feat: add sdf read options (#161)

* feat: support domtab
* feat: add sdf read options
* fix: fix for tests to run

Cargo.toml

@@ -8,12 +8,12 @@ crate-type = ["cdylib"]
 name = "biobear"
 
 [dependencies]
-arrow = { version = "52.0.0", features = ["pyarrow"] }
-datafusion = "39"
-exon = { version = "0.26", features = ["default"] }
+arrow = { version = "52.1.0", features = ["pyarrow"] }
+datafusion = "40"
+exon = { version = "0.29", features = ["default"] }
 pyo3 = "0.21.2"
 tokio = { version = "1", features = ["rt"] }
-noodles = { version = "0.77", features = ["core"] }
+noodles = { version = "0.78", features = ["core"] }
 
 [profile.release]
 codegen-units = 1

python/biobear/__init__.py

@@ -43,6 +43,7 @@
 from .biobear import GenBankReadOptions
 from .biobear import FCSReadOptions
 from .biobear import CRAMReadOptions
+from .biobear import SDFReadOptions
 from .biobear import connect
 from .biobear import new_session
 from .biobear import __runtime
@@ -72,6 +73,7 @@
     "BCFReadOptions",
     "VCFReadOptions",
     "BEDReadOptions",
+    "SDFReadOptions",
     "FCSReadOptions",
     "CRAMReadOptions",
     "BigWigReadOptions",

python/biobear/biobear.pyi

@@ -116,7 +116,7 @@ class VCFReadOptions:
         file_compression_type: Optional[FileCompressionType] = None,
         parse_info: bool = False,
         parse_formats: bool = False,
-        partition_cols: list[str | None] = None,
+        partition_cols: list[str] | None = None,
     ) -> None: ...
 
 class BCFReadOptions:
@@ -141,6 +141,16 @@ class BAMReadOptions:
         region: Optional[str] = None,
     ) -> None: ...
 
+class SDFReadOptions:
+    """Options for reading SDF data."""
+    def __init__(
+        self,
+        /,
+        file_compression_type: Optional[FileCompressionType] = None,
+        file_extension: Optional[str] = None,
+        partition_cols: list[str] | None = None,
+    ) -> None: ...
+
 class BEDReadOptions:
     """Options for reading BED data."""
     def __init__(
@@ -187,6 +197,10 @@ class BioBearSessionContext:
         self, file_path: str, /, options: Optional[FASTQReadOptions] = None
     ) -> ExecutionResult:
         """Reads one or more FASTQ files and returns an ExecutionResult."""
+    def read_sdf_file(
+        self, file_path: str, /, options: Optional[SDFReadOptions] = None
+    ) -> ExecutionResult:
+        """Reads one or more SDF files and returns an ExecutionResult."""
     def read_fasta_file(
         self, file_path: str, /, options: Optional[FASTAReadOptions] = None
     ) -> ExecutionResult: