[med-svn] [Git][med-team/flye][upstream] New upstream version 2.9.5+dfsg

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch upstream at Debian Med / flye


Commits:
8dc07ac6 by Étienne Mollier at 2024-08-31T12:32:55+02:00
New upstream version 2.9.5+dfsg
- - - - -


6 changed files:

- README.md
- docs/NEWS.md
- flye/__build__.py
- flye/__version__.py
- flye/main.py
- src/common/bfcontainer.h


Changes:

=====================================
README.md
=====================================
@@ -3,7 +3,7 @@ Flye assembler
 
 [![BioConda Install](https://img.shields.io/conda/dn/bioconda/flye.svg?style=flag&label=BioConda%20install)](https://anaconda.org/bioconda/flye)
 
-### Version: 2.9.4
+### Version: 2.9.5
 
 Flye is a de novo assembler for single-molecule sequencing reads,
 such as those produced by PacBio and Oxford Nanopore Technologies.
@@ -26,6 +26,15 @@ Manuals
 Latest updates
 --------------
 
+Flye 2.9.5 release (27 Aug 2024)
+===============================
+* Python 3.12 support, Python 2 dropped
+
+Flye 2.9.4 release (14 May 2024)
+===============================
+* Minor technical changes
+
+
 ### Flye 2.9.3 release (28 November 2023)
 * Disjointig step speedup for `--nano-hq` mode
 * Improved `--keep-haplotypes` mode preserves more heterozygous SVs
@@ -200,5 +209,3 @@ has already been answered.
 
 If you are reporting a problem, please include the `flye.log` file and provide
 details about your dataset.
-
-In case you prefer personal communication, please contact Mikhail at mikolmogorov at gmail.com.


=====================================
docs/NEWS.md
=====================================
@@ -1,3 +1,7 @@
+Flye 2.9.5 release (27 Aug 2024)
+===============================
+* Python 3.12 support, Python 2 dropped
+
 Flye 2.9.4 release (14 May 2024)
 ===============================
 * Minor technical changes


=====================================
flye/__build__.py
=====================================
@@ -1 +1 @@
-__build__ = 1799
+__build__ = 1801


=====================================
flye/__version__.py
=====================================
@@ -1 +1 @@
-__version__ = "2.9.4"
+__version__ = "2.9.5"


=====================================
flye/main.py
=====================================
@@ -35,6 +35,9 @@ import flye.utils.fasta_parser as fp
 from flye.repeat_graph.repeat_graph import RepeatGraph
 from flye.six.moves import range
 
+if sys.version_info[0] == 2:
+    raise Exception("Python 2 is unsupported")
+
 logger = logging.getLogger()
 
 class ResumeException(Exception):


=====================================
src/common/bfcontainer.h
=====================================
@@ -177,7 +177,7 @@ public:
 			return *this += -n;
 		}
 
-		BFIterator operator+(difference_type n) 
+		BFIterator operator+(difference_type n) const
 		{
 			auto tmp = *this;
 			return tmp += n;
@@ -188,13 +188,13 @@ public:
 			return rhs + lhs;
 		}
 		
-        BFIterator operator-(difference_type n) 
+        BFIterator operator-(difference_type n) const
 		{
 			auto tmp = *this;
 			return tmp -= n;
 		}
 
-        difference_type operator-(const BFIterator& rhs) 
+        difference_type operator-(const BFIterator& rhs) const
 		{
 			return difference_type(ChunkSize) * (_map - rhs._map - 1) + 
 						(_chunkCur - _chunkStart) +
@@ -239,8 +239,8 @@ public:
 
 		T& operator[](difference_type n) {return *(*this += n);}
 
-		T& operator*() {return *_chunkCur;}
-        T* operator->() {return _chunkCur;}
+		T& operator*() const {return *_chunkCur;}
+        T* operator->() const {return _chunkCur;}
 
     	bool operator==(const BFIterator& rhs) const
 		{



View it on GitLab: https://salsa.debian.org/med-team/flye/-/commit/8dc07ac618cf371aac914a948d48407b73eeeecb

-- 
View it on GitLab: https://salsa.debian.org/med-team/flye/-/commit/8dc07ac618cf371aac914a948d48407b73eeeecb
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