diff --git a/Cargo.lock b/Cargo.lock
index 5d6b0dac0..a9639e409 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -128,9 +128,9 @@ checksum = "23b62fc65de8e4e7f52534fb52b0f3ed04746ae267519eef2a83941e8085068b"
 
 [[package]]
 name = "assert_cmd"
-version = "2.2.0"
+version = "2.2.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9a686bbee5efb88a82df0621b236e74d925f470e5445d3220a5648b892ec99c9"
+checksum = "39bae1d3fa576f7c6519514180a72559268dd7d1fe104070956cb687bc6673bd"
 dependencies = [
  "anstyle",
  "bstr",
@@ -257,9 +257,9 @@ checksum = "1fd0f2584146f6f2ef48085050886acf353beff7305ebd1ae69500e27c67f64b"
 
 [[package]]
 name = "capnp"
-version = "0.25.2"
+version = "0.25.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c982cc37b8f646c753f3b0a24d4d40ca2eac8a9c2b9ea6fff524be67ddc184cb"
+checksum = "63da65e5e9ffc3b8f993d4ad222a548152549351a643f6b850a7773cb6ff2809"
 dependencies = [
  "embedded-io",
 ]
@@ -272,9 +272,9 @@ checksum = "37b2a672a2cb129a2e41c10b1224bb368f9f37a2b16b612598138befd7b37eb5"
 
 [[package]]
 name = "cc"
-version = "1.2.57"
+version = "1.2.61"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7a0dd1ca384932ff3641c8718a02769f1698e7563dc6974ffd03346116310423"
+checksum = "d16d90359e986641506914ba71350897565610e87ce0ad9e6f28569db3dd5c6d"
 dependencies = [
  "find-msvc-tools",
  "jobserver",
@@ -346,9 +346,9 @@ dependencies = [
 
 [[package]]
 name = "clap"
-version = "4.6.0"
+version = "4.6.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b193af5b67834b676abd72466a96c1024e6a6ad978a1f484bd90b85c94041351"
+checksum = "1ddb117e43bbf7dacf0a4190fef4d345b9bad68dfc649cb349e7d17d28428e51"
 dependencies = [
  "clap_builder",
  "clap_derive",
@@ -378,9 +378,9 @@ dependencies = [
 
 [[package]]
 name = "clap_derive"
-version = "4.6.0"
+version = "4.6.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1110bd8a634a1ab8cb04345d8d878267d57c3cf1b38d91b71af6686408bbca6a"
+checksum = "f2ce8604710f6733aa641a2b3731eaa1e8b3d9973d5e3565da11800813f997a9"
 dependencies = [
  "heck",
  "proc-macro2",
@@ -768,9 +768,9 @@ dependencies = [
 
 [[package]]
 name = "fancy-regex"
-version = "0.17.0"
+version = "0.18.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "72cf461f865c862bb7dc573f643dd6a2b6842f7c30b07882b56bd148cc2761b8"
+checksum = "e1e1dacd0d2082dfcf1351c4bdd566bbe89a2b263235a2b50058f1e130a47277"
 dependencies = [
  "bit-set",
  "regex-automata",
@@ -1490,9 +1490,9 @@ dependencies = [
 
 [[package]]
 name = "jsonschema"
-version = "0.46.2"
+version = "0.46.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "50180452e7808015fe083eae3efcf1ec98b89b45dd8cc204f7b4a6b7b81ea675"
+checksum = "fc59d2432e047d6090ba1d83c782d0128bd6203857978218f5614dbd3287281f"
 dependencies = [
  "ahash",
  "bytecount",
@@ -1767,9 +1767,9 @@ dependencies = [
 
 [[package]]
 name = "pastey"
-version = "0.2.1"
+version = "0.2.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b867cad97c0791bbd3aaa6472142568c6c9e8f71937e98379f584cfb0cf35bec"
+checksum = "c5a797f0e07bdf071d15742978fc3128ec6c22891c31a3a931513263904c982a"
 
 [[package]]
 name = "percent-encoding"
@@ -1880,9 +1880,9 @@ checksum = "c33a9471896f1c69cecef8d20cbe2f7accd12527ce60845ff44c153bb2a21b49"
 
 [[package]]
 name = "portgraph"
-version = "0.16.0"
+version = "0.16.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c4d6244193810d114467998a979f0f763e5422ea546586d309fb70a68c036fb5"
+checksum = "6a1395575e261a0c0dd2d360ac4e3b14a4c9f68647ee12e59d96af959e4c0f79"
 dependencies = [
  "bitvec",
  "delegate",
@@ -2051,9 +2051,9 @@ dependencies = [
 
 [[package]]
 name = "pyo3"
-version = "0.28.2"
+version = "0.28.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "cf85e27e86080aafd5a22eae58a162e133a589551542b3e5cee4beb27e54f8e1"
+checksum = "91fd8e38a3b50ed1167fb981cd6fd60147e091784c427b8f7183a7ee32c31c12"
 dependencies = [
  "libc",
  "once_cell",
@@ -2065,18 +2065,18 @@ dependencies = [
 
 [[package]]
 name = "pyo3-build-config"
-version = "0.28.2"
+version = "0.28.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "8bf94ee265674bf76c09fa430b0e99c26e319c945d96ca0d5a8215f31bf81cf7"
+checksum = "e368e7ddfdeb98c9bca7f8383be1648fd84ab466bf2bc015e94008db6d35611e"
 dependencies = [
  "target-lexicon",
 ]
 
 [[package]]
 name = "pyo3-ffi"
-version = "0.28.2"
+version = "0.28.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "491aa5fc66d8059dd44a75f4580a2962c1862a1c2945359db36f6c2818b748dc"
+checksum = "7f29e10af80b1f7ccaf7f69eace800a03ecd13e883acfacc1e5d0988605f651e"
 dependencies = [
  "libc",
  "pyo3-build-config",
@@ -2084,9 +2084,9 @@ dependencies = [
 
 [[package]]
 name = "pyo3-macros"
-version = "0.28.2"
+version = "0.28.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f5d671734e9d7a43449f8480f8b38115df67bef8d21f76837fa75ee7aaa5e52e"
+checksum = "df6e520eff47c45997d2fc7dd8214b25dd1310918bbb2642156ef66a67f29813"
 dependencies = [
  "proc-macro2",
  "pyo3-macros-backend",
@@ -2096,9 +2096,9 @@ dependencies = [
 
 [[package]]
 name = "pyo3-macros-backend"
-version = "0.28.2"
+version = "0.28.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "22faaa1ce6c430a1f71658760497291065e6450d7b5dc2bcf254d49f66ee700a"
+checksum = "c4cdc218d835738f81c2338f822078af45b4afdf8b2e33cbb5916f108b813acb"
 dependencies = [
  "heck",
  "proc-macro2",
@@ -2242,9 +2242,9 @@ dependencies = [
 
 [[package]]
 name = "referencing"
-version = "0.46.2"
+version = "0.46.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "acb0c66c7b78c1da928bee668b5cc638c678642ff587faff6e6222f797be9d4c"
+checksum = "cb674900ca31acd75c4aaf63f48e43e719631c0539ea5a9e64163d1296bcb730"
 dependencies = [
  "ahash",
  "fluent-uri",
@@ -2345,9 +2345,9 @@ dependencies = [
 
 [[package]]
 name = "rustc-hash"
-version = "2.1.1"
+version = "2.1.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "357703d41365b4b27c590e3ed91eabb1b663f07c4c084095e60cbed4362dff0d"
+checksum = "94300abf3f1ae2e2b8ffb7b58043de3d399c73fa6f4b73826402a5c457614dbe"
 
 [[package]]
 name = "rustc_version"
@@ -2449,9 +2449,9 @@ checksum = "94143f37725109f92c262ed2cf5e59bce7498c01bcc1502d7b9afe439a4e9f49"
 
 [[package]]
 name = "semver"
-version = "1.0.27"
+version = "1.0.28"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d767eb0aabc880b29956c35734170f26ed551a859dbd361d140cdbeca61ab1e2"
+checksum = "8a7852d02fc848982e0c167ef163aaff9cd91dc640ba85e263cb1ce46fae51cd"
 dependencies = [
  "serde",
  "serde_core",
diff --git a/Cargo.toml b/Cargo.toml
index 4d547f037..3b1700515 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -42,7 +42,7 @@ too_long_first_doc_paragraph = "warn"
 anyhow = "1.0.101"
 insta = { version = "1.47.2" }
 bitvec = "1.0.1"
-capnp = "0.25.2"
+capnp = "0.25.4"
 cgmath = "0.18.0"
 cool_asserts = "2.0.4"
 delegate = "0.13.5"
@@ -51,15 +51,15 @@ downcast-rs = "2.0.2"
 enum_dispatch = "0.3.11"
 html-escape = "0.2.13"
 itertools = "0.14.0"
-jsonschema = { version = "0.46.2", default-features = false }
+jsonschema = { version = "0.46.4", default-features = false }
 num-rational = "0.4.1"
-pastey = "0.2.1"
+pastey = "0.2.2"
 proptest = "1.11.0"
 proptest-derive = "0.8.0"
 regex = "1.12.3"
 regex-syntax = "0.8.9"
 rstest = "0.26.1"
-semver = "1.0.27"
+semver = "1.0.28"
 serde = "1.0.228"
 serde_json = "1.0.149"
 serde_with = "3.18.0"
@@ -70,14 +70,14 @@ static_assertions = "1.1.0"
 tempfile = "3.27"
 thiserror = "2.0.18"
 typetag = "0.2.21"
-clap = { version = "4.6.0" }
+clap = { version = "4.6.1" }
 clio = "0.3.5"
 clap-verbosity-flag = "3.0.4"
 assert_cmd = "2.2"
 assert_fs = "1.1.3"
 predicates = "3.1.4"
 indexmap = "2.14.0"
-rustc-hash = "2.1.1"
+rustc-hash = "2.1.2"
 bumpalo = "3.20.1"
 pathsearch = "0.2.0"
 base64 = "0.22.1"
@@ -94,7 +94,7 @@ schemars = "1.2.1"
 
 # These public dependencies usually require breaking changes downstream, so we
 # try to be as permissive as possible.
-portgraph = { version = "0.16.0" }
+portgraph = { version = "0.16.1" }
 petgraph = { version = ">= 0.8.3, < 0.9", default-features = false }
 # There can only be one `pyo3` dependency in the whole workspace, so we use a
 # loose version constraint to prevent breaking changes in dependent crates where possible.
diff --git a/hugr-llvm/Cargo.toml b/hugr-llvm/Cargo.toml
index 7f6c79d53..ba3369365 100644
--- a/hugr-llvm/Cargo.toml
+++ b/hugr-llvm/Cargo.toml
@@ -42,4 +42,4 @@ derive_more = { workspace = true, features = ["debug"] }
 hugr-llvm = { "path" = ".", features = ["test-utils"] }
 
 [build-dependencies]
-cc = "1.2.57"
+cc = "1.2.61"