[med-svn] [Git][med-team/cyvcf2][upstream] New upstream version 0.11.6

[Steffen Möller]

Steffen Möller pushed to branch upstream at Debian Med / cyvcf2


Commits:
f70b6513 by Steffen Moeller at 2020-02-25T14:57:30+01:00
New upstream version 0.11.6
- - - - -


5 changed files:

- .travis.yml
- cyvcf2/__init__.py
- cyvcf2/cyvcf2.pyx
- cyvcf2/relatedness.h
- 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;
     }


=====================================
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/-/commit/f70b6513a9575929831bfff9ad8de2fa8af3252a

-- 
View it on GitLab: https://salsa.debian.org/med-team/cyvcf2/-/commit/f70b6513a9575929831bfff9ad8de2fa8af3252a
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