Update dependencies (and rename of custom_error to context_error)

douweschulte · douweschulte · commit b1a6d91fd802 · 2025-09-25T17:14:07.000+02:00
diff --git a/Cargo.toml b/Cargo.toml
@@ -16,7 +16,7 @@ package.authors = [
 package.edition = "2024"
 package.license = "MIT OR Apache-2.0"
 package.rust-version = "1.88.0"
-package.version = "0.10.0"
+package.version = "0.11.0"
 default-members = ["rustyms"]
 
 [profile.release]
@@ -31,18 +31,17 @@ afl = "0.15"
 base64 = "0.22"
 bincode = { version = "2.0", features = ["serde"] }
 clap = { version = "4.5", features = ["derive", "cargo"] }
-custom_error = {git="https://github.com/douweschulte/custom_error", features = ["serde"]}
-#custom_error = {path="../custom_error", features = ["serde"]}
+context_error = {version = "0.1", features = ["serde"]}
 directories = "6.0"
 flate2 = "1.0"
 itertools = "0.14"
-mzdata = {version="0.57", default-features = false, features = ["miniz_oxide"]}
+mzdata = {version="0.59", default-features = false}
 ndarray = "0.16"
 ordered-float = { version = "5.0", features = ["serde"] }
 paste = "1.0"
-png = "0.17"
+png = "0.18"
 probability = "0.20"
-pyo3 = "0.25"
+pyo3 = "0.26"
 rand = "0.9"
 rayon = "1.10"
 regex = "1.11"
diff --git a/examples/multi-annotator/Cargo.toml b/examples/multi-annotator/Cargo.toml
@@ -8,7 +8,7 @@ publish = false
 
 [dependencies]
 clap = { workspace = true }
-custom_error = { workspace = true }
+context_error = { workspace = true }
 directories = { workspace = true }
 itertools = { workspace = true }
 mzdata = { workspace = true, default-features=false, features = ["mgf", "mzml", "thermo", "bruker_tdf"] }
diff --git a/examples/multi-annotator/src/main.rs b/examples/multi-annotator/src/main.rs
@@ -13,7 +13,7 @@ use std::{
     },
 };
 
-use custom_error::CombineErrorsExtender;
+use context_error::CombineErrorsExtender;
 
 use clap::Parser;
 use directories::ProjectDirs;
diff --git a/examples/peptidoform-file-converter/Cargo.toml b/examples/peptidoform-file-converter/Cargo.toml
@@ -8,7 +8,7 @@ publish = false
 
 [dependencies]
 clap = { workspace = true }
-custom_error = { workspace = true }
+context_error = { workspace = true }
 directories = { workspace = true }
 rustyms = { path = "../../rustyms", default-features=false, features = ["identification", "coloured-errors"] }
 
diff --git a/examples/peptidoform-file-converter/src/main.rs b/examples/peptidoform-file-converter/src/main.rs
@@ -7,7 +7,7 @@ use std::{
 };
 
 use clap::Parser;
-use custom_error::{BasicKind, BoxedError, Context, CreateError};
+use context_error::{BasicKind, BoxedError, Context, CreateError};
 use directories::ProjectDirs;
 use rustyms::{
     identification::{
@@ -126,7 +126,7 @@ fn main() {
                 .compound_peptidoform_ion()
                 .map(std::borrow::Cow::into_owned),))
         }) {
-            custom_error::combine_error(&mut errors, error, ());
+            context_error::combine_error(&mut errors, error, ());
         }
     }
     if errors.is_empty() {
diff --git a/rustyms-py/Cargo.toml b/rustyms-py/Cargo.toml
@@ -11,7 +11,7 @@ name = "rustyms_py"
 crate-type = ["cdylib"]
 
 [dependencies]
-custom_error = { workspace = true }
+context_error = { workspace = true }
 ordered-float = { workspace = true }
 pyo3 = { workspace = true }
 rustyms = { path = "../rustyms" }
diff --git a/rustyms-py/src/lib.rs b/rustyms-py/src/lib.rs
@@ -1798,7 +1798,7 @@ fn rustyms_py03(_py: Python, m: &Bound<'_, PyModule>) -> PyResult<()> {
 /// An error with context where it originated
 #[pyclass]
 #[derive(Debug)]
-pub struct BoxedError(custom_error::BoxedError<'static, custom_error::BasicKind>);
+pub struct BoxedError(context_error::BoxedError<'static, context_error::BasicKind>);
 
 impl std::error::Error for BoxedError {}
 
diff --git a/rustyms/Cargo.toml b/rustyms/Cargo.toml
@@ -15,7 +15,7 @@ include = ["src/**/*", "images/**/*", "README.md", "build.rs", "benches/**/*"]
 
 [dependencies]
 bincode = { workspace = true }
-custom_error = { workspace = true }
+context_error = { workspace = true }
 flate2 = { workspace = true }
 itertools = { workspace = true }
 mzdata = { workspace = true, optional = true }
@@ -58,7 +58,7 @@ isotopes = ["probability", "ndarray"]
 glycan-render = []
 glycan-render-bitmap = ["zeno", "swash", "glycan-render"]
 internal-no-data = []
-coloured-errors = ["custom_error/colored"]
+coloured-errors = ["context_error/colored"]
 
 [lints]
 workspace = true
diff --git a/rustyms/README.md b/rustyms/README.md
@@ -28,7 +28,7 @@ reading of [mgf](spectrum::mgf), doing [spectrum annotation](crate::annotation::
 ## Example usage
 
 ```rust
-# fn main() -> Result<(), custom_error::BoxedError<'static, custom_error::BasicKind>> {
+# fn main() -> Result<(), context_error::BoxedError<'static, context_error::BasicKind>> {
 # let raw_file_path = "data/annotated_example.mgf";
 use rustyms::{prelude::*, system::{isize::Charge, e}};
 // Open example raw data (this is the built in mgf reader, look into mzdata for more advanced raw file readers)
@@ -50,7 +50,7 @@ assert!(fdr.peaks_sigma() > 2.0);
 ```
 
 ```rust
-# fn main() -> Result<(), custom_error::BoxedError<'static, custom_error::BasicKind>> {
+# fn main() -> Result<(), context_error::BoxedError<'static, context_error::BasicKind>> {
 use rustyms::{prelude::*, sequence::SimpleLinear, align::*};
 // Check how this peptide compares to a similar peptide (using the feature `align`)
 let first_peptide = Peptidoform::pro_forma("IVQEVT", None)?.into_simple_linear().unwrap();
diff --git a/rustyms/src/annotation/model/custom_models.rs b/rustyms/src/annotation/model/custom_models.rs
@@ -1,6 +1,6 @@
 use std::path::Path;
 
-use custom_error::*;
+use context_error::*;
 
 use crate::{annotation::model::FragmentationModel, parse_json::ParseJson};
 
diff --git a/rustyms/src/annotation/model/json.rs b/rustyms/src/annotation/model/json.rs
@@ -1,6 +1,6 @@
 use std::ops::RangeInclusive;
 
-use custom_error::*;
+use context_error::*;
 use itertools::Itertools;
 use serde_json::Value;
 
diff --git a/rustyms/src/chemistry/formula/formula.rs b/rustyms/src/chemistry/formula/formula.rs
@@ -111,7 +111,7 @@ impl MolecularFormula {
 impl ParseJson for MolecularFormula {
     fn from_json_value(
         value: serde_json::Value,
-    ) -> Result<Self, custom_error::BoxedError<'static, custom_error::BasicKind>> {
+    ) -> Result<Self, context_error::BoxedError<'static, context_error::BasicKind>> {
         use_serde(value)
     }
 }
diff --git a/rustyms/src/chemistry/formula/pro_forma.rs b/rustyms/src/chemistry/formula/pro_forma.rs
@@ -1,6 +1,6 @@
 use std::{num::NonZeroU16, ops::RangeBounds};
 
-use custom_error::*;
+use context_error::*;
 
 use crate::{
     chemistry::{COMMON_ELEMENT_PARSE_LIST, ELEMENT_PARSE_LIST, Element, MolecularFormula},
diff --git a/rustyms/src/chemistry/formula/psi_mod.rs b/rustyms/src/chemistry/formula/psi_mod.rs
@@ -1,6 +1,6 @@
 use std::{num::NonZeroU16, ops::RangeBounds};
 
-use custom_error::*;
+use context_error::*;
 
 use crate::{
     chemistry::{ELEMENT_PARSE_LIST, MolecularFormula},
diff --git a/rustyms/src/chemistry/formula/resid.rs b/rustyms/src/chemistry/formula/resid.rs
@@ -1,6 +1,6 @@
 use std::ops::RangeBounds;
 
-use custom_error::*;
+use context_error::*;
 
 use crate::{
     chemistry::{ELEMENT_PARSE_LIST, Element, MolecularFormula},
diff --git a/rustyms/src/chemistry/formula/unimod.rs b/rustyms/src/chemistry/formula/unimod.rs
@@ -3,7 +3,7 @@ use std::{
     ops::{Range, RangeBounds},
 };
 
-use custom_error::*;
+use context_error::*;
 
 use crate::{
     chemistry::{Chemical, Element, MolecularFormula},
diff --git a/rustyms/src/chemistry/formula/xlmod.rs b/rustyms/src/chemistry/formula/xlmod.rs
@@ -1,6 +1,6 @@
 use std::{num::NonZeroU16, ops::RangeBounds};
 
-use custom_error::*;
+use context_error::*;
 
 use crate::{
     chemistry::{ELEMENT_PARSE_LIST, Element, MolecularFormula},
diff --git a/rustyms/src/fragment/mzpaf/read.rs b/rustyms/src/fragment/mzpaf/read.rs
@@ -1,7 +1,7 @@
 //! WIP: mzPAF parser
 use std::{num::NonZeroU16, ops::Range, sync::LazyLock};
 
-use custom_error::*;
+use context_error::*;
 use serde::{Deserialize, Serialize};
 
 use crate::{
diff --git a/rustyms/src/fragment/neutral_loss.rs b/rustyms/src/fragment/neutral_loss.rs
@@ -5,7 +5,7 @@ use std::{
     str::FromStr,
 };
 
-use custom_error::*;
+use context_error::*;
 use itertools::Itertools;
 use serde::{Deserialize, Serialize};
 use serde_json::Value;
diff --git a/rustyms/src/glycan/glycan.rs b/rustyms/src/glycan/glycan.rs
@@ -1,6 +1,6 @@
 use std::{fmt::Display, hash::Hash};
 
-use custom_error::*;
+use context_error::*;
 use itertools::Itertools;
 use serde::{Deserialize, Serialize};
 
diff --git a/rustyms/src/glycan/glycan_structure.rs b/rustyms/src/glycan/glycan_structure.rs
@@ -5,7 +5,7 @@ use std::{
     {fmt::Display, hash::Hash},
 };
 
-use custom_error::*;
+use context_error::*;
 use itertools::Itertools;
 use serde::{Deserialize, Serialize};
 
diff --git a/rustyms/src/identification/common_parser.rs b/rustyms/src/identification/common_parser.rs
@@ -1,6 +1,6 @@
 use std::{borrow::Cow, ops::Range, str::FromStr};
 
-use custom_error::*;
+use context_error::*;
 
 use crate::identification::csv::CsvLine;
 
@@ -35,7 +35,7 @@ macro_rules! format_family {
      optional { $($(#[doc = $odoc:expr])? $oname:ident: $otyp:ty, $of:expr;)*}
      $($post_process:item)?) => {paste::paste!{
         #[allow(unused_imports)] // Needed sometimes, but not all invocations of the macro
-        use custom_error::*;
+        use context_error::*;
 
         use super::super::common_parser::HasLocation;
 
diff --git a/rustyms/src/identification/csv.rs b/rustyms/src/identification/csv.rs
@@ -11,7 +11,7 @@ use std::{
     sync::Arc,
 };
 
-use custom_error::*;
+use context_error::*;
 use flate2::bufread::GzDecoder;
 use itertools::Itertools;
 use serde::{Deserialize, Serialize};
diff --git a/rustyms/src/identification/file_format.rs b/rustyms/src/identification/file_format.rs
@@ -1,6 +1,6 @@
 use std::{fmt::Display, path::Path};
 
-use custom_error::{BasicKind, BoxedError};
+use context_error::{BasicKind, BoxedError};
 use serde::{Deserialize, Serialize};
 
 use crate::{
diff --git a/rustyms/src/identification/formats/fasta.rs b/rustyms/src/identification/formats/fasta.rs
@@ -8,7 +8,7 @@ use std::{
     str::FromStr,
 };
 
-use custom_error::*;
+use context_error::*;
 use itertools::Itertools;
 use serde::{Deserialize, Serialize};
 
diff --git a/rustyms/src/identification/formats/mztab.rs b/rustyms/src/identification/formats/mztab.rs
@@ -9,7 +9,7 @@ use std::{
     sync::Arc,
 };
 
-use custom_error::*;
+use context_error::*;
 use flate2::bufread::GzDecoder;
 use itertools::Itertools;
 use ordered_float::OrderedFloat;
diff --git a/rustyms/src/identification/formats/mztab_test.rs b/rustyms/src/identification/formats/mztab_test.rs
@@ -1,7 +1,7 @@
 #![allow(clippy::missing_panics_doc)]
 use std::io::{BufRead, BufReader};
 
-use custom_error::{BasicKind, BoxedError};
+use context_error::{BasicKind, BoxedError};
 
 use crate::{
     identification::{
diff --git a/rustyms/src/identification/formats/opair.rs b/rustyms/src/identification/formats/opair.rs
@@ -5,7 +5,7 @@ use std::{
     path::{Path, PathBuf},
 };
 
-use custom_error::*;
+use context_error::*;
 use serde::{Deserialize, Serialize};
 
 use crate::{
diff --git a/rustyms/src/identification/formats/plink.rs b/rustyms/src/identification/formats/plink.rs
@@ -6,7 +6,7 @@ use std::{
     sync::{Arc, LazyLock},
 };
 
-use custom_error::*;
+use context_error::*;
 use itertools::Itertools;
 use serde::{Deserialize, Serialize};
 use uom::ConstZero;
diff --git a/rustyms/src/identification/general.rs b/rustyms/src/identification/general.rs
@@ -1,6 +1,6 @@
 use std::path::Path;
 
-use custom_error::*;
+use context_error::*;
 
 use crate::{
     identification::*,
diff --git a/rustyms/src/identification/source.rs b/rustyms/src/identification/source.rs
@@ -1,6 +1,6 @@
 use std::fmt::Display;
 
-use custom_error::{BasicKind, BoxedError};
+use context_error::{BasicKind, BoxedError};
 
 use crate::{
     identification::{IdentifiedPeptidoform, MaybePeptidoform, MetaData},
diff --git a/rustyms/src/imgt/species.rs b/rustyms/src/imgt/species.rs
@@ -1,7 +1,7 @@
 #![allow(dead_code, unreachable_patterns)]
 use std::{error::Error, fmt::Display};
 
-use custom_error::*;
+use context_error::*;
 use serde::{Deserialize, Serialize};
 
 /// Error type to indicate that the given name was not a recognised species from the IMGT database
diff --git a/rustyms/src/ontology.rs b/rustyms/src/ontology.rs
@@ -1,6 +1,6 @@
 //! The available ontologies
 
-use custom_error::*;
+use context_error::*;
 use itertools::Itertools;
 use serde::{Deserialize, Serialize};
 
diff --git a/rustyms/src/parse_json.rs b/rustyms/src/parse_json.rs
@@ -4,7 +4,7 @@ use itertools::Itertools;
 use serde::de::DeserializeOwned;
 use serde_json::Value;
 
-use custom_error::*;
+use context_error::*;
 
 /// Custom JSON parser, needed to allow backwards compatibility to older version of JSON formats.
 pub(crate) trait ParseJson: Sized {
diff --git a/rustyms/src/sequence/aminoacid/aminoacid.rs b/rustyms/src/sequence/aminoacid/aminoacid.rs
@@ -959,7 +959,7 @@ impl AminoAcid {
 impl ParseJson for AminoAcid {
     fn from_json_value(
         value: serde_json::Value,
-    ) -> Result<Self, custom_error::BoxedError<'static, custom_error::BasicKind>> {
+    ) -> Result<Self, context_error::BoxedError<'static, context_error::BasicKind>> {
         use_serde(value)
     }
 }
diff --git a/rustyms/src/sequence/cross_link.rs b/rustyms/src/sequence/cross_link.rs
@@ -1,6 +1,6 @@
 use std::{cmp::Ordering, collections::BTreeSet};
 
-use custom_error::*;
+use context_error::*;
 use itertools::Itertools;
 use serde::{Deserialize, Serialize};
 use serde_json::Value;
diff --git a/rustyms/src/sequence/modification.rs b/rustyms/src/sequence/modification.rs
@@ -7,7 +7,7 @@ use std::{
     sync::Arc,
 };
 
-use custom_error::*;
+use context_error::*;
 use itertools::Itertools;
 use ordered_float::OrderedFloat;
 use serde::{Deserialize, Serialize};
diff --git a/rustyms/src/sequence/peptidoform/parse.rs b/rustyms/src/sequence/peptidoform/parse.rs
@@ -1,6 +1,6 @@
 use std::{collections::BTreeMap, num::NonZeroU16};
 
-use custom_error::*;
+use context_error::*;
 use itertools::Itertools;
 use ordered_float::OrderedFloat;
 
diff --git a/rustyms/src/sequence/peptidoform/parse_modification.rs b/rustyms/src/sequence/peptidoform/parse_modification.rs
@@ -4,7 +4,7 @@ use std::{
     sync::{Arc, LazyLock},
 };
 
-use custom_error::*;
+use context_error::*;
 use ordered_float::OrderedFloat;
 use regex::Regex;
 use serde::{Deserialize, Serialize};
diff --git a/rustyms/src/sequence/peptidoform/parse_sloppy.rs b/rustyms/src/sequence/peptidoform/parse_sloppy.rs
diff --git a/rustyms/src/sequence/peptidoform/tests/parse.rs b/rustyms/src/sequence/peptidoform/tests/parse.rs
diff --git a/rustyms/src/sequence/peptidoform/validate.rs b/rustyms/src/sequence/peptidoform/validate.rs
diff --git a/rustyms/src/sequence/placement_rule.rs b/rustyms/src/sequence/placement_rule.rs
diff --git a/rustyms/src/sequence/sequence_element.rs b/rustyms/src/sequence/sequence_element.rs
diff --git a/rustyms/src/sequence/sequence_position.rs b/rustyms/src/sequence/sequence_position.rs
diff --git a/rustyms/src/sequence/simple_modification.rs b/rustyms/src/sequence/simple_modification.rs
diff --git a/rustyms/src/spectrum/mgf.rs b/rustyms/src/spectrum/mgf.rs
