From fdf07ca3af8ebe85346f8b12b71dd405dc555782 Mon Sep 17 00:00:00 2001 From: Zachary Charlop-Powers Date: Fri, 6 Dec 2024 20:16:11 -0500 Subject: [PATCH 1/2] add Readme.md --- Readme.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Readme.md b/Readme.md index e0e84e67..137bfd36 100644 --- a/Readme.md +++ b/Readme.md @@ -2,4 +2,4 @@ Protein utilities for Rust -![](ferritin.png) + From 3a2b95731841ef889c6246838eed3a0237ca9b7e Mon Sep 17 00:00:00 2001 From: Zachary Charlop-Powers Date: Sat, 7 Dec 2024 15:50:57 -0500 Subject: [PATCH 2/2] upate to Candle 0.8.1 --- Cargo.lock | 25 +++++++++++++++---------- Cargo.toml | 10 +++++----- ferritin-amplify/Cargo.toml | 3 ++- ferritin-esm/Cargo.toml | 3 ++- ferritin-examples/Cargo.toml | 4 +++- ferritin-ligandmpnn/Cargo.toml | 4 +++- 6 files changed, 30 insertions(+), 19 deletions(-) diff --git a/Cargo.lock b/Cargo.lock index 1324805e..fbdd505b 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -1563,8 +1563,9 @@ dependencies = [ [[package]] name = "candle-core" -version = "0.8.0" -source = "git+https://github.com/huggingface/candle.git#1807be84f4d9e388b19710a9282eb6501ce55f80" +version = "0.8.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "d1e306c8a4276ba57ce9fac76d823cc8c8a7fca14bf222ac20ad8b12c4273152" dependencies = [ "byteorder", "candle-metal-kernels", @@ -1587,8 +1588,9 @@ dependencies = [ [[package]] name = "candle-examples" -version = "0.8.0" -source = "git+https://github.com/huggingface/candle.git#1807be84f4d9e388b19710a9282eb6501ce55f80" +version = "0.8.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "3bdceca3faa253f7140230f8eb9ac05ed0c10c7e33afeb9ee0d7fa6305a5d946" dependencies = [ "anyhow", "candle-core", @@ -1628,8 +1630,9 @@ dependencies = [ [[package]] name = "candle-metal-kernels" -version = "0.8.0" -source = "git+https://github.com/huggingface/candle.git#1807be84f4d9e388b19710a9282eb6501ce55f80" +version = "0.8.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "cbc6621c7e2202f4f129bcc3185c2c6d4fa2fc6b8f3f2b07eaf7c06042910c83" dependencies = [ "metal 0.27.0", "once_cell", @@ -1639,8 +1642,9 @@ dependencies = [ [[package]] name = "candle-nn" -version = "0.8.0" -source = "git+https://github.com/huggingface/candle.git#1807be84f4d9e388b19710a9282eb6501ce55f80" +version = "0.8.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "39d417059c44d719fd03a0f711ccfe148d341469c9273d4b5731ebe965b2c97e" dependencies = [ "candle-core", "candle-metal-kernels", @@ -1655,8 +1659,9 @@ dependencies = [ [[package]] name = "candle-transformers" -version = "0.8.0" -source = "git+https://github.com/huggingface/candle.git#1807be84f4d9e388b19710a9282eb6501ce55f80" +version = "0.8.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "962a277e90dea20968164175138b836bba8b51b57505579fd628d79933da2b70" dependencies = [ "byteorder", "candle-core", diff --git a/Cargo.toml b/Cargo.toml index 0c16bf2c..8dc5781c 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -17,12 +17,12 @@ resolver = "2" [workspace.dependencies] anyhow = "1.0" bitflags = "2.6.0" -candle-core = { git = "https://github.com/huggingface/candle.git", package = "candle-core", features = [ -] } -candle-examples = { git = "https://github.com/huggingface/candle.git", package = "candle-examples" } +candle-core = "0.8.1" +candle-examples = "0.8.1" candle-hf-hub = "0.3.3" -candle-nn = { git = "https://github.com/huggingface/candle.git", package = "candle-nn" } -candle-transformers = { git = "https://github.com/huggingface/candle.git", package = "candle-transformers" } +candle-metal-kernels = "0.8.1" +candle-nn = "0.8.1" +candle-transformers = "0.8.1" itertools = "0.13.0" once_cell = "1.20.2" pdbtbx = "0.12.0" diff --git a/ferritin-amplify/Cargo.toml b/ferritin-amplify/Cargo.toml index 1b2524b4..07c54cdc 100644 --- a/ferritin-amplify/Cargo.toml +++ b/ferritin-amplify/Cargo.toml @@ -12,6 +12,7 @@ metal = ["candle-core/metal", "candle-nn/metal", "candle-metal-kernels"] [dependencies] anyhow.workspace = true candle-core.workspace = true +candle-metal-kernels = { workspace = true, optional = true } candle-nn.workspace = true ferritin-test-data = { path = "../ferritin-test-data" } rand.workspace = true @@ -22,7 +23,7 @@ serde.workspace = true metal = [] [target.'cfg(target_os = "macos")'.dependencies] -candle-metal-kernels = { git = "https://github.com/huggingface/candle.git", package = "candle-metal-kernels", optional = true } +candle-metal-kernels.workspace = true [target.'cfg(target_arch = "wasm32")'.dependencies] tokenizers = { version = "0.21.0", default-features = false, features = [ diff --git a/ferritin-esm/Cargo.toml b/ferritin-esm/Cargo.toml index 29f9b8c9..3e374072 100644 --- a/ferritin-esm/Cargo.toml +++ b/ferritin-esm/Cargo.toml @@ -18,13 +18,14 @@ ferritin-test-data = { path = "../ferritin-test-data" } rand.workspace = true safetensors.workspace = true tokenizers.workspace = true +candle-metal-kernels = { workspace = true, optional = true } [target.'cfg(target_os = "macos")'.features] metal = [] [target.'cfg(target_os = "macos")'.dependencies] -candle-metal-kernels = { git = "https://github.com/huggingface/candle.git", package = "candle-metal-kernels", optional = true } +candle-metal-kernels.workspace = true [dev-dependencies] candle-examples.workspace = true diff --git a/ferritin-examples/Cargo.toml b/ferritin-examples/Cargo.toml index 44ca701b..9747aa19 100644 --- a/ferritin-examples/Cargo.toml +++ b/ferritin-examples/Cargo.toml @@ -16,12 +16,14 @@ candle-nn.workspace = true clap = { version = "4.5.23", features = ["derive"] } ferritin-amplify = { path = "../ferritin-amplify" } serde_json.workspace = true +candle-metal-kernels = { workspace = true, optional = true } + [target.'cfg(target_os = "macos")'.features] metal = [] [target.'cfg(target_os = "macos")'.dependencies] -candle-metal-kernels = { git = "https://github.com/huggingface/candle.git", package = "candle-metal-kernels", optional = true } +candle-metal-kernels.workspace = true [target.'cfg(target_arch = "wasm32")'.dependencies] tokenizers = { version = "0.21.0", default-features = false, features = [ diff --git a/ferritin-ligandmpnn/Cargo.toml b/ferritin-ligandmpnn/Cargo.toml index 5b408726..667e5fd4 100644 --- a/ferritin-ligandmpnn/Cargo.toml +++ b/ferritin-ligandmpnn/Cargo.toml @@ -17,6 +17,7 @@ metal = [ [dependencies] anyhow.workspace = true candle-core.workspace = true +candle-metal-kernels = { workspace = true, optional = true } candle-nn.workspace = true candle-transformers.workspace = true clap = "4.5.23" @@ -33,7 +34,8 @@ strum = { version = "0.26", features = ["derive"] } metal = [] [target.'cfg(target_os = "macos")'.dependencies] -candle-metal-kernels = { git = "https://github.com/huggingface/candle.git", package = "candle-metal-kernels", optional = true } +candle-metal-kernels.workspace = true + [dev-dependencies] candle-examples.workspace = true