diff --git a/.github/workflows/sirius.yml b/.github/workflows/sirius.yml index c7b64d03..9fa910f1 100644 --- a/.github/workflows/sirius.yml +++ b/.github/workflows/sirius.yml @@ -39,5 +39,5 @@ jobs: SIRIUS_PASSWORD: ${{secrets.SIRIUS_PASSWORD}} run: | export SIRIUS_PATH=${{vars.SIRIUS_PATH}} - cargo test --test test_sirius + cargo test diff --git a/bindings/sirius-bindings/README.md b/bindings/sirius-bindings/README.md index 36f79651..da3b44f4 100644 --- a/bindings/sirius-bindings/README.md +++ b/bindings/sirius-bindings/README.md @@ -1,5 +1,5 @@ # Sirius -[![Build status](https://github.com/earth-metabolome-initiative/sirius-bindings/actions/workflows/sirius.yml/badge.svg)](https://github.com/earth-metabolome-initiative/sirius-bindings/actions) +[![Build status](https://github.com/earth-metabolome-initiative/emi-monorepo/actions/workflows/sirius.yml/badge.svg)](https://github.com/earth-metabolome-initiative/emi-monorepo/actions) [![Crates.io](https://img.shields.io/crates/v/sirius-bindings.svg)](https://crates.io/crates/sirius-bindings) [![Documentation](https://docs.rs/sirius-bindings/badge.svg)](https://docs.rs/sirius-bindings) @@ -30,7 +30,7 @@ sirius = "0.1" ``` and this to your crate root: ```rust -use sirius::prelude::*; +use sirius_bindings::prelude::*; ``` ## Examples @@ -41,7 +41,7 @@ sirius -i tests/data/input_sirius.mgf --output tests/data/output_sirius_default The equivalent Rust code is: ```rust -use sirius::prelude::*; +use sirius_bindings::prelude::*; use std::path::Path; let sirius = SiriusBuilder::::default() .maximal_mz_default().unwrap() @@ -84,7 +84,7 @@ config --IsotopeSettings.filter=true --FormulaSearchDB=BIO --Timeout.secondsPerT The equivalent Rust code is: ```rust -use sirius::prelude::*; +use sirius_bindings::prelude::*; use std::path::Path; let sirius = SiriusBuilder::default() .maximal_mz(800.0).unwrap() @@ -161,7 +161,7 @@ This binding also provides error handling before running the Sirius CLI. The following example will throw an error because the `maximal_mz` is added twice: ```should_panic -use sirius::prelude::*; +use sirius_bindings::prelude::*; use std::path::Path; let sirius = SiriusBuilder::::default() .maximal_mz_default().unwrap() diff --git a/bindings/sirius-bindings/fuzz/fuzz_targets/random.rs b/bindings/sirius-bindings/fuzz/fuzz_targets/random.rs index f3c569cf..43a81315 100644 --- a/bindings/sirius-bindings/fuzz/fuzz_targets/random.rs +++ b/bindings/sirius-bindings/fuzz/fuzz_targets/random.rs @@ -5,7 +5,7 @@ use libfuzzer_sys::fuzz_target; use rand::rngs::SmallRng; use rand::Rng; use rand::SeedableRng; -use sirius::prelude::*; +use sirius_bindings::prelude::*; #[derive(Arbitrary, Debug)] struct FuzzCase { diff --git a/bindings/sirius-bindings/src/builder.rs b/bindings/sirius-bindings/src/builder.rs index e4ef7d0e..1c6e3430 100644 --- a/bindings/sirius-bindings/src/builder.rs +++ b/bindings/sirius-bindings/src/builder.rs @@ -22,7 +22,7 @@ impl SiriusBuilder { /// # Example /// /// ``` - /// use sirius::prelude::*; + /// use sirius_bindings::prelude::*; /// /// let sirius = SiriusBuilder::default() /// .maximal_mz(1000.0).unwrap() @@ -61,7 +61,7 @@ impl SiriusBuilder { /// * `n_cores` - The number of cores to use. /// # Example /// ``` - /// use sirius::prelude::*; + /// use sirius_bindings::prelude::*; /// let sirius = SiriusBuilder::default() /// .max_cpus(4).unwrap() /// .build(); @@ -77,7 +77,7 @@ impl SiriusBuilder { /// /// # Example /// ``` - /// use sirius::prelude::*; + /// use sirius_bindings::prelude::*; /// let sirius = SiriusBuilder::default() /// .isotope_settings_filter(true).unwrap() /// .build(); @@ -96,7 +96,7 @@ impl SiriusBuilder { /// * `formula_search_db` - The database to be used for formula search. /// # Example /// ``` - /// use sirius::prelude::*; + /// use sirius_bindings::prelude::*; /// let sirius = SiriusBuilder::default() /// .formula_search_db(DBVector::from(vec![SearchDB::Hmdb])).unwrap() /// .build(); @@ -117,7 +117,7 @@ impl SiriusBuilder { /// * `structure_search_db` - The database to be used for the structure search. /// # Example /// ``` - /// use sirius::prelude::*; + /// use sirius_bindings::prelude::*; /// let sirius = SiriusBuilder::default() /// .structure_search_db(DBVector::from(vec![SearchDB::Zincbio])).unwrap() /// .build(); @@ -136,7 +136,7 @@ impl SiriusBuilder { /// * `timeout_seconds_per_tree` - The timeout seconds for each tree. /// # Example /// ``` - /// use sirius::prelude::*; + /// use sirius_bindings::prelude::*; /// let sirius = SiriusBuilder::default() /// .timeout_seconds_per_tree(100).unwrap() /// .build(); @@ -515,7 +515,7 @@ impl SiriusBuilder { /// * `zodiac_library_scoring_min_cosine` - The minimal cosine value. /// # Example /// ``` - /// use sirius::prelude::*; + /// use sirius_bindings::prelude::*; /// let sirius = SiriusBuilder::default() /// .zodiac_library_scoring_min_cosine(0.5).unwrap() /// .build(); @@ -524,7 +524,7 @@ impl SiriusBuilder { /// If the value is not in the range 0 and 1. /// # Example /// ``` - /// use sirius::prelude::*; + /// use sirius_bindings::prelude::*; /// assert!(SiriusBuilder::default().zodiac_library_scoring_min_cosine(1.1).is_err()); /// assert!(SiriusBuilder::default().zodiac_library_scoring_min_cosine(-0.1).is_err()); /// ``` @@ -1070,7 +1070,7 @@ impl SiriusBuilder { /// Build the Sirius instance from the configuration. /// # Example /// ``` - /// use sirius::prelude::*; + /// use sirius_bindings::prelude::*; /// let sirius = SiriusBuilder::::default().build(); /// ``` pub fn build(self) -> Sirius { @@ -1084,7 +1084,7 @@ impl SiriusBuilder { /// # Example /// /// ``` - /// use sirius::prelude::*; + /// use sirius_bindings::prelude::*; /// /// let sirius = SiriusBuilder::default() /// .maximal_mz_default().unwrap() diff --git a/bindings/sirius-bindings/src/sirius_types/mass_deviation.rs b/bindings/sirius-bindings/src/sirius_types/mass_deviation.rs index 0e1ae447..84302a67 100644 --- a/bindings/sirius-bindings/src/sirius_types/mass_deviation.rs +++ b/bindings/sirius-bindings/src/sirius_types/mass_deviation.rs @@ -17,13 +17,13 @@ impl MassDeviation { /// If the value is negative /// # Example /// ``` - /// use sirius::prelude::*; + /// use sirius_bindings::prelude::*; /// let ppm = MassDeviation::ppm(10.0); /// ``` /// # Panics /// If the value is negative /// ```should_panic - /// use sirius::prelude::*; + /// use sirius_bindings::prelude::*; /// let ppm = MassDeviation::ppm(-10.0); /// ``` pub fn ppm(value: f32) -> Self { @@ -39,13 +39,13 @@ impl MassDeviation { /// If the value is negative /// # Example /// ``` - /// use sirius::prelude::*; + /// use sirius_bindings::prelude::*; /// let da = MassDeviation::da(0.1); /// ``` /// # Panics /// If the value is negative /// ```should_panic - /// use sirius::prelude::*; + /// use sirius_bindings::prelude::*; /// let x = MassDeviation::da(-0.1); /// ``` pub fn da(value: f32) -> Self { @@ -61,14 +61,14 @@ impl MassDeviation { /// If the value is negative /// # Example /// ``` - /// use sirius::prelude::*; + /// use sirius_bindings::prelude::*; /// let ppm = MassDeviation::ppm(10.0); /// assert_eq!(ppm.must_be_positive().unwrap(), MassDeviation::Ppm(10.0)); /// ``` /// # Errors /// If the value is negative /// ``` - /// use sirius::prelude::*; + /// use sirius_bindings::prelude::*; /// let ppm = MassDeviation::Ppm(-10.0); /// assert!(ppm.must_be_positive().is_err()); /// ```