[med-svn] [Git][med-team/biomaj3][upstream] New upstream version 3.1.24
Charles Plessy (@plessy)
gitlab at salsa.debian.org
Fri Apr 19 05:24:25 BST 2024
Charles Plessy pushed to branch upstream at Debian Med / biomaj3
Commits:
5313243e by Charles Plessy at 2024-04-19T09:18:39+09:00
New upstream version 3.1.24
- - - - -
16 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
- 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
"""
=====================================
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/-/commit/5313243e2e6320700f683183dda082eddb1e9e0a
--
View it on GitLab: https://salsa.debian.org/med-team/biomaj3/-/commit/5313243e2e6320700f683183dda082eddb1e9e0a
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