build: update exon (#67)

Cargo.toml

@@ -8,9 +8,9 @@ crate-type = ["cdylib"]
 name = "biobear"
 
 [dependencies]
-arrow = {version = "46", features = ["pyarrow"]}
-datafusion = "31"
-exon = {version = "0.3.4-beta.3", features = ["all"]}
+arrow = {version = "47", features = ["pyarrow"]}
+datafusion = "32"
+exon = {version = "0.3.8-beta.4", features = ["all"]}
 pyo3 = "0.19"
 thiserror = "1.0"
 tokio = {version = "1", features = ["rt"]}

src/bcf_reader.rs

@@ -64,7 +64,7 @@ impl BCFIndexedReader {
             config = config.with_batch_size(batch_size);
         }
 
-        let ctx = SessionContext::with_config(config);
+        let ctx = SessionContext::new_with_config(config);
 
         let df = self._runtime.block_on(async {
             match ctx.query_bcf_file(self.path.as_str(), region).await {

src/execution_result.rs

@@ -56,6 +56,7 @@ impl PyExecutionResult {
         Python::with_gil(|py| {
             // Instantiate pyarrow Table object and use its from_batches method
             let table_class = py.import("pyarrow")?.getattr("Table")?;
+
             let args = PyTuple::new(py, &[batches]);
             let table: PyObject = table_class.call_method1("from_batches", args)?.into();
             Ok(table)

src/exon_reader.rs

@@ -18,7 +18,7 @@ use std::sync::Arc;
 
 use arrow::ffi_stream::{export_reader_into_raw, ArrowArrayStreamReader, FFI_ArrowArrayStream};
 use arrow::pyarrow::IntoPyArrow;
-use datafusion::common::FileCompressionType;
+use datafusion::datasource::file_format::file_compression_type::FileCompressionType;
 use datafusion::prelude::{SessionConfig, SessionContext};
 use exon::datasources::ExonFileType;
 use exon::ffi::DataFrameRecordBatchStream;