[med-svn] [Git][med-team/biomaj3-core][master] 6 commits: New upstream version 3.0.26
Andreas Tille
gitlab at salsa.debian.org
Sun Jan 17 08:32:13 GMT 2021
Andreas Tille pushed to branch master at Debian Med / biomaj3-core
Commits:
921d3c65 by Andreas Tille at 2021-01-17T09:28:52+01:00
New upstream version 3.0.26
- - - - -
57bcf437 by Andreas Tille at 2021-01-17T09:28:52+01:00
routine-update: New upstream version
- - - - -
bd504c97 by Andreas Tille at 2021-01-17T09:28:53+01:00
Update upstream source from tag 'upstream/3.0.26'
Update to upstream version '3.0.26'
with Debian dir 60069e0a8babf20d6a123b1b251cb833ac001473
- - - - -
28dc4da8 by Andreas Tille at 2021-01-17T09:28:53+01:00
routine-update: Standards-Version: 4.5.1
- - - - -
3bb1cb84 by Andreas Tille at 2021-01-17T09:28:56+01:00
routine-update: Add salsa-ci file
- - - - -
78cccfb2 by Andreas Tille at 2021-01-17T09:30:24+01:00
routine-update: Ready to upload to unstable
- - - - -
9 changed files:
- .travis.yml
- CHANGES.txt
- biomaj_core/config.py
- biomaj_core/utils.py
- debian/changelog
- debian/control
- + debian/salsa-ci.yml
- requirements.txt
- setup.py
Changes:
=====================================
.travis.yml
=====================================
@@ -1,10 +1,14 @@
language: python
+arch:
+ - ppc64le
+ - amd64
sudo: false
python:
- '2.7'
- - '3.4'
- '3.5'
- '3.6'
+ - '3.7'
+ - '3.8'
branches:
except:
- "/^feature.*$/"
=====================================
CHANGES.txt
=====================================
@@ -1,7 +1,24 @@
-3.0.19 [unreleased]:
+3.0.26:
+ check use_ldap and use_elastic as bool (true/false or 0/1)
+3.0.25:
+ utils/get_folder_size: if file not found, catch error and continue
+3.0.24:
+ get_more_recent_file, return also file info
+3.0.23:
+ PR #9 Add missing ssh defaults for download
+3.0.21 [3.0.22 ,tag issue]:
+ Pin elasticsearch dependency, v7 breaks some API calls
+3.0.20:
+ PR #7 from institut-de-genomique/retry_method, rename default values of retryer.
+ Rename wait_condition to wait_policy in default values
+ PR #6 from institut-de-genomique/retry_method, add default values for retryer
+ Add default values for retryer (see the corresponding branch biomaj-download).
+3.0.19:
Add ftps and directftps protocols
#4 Harden hardlinks
copy_files_with_regexp: remove duplicates
+ Add utils fonctions
+ Code cleanup
3.0.18:
Allow to use hardlinks in copy_files and copy_files_with_regexp
3.0.17:
=====================================
biomaj_core/config.py
=====================================
@@ -44,7 +44,11 @@ class BiomajConfig(object):
'keep.old.sessions': 0,
'docker.sudo': '1',
'auto_publish': 0,
- 'use_hardlinks': 0
+ 'use_hardlinks': 0,
+ 'wait_policy': 'wait_fixed(3)',
+ 'stop_condition': 'stop_after_attempt(3)',
+ 'ssh_hosts_file': os.path.expanduser('~/.ssh/known_hosts'),
+ 'ssh_new_host': 'reject',
}
# Old biomaj level compatibility
@@ -361,12 +365,12 @@ class BiomajConfig(object):
logging.warn('db.fullname is not set')
if not self.get('db.formats'):
logging.warn('db.formats is not set')
- if self.get('use_ldap'):
+ if self.get_bool('use_ldap'):
if not self.get('ldap.host') or not self.get('ldap.port') or \
not self.get('ldap.dn'):
logging.error('use_ldap set to 1 but missing configuration')
status = False
- if self.get('use_elastic'):
+ if self.get_bool('use_elastic'):
if not self.get('elastic_nodes') or not self.get('elastic_index'):
logging.error('use_elastic set to 1 but missing configuration')
status = False
=====================================
biomaj_core/utils.py
=====================================
@@ -126,13 +126,17 @@ class Utils(object):
:param folder: directory path
:type folder: str
"""
+ logger = logging.getLogger('biomaj')
if not os.path.exists(folder):
return -1
folder_size = 0
for (path, dirs, files) in os.walk(folder):
for ffile in files:
filename = os.path.join(path, ffile)
- folder_size += os.path.getsize(filename)
+ try:
+ folder_size += os.path.getsize(filename)
+ except Exception:
+ logger.error('[stat][size] file not found %s' % filename)
return folder_size
@staticmethod
@@ -157,7 +161,7 @@ class Utils(object):
return None
# release = None
rfile = files[0]
- release = {'year': rfile['year'], 'month': rfile['month'], 'day': rfile['day']}
+ release = {'year': rfile['year'], 'month': rfile['month'], 'day': rfile['day'], 'file': rfile}
for rfile in files:
rel_date = datetime.date(int(release['year']), int(release['month']), int(release['day']))
file_date = datetime.date(int(rfile['year']), int(rfile['month']), int(rfile['day']))
@@ -165,6 +169,7 @@ class Utils(object):
release['year'] = rfile['year']
release['month'] = rfile['month']
release['day'] = rfile['day']
+ release['file'] = rfile
return release
@staticmethod
=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+biomaj3-core (3.0.26-1) unstable; urgency=medium
+
+ * Team upload.
+ * New upstream version
+ * Standards-Version: 4.5.1 (routine-update)
+ * Add salsa-ci file (routine-update)
+
+ -- Andreas Tille <tille at debian.org> Sun, 17 Jan 2021 09:28:57 +0100
+
biomaj3-core (3.0.19-2) unstable; urgency=medium
* Team Upload.
=====================================
debian/control
=====================================
@@ -12,7 +12,7 @@ Build-Depends: debhelper-compat (= 13),
python3-nose,
python3-requests,
python3-setuptools
-Standards-Version: 4.5.0
+Standards-Version: 4.5.1
Vcs-Browser: https://salsa.debian.org/med-team/biomaj3-core
Vcs-Git: https://salsa.debian.org/med-team/biomaj3-core.git
Homepage: https://github.com/genouest/biomaj-core
=====================================
debian/salsa-ci.yml
=====================================
@@ -0,0 +1,4 @@
+---
+include:
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml
=====================================
requirements.txt
=====================================
@@ -1,5 +1,5 @@
nose
mock
future
-elasticsearch
+elasticsearch==5.5.3
requests
=====================================
setup.py
=====================================
@@ -17,11 +17,12 @@ with open(os.path.join(here, 'CHANGES.txt')) as f:
config = {
'description': 'BioMAJ core library',
'long_description': README + '\n\n' + CHANGES,
+ 'long_description_content_type': 'text/markdown',
'author': 'Olivier Sallou',
'url': 'http://biomaj.genouest.org',
'download_url': 'http://biomaj.genouest.org',
'author_email': 'olivier.sallou at irisa.fr',
- 'version': '3.0.19',
+ 'version': '3.0.26',
'classifiers': [
'Development Status :: 5 - Production/Stable',
'Environment :: Console',
@@ -36,8 +37,7 @@ config = {
# 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',
- 'Programming Language :: Python :: 3.4'
+ 'Programming Language :: Python :: 3'
],
'install_requires': [
'future',
View it on GitLab: https://salsa.debian.org/med-team/biomaj3-core/-/compare/f983aab124b346b2d72ce1d8bdaa9c55ef41bb19...78cccfb24e553f21cd2b5fb1ee53651e40e874b6
--
View it on GitLab: https://salsa.debian.org/med-team/biomaj3-core/-/compare/f983aab124b346b2d72ce1d8bdaa9c55ef41bb19...78cccfb24e553f21cd2b5fb1ee53651e40e874b6
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