diff --git a/.github/workflows/rust.yml b/.github/workflows/rust.yml index 7b954739..8844d2a5 100644 --- a/.github/workflows/rust.yml +++ b/.github/workflows/rust.yml @@ -79,8 +79,8 @@ jobs: - name: Run cargo-tarpaulin uses: actions-rs/tarpaulin@v0.1 with: - version: 0.16.0 - args: "-- --test-threads 1" + version: 0.21.0 + args: "--skip-clean -- --test-threads 1" - name: Codecov uses: codecov/codecov-action@v3 diff --git a/Cargo.lock b/Cargo.lock index d2e09d09..33348446 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -253,48 +253,6 @@ dependencies = [ "libc", ] -[[package]] -name = "annonars" -version = "0.20.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "856d2a30152c991d240d14a38c724f0f800e65d44a5b9ea34279cd67a9e6f912" -dependencies = [ - "actix-web", - "anyhow", - "bgzip", - "boolvec", - "byteorder", - "chrono", - "clap", - "clap-verbosity-flag", - "csv", - "enum-map 2.6.3", - "env_logger", - "flate2", - "hgvs", - "indexmap 2.0.2", - "indicatif", - "log", - "noodles-bed", - "noodles-bgzf", - "noodles-core", - "noodles-csi", - "noodles-tabix", - "noodles-vcf 0.39.0", - "prost", - "prost-build", - "rayon", - "rocksdb", - "rocksdb-utils-lookup", - "serde", - "serde_json", - "serde_with", - "strum", - "thiserror", - "tracing", - "tracing-subscriber", -] - [[package]] name = "annonars" version = "0.21.0" @@ -322,7 +280,7 @@ dependencies = [ "noodles-core", "noodles-csi", "noodles-tabix", - "noodles-vcf 0.40.0", + "noodles-vcf", "prost", "prost-build", "rayon", @@ -882,9 +840,9 @@ dependencies = [ [[package]] name = "csv" -version = "1.2.2" +version = "1.3.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "626ae34994d3d8d668f4269922248239db4ae42d538b14c398b74a52208e8086" +checksum = "ac574ff4d437a7b5ad237ef331c17ccca63c46479e5b5453eb8e10bb99a759fe" dependencies = [ "csv-core", "itoa", @@ -894,9 +852,9 @@ dependencies = [ [[package]] name = "csv-core" -version = "0.1.10" +version = "0.1.11" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "2b2466559f260f48ad25fe6317b3c8dac77b5bdb5763ac7d9d6103530663bc90" +checksum = "5efa2b3d7902f4b634a20cae3c9c4e6209dc4779feb6863329607560143efa70" dependencies = [ "memchr", ] @@ -1614,7 +1572,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "cb0889898416213fab133e1d33a0e5858a48177452750691bde3666d0fdbaf8b" dependencies = [ "hermit-abi", - "rustix 0.38.15", + "rustix 0.38.17", "windows-sys 0.48.0", ] @@ -1831,12 +1789,12 @@ dependencies = [ [[package]] name = "mehari" -version = "0.7.0" +version = "0.8.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "4a26fc67865c0e7536b74f167bc78ed179d21eb28f0c7f0f8dbe9ad20b3dc0a0" +checksum = "876048178b1469372ec642af0d6c616aeac0f7dc18c405518a5779d41077ea5d" dependencies = [ "actix-web", - "annonars 0.20.0", + "annonars", "anyhow", "bgzip", "bio", @@ -1861,7 +1819,7 @@ dependencies = [ "noodles-csi", "noodles-fasta", "noodles-tabix", - "noodles-vcf 0.39.0", + "noodles-vcf", "parse-display", "procfs", "prost", @@ -2076,21 +2034,6 @@ dependencies = [ "noodles-csi", ] -[[package]] -name = "noodles-vcf" -version = "0.39.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "1a056c06c7b33d5ba10bb59c09cca9500b02c3e0ead964dd4cf8f0068159783a" -dependencies = [ - "indexmap 2.0.2", - "memchr", - "noodles-bgzf", - "noodles-core", - "noodles-csi", - "noodles-tabix", - "percent-encoding", -] - [[package]] name = "noodles-vcf" version = "0.40.0" @@ -2796,9 +2739,9 @@ dependencies = [ [[package]] name = "rustix" -version = "0.38.15" +version = "0.38.17" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "d2f9da0cbd88f9f09e7814e388301c8414c51c62aa6ce1e4b5c551d49d96e531" +checksum = "f25469e9ae0f3d0047ca8b93fc56843f38e6774f0914a107ff8b41be8be8e0b7" dependencies = [ "bitflags 2.4.0", "errno", @@ -2977,9 +2920,9 @@ dependencies = [ [[package]] name = "sharded-slab" -version = "0.1.6" +version = "0.1.7" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "c1b21f559e07218024e7e9f90f96f601825397de0e25420135f7f952453fed0b" +checksum = "f40ca3c46823713e0d4209592e8d6e826aa57e928f09752619fc696c499637f6" dependencies = [ "lazy_static", ] @@ -3186,7 +3129,7 @@ dependencies = [ "cfg-if", "fastrand", "redox_syscall 0.3.5", - "rustix 0.38.15", + "rustix 0.38.17", "windows-sys 0.48.0", ] @@ -3477,7 +3420,7 @@ checksum = "830b7e5d4d90034032940e4ace0d9a9a057e7a45cd94e6c007832e39edb82f6d" name = "varfish-server-worker" version = "0.10.2" dependencies = [ - "annonars 0.21.0", + "annonars", "anyhow", "base16ct", "bio", @@ -3623,7 +3566,7 @@ dependencies = [ "either", "home", "once_cell", - "rustix 0.38.15", + "rustix 0.38.17", ] [[package]] diff --git a/Cargo.toml b/Cargo.toml index 011d710e..a6a964d9 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -30,7 +30,7 @@ indexmap = { version = "2.0", features = ["serde"] } itertools = "0.11" lazy_static = "1.4" log = "0.4" -mehari = "0.7" +mehari = "0.8" multimap = "0.9" procfs = "0.15" prost = "0.12"