Version bump & doc_cfg removed

rustyms-imgt-generate/src/main.rs

@@ -1,3 +1,5 @@
+#![allow(clippy::redundant_pub_crate)]
+
 use std::{
     collections::HashMap,
     fmt::Display,
@@ -14,7 +16,11 @@ mod shared;
 use crate::shared::*;
 
 use itertools::Itertools;
-use rustyms::*;
+use rustyms::{
+    align::Alignment,
+    system::{dalton, Mass},
+    *,
+};
 
 fn main() {
     let file = File::open("../rustyms/databases/imgt.dat")
@@ -176,10 +182,9 @@ pub fn all_germlines() -> impl std::iter::Iterator<Item = &'static Germlines> {{
     writeln!(
         output,
 "/// Get all germlines in one parallel iterator, see the main documentation for more information about the available germlines
-use doc_cfg::doc_cfg;
 #[cfg(feature = \"rayon\")]
 use rayon::prelude::*;
-#[doc_cfg(feature = \"rayon\")]
+#[cfg(feature = \"rayon\")]
 pub fn par_germlines() -> impl rayon::prelude::ParallelIterator<Item = &'static Germlines> {{"
     )
     .unwrap();
@@ -1122,12 +1127,12 @@ impl std::fmt::Display for TemporaryGermline {
                     )?;
                 }
                 if let Some(first_allele) = first_allele {
-                    let alignment = rustyms_align::align::<1>(
+                    let alignment = rustyms::align::align::<1>(
                         first_allele,
                         &seq.sequence,
-                        rustyms_align::BLOSUM90,
+                        rustyms::align::matrix::BLOSUM90,
                         crate::Tolerance::new_absolute(Mass::new::<dalton>(0.01)),
-                        rustyms_align::AlignType::GLOBAL,
+                        rustyms::align::AlignType::GLOBAL,
                     )
                     .stats();
                     writeln!(
@@ -1138,12 +1143,12 @@ impl std::fmt::Display for TemporaryGermline {
                     )?;
                 }
                 if let Some(reference) = reference {
-                    let alignment = rustyms_align::align::<1>(
+                    let alignment = rustyms::align::align::<1>(
                         reference,
                         &seq.sequence,
-                        rustyms_align::BLOSUM90,
+                        rustyms::align::matrix::BLOSUM90,
                         crate::Tolerance::new_absolute(Mass::new::<dalton>(0.01)),
-                        rustyms_align::AlignType::GLOBAL,
+                        rustyms::align::AlignType::GLOBAL,
                     )
                     .stats();
                     writeln!(

rustyms/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "rustyms"
-version = "0.8.0"
+version = "0.8.1"
 edition = "2021"
 license = "MIT OR Apache-2.0"
 authors = ["Douwe Schulte <[email protected]>"]
@@ -20,7 +20,6 @@ rust-version = "1.70.0"
 
 [dependencies]
 bincode = "1.3"
-doc-cfg = { version = "0.1" }
 flate2 = "1.0"
 itertools = "0.12"
 ordered-float = { version = "4.2", features = ["serde"] }
@@ -48,10 +47,6 @@ default = ["imgt", "align", "identification", "rayon"]
 imgt = []
 align = []
 identification = []
-unstable-doc-cfg = []
-
-[package.metadata.docs.rs]
-features = ["unstable-doc-cfg"]
 
 [[bench]]
 name = "iai"

rustyms/src/align/consecutive.rs

@@ -4,13 +4,12 @@ use crate::itertools_extension::ItertoolsExt;
 use crate::*;
 use std::collections::HashSet;
 
-use doc_cfg::doc_cfg;
 use itertools::Itertools;
 
 /// Only available with if features `align` and `imgt` are turned on.
 /// Align one sequence to multiple consecutive genes. Each gene can be controlled to be global to the left or free to allow unmatched residues between it and the previous gene.
 /// If the sequence is too short to cover all genes only the genes that could be matched are returned.
-#[doc_cfg(feature = "imgt")]
+#[cfg(feature = "imgt")]
 pub fn consecutive_align<const STEPS: u16>(
     sequence: &LinearPeptide,
     genes: &[(GeneType, AlignType)],
@@ -64,7 +63,7 @@ pub fn consecutive_align<const STEPS: u16>(
 /// Only available with if features `align`, `rayon`, and `imgt` are turned on.
 /// Align one sequence to multiple consecutive genes. Each gene can be controlled to be global to the left or free to allow unmatched residues between it and the previous gene.
 /// If the sequence is too short to cover all genes only the genes that could be matched are returned.
-#[doc_cfg(all(feature = "rayon", feature = "imgt"))]
+#[cfg(all(feature = "rayon", feature = "imgt"))]
 pub fn par_consecutive_align<const STEPS: u16>(
     sequence: &LinearPeptide,
     genes: &[(GeneType, AlignType)],

rustyms/src/imgt/germlines/mod.rs

@@ -77,11 +77,10 @@ pub fn all_germlines() -> impl std::iter::Iterator<Item = &'static Germlines> {
         .chain(std::iter::once(lock_SusScrofa()))
         .chain(std::iter::once(lock_VicugnaPacos()))
 }
-use doc_cfg::doc_cfg;
-/// Get all germlines in one parallel iterator, see the main documentation for more information about the available germlines
+/// Get all germlines in one parallel iterator, see the main documentation for more information about the available germlines, only available with feature "rayon" (on by default)
 #[cfg(feature = "rayon")]
 use rayon::prelude::*;
-#[doc_cfg(feature = "rayon")]
+#[cfg(feature = "rayon")]
 pub fn par_germlines() -> impl rayon::prelude::ParallelIterator<Item = &'static Germlines> {
     rayon::iter::once(lock_BosTaurus())
         .chain(rayon::iter::once(lock_CamelusDromedarius()))

rustyms/src/imgt/mod.rs

@@ -23,9 +23,8 @@ mod germlines;
 mod select;
 mod shared;
 
-use doc_cfg::doc_cfg;
 pub use fancy::*;
-#[doc_cfg(feature = "rayon")]
+#[cfg(feature = "rayon")]
 use germlines::par_germlines;
 use germlines::{all_germlines, germlines};
 

rustyms/src/imgt/select.rs

@@ -1,4 +1,3 @@
-use doc_cfg::doc_cfg;
 #[cfg(feature = "rayon")]
 use rayon::prelude::*;
 use std::collections::HashSet;
@@ -86,7 +85,7 @@ impl Selection {
             .map(Into::into)
     }
 
-    #[doc_cfg(feature = "rayon")]
+    #[cfg(feature = "rayon")]
     /// Get the selected alleles in parallel fashion, only available if you enable the feature "rayon" (on by default)
     pub fn par_germlines(self) -> impl ParallelIterator<Item = Allele<'static>> {
         super::par_germlines()