Revert unintended commits to main branch

Revert "Implement file like object compatibility for fastq reader"
This reverts commit 9ff35a8.

Revert "Restructure imports and remove unused code"
This reverts commit 2279ab7.

oxbow/src/fastq.rs

@@ -1,35 +1,31 @@
 use arrow::array::{ArrayRef, GenericStringBuilder};
 use arrow::{error::ArrowError, record_batch::RecordBatch};
+// use noodles::core::Region;
 use noodles::fastq;
-use std::{
-    fs::File,
-    io::{self, BufReader, Read, Seek},
-    str,
-    sync::Arc,
-};
+// use noodles::fastq::fai;
+use std::sync::Arc;
 
 use crate::batch_builder::{write_ipc, BatchBuilder};
 
-/// A FASTQ reader.
-pub struct FastqReader<R> {
-    reader: fastq::Reader<BufReader<R>>,
-}
+type BufferedReader = std::io::BufReader<std::fs::File>;
 
-impl FastqReader<BufReader<File>> {
-    /// Creates a Fasta reader from a given file path.
-    pub fn new_from_path(path: &str) -> io::Result<Self> {
-        let reader = File::open(path)
-            .map(BufReader::new)
-            .map(BufReader::new)
-            .map(fastq::Reader::new)?;
-        Ok(Self { reader })
-    }
+/// A FASTQ reader.
+pub struct FastqReader {
+    reader: fastq::Reader<BufferedReader>,
+    // index: fai::Reader<std::io::BufReader<std::fs::File>>,
 }
 
-impl<R: Read + Seek> FastqReader<R> {
+impl FastqReader {
     /// Creates a Fastq Reader.
-    pub fn new(read: R) -> io::Result<Self> {
-        let reader = fastq::Reader::new(BufReader::new(read));
+    pub fn new(path: &str) -> std::io::Result<Self> {
+        // let index_file = std::fs::File::open(format!("{}.fai", path))?;
+        // let index_bufreader = std::io::BufReader::with_capacity(1024 * 1024, index_file);
+        // let index = fai::Reader::new(index_bufreader);
+
+        let file = std::fs::File::open(path)?;
+        let bufreader = std::io::BufReader::with_capacity(1024 * 1024, file);
+        let reader = fastq::reader::Reader::new(bufreader);
+
         Ok(Self { reader })
     }
 
@@ -75,13 +71,13 @@ impl BatchBuilder for FastqBatchBuilder {
 
     fn push(&mut self, record: Self::Record<'_>) {
         self.name
-            .append_value(str::from_utf8(record.name()).unwrap());
+            .append_value(std::str::from_utf8(record.name()).unwrap());
         self.description
-            .append_value(str::from_utf8(record.description()).unwrap());
+            .append_value(std::str::from_utf8(record.description()).unwrap());
         self.sequence
-            .append_value(str::from_utf8(record.sequence()).unwrap());
+            .append_value(std::str::from_utf8(record.sequence()).unwrap());
         self.quality_scores
-            .append_value(str::from_utf8(record.quality_scores()).unwrap());
+            .append_value(std::str::from_utf8(record.quality_scores()).unwrap());
     }
 
     fn finish(mut self) -> Result<RecordBatch, ArrowError> {

py-oxbow/src/lib.rs

@@ -39,22 +39,10 @@ fn read_fasta(path: &str, region: Option<&str>) -> PyObject {
 }
 
 #[pyfunction]
-fn read_fastq(py: Python, path_or_file_like: PyObject) -> PyObject {
-    if let Ok(string_ref) = path_or_file_like.downcast::<PyString>(py) {
-        // If it's a string, treat it like a path
-        let mut reader = FastqReader::new_from_path(string_ref.to_str().unwrap()).unwrap();
-        let ipc = reader.records_to_ipc().unwrap();
-        Python::with_gil(|py| PyBytes::new(py, &ipc).into())
-    } else {
-        // Otherwise, treat it as file-like
-        let file_like = match PyFileLikeObject::new(path_or_file_like, true, false, true) {
-	    Ok(file_like) => file_like,
-            Err(_) => panic!("Unknown argument for `path_url_or_file_like`. Not a file path string or url, and not a file-like object."),
-	};
-        let mut reader = FastqReader::new(file_like).unwrap();
-        let ipc = reader.records_to_ipc().unwrap();
-        Python::with_gil(|py| PyBytes::new(py, &ipc).into())
-    }
+fn read_fastq(path: &str) -> PyObject {
+    let mut reader = FastqReader::new(path).unwrap();
+    let ipc = reader.records_to_ipc().unwrap();
+    Python::with_gil(|py| PyBytes::new(py, &ipc).into())
 }
 
 #[pyfunction]