Update Deps incuding HF-hub (#103)

* bump deps * cand;e_hf_hub- -> hf-hub
ferritin-bio · Jan 5, 2025 · 830a3a8 · 830a3a8
1 parent 208a766
commit 830a3a8
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Showing 12 changed files with 219 additions and 159 deletions.
diff --git a/Cargo.lock b/Cargo.lock
diff --git a/Cargo.toml b/Cargo.toml
@@ -24,10 +24,10 @@ anyhow = "1.0"
 bitflags = "2.6.0"
 candle-core = "0.8.1"
 candle-examples = "0.8.1"
-candle-hf-hub = "0.3.3"
 candle-metal-kernels = "0.8.1"
 candle-nn = "0.8.1"
 candle-transformers = "0.8.1"
+hf-hub = "0.4.1"
 itertools = "0.14.0"
 once_cell = "1.20.2"
 pdbtbx = "0.12.0"

diff --git a/ferritin-bevy/Cargo.toml b/ferritin-bevy/Cargo.toml
@@ -7,7 +7,7 @@ license.workspace = true
 description.workspace = true
 
 [dependencies]
-bevy = "0.15.0"
+bevy = "0.15.1"
 bon = "3.3.2"
 ferritin-core = { path = "../ferritin-core" }
 pdbtbx.workspace = true

diff --git a/ferritin-examples/Cargo.toml b/ferritin-examples/Cargo.toml
@@ -11,16 +11,16 @@ metal = ["candle-core/metal", "candle-nn/metal", "candle-metal-kernels"]
 
 [dependencies]
 anyhow.workspace = true
-bevy = "0.15.0"
+bevy = "0.15.1"
 candle-core.workspace = true
-candle-hf-hub.workspace = true
 candle-metal-kernels = { workspace = true, optional = true }
 candle-nn.workspace = true
 clap = { version = "4.5.23", features = ["derive"] }
 ferritin-bevy = { path = "../ferritin-bevy" }
 ferritin-core = { path = "../ferritin-core" }
 ferritin-plms = { path = "../ferritin-plms" }
 ferritin-onnx-models = { path = "../ferritin-onnx-models" }
+hf-hub.workspace = true
 ndarray = "0.16"
 ort = "=2.0.0-rc.9"
 pdbtbx.workspace = true
@@ -39,8 +39,8 @@ tokenizers = { version = "0.21.0", default-features = false, features = [
 ] }
 
 [target.'cfg(not(target_arch = "wasm32"))'.dependencies]
-candle-hf-hub = { workspace = true }
-tokenizers = { version = "0.21.0" }  # full features for non-wasm
+hf-hub.workspace = true
+tokenizers = { version = "0.21.0" } # full features for non-wasm
 
 
 [dev-dependencies]

diff --git a/ferritin-examples/examples/esm2/main.rs b/ferritin-examples/examples/esm2/main.rs
@@ -2,10 +2,10 @@ use anyhow::{Error as E, Result};
 use candle_core::safetensors::load;
 use candle_core::{DType, Tensor};
 use candle_examples::device;
-use candle_hf_hub::{api::sync::Api, Repo, RepoType};
 use candle_nn::VarBuilder;
 use clap::Parser;
 use ferritin_plms::{ESM2Config as Config, ESM2};
+use hf_hub::{api::sync::Api, Repo, RepoType};
 use tokenizers::Tokenizer;
 
 pub const DTYPE: DType = DType::F32;

diff --git a/ferritin-examples/examples/esmc/main.rs b/ferritin-examples/examples/esmc/main.rs
@@ -1,8 +1,8 @@
 use anyhow::Result;
 use candle_core::pickle::PthTensors;
 use candle_core::{DType, Device};
-use candle_hf_hub::{api::sync::Api, Repo, RepoType};
 use candle_nn::VarBuilder;
+use hf_hub::{api::sync::Api, Repo, RepoType};
 use ferritin_plms::{ESMCConfig, ESMC};
 
 // pub fn esmc_300m_202412(device: &Device) -> Result<Box<dyn Model>> {

diff --git a/ferritin-onnx-models/Cargo.toml b/ferritin-onnx-models/Cargo.toml
@@ -10,9 +10,9 @@ description.workspace = true
 anyhow.workspace = true
 candle-core.workspace = true
 candle-nn.workspace = true
-candle-hf-hub.workspace = true
+hf-hub.workspace = true
 ndarray = "0.16"
-ndarray-safetensors = "0.2.0"
+ndarray-safetensors = "0.2.1"
 ort = "=2.0.0-rc.9"
 safetensors.workspace = true
 serde.workspace = true

diff --git a/ferritin-onnx-models/src/models/amplify/mod.rs b/ferritin-onnx-models/src/models/amplify/mod.rs
@@ -18,7 +18,7 @@
 //! - [Paper](https://www.biorxiv.org/content/10.1101/2024.09.23.614603v1)
 //!
 use anyhow::{anyhow, Result};
-use candle_hf_hub::api::sync::Api;
+use hf_hub::api::sync::Api;
 use std::path::PathBuf;
 use tokenizers::Tokenizer;
 

diff --git a/ferritin-onnx-models/src/models/esm2/mod.rs b/ferritin-onnx-models/src/models/esm2/mod.rs
@@ -11,9 +11,9 @@
 use super::super::utilities::ndarray_to_tensor_f32;
 use anyhow::{anyhow, Result};
 use candle_core::{Tensor, D};
-use candle_hf_hub::api::sync::Api;
 use candle_nn::ops;
 use ferritin_plms::types::PseudoProbability;
+use hf_hub::api::sync::Api;
 use ndarray::Array2;
 use ort::{
     execution_providers::CUDAExecutionProvider,

diff --git a/ferritin-onnx-models/src/models/ligandmpnn/mod.rs b/ferritin-onnx-models/src/models/ligandmpnn/mod.rs
@@ -9,11 +9,11 @@
 use crate::{ndarray_to_tensor_f32, tensor_to_ndarray_f32, tensor_to_ndarray_i64};
 use anyhow::Result;
 use candle_core::{Device, Tensor};
-use candle_hf_hub::api::sync::Api;
 use candle_nn::ops;
 use ferritin_core::{AtomCollection, StructureFeatures};
 use ferritin_plms::ligandmpnn::utilities::int_to_aa1;
 use ferritin_plms::types::PseudoProbability;
+use hf_hub::api::sync::Api;
 use ndarray::ArrayBase;
 use ort::{
     execution_providers::CUDAExecutionProvider,

diff --git a/ferritin-plms/Cargo.toml b/ferritin-plms/Cargo.toml
@@ -18,13 +18,13 @@ metal = [
 [dependencies]
 anyhow.workspace = true
 candle-core.workspace = true
-candle-hf-hub.workspace = true
 candle-metal-kernels = { workspace = true, optional = true }
 candle-nn.workspace = true
 candle-transformers.workspace = true
 clap = { version = "4.5", features = ["derive"] }
 ferritin-core = { path = "../ferritin-core" }
 ferritin-test-data = { path = "../ferritin-test-data" }
+hf-hub.workspace = true
 itertools.workspace = true
 pdbtbx.workspace = true
 rand.workspace = true

diff --git a/ferritin-plms/src/amplify/amplify_runner.rs b/ferritin-plms/src/amplify/amplify_runner.rs
@@ -8,9 +8,9 @@ use super::config::AMPLIFYConfig;
 use super::outputs::ModelOutput;
 use anyhow::{anyhow, Error as E, Result};
 use candle_core::{DType, Device, Tensor, D};
-use candle_hf_hub::{api::sync::Api, Repo, RepoType};
 use candle_nn::ops;
 use candle_nn::VarBuilder;
+use hf_hub::{api::sync::Api, Repo, RepoType};
 use tokenizers::Tokenizer;
 
 pub enum AmplifyModels {