[med-svn] [Git][med-team/python-datacache][master] 7 commits: New upstream version 1.2.1
Andreas Tille (@tille)
gitlab at salsa.debian.org
Sun Dec 25 21:44:37 GMT 2022
Andreas Tille pushed to branch master at Debian Med / python-datacache
Commits:
98df5f10 by Andreas Tille at 2022-12-25T22:34:03+01:00
New upstream version 1.2.1
- - - - -
01bb5dec by Andreas Tille at 2022-12-25T22:34:03+01:00
routine-update: New upstream version
- - - - -
c12c35b0 by Andreas Tille at 2022-12-25T22:34:03+01:00
Update upstream source from tag 'upstream/1.2.1'
Update to upstream version '1.2.1'
with Debian dir c1c8b2e731e67f3bd16b35472098434d50a0ad07
- - - - -
c8dbcc7c by Andreas Tille at 2022-12-25T22:34:03+01:00
routine-update: Standards-Version: 4.6.2
- - - - -
46d0e7b0 by Andreas Tille at 2022-12-25T22:34:05+01:00
routine-update: Remove trailing whitespace in debian/changelog
- - - - -
98a52bf1 by Andreas Tille at 2022-12-25T22:39:12+01:00
Refresh patches
- - - - -
32bd7956 by Andreas Tille at 2022-12-25T22:40:25+01:00
Upload to unstable
- - - - -
22 changed files:
- + LICENSE
- PKG-INFO
- datacache.egg-info/PKG-INFO
- datacache.egg-info/SOURCES.txt
- datacache/__init__.py
- datacache/cache.py
- datacache/common.py
- datacache/database_helpers.py
- datacache/database_table.py
- datacache/database_types.py
- datacache/download.py
- + datacache/version.py
- debian/changelog
- debian/control
- debian/patches/noInternetAccessForDownloads.patch
- debian/patches/python3.10.patch
- debian/patches/switch-to-pytest.patch
- setup.py
- test/test_cache_object.py
- test/test_database_objects.py
- test/test_database_types.py
- test/test_db_from_dataframes.py
Changes:
=====================================
LICENSE
=====================================
@@ -0,0 +1,201 @@
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\ No newline at end of file
=====================================
PKG-INFO
=====================================
@@ -1,35 +1,43 @@
-Metadata-Version: 1.1
+Metadata-Version: 2.1
Name: datacache
-Version: 1.1.5
+Version: 1.2.1
Summary: Helpers for transparently downloading datasets
Home-page: https://github.com/openvax/datacache
Author: Alex Rubinsteyn
-Author-email: alex.rubinsteyn at mssm.edu
+Author-email: alex.rubinsteyn at unc.edu
License: http://www.apache.org/licenses/LICENSE-2.0.html
-Description: DataCache
- =========
-
- Helpers for transparently downloading datasets
-
- API
- ---
-
- - **fetch_file**\ (download_url, filename = *None*, decompress =
- *False*, subdir = *None*)
- - **fetch_and_transform**\ (transformed_filename, transformer, loader,
- source_filename, source_url, subdir = *None*)
- - **fetch_fasta_dict**\ (download_url, filename = *None*, subdir =
- *None*)
- - **fetch_fasta_db**\ (table_name, download_url, fasta_filename =
- *None*, key_column = *‘id’*, value_column = *‘seq’*, subdir = *None*)
- - **fetch_csv_db**\ (table_name, download_url, csv_filename = *None*,
- subdir = *None*, \**pandas_kwargs)
-
-Platform: UNKNOWN
-Classifier: Development Status :: 3 - Alpha
+Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Operating System :: OS Independent
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Programming Language :: Python
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Description-Content-Type: text/markdown
+License-File: LICENSE
+
+<a href="https://travis-ci.org/openvax/datacache">
+ <img src="https://travis-ci.org/openvax/datacache.svg?branch=master" alt="Build Status" />
+</a>
+<a href="https://coveralls.io/github/openvax/datacache?branch=master">
+ <img src="https://coveralls.io/repos/openvax/datacache/badge.svg?branch=master&service=github" alt="Coverage Status" />
+</a>
+<a href="https://pypi.python.org/pypi/datacache/">
+ <img src="https://img.shields.io/pypi/v/datacache.svg?maxAge=1000" alt="PyPI" />
+</a>
+
+DataCache
+=========
+
+Helpers for transparently downloading datasets
+
+## API
+
+* **fetch_file**(download_url, filename = *None*, decompress = *False*, subdir = *None*)
+* **fetch_and_transform**(transformed_filename, transformer, loader,
+ source_filename, source_url, subdir = *None*)
+* **fetch_fasta_dict**(download_url, filename = *None*, subdir = *None*)
+* **fetch_fasta_db**(table_name, download_url, fasta_filename = *None*,
+ key_column = *'id'*, value_column = *'seq'*, subdir = *None*)
+* **fetch_csv_db**(table_name, download_url, csv_filename = *None*, subdir = *None*,
+ \*\*pandas_kwargs)
=====================================
datacache.egg-info/PKG-INFO
=====================================
@@ -1,35 +1,43 @@
-Metadata-Version: 1.1
+Metadata-Version: 2.1
Name: datacache
-Version: 1.1.5
+Version: 1.2.1
Summary: Helpers for transparently downloading datasets
Home-page: https://github.com/openvax/datacache
Author: Alex Rubinsteyn
-Author-email: alex.rubinsteyn at mssm.edu
+Author-email: alex.rubinsteyn at unc.edu
License: http://www.apache.org/licenses/LICENSE-2.0.html
-Description: DataCache
- =========
-
- Helpers for transparently downloading datasets
-
- API
- ---
-
- - **fetch_file**\ (download_url, filename = *None*, decompress =
- *False*, subdir = *None*)
- - **fetch_and_transform**\ (transformed_filename, transformer, loader,
- source_filename, source_url, subdir = *None*)
- - **fetch_fasta_dict**\ (download_url, filename = *None*, subdir =
- *None*)
- - **fetch_fasta_db**\ (table_name, download_url, fasta_filename =
- *None*, key_column = *‘id’*, value_column = *‘seq’*, subdir = *None*)
- - **fetch_csv_db**\ (table_name, download_url, csv_filename = *None*,
- subdir = *None*, \**pandas_kwargs)
-
-Platform: UNKNOWN
-Classifier: Development Status :: 3 - Alpha
+Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Operating System :: OS Independent
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Programming Language :: Python
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Description-Content-Type: text/markdown
+License-File: LICENSE
+
+<a href="https://travis-ci.org/openvax/datacache">
+ <img src="https://travis-ci.org/openvax/datacache.svg?branch=master" alt="Build Status" />
+</a>
+<a href="https://coveralls.io/github/openvax/datacache?branch=master">
+ <img src="https://coveralls.io/repos/openvax/datacache/badge.svg?branch=master&service=github" alt="Coverage Status" />
+</a>
+<a href="https://pypi.python.org/pypi/datacache/">
+ <img src="https://img.shields.io/pypi/v/datacache.svg?maxAge=1000" alt="PyPI" />
+</a>
+
+DataCache
+=========
+
+Helpers for transparently downloading datasets
+
+## API
+
+* **fetch_file**(download_url, filename = *None*, decompress = *False*, subdir = *None*)
+* **fetch_and_transform**(transformed_filename, transformer, loader,
+ source_filename, source_url, subdir = *None*)
+* **fetch_fasta_dict**(download_url, filename = *None*, subdir = *None*)
+* **fetch_fasta_db**(table_name, download_url, fasta_filename = *None*,
+ key_column = *'id'*, value_column = *'seq'*, subdir = *None*)
+* **fetch_csv_db**(table_name, download_url, csv_filename = *None*, subdir = *None*,
+ \*\*pandas_kwargs)
=====================================
datacache.egg-info/SOURCES.txt
=====================================
@@ -1,3 +1,4 @@
+LICENSE
README.md
setup.py
datacache/__init__.py
@@ -8,6 +9,7 @@ datacache/database_helpers.py
datacache/database_table.py
datacache/database_types.py
datacache/download.py
+datacache/version.py
datacache.egg-info/PKG-INFO
datacache.egg-info/SOURCES.txt
datacache.egg-info/dependency_links.txt
=====================================
datacache/__init__.py
=====================================
@@ -1,5 +1,3 @@
-# Copyright (c) 2015-2018. Mount Sinai School of Medicine
-#
# 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
@@ -12,8 +10,6 @@
# See the License for the specific language governing permissions and
# limitations under the License.
-from __future__ import print_function, division, absolute_import
-
from .download import fetch_file, fetch_and_transform, fetch_csv_dataframe
from .database_helpers import (
db_from_dataframe,
@@ -30,8 +26,7 @@ from .common import (
build_local_filename
)
from .cache import Cache
-
-__version__ = '1.1.5'
+from .version import __version__
__all__ = [
'fetch_file',
=====================================
datacache/cache.py
=====================================
@@ -1,5 +1,3 @@
-# Copyright (c) 2015-2018. Mount Sinai School of Medicine
-#
# 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
@@ -12,8 +10,6 @@
# See the License for the specific language governing permissions and
# limitations under the License.
-from __future__ import print_function, division, absolute_import
-
from os.path import exists, join
from os import remove
=====================================
datacache/common.py
=====================================
@@ -1,5 +1,3 @@
-# Copyright (c) 2015-2018. Mount Sinai School of Medicine
-#
# 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
@@ -12,8 +10,6 @@
# See the License for the specific language governing permissions and
# limitations under the License.
-from __future__ import print_function, division, absolute_import
-
import hashlib
from os import makedirs, environ
from os.path import join, exists, split, splitext
=====================================
datacache/database_helpers.py
=====================================
@@ -1,5 +1,3 @@
-# Copyright (c) 2015-2018. Mount Sinai School of Medicine
-#
# 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
=====================================
datacache/database_table.py
=====================================
@@ -1,5 +1,3 @@
-# Copyright (c) 2015-2018. Mount Sinai School of Medicine
-#
# 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
@@ -12,8 +10,6 @@
# See the License for the specific language governing permissions and
# limitations under the License.
-from __future__ import print_function, division, absolute_import
-
from .database_types import db_type
class DatabaseTable(object):
=====================================
datacache/database_types.py
=====================================
@@ -1,5 +1,3 @@
-# Copyright (c) 2015-2018. Mount Sinai School of Medicine
-#
# 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
@@ -58,13 +56,6 @@ def _candidate_type_names(python_type_representation):
Any Python object which represents a type, such as `int`,
`dtype('int8')`, `np.int8`, or `"int8"`.
"""
- # if we get a single character code we should normalize to a NumPy type
- # using np.typeDict, which maps string representations of types to NumPy
- # type objects
- if python_type_representation in np.typeDict:
- python_type_representation = np.typeDict[python_type_representation]
- yield python_type_representation.__name__
-
# if we get a dtype object i.e. dtype('int16'), then pull out its name
if hasattr(python_type_representation, 'name'):
yield python_type_representation.name
=====================================
datacache/download.py
=====================================
@@ -1,5 +1,3 @@
-# Copyright (c) 2015-2018. Mount Sinai School of Medicine
-#
# 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
@@ -12,8 +10,6 @@
# See the License for the specific language governing permissions and
# limitations under the License.
-from __future__ import print_function, division, absolute_import
-
import gzip
import logging
import os
@@ -21,11 +17,10 @@ import subprocess
from shutil import move
from tempfile import NamedTemporaryFile
import zipfile
-
+import urllib
import requests
import pandas as pd
-from six.moves import urllib
from .common import build_path, build_local_filename
=====================================
datacache/version.py
=====================================
@@ -0,0 +1,3 @@
+__version__ = '1.2.1'
+
+
=====================================
debian/changelog
=====================================
@@ -1,9 +1,18 @@
+python-datacache (1.2.1-1) unstable; urgency=medium
+
+ * Team upload.
+ * New upstream version
+ * Standards-Version: 4.6.2 (routine-update)
+ * Remove trailing whitespace in debian/changelog (routine-update)
+
+ -- Andreas Tille <tille at debian.org> Sun, 25 Dec 2022 22:39:23 +0100
+
python-datacache (1.1.5-2) unstable; urgency=medium
[ Mohammed Bilal ]
* Team Upload.
* Add autopkgtest
-
+
[ Nilesh Patra ]
* Switch from nose to pytest
=====================================
debian/control
=====================================
@@ -13,7 +13,7 @@ Build-Depends: debhelper-compat (= 13),
python3-biopython <!nocheck>,
python3-typechecks <!nocheck>,
python3-mock <!nocheck>,
-Standards-Version: 4.6.0
+Standards-Version: 4.6.2
Homepage: https://github.com/openvax/datacache
Vcs-Browser: https://salsa.debian.org/med-team/python-datacache
Vcs-Git: https://salsa.debian.org/med-team/python-datacache.git
=====================================
debian/patches/noInternetAccessForDownloads.patch
=====================================
@@ -43,7 +43,7 @@ Description: Exclude tests accessing network
+ assert filename_yahoo != filename_google
--- a/test/test_cache_object.py
+++ b/test/test_cache_object.py
-@@ -19,7 +19,7 @@ def test_cache_object_local_filename():
+@@ -21,7 +21,7 @@ def test_cache_object_local_filename():
filename = Cache(CACHE_DIR).local_filename(filename="test")
assert filename.endswith("test")
@@ -52,7 +52,7 @@ Description: Exclude tests accessing network
cache = Cache(CACHE_DIR)
path = cache.fetch(TEST_URL, filename=TEST_FILENAME)
assert path.endswith(TEST_FILENAME), \
-@@ -37,7 +37,7 @@ def test_cache_fetch_force(mock_download
+@@ -39,7 +39,7 @@ def test_cache_fetch_force(mock_download
assert len(mock_download.call_args_list) == 2, \
"Expected two separate calls to _download, given force=True"
@@ -61,7 +61,7 @@ Description: Exclude tests accessing network
cache = Cache(CACHE_DIR)
path = cache.fetch(TEST_URL, filename=TEST_FILENAME)
assert exists(path), "Expected %s to exist after download" % path
-@@ -45,7 +45,7 @@ def test_cache_delete_url():
+@@ -47,7 +47,7 @@ def test_cache_delete_url():
assert not exists(path), \
"Expected %s to be deleted after call to delete_url" % path
=====================================
debian/patches/python3.10.patch
=====================================
@@ -4,7 +4,7 @@ Description: There is no os.errno any more
--- a/datacache/download.py
+++ b/datacache/download.py
-@@ -17,6 +17,7 @@ from __future__ import print_function, d
+@@ -13,6 +13,7 @@
import gzip
import logging
import os
@@ -12,7 +12,7 @@ Description: There is no os.errno any more
import subprocess
from shutil import move
from tempfile import NamedTemporaryFile
-@@ -83,7 +84,7 @@ def _download_to_temp_file(
+@@ -78,7 +79,7 @@ def _download_to_temp_file(
logger.info("Running: %s" % (" ".join(wget_command_list)))
subprocess.call(wget_command_list)
except OSError as e:
=====================================
debian/patches/switch-to-pytest.patch
=====================================
@@ -3,15 +3,7 @@ Author: Nilesh Patra <nilesh at debian.org>
Last-Update: 2022-03-29
--- a/test/test_cache_object.py
+++ b/test/test_cache_object.py
-@@ -1,7 +1,6 @@
- from os import remove
- from os.path import exists
- from mock import patch
--from nose.tools import eq_
-
- from datacache import Cache
-
-@@ -26,7 +25,7 @@
+@@ -28,7 +28,7 @@ def notest_cache_fetch_google():
"Expected local file to be named %s but got %s" % (
TEST_FILENAME, path)
assert exists(path), "File not found: %s" % path
@@ -20,34 +12,9 @@ Last-Update: 2022-03-29
@patch('datacache.cache.download._download_and_decompress_if_necessary')
---- a/test/test_database_types.py
-+++ b/test/test_database_types.py
-@@ -1,4 +1,3 @@
--from nose.tools import eq_
- import numpy as np
- from datacache.database_types import db_type
-
-@@ -7,9 +6,9 @@
- int,
- np.int8, np.int16, np.int32, np.int64,
- np.uint8, np.uint16, np.uint32, np.uint64]:
-- eq_(db_type(int_type), "INT")
-+ assert(db_type(int_type) == "INT")
-
- for float_type in [float, np.float32, np.float64]:
-- eq_(db_type(float), "FLOAT")
-+ assert(db_type(float) == "FLOAT")
-
-- eq_(db_type(str), "TEXT")
-+ assert(db_type(str) == "TEXT")
--- a/test/test_db_from_dataframes.py
+++ b/test/test_db_from_dataframes.py
-@@ -1,4 +1,3 @@
--from nose.tools import eq_
- import pandas as pd
- from tempfile import NamedTemporaryFile
- from datacache import db_from_dataframes, db_from_dataframe
-@@ -16,10 +15,10 @@
+@@ -18,10 +18,10 @@ def test_database_from_dataframes():
subdir="test_datacache")
cursor_A = db.execute("SELECT * FROM A")
results_A = cursor_A.fetchall()
@@ -60,7 +27,7 @@ Last-Update: 2022-03-29
def test_database_from_single_dataframe():
with NamedTemporaryFile(suffix="test.db") as f:
-@@ -32,4 +31,4 @@
+@@ -34,4 +34,4 @@ def test_database_from_single_dataframe(
subdir="test_datacache")
cursor = db.execute("SELECT * FROM A")
results = cursor.fetchall()
@@ -68,15 +35,7 @@ Last-Update: 2022-03-29
+ assert(results == [(1, "a"), (2, "b"), (3, "c")])
--- a/test/test_database_objects.py
+++ b/test/test_database_objects.py
-@@ -6,7 +6,6 @@
-
- import datacache
-
--from nose.tools import eq_
-
- TABLE_NAME = "test"
- INT_COL_NAME = "int_col"
-@@ -29,11 +28,11 @@
+@@ -30,11 +30,11 @@ def make_table_object():
def test_database_table_object():
table = make_table_object()
@@ -93,7 +52,7 @@ Last-Update: 2022-03-29
def test_create_db():
with tempfile.NamedTemporaryFile(suffix="test.db") as f:
-@@ -49,4 +48,4 @@
+@@ -50,4 +50,4 @@ def test_create_db():
cursor = db.connection.execute(sql)
int_result_tuple = cursor.fetchone()
int_result = int_result_tuple[0]
=====================================
setup.py
=====================================
@@ -1,5 +1,3 @@
-# Copyright (c) 2014-2018. Mount Sinai School of Medicine
-#
# 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
@@ -21,7 +19,7 @@ from setuptools import setup
readme_filename = "README.md"
current_directory = os.path.dirname(__file__)
readme_path = os.path.join(current_directory, readme_filename)
-
+project_name = "datacache"
try:
with open(readme_path, "r") as f:
@@ -30,14 +28,7 @@ except:
logging.warn("Failed to load %s", readme_filename)
readme_markdown = ""
-try:
- import pypandoc
- readme_restructured = pypandoc.convert(readme_markdown, to="rst", format="md")
-except:
- readme_restructured = readme_markdown
- logging.warn("Failed to convert %s to reStructuredText", readme_filename)
-
-with open('datacache/__init__.py', 'r') as f:
+with open('%s/version.py' % project_name, 'r') as f:
version = re.search(
r'^__version__\s*=\s*[\'"]([^\'"]*)[\'"]',
f.read(),
@@ -45,15 +36,15 @@ with open('datacache/__init__.py', 'r') as f:
if __name__ == "__main__":
setup(
- name="datacache",
+ name=project_name,
version=version,
description="Helpers for transparently downloading datasets",
author="Alex Rubinsteyn",
- author_email="alex.rubinsteyn at mssm.edu",
- url="https://github.com/openvax/datacache",
+ author_email="alex.rubinsteyn at unc.edu",
+ url="https://github.com/openvax/%s" % project_name,
license="http://www.apache.org/licenses/LICENSE-2.0.html",
classifiers=[
- "Development Status :: 3 - Alpha",
+ "Development Status :: 4 - Beta",
"Environment :: Console",
"Operating System :: OS Independent",
"Intended Audience :: Science/Research",
@@ -69,6 +60,7 @@ if __name__ == "__main__":
"typechecks>=0.0.2",
"mock",
],
- long_description=readme_restructured,
- packages=["datacache"],
+ long_description=readme_markdown,
+ long_description_content_type='text/markdown',
+ packages=[project_name],
)
=====================================
test/test_cache_object.py
=====================================
@@ -1,7 +1,6 @@
from os import remove
from os.path import exists
from mock import patch
-from nose.tools import eq_
from datacache import Cache
@@ -9,6 +8,9 @@ CACHE_DIR = "datacache_test"
TEST_URL = "http://www.google.com"
TEST_FILENAME = "google"
+def eq_(x, y):
+ assert x == y
+
def test_cache_object_path():
cache = Cache(CACHE_DIR)
assert cache.cache_directory_path.endswith(CACHE_DIR), \
=====================================
test/test_database_objects.py
=====================================
@@ -6,7 +6,8 @@ import tempfile
import datacache
-from nose.tools import eq_
+def eq_(x, y):
+ assert x == y
TABLE_NAME = "test"
INT_COL_NAME = "int_col"
=====================================
test/test_database_types.py
=====================================
@@ -1,4 +1,3 @@
-from nose.tools import eq_
import numpy as np
from datacache.database_types import db_type
@@ -7,9 +6,9 @@ def test_db_types():
int,
np.int8, np.int16, np.int32, np.int64,
np.uint8, np.uint16, np.uint32, np.uint64]:
- eq_(db_type(int_type), "INT")
+ assert db_type(int_type) == "INT"
for float_type in [float, np.float32, np.float64]:
- eq_(db_type(float), "FLOAT")
+ assert db_type(float) == "FLOAT"
- eq_(db_type(str), "TEXT")
+ assert db_type(str) == "TEXT"
=====================================
test/test_db_from_dataframes.py
=====================================
@@ -1,4 +1,3 @@
-from nose.tools import eq_
import pandas as pd
from tempfile import NamedTemporaryFile
from datacache import db_from_dataframes, db_from_dataframe
@@ -6,6 +5,9 @@ from datacache import db_from_dataframes, db_from_dataframe
dfA = pd.DataFrame({"numbers": [1, 2, 3], "strings": ["a", "b", "c"]})
dfB = pd.DataFrame({"wuzzles": ["nuzzle", "ruzzle"]})
+def eq_(x, y):
+ assert x == y
+
def test_database_from_dataframes():
with NamedTemporaryFile(suffix="test.db") as f:
db = db_from_dataframes(
View it on GitLab: https://salsa.debian.org/med-team/python-datacache/-/compare/4e5a8695789c8261e461fb7e6d775652e5db6c92...32bd7956745a9dd40933322403a55affcd7ea7cd
--
View it on GitLab: https://salsa.debian.org/med-team/python-datacache/-/compare/4e5a8695789c8261e461fb7e6d775652e5db6c92...32bd7956745a9dd40933322403a55affcd7ea7cd
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