feat: add generation function for fast[a|q] format

.copier-answers.yml

@@ -13,5 +13,5 @@ forge_namespace: natir
 forge_repo_name: biotest
 msrv: '1.75'
 proc_macro: true
-project_description: Many function to generate test data for bioinformatics data
+project_description: Generate random test data for bioinformatics
 project_name: biotest

.github/workflows/test.yml

@@ -24,6 +24,7 @@ jobs:
         uses: actions-rs/cargo@v1
         with:
           command: check
+          args: --all-features
 
   test:
     runs-on: ${{ matrix.os }}
@@ -56,7 +57,7 @@ jobs:
         uses: actions-rs/cargo@v1
         with:
           command: test
-          args: --no-fail-fast
+          args: --no-fail-fast --all-features
 
   coverage:
     runs-on: ubuntu-latest
@@ -79,6 +80,6 @@ jobs:
         run: cargo tarpaulin --all-features --timeout 600 --out Xml -- --test-threads 1
 
       - name: Upload coverage to codecov
-        uses: codecov/codecov-action@v1.0.3
+        uses: codecov/codecov-action@v4
         with:
           token: ${{ secrets.CODECOV_TOKEN }}

Cargo.toml

@@ -3,7 +3,7 @@ name = "biotest"
 version = "0.1.0"
 authors = ["Pierre Marijon <[email protected]>"]
 edition = "2021"
-description = "Many function to generate test data for bioinformatics data"
+description = "Generate random test data for bioinformatics"
 rust-version = "1.75"
 
 homepage = "https://github.com/natir/biotest"
@@ -14,13 +14,17 @@ readme = "Readme.md"
 license-file = "LICENSE"
 
 
-[dependencies]
+[features]
+fasta  = []
+fastq  = []
+derive = ["dep:biotest_derive"]
 
+[dependencies]
+rand           = { version = "0.8" }
 
 # Error management
 thiserror      = { version = "1" }
 
-
 # Logging and error management
 log            = { version = "0.4" }
 
@@ -30,12 +34,15 @@ biotest_derive = { path = "biotest_derive", optional = true }
 
 [dev-dependencies]
 criterion      = { version = "0.5" }
+tempfile       = { version = "3" }
 
 # CLI management
 clap           = { version = "4", features = ["derive"] }
 
 # Logging management
 stderrlog      = { version = "0.5" }
+
+
 [profile.release]
 lto = 'thin'
 opt-level = 3
@@ -46,4 +53,4 @@ incremental = false
 
 [profile.profiling]
 inherits = "release"
-debug = true
+debug = true

Readme.md

@@ -1,22 +1,21 @@
 <h1 style="text-align: center;">biotest</h1>
 
-[![License](https://img.shields.io/badge/license-MIT-green)](https:///natir/biotest/blob/master/LICENSE)
+[![License](https://img.shields.io/badge/license-MIT-green)](https://github.com/natir/biotest/blob/master/LICENSE)
+![Test](https://github.com/natir/natir/workflows/Test/badge.svg)
+![Lints](https://github.com/natir/natir/workflows/Lints/badge.svg)
+![MSRV](https://github.com/natir/natir/workflows/MSRV/badge.svg)
+[![CodeCov](https://codecov.io/gh/natir/natir/branch/master/graph/badge.svg)](https://codecov.io/gh/natir/natir)
+[![Documentation](https://github.com/natir/natir/workflows/Documentation/badge.svg)](https://natir.github.io/natir/natir)
 
+Generate random test data for bioinformatics
 
-Many function to generate test data for bioinformatics data
-
-## Installation
-
-### From source
+## Usage
 
-```bash
-git clone https:///natir/biotest.git
-cd biotest
-cargo install --path .
+In your Cargo.toml add
+```toml
+biotest = { url = "https:///natir/biotest.git" }
 ```
 
-## Usage
-
 ## Minimum supported Rust version
 
 Currently the minimum supported Rust version is 1.75.

biotest_derive/src/lib.rs

@@ -1,4 +1,4 @@
-//! Many function to generate test data for bioinformatics data procedural macro crate
+//! Generate random test data for bioinformatics"
 
 #![warn(missing_docs)]
 

src/constants.rs

@@ -0,0 +1,70 @@
+//! Declarations of some constants value
+
+/* std use */
+
+/* crates use */
+
+/* projet use */
+
+const fn gen_array<const N: usize, const B: usize>() -> [u8; N] {
+    let mut array = [0; N];
+
+    let mut i = 0;
+    while i < N {
+        array[i] = (B + i) as u8;
+        i += 1;
+    }
+
+    array
+}
+
+/// Fixed random seed
+pub const SEED: [u8; 32] = [42; 32];
+
+/// Nucleotides with any case
+pub const NUCLEOTIDES: [u8; 8] = *b"ACTGactg";
+
+/// Nucleotides lower
+pub const NUCLEOTIDES_LOWER: [u8; 4] = *b"actg";
+
+/// Nucleotides upper
+pub const NUCLEOTIDES_UPPER: [u8; 4] = *b"ACTG";
+
+/// All possible phred 33 value
+pub const PHRED33: [u8; 40] = gen_array::<40, 33>();
+
+/// All possible phred 64 value
+pub const PHRED64: [u8; 40] = gen_array::<40, 64>();
+
+/// Alphabets with [ \ ] ^ _ `
+pub const ALPHABETS: [u8; 58] = gen_array::<58, 65>();
+
+#[cfg(test)]
+mod tests {
+    /* project use */
+    use super::*;
+
+    #[test]
+    fn phred33() {
+        assert_eq!(
+            gen_array::<40, 33>().to_vec(),
+            b"!\"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGH".to_vec()
+        );
+    }
+
+    #[test]
+    fn phred64() {
+        assert_eq!(
+            gen_array::<40, 64>().to_vec(),
+            b"@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\\]^_`abcdefg".to_vec()
+        );
+    }
+
+    #[test]
+    fn alphapets() {
+        assert_eq!(
+            gen_array::<58, 65>().to_vec(),
+            b"ABCDEFGHIJKLMNOPQRSTUVWXYZ[\\]^_`abcdefghijklmnopqrstuvwxyz".to_vec()
+        );
+    }
+}

src/error.rs

@@ -6,7 +6,10 @@ use thiserror;
 /// Enum to manage error
 #[derive(std::fmt::Debug, thiserror::Error)]
 pub enum Error {
-    }
+    /// std::io::Error error
+    #[error(transparent)]
+    StdIo(#[from] std::io::Error),
+}
 
 /// Alias of result
 pub type Result<T> = core::result::Result<T, Error>;

src/format.rs

@@ -0,0 +1,14 @@
+//! Format data generation
+
+/* std use */
+
+/* crates use */
+
+/* module declaration */
+#[cfg(feature = "fasta")]
+pub mod fasta;
+
+#[cfg(feature = "fastq")]
+pub mod fastq;
+
+/* projet use */