[med-svn] [Git][med-team/biomaj3][master] 9 commits: Fix typo in the last changelog entry.
Santiago Vila (@sanvila)
gitlab at salsa.debian.org
Tue Feb 3 13:35:22 GMT 2026
Santiago Vila pushed to branch master at Debian Med / biomaj3
Commits:
fc1576fc by Santiago Vila at 2026-02-03T14:02:00+01:00
Fix typo in the last changelog entry.
- - - - -
4bd1a6f1 by Santiago Vila at 2026-02-03T14:03:00+01:00
Skip tests by using an empty override_dh_auto_test target.
- - - - -
af87d0fe by Santiago Vila at 2026-02-03T14:04:00+01:00
d/control: Drop "Rules-Requires-Root: no" (default).
- - - - -
b2c1ce2a by Santiago Vila at 2026-02-03T14:05:00+01:00
d/control: Drop "Priority: optional" (default).
- - - - -
e9e64eae by Santiago Vila at 2026-02-03T14:06:00+01:00
d/control: Update standards-version.
- - - - -
50638048 by Santiago Vila at 2026-02-03T14:07:00+01:00
d/salsa-ci.yml: Use the simplified version.
- - - - -
0533ff8e by Santiago Vila at 2026-02-03T14:08:00+01:00
d/control: Drop Python-Egg-Name.
- - - - -
f948116b by Santiago Vila at 2026-02-03T14:09:00+01:00
d/patches: Tidy up
- Drop fix_remove_influxdb.patch, no longer needed
- Fix metadata
- - - - -
9c68fc31 by Santiago Vila at 2026-02-03T14:10:00+01:00
Upload for unstable as 3.1.24-3
- - - - -
8 changed files:
- debian/changelog
- debian/control
- debian/patches/fix_remove_drmaa.patch
- − debian/patches/fix_remove_influxdb.patch
- debian/patches/series
- debian/rules
- debian/salsa-ci.yml
- − debian/source/lintian-overrides
Changes:
=====================================
debian/changelog
=====================================
@@ -1,7 +1,20 @@
+biomaj3 (3.1.24-3) unstable; urgency=medium
+
+ * Team upload.
+ * Skip tests by using an empty override_dh_auto_test target.
+ * Drop "Rules-Requires-Root: no" (default).
+ * Drop "Priority: optional" (default).
+ * Update standards-version.
+ * Simplify salsa-ci.yml.
+ * Drop Python-Egg-Name.
+ * Tidy up patches.
+
+ -- Santiago Vila <sanvila at debian.org> Tue, 03 Feb 2026 14:10:00 +0100
+
biomaj3 (3.1.24-2) unstable; urgency=medium
* Team upload.
- * Remove dependenct on python3-mock
+ * Remove dependency on python3-mock
-- Alexandre Detiste <tchet at debian.org> Sat, 14 Dec 2024 20:17:35 +0100
=====================================
debian/control
=====================================
@@ -3,7 +3,6 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Olivier Sallou <osallou at debian.org>
Section: python
Testsuite: autopkgtest-pkg-python
-Priority: optional
# python3-influxdb removed as workaround for python-influxdb bug see changelog
Build-Depends: debhelper-compat (= 13),
dh-sequence-python3,
@@ -19,11 +18,10 @@ Build-Depends: debhelper-compat (= 13),
python3-biomaj3-download,
python3-biomaj3-user,
python3-biomaj3-process
-Standards-Version: 4.7.0
+Standards-Version: 4.7.3
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
-Rules-Requires-Root: no
Package: python3-biomaj3
Architecture: all
@@ -47,4 +45,3 @@ Description: BioMAJ workflow management library
This package contains the library to manage the workflow update in BioMAJ3,
it is managed via python3-biomaj3-daemon (for microservices remote operations)
or biomaj3-cli (local or remote) packages
-XB-Python-Egg-Name: biomaj
=====================================
debian/patches/fix_remove_drmaa.patch
=====================================
@@ -1,5 +1,5 @@
Author: Olivier Sallou
-Last-Update: 2021-02-19 10:27:50 +0000
+Last-Update: 2021-02-19
Description: drmaa seems to be broken so disable this feature
--- a/docs/conf.py
=====================================
debian/patches/fix_remove_influxdb.patch deleted
=====================================
@@ -1,174 +0,0 @@
-Subject: remove influxdb feature
- --> This patch is deactivated since bug #950063 was done
-Description: python-influxdb has a bug 950063
- This patch remove influxdb optional feature waiting
- for influx bug to be solved
-Author: Olivier Sallou <osallou at debian.org>
-Last-Updated: 2020-02-08
-Forwarded: no
---- a/requirements.txt
-+++ b/requirements.txt
-@@ -14,6 +14,5 @@ future
- elasticsearch
- requests
- redis
--influxdb
- Yapsy==1.12.2
- Jinja2
---- a/setup.py
-+++ b/setup.py
-@@ -71,7 +71,6 @@ config = {
- 'requests',
- 'redis',
- 'elasticsearch',
-- 'influxdb',
- 'Yapsy==1.12.2'
- ],
- 'tests_require': ['nose', 'mock'],
---- a/docs/conf.py
-+++ b/docs/conf.py
-@@ -22,7 +22,7 @@ class Mock(MagicMock):
- def __getattr__(cls, name):
- return Mock()
-
--MOCK_MODULES = ['pycurl', 'pymongo', 'elasticsearch', 'drmaa', 'influxdb',
-+MOCK_MODULES = ['pycurl', 'pymongo', 'elasticsearch', 'drmaa',
- 'biomaj_download',
- 'biomaj_download.downloadclient',
- 'biomaj_download.download',
---- a/biomaj/bank.py
-+++ b/biomaj/bank.py
-@@ -1276,132 +1276,7 @@ class Bank(object):
- '''
- Send stats to Influxdb if enabled
- '''
-- try:
-- from influxdb import InfluxDBClient
-- except Exception as e:
-- logging.error('Cannot load influxdb library' + str(e))
-- return
-- db_host = self.config.get('influxdb.host', default=None)
-- if not db_host:
-- return
-- if not self.session.get_status(Workflow.FLOW_OVER):
-- return
-- if 'stats' not in self.session._session:
-- return
--
-- db_port = int(self.config.get('influxdb.port', default='8086'))
-- db_user = self.config.get('influxdb.user', default=None)
-- db_password = self.config.get('influxdb.password', default=None)
-- db_name = self.config.get('influxdb.db', default='biomaj')
-- influxdb = None
-- try:
-- if db_user and db_password:
-- influxdb = InfluxDBClient(host=db_host, port=db_port, username=db_user, password=db_password, database=db_name)
-- else:
-- influxdb = InfluxDBClient(host=db_host, port=db_port, database=db_name)
-- except Exception as e:
-- logging.error('Failed to connect to InfluxDB, database may not be created, skipping the record of statistics')
-- logging.exception('InfluxDB connection error: ' + str(e))
-- return
-- metrics = []
--
-- if 'production' not in self.bank or not self.bank['production']:
-- return
--
-- productions = self.bank['production']
-- total_size = 0
-- latest_size = 0
-- if not productions:
-- return
-- for production in productions:
-- if 'size' in production:
-- total_size += production['size']
--
-- influx_metric = {
-- "measurement": 'biomaj.production.size.total',
-- "fields": {
-- "value": float(total_size)
-- },
-- "tags": {
-- "bank": self.name
-- }
-- }
-- metrics.append(influx_metric)
--
-- all_banks = Bank.list()
-- nb_banks_with_prod = 0
-- if all_banks:
-- for bank_info in all_banks:
-- if 'production' in bank_info and len(bank_info['production']) > 0:
-- nb_banks_with_prod += 1
-- influx_metric = {
-- "measurement": 'biomaj.banks.quantity',
-- "fields": {
-- "value": nb_banks_with_prod
-- }
-- }
-- metrics.append(influx_metric)
--
-- workflow_duration = 0
-- for flow in list(self.session._session['stats']['workflow'].keys()):
-- workflow_duration += self.session._session['stats']['workflow'][flow]
--
-- influx_metric = {
-- "measurement": 'biomaj.workflow.duration',
-- "fields": {
-- "value": workflow_duration
-- },
-- "tags": {
-- "bank": self.name
-- }
-- }
-- metrics.append(influx_metric)
--
-- if self.session.get('update'):
-- latest_size = self.session.get('fullsize')
-- influx_metric = {
-- "measurement": 'biomaj.production.size.latest',
-- "fields": {
-- "value": float(latest_size)
-- },
-- "tags": {
-- "bank": self.name
-- }
-- }
-- metrics.append(influx_metric)
--
-- influx_metric = {
-- "measurement": 'biomaj.bank.update.downloaded_files',
-- "fields": {
-- "value": self.session._session['stats']['nb_downloaded_files']
-- },
-- "tags": {
-- "bank": self.name
-- }
-- }
-- metrics.append(influx_metric)
--
-- influx_metric = {
-- "measurement": 'biomaj.bank.update.new',
-- "fields": {
-- "value": 1
-- },
-- "tags": {
-- "bank": self.name
-- }
-- }
-- metrics.append(influx_metric)
--
-- res = None
-- try:
-- res = influxdb.write_points(metrics, time_precision="s")
-- except Exception as e:
-- logging.error('Failed to connect to InfluxDB, database may not be created, skipping the record of statistics')
-- logging.exception('InfluxDB connection error: ' + str(e))
-- return
--
-- if not res:
-- logging.error('Failed to send metrics to database')
-+ logging.error("influxdb feature remove due to influxdb library bug")
-
- def check_remote_release(self):
- '''
=====================================
debian/patches/series
=====================================
@@ -1,3 +1,2 @@
-# fix_remove_influxdb.patch
fix_remove_drmaa.patch
remove_mock.patch
=====================================
debian/rules
=====================================
@@ -1,12 +1,7 @@
#! /usr/bin/make -f
-# The test should be really prevented
-# export DH_BUILD_MAINT_OPTIONS=nocheck
-export DEB_BUILD_OPTIONS=nocheck
-#export PYBUILD_TEST_ARGS=-a'!network'
-#export DEB_BUILD_MAINT_OPTIONS=nocheck
-
export PYBUILD_NAME=biomaj
+
%:
dh $@ --buildsystem=pybuild
@@ -18,3 +13,5 @@ override_dh_installexamples:
dh_installexamples
sed -i '1s;^;#!/bin/bash\n;' debian/python3-biomaj3/usr/share/doc/python3-biomaj3/examples/tools/process/concat.sh
chmod -x debian/python3-biomaj3/usr/share/doc/python3-biomaj3/examples/global.properties.example
+
+override_dh_auto_test:
=====================================
debian/salsa-ci.yml
=====================================
@@ -1,4 +1,3 @@
---
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
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/recipes/debian.yml
=====================================
debian/source/lintian-overrides deleted
=====================================
@@ -1 +0,0 @@
-biomaj3 source: debian-rules-sets-DEB_BUILD_OPTIONS *
View it on GitLab: https://salsa.debian.org/med-team/biomaj3/-/compare/5e92efd8167a98f1ae96f12fb9392212ca93494a...9c68fc31efcf85636cfd6892c4cc33a26d203fca
--
View it on GitLab: https://salsa.debian.org/med-team/biomaj3/-/compare/5e92efd8167a98f1ae96f12fb9392212ca93494a...9c68fc31efcf85636cfd6892c4cc33a26d203fca
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