Merge pull request #65 from anergictcell/refactor/remove-aquamarine

Add `Builder` struct and refactor documentation

Cargo.toml

@@ -14,7 +14,6 @@ categories = ["science", "data-structures", "parser-implementations"]
 
 [dependencies]
 thiserror = "1.0"
-aquamarine = "0" # used in Docs
 tracing = "0.1"
 smallvec = "1"
 

README.md

@@ -51,16 +51,20 @@ HPO data must be downloaded first from  [Jax HPO](https://hpo.jax.org/) itself.
 
 1. Data can be loaded directly from the code with  [`Ontology::from_standard`]:
 ```no_run
-    use hpo::Ontology;
-    let ontology = Ontology::from_standard("/path/to/master-data/").unwrap();
+use hpo::Ontology;
+let ontology = Ontology::from_standard("/path/to/master-data/").unwrap();
+```
+
+2. Or it can be converted to a localy binary by copy  `examples/obo_to_bin.rs` into your project, then run 
+```sh
+cargo run --example --release obo_to_bin <PATH TO FOLDER WITH JAX DATA> <OUTPUT FILENAME>`
 ```
 
-2. Or it can be converted to a localy binary by copy  `examples/obo_to_bin.rs` into your project, then run .
-`cargo run --example --release obo_to_bin <PATH TO FOLDER WITH JAX DATA> <OUTPUT FILENAME>`
 Finally, load the data using [`Ontology::from_binary`]:
+
 ```no_run
-    use hpo::Ontology;
-    let ontology = Ontology::from_binary("your-hpo-binary.hpo").unwrap();
+use hpo::Ontology;
+let ontology = Ontology::from_binary("your-hpo-binary.hpo").unwrap();
 ```
 
 3. Another possibility is to use the snapshot from the [Github repository](https://github.com/anergictcell/hpo) of this crate which contains a binary build of the ontology <https://github.com/anergictcell/hpo/blob/main/tests/ontology.hpo>. IT will not always be up to date, so please double-check yourself.
@@ -164,7 +168,7 @@ fn example() {
 ```
 
 ### Enrichment
-Identify which genes (or diseases) are enriched in a set of HpoTerms, e.g. in
+Identify which genes (or diseases) are enriched in a set of `HpoTerm`s, e.g. in
 the clinical information of a patient or patient cohort
 
 ```rust

clippy.toml

@@ -0,0 +1 @@
+doc-valid-idents = ["MacBook", ".."]

src/annotations.rs

@@ -30,7 +30,17 @@ pub use orpha_disease::{OrphaDisease, OrphaDiseaseId, OrphaDiseaseIterator, Orph
 /// The ID must be unique only within the annotation type, i.e. a gene and a disease
 /// can have the same ID.
 pub trait AnnotationId:
-    Clone + Copy + Debug + Hash + PartialEq + PartialOrd + Eq + Ord + Display + From<u32>
+    Clone
+    + Copy
+    + Debug
+    + Hash
+    + PartialEq
+    + PartialOrd
+    + Eq
+    + Ord
+    + Display
+    + From<u32>
+    + for<'a> TryFrom<&'a str>
 {
     /// Return the integer representation of the annotation ID
     fn as_u32(&self) -> u32;

src/annotations/gene.rs

@@ -77,7 +77,7 @@ impl Gene {
     /// Initializes a new Gene
     ///
     /// This method should rarely, if ever, be used directly. The
-    /// preferred way to create new genes is through [`Ontology::add_gene`]
+    /// preferred way to create new genes is through [`Builder::annotate_gene`](`crate::builder::Builder::annotate_gene`)
     /// to ensure that each gene exists only once.
     pub fn new(id: GeneId, name: &str) -> Gene {
         Gene {
@@ -90,7 +90,7 @@ impl Gene {
     /// Initializes a new Gene from `str` values
     ///
     /// This method should rarely, if ever, be used directly. The
-    /// preferred way to create new genes is through [`Ontology::add_gene`]
+    /// preferred way to create new genes is through [`Builder::annotate_gene`](`crate::builder::Builder::annotate_gene`)
     /// to ensure that each gene exists only once.
     ///
     /// # Errors

src/annotations/omim_disease.rs

@@ -72,7 +72,7 @@ impl Disease for OmimDisease {
     /// Initializes a new OMIM disease
     ///
     /// This method should rarely, if ever, be used directly. The
-    /// preferred way to create new genes is through [`crate::Ontology::add_omim_disease`]
+    /// preferred way to create new genes is through [`Builder::annotate_omim_disease`](`crate::builder::Builder::annotate_omim_disease`)
     /// to ensure that each disease exists only once.
     fn new(id: Self::AnnoID, name: &str) -> OmimDisease {
         Self {

src/annotations/orpha_disease.rs

@@ -72,7 +72,7 @@ impl Disease for OrphaDisease {
     /// Initializes a new Orpha disease
     ///
     /// This method should rarely, if ever, be used directly. The
-    /// preferred way to create new genes is through [`crate::Ontology::add_orpha_disease`]
+    /// preferred way to create new genes is through [`Builder::annotate_orpha_disease`](`crate::builder::Builder::annotate_orpha_disease`)
     /// to ensure that each disease exists only once.
     fn new(id: Self::AnnoID, name: &str) -> OrphaDisease {
         Self {

src/lib.rs

@@ -18,6 +18,7 @@ pub mod stats;
 pub mod term;
 pub mod utils;
 
+pub use ontology::builder;
 pub use ontology::comparison;
 pub use ontology::Ontology;
 pub use set::HpoSet;