[med-svn] [Git][med-team/biomaj3][master] 8 commits: fix merge 3.1.23
Charles Plessy (@plessy)
gitlab at salsa.debian.org
Fri Apr 19 05:24:06 BST 2024
Charles Plessy pushed to branch master at Debian Med / biomaj3
Commits:
85e04d93 by Olivier Sallou at 2022-08-29T13:50:50+00:00
fix merge 3.1.23
- - - - -
5313243e by Charles Plessy at 2024-04-19T09:18:39+09:00
New upstream version 3.1.24
- - - - -
f3434ef6 by Charles Plessy at 2024-04-19T09:18:39+09:00
routine-update: New upstream version
- - - - -
b1dcfc96 by Charles Plessy at 2024-04-19T09:18:39+09:00
Update upstream source from tag 'upstream/3.1.24'
Update to upstream version '3.1.24'
with Debian dir 017e6529ee9ed83ca5a462c61be3d5b8c5bf60c2
- - - - -
466404a1 by Charles Plessy at 2024-04-19T09:18:40+09:00
routine-update: Standards-Version: 4.7.0
- - - - -
445e84f2 by Charles Plessy at 2024-04-19T13:06:31+09:00
Refresh patch
- - - - -
714b8125 by Charles Plessy at 2024-04-19T13:06:56+09:00
Remove patch applied upstream.
- - - - -
e5865331 by Charles Plessy at 2024-04-19T13:14:15+09:00
routine-update: Ready to upload to unstable
- - - - -
21 changed files:
- CHANGES.txt
- README.md
- biomaj/bank.py
- biomaj/mongo_connector.py
- biomaj/notify.py
- biomaj/options.py
- biomaj/process/metaprocess.py
- biomaj/process/processfactory.py
- biomaj/schema_version.py
- biomaj/session.py
- biomaj/workflow.py
- debian/changelog
- debian/control
- − debian/patches/c27f7a2283460a919bc72f400fc610bd45c2df23.patch
- debian/patches/fix_remove_drmaa.patch
- debian/patches/series
- docs/requirements.txt
- requirements.txt
- setup.py
- tests/biomaj_tests.py
- tests/alu.properties → tests/pdbaa.properties
Changes:
=====================================
CHANGES.txt
=====================================
@@ -1,3 +1,7 @@
+3.1.24
+ Update documentation
+ Fix tests
+ Remove dependency on python3-future
3.1.23:
Use pytest instead of nose
3.1.21:
=====================================
README.md
=====================================
@@ -110,7 +110,7 @@ From source:
After dependencies installation, go in BioMAJ source directory:
- python setup.py install
+ pip install .
From packages:
=====================================
biomaj/bank.py
=====================================
@@ -1,5 +1,3 @@
-from builtins import str
-from builtins import object
import os
import logging
import time
@@ -25,7 +23,7 @@ from biomaj_core.bmajindex import BmajIndex
import getpass
-class Bank(object):
+class Bank:
"""
BioMAJ bank
"""
=====================================
biomaj/mongo_connector.py
=====================================
@@ -1,8 +1,7 @@
-from builtins import object
from pymongo import MongoClient
-class MongoConnector(object):
+class MongoConnector:
"""
Connector to mongodb
"""
=====================================
biomaj/notify.py
=====================================
@@ -1,5 +1,3 @@
-from builtins import str
-from builtins import object
import smtplib
import email.utils
from biomaj.workflow import Workflow
@@ -8,16 +6,13 @@ import os
import sys
from email.mime.base import MIMEBase
from email.mime.multipart import MIMEMultipart
+from email.mime.text import MIMEText
from email import encoders
-from jinja2 import Template
-if sys.version < '3':
- from email.MIMEText import MIMEText
-else:
- from email.mime.text import MIMEText
+from jinja2 import Template
-class Notify(object):
+class Notify:
"""
Send notifications
"""
=====================================
biomaj/options.py
=====================================
@@ -1,7 +1,4 @@
-from builtins import object
-
-
-class Options(object):
+class Options:
"""
Available options
"""
=====================================
biomaj/process/metaprocess.py
=====================================
@@ -1,4 +1,3 @@
-from builtins import str
import threading
import logging
import os
=====================================
biomaj/process/processfactory.py
=====================================
@@ -1,12 +1,10 @@
-from builtins import range
-from builtins import object
import threading
import logging
import os
from biomaj.process.metaprocess import MetaProcess
-class ProcessFactory(object):
+class ProcessFactory:
'''
Manage process execution
'''
=====================================
biomaj/schema_version.py
=====================================
@@ -1,4 +1,3 @@
-from __future__ import print_function
import pkg_resources
import string
import random
@@ -12,7 +11,7 @@ from biomaj_core.utils import Utils
import logging
-class SchemaVersion(object):
+class SchemaVersion:
"""
BioMAJ database schema version. This package can be used to make some schema modification if needed during
=====================================
biomaj/session.py
=====================================
@@ -1,6 +1,3 @@
-from future import standard_library
-from builtins import str
-from builtins import object
import os
import time
import copy
@@ -8,10 +5,9 @@ import sys
from biomaj.workflow import Workflow
-standard_library.install_aliases()
-class Session(object):
+class Session:
"""
BioMAJ bank session
"""
=====================================
biomaj/workflow.py
=====================================
@@ -1,6 +1,3 @@
-from builtins import str
-from builtins import range
-from builtins import object
import logging
import datetime
import time
@@ -29,7 +26,7 @@ from yapsy.PluginManager import PluginManager
from packaging.version import parse
-class Workflow(object):
+class Workflow:
"""
Bank update workflow
"""
=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+biomaj3 (3.1.24-1) unstable; urgency=medium
+
+ * Team upload.
+ * New upstream version
+ * Standards-Version: 4.7.0 (routine-update)
+
+ -- Charles Plessy <plessy at debian.org> Fri, 19 Apr 2024 13:13:23 +0900
+
biomaj3 (3.1.23-2) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -20,7 +20,7 @@ Build-Depends: debhelper-compat (= 13),
python3-biomaj3-download,
python3-biomaj3-user,
python3-biomaj3-process
-Standards-Version: 4.6.2
+Standards-Version: 4.7.0
Vcs-Browser: https://salsa.debian.org/med-team/biomaj3
Vcs-Git: https://salsa.debian.org/med-team/biomaj3.git
Homepage: https://github.com/genouest/biomaj
=====================================
debian/patches/c27f7a2283460a919bc72f400fc610bd45c2df23.patch deleted
=====================================
@@ -1,194 +0,0 @@
-From: Alexandre Detiste <alexandre.detiste at gmail.com>
-Origin: https://github.com/genouest/biomaj/pull/134
-Bug-Debian: https://bugs.debian.org/1058564
-Date: Wed, 13 Dec 2023 01:31:24 +0100
-Subject: [PATCH] remove dependency on python3-future
-
----
- biomaj/bank.py | 4 +---
- biomaj/mongo_connector.py | 3 +--
- biomaj/notify.py | 11 +++--------
- biomaj/options.py | 5 +----
- biomaj/process/metaprocess.py | 1 -
- biomaj/process/processfactory.py | 4 +---
- biomaj/schema_version.py | 3 +--
- biomaj/session.py | 5 +----
- biomaj/workflow.py | 5 +----
- docs/requirements.txt | 1 -
- requirements.txt | 1 -
- setup.py | 1 -
- 12 files changed, 10 insertions(+), 34 deletions(-)
-
---- a/biomaj/bank.py
-+++ b/biomaj/bank.py
-@@ -1,5 +1,3 @@
--from builtins import str
--from builtins import object
- import os
- import logging
- import time
-@@ -25,7 +23,7 @@ from biomaj_core.bmajindex import BmajIn
- import getpass
-
-
--class Bank(object):
-+class Bank:
- """
- BioMAJ bank
- """
---- a/biomaj/mongo_connector.py
-+++ b/biomaj/mongo_connector.py
-@@ -1,8 +1,7 @@
--from builtins import object
- from pymongo import MongoClient
-
-
--class MongoConnector(object):
-+class MongoConnector:
- """
- Connector to mongodb
- """
---- a/biomaj/notify.py
-+++ b/biomaj/notify.py
-@@ -1,5 +1,3 @@
--from builtins import str
--from builtins import object
- import smtplib
- import email.utils
- from biomaj.workflow import Workflow
-@@ -8,16 +6,13 @@ import os
- import sys
- from email.mime.base import MIMEBase
- from email.mime.multipart import MIMEMultipart
-+from email.mime.text import MIMEText
- from email import encoders
--from jinja2 import Template
-
--if sys.version < '3':
-- from email.MIMEText import MIMEText
--else:
-- from email.mime.text import MIMEText
-+from jinja2 import Template
-
-
--class Notify(object):
-+class Notify:
- """
- Send notifications
- """
---- a/biomaj/options.py
-+++ b/biomaj/options.py
-@@ -1,7 +1,4 @@
--from builtins import object
--
--
--class Options(object):
-+class Options:
- """
- Available options
- """
---- a/biomaj/process/metaprocess.py
-+++ b/biomaj/process/metaprocess.py
-@@ -1,4 +1,3 @@
--from builtins import str
- import threading
- import logging
- import os
---- a/biomaj/process/processfactory.py
-+++ b/biomaj/process/processfactory.py
-@@ -1,12 +1,10 @@
--from builtins import range
--from builtins import object
- import threading
- import logging
- import os
- from biomaj.process.metaprocess import MetaProcess
-
-
--class ProcessFactory(object):
-+class ProcessFactory:
- '''
- Manage process execution
- '''
---- a/biomaj/schema_version.py
-+++ b/biomaj/schema_version.py
-@@ -1,4 +1,3 @@
--from __future__ import print_function
- import pkg_resources
- import string
- import random
-@@ -12,7 +11,7 @@ from biomaj_core.utils import Utils
- import logging
-
-
--class SchemaVersion(object):
-+class SchemaVersion:
-
- """
- BioMAJ database schema version. This package can be used to make some schema modification if needed during
---- a/biomaj/session.py
-+++ b/biomaj/session.py
-@@ -1,6 +1,3 @@
--from future import standard_library
--from builtins import str
--from builtins import object
- import os
- import time
- import copy
-@@ -11,7 +8,7 @@ from biomaj.workflow import Workflow
- standard_library.install_aliases()
-
-
--class Session(object):
-+class Session:
- """
- BioMAJ bank session
- """
---- a/biomaj/workflow.py
-+++ b/biomaj/workflow.py
-@@ -1,6 +1,3 @@
--from builtins import str
--from builtins import range
--from builtins import object
- import logging
- import datetime
- import time
-@@ -29,7 +26,7 @@ from yapsy.PluginManager import PluginMa
- from packaging.version import parse
-
-
--class Workflow(object):
-+class Workflow:
- """
- Bank update workflow
- """
---- a/docs/requirements.txt
-+++ b/docs/requirements.txt
-@@ -4,7 +4,6 @@ pymongo==3.2
- tabulate
- ldap3
- py-bcrypt
--future
- elasticsearch
- biomaj_core
- biomaj_user
---- a/requirements.txt
-+++ b/requirements.txt
-@@ -9,7 +9,6 @@ pymongo==3.12.3
- pycurl
- tabulate
- py-bcrypt
--future
- elasticsearch
- requests
- redis
---- a/setup.py
-+++ b/setup.py
-@@ -65,7 +65,6 @@ config = {
- 'pymongo >=3.2, <4',
- 'pycurl',
- 'py-bcrypt',
-- 'future',
- 'tabulate',
- 'requests',
- 'redis',
=====================================
debian/patches/fix_remove_drmaa.patch
=====================================
@@ -4,7 +4,7 @@ Description: drmaa seems to be broken so disable this feature
--- a/docs/conf.py
+++ b/docs/conf.py
-@@ -22,7 +22,7 @@ class Mock(MagicMock):
+@@ -22,7 +22,7 @@
def __getattr__(cls, name):
return Mock()
@@ -15,31 +15,31 @@ Description: drmaa seems to be broken so disable this feature
'biomaj_download.download',
--- a/docs/requirements.txt
+++ b/docs/requirements.txt
-@@ -4,7 +4,6 @@ pymongo==3.2
+@@ -4,7 +4,6 @@
tabulate
ldap3
py-bcrypt
-drmaa
- future
elasticsearch
biomaj_core
+ biomaj_user
--- a/requirements.txt
+++ b/requirements.txt
-@@ -9,7 +9,6 @@ pymongo==3.12.3
+@@ -9,7 +9,6 @@
pycurl
tabulate
py-bcrypt
-drmaa
- future
elasticsearch
requests
+ redis
--- a/setup.py
+++ b/setup.py
-@@ -65,7 +65,6 @@ config = {
+@@ -65,7 +65,6 @@
'pymongo >=3.2, <4',
'pycurl',
'py-bcrypt',
- 'drmaa',
- 'future',
'tabulate',
'requests',
+ 'redis',
=====================================
debian/patches/series
=====================================
@@ -1,3 +1,2 @@
# fix_remove_influxdb.patch
fix_remove_drmaa.patch
-c27f7a2283460a919bc72f400fc610bd45c2df23.patch
=====================================
docs/requirements.txt
=====================================
@@ -5,7 +5,6 @@ tabulate
ldap3
py-bcrypt
drmaa
-future
elasticsearch
biomaj_core
biomaj_user
=====================================
requirements.txt
=====================================
@@ -10,7 +10,6 @@ pycurl
tabulate
py-bcrypt
drmaa
-future
elasticsearch
requests
redis
=====================================
setup.py
=====================================
@@ -36,7 +36,7 @@ config = {
'url': 'http://biomaj.genouest.org',
'download_url': 'http://biomaj.genouest.org',
'author_email': 'olivier.sallou at irisa.fr',
- 'version': '3.1.23',
+ 'version': '3.1.24',
'classifiers': [
# How mature is this project? Common values are
# 3 - Alpha
@@ -66,7 +66,6 @@ config = {
'pycurl',
'py-bcrypt',
'drmaa',
- 'future',
'tabulate',
'requests',
'redis',
=====================================
tests/biomaj_tests.py
=====================================
@@ -77,7 +77,7 @@ class UtilsForTest():
def __copy_test_bank_properties(self):
if self.bank_properties is not None:
return
- self.bank_properties = ['alu', 'local', 'testhttp','directhttp',
+ self.bank_properties = ['pdbaa', 'local', 'testhttp','directhttp',
'alu_list_error']
curdir = os.path.dirname(os.path.realpath(__file__))
for b in self.bank_properties:
@@ -146,10 +146,10 @@ class TestBiomajSetup():
BiomajConfig.load_config(self.utils.global_properties, allow_user_config=False)
# Delete all banks
- b = Bank('alu')
+ b = Bank('pdbaa')
b.banks.remove({})
- self.config = BiomajConfig('alu')
+ self.config = BiomajConfig('pdbaa')
data_dir = self.config.get('data.dir')
lock_file = os.path.join(data_dir,'alu.lock')
if os.path.exists(lock_file):
@@ -166,13 +166,13 @@ class TestBiomajSetup():
"""
Checks bank init
"""
- b = Bank('alu')
+ b = Bank('pdbaa')
def test_new_session(self):
"""
Checks an empty session is created
"""
- b = Bank('alu')
+ b = Bank('pdbaa')
b.load_session(UpdateWorkflow.FLOW)
for key in b.session._session['status'].keys():
assert not(b.session.get_status(key))
@@ -181,14 +181,14 @@ class TestBiomajSetup():
"""
Checks a session is used if present
"""
- b = Bank('alu')
+ b = Bank('pdbaa')
for i in range(1, 5):
- s = Session('alu', self.config, UpdateWorkflow.FLOW)
+ s = Session('pdbaa', self.config, UpdateWorkflow.FLOW)
s._session['status'][Workflow.FLOW_INIT] = True
b.session = s
b.save_session()
- b = Bank('alu')
+ b = Bank('pdbaa')
b.load_session(UpdateWorkflow.FLOW)
assert (b.session.get_status(Workflow.FLOW_INIT))
@@ -198,7 +198,7 @@ class TestBiomajSetup():
"""
b = Bank('local')
for i in range(1,5):
- s = Session('alu', self.config, UpdateWorkflow.FLOW)
+ s = Session('pdbaa', self.config, UpdateWorkflow.FLOW)
s._session['status'][Workflow.FLOW_INIT] = True
b.session = s
b.save_session()
@@ -211,20 +211,20 @@ class TestBiomajSetup():
"""
Checks a session if is not over
"""
- b = Bank('alu')
+ b = Bank('pdbaa')
for i in range(1,5):
- s = Session('alu', self.config, UpdateWorkflow.FLOW)
+ s = Session('pdbaa', self.config, UpdateWorkflow.FLOW)
s._session['status'][Workflow.FLOW_INIT] = True
s._session['status'][Workflow.FLOW_OVER] = True
b.session = s
b.save_session()
- b = Bank('alu')
+ b = Bank('pdbaa')
b.load_session(UpdateWorkflow.FLOW)
assert not (b.session.get_status(Workflow.FLOW_INIT))
def test_bank_list(self):
- b1 = Bank('alu')
+ b1 = Bank('pdbaa')
b2 = Bank('local')
banks = Bank.list()
assert (len(banks) == 2)
@@ -237,7 +237,7 @@ class TestBiomajSetup():
"""
Get release
"""
- b = Bank('alu')
+ b = Bank('pdbaa')
b.load_session(UpdateWorkflow.FLOW)
res = b.update()
assert (b.session.get('update'))
@@ -249,9 +249,9 @@ class TestBiomajSetup():
reason='network tests disabled'
)
def test_remove_session(self):
- b = Bank('alu')
+ b = Bank('pdbaa')
for i in range(1,5):
- s = Session('alu', self.config, UpdateWorkflow.FLOW)
+ s = Session('pdbaa', self.config, UpdateWorkflow.FLOW)
s._session['status'][Workflow.FLOW_INIT] = True
b.session = s
b.save_session()
=====================================
tests/alu.properties → tests/pdbaa.properties
=====================================
@@ -3,11 +3,11 @@
### Initialization ###
db.fullname="alu.n : alu repeat element. alu.a : translation of alu.n repeats"
-db.name=alu
+db.name=pdbaa
db.type=nucleic_protein
-offline.dir.name=offline/ncbi/blast/alu_tmp
-dir.version=ncbi/blast/alu
+offline.dir.name=offline/ncbi/blast/pdbaa_tmp
+dir.version=ncbi/blast/pdbaa
frequency.update=0
@@ -24,12 +24,12 @@ release.file=
release.regexp=
release.file.compressed=
-remote.files=^alu.*\.gz$
+remote.files=^pdbaa.*\.gz$
#Uncomment if you don't want to extract the data files.
#no.extract=true
-local.files=^alu\.(a|n).*
+local.files=^pdbaa\.*$
## Post Process ## The files should be located in the projectfiles/process directory
View it on GitLab: https://salsa.debian.org/med-team/biomaj3/-/compare/b8775b5ac74ad13afa3a341dde3ea3c12cad57f9...e5865331eea6203513af3a2ba407b0b8ac720bf0
--
View it on GitLab: https://salsa.debian.org/med-team/biomaj3/-/compare/b8775b5ac74ad13afa3a341dde3ea3c12cad57f9...e5865331eea6203513af3a2ba407b0b8ac720bf0
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20240419/26426313/attachment-0001.htm>
More information about the debian-med-commit
mailing list