[med-svn] [Git][med-team/biomaj3-core][upstream] 2 commits: New upstream version 3.0.28
Olivier Sallou (@osallou)
gitlab at salsa.debian.org
Mon Aug 29 08:59:10 BST 2022
Olivier Sallou pushed to branch upstream at Debian Med / biomaj3-core
Commits:
936792ca by Olivier Sallou at 2022-08-29T07:50:48+00:00
New upstream version 3.0.28
- - - - -
f9ca1199 by Olivier Sallou at 2022-08-29T07:58:37+00:00
new upstream release 3.0.28
- - - - -
5 changed files:
- CHANGES.txt
- biomaj_core/config.py
- requirements.txt
- setup.py
- tests/biomaj_tests.py → tests/test_biomaj.py
Changes:
=====================================
CHANGES.txt
=====================================
@@ -1,3 +1,7 @@
+3.0.28:
+ use pytest instead of nose (deprecated)
+ python3 only support
+
3.0.27:
add .tgz extension support
=====================================
biomaj_core/config.py
=====================================
@@ -1,5 +1,3 @@
-from __future__ import print_function
-from future import standard_library
from builtins import str
from builtins import object
import logging
@@ -11,12 +9,7 @@ import sys
from biomaj_core.utils import Utils
from biomaj_core.bmajindex import BmajIndex
-if sys.version < '3':
- import ConfigParser as configparser
-else:
- import configparser
-
-standard_library.install_aliases()
+import configparser
class BiomajConfig(object):
=====================================
requirements.txt
=====================================
@@ -1,5 +1,4 @@
-nose
+pytest
mock
-future
elasticsearch==5.5.3
requests
=====================================
setup.py
=====================================
@@ -22,7 +22,7 @@ config = {
'url': 'http://biomaj.genouest.org',
'download_url': 'http://biomaj.genouest.org',
'author_email': 'olivier.sallou at irisa.fr',
- 'version': '3.0.27',
+ 'version': '3.0.28',
'classifiers': [
'Development Status :: 5 - Production/Stable',
'Environment :: Console',
@@ -35,17 +35,14 @@ config = {
'License :: OSI Approved :: GNU Affero General Public License v3 or later (AGPLv3+)',
# Specify the Python versions you support here. In particular, ensure
# that you indicate whether you support Python 2, Python 3 or both.
- 'Programming Language :: Python :: 2',
- 'Programming Language :: Python :: 2.7',
'Programming Language :: Python :: 3'
],
+ 'python_requires': '>=3',
'install_requires': [
- 'future',
'elasticsearch',
'requests'
],
- 'tests_require': ['nose', 'mock'],
- 'test_suite': 'nose.collector',
+ 'tests_require': ['pytest', 'mock'],
'packages': find_packages(),
'include_package_data': True,
'name': 'biomaj_core'
=====================================
tests/biomaj_tests.py → tests/test_biomaj.py
=====================================
@@ -1,19 +1,14 @@
-from __future__ import print_function
-
-from nose.tools import *
-from nose.plugins.attrib import attr
-
import shutil
import os
import sys
import tempfile
import stat
+import pytest
from biomaj_core.config import BiomajConfig
from biomaj_core.utils import Utils
from biomaj_core.bmajindex import BmajIndex
-import unittest
class UtilsForTest:
@@ -98,8 +93,8 @@ class UtilsForTest:
for prop in properties:
from_file = os.path.join(curdir, prop)
to_file = os.path.join(self.conf_dir, prop)
- fout = open(to_file,'w')
- with open(from_file,'r') as fin:
+ fout = open(to_file,'w', encoding='UTF-8')
+ with open(from_file,'r', encoding='UTF-8') as fin:
for line in fin:
if line.startswith('remote.dir'):
fout.write("remote.dir="+os.path.join(curdir,
@@ -117,8 +112,8 @@ class UtilsForTest:
self.global_properties = os.path.join(self.conf_dir, 'global.properties')
curdir = os.path.dirname(os.path.realpath(__file__))
global_template = os.path.join(curdir, 'global.properties')
- fout = open(self.global_properties, 'w')
- with open(global_template,'r') as fin:
+ fout = open(self.global_properties, 'w', encoding='UTF-8')
+ with open(global_template,'r', encoding='UTF-8') as fin:
for line in fin:
if line.startswith('conf.dir'):
fout.write("conf.dir="+self.conf_dir+"\n")
@@ -140,8 +135,8 @@ class UtilsForTest:
self.global_properties_hl = os.path.join(self.conf_dir, 'global_hardlinks.properties')
curdir = os.path.dirname(os.path.realpath(__file__))
global_template = os.path.join(curdir, 'global_hardlinks.properties')
- fout = open(self.global_properties_hl, 'w')
- with open(global_template,'r') as fin:
+ fout = open(self.global_properties_hl, 'w', encoding='UTF-8')
+ with open(global_template,'r', encoding='UTF-8') as fin:
for line in fin:
if line.startswith('conf.dir'):
fout.write("conf.dir="+self.conf_dir+"\n")
@@ -158,12 +153,12 @@ class UtilsForTest:
fout.close()
-class TestBiomajUtils(unittest.TestCase):
+class TestBiomajUtils():
- def setUp(self):
+ def setup_method(self, m):
self.utils = UtilsForTest()
- def tearDown(self):
+ def teardown_method(self, m):
self.utils.clean()
def test_properties_override(self):
@@ -171,10 +166,10 @@ class TestBiomajUtils(unittest.TestCase):
allow_user_config=False)
config = BiomajConfig('local')
ldap_host = config.get('ldap.host')
- self.assertTrue(ldap_host == 'localhost')
+ assert (ldap_host == 'localhost')
os.environ['BIOMAJ_LDAP_HOST'] = 'someserver'
ldap_host = config.get('ldap.host')
- self.assertTrue(ldap_host == 'someserver')
+ assert (ldap_host == 'someserver')
def test_service_config_override(self):
config = {
@@ -182,17 +177,17 @@ class TestBiomajUtils(unittest.TestCase):
'web': {'local_endpoint': 'http://localhost'}
}
Utils.service_config_override(config)
- self.assertTrue(config['rabbitmq']['host'] == '1.2.3.4')
+ assert (config['rabbitmq']['host'] == '1.2.3.4')
os.environ['RABBITMQ_HOST'] = '4.3.2.1'
Utils.service_config_override(config)
- self.assertTrue(config['rabbitmq']['host'] == '4.3.2.1')
+ assert (config['rabbitmq']['host'] == '4.3.2.1')
os.environ['WEB_LOCAL_ENDPOINT_DOWNLOAD'] = 'http://download'
Utils.service_config_override(config)
- self.assertTrue(config['web']['local_endpoint_download'] == 'http://download')
+ assert (config['web']['local_endpoint_download'] == 'http://download')
endpoint = Utils.get_service_endpoint(config, 'download')
- self.assertTrue(endpoint == 'http://download')
+ assert (endpoint == 'http://download')
endpoint = Utils.get_service_endpoint(config, 'process')
- self.assertTrue(endpoint == 'http://localhost')
+ assert (endpoint == 'http://localhost')
def test_use_hardlinks_config(self):
"""
@@ -202,23 +197,22 @@ class TestBiomajUtils(unittest.TestCase):
allow_user_config=False)
# Must be disabled in local.properties
config = BiomajConfig('local')
- self.assertFalse(config.get_bool("use_hardlinks"))
+ assert not config.get_bool("use_hardlinks")
# Must be enabled for hardlinks.properties (override)
config = BiomajConfig('hardlinks')
- self.assertTrue(config.get_bool("use_hardlinks"))
+ assert config.get_bool("use_hardlinks")
# Reload file with use_hardlinks=1
BiomajConfig.load_config(self.utils.global_properties_hl,
allow_user_config=False)
config = BiomajConfig('local')
- self.assertTrue(config.get_bool("use_hardlinks"))
+ assert config.get_bool("use_hardlinks")
def test_mimes(self):
fasta_file = os.path.join(os.path.dirname(os.path.realpath(__file__)),
'bank/test2.fasta')
- (mime, encoding) = Utils.detect_format(fasta_file)
- self.assertTrue('application/fasta' == mime)
+ (mime, _) = Utils.detect_format(fasta_file)
+ assert 'application/fasta' == mime
- @attr('compress')
def test_uncompress(self):
from_file = { 'root': os.path.dirname(os.path.realpath(__file__)),
'name': 'bank/test.fasta.gz'
@@ -227,13 +221,13 @@ class TestBiomajUtils(unittest.TestCase):
to_dir = self.utils.data_dir
Utils.copy_files([from_file], to_dir)
Utils.uncompress(os.path.join(to_dir, from_file['name']))
- self.assertTrue(os.path.exists(to_dir+'/bank/test.fasta'))
+ assert os.path.exists(to_dir+'/bank/test.fasta')
def test_copy_with_regexp(self):
from_dir = os.path.dirname(os.path.realpath(__file__))
to_dir = self.utils.data_dir
- Utils.copy_files_with_regexp(from_dir, to_dir, ['.*\.py'])
- self.assertTrue(os.path.exists(to_dir+'/biomaj_tests.py'))
+ Utils.copy_files_with_regexp(from_dir, to_dir, [r'.*\.py'])
+ assert os.path.exists(to_dir+'/test_biomaj.py')
def test_copy_with_regexp_hardlink(self):
"""
@@ -257,24 +251,24 @@ class TestBiomajUtils(unittest.TestCase):
use_hardlinks=True)
# Check if files was copied
for orig, new in zip(orig_file_full, new_file_full):
- self.assertTrue(os.path.exists(new))
+ assert (os.path.exists(new))
# Check if it's really a hardlink. This may fail so we catch
# any exceptions.
orig_file_stat = os.stat(orig)
new_file_stat = os.stat(new)
try:
- self.assertTrue(orig_file_stat.st_ino == new_file_stat.st_ino)
+ assert (orig_file_stat.st_ino == new_file_stat.st_ino)
except Exception:
- msg = "In %s: copy worked but hardlinks were not used." % self.id()
+ msg = "In %s: copy worked but hardlinks were not used." % orig_file_full
print(msg, file=sys.stderr)
def test_copy(self):
from_dir = os.path.dirname(os.path.realpath(__file__))
- local_file = 'biomaj_tests.py'
+ local_file = 'test_biomaj.py'
files_to_copy = [ {'root': from_dir, 'name': local_file}]
to_dir = self.utils.data_dir
Utils.copy_files(files_to_copy, to_dir)
- self.assertTrue(os.path.exists(to_dir+'/biomaj_tests.py'))
+ assert os.path.exists(to_dir+'/test_biomaj.py')
def test_copy_hardlink(self):
"""
@@ -292,18 +286,17 @@ class TestBiomajUtils(unittest.TestCase):
files_to_copy = [{'root': from_dir, 'name': orig_file}]
Utils.copy_files(files_to_copy, to_dir, use_hardlinks=True)
# Check if file was copied
- self.assertTrue(os.path.exists(new_file_full))
+ assert (os.path.exists(new_file_full))
# Check if it's really a hardlink. This may fail so we catch
# any exceptions.
orig_file_stat = os.stat(orig_file_full)
new_file_stat = os.stat(new_file_full)
try:
- self.assertTrue(orig_file_stat.st_ino == new_file_stat.st_ino)
+ assert orig_file_stat.st_ino == new_file_stat.st_ino
except Exception:
- msg = "In %s: copy worked but hardlinks were not used." % self.id()
+ msg = "In %s: copy worked but hardlinks were not used." % orig_file_full
print(msg, file=sys.stderr)
- @attr('check')
def test_check_method(self):
"""Check .name, .exe and .args are well check during bank configuration
checking"""
@@ -311,39 +304,38 @@ class TestBiomajUtils(unittest.TestCase):
for conf in ['noname', 'noexe', 'noargs', 'prenoname', 'prenoexe',
'prenoargs', 'rmnoname', 'rmnoexe', 'rmnoargs']:
config = BiomajConfig(conf)
- self.assertFalse(config.check())
+ assert not config.check()
- at attr('elastic')
-class TestElastic(unittest.TestCase):
+class TestElastic():
"""
test indexing and search
"""
- def setUp(self):
+ def setup_method(self, m):
BmajIndex.es = None
self.utils = UtilsForTest()
- curdir = os.path.dirname(os.path.realpath(__file__))
+ # curdir = os.path.dirname(os.path.realpath(__file__))
BiomajConfig.load_config(self.utils.global_properties,
allow_user_config=False)
if BmajIndex.do_index == False:
- self.skipTest("Skipping indexing tests due to elasticsearch not available")
+ pytest.skip("Skipping indexing tests due to elasticsearch not available")
# Delete all banks
- b = Bank('local')
- b.banks.remove({})
+ # b = Bank('local')
+ # b.banks.remove({})
BmajIndex.delete_all_bank('local')
self.config = BiomajConfig('local')
data_dir = self.config.get('data.dir')
lock_file = os.path.join(data_dir,'local.lock')
if os.path.exists(lock_file):
- os.remove(lock_file)
+ os.remove(lock_file)
- def tearDown(self):
+ def teardown_method(self, m):
data_dir = self.config.get('data.dir')
lock_file = os.path.join(data_dir,'local.lock')
if os.path.exists(lock_file):
- os.remove(lock_file)
+ os.remove(lock_file)
self.utils.clean()
BmajIndex.delete_all_bank('test')
@@ -399,7 +391,7 @@ class TestElastic(unittest.TestCase):
}
}
res = BmajIndex.search(query)
- self.assertTrue(len(res)==2)
+ assert len(res)==2
def test_remove_all(self):
@@ -411,4 +403,4 @@ class TestElastic(unittest.TestCase):
}
BmajIndex.delete_all_bank('test')
res = BmajIndex.search(query)
- self.assertTrue(len(res)==0)
+ assert len(res)==0
View it on GitLab: https://salsa.debian.org/med-team/biomaj3-core/-/compare/7e1c9a4df474ebf6609378600994a56c3c5d78b0...f9ca11995708fd6321a83de5da7e53c6bedf7417
--
View it on GitLab: https://salsa.debian.org/med-team/biomaj3-core/-/compare/7e1c9a4df474ebf6609378600994a56c3c5d78b0...f9ca11995708fd6321a83de5da7e53c6bedf7417
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