Update README with downloading HPO data

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "hpo"
-version = "0.8.0"
+version = "0.8.1"
 edition = "2021"
 authors = ["Jonas Marcello <jonas.marcello@esbme.com>"]
 description = "Human Phenotype Ontology Similarity"

README.md

@@ -43,6 +43,27 @@ The most relevant modules are:
 ## Examples
 Some (more or less random) examples are included in the [`examples` folder](https://github.com/anergictcell/hpo/tree/main/examples).
 
+HPO data must be downloaded first from  [Jax HPO](https://hpo.jax.org/) itself. You need the following files:
+- [phenotype.hpoa](https://hpo.jax.org/app/data/annotations) available as "Download HPO annotations" (Required to connect [`OmimDisease`]s to [`HpoTerm`]s)
+- [phenotype_to_genes.txt](https://hpo.jax.org/app/data/annotations) available as "Phenotype to genes" (Required to connect [`Gene`]s to [`HpoTerm`]s)
+- [hp.obo](https://hpo.jax.org/app/data/ontology) (Required for [`HpoTerm`]s and their connection to each other)
+
+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();
+```
+
+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();
+```
+
+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.
+
 ### Ontology
 ```rust
 use hpo::{Ontology, HpoTermId};

src/annotations/omim_disease.rs

@@ -150,7 +150,7 @@ impl OmimDisease {
         res.append(&mut usize_to_u32(name_length).to_be_bytes().to_vec());
 
         // OMIM Disease name (n bytes)
-        for c in name.iter() {
+        for c in name {
             res.push(*c);
         }
 

src/parser/binary/term.rs

@@ -33,7 +33,7 @@ pub(crate) fn from_bytes_v1(bytes: Bytes) -> Result<HpoTermInternal, HpoError> {
     }
 
     let Ok(name) = String::from_utf8(bytes[9..total_len as usize].to_vec()) else {
-        return Err(HpoError::ParseBinaryError)
+        return Err(HpoError::ParseBinaryError);
     };
     Ok(HpoTermInternal::new(name, id.into()))
 }
@@ -67,7 +67,7 @@ pub(crate) fn from_bytes_v2(bytes: Bytes) -> Result<HpoTermInternal, HpoError> {
     }
 
     let Ok(name) = String::from_utf8(bytes[9..9 + name_len].to_vec()) else {
-        return Err(HpoError::ParseBinaryError)
+        return Err(HpoError::ParseBinaryError);
     };
     let mut term = HpoTermInternal::new(name, id.into());
 

src/parser/hp_obo.rs

@@ -28,7 +28,7 @@ pub(super) fn read_obo_file<P: AsRef<Path>>(filename: P, ontology: &mut Ontology
     let Ok(file_content) = fs::read_to_string(&filename) else {
         return Err(HpoError::CannotOpenFile(
             filename.as_ref().display().to_string(),
-        ))
+        ));
     };
 
     for term in file_content.split("\n\n") {

src/set.rs

@@ -115,6 +115,8 @@ impl<'a> HpoSet<'a> {
     /// let children = set.child_nodes();
     /// assert_eq!(children.len(), 4);
     /// ```
+    /// # Panics
+    /// TODO
     pub fn child_nodes(&self) -> Self {
         let group = self
             .group

src/term/hpoterm.rs

@@ -920,6 +920,8 @@ impl<'a> HpoTerm<'a> {
     ///     ]
     /// );
     /// ```
+    /// # Panics
+    /// TODO    
     pub fn path_to_term(&self, other: &HpoTerm) -> Option<Vec<HpoTermId>> {
         if other.parent_of(self) {
             return self.path_to_ancestor(other);