[med-svn] [Git][med-team/biomaj3][master] 6 commits: Apply patch to remove future
Andreas Tille (@tille)
gitlab at salsa.debian.org
Sat Dec 16 15:31:50 GMT 2023
Andreas Tille pushed to branch master at Debian Med / biomaj3
Commits:
5be00dcf by Andreas Tille at 2023-12-16T09:13:59+01:00
Apply patch to remove future
- - - - -
d0e58500 by Andreas Tille at 2023-12-16T09:16:55+01:00
Remove need for future
- - - - -
aac9396b by Andreas Tille at 2023-12-16T09:21:04+01:00
routine-update: Standards-Version: 4.6.2
- - - - -
b8bfba0a by Andreas Tille at 2023-12-16T09:33:25+01:00
routine-update: Remove trailing whitespace in debian/changelog
- - - - -
264eecd5 by Andreas Tille at 2023-12-16T09:33:25+01:00
routine-update: Build-Depends: s/dh-python/dh-sequence-python3/
- - - - -
b8775b5a by Andreas Tille at 2023-12-16T16:31:21+01:00
Upload to unstable
- - - - -
5 changed files:
- debian/changelog
- debian/control
- + debian/patches/c27f7a2283460a919bc72f400fc610bd45c2df23.patch
- debian/patches/series
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,6 +1,17 @@
+biomaj3 (3.1.23-2) unstable; urgency=medium
+
+ * Team upload.
+ * Remove need for future
+ Closes: #1058565
+ * Standards-Version: 4.6.2 (routine-update)
+ * Remove trailing whitespace in debian/changelog (routine-update)
+ * Build-Depends: s/dh-python/dh-sequence-python3/ (routine-update)
+
+ -- Andreas Tille <tille at debian.org> Sat, 16 Dec 2023 09:36:54 +0100
+
biomaj3 (3.1.23-1) unstable; urgency=medium
- * New upstream release using pytest vs nose (Closes: #1018320).
+ * New upstream release using pytest vs nose (Closes: #1018320).
-- Olivier Sallou <osallou at debian.org> Mon, 29 Aug 2022 13:44:33 +0000
=====================================
debian/control
=====================================
@@ -6,7 +6,7 @@ Testsuite: autopkgtest-pkg-python
Priority: optional
# python3-influxdb removed as workaround for python-influxdb bug see changelog
Build-Depends: debhelper-compat (= 13),
- dh-python,
+ dh-sequence-python3,
python3-all,
python3-bcrypt,
python3-mock,
@@ -20,7 +20,7 @@ Build-Depends: debhelper-compat (= 13),
python3-biomaj3-download,
python3-biomaj3-user,
python3-biomaj3-process
-Standards-Version: 4.6.1
+Standards-Version: 4.6.2
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
=====================================
@@ -0,0 +1,194 @@
+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/series
=====================================
@@ -1,2 +1,3 @@
# fix_remove_influxdb.patch
fix_remove_drmaa.patch
+c27f7a2283460a919bc72f400fc610bd45c2df23.patch
=====================================
debian/rules
=====================================
@@ -8,7 +8,7 @@ export DEB_BUILD_OPTIONS=nocheck
export PYBUILD_NAME=biomaj
%:
- dh $@ --with python3 --buildsystem=pybuild
+ dh $@ --buildsystem=pybuild
override_dh_install:
dh_install
View it on GitLab: https://salsa.debian.org/med-team/biomaj3/-/compare/4732e0d5be48e14f05114c51d633c3de7243837f...b8775b5ac74ad13afa3a341dde3ea3c12cad57f9
--
View it on GitLab: https://salsa.debian.org/med-team/biomaj3/-/compare/4732e0d5be48e14f05114c51d633c3de7243837f...b8775b5ac74ad13afa3a341dde3ea3c12cad57f9
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