gtfreader 0.1.0__tar.gz → 0.1.2__tar.gz

{gtfreader-0.1.0 → gtfreader-0.1.2}/PKG-INFO

@@ -1,14 +1,16 @@
 Metadata-Version: 2.4
 Name: gtfreader
-Version: 0.1.0
+Version: 0.1.2
 Summary: Fast Cython-backed parsing for GTF attribute columns.
 Author: Endre Bakken Stovner
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Cython
 Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 Classifier: Operating System :: OS Independent
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
-Requires-Python: >=3.9
+Requires-Python: >=3.12
 Description-Content-Type: text/markdown
 Requires-Dist: pandas>=2.0
 
@@ -16,6 +18,8 @@ Requires-Dist: pandas>=2.0
 
 `gtfreader` is a small package for parsing and reading GTF files into pandas dataframes.
 
+Requires Python 3.12 or newer.
+
 ## Install
 
 ```bash
@@ -47,6 +51,7 @@ attribute_lines = pd.read_csv(
     header=None,
     usecols=[8],
     names=["Attribute"],
+    comment="#",
     skiprows=skiprows,
 )["Attribute"].tolist()
 

{gtfreader-0.1.0 → gtfreader-0.1.2}/README.md

@@ -2,6 +2,8 @@
 
 `gtfreader` is a small package for parsing and reading GTF files into pandas dataframes.
 
+Requires Python 3.12 or newer.
+
 ## Install
 
 ```bash
@@ -33,6 +35,7 @@ attribute_lines = pd.read_csv(
     header=None,
     usecols=[8],
     names=["Attribute"],
+    comment="#",
     skiprows=skiprows,
 )["Attribute"].tolist()
 

{gtfreader-0.1.0 → gtfreader-0.1.2}/gtfreader/readers.py

@@ -162,6 +162,7 @@ def _open_gtf_reader(
         header=None,
         names=GTF_NAMES,
         dtype=GTF_DTYPES,
+        comment="#",
         chunksize=chunksize,
         skiprows=skiprows,
         nrows=nrows,

{gtfreader-0.1.0 → gtfreader-0.1.2}/gtfreader.egg-info/PKG-INFO

@@ -1,14 +1,16 @@
 Metadata-Version: 2.4
 Name: gtfreader
-Version: 0.1.0
+Version: 0.1.2
 Summary: Fast Cython-backed parsing for GTF attribute columns.
 Author: Endre Bakken Stovner
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Cython
 Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 Classifier: Operating System :: OS Independent
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
-Requires-Python: >=3.9
+Requires-Python: >=3.12
 Description-Content-Type: text/markdown
 Requires-Dist: pandas>=2.0
 
@@ -16,6 +18,8 @@ Requires-Dist: pandas>=2.0
 
 `gtfreader` is a small package for parsing and reading GTF files into pandas dataframes.
 
+Requires Python 3.12 or newer.
+
 ## Install
 
 ```bash
@@ -47,6 +51,7 @@ attribute_lines = pd.read_csv(
     header=None,
     usecols=[8],
     names=["Attribute"],
+    comment="#",
     skiprows=skiprows,
 )["Attribute"].tolist()
 

{gtfreader-0.1.0 → gtfreader-0.1.2}/gtfreader.egg-info/SOURCES.txt

@@ -3,7 +3,6 @@ README.md
 pyproject.toml
 setup.py
 gtfreader/__init__.py
-gtfreader/_parser.c
 gtfreader/_parser.pyx
 gtfreader/readers.py
 gtfreader.egg-info/PKG-INFO

{gtfreader-0.1.0 → gtfreader-0.1.2}/pyproject.toml

@@ -8,10 +8,10 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "gtfreader"
-version = "0.1.0"
+version = "0.1.2"
 description = "Fast Cython-backed parsing for GTF attribute columns."
 readme = "README.md"
-requires-python = ">=3.9"
+requires-python = ">=3.12"
 authors = [
     { name = "Endre Bakken Stovner" },
 ]
@@ -22,6 +22,8 @@ classifiers = [
     "Programming Language :: Python :: 3",
     "Programming Language :: Cython",
     "Programming Language :: Python :: 3 :: Only",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
     "Operating System :: OS Independent",
     "Topic :: Scientific/Engineering :: Bio-Informatics",
 ]
@@ -39,7 +41,7 @@ include = ["gtfreader*"]
 testpaths = ["tests"]
 
 [tool.cibuildwheel]
-build = "cp39-* cp310-* cp311-* cp312-* cp313-*"
+build = "cp312-* cp313-*"
 skip = "pp* *-musllinux_* *-manylinux_i686"
 test-command = "pytest -q {project}/tests"
 test-requires = ["pytest"]

{gtfreader-0.1.0 → gtfreader-0.1.2}/tests/test_readers.py

@@ -120,6 +120,23 @@ def test_full_readers_support_mixed_attribute_formats(tmp_path: Path, reader):
     assert result.iloc[1]["exon_id"] == "EX2"
 
 
+@pytest.mark.parametrize("reader", [read_gtf, read_gtf_python], ids=["default", "python"])
+def test_readers_ignore_comment_lines_inside_body(tmp_path: Path, reader):
+    path = _write_temp_gtf(
+        tmp_path,
+        "# header\n"
+        'chr1\thavana\tgene\t11869\t14409\t.\t+\t.\tgene_id "G1";\n'
+        "# another comment\n"
+        'chr1\thavana\ttranscript\t11869\t14409\t.\t+\t.\tgene_id "G1"; transcript_id "T1";\n',
+    )
+
+    result = _normalize_frame_for_compare(reader(path))
+
+    assert list(result["Feature"]) == ["gene", "transcript"]
+    assert list(result["gene_id"]) == ["G1", "G1"]
+    assert list(result["transcript_id"]) == [None, "T1"]
+
+
 def test_read_gtf_duplicate_attr_keeps_all_values(tmp_path: Path):
     path = _write_temp_gtf(
         tmp_path,