chore: upgrade deps

Cargo.toml

@@ -27,9 +27,9 @@ keywords = [
 authors = ["NeherLab team"]
 
 [workspace.dependencies]
-bzip2 = { version = "=0.5.1", features = ["static"] }
-flate2 = "=1.1.0"
-libz-sys = { version = "=1.1.21", features = ["static", "stock-zlib", "cmake"] }
+bzip2 = { version = "=0.6.0", features = ["static"] }
+flate2 = "=1.1.2"
+libz-sys = { version = "=1.1.22", features = ["static", "stock-zlib", "cmake"] }
 xz2 = { version = "=0.1.7", features = ["static"] }
 zstd = { version = "=0.13.3", features = ["zstdmt"] }
 
@@ -41,54 +41,54 @@ minimap2-sys = { path = "packages/minimap2-sys", features = ["simde", "static",
 approx = "=0.5.1"
 atty = "=0.2.14"
 auto_ops = "=0.3.0"
-bio = "=2.0.3"
-chrono = { version = "=0.4.39", default-features = false, features = ["clock", "std", "wasmbind"] }
-clap = { version = "=4.5.30", features = ["derive", "color", "unicode", "unstable-styles"] }
-clap-markdown = "=0.1.4"
-clap_complete = "=4.5.45"
+bio = "=3.0.0"
+chrono = { version = "=0.4.42", default-features = false, features = ["clock", "std", "wasmbind"] }
+clap = { version = "=4.5.48", features = ["derive", "color", "unicode", "unstable-styles"] }
+clap-markdown = "=0.1.5"
+clap_complete = "=4.5.58"
 clap_complete_fig = "=4.5.2"
-cmd_lib = "=1.9.5"
-color-eyre = "=0.6.3"
+cmd_lib = "=2.0.0"
+color-eyre = "=0.6.5"
 csv = "=1.3.1"
-ctor = "=0.3.6"
+ctor = "=0.5.0"
 derive_more = { version = "=2.0.1", features = ["full"] }
-env_logger = "=0.11.6"
+env_logger = "=0.11.8"
 eyre = "=0.6.12"
 gcollections = "=1.5.0"
-getset = "=0.1.4"
-indicatif = "0.17.11"
+getset = "=0.1.6"
+indicatif = "0.18.0"
 indicatif-log-bridge = "0.2.3"
-indoc = "=2.0.5"
-intervallum = "=1.4.1"
+indoc = "=2.0.6"
+intervallum = "=1.4.4"
 itertools = "=0.14.0"
-log = "=0.4.26"
+log = "=0.4.28"
 maplit = "=1.0.2"
 ndarray = { version = "=0.16.1", features = ["rayon", "serde", "blas", "approx"] }
 ndarray-stats = "=0.6.0"
 noodles = { version = "=0.60.0", features = ["core", "sam"] }
 num = "=0.4.3"
 num-traits = "=0.2.19"
-num_cpus = "=1.16.0"
+num_cpus = "=1.17.0"
 ordered-float = { version = "=5.0.0", features = ["serde"] }
-parking_lot = { version = "=0.12.3", features = ["deadlock_detection", "hardware-lock-elision", "serde", "arc_lock"] }
+parking_lot = { version = "=0.12.4", features = ["deadlock_detection", "hardware-lock-elision", "serde", "arc_lock"] }
 pretty_assertions = "=1.4.1"
 pretty_dtoa = "=0.3.0"
-rand = { version = "=0.9.0", features = ["serde", "log"] }
+rand = { version = "=0.9.2", features = ["serde", "log"] }
 rand_isaac = { version = "=0.4.0", features = ["serde"] }
-rayon = "=1.10.0"
-regex = "=1.11.1"
-rstest = "=0.24.0"
-schemars = { version = "=1.0.0-alpha.17", features = ["chrono04", "either1", "indexmap2", "raw_value", "schemars_derive", "preserve_order"] }
-serde = { version = "=1.0.218", features = ["derive"] }
-serde-aux = "=4.6.0"
-serde_json = { version = "=1.0.139", features = ["preserve_order", "unbounded_depth"] }
-serde_stacker = { version = "=0.1.11" }
+rayon = "=1.11.0"
+regex = "=1.11.2"
+rstest = "=0.26.1"
+schemars = { version = "=1.0.4", features = ["chrono04", "either1", "indexmap2", "raw_value", "schemars_derive", "preserve_order"] }
+serde = { version = "=1.0.225", features = ["derive"] }
+serde-aux = "=4.7.0"
+serde_json = { version = "=1.0.145", features = ["preserve_order", "unbounded_depth"] }
+serde_stacker = { version = "=0.1.14" }
 serde_yaml = "=0.9.34"
 smart-default = "=0.7.1"
-strum = "=0.27.1"
-strum_macros = "=0.27.1"
-tempfile = "=3.17.1"
-twox-hash = { version = "=2.1.0", features = ["serialize"] }
+strum = "=0.27.2"
+strum_macros = "=0.27.2"
+tempfile = "=3.22.0"
+twox-hash = { version = "=2.1.2", features = ["serialize"] }
 
 
 [workspace.lints.rust]

packages/minimap2-sys/Cargo.toml

@@ -30,11 +30,11 @@ exclude = [
 ]
 
 [dependencies]
-libz-sys = { version = "1.1.21", default-features = false }
+libz-sys = { version = "1.1.22", default-features = false }
 
 [build-dependencies]
-bindgen = { version = "0.71.1", features = ["which-rustfmt", "runtime"] }
-cc = { version = "1.2.15" }
+bindgen = { version = "0.72.1", features = ["runtime"] }
+cc = { version = "1.2.38" }
 
 [features]
 default = ["libz-sys/libc"]
@@ -44,4 +44,3 @@ noopt = []
 zlib-ng = ["libz-sys/zlib-ng"]
 static = ["libz-sys/static"]
 stock-zlib = ["libz-sys/stock-zlib"]
-

packages/pangraph-schemas/Pangraph.schema.json

@@ -1,7 +1,7 @@
 {
   "$schema": "https://json-schema.org/draft/2020-12/schema",
   "title": "_PangraphSchemaRoot",
-  "description": "AUTOGENERATED! This JSON schema file is generated automatically from Rust types.\n The root object definition is a dummy container for the types being exposed. Disregard\n it. Instead, see the actual types in the `definitions` property of that container.",
+  "description": "AUTOGENERATED! This JSON schema file is generated automatically from Rust types.\nThe root object definition is a dummy container for the types being exposed. Disregard\nit. Instead, see the actual types in the `definitions` property of that container.",
   "type": "object",
   "properties": {
     "pangraph": {
@@ -17,21 +17,30 @@
       "properties": {
         "paths": {
           "type": "object",
-          "additionalProperties": {
-            "$ref": "#/$defs/PangraphPath"
-          }
+          "patternProperties": {
+            "^\\d+$": {
+              "$ref": "#/$defs/PangraphPath"
+            }
+          },
+          "additionalProperties": false
         },
         "blocks": {
           "type": "object",
-          "additionalProperties": {
-            "$ref": "#/$defs/PangraphBlock"
-          }
+          "patternProperties": {
+            "^\\d+$": {
+              "$ref": "#/$defs/PangraphBlock"
+            }
+          },
+          "additionalProperties": false
         },
         "nodes": {
           "type": "object",
-          "additionalProperties": {
-            "$ref": "#/$defs/PangraphNode"
-          }
+          "patternProperties": {
+            "^\\d+$": {
+              "$ref": "#/$defs/PangraphNode"
+            }
+          },
+          "additionalProperties": false
         }
       },
       "required": [
@@ -101,9 +110,12 @@
         },
         "alignments": {
           "type": "object",
-          "additionalProperties": {
-            "$ref": "#/$defs/Edit"
-          }
+          "patternProperties": {
+            "^\\d+$": {
+              "$ref": "#/$defs/Edit"
+            }
+          },
+          "additionalProperties": false
         }
       },
       "required": [

packages/pangraph-schemas/README.md

@@ -26,7 +26,7 @@ cd pangraph-schemas/
 pip3 install dacite datamodel-code-generator pydantic
 
 # Generate Python classes
-datamodel-codegen --input-file-type "jsonschema" --input "Pangraph.schema.json" --output-model-type "dataclasses.dataclass" --enum-field-as-literal=all --output "python/Pangraph.py"
+datamodel-codegen --input-file-type "jsonschema" --input "Pangraph.schema.json" --output-model-type "dataclasses.dataclass" --enum-field-as-literal=all --output "python/Pangraph_model.py"
 
 # Run the example using the generated Python classes
 python3 python/example.py path/to/your/pangraph/output.json

packages/pangraph-schemas/python/Pangraph_model.py

@@ -1,6 +1,6 @@
 # generated by datamodel-codegen:
 #   filename:  Pangraph.schema.json
-#   timestamp: 2024-10-23T22:10:52+00:00
+#   timestamp: 2025-09-20T00:33:52+00:00
 
 from __future__ import annotations
 
@@ -44,6 +44,7 @@ class PangraphPath:
     tot_len: int
     circular: bool
     name: Optional[str] = None
+    desc: Optional[str] = None
 
 
 @dataclass

packages/pangraph/src/bin/merge_two_graphs.rs

@@ -67,7 +67,7 @@ fn main() -> Result<(), Report> {
   #[cfg(debug_assertions)]
   merged.sanity_check()?;
 
-  info!("Writing merged graph to {:?}", args.build_args.output_json);
+  info!("Writing merged graph to {}", args.build_args.output_json.display());
 
   json_write_file(&args.build_args.output_json, &merged, JsonPretty(true))?;
 

packages/pangraph/src/io/file.rs

@@ -66,7 +66,7 @@ pub fn create_file_or_stdout(filepath: impl AsRef<Path>) -> Result<Box<dyn Write
   let filepath = filepath.as_ref();
 
   let file: Box<dyn Write + Sync + Send> = if is_path_stdout(filepath) {
-    info!("File path is {filepath:?}. Writing to standard output.");
+    info!("File path is {}. Writing to standard output.", filepath.display());
     Box::new(BufWriter::with_capacity(DEFAULT_FILE_BUF_SIZE, stdout()))
   } else {
     ensure_dir(filepath)?;

packages/pangraph/src/representation/seq.rs

@@ -550,7 +550,7 @@ impl<'de> serde::Deserialize<'de> for Seq {
 }
 
 impl JsonSchema for Seq {
-  fn always_inline_schema() -> bool {
+  fn inline_schema() -> bool {
     true
   }
 

packages/pangraph/src/representation/seq_char.rs

@@ -127,7 +127,7 @@ impl<'de> serde::Deserialize<'de> for AsciiChar {
 }
 
 impl JsonSchema for AsciiChar {
-  fn always_inline_schema() -> bool {
+  fn inline_schema() -> bool {
     true
   }