gtfparse 2.0.1__tar.gz → 2.1.0__tar.gz

{gtfparse-2.0.1 → gtfparse-2.1.0}/PKG-INFO

@@ -1,10 +1,10 @@
 Metadata-Version: 2.1
 Name: gtfparse
-Version: 2.0.1
-Summary: GTF Parsing
-Home-page: https://github.com/openvax/gtfparse
-Author: Alex Rubinsteyn
-License: http://www.apache.org/licenses/LICENSE-2.0.html
+Version: 2.1.0
+Summary: Parsing library for extracting data frames of genomic features from GTF files
+Author-email: Alex Rubinsteyn <alex.rubinsteyn@unc.edu>
+Project-URL: Homepage, https://github.com/openvax/gtfparse
+Project-URL: Bug Tracker, https://github.com/openvax/gtfparse
 Classifier: Development Status :: 4 - Beta
 Classifier: Environment :: Console
 Classifier: Operating System :: OS Independent
@@ -12,8 +12,11 @@ Classifier: Intended Audience :: Science/Research
 Classifier: License :: OSI Approved :: Apache Software License
 Classifier: Programming Language :: Python
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.7
 Description-Content-Type: text/markdown
 License-File: LICENSE
+Requires-Dist: polars<0.21.0,>=0.20.2
+Requires-Dist: pyarrow<14.1.0,>=14.0.2
 
 [![Build Status](https://travis-ci.org/openvax/gtfparse.svg?branch=master)](https://travis-ci.org/openvax/gtfparse) [![Coverage Status](https://coveralls.io/repos/openvax/gtfparse/badge.svg?branch=master&service=github)](https://coveralls.io/github/openvax/gtfparse?branch=master)
 <a href="https://pypi.python.org/pypi/gtfparse/">

{gtfparse-2.0.1 → gtfparse-2.1.0}/gtfparse/__init__.py

@@ -21,9 +21,10 @@ from .read_gtf import (
     REQUIRED_COLUMNS,
 )
 
-
+__version__ = "2.1.0"
 
 __all__ = [
+    "__version__",
     "expand_attribute_strings",
     "create_missing_features",
 

{gtfparse-2.0.1 → gtfparse-2.1.0}/gtfparse/read_gtf.py

@@ -84,11 +84,11 @@ def parse_with_polars_lazy(
         fix_quotes_columns=["attribute"]):
     # use a global string cache so that all strings get intern'd into
     # a single numbering system
-    polars.toggle_string_cache(True)
+    polars.enable_string_cache()
     kwargs = dict(
         has_header=False,
-        sep="\t",
-        comment_char="#",
+        separator="\t",
+        comment_prefix="#",
         null_values=".",
         dtypes={
             "seqname": polars.Categorical, 
@@ -202,7 +202,7 @@ def parse_gtf_and_expand_attributes(
         expand_attribute_strings(attribute_pairs).items()
         if restrict_attribute_columns is None or k in restrict_attribute_columns
     ])
-
+    
 
 def read_gtf(
         filepath_or_buffer,
@@ -260,7 +260,7 @@ def read_gtf(
 
     result_df = result_df.with_columns(
         [
-            polars.col(column_name).apply(lambda x: column_type(x) if len(x) > 0 else None)
+            polars.col(column_name).map_elements(lambda x: column_type(x) if len(x) > 0 else None)
             for column_name, column_type in column_converters.items()
         ]
     )

{gtfparse-2.0.1 → gtfparse-2.1.0}/gtfparse.egg-info/PKG-INFO

@@ -1,10 +1,10 @@
 Metadata-Version: 2.1
 Name: gtfparse
-Version: 2.0.1
-Summary: GTF Parsing
-Home-page: https://github.com/openvax/gtfparse
-Author: Alex Rubinsteyn
-License: http://www.apache.org/licenses/LICENSE-2.0.html
+Version: 2.1.0
+Summary: Parsing library for extracting data frames of genomic features from GTF files
+Author-email: Alex Rubinsteyn <alex.rubinsteyn@unc.edu>
+Project-URL: Homepage, https://github.com/openvax/gtfparse
+Project-URL: Bug Tracker, https://github.com/openvax/gtfparse
 Classifier: Development Status :: 4 - Beta
 Classifier: Environment :: Console
 Classifier: Operating System :: OS Independent
@@ -12,8 +12,11 @@ Classifier: Intended Audience :: Science/Research
 Classifier: License :: OSI Approved :: Apache Software License
 Classifier: Programming Language :: Python
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.7
 Description-Content-Type: text/markdown
 License-File: LICENSE
+Requires-Dist: polars<0.21.0,>=0.20.2
+Requires-Dist: pyarrow<14.1.0,>=14.0.2
 
 [![Build Status](https://travis-ci.org/openvax/gtfparse.svg?branch=master)](https://travis-ci.org/openvax/gtfparse) [![Coverage Status](https://coveralls.io/repos/openvax/gtfparse/badge.svg?branch=master&service=github)](https://coveralls.io/github/openvax/gtfparse?branch=master)
 <a href="https://pypi.python.org/pypi/gtfparse/">

{gtfparse-2.0.1 → gtfparse-2.1.0}/gtfparse.egg-info/SOURCES.txt

@@ -1,22 +1,22 @@
 LICENSE
 README.md
-setup.py
+pyproject.toml
+requirements.txt
 gtfparse/__init__.py
 gtfparse/attribute_parsing.py
 gtfparse/create_missing_features.py
 gtfparse/parsing_error.py
 gtfparse/read_gtf.py
-gtfparse/version.py
 gtfparse.egg-info/PKG-INFO
 gtfparse.egg-info/SOURCES.txt
 gtfparse.egg-info/dependency_links.txt
 gtfparse.egg-info/requires.txt
 gtfparse.egg-info/top_level.txt
 gtfparse/../requirements.txt
-test/test_create_missing_features.py
-test/test_ensembl_gtf.py
-test/test_expand_attributes.py
-test/test_multiple_values_for_tag_attribute.py
-test/test_parse_gtf_lines.py
-test/test_read_stringtie_gtf.py
-test/test_refseq_gtf.py
+tests/test_create_missing_features.py
+tests/test_ensembl_gtf.py
+tests/test_expand_attributes.py
+tests/test_multiple_values_for_tag_attribute.py
+tests/test_parse_gtf_lines.py
+tests/test_read_stringtie_gtf.py
+tests/test_refseq_gtf.py

gtfparse-2.1.0/gtfparse.egg-info/requires.txt

@@ -0,0 +1,2 @@
+polars<0.21.0,>=0.20.2
+pyarrow<14.1.0,>=14.0.2

gtfparse-2.1.0/pyproject.toml

@@ -0,0 +1,27 @@
+[project]
+name = "gtfparse"
+requires-python = ">=3.7"
+authors = [ {name="Alex Rubinsteyn", email="alex.rubinsteyn@unc.edu" } ]
+description = "Parsing library for extracting data frames of genomic features from GTF files"
+classifiers = [
+            'Development Status :: 4 - Beta',
+            'Environment :: Console',
+            'Operating System :: OS Independent',
+            'Intended Audience :: Science/Research',
+            'License :: OSI Approved :: Apache Software License',
+            'Programming Language :: Python',
+            'Topic :: Scientific/Engineering :: Bio-Informatics',
+]
+readme = "README.md"
+dynamic = ["version", "dependencies"]
+
+[tool.setuptools.dynamic]
+version = {attr = "gtfparse.__version__"}
+dependencies = {file = ["requirements.txt"]}
+
+[tool.setuptools]
+packages = ["gtfparse"]
+
+[project.urls]
+"Homepage" = "https://github.com/openvax/gtfparse"
+"Bug Tracker" = "https://github.com/openvax/gtfparse"

gtfparse-2.1.0/requirements.txt

@@ -0,0 +1,2 @@
+polars>=0.20.2,<0.21.0
+pyarrow>=14.0.2,<14.1.0

{gtfparse-2.0.1/test → gtfparse-2.1.0/tests}/test_create_missing_features.py

@@ -18,7 +18,8 @@ GTF_TEXT = "\n".join([
 ])
 
 
-GTF_DATAFRAME = parse_gtf_and_expand_attributes(StringIO(GTF_TEXT)).to_pandas()
+GTF_DATAFRAME = parse_gtf_and_expand_attributes(StringIO(GTF_TEXT))
+GTF_DATAFRAME = GTF_DATAFRAME.to_pandas()
 
 def test_create_missing_features_identity():
     df_should_be_same = create_missing_features(GTF_DATAFRAME, {})

gtfparse-2.0.1/gtfparse/version.py

@@ -1 +0,0 @@
-__version__ = "2.0.1"

gtfparse-2.0.1/gtfparse.egg-info/requires.txt

@@ -1 +0,0 @@
-polars

gtfparse-2.0.1/requirements.txt

@@ -1 +0,0 @@
-polars

gtfparse-2.0.1/setup.py

@@ -1,69 +0,0 @@
-# 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 os
-import re
-
-from setuptools import setup, find_packages
-
-
-
-package_name = "gtfparse"
-current_directory = os.path.dirname(__file__)
-readme_filename = 'README.md'
-readme_path = os.path.join(current_directory, readme_filename)
-github_url = "https://github.com/openvax/%s" % package_name
-
-
-readme_markdown = ""
-try:
-    with open(readme_path, 'r') as f:
-        readme_markdown = f.read()
-except Exception as e:
-    print(e)
-    print("Failed to open %s" % readme_path)
-
-with open('gtfparse/version.py', 'r') as f:
-    version = re.search(
-        r'^__version__\s*=\s*[\'"]([^\'"]*)[\'"]',
-        f.read(),
-        re.MULTILINE).group(1)
-
-with open("requirements.txt") as f:
-    requirements = [l.strip() for l in f]
-
-
-if __name__ == '__main__':
-    setup(
-        name=package_name,
-        packages=find_packages(),
-        version=version,
-        description="GTF Parsing",
-        long_description=readme_markdown,
-        long_description_content_type='text/markdown',
-        url=github_url,
-        author="Alex Rubinsteyn",
-        license="http://www.apache.org/licenses/LICENSE-2.0.html",
-        classifiers=[
-            'Development Status :: 4 - Beta',
-            'Environment :: Console',
-            'Operating System :: OS Independent',
-            'Intended Audience :: Science/Research',
-            'License :: OSI Approved :: Apache Software License',
-            'Programming Language :: Python',
-            'Topic :: Scientific/Engineering :: Bio-Informatics',
-        ],
-        install_requires=requirements,
-        package_data={
-            package_name: ['../requirements.txt'],
-        },
-    )