[med-svn] [Git][med-team/python-py2bit][upstream] New upstream version 0.3.2

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch upstream at Debian Med / python-py2bit


Commits:
2d49dd5d by Étienne Mollier at 2024-11-18T19:50:17+01:00
New upstream version 0.3.2
- - - - -


7 changed files:

- azure-pipelines.yml
- lib2bit/2bit.c
- py2bit.c
- py2bit.h
- py2bitTest/test.py
- setup.cfg
- setup.py


Changes:

=====================================
azure-pipelines.yml
=====================================
@@ -8,16 +8,14 @@ jobs:
     vmImage: 'ubuntu-latest'
   strategy:
     matrix:
-      Python36:
-        python.version: '3.6'
-      Python37:
-        python.version: '3.7'
       Python38:
         python.version: '3.8'
       Python39:
         python.version: '3.9'
       Python310:
         python.version: '3.10'
+      Python311:
+        python.version: '3.11'
     maxParallel: 5
 
   steps:


=====================================
lib2bit/2bit.c
=====================================
@@ -69,7 +69,7 @@ void bytes2bases(char *seq, uint8_t *byte, uint32_t sz, int offset) {
 
     // Deal with the first partial byte
     if(offset != 0) {
-        while(offset < 4) {
+        while(offset < 4 && pos < sz) {
            seq[pos++] = byte2base(foo, offset++);
         }
         if(pos >= sz) return;


=====================================
py2bit.c
=====================================
@@ -32,9 +32,9 @@ error:
 }
 
 PyObject *py2bitEnter(pyTwoBit_t *self, PyObject *args) {
-    pyTwoBit_t *pytb = self->tb;
+    TwoBit *tb = self->tb;
 
-    if(!pytb) {
+    if(!tb) {
         PyErr_SetString(PyExc_RuntimeError, "The 2bit file handle is not open!");
         return NULL;
     }


=====================================
py2bit.h
=====================================
@@ -1,7 +1,7 @@
 #include <Python.h>
 #include "2bit.h"
 
-#define pyTwoBitVersion "0.3.1"
+#define pyTwoBitVersion "0.3.2"
 
 typedef struct {
     PyObject_HEAD


=====================================
py2bitTest/test.py
=====================================
@@ -42,6 +42,8 @@ class Test():
         assert(tb.bases("chr1") == {'A': 0.08, 'C': 0.08, 'T': 0.08666666666666667, 'G': 0.08666666666666667})
         assert(tb.bases("chr1", 24, 74) == {'A': 0.12, 'C': 0.12, 'T': 0.12, 'G': 0.12})
         assert(tb.bases("chr1", 24, 74, False) == {'A': 6, 'C': 6, 'T': 6, 'G': 6})
+        assert(tb.bases("chr2", 10, 20) == {'A': 0.2, 'C': 0.2, 'T': 0.3, 'G': 0.3})
+        assert(tb.bases("chr2", 10, 20, False) == {'A': 2, 'C': 2, 'T': 3, 'G': 3})
         tb.close()
 
     def testHardMaskedBlocks(self):


=====================================
setup.cfg
=====================================
@@ -1,2 +1,2 @@
 [metadata]
-description-file = README.md
+description_file = README.md


=====================================
setup.py
=====================================
@@ -17,7 +17,7 @@ module1 = Extension('py2bit',
                     include_dirs = ['lib2bit', sysconfig.get_config_var("INCLUDEPY")])
 
 setup(name = 'py2bit',
-       version = '0.3.1',
+       version = '0.3.2',
        description = 'A package for accessing 2bit files using lib2bit',
        author = "Devon P. Ryan",
        author_email = "dpryan79 at gmail.com",



View it on GitLab: https://salsa.debian.org/med-team/python-py2bit/-/commit/2d49dd5dad00bdd10372abacd2550980d25cc6be

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View it on GitLab: https://salsa.debian.org/med-team/python-py2bit/-/commit/2d49dd5dad00bdd10372abacd2550980d25cc6be
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