From 01ab856d120f3d3d1b45730081b63e810f9cdd69 Mon Sep 17 00:00:00 2001 From: Trent Hauck Date: Thu, 6 Jul 2023 09:41:16 -0700 Subject: [PATCH] build: update depdencies --- Cargo.toml | 10 +++++----- python/biobear/genbank_reader.py | 3 ++- src/bam_reader.rs | 4 ++-- src/bcf_reader.rs | 8 +++----- src/exon_reader.rs | 4 ++-- src/vcf_reader.rs | 8 +++----- 6 files changed, 17 insertions(+), 20 deletions(-) diff --git a/Cargo.toml b/Cargo.toml index d191918..162b8a1 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -8,10 +8,10 @@ crate-type = ["cdylib"] name = "biobear" [dependencies] -arrow = {version = "40", features = ["pyarrow"]} -datafusion = "26" -exon = {version = "0.1.2", features = ["all"]} -object_store = {version = "0.5.4", features = ["aws", "gcp", "azure", "aws_profile"]} -pyo3 = "0.18.3" +arrow = {version = "42", features = ["pyarrow"]} +datafusion = "27" +exon = {version = "0.2.3", features = ["all"]} +object_store = {version = "0.6.1", features = ["aws", "gcp"]} +pyo3 = "0.19" tokio = {version = "1", features = ["rt"]} url = "2.4.0" diff --git a/python/biobear/genbank_reader.py b/python/biobear/genbank_reader.py index 84e1e5f..5ec46a2 100644 --- a/python/biobear/genbank_reader.py +++ b/python/biobear/genbank_reader.py @@ -13,10 +13,11 @@ class GenbankReader(Reader): def __init__( self, path: os.PathLike, compression: Compression = Compression.INFERRED ): - """Read a fasta file. + """Read a genbank file. Args: path (Path): Path to the fasta file. + compression (Compression): Compression type of the file. """ self.compression = compression.infer_or_use(path) diff --git a/src/bam_reader.rs b/src/bam_reader.rs index e99fd95..bf57db8 100644 --- a/src/bam_reader.rs +++ b/src/bam_reader.rs @@ -14,7 +14,7 @@ use arrow::ffi_stream::ArrowArrayStreamReader; use arrow::ffi_stream::FFI_ArrowArrayStream; -use arrow::pyarrow::PyArrowConvert; +use arrow::pyarrow::IntoPyArrow; use datafusion::prelude::SessionConfig; use datafusion::prelude::SessionContext; use exon::context::ExonSessionExt; @@ -97,7 +97,7 @@ impl BamIndexedReader { Python::with_gil(|py| unsafe { match ArrowArrayStreamReader::from_raw(stream_ptr) { - Ok(stream_reader) => stream_reader.to_pyarrow(py), + Ok(stream_reader) => stream_reader.into_pyarrow(py), Err(err) => Err(PyErr::new::(format!( "Error converting to pyarrow: {err}" ))), diff --git a/src/bcf_reader.rs b/src/bcf_reader.rs index 82e5c26..76036eb 100644 --- a/src/bcf_reader.rs +++ b/src/bcf_reader.rs @@ -12,10 +12,8 @@ // See the License for the specific language governing permissions and // limitations under the License. -use arrow::{ - ffi_stream::{ArrowArrayStreamReader, FFI_ArrowArrayStream}, - pyarrow::PyArrowConvert, -}; +use arrow::ffi_stream::{ArrowArrayStreamReader, FFI_ArrowArrayStream}; +use arrow::pyarrow::IntoPyArrow; use datafusion::prelude::{SessionConfig, SessionContext}; use pyo3::prelude::*; use tokio::runtime::Runtime; @@ -92,7 +90,7 @@ impl BCFIndexedReader { Python::with_gil(|py| unsafe { match ArrowArrayStreamReader::from_raw(stream_ptr) { - Ok(stream_reader) => stream_reader.to_pyarrow(py), + Ok(stream_reader) => stream_reader.into_pyarrow(py), Err(err) => Err(PyErr::new::(format!( "Error converting to pyarrow: {err}" ))), diff --git a/src/exon_reader.rs b/src/exon_reader.rs index d36791e..a77b3d2 100644 --- a/src/exon_reader.rs +++ b/src/exon_reader.rs @@ -18,7 +18,7 @@ use std::str::FromStr; use std::sync::Arc; use arrow::ffi_stream::{ArrowArrayStreamReader, FFI_ArrowArrayStream}; -use arrow::pyarrow::PyArrowConvert; +use arrow::pyarrow::IntoPyArrow; use datafusion::datasource::file_format::file_type::FileCompressionType; use datafusion::prelude::{SessionConfig, SessionContext}; use exon::context::ExonSessionExt; @@ -168,7 +168,7 @@ impl ExonReader { Python::with_gil(|py| unsafe { match ArrowArrayStreamReader::from_raw(stream_ptr) { - Ok(stream_reader) => stream_reader.to_pyarrow(py), + Ok(stream_reader) => stream_reader.into_pyarrow(py), Err(err) => Err(PyErr::new::(format!( "Error converting to pyarrow: {err}" ))), diff --git a/src/vcf_reader.rs b/src/vcf_reader.rs index e9030c7..d079133 100644 --- a/src/vcf_reader.rs +++ b/src/vcf_reader.rs @@ -12,10 +12,8 @@ // See the License for the specific language governing permissions and // limitations under the License. -use arrow::{ - ffi_stream::{ArrowArrayStreamReader, FFI_ArrowArrayStream}, - pyarrow::PyArrowConvert, -}; +use arrow::ffi_stream::{ArrowArrayStreamReader, FFI_ArrowArrayStream}; +use arrow::pyarrow::IntoPyArrow; use datafusion::prelude::{SessionConfig, SessionContext}; use pyo3::prelude::*; use tokio::runtime::Runtime; @@ -92,7 +90,7 @@ impl VCFIndexedReader { Python::with_gil(|py| unsafe { match ArrowArrayStreamReader::from_raw(stream_ptr) { - Ok(stream_reader) => stream_reader.to_pyarrow(py), + Ok(stream_reader) => stream_reader.into_pyarrow(py), Err(err) => Err(PyErr::new::(format!( "Error converting to pyarrow: {err}" ))),