rust-sasa-python 0.7.1__tar.gz → 0.7.3__tar.gz

{rust_sasa_python-0.7.1 → rust_sasa_python-0.7.3}/Cargo.lock

@@ -160,12 +160,6 @@ dependencies = [
  "hashbrown",
 ]
 
-[[package]]
-name = "indoc"
-version = "2.0.5"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b248f5224d1d606005e02c97f5aa4e88eeb230488bcc03bc9ca4d7991399f2b5"
-
 [[package]]
 name = "libc"
 version = "0.2.153"
@@ -188,15 +182,6 @@ dependencies = [
  "libc",
 ]
 
-[[package]]
-name = "memoffset"
-version = "0.9.1"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "488016bfae457b036d996092f6cb448677611ce4449e970ceaf42695203f218a"
-dependencies = [
- "autocfg",
-]
-
 [[package]]
 name = "mimalloc"
 version = "0.1.48"
@@ -237,9 +222,9 @@ dependencies = [
 
 [[package]]
 name = "once_cell"
-version = "1.19.0"
+version = "1.21.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "3fdb12b2476b595f9358c5161aa467c2438859caa136dec86c26fdd2efe17b92"
+checksum = "9f7c3e4beb33f85d45ae3e3a1792185706c8e16d043238c593331cc7cd313b50"
 
 [[package]]
 name = "paste"
@@ -310,36 +295,32 @@ checksum = "40e24eee682d89fb193496edf918a7f407d30175b2e785fe057e4392dfd182e0"
 
 [[package]]
 name = "pyo3"
-version = "0.25.1"
+version = "0.29.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "8970a78afe0628a3e3430376fc5fd76b6b45c4d43360ffd6cdd40bdde72b682a"
+checksum = "700d18fa267b73b9b521fd7e13580e2f446916f176cacee1ab63fcc8191f1655"
 dependencies = [
- "indoc",
  "libc",
- "memoffset",
  "once_cell",
  "portable-atomic",
  "pyo3-build-config",
  "pyo3-ffi",
  "pyo3-macros",
- "unindent",
 ]
 
 [[package]]
 name = "pyo3-build-config"
-version = "0.25.1"
+version = "0.29.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "458eb0c55e7ece017adeba38f2248ff3ac615e53660d7c71a238d7d2a01c7598"
+checksum = "7b3fc0c4d08f6bb10e71fe39dfb9e2f59c6eb6854e22ec8092f50c69a4499adb"
 dependencies = [
- "once_cell",
  "target-lexicon",
 ]
 
 [[package]]
 name = "pyo3-ffi"
-version = "0.25.1"
+version = "0.29.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7114fe5457c61b276ab77c5055f206295b812608083644a5c5b2640c3102565c"
+checksum = "dfc0b8e19df29aad7086cf977bb0c2a2f143e30567eb113e9cf72b62ca698330"
 dependencies = [
  "libc",
  "pyo3-build-config",
@@ -347,26 +328,25 @@ dependencies = [
 
 [[package]]
 name = "pyo3-macros"
-version = "0.25.1"
+version = "0.29.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a8725c0a622b374d6cb051d11a0983786448f7785336139c3c94f5aa6bef7e50"
+checksum = "6100e8a4b5eba53afaa5ed078364851a0b2499c553a44c31026b929049b49dc6"
 dependencies = [
  "proc-macro2 1.0.95",
  "pyo3-macros-backend",
- "quote 1.0.36",
+ "quote 1.0.47",
  "syn",
 ]
 
 [[package]]
 name = "pyo3-macros-backend"
-version = "0.25.1"
+version = "0.29.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "4109984c22491085343c05b0dbc54ddc405c3cf7b4374fc533f5c3313a572ccc"
+checksum = "6143877a16e82b5a727b7127ff4cd86858a24a28d745d72f43e6f227c7b1bdb3"
 dependencies = [
  "heck",
  "proc-macro2 1.0.95",
- "pyo3-build-config",
- "quote 1.0.36",
+ "quote 1.0.47",
  "syn",
 ]
 
@@ -381,9 +361,9 @@ dependencies = [
 
 [[package]]
 name = "quote"
-version = "1.0.36"
+version = "1.0.47"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "0fa76aaf39101c457836aec0ce2316dbdc3ab723cdda1c6bd4e6ad4208acaca7"
+checksum = "1fbf4db142a473a8d80c26bbf18454ed458bf8d26c8219c331daecfdbd079001"
 dependencies = [
  "proc-macro2 1.0.95",
 ]
@@ -436,9 +416,9 @@ dependencies = [
 
 [[package]]
 name = "rust-sasa"
-version = "0.9.1"
+version = "0.9.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c6f7a7e52e93d1869826869f1a3d9212ddf40b829c318d9fc9ee1466f1cb9bbe"
+checksum = "f670125d1727b9c8d30dc66558a669b2278bb03a03b608282c5031147b860684"
 dependencies = [
  "fnv",
  "pdbtbx",
@@ -449,7 +429,7 @@ dependencies = [
 
 [[package]]
 name = "rust-sasa-python"
-version = "0.7.1"
+version = "0.7.3"
 dependencies = [
  "mimalloc",
  "num-complex",
@@ -485,7 +465,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "d540f220d3187173da220f885ab66608367b6574e925011a9353e4badda91d79"
 dependencies = [
  "proc-macro2 1.0.95",
- "quote 1.0.36",
+ "quote 1.0.47",
  "syn",
 ]
 
@@ -518,7 +498,7 @@ checksum = "c1c97747dbf44bb1ca44a561ece23508e99cb592e862f22222dcf42f51d1e451"
 dependencies = [
  "heck",
  "proc-macro2 1.0.95",
- "quote 1.0.36",
+ "quote 1.0.47",
  "syn",
 ]
 
@@ -535,15 +515,15 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "17b6f705963418cdb9927482fa304bc562ece2fdd4f616084c50b7023b435a40"
 dependencies = [
  "proc-macro2 1.0.95",
- "quote 1.0.36",
+ "quote 1.0.47",
  "unicode-ident",
 ]
 
 [[package]]
 name = "target-lexicon"
-version = "0.13.2"
+version = "0.13.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e502f78cdbb8ba4718f566c418c52bc729126ffd16baee5baa718cf25dd5a69a"
+checksum = "adb6935a6f5c20170eeceb1a3835a49e12e19d792f6dd344ccc76a985ca5a6ca"
 
 [[package]]
 name = "unicode-ident"
@@ -557,12 +537,6 @@ version = "0.1.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "fc72304796d0818e357ead4e000d19c9c174ab23dc11093ac919054d20a6a7fc"
 
-[[package]]
-name = "unindent"
-version = "0.2.3"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c7de7d73e1754487cb58364ee906a499937a0dfabd86bcb980fa99ec8c8fa2ce"
-
 [[package]]
 name = "version_check"
 version = "0.9.5"

{rust_sasa_python-0.7.1 → rust_sasa_python-0.7.3}/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "rust-sasa-python"
-version = "0.7.1"
+version = "0.7.3"
 edition = "2024"
 readme = "README.md"
 
@@ -11,8 +11,8 @@ crate-type = ["cdylib"]
 
 [dependencies]
 pdbtbx = "0.12.0"
-pyo3 = "0.25.1"
-rust-sasa = "0.9.1"
+pyo3 = "0.29.3"
+rust-sasa = "0.9.2"
 mimalloc = "0.1.47"
 num-complex = "0.4.6"
 pulp = "0.22.2"

{rust_sasa_python-0.7.1 → rust_sasa_python-0.7.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rust-sasa-python
-Version: 0.7.1
+Version: 0.7.3
 Classifier: Programming Language :: Rust
 Classifier: Programming Language :: Python :: Implementation :: CPython
 Classifier: Programming Language :: Python :: Implementation :: PyPy
@@ -16,20 +16,27 @@ Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
 
 # rust-sasa-python
 
-A high-performance **Python library** for computing SASA (Solvent Accessible Surface Area) using Rust as the backend. This library provides a clean, Pythonic interface to the fast RustSASA calculation engine.
+A high-performance **Python library** for computing SASA (Solvent Accessible Surface Area) using Rust as the backend. This library provides a clean, Pythonic interface to the fast RustSASA calculation engine. If you use RustSASA in your research, please [cite it](https://github.com/maxall41/RustSASA#how-to-cite).
 
 ## Features
 
-- 🦀 **Powered by [RustSASA](https://github.com/maxall41/RustSASA)**: Leverages Rust's performance and safety.
-- ⚡️ **Ludicrous Speed**: **63X** faster than Biopython, **5X** faster than Freesasa.
-- 🐍 **Pythonic Interface**: Clean, intuitive API.
-- 🔧 **Configurable**: Customizable probe radius and sampling points.
-- 📁 **PDB and mmCIF SUPPORT**: Supports both PDB and mmCIF files.
+- **Powered by [RustSASA](https://github.com/maxall41/RustSASA)**: Leverages Rust's performance and safety.
+- **Ludicrous Speed**: **63X** faster than Biopython, **5X** faster than Freesasa.
+- **Pythonic Interface**: Clean, intuitive API.
+- **Configurable**: Customizable probe radius and sampling points.
+- **PDB and mmCIF SUPPORT**: Supports both PDB and mmCIF files.
 
 ## Installation
 
-```bash
+```shell
+# PyPI
 pip install rust-sasa-python
+
+# conda
+conda install -c conda-forge rust-sasa-python
+
+# mamba
+mamba install -c conda-forge rust-sasa-python
 ```
 
 ## Quick Start

{rust_sasa_python-0.7.1 → rust_sasa_python-0.7.3}/README.md

@@ -1,19 +1,26 @@
 # rust-sasa-python
 
-A high-performance **Python library** for computing SASA (Solvent Accessible Surface Area) using Rust as the backend. This library provides a clean, Pythonic interface to the fast RustSASA calculation engine.
+A high-performance **Python library** for computing SASA (Solvent Accessible Surface Area) using Rust as the backend. This library provides a clean, Pythonic interface to the fast RustSASA calculation engine. If you use RustSASA in your research, please [cite it](https://github.com/maxall41/RustSASA#how-to-cite).
 
 ## Features
 
-- 🦀 **Powered by [RustSASA](https://github.com/maxall41/RustSASA)**: Leverages Rust's performance and safety.
-- ⚡️ **Ludicrous Speed**: **63X** faster than Biopython, **5X** faster than Freesasa.
-- 🐍 **Pythonic Interface**: Clean, intuitive API.
-- 🔧 **Configurable**: Customizable probe radius and sampling points.
-- 📁 **PDB and mmCIF SUPPORT**: Supports both PDB and mmCIF files.
+- **Powered by [RustSASA](https://github.com/maxall41/RustSASA)**: Leverages Rust's performance and safety.
+- **Ludicrous Speed**: **63X** faster than Biopython, **5X** faster than Freesasa.
+- **Pythonic Interface**: Clean, intuitive API.
+- **Configurable**: Customizable probe radius and sampling points.
+- **PDB and mmCIF SUPPORT**: Supports both PDB and mmCIF files.
 
 ## Installation
 
-```bash
+```shell
+# PyPI
 pip install rust-sasa-python
+
+# conda
+conda install -c conda-forge rust-sasa-python
+
+# mamba
+mamba install -c conda-forge rust-sasa-python
 ```
 
 ## Quick Start

{rust_sasa_python-0.7.1 → rust_sasa_python-0.7.3}/src/lib.rs

@@ -12,7 +12,7 @@ mod simd;
 #[global_allocator]
 static GLOBAL: mimalloc::MiMalloc = mimalloc::MiMalloc;
 
-#[pyclass]
+#[pyclass(from_py_object)]
 #[derive(Clone)]
 pub struct Protein {
     #[pyo3(get)]
@@ -33,7 +33,7 @@ impl Protein {
     }
 }
 
-#[pyclass]
+#[pyclass(from_py_object)]
 #[derive(Clone)]
 pub struct Residue {
     #[pyo3(get)]
@@ -56,7 +56,7 @@ impl Residue {
     }
 }
 
-#[pyclass]
+#[pyclass(from_py_object)]
 #[derive(Clone)]
 pub struct Chain {
     #[pyo3(get)]
@@ -72,7 +72,7 @@ impl Chain {
     }
 }
 
-#[pyclass]
+#[pyclass(from_py_object)]
 #[derive(Clone)]
 pub struct SASACalculator {
     pdb_path: String,