[med-svn] [Git][med-team/python-datacache][master] 4 commits: New upstream version 1.4.1

Sun Sep 22 12:44:02 BST 2024


Alexandre Detiste pushed to branch master at Debian Med / python-datacache


Commits:
1b2c5769 by Alexandre Detiste at 2024-09-22T13:37:10+02:00
New upstream version 1.4.1
- - - - -
d8723198 by Alexandre Detiste at 2024-09-22T13:37:11+02:00
Update upstream source from tag 'upstream/1.4.1'

Update to upstream version '1.4.1'
with Debian dir 2596723998d9a6fd2c51566cd25b5c7eaefcd985
- - - - -
b771b8aa by Alexandre Detiste at 2024-09-22T13:43:48+02:00
refresh patches

- - - - -
34cf2d02 by Alexandre Detiste at 2024-09-22T13:43:52+02:00
release

- - - - -


22 changed files:

- PKG-INFO
- README.md
- datacache.egg-info/PKG-INFO
- datacache.egg-info/SOURCES.txt
- datacache/__init__.py
- datacache/common.py
- datacache/database_types.py
- datacache/download.py
- datacache/version.py
- debian/changelog
- debian/patches/noInternetAccessForDownloads.patch
- − debian/patches/python3.10.patch
- debian/patches/remove-mock.patch
- debian/patches/series
- debian/patches/switch-to-pytest.patch
- test/test_cache_object.py → tests/test_cache_object.py
- test/test_database_objects.py → tests/test_database_objects.py
- test/test_database_types.py → tests/test_database_types.py
- test/test_db_from_dataframes.py → tests/test_db_from_dataframes.py
- test/test_download.py → tests/test_download.py
- test/test_fasta_dict.py → tests/test_fasta_dict.py
- test/test_names.py → tests/test_names.py


Changes:

=====================================
PKG-INFO
=====================================
@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: datacache
-Version: 1.2.1
+Version: 1.4.1
 Summary: Helpers for transparently downloading datasets
 Home-page: https://github.com/openvax/datacache
 Author: Alex Rubinsteyn
@@ -15,29 +15,32 @@ Classifier: Programming Language :: Python
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Description-Content-Type: text/markdown
 License-File: LICENSE
+Requires-Dist: pandas>=0.15.2
+Requires-Dist: appdirs>=1.4.0
+Requires-Dist: progressbar33>=2.4
+Requires-Dist: requests>=2.5.1
+Requires-Dist: typechecks>=0.0.2
+Requires-Dist: mock
 
-<a href="https://travis-ci.org/openvax/datacache">
-    <img src="https://travis-ci.org/openvax/datacache.svg?branch=master" alt="Build Status" />
-</a>
+[![Tests](https://github.com/openvax/datacache/actions/workflows/tests.yml/badge.svg)](https://github.com/openvax/datacache/actions/workflows/tests.yml)
 <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" />
+<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" />
+<img src="https://img.shields.io/pypi/v/datacache.svg?maxAge=1000" alt="PyPI" />
 </a>
 
-DataCache
-=========
+# 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)
+- **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)


=====================================
README.md
=====================================
@@ -1,25 +1,22 @@
-<a href="https://travis-ci.org/openvax/datacache">
-    <img src="https://travis-ci.org/openvax/datacache.svg?branch=master" alt="Build Status" />
-</a>
+[![Tests](https://github.com/openvax/datacache/actions/workflows/tests.yml/badge.svg)](https://github.com/openvax/datacache/actions/workflows/tests.yml)
 <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" />
+<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" />
+<img src="https://img.shields.io/pypi/v/datacache.svg?maxAge=1000" alt="PyPI" />
 </a>
 
-DataCache
-=========
+# 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)
+- **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
=====================================
@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: datacache
-Version: 1.2.1
+Version: 1.4.1
 Summary: Helpers for transparently downloading datasets
 Home-page: https://github.com/openvax/datacache
 Author: Alex Rubinsteyn
@@ -15,29 +15,32 @@ Classifier: Programming Language :: Python
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Description-Content-Type: text/markdown
 License-File: LICENSE
+Requires-Dist: pandas>=0.15.2
+Requires-Dist: appdirs>=1.4.0
+Requires-Dist: progressbar33>=2.4
+Requires-Dist: requests>=2.5.1
+Requires-Dist: typechecks>=0.0.2
+Requires-Dist: mock
 
-<a href="https://travis-ci.org/openvax/datacache">
-    <img src="https://travis-ci.org/openvax/datacache.svg?branch=master" alt="Build Status" />
-</a>
+[![Tests](https://github.com/openvax/datacache/actions/workflows/tests.yml/badge.svg)](https://github.com/openvax/datacache/actions/workflows/tests.yml)
 <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" />
+<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" />
+<img src="https://img.shields.io/pypi/v/datacache.svg?maxAge=1000" alt="PyPI" />
 </a>
 
-DataCache
-=========
+# 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)
+- **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
=====================================
@@ -15,10 +15,10 @@ datacache.egg-info/SOURCES.txt
 datacache.egg-info/dependency_links.txt
 datacache.egg-info/requires.txt
 datacache.egg-info/top_level.txt
-test/test_cache_object.py
-test/test_database_objects.py
-test/test_database_types.py
-test/test_db_from_dataframes.py
-test/test_download.py
-test/test_fasta_dict.py
-test/test_names.py
\ No newline at end of file
+tests/test_cache_object.py
+tests/test_database_objects.py
+tests/test_database_types.py
+tests/test_db_from_dataframes.py
+tests/test_download.py
+tests/test_fasta_dict.py
+tests/test_names.py
\ No newline at end of file


=====================================
datacache/__init__.py
=====================================
@@ -29,6 +29,7 @@ from .cache import Cache
 from .version import __version__
 
 __all__ = [
+    '__version__',
     'fetch_file',
     'fetch_and_transform',
     'fetch_csv_dataframe',


=====================================
datacache/common.py
=====================================
@@ -45,7 +45,7 @@ def normalize_filename(filename):
     Remove special characters and shorten if name is too long
     """
     # if the url pointed to a directory then just replace all the special chars
-    filename = re.sub("/|\\|;|:|\?|=", "_", filename)
+    filename = re.sub(r"/|\\|;|:|\?|=", "_", filename)
 
     if len(filename) > 150:
         prefix = hashlib.md5(filename).hexdigest()


=====================================
datacache/database_types.py
=====================================
@@ -38,6 +38,7 @@ _dtype_to_db_type_dict = {
     'object_': 'TEXT',
     'string_': 'TEXT',
     'str': 'TEXT',
+    'category': 'TEXT',
 }
 
 def _lookup_type_name(type_name):


=====================================
datacache/download.py
=====================================
@@ -13,6 +13,7 @@
 import gzip
 import logging
 import os
+import errno
 import subprocess
 from shutil import move
 from tempfile import NamedTemporaryFile
@@ -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:
-            if e.errno == os.errno.ENOENT:
+            if e.errno == errno.ENOENT:
                 # wget not found
                 download_using_python()
             else:


=====================================
datacache/version.py
=====================================
@@ -1,3 +1,3 @@
-__version__ = '1.2.1'
+__version__ = '1.4.1'
 
 


=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+python-datacache (1.4.1-1) unstable; urgency=medium
+
+  * Team upload.
+  * New upstream version 1.4.1
+  * Refresh patches
+
+ -- Alexandre Detiste <tchet at debian.org>  Sun, 22 Sep 2024 13:42:56 +0200
+
 python-datacache (1.2.1-2) unstable; urgency=medium
 
   * Team upload.


=====================================
debian/patches/noInternetAccessForDownloads.patch
=====================================
@@ -3,8 +3,8 @@ Author: Steffen Möller <moeller at debian.org>
 Last-Update: Fri, 18 Feb 2022 18:46:02 +0100
 Description: Exclude tests accessing network
 
---- a/test/test_download.py
-+++ b/test/test_download.py
+--- a/tests/test_download.py
++++ b/tests/test_download.py
 @@ -19,7 +19,7 @@ URL = \
      'ftp://ftp.ensembl.org/pub/release-75/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.75.dna_rm.chromosome.MT.fa.gz'
  
@@ -23,8 +23,8 @@ Description: Exclude tests accessing network
      path = fetch_file(URL, decompress=True, subdir="datacache")
      assert path.endswith(FASTA_FILENAME)
  
---- a/test/test_names.py
-+++ b/test/test_names.py
+--- a/tests/test_names.py
++++ b/tests/test_names.py
 @@ -5,7 +5,7 @@ def test_url_without_filename():
      assert filename
      assert "google" in filename
@@ -41,8 +41,8 @@ Description: Exclude tests accessing network
 -    assert filename_yahoo != filename_google
 \ No newline at end of file
 +    assert filename_yahoo != filename_google
---- a/test/test_cache_object.py
-+++ b/test/test_cache_object.py
+--- a/tests/test_cache_object.py
++++ b/tests/test_cache_object.py
 @@ -21,7 +21,7 @@ def test_cache_object_local_filename():
      filename = Cache(CACHE_DIR).local_filename(filename="test")
      assert filename.endswith("test")
@@ -70,8 +70,8 @@ Description: Exclude tests accessing network
      """test_cache_missing_file : Files can be deleted from the file system,
      Cache should be aware that these files no longer exist
      """
---- a/test/test_fasta_dict.py
-+++ b/test/test_fasta_dict.py
+--- a/tests/test_fasta_dict.py
++++ b/tests/test_fasta_dict.py
 @@ -46,6 +46,3 @@ def fetch_fasta_dict(path_or_url):
      return d
  


=====================================
debian/patches/python3.10.patch deleted
=====================================
@@ -1,23 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Fri, 18 Feb 2022 18:46:02 +0100
-Description: There is no os.errno any more
-
---- a/datacache/download.py
-+++ b/datacache/download.py
-@@ -13,6 +13,7 @@
- import gzip
- import logging
- import os
-+import errno
- import subprocess
- from shutil import move
- from tempfile import NamedTemporaryFile
-@@ -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:
--            if e.errno == os.errno.ENOENT:
-+            if e.errno == errno.ENOENT:
-                 # wget not found
-                 download_using_python()
-             else:


=====================================
debian/patches/remove-mock.patch
=====================================
@@ -20,8 +20,8 @@ Description: remove usage of old python3-mock
          ],
          long_description=readme_markdown,
          long_description_content_type='text/markdown',
---- a/test/test_cache_object.py
-+++ b/test/test_cache_object.py
+--- a/tests/test_cache_object.py
++++ b/tests/test_cache_object.py
 @@ -1,6 +1,6 @@
  from os import remove
  from os.path import exists


=====================================
debian/patches/series
=====================================
@@ -1,4 +1,3 @@
 noInternetAccessForDownloads.patch
-python3.10.patch
 switch-to-pytest.patch
 remove-mock.patch


=====================================
debian/patches/switch-to-pytest.patch
=====================================
@@ -1,8 +1,8 @@
 Description: nose is being deprecated hence remove its usage
 Author: Nilesh Patra <nilesh at debian.org>
 Last-Update: 2022-03-29
---- a/test/test_cache_object.py
-+++ b/test/test_cache_object.py
+--- a/tests/test_cache_object.py
++++ b/tests/test_cache_object.py
 @@ -28,7 +28,7 @@ def notest_cache_fetch_google():
          "Expected local file to be named %s but got %s" % (
              TEST_FILENAME, path)
@@ -12,8 +12,8 @@ Last-Update: 2022-03-29
  
  
  @patch('datacache.cache.download._download_and_decompress_if_necessary')
---- a/test/test_db_from_dataframes.py
-+++ b/test/test_db_from_dataframes.py
+--- a/tests/test_db_from_dataframes.py
++++ b/tests/test_db_from_dataframes.py
 @@ -18,10 +18,10 @@ def test_database_from_dataframes():
              subdir="test_datacache")
          cursor_A = db.execute("SELECT * FROM A")
@@ -33,8 +33,8 @@ Last-Update: 2022-03-29
          results = cursor.fetchall()
 -        eq_(results, [(1, "a"), (2, "b"), (3, "c")])
 +        assert(results == [(1, "a"), (2, "b"), (3, "c")])
---- a/test/test_database_objects.py
-+++ b/test/test_database_objects.py
+--- a/tests/test_database_objects.py
++++ b/tests/test_database_objects.py
 @@ -30,11 +30,11 @@ def make_table_object():
  
  def test_database_table_object():


=====================================
test/test_cache_object.py → tests/test_cache_object.py
=====================================


=====================================
test/test_database_objects.py → tests/test_database_objects.py
=====================================


=====================================
test/test_database_types.py → tests/test_database_types.py
=====================================


=====================================
test/test_db_from_dataframes.py → tests/test_db_from_dataframes.py
=====================================


=====================================
test/test_download.py → tests/test_download.py
=====================================


=====================================
test/test_fasta_dict.py → tests/test_fasta_dict.py
=====================================


=====================================
test/test_names.py → tests/test_names.py
=====================================



View it on GitLab: https://salsa.debian.org/med-team/python-datacache/-/compare/1de2f2ea6ac07b26842996deb4bb425d0453f91e...34cf2d02a708b9b1f495a99ba45b3d2fda4bbcbc

-- 
View it on GitLab: https://salsa.debian.org/med-team/python-datacache/-/compare/1de2f2ea6ac07b26842996deb4bb425d0453f91e...34cf2d02a708b9b1f495a99ba45b3d2fda4bbcbc
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