Merge pull request #102 from databio/hf_to_str

Hot fix for python bindings failing (resolve #104)

Author: nleroy917

bindings/python/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "gtars-py"
-version = "0.2.3"
+version = "0.2.4"
 edition = "2021"
 
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html

bindings/python/src/digests/mod.rs

@@ -4,13 +4,13 @@ use gtars::digests::{md5, sha512t24u, DigestResult};
 use pyo3::prelude::*;
 
 use pyo3::exceptions::PyTypeError;
-use pyo3::prelude::*;
 use pyo3::types::{PyBytes, PyString};
 
 #[pyfunction]
 pub fn sha512t24u_digest(readable: &Bound<'_, PyAny>) -> PyResult<String> {
     if let Ok(s) = readable.downcast::<PyString>() {
-        Ok(sha512t24u(s.to_str()?)) // Borrowed, no copying
+        // https://discord.com/channels/1209263839632424990/1229461480873922681/1229465185270370376
+        Ok(sha512t24u(s.encode_utf8()?.as_bytes())) // Borrowed, no copying
     } else if let Ok(b) = readable.downcast::<PyBytes>() {
         Ok(sha512t24u(b.as_bytes())) // Borrowed, no copying
     } else {
@@ -21,7 +21,8 @@ pub fn sha512t24u_digest(readable: &Bound<'_, PyAny>) -> PyResult<String> {
 #[pyfunction]
 pub fn md5_digest(readable: &Bound<'_, PyAny>) -> PyResult<String> {
     if let Ok(s) = readable.downcast::<PyString>() {
-        Ok(md5(s.to_str()?)) // Borrowed, no copying
+        // https://discord.com/channels/1209263839632424990/1229461480873922681/1229465185270370376
+        Ok(md5(s.encode_utf8()?.as_bytes())) // Borrowed, no copying
     } else if let Ok(b) = readable.downcast::<PyBytes>() {
         Ok(md5(b.as_bytes())) // Borrowed, no copying
     } else {

bindings/r/DESCRIPTION

@@ -1,6 +1,6 @@
 Package: gtars
 Title: Performance critical genomic interval analysis using Rust, in R
-Version: 0.2.3
+Version: 0.2.4
 Authors@R: 
     person("Nathan", "LeRoy", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-7354-7213"))

bindings/r/src/rust/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = 'gtars-r'
-version = '0.2.3'
+version = '0.2.4'
 edition = '2021'
 
 [lib]

gtars/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "gtars"
-version = "0.2.3"
+version = "0.2.4"
 edition = "2021"
 description = "Performance-critical tools to manipulate, analyze, and process genomic interval data. Primarily focused on building tools for geniml - our genomic machine learning python package."
 license = "MIT"

gtars/docs/changelog.md

@@ -4,6 +4,9 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.2.4]
+- Attempt to fix failing python bindings in CI linux [#104](https://github.com/databio/gtars/issues/104)
+
 ## [0.2.3]
 - Improved RegionSet, by adding a multiple new methods: `to_bed`, `to_bed_gz`, `to_bigbed`, `identifier()`, and others.
 - Fixed allowed `fasta_digest` to accept `Path` or `bytes` [#93](https://github.com/databio/gtars/issues/93)