[med-svn] [Git][med-team/cyvcf2][master] 5 commits: routine-update: New upstream version
Steffen Möller
gitlab at salsa.debian.org
Tue Feb 25 14:49:42 GMT 2020
Steffen Möller pushed to branch master at Debian Med / cyvcf2
Commits:
490040c1 by Steffen Moeller at 2020-02-25T14:57:29+01:00
routine-update: New upstream version
- - - - -
f70b6513 by Steffen Moeller at 2020-02-25T14:57:30+01:00
New upstream version 0.11.6
- - - - -
abb7fbfa by Steffen Moeller at 2020-02-25T14:57:31+01:00
Update upstream source from tag 'upstream/0.11.6'
Update to upstream version '0.11.6'
with Debian dir 6e116b7dbf8993e8c5f724dd0068145b20d6d249
- - - - -
479de503 by Steffen Moeller at 2020-02-25T14:57:31+01:00
routine-update: Standards-Version: 4.5.0
- - - - -
b081a266 by Steffen Moeller at 2020-02-25T15:11:22+01:00
Adjusted patch for spelling. Ready to upload.
- - - - -
9 changed files:
- .travis.yml
- cyvcf2/__init__.py
- cyvcf2/cyvcf2.pyx
- cyvcf2/relatedness.h
- debian/changelog
- debian/control
- debian/patches/series
- debian/patches/spelling
- docs/source/conf.py
Changes:
=====================================
.travis.yml
=====================================
@@ -1,10 +1,11 @@
language: python
-dist: xenial
+dist: bionic
python:
- "2.7"
- "3.5"
- "3.6"
- "3.7"
+ - "3.8"
install:
- sudo apt-get install libcurl4-openssl-dev
=====================================
cyvcf2/__init__.py
=====================================
@@ -2,4 +2,4 @@ from .cyvcf2 import (VCF, Variant, Writer, r_ as r_unphased, par_relatedness,
par_het)
Reader = VCFReader = VCF
-__version__ = "0.11.5"
+__version__ = "0.11.6"
=====================================
cyvcf2/cyvcf2.pyx
=====================================
@@ -1126,7 +1126,7 @@ cdef class Variant(object):
&hets[0], self.vcf.n_samples, &alt_freqs[0])
property num_called:
- "number of samples that were not UKNOWN."
+ "number of samples that were not UNKNOWN."
def __get__(self):
if self._gt_types == NULL:
self.gt_types
@@ -1142,7 +1142,7 @@ cdef class Variant(object):
return n
property call_rate:
- "proprtion of samples that were not UKNOWN."
+ "proprtion of samples that were not UNKNOWN."
def __get__(self):
if self.vcf.n_samples > 0:
return float(self.num_called) / self.vcf.n_samples
@@ -1394,7 +1394,7 @@ cdef class Variant(object):
property gt_types:
"""gt_types returns a numpy array indicating the type of each sample.
- HOM_REF=0, HET=1. For `gts012=True` HOM_ALT=2, UKNOWN=3
+ HOM_REF=0, HET=1. For `gts012=True` HOM_ALT=2, UNKNOWN=3
"""
def __get__(self):
cdef int ndst = 0, ngts, n, i, nper, j = 0, k = 0
=====================================
cyvcf2/relatedness.h
=====================================
@@ -7,7 +7,7 @@
#define _UNKNOWN 3
// internal calculate of alternate allele frequency.
-inline float aaf(int *gt_types, int32_t n_samples){
+static inline float aaf(int *gt_types, int32_t n_samples){
float af = 0;
int i, n_called = 0;
@@ -134,7 +134,7 @@ int related(int *gt_types, double *asum, int32_t *N, int32_t *ibs0, int32_t *ibs
}
// returns 1 if this is a usable site.
-inline int ab_ok(double ab, int ab_missing) {
+static inline int ab_ok(double ab, int ab_missing) {
if (ab_missing) {
return 1;
}
=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+cyvcf2 (0.11.6-1) unstable; urgency=medium
+
+ * New upstream version
+ * Standards-Version: 4.5.0 (routine-update)
+ * Adjusted spelling fixes - 4 already fixed upstream,
+ submitted PR for the last on
+ https://github.com/brentp/cyvcf2/pull/140
+
+ -- Steffen Moeller <moeller at debian.org> Tue, 25 Feb 2020 14:57:29 +0100
+
cyvcf2 (0.11.5-2) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -20,7 +20,7 @@ Build-Depends: debhelper-compat (= 12),
libhts-dev,
libbz2-dev,
help2man <!nodoc>
-Standards-Version: 4.3.0
+Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/cyvcf2
Vcs-Git: https://salsa.debian.org/med-team/cyvcf2.git
Homepage: https://github.com/brentp/cyvcf2
=====================================
debian/patches/series
=====================================
@@ -1,2 +1,2 @@
add_htslib_link_dependency.patch
-spelling
+#spelling
=====================================
debian/patches/spelling
=====================================
@@ -1,34 +1,5 @@
From: Michael R. Crusoe <michael.crusoe at gmail.com>
Subject: Fix a few typos
---- cyvcf2.orig/cyvcf2/cyvcf2.pyx
-+++ cyvcf2/cyvcf2/cyvcf2.pyx
-@@ -1126,7 +1126,7 @@
- &hets[0], self.vcf.n_samples, &alt_freqs[0])
-
- property num_called:
-- "number of samples that were not UKNOWN."
-+ "number of samples that were not UNKNOWN."
- def __get__(self):
- if self._gt_types == NULL:
- self.gt_types
-@@ -1142,7 +1142,7 @@
- return n
-
- property call_rate:
-- "proprtion of samples that were not UKNOWN."
-+ "proprtion of samples that were not UNKNOWN."
- def __get__(self):
- if self.vcf.n_samples > 0:
- return float(self.num_called) / self.vcf.n_samples
-@@ -1394,7 +1394,7 @@
- property gt_types:
- """gt_types returns a numpy array indicating the type of each sample.
-
-- HOM_REF=0, HET=1. For `gts012=True` HOM_ALT=2, UKNOWN=3
-+ HOM_REF=0, HET=1. For `gts012=True` HOM_ALT=2, UNKNOWN=3
- """
- def __get__(self):
- cdef int ndst = 0, ngts, n, i, nper, j = 0, k = 0
@@ -1684,7 +1684,7 @@
return depth
=====================================
docs/source/conf.py
=====================================
@@ -14,6 +14,7 @@
import sys
import os
+import re
# If extensions (or modules to document with autodoc) are in another directory,
# add these directories to sys.path here. If the directory is relative to the
@@ -60,13 +61,20 @@ author = u'Brent Pedersen'
# built documents.
#
#
-#sys.path.insert(0, os.path.join(os.path.dirname(__file__), "../../"))
-#import cyvcf2
-#
+init_file = os.path.abspath(
+ os.path.join(os.path.dirname(__file__), "../../cyvcf2/__init__.py")
+)
+with open(init_file, 'r') as f:
+ version_file = f.read()
+ version_match = re.search(r"^__version__ = ['\"]([^'\"]*)['\"]",
+ version_file, re.M)
+ if version_match:
+ pkg_version = version_match.group(1)
+
# The short X.Y version.
-version = u'0.6.5'
+version = pkg_version
# The full version, including alpha/beta/rc tags.
-release = u'0.6.5'
+release = pkg_version
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
View it on GitLab: https://salsa.debian.org/med-team/cyvcf2/-/compare/36e85baaf2e86e1723fc984b0d0e58322546aa6d...b081a266a25a4dc886e5427d2ae3b6469a2081dc
--
View it on GitLab: https://salsa.debian.org/med-team/cyvcf2/-/compare/36e85baaf2e86e1723fc984b0d0e58322546aa6d...b081a266a25a4dc886e5427d2ae3b6469a2081dc
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