[med-svn] [Git][med-team/python-cgecore][master] 11 commits: routine-update: New upstream version
Steffen Möller
gitlab at salsa.debian.org
Tue Mar 17 12:36:25 GMT 2020
Steffen Möller pushed to branch master at Debian Med / python-cgecore
Commits:
bd72db30 by Steffen Moeller at 2020-03-17T13:15:13+01:00
routine-update: New upstream version
- - - - -
c6a1da3b by Steffen Moeller at 2020-03-17T13:15:13+01:00
Update upstream source from tag 'upstream/1.5.3'
Update to upstream version '1.5.3'
with Debian dir 425b806f7c4568e7aaf110cbdf208a8e84ef6e2f
- - - - -
3b828448 by Steffen Moeller at 2020-03-17T13:15:13+01:00
New upstream version 1.5.3
- - - - -
3af347a5 by Steffen Moeller at 2020-03-17T13:15:14+01:00
routine-update: Standards-Version: 4.5.0
- - - - -
c5ccdd17 by Steffen Moeller at 2020-03-17T13:15:16+01:00
routine-update: Add salsa-ci file
- - - - -
e4e82524 by Steffen Moeller at 2020-03-17T13:15:16+01:00
routine-update: Rules-Requires-Root: no
- - - - -
e3728ba3 by Steffen Moeller at 2020-03-17T13:15:25+01:00
routine-update: Ready to upload to unstable
- - - - -
63f1fda4 by Steffen Moeller at 2020-03-17T13:23:14+01:00
Adjustments for new release
- - - - -
918eda8f by Steffen Moeller at 2020-03-17T13:23:57+01:00
New upstream version 1.5.3+ds
- - - - -
71a8a258 by Steffen Moeller at 2020-03-17T13:23:57+01:00
Update upstream source from tag 'upstream/1.5.3+ds'
Update to upstream version '1.5.3+ds'
with Debian dir 1e3ed5c6b679de57da1a6bbca79c4c8026025c08
- - - - -
cbf0bdd8 by Steffen Moeller at 2020-03-17T13:24:56+01:00
Ready to upload
- - - - -
12 changed files:
- PKG-INFO
- − cgecore.egg-info/PKG-INFO
- − cgecore.egg-info/SOURCES.txt
- − cgecore.egg-info/dependency_links.txt
- − cgecore.egg-info/top_level.txt
- cgecore/__init__.py
- cgecore/blaster/blaster.py
- debian/changelog
- debian/control
- debian/copyright
- + debian/salsa-ci.yml
- debian/watch
Changes:
=====================================
PKG-INFO
=====================================
@@ -1,6 +1,6 @@
Metadata-Version: 1.0
Name: cgecore
-Version: 1.5.2
+Version: 1.5.3
Summary: Center for Genomic Epidemiology Core Module
Home-page: https://bitbucket.org/genomicepidemiology/cge_core_module
Author: Center for Genomic Epidemiology
=====================================
cgecore.egg-info/PKG-INFO deleted
=====================================
@@ -1,38 +0,0 @@
-Metadata-Version: 1.0
-Name: cgecore
-Version: 1.5.2
-Summary: Center for Genomic Epidemiology Core Module
-Home-page: https://bitbucket.org/genomicepidemiology/cge_core_module
-Author: Center for Genomic Epidemiology
-Author-email: cgehelp at cbs.dtu.dk
-License: Apache License, Version 2.0
-Description: # cge_core_module
-
- Core module for the Center for Genomic Epidemiology
-
- This module contains classes and functions needed to run the service wrappers and pipeline scripts
-
- The pypi project can be found here:
- https://pypi.org/project/cgecore/
-
- # How to update:
- 1. Make changes to the modules
- 2. Bump the version number accordingly in cgecore/__init__.py
- 3. Install package locally
- 4. Test the changes locally (for both python2 and python3)
- 5. Distribute to Pypi
-
- # Install package locally
- python2 setup.py install
-
- python3 setup.py install
-
- # Distribute to PyPi
- python3 setup.py sdist bdist_wheel
-
- twine upload dist/*
-
- *deprecated:*
- ~~python setup.py sdist upload -r pypi~~
-
-Platform: UNKNOWN
=====================================
cgecore.egg-info/SOURCES.txt deleted
=====================================
@@ -1,29 +0,0 @@
-PKG-INFO
-README.md
-setup.cfg
-setup.py
-cgecore/__init__.py
-cgecore/alignment.py
-cgecore/argumentparsing.py
-cgecore/cgefinder.py
-cgecore/cmdline.py
-cgecore/utility.py
-cgecore.egg-info/PKG-INFO
-cgecore.egg-info/SOURCES.txt
-cgecore.egg-info/dependency_links.txt
-cgecore.egg-info/top_level.txt
-cgecore/blaster/__init__.py
-cgecore/blaster/blaster.py
-cgecore/blaster/run_blaster.py
-cgecore/organisminfo/__init__.py
-cgecore/organisminfo/gram_neg.txt
-cgecore/organisminfo/gram_pos.txt
-cgecore/organisminfo/gramstain.py
-cgecore/organisminfo/species.py
-debian/changelog
-debian/control
-debian/copyright
-debian/rules
-debian/watch
-debian/source/format
-debian/upstream/metadata
\ No newline at end of file
=====================================
cgecore.egg-info/dependency_links.txt deleted
=====================================
@@ -1 +0,0 @@
-
=====================================
cgecore.egg-info/top_level.txt deleted
=====================================
@@ -1 +0,0 @@
-cgecore
=====================================
cgecore/__init__.py
=====================================
@@ -13,7 +13,7 @@ from .argumentparsing import (check_file_type, get_arguments, get_string,
)
#####################
-__version__ = "1.5.2"
+__version__ = "1.5.3"
__all__ = [
"argumentparsing",
"cmdline",
=====================================
cgecore/blaster/blaster.py
=====================================
@@ -194,31 +194,32 @@ class Blaster():
'strand': strand,
'perc_coverage': perc_coverage
}
-
-
-
- # Saving the result if any
- if best_hsp:
- save = 1
-
- # If there are other gene alignments they are compared
- if gene_results:
- tmp_gene_split = gene_split
- tmp_results = gene_results
- # Compare the hit results
- save, gene_split, gene_results = (
- self.compare_results(save, best_hsp,
- tmp_results,
- tmp_gene_split,
- allowed_overlap)
- )
-
- # If the hit is not overlapping with other hit
- # seqeunces it is kept
- if save == 1:
- # DEBUG
- print("Saving: {}".format(hit_id))
- gene_results[hit_id] = best_hsp
+ else:
+ best_hsp={}
+ continue
+
+ # Saving the result if any
+ if best_hsp:
+ save = 1
+
+ # If there are other gene alignments they are compared
+ if gene_results:
+ tmp_gene_split = gene_split
+ tmp_results = gene_results
+ # Compare the hit results
+ save, gene_split, gene_results = (
+ self.compare_results(save, best_hsp,
+ tmp_results,
+ tmp_gene_split,
+ allowed_overlap)
+ )
+
+ # If the hit is not overlapping with other hit
+ # seqeunces it is kept
+ if save == 1:
+ # DEBUG
+ print("Saving: {}".format(hit_id))
+ gene_results[hit_id] = best_hsp
result_handle.close()
@@ -463,7 +464,7 @@ class Blaster():
# TODO
# If new_score == old_score but identity and coverages are not the same.
- # which gene should be chosen?? Now they are both keept.
+ # which gene should be chosen?? Now they are both kept.
# Save a split if the new hit creats one - both
# hits are saved
=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+python-cgecore (1.5.3+ds-1) unstable; urgency=medium
+
+ * Team upload.
+ * New upstream version
+ * Standards-Version: 4.5.0 (routine-update)
+ * Add salsa-ci file (routine-update)
+ * Rules-Requires-Root: no (routine-update)
+ * Remove egg-info files removed at d/rules clean
+
+ -- Steffen Moeller <moeller at debian.org> Tue, 17 Mar 2020 13:15:17 +0100
+
python-cgecore (1.5.2-1) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -9,10 +9,11 @@ Build-Depends: debhelper-compat (= 12),
python3,
python3-setuptools,
python3-biopython
-Standards-Version: 4.4.1
+Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/python-cgecore
Vcs-Git: https://salsa.debian.org/med-team/python-cgecore.git
Homepage: https://bitbucket.org/genomicepidemiology/cge_core_module/
+Rules-Requires-Root: no
Package: python3-cgecore
Architecture: all
=====================================
debian/copyright
=====================================
@@ -1,6 +1,11 @@
Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: python-cgecore
Source: https://pypi.python.org/simple/cgecore
+Files-Excluded:
+ cgecore.egg-info/PKG-INFO
+ cgecore.egg-info/SOURCES.txt
+ cgecore.egg-info/dependency_links.txt
+ cgecore.egg-info/top_level.txt
Files: *
Copyright: 2012-2019 Center for Genomic Epidemiology
=====================================
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
=====================================
debian/watch
=====================================
@@ -1,3 +1,4 @@
version=4
+opts="oversionmangle=s/$/+ds/,dversionmangle=s/\+ds$//,repack" \
https://pypi.python.org/simple/cgecore .*/cgecore- at ANY_VERSION@@ARCHIVE_EXT@#sha256=.*
View it on GitLab: https://salsa.debian.org/med-team/python-cgecore/-/compare/182ac7d7dbdb5908086efd8f7d57c1a46aa59189...cbf0bdd8cd64faa14babb70bc98ab05a25583572
--
View it on GitLab: https://salsa.debian.org/med-team/python-cgecore/-/compare/182ac7d7dbdb5908086efd8f7d57c1a46aa59189...cbf0bdd8cd64faa14babb70bc98ab05a25583572
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/20200317/8b5924f4/attachment-0001.html>
More information about the debian-med-commit
mailing list