pub annotation: Option<Annotation>,
 }

src/lib.rs

@@ -97,8 +97,6 @@ pub use base_types::{
 pub use unit::{Unit, UnitSId, UnitSIdRef};
 
 pub use model::{parse_document, Model, ModelRaw, ModelUnits};
-#[cfg(feature = "default")]
-pub use pyo::*;
 
 #[cfg(test)]
 mod tests {

src/model.rs

@@ -160,7 +160,7 @@ impl Model {
     /// println!("{:?}", document.get_list_of_compartments())
     /// ```
     pub fn get_list_of_compartments(&self) -> Vec<&Compartment> {
-        self.compartments.iter().map(|(_key, val)| val).collect()
+        self.compartments.values().collect()
     }
     /// Emulating the API of libSBML
     ///
@@ -175,7 +175,7 @@ impl Model {
     /// println!("{:?}", document.get_list_of_species())
     /// ```
     pub fn get_list_of_species(&self) -> Vec<&Species> {
-        self.species.iter().map(|(_key, val)| val).collect()
+        self.species.values().collect()
     }
     /// Emulating the API of libSBML
     ///
@@ -190,7 +190,7 @@ impl Model {
     /// println!("{:?}", document.get_list_of_reactions())
     /// ```
     pub fn get_list_of_reactions(&self) -> Vec<&Reaction> {
-        self.reactions.iter().map(|(_key, val)| val).collect()
+        self.reactions.values().collect()
     }
     /// Use [`ModelRaw`] to parse the SBML document
     /// and then format it into `Model`.
@@ -259,7 +259,7 @@ impl Model {
                 objs.objectives
                     .iter()
                     .flat_map(|n| {
-                        (*n).list_of_flux_objectives
+                        n.list_of_flux_objectives
                             .flux_objectives
                             .iter()
                             .map(|fr| fr.reaction.to_owned().unwrap())

src/pyo.rs

@@ -94,16 +94,13 @@ impl Model {
         }
     }
     fn getListOfCompartments(&self) -> Vec<Compartment> {
-        self.compartments
-            .iter()
-            .map(|(_, n)| n.to_owned())
-            .collect()
+        self.compartments.values().cloned().collect()
     }
     fn getListOfSpecies(&self) -> Vec<Species> {
-        self.species.iter().map(|(_, n)| n.to_owned()).collect()
+        self.species.values().cloned().collect()
     }
     fn getListOfReactions(&self) -> Vec<Reaction> {
-        self.reactions.iter().map(|(_, n)| n.to_owned()).collect()
+        self.reactions.values().cloned().collect()
     }
     fn getParameter(&self, query: String) -> Option<Parameter> {
         self.parameters.get(&query).cloned()
@@ -126,7 +123,7 @@ impl Model {
 }
 
 #[pymodule]
-fn rust_sbml(_py: Python, m: &PyModule) -> PyResult<()> {
+fn rust_sbml(_py: Python, m: &Bound<'_, PyModule>) -> PyResult<()> {
     m.add_class::<Model>()?;
     m.add_class::<Reaction>()?;
     m.add_class::<Species>()?;