Fix clippy issues and update several dependenices

CHANGELOG.md

@@ -9,6 +9,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - Include token in subgraph even if not covered by segmentation node #334.
 
+### Changed
+
+- Updated several internal dependencies.
+
 ## [4.1.1] - 2026-01-13
 
 ### Added

capi/Cargo.toml

@@ -10,10 +10,11 @@ version = "4.1.1"
 
 [lib]
 crate-type = ["staticlib", "cdylib"]
+test = false
 
 [dependencies]
 graphannis = { path = "../graphannis/", version = "^4" }
-itertools = "0.10"
+itertools = "0.14"
 libc = "0.2"
 log = "0.4"
 simplelog = { version = "0.12" }

cli/Cargo.toml

@@ -13,29 +13,25 @@ version = "4.1.1"
 anyhow = "1"
 clap = { version = "2", default-features = false }
 compound_duration = "1"
-criterion = "0.3"
+criterion = "0.8.2"
 graphannis = { path = "../graphannis/", version = "^4" }
 log = "0.4"
 prettytable-rs = "0.10.0"
 rustyline = "9"
 rustyline-derive = "0.5"
 simplelog = "0.12"
-toml = "0.5"
+toml = "1.1.2"
 
 [target.'cfg(not(target_env = "msvc"))'.dependencies]
-tikv-jemallocator = "0.5"
+tikv-jemallocator = "0.6.1"
 
 [dev-dependencies]
 assert_cmd = "2.1"
 insta = { version = "1.34.0", features = ["filters"] }
-insta-cmd = "0.5"
 serial_test = "2"
 
 [[bin]]
 name = "annis"
 
 [[bin]]
 name = "annis_bench_queries"
-
-[package.metadata.cargo-machete]
-ignored = ["prettytable-rs"]

cli/src/bin/annis_bench_queries.rs

@@ -115,7 +115,7 @@ fn main() {
     if let Some(baseline) = matches.value_of("save-baseline") {
         crit = crit.save_baseline(baseline.to_string());
     } else if let Some(baseline) = matches.value_of("baseline") {
-        crit = crit.retain_baseline(baseline.to_string());
+        crit = crit.retain_baseline(baseline.to_string(), false);
     }
 
     if matches.is_present("measurement-time") {

cli/tests/snapshots/cli__export_to_zip_file.snap

@@ -1,14 +1,8 @@
 ---
 source: cli/tests/cli.rs
-info:
-  program: annis
-  args:
-    - "../graphannis/tests/data/"
-    - "-c"
-    - corpus sample-disk-based-3.3
-    - "-c"
-    - export sample-disk-based-3.3.zip
+expression: actual
 ---
+
 success: true
 exit_code: 0
 ----- stdout -----

cli/tests/snapshots/cli__list_corpora_fully_loaded.snap

@@ -1,16 +1,8 @@
 ---
 source: cli/tests/cli.rs
-info:
-  program: annis
-  args:
-    - "../graphannis/tests/data/"
-    - "-c"
-    - corpus sample-disk-based-3.3
-    - "-c"
-    - preload
-    - "-c"
-    - list
+expression: actual
 ---
+
 success: true
 exit_code: 0
 ----- stdout -----

cli/tests/snapshots/cli__list_corpora_not_loaded.snap

@@ -1,12 +1,8 @@
 ---
 source: cli/tests/cli.rs
-info:
-  program: annis
-  args:
-    - "../graphannis/tests/data/"
-    - "-c"
-    - list
+expression: actual
 ---
+
 success: true
 exit_code: 0
 ----- stdout -----

cli/tests/snapshots/cli__list_corpora_partially_loaded.snap

@@ -1,16 +1,8 @@
 ---
 source: cli/tests/cli.rs
-info:
-  program: annis
-  args:
-    - "../graphannis/tests/data/"
-    - "-c"
-    - corpus sample-disk-based-3.3
-    - "-c"
-    - count tok
-    - "-c"
-    - list
+expression: actual
 ---
+
 success: true
 exit_code: 0
 ----- stdout -----

cli/tests/snapshots/cli__show_corpus_info.snap

@@ -1,16 +1,8 @@
 ---
 source: cli/tests/cli.rs
-info:
-  program: annis
-  args:
-    - "../graphannis/tests/data/"
-    - "-c"
-    - corpus sample-disk-based-3.8
-    - "-c"
-    - preload
-    - "-c"
-    - info
+expression: actual
 ---
+
 success: true
 exit_code: 0
 ----- stdout -----

core/Cargo.toml

@@ -12,38 +12,35 @@ version = "4.1.1"
 
 [dependencies]
 binary-layout = "4.0.1"
-bincode = "1.2"
+bincode = "1.3"
 clru = "0.6.1"
-facet = "0.28.0"
-itertools = "0.10"
+facet = "0.46.0"
+itertools = "0.14"
 lazy_static = "1.4"
 log = "0.4"
 memmap2 = "0.9"
 normpath = "1.1.1"
 num-traits = "0.2"
 percent-encoding = "2.1"
-quick-xml = "0.28"
-rand = { version = "0.9", features = ["small_rng"] }
+quick-xml = "0.39"
+rand = "0.10"
 rayon = { version = "1.3", default-features = false }
 regex = "1"
 regex-syntax = "0.8"
-rustc-hash = "1.0"
+rustc-hash = "2.1.2"
 serde = { version = "1.0", features = ["rc"] }
 serde_bytes = "0.11"
 serde_derive = "1.0"
 smallvec = "1.6"
 sstable = "0.11"
 tempfile = "3.1"
-thiserror = "1"
-toml = "0.8"
+thiserror = "2"
+toml = "1.1.2"
 transient-btree-index = "0.5"
 
-[target.'cfg(windows)'.dependencies]
-winapi = { version = "0.3", features = ["heapapi"] }
-
 [dev-dependencies]
-env_logger = "0.9"
-fake = "2.2"
+env_logger = "0.11"
+fake = "5.1"
 insta = { version = "1.38.0", features = ["json"] }
 pretty_assertions = "1.3"
 serde_json = "1.0"

core/src/annostorage/inmemory.rs

@@ -180,8 +180,8 @@ where
                 // flatten the hash set of all items of the value map
                 .flat_map(|(key, values)| {
                     values
-                        .iter()
-                        .flat_map(|(_, items)| items.iter().cloned())
+                        .values()
+                        .flat_map(|items| items.iter().cloned())
                         .zip(std::iter::repeat(key))
                 })
                 .map(Ok);
@@ -572,8 +572,8 @@ where
                 // flatten the hash set of all items of the value map
                 .flat_map(|(key, values)| {
                     values
-                        .iter()
-                        .flat_map(|(_, items)| items.iter().cloned())
+                        .values()
+                        .flat_map(|items| items.iter().cloned())
                         .zip(std::iter::repeat(key))
                 });
 
@@ -796,7 +796,7 @@ where
                         if let Some(histo) = self.histogram_bounds.get(&anno_key_symbol)
                             && !histo.is_empty()
                         {
-                            let sampled_values = histo.iter().choose_multiple(&mut rng, 20);
+                            let sampled_values = histo.iter().sample(&mut rng, 20);
                             let matches = sampled_values
                                 .iter()
                                 .filter(|v| pattern.is_match(v))
@@ -889,8 +889,8 @@ where
                 return Ok(result);
             } else {
                 let result = values_for_key
-                    .iter()
-                    .filter_map(|(val, _items)| self.anno_values.get_value_ref(*val))
+                    .keys()
+                    .filter_map(|val| self.anno_values.get_value_ref(*val))
                     .map(|val| Cow::Borrowed(&val[..]))
                     .collect();
                 return Ok(result);

core/src/annostorage/ondisk.rs

@@ -942,7 +942,7 @@ where
                         if let Some(histo) = self.histogram_bounds.get(&anno_key)
                             && !histo.is_empty()
                         {
-                            let sampled_values = histo.iter().choose_multiple(&mut rng, 20);
+                            let sampled_values = histo.iter().sample(&mut rng, 20);
 
                             let matches = sampled_values
                                 .iter()
@@ -1071,7 +1071,7 @@ where
             let all_values_for_key = self.get_by_anno_qname_range(anno_key);
 
             let sampled_anno_values: Result<Vec<String>> = all_values_for_key
-                .choose_multiple(&mut rng, max_sampled_annotations)
+                .sample(&mut rng, max_sampled_annotations)
                 .into_iter()
                 .map(|data| {
                     let (data, _) = data?;

core/src/errors.rs

@@ -46,6 +46,8 @@ pub enum GraphAnnisCoreError {
     #[error(transparent)]
     Xml(#[from] quick_xml::Error),
     #[error(transparent)]
+    XmlEncoding(#[from] quick_xml::encoding::EncodingError),
+    #[error(transparent)]
     XmlAttr(#[from] quick_xml::events::attributes::AttrError),
     #[error("Cache error: {0}")]
     LfuCache(String),

core/src/graph/serialization/graphml.rs

@@ -510,7 +510,7 @@ fn read_graphml<CT: ComponentType, R: std::io::BufRead, F: Fn(&str)>(
     progress_callback: &F,
 ) -> Result<Option<String>> {
     let mut reader = Reader::from_reader(input);
-    reader.expand_empty_elements(true);
+    reader.config_mut().expand_empty_elements = true;
 
     let mut keys = BTreeMap::new();
 
@@ -535,48 +535,42 @@ fn read_graphml<CT: ComponentType, R: std::io::BufRead, F: Fn(&str)>(
                 level += 1;
 
                 match e.name().0 {
-                    b"graph" => {
-                        if level == 2 {
-                            in_graph = true;
-                        }
+                    b"graph" if level == 2 => {
+                        in_graph = true;
                     }
-                    b"key" => {
-                        if level == 2 {
-                            add_annotation_key(&mut keys, e.attributes())?;
-                        }
+                    b"key" if level == 2 => {
+                        add_annotation_key(&mut keys, e.attributes())?;
                     }
-                    b"node" => {
-                        if in_graph && level == 3 {
-                            data.clear();
-                            // Get the ID of this node
-                            for att in e.attributes() {
-                                let att = att?;
-                                if att.key.0 == b"id" {
-                                    current_node_id =
-                                        Some(String::from_utf8_lossy(&att.value).to_string());
-                                }
+                    b"node" if in_graph && level == 3 => {
+                        data.clear();
+                        // Get the ID of this node
+                        for att in e.attributes() {
+                            let att = att?;
+                            if att.key.0 == b"id" {
+                                current_node_id =
+                                    Some(String::from_utf8_lossy(&att.value).to_string());
                             }
                         }
                     }
-                    b"edge" => {
-                        if in_graph && level == 3 {
-                            data.clear();
-                            // Get the source and target node IDs
-                            for att in e.attributes() {
-                                let att = att?;
-                                if att.key.0 == b"source" {
-                                    current_source_id =
-                                        Some(String::from_utf8_lossy(&att.value).to_string());
-                                } else if att.key.0 == b"target" {
-                                    current_target_id =
-                                        Some(String::from_utf8_lossy(&att.value).to_string());
-                                } else if att.key.0 == b"label" {
-                                    current_component =
-                                        Some(String::from_utf8_lossy(&att.value).to_string());
-                                }
+
+                    b"edge" if in_graph && level == 3 => {
+                        data.clear();
+                        // Get the source and target node IDs
+                        for att in e.attributes() {
+                            let att = att?;
+                            if att.key.0 == b"source" {
+                                current_source_id =
+                                    Some(String::from_utf8_lossy(&att.value).to_string());
+                            } else if att.key.0 == b"target" {
+                                current_target_id =
+                                    Some(String::from_utf8_lossy(&att.value).to_string());
+                            } else if att.key.0 == b"label" {
+                                current_component =
+                                    Some(String::from_utf8_lossy(&att.value).to_string());
                             }
                         }
                     }
+
                     b"data" => {
                         for att in e.attributes() {
                             let att = att?;
@@ -589,11 +583,10 @@ fn read_graphml<CT: ComponentType, R: std::io::BufRead, F: Fn(&str)>(
                     _ => {}
                 }
             }
-            Event::Text(t) => {
-                if in_graph && level == 4 && current_data_key.is_some() {
-                    current_data_value = Some(t.unescape()?.to_string());
-                }
+            Event::Text(t) if in_graph && level == 4 && current_data_key.is_some() => {
+                current_data_value = Some(t.decode()?.to_string());
             }
+
             Event::CData(t) => {
                 if let Some(current_data_key) = &current_data_key
                     && in_graph

core/src/graph/storage/linear.rs

@@ -134,8 +134,8 @@ where
         // because the last element is only a target node, not a source node
         let it = self
             .node_chains
-            .iter()
-            .flat_map(|(_root, chain)| chain.iter().rev().skip(1))
+            .values()
+            .flat_map(|chain| chain.iter().rev().skip(1))
             .cloned()
             .map(Ok);
 

core/src/graph/storage/prepost.rs

@@ -162,8 +162,8 @@ where
     fn source_nodes<'a>(&'a self) -> Box<dyn Iterator<Item = Result<NodeID>> + 'a> {
         let it = self
             .node_to_order
-            .iter()
-            .filter_map(move |(n, _order)| {
+            .keys()
+            .filter_map(move |n| {
                 // check if this is actual a source node (and not only a target node)
                 if self.get_outgoing_edges(*n).next().is_some() {
                     Some(*n)