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build: update deps #40

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Jul 6, 2023
Merged

build: update deps #40

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10 changes: 5 additions & 5 deletions Cargo.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -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"
3 changes: 2 additions & 1 deletion python/biobear/genbank_reader.py
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Expand Up @@ -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)
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4 changes: 2 additions & 2 deletions src/bam_reader.rs
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Expand Up @@ -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;
Expand Down Expand Up @@ -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::<pyo3::exceptions::PyValueError, _>(format!(
"Error converting to pyarrow: {err}"
))),
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8 changes: 3 additions & 5 deletions src/bcf_reader.rs
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Expand Up @@ -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;
Expand Down Expand Up @@ -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::<pyo3::exceptions::PyValueError, _>(format!(
"Error converting to pyarrow: {err}"
))),
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4 changes: 2 additions & 2 deletions src/exon_reader.rs
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Expand Up @@ -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;
Expand Down Expand Up @@ -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::<pyo3::exceptions::PyValueError, _>(format!(
"Error converting to pyarrow: {err}"
))),
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8 changes: 3 additions & 5 deletions src/vcf_reader.rs
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Expand Up @@ -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;
Expand Down Expand Up @@ -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::<pyo3::exceptions::PyValueError, _>(format!(
"Error converting to pyarrow: {err}"
))),
Expand Down
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