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Start updating dependencies (#1163)
Progress towards #1162 and fixing security alerts. - `cargo update`: bumps versions in the lockfile - `cargo upgrade`: bumps manifest versions within current semranges - Then a few incompatible bumps (`dashmap 6`, `embed-resource 3`, `env_logger 0.11`,`itertools 0.14`, `libloading 0.9`, `strum 0.28`, `winsafe 0.0.27`,`xdg 3`) - Switched to rust-yaml2 as rust-yaml is unmaintained - More updates (base64 0.21 to 0.22, dirs 4 to 6, http 0.2 removed, rand 0.8 to 0.10,
2 parents 3278258 + 13277eb commit a168b38

16 files changed

Lines changed: 1387 additions & 1230 deletions

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‎Cargo.lock‎

Lines changed: 1309 additions & 1142 deletions
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‎Cargo.toml‎

Lines changed: 56 additions & 59 deletions
Original file line numberDiff line numberDiff line change
@@ -24,101 +24,98 @@ result_large_err = "allow"
2424
too_many_arguments = "allow"
2525

2626
[workspace.dependencies]
27-
actix-web = "4.4.0"
27+
actix-web = "4.13.0"
2828
aether_factory = { git = "https://github.com/posit-dev/air", package = "air_r_factory", rev = "4cbd36d552e27d8930cff1602d56bfd9ce4c1ed1" }
2929
aether_lsp_utils = { git = "https://github.com/posit-dev/air", rev = "4cbd36d552e27d8930cff1602d56bfd9ce4c1ed1" }
3030
aether_parser = { git = "https://github.com/posit-dev/air", package = "air_r_parser", rev = "4cbd36d552e27d8930cff1602d56bfd9ce4c1ed1" }
3131
aether_syntax = { git = "https://github.com/posit-dev/air", package = "air_r_syntax", rev = "4cbd36d552e27d8930cff1602d56bfd9ce4c1ed1" }
3232
amalthea = { path = "crates/amalthea" }
33-
anyhow = "1.0.100"
33+
anyhow = "1.0.102"
3434
ark = { path = "crates/ark" }
3535
ark_test = { path = "crates/ark_test" }
3636
assert_matches = "1.5.0"
37-
async-trait = "0.1.66"
38-
base64 = "0.21.0"
37+
async-trait = "0.1.89"
38+
base64 = "0.22.1"
3939
biome_line_index = { git = "https://github.com/lionel-/biome", rev = "41d799cfa4cedd25625fc3f6bd7898532873f051" }
4040
biome_rowan = { git = "https://github.com/lionel-/biome", rev = "41d799cfa4cedd25625fc3f6bd7898532873f051" }
41-
blake3 = "1.8.2"
42-
bus = "2.3.0"
43-
cc = "1.1.22"
44-
cfg-if = "1.0.0"
41+
blake3 = "1.8.4"
42+
bus = "2.4.1"
43+
cc = "1.2.60"
44+
cfg-if = "1.0.4"
4545
chrono = "0.4.44"
4646
crossbeam = { version = "0.8.4", features = ["crossbeam-channel"] }
47-
crypto-common = "0.1.6"
4847
ctor = "0.1.26"
4948
dap = { branch = "main", git = "https://github.com/sztomi/dap-rs" }
50-
dashmap = "5.4.0"
51-
dirs = "4.0.0"
52-
ego-tree = "0.6.2"
53-
embed-resource = "2.5.0"
54-
env_logger = "0.10.0"
49+
dashmap = "6.1.0"
50+
dirs = "6.0.0"
51+
ego-tree = "0.11.0"
52+
embed-resource = "3.0.8"
53+
env_logger = "0.11.10"
5554
etcetera = "0.11.0"
56-
flate2 = "1.1.1"
57-
futures = "0.3.30"
58-
generic-array = "0.14.6"
55+
flate2 = "1.1.9"
56+
futures = "0.3.32"
5957
harp = { path = "crates/harp" }
6058
harp-macros = { path = "crates/harp/harp-macros" }
6159
hex = "0.4.3"
62-
hmac = "0.12.1"
63-
home = "0.5.5"
64-
http = "0.2.9"
65-
insta = "1.39.0"
66-
itertools = "0.10.5"
67-
libc = "0.2.152"
68-
libloading = "0.8.1"
60+
hmac = "0.13.0"
61+
home = "0.5.12"
62+
insta = "1.47.2"
63+
itertools = "0.14.0"
64+
libc = "0.2.185"
65+
libloading = "0.9.0"
6966
libr = { path = "crates/libr" }
70-
log = "0.4.18"
71-
mime_guess = "2.0.4"
72-
nix = { version = "0.26.2", features = ["signal"] }
73-
notify = "6.0.0"
67+
log = "0.4.29"
68+
mime_guess = "2.0.5"
69+
nix = { version = "0.26.4", features = ["signal"] }
70+
notify = "8.2.0"
7471
oak_core = { path = "crates/oak_core" }
7572
oak_fs = { path = "crates/oak_fs" }
7673
oak_ide = { path = "crates/oak_ide" }
7774
oak_index = { path = "crates/oak_index" }
7875
oak_package = { path = "crates/oak_package" }
7976
oak_r_process = { path = "crates/oak_r_process" }
8077
oak_sources = { path = "crates/oak_sources" }
81-
once_cell = "1.17.1"
82-
parking_lot = "0.12.3"
83-
paste = "1.0.14"
84-
quote = "1.0.42"
85-
rand = "0.8.5"
86-
regex = "1.10.0"
78+
once_cell = "1.21.4"
79+
parking_lot = "0.12.5"
80+
paste = "1.0.15"
81+
quote = "1.0.45"
82+
rand = "0.10"
83+
regex = "1.12.3"
8784
reqwest = { version = "0.13.2", default-features = false, features = ["json"] }
8885
reqwest-middleware = "0.5.1"
8986
reqwest-retry = "0.9.1"
90-
rust-embed = "8.2.0"
91-
rustc-hash = "2.1.1"
92-
scraper = "0.15.0"
93-
semver = "1.0.19"
94-
serde = { version = "1.0.183", features = ["derive"] }
95-
serde_json = { version = "1.0.94", features = ["preserve_order"] }
96-
serde_repr = "0.1.17"
97-
serde_with = "3.0.0"
98-
sha2 = "0.10.6"
99-
smallvec = "1.13.2"
87+
rust-embed = "8.11.0"
88+
rustc-hash = "2.1.2"
89+
scraper = "0.26.0"
90+
semver = "1.0.28"
91+
serde = { version = "1.0.228", features = ["derive"] }
92+
serde_json = { version = "1.0.149", features = ["preserve_order"] }
93+
serde_repr = "0.1.20"
94+
serde_with = "3.18.0"
95+
sha2 = "0.11.0"
96+
smallvec = "1.15.1"
10097
stdext = { path = "crates/stdext" }
10198
streaming-iterator = "0.1.9"
102-
strum = "0.26.2"
103-
strum_macros = "0.26.2"
104-
syn = { version = "2.0.111", features = ["full"] }
105-
tar = "0.4.44"
106-
tempfile = "3.13.0"
107-
tokio = { version = "1.26.0", features = ["full"] }
99+
strum = "0.28.0"
100+
strum_macros = "0.28.0"
101+
syn = { version = "2.0.117", features = ["full"] }
102+
tar = "0.4.45"
103+
tempfile = "3.27.0"
104+
tokio = { version = "1.52.1", features = ["full"] }
108105
# For https://github.com/ebkalderon/tower-lsp/pull/428
109106
tower-lsp = { branch = "bugfix/patches", git = "https://github.com/lionel-/tower-lsp" }
110-
tracing = "0.1.40"
111-
tracing-appender = "0.2.3"
112-
tracing-error = "0.2.0"
113-
tracing-subscriber = { version = "0.3.18", features = ["env-filter"] }
107+
tracing = "0.1.44"
108+
tracing-appender = "0.2.5"
109+
tracing-error = "0.2.1"
110+
tracing-subscriber = { version = "0.3.23", features = ["env-filter"] }
114111
tree-sitter = "0.24.7"
115112
tree-sitter-r = { git = "https://github.com/r-lib/tree-sitter-r", rev = "95aff097aa927a66bb357f715b58cde821be8867" }
116113
ureq = "3.3.0"
117-
url = "2.5.7"
118-
uuid = { version = "1.3.0", features = ["v4"] }
114+
url = "2.5.8"
115+
uuid = { version = "1.23.1", features = ["v4"] }
119116
walkdir = "2"
120117
windows-sys ="0.61.2"
121-
winsafe = { version = "0.0.19", features = ["kernel"] }
122-
xdg = "2.5.2"
123-
yaml-rust = "0.4.5"
118+
winsafe = { version = "0.0.27", features = ["kernel"] }
119+
xdg = "3.0.0"
120+
yaml-rust2 = "0.9"
124121
zmq = "0.10.0"

‎crates/amalthea/Cargo.toml‎

Lines changed: 0 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -17,10 +17,8 @@ async-trait.workspace = true
1717
cfg-if.workspace = true
1818
chrono.workspace = true
1919
crossbeam.workspace = true
20-
crypto-common.workspace = true
2120
dirs.workspace = true
2221
futures.workspace = true
23-
generic-array.workspace = true
2422
hex.workspace = true
2523
hmac.workspace = true
2624
log.workspace = true

‎crates/amalthea/src/error.rs‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -29,7 +29,7 @@ pub enum Error {
2929
JsonSerializeSpecFailed(serde_json::Error),
3030
CreateSpecFailed(std::io::Error),
3131
WriteSpecFailed(std::io::Error),
32-
HmacKeyInvalid(String, crypto_common::InvalidLength),
32+
HmacKeyInvalid(String, hmac::digest::InvalidLength),
3333
CreateSocketFailed(String, zmq::Error),
3434
SocketBindError(String, String, zmq::Error),
3535
SocketConnectError(String, String, zmq::Error),

‎crates/amalthea/src/fixtures/dummy_frontend.rs‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -6,7 +6,7 @@
66
*/
77

88
use assert_matches::assert_matches;
9-
use rand::Rng;
9+
use rand::RngExt;
1010
use serde_json::Value;
1111

1212
use crate::connection_file::ConnectionFile;
@@ -65,7 +65,7 @@ impl Default for DummyConnection {
6565
impl DummyConnection {
6666
pub fn new() -> Self {
6767
// Create a random HMAC key for signing messages.
68-
let key_bytes = rand::thread_rng().gen::<[u8; 16]>();
68+
let key_bytes = rand::rng().random::<[u8; 16]>();
6969
let key = hex::encode(key_bytes);
7070

7171
// Create a new kernel session from the key
@@ -144,7 +144,7 @@ impl DummyFrontend {
144144

145145
// Create a random socket identity for the shell and stdin sockets. Per
146146
// the Jupyter specification, these must share a ZeroMQ identity.
147-
let shell_id = rand::thread_rng().gen::<[u8; 16]>();
147+
let shell_id = rand::rng().random::<[u8; 16]>();
148148

149149
let control_socket = Socket::new(
150150
connection.session.clone(),

‎crates/amalthea/src/session.rs‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -6,7 +6,7 @@
66
*/
77

88
use hmac::Hmac;
9-
use hmac::Mac;
9+
use hmac::KeyInit;
1010
use sha2::Sha256;
1111
use uuid::Uuid;
1212

‎crates/amalthea/src/wire/wire_message.rs‎

Lines changed: 1 addition & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -5,7 +5,6 @@
55
*
66
*/
77

8-
use generic_array::GenericArray;
98
use hmac::Hmac;
109
use log::trace;
1110
use serde::de::DeserializeOwned;
@@ -162,7 +161,7 @@ impl WireMessage {
162161
hmac_validator.update(buf);
163162
}
164163
// Verify the signature
165-
if let Err(err) = hmac_validator.verify(GenericArray::from_slice(&decoded)) {
164+
if let Err(err) = hmac_validator.verify_slice(&decoded) {
166165
return Err(Error::BadSignature(decoded, err));
167166
}
168167

‎crates/ark/Cargo.toml‎

Lines changed: 1 addition & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -36,7 +36,6 @@ ego-tree.workspace = true
3636
futures.workspace = true
3737
harp.workspace = true
3838
home.workspace = true
39-
http.workspace = true
4039
itertools.workspace = true
4140
libc.workspace = true
4241
libr.workspace = true
@@ -74,7 +73,7 @@ url.workspace = true
7473
uuid.workspace = true
7574
walkdir.workspace = true
7675
winsafe.workspace = true
77-
yaml-rust.workspace = true
76+
yaml-rust2.workspace = true
7877

7978
[dev-dependencies]
8079
ark_test.workspace = true

‎crates/ark/build.rs‎

Lines changed: 3 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -65,7 +65,9 @@ fn main() {
6565
let resource = Path::new("resources")
6666
.join("manifest")
6767
.join("ark-manifest.rc");
68-
embed_resource::compile_for_everything(resource, embed_resource::NONE);
68+
embed_resource::compile_for_everything(resource, embed_resource::NONE)
69+
.manifest_required()
70+
.unwrap();
6971

7072
cc::Build::new().file("src/debug.c").compile("debug");
7173
}

‎crates/ark/src/help_proxy.rs‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -9,14 +9,14 @@ use std::net::TcpListener;
99

1010
use actix_web::get;
1111
use actix_web::http::header::ContentType;
12+
use actix_web::http::uri::PathAndQuery;
1213
use actix_web::web;
1314
use actix_web::App;
1415
use actix_web::HttpRequest;
1516
use actix_web::HttpResponse;
1617
use actix_web::HttpServer;
1718
use harp::exec::RFunction;
1819
use harp::exec::RFunctionExt;
19-
use http::uri::PathAndQuery;
2020
use mime_guess::from_path;
2121
use reqwest::Client;
2222
use reqwest_middleware::ClientBuilder;

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