chore: Update Plonky3 dependency and adapt to breaking API changes: (#43)

- AirBuilder: replace type M with PreprocessedWindow, MainWindow, PublicVar
- Use RowWindow/WindowAccess instead of VerticalPair for preprocessed traces
- MerkleTreeMmcs: add arity generic parameter and cap_height constructor arg
- FriParameters: add max_log_arity field
- MerkleCap no longer Copy: add .clone() where needed
- Remove PreprocessedBuilder, AirBuilderWithPublicValues, BaseAirWithPublicValues
  (functionality merged into AirBuilder/BaseAir)
- Expose cap_height and max_log_arity in public CommitmentParameters/FriParameters
- Add documentation to public types and fix stale doc comments

Author: arthurpaulino

Cargo.lock

@@ -11,19 +11,19 @@ rust-version = "1.88"
 [dependencies]
 serde = { version = "1", features = ["derive"] }
 bincode = { version = "2", features = ["serde"] }
-p3-air = { git = "https://github.com/Plonky3/Plonky3", rev = "0835481398d2b481bef0c6d0e8188b484ab9a636" }
-p3-goldilocks = { git = "https://github.com/Plonky3/Plonky3", rev = "0835481398d2b481bef0c6d0e8188b484ab9a636" }
-p3-challenger = { git = "https://github.com/Plonky3/Plonky3", rev = "0835481398d2b481bef0c6d0e8188b484ab9a636" }
-p3-commit = { git = "https://github.com/Plonky3/Plonky3", rev = "0835481398d2b481bef0c6d0e8188b484ab9a636" }
-p3-dft = { git = "https://github.com/Plonky3/Plonky3", rev = "0835481398d2b481bef0c6d0e8188b484ab9a636" }
-p3-field = { git = "https://github.com/Plonky3/Plonky3", rev = "0835481398d2b481bef0c6d0e8188b484ab9a636" }
-p3-fri = { git = "https://github.com/Plonky3/Plonky3", rev = "0835481398d2b481bef0c6d0e8188b484ab9a636" }
-p3-keccak = { git = "https://github.com/Plonky3/Plonky3", rev = "0835481398d2b481bef0c6d0e8188b484ab9a636" }
-p3-matrix = { git = "https://github.com/Plonky3/Plonky3", rev = "0835481398d2b481bef0c6d0e8188b484ab9a636" }
-p3-maybe-rayon = { git = "https://github.com/Plonky3/Plonky3", rev = "0835481398d2b481bef0c6d0e8188b484ab9a636" }
-p3-merkle-tree = { git = "https://github.com/Plonky3/Plonky3", rev = "0835481398d2b481bef0c6d0e8188b484ab9a636" }
-p3-symmetric = { git = "https://github.com/Plonky3/Plonky3", rev = "0835481398d2b481bef0c6d0e8188b484ab9a636" }
-p3-util = { git = "https://github.com/Plonky3/Plonky3", rev = "0835481398d2b481bef0c6d0e8188b484ab9a636" }
+p3-air = { git = "https://github.com/Plonky3/Plonky3", rev = "e52636ec09663fd7d3bd4eaabb21dba8698f129a" }
+p3-goldilocks = { git = "https://github.com/Plonky3/Plonky3", rev = "e52636ec09663fd7d3bd4eaabb21dba8698f129a" }
+p3-challenger = { git = "https://github.com/Plonky3/Plonky3", rev = "e52636ec09663fd7d3bd4eaabb21dba8698f129a" }
+p3-commit = { git = "https://github.com/Plonky3/Plonky3", rev = "e52636ec09663fd7d3bd4eaabb21dba8698f129a" }
+p3-dft = { git = "https://github.com/Plonky3/Plonky3", rev = "e52636ec09663fd7d3bd4eaabb21dba8698f129a" }
+p3-field = { git = "https://github.com/Plonky3/Plonky3", rev = "e52636ec09663fd7d3bd4eaabb21dba8698f129a" }
+p3-fri = { git = "https://github.com/Plonky3/Plonky3", rev = "e52636ec09663fd7d3bd4eaabb21dba8698f129a" }
+p3-keccak = { git = "https://github.com/Plonky3/Plonky3", rev = "e52636ec09663fd7d3bd4eaabb21dba8698f129a" }
+p3-matrix = { git = "https://github.com/Plonky3/Plonky3", rev = "e52636ec09663fd7d3bd4eaabb21dba8698f129a" }
+p3-maybe-rayon = { git = "https://github.com/Plonky3/Plonky3", rev = "e52636ec09663fd7d3bd4eaabb21dba8698f129a" }
+p3-merkle-tree = { git = "https://github.com/Plonky3/Plonky3", rev = "e52636ec09663fd7d3bd4eaabb21dba8698f129a" }
+p3-symmetric = { git = "https://github.com/Plonky3/Plonky3", rev = "e52636ec09663fd7d3bd4eaabb21dba8698f129a" }
+p3-util = { git = "https://github.com/Plonky3/Plonky3", rev = "e52636ec09663fd7d3bd4eaabb21dba8698f129a" }
 
 [features]
 parallel = ["p3-maybe-rayon/parallel"]

Cargo.toml

@@ -71,6 +71,7 @@ feature-depth = 1
 # output a note when they are encountered.
 ignore = [
     "RUSTSEC-2024-0436", # `paste` crate is unmaintained
+    "RUSTSEC-2025-0141", # `bincode` crate is unmaintained
     #"RUSTSEC-0000-0000",
     #{ id = "RUSTSEC-0000-0000", reason = "you can specify a reason the advisory is ignored" },
     #"a-crate-that-is-yanked@0.1.1", # you can also ignore yanked crate versions if you wish
@@ -95,7 +96,7 @@ allow = [
     "Unicode-3.0",
     "CC0-1.0",
     #"Apache-2.0 WITH LLVM-exception",
-    "BSD-2-Clause",
+    #"BSD-2-Clause",
 ]
 # The confidence threshold for detecting a license from license text.
 # The higher the value, the more closely the license text must be to the