build: update build for biobear (#79)

Cargo.toml

@@ -8,9 +8,9 @@ crate-type = ["cdylib"]
 name = "biobear"
 
 [dependencies]
-arrow = {version = "48.0.1", features = ["pyarrow"]}
-datafusion = "33"
-exon = {version = "0.5.3", features = ["all"]}
+arrow = {version = "49.0.0", features = ["pyarrow"]}
+datafusion = "34"
+exon = {version = "0.5.5", features = ["all"]}
 pyo3 = "0.20"
 thiserror = "1.0"
 tokio = {version = "1", features = ["rt"]}

python/biobear/bam_reader.py

@@ -19,9 +19,11 @@
 import pyarrow as pa
 
 from biobear.reader import Reader
+from biobear.deprecated import deprecated
 from .biobear import _BamIndexedReader, _ExonReader
 
 
+@deprecated
 class BamReader(Reader):
     """A BAM File Reader."""
 

python/biobear/bcf_reader.py

@@ -21,10 +21,12 @@
 
 
 from biobear.reader import Reader
+from biobear.deprecated import deprecated
 
 from .biobear import _ExonReader, _BCFIndexedReader
 
 
+@deprecated
 class BCFReader(Reader):
     """A BCF File Reader.
 
@@ -46,6 +48,7 @@ def inner(self):
         return self._bcf_reader
 
 
+@deprecated
 class BCFIndexedReader(Reader):
     """An Indexed BCF File Reader.
 

python/biobear/deprecated.py

@@ -0,0 +1,32 @@
+# Copyright 2023 WHERE TRUE Technologies.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+import warnings
+import functools
+
+
+def deprecated(cls):
+    orig_init = cls.__init__
+
+    @functools.wraps(orig_init)
+    def new_init(self, *args, **kwargs):
+        warnings.warn(
+            f"{cls.__name__} is deprecated, use a table function via the session",
+            category=DeprecationWarning,
+            stacklevel=2,
+        )
+        orig_init(self, *args, **kwargs)
+
+    cls.__init__ = new_init
+    return cls

python/biobear/fasta_reader.py

@@ -17,10 +17,12 @@
 
 from biobear.reader import Reader
 from biobear.compression import Compression
+from biobear.deprecated import deprecated
 
 from .biobear import _ExonReader
 
 
+@deprecated
 class FastaReader(Reader):
     """FASTA file reader."""
 

python/biobear/fastq_reader.py

@@ -17,10 +17,12 @@
 
 from biobear.reader import Reader
 from biobear.compression import Compression
+from biobear.deprecated import deprecated
 
 from .biobear import _ExonReader
 
 
+@deprecated
 class FastqReader(Reader):
     """FASTQ file reader."""
 

python/biobear/genbank_reader.py

@@ -3,10 +3,12 @@
 
 from biobear.reader import Reader
 from biobear.compression import Compression
+from biobear.deprecated import deprecated
 
 from .biobear import _ExonReader
 
 
+@deprecated
 class GenbankReader(Reader):
     """Genbank file reader."""
 

python/biobear/gff_reader.py

@@ -7,10 +7,12 @@
 
 from biobear.compression import Compression
 from biobear.reader import Reader
+from biobear.deprecated import deprecated
 
 from .biobear import _ExonReader
 
 
+@deprecated
 class GFFReader(Reader):
     """A GFF File Reader."""
 

python/biobear/gtf_reader.py

@@ -7,10 +7,12 @@
 
 from biobear.compression import Compression
 from biobear.reader import Reader
+from biobear.deprecated import deprecated
 
 from .biobear import _ExonReader
 
 
+@deprecated
 class GTFReader(Reader):
     """A GTF File Reader."""
 

python/biobear/mzml_reader.py

@@ -4,10 +4,12 @@
 
 from biobear.compression import Compression
 from biobear.reader import Reader
+from biobear.deprecated import deprecated
 
 from .biobear import _ExonReader
 
 
+@deprecated
 class MzMLReader(Reader):
     """A MzML File Reader."""
 

python/biobear/vcf_reader.py

@@ -19,10 +19,12 @@
 import pyarrow as pa
 
 from biobear.reader import Reader
+from biobear.deprecated import deprecated
 
 from .biobear import _ExonReader, _VCFIndexedReader
 
 
+@deprecated
 class VCFReader(Reader):
     """A VCF File Reader.
 
@@ -44,6 +46,7 @@ def inner(self):
         return self._vcf_reader
 
 
+@deprecated
 class VCFIndexedReader(Reader):
     """An Indexed VCF File Reader.
 

python/tests/test_bam_reader.py

@@ -32,18 +32,8 @@ def test_bam_reader_to_pandas():
     assert len(df) == 61
 
 
-def test_bam_reader_no_file():
-    with pytest.raises(OSError):
-        BamReader("test.bam")
-
-
 def test_bam_indexed_reader():
     reader = BamIndexedReader(DATA / "bedcov.bam")
     rbr = reader.query("chr1:12203700-12205426")
 
     assert 1 == sum(b.num_rows for b in rbr)
-
-
-def test_bam_indexed_reader_no_file():
-    with pytest.raises(OSError):
-        BamIndexedReader("test.bam")

python/tests/test_bcf_reader.py

@@ -47,12 +47,6 @@ def test_bcf_reader_to_pandas():
     assert len(df) == 621
 
 
-def test_bcf_reader_missing_file():
-    """Test the BCFReader with a missing file."""
-    with pytest.raises(OSError):
-        BCFReader("test.bcf")
-
-
 def test_bcf_indexed_reader_query():
     """Test the BCFIndexedReader.query() method."""
     reader = BCFIndexedReader(DATA / "index.bcf")

python/tests/test_fasta_reader.py

@@ -63,11 +63,6 @@ def test_fasta_reader_to_arrow():
     assert arrow_reader.read_all().num_rows == 2
 
 
-def test_fasta_reader_no_file():
-    with pytest.raises(OSError):
-        FastaReader("test.fasta")
-
-
 @pytest.mark.skipif(
     not importlib.util.find_spec("polars"), reason="polars not installed"
 )

python/tests/test_fastq_reader.py

@@ -59,8 +59,3 @@ def test_to_arrow_scanner():
     scanner = gzipped_fastq_reader.to_arrow_scanner()
 
     assert scanner.count_rows() == 2
-
-
-def test_fastq_reader_no_file():
-    with pytest.raises(OSError):
-        FastqReader("test.fastq")

python/tests/test_genbank_reader.py

@@ -28,8 +28,3 @@ def test_genbank_reader_to_pandas():
     df = reader.to_pandas()
 
     assert len(df) == 1
-
-
-def test_genbank_missing_file():
-    with pytest.raises(OSError):
-        GenbankReader(DATA / "missing.gbk")

python/tests/test_gff_reader.py

@@ -52,11 +52,6 @@ def test_gff_reader_to_scanner():
     assert scanner.count_rows() == 2
 
 
-def test_gff_reader_no_file():
-    with pytest.raises(OSError):
-        GFFReader("")
-
-
 @pytest.mark.skipif(
     not importlib.util.find_spec("polars"), reason="polars not installed"
 )
@@ -72,8 +67,3 @@ def test_gff_reader_gz_to_scanner():
     scanner = reader.to_arrow_scanner()
 
     assert scanner.count_rows() == 2
-
-
-def test_gff_gz_no_file():
-    with pytest.raises(OSError):
-        GFFReader("test.gff.gz")

python/tests/test_gtf_reader.py

@@ -53,11 +53,6 @@ def test_gtf_reader_to_scanner():
     assert scanner.count_rows() == 77
 
 
-def test_gtf_reader_no_file():
-    with pytest.raises(OSError):
-        GTFReader("test.gtf")
-
-
 @pytest.mark.skipif(
     not importlib.util.find_spec("polars"), reason="polars not installed"
 )
@@ -73,8 +68,3 @@ def test_gtf_reader_gz_to_scanner():
     scanner = reader.to_arrow_scanner()
 
     assert scanner.count_rows() == 77
-
-
-def test_gtf_gz_no_file():
-    with pytest.raises(OSError):
-        GTFReader("test.gtf.gz")

python/tests/test_mzml_reader.py

@@ -37,11 +37,6 @@ def test_mzml_reader_to_scanner():
     assert scanner.count_rows() == 2
 
 
-def test_mzml_reader_no_file():
-    with pytest.raises(OSError):
-        MzMLReader("test.mzML")
-
-
 @pytest.mark.skipif(
     not importlib.util.find_spec("polars"), reason="polars not installed"
 )
@@ -57,8 +52,3 @@ def test_mzml_reader_gz_to_scanner():
     scanner = reader.to_arrow_scanner()
 
     assert scanner.count_rows() == 2
-
-
-def test_mzml_gz_no_file():
-    with pytest.raises(OSError):
-        MzMLReader("test.mzML.gz")

python/tests/test_vcf_reader.py

@@ -30,11 +30,6 @@ def test_vcf_reader_to_pandas():
     assert len(df) == 15
 
 
-def test_vcf_reader_missing_file():
-    with pytest.raises(OSError):
-        VCFReader("test.vcf")
-
-
 def test_vcf_indexed_reader_query():
     reader = VCFIndexedReader(DATA / "vcf_file.vcf.gz")
     rbr = reader.query("1")