[med-svn] [Git][med-team/obitools][master] 7 commits: New upstream version 1.2.13+dfsg
Steffen Möller
gitlab at salsa.debian.org
Sat Jul 27 12:17:07 BST 2019
Steffen Möller pushed to branch master at Debian Med / obitools
Commits:
f179fe77 by Steffen Moeller at 2019-07-27T11:10:58Z
New upstream version 1.2.13+dfsg
- - - - -
25d3aa23 by Steffen Moeller at 2019-07-27T11:10:59Z
Update upstream source from tag 'upstream/1.2.13+dfsg'
Update to upstream version '1.2.13+dfsg'
with Debian dir 45a5e18b4c764771a824829447ace78309e2ca4c
- - - - -
76984bbf by Steffen Moeller at 2019-07-27T11:10:59Z
New upstream version
- - - - -
14a7b38f by Steffen Moeller at 2019-07-27T11:11:00Z
debhelper-compat 12
- - - - -
61370b46 by Steffen Moeller at 2019-07-27T11:11:01Z
Standards-Version: 4.4.0
- - - - -
afb00b4d by Steffen Moeller at 2019-07-27T11:11:02Z
Build-Depends: s/python-sphinx/python3-sphinx/
- - - - -
a8044e7e by Steffen Moeller at 2019-07-27T11:16:13Z
Upload to unstable
- - - - -
13 changed files:
- PKG-INFO
- debian/changelog
- − debian/compat
- debian/control
- distutils.ext/obidistutils/command/build_sphinx.py
- requirements.txt
- setup.py
- src/obiconvert.py
- src/obitaxonomy.py
- src/obitools/format/sequence/__init__.py
- src/obitools/seqdb/embl/parser.py
- src/obitools/seqdb/genbank/parser.py
- src/obitools/version.py
Changes:
=====================================
PKG-INFO
=====================================
@@ -1,6 +1,6 @@
Metadata-Version: 1.1
Name: OBITools
-Version: 1.2.12
+Version: 1.2.13
Summary: Scripts and library for sequence analysis
Home-page: http://metabarcoding.org/obitools
Author: Eric Coissac
=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+obitools (1.2.13+dfsg-1) unstable; urgency=medium
+
+ * Team upload.
+ * New upstream version
+ * Created with routine-update script
+ * debhelper-compat 12
+ * Standards-Version: 4.4.0
+ * Build-Depends: s/python-sphinx/python3-sphinx/
+
+ -- Steffen Moeller <moeller at debian.org> Sat, 27 Jul 2019 13:11:02 +0200
+
obitools (1.2.12+dfsg-2) unstable; urgency=medium
* Drop ecoPCR.1.gz and ecofind.1 from package
=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-12
=====================================
debian/control
=====================================
@@ -4,15 +4,15 @@ Uploaders: Olivier Sallou <osallou at debian.org>,
Andreas Tille <tille at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 12~),
+Build-Depends: debhelper-compat (= 12),
dh-python,
python-dev,
- python-sphinx,
+ python3-sphinx,
cython,
ipython,
python-wheel,
python-virtualenv
-Standards-Version: 4.3.0
+Standards-Version: 4.4.0
Vcs-Browser: https://salsa.debian.org/med-team/obitools
Vcs-Git: https://salsa.debian.org/med-team/obitools.git
Homepage: https://pypi.python.org/pypi/OBITools
=====================================
distutils.ext/obidistutils/command/build_sphinx.py
=====================================
@@ -13,26 +13,29 @@ import sys
try:
from sphinx.setup_command import BuildDoc as ori_build_sphinx
+
+ class build_sphinx(ori_build_sphinx):
+ '''
+ Build Sphinx documentation in html, epub and man formats
+ '''
+
+ description = __doc__
+
+ def run(self):
+ self.builder='html'
+ self.finalize_options()
+ ori_build_sphinx.run(self)
+ self.builder='epub'
+ self.finalize_options()
+ ori_build_sphinx.run(self)
+ self.builder='man'
+ self.finalize_options()
+ ori_build_sphinx.run(self)
+
except ImportError:
if not is_serenity() and install_requirements():
log.info("Restarting installation with all dependencies ok")
rerun_with_anothe_python(os.path.realpath(sys.executable))
+
-class build_sphinx(ori_build_sphinx):
- '''
- Build Sphinx documentation in html, epub and man formats
- '''
-
- description = __doc__
-
- def run(self):
- self.builder='html'
- self.finalize_options()
- ori_build_sphinx.run(self)
- self.builder='epub'
- self.finalize_options()
- ori_build_sphinx.run(self)
- self.builder='man'
- self.finalize_options()
- ori_build_sphinx.run(self)
\ No newline at end of file
=====================================
requirements.txt
=====================================
@@ -1,6 +1,6 @@
--extra-index-url https://pypi.python.org/simple/
Cython>=0.24
-Sphinx>=1.2.0
+Sphinx<2.0
wheel>=0.24.0
virtualenv>=1.11.0
ipython<6.0
=====================================
setup.py
=====================================
@@ -19,7 +19,7 @@ from os import path
PACKAGE = "OBITools"
-VERSION = "1.2.12"
+VERSION = "1.2.13"
AUTHOR = 'Eric Coissac'
EMAIL = 'eric at coissac.eu'
URL = 'http://metabarcoding.org/obitools'
=====================================
src/obiconvert.py
=====================================
@@ -47,7 +47,7 @@ if __name__ == '__main__':
try:
writer(entry)
except:
- print >>stderr,"Skip writing of sequence : %s" % entry.id
+ print >>stderr,"Skipping an entry"
else:
writer(entry)
=====================================
src/obitaxonomy.py
=====================================
@@ -331,7 +331,7 @@ if __name__ == '__main__':
for t in options.newspecies:
genus,species = t.split(" ",1)
- parent = options.taxonomy.findTaxonByName(genus)
+ parent = options.taxonomy.findTaxonByName(genus)[0]
taxid = options.taxonomy.addLocalTaxon(t,'species',parent[0],options.taxashift)
taxon = options.taxonomy.findTaxonByTaxid(taxid)
parent= options.taxonomy._taxonomy[taxon[2]]
@@ -347,4 +347,4 @@ if __name__ == '__main__':
ecoTaxonomyWriter(options.ecodb,options.taxonomy,onlyLocal=True)
-
\ No newline at end of file
+
=====================================
src/obitools/format/sequence/__init__.py
=====================================
@@ -14,7 +14,6 @@ def skipOnErrorIterator(seqIterator):
seq = si.next()
yield seq
except Exception,e:
- print >>sys.stderr,"coucou"
if isinstance(e,StopIteration):
raise e
else:
=====================================
src/obitools/seqdb/embl/parser.py
=====================================
@@ -29,20 +29,24 @@ def __emblparser(text):
acs = acs.split()
ac = acs[0]
acs = acs[1:]
-
de = _deMatcher.search(header).group()
de = _cleanDe.sub(' ',de).strip().strip('.')
- except AttributeError,e:
- print >>sys.stderr,'======================================================='
- print >>sys.stderr,text
- print >>sys.stderr,'======================================================='
- raise e
+ except Exception as e:
+ print>>sys.stderr, "\nCould not import sequence id:", text.split()[1], "(error raised:", e, ")"
+ # Do not raise any Exception if you need the possibility to resume the generator
+ # (Python generators can't resume after any exception is raised)
+ return None
return (ac,seq,de,header,ft,acs)
+
def emblParser(text):
- return embl.EmblSequence(*__emblparser(text))
+ parsed_text = __emblparser(text)
+ if parsed_text is not None:
+ return embl.EmblSequence(*parsed_text)
+ else:
+ return None
def emblIterator(file):
=====================================
src/obitools/seqdb/genbank/parser.py
=====================================
@@ -25,16 +25,21 @@ def __gbparser(text):
acs = acs[1:]
de = _deMatcher.search(header).group()
de = _cleanDe.sub(' ',de).strip().strip('.')
- except AttributeError,e:
- print >>sys.stderr,'======================================================='
- print >>sys.stderr,text
- print >>sys.stderr,'======================================================='
- raise e
+ except Exception as e:
+ print>>sys.stderr, "\nCould not import sequence id:", text.split()[1], "(error raised:", e, ")"
+ # Do not raise any Exception if you need the possibility to resume the generator
+ # (Python generators can't resume after any exception is raised)
+ return None
return (ac,seq,de,header,ft,acs)
+
def genbankParser(text):
- return gb.GbSequence(*__gbparser(text))
+ parsed_text = __gbparser(text)
+ if parsed_text is not None:
+ return gb.GbSequence(*parsed_text)
+ else:
+ return None
def genbankIterator(file):
@@ -43,7 +48,11 @@ def genbankIterator(file):
def genpepParser(text):
- return gb.GpepSequence(*__gbparser(text))
+ parsed_text = __gbparser(text)
+ if parsed_text is not None:
+ return gb.GpepSequence(*parsed_text)
+ else:
+ return None
def genpepIterator(file):
=====================================
src/obitools/version.py
=====================================
@@ -1,5 +1,5 @@
major = 1
minor = 2
-serial= '12'
+serial= '13'
version = "%2d.%02d %s" % (major,minor,serial)
View it on GitLab: https://salsa.debian.org/med-team/obitools/compare/59d02fc4823570980cf0d87555c828d79f6e1b57...a8044e7eb209e6bc957d9831ab62ce166d81c766
--
View it on GitLab: https://salsa.debian.org/med-team/obitools/compare/59d02fc4823570980cf0d87555c828d79f6e1b57...a8044e7eb209e6bc957d9831ab62ce166d81c766
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