Fixed the doctests import name

earth-metabolome-initiative · Feb 13, 2024 · efad997 · efad997
1 parent 9894f6f
commit efad997
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diff --git 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
@@ -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::<Version5>::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::<Version5>::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
@@ -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
@@ -22,7 +22,7 @@ impl SiriusBuilder<Version5> {
     /// # Example
     ///
     /// ```
-    /// use sirius::prelude::*;
+    /// use sirius_bindings::prelude::*;
     ///
     /// let sirius = SiriusBuilder::default()
     ///    .maximal_mz(1000.0).unwrap()
@@ -61,7 +61,7 @@ impl SiriusBuilder<Version5> {
     /// * `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<Version5> {
     ///
     /// # Example
     /// ```
-    /// use sirius::prelude::*;
+    /// use sirius_bindings::prelude::*;
     /// let sirius = SiriusBuilder::default()
     ///   .isotope_settings_filter(true).unwrap()
     ///   .build();
@@ -96,7 +96,7 @@ impl SiriusBuilder<Version5> {
     /// * `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<Version5> {
     /// * `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<Version5> {
     /// * `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<Version5> {
     /// * `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<Version5> {
     /// 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<V: Version> SiriusBuilder<V> {
     /// Build the Sirius instance from the configuration.
     /// # Example
     /// ```
-    /// use sirius::prelude::*;
+    /// use sirius_bindings::prelude::*;
     /// let sirius = SiriusBuilder::<Version5>::default().build();
     /// ```
     pub fn build(self) -> Sirius<V> {
@@ -1084,7 +1084,7 @@ impl SiriusBuilder<Version5> {
     /// # 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
@@ -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());
     /// ```