[med-svn] [Git][med-team/flye][master] 5 commits: New upstream version 2.9.5+dfsg

Étienne Mollier (@emollier) gitlab at salsa.debian.org
Sat Aug 31 11:45:10 BST 2024 


Étienne Mollier pushed to branch master at Debian Med / flye


Commits:
8dc07ac6 by Étienne Mollier at 2024-08-31T12:32:55+02:00
New upstream version 2.9.5+dfsg
- - - - -
24890ebd by Étienne Mollier at 2024-08-31T12:33:14+02:00
Update upstream source from tag 'upstream/2.9.5+dfsg'

Update to upstream version '2.9.5+dfsg'
with Debian dir c00701f5ce42235ad7f04a77d118f280eff0ec62
- - - - -
4119e4ac by Étienne Mollier at 2024-08-31T12:37:54+02:00
python3.12.patch: unfuzz.

- - - - -
940d99f5 by Étienne Mollier at 2024-08-31T12:42:18+02:00
python3.12.patch: forwarding not needed.

This is because most of the changes are vendoring removal; upstream
did move to Python 3.12 in the present version.

- - - - -
77d0e909 by Étienne Mollier at 2024-08-31T12:43:52+02:00
Ready for upload to unstable.

- - - - -


8 changed files:

- README.md
- debian/changelog
- debian/patches/python3.12.patch
- 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.


=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+flye (2.9.5+dfsg-1) unstable; urgency=medium
+
+  * New upstream version 2.9.5+dfsg
+  * python3.12.patch: unfuzz.
+  * python3.12.patch: forwarding not needed.
+    This is because most of the changes are vendoring removal; upstream
+    did move to Python 3.12 in the present version.
+
+ -- Étienne Mollier <emollier at debian.org>  Sat, 31 Aug 2024 12:43:43 +0200
+
 flye (2.9.4+dfsg-1) unstable; urgency=medium
 
   * Team upload.


=====================================
debian/patches/python3.12.patch
=====================================
@@ -1,11 +1,15 @@
 Description: Port to Python3.12 by removing vendored six.py
+ Since most part of the fix involve unvendoring six.py, forwarding does
+ not seem too relevant.
+
 Bug-Debian: https://bugs.debian.org/#1061797
 Author: Andreas Tille <tille at debian.org>
+Reviewed-By: Étienne Mollier <emollier at debian.org>
 Last-Update: Fri, 02 Feb 2024 10:40:30 +0100
 
 
---- a/flye/assembly/scaffolder.py
-+++ b/flye/assembly/scaffolder.py
+--- flye.orig/flye/assembly/scaffolder.py
++++ flye/flye/assembly/scaffolder.py
 @@ -12,7 +12,7 @@
  
  import flye.utils.fasta_parser as fp
@@ -15,8 +19,8 @@ Last-Update: Fri, 02 Feb 2024 10:40:30 +0100
  
  logger = logging.getLogger()
  
---- a/flye/config/configurator.py
-+++ b/flye/config/configurator.py
+--- flye.orig/flye/config/configurator.py
++++ flye/flye/config/configurator.py
 @@ -12,7 +12,7 @@
  
  import flye.utils.fasta_parser as fp
@@ -26,8 +30,8 @@ Last-Update: Fri, 02 Feb 2024 10:40:30 +0100
  
  
  logger = logging.getLogger()
---- a/flye/main.py
-+++ b/flye/main.py
+--- flye.orig/flye/main.py
++++ flye/flye/main.py
 @@ -33,7 +33,7 @@
  #import flye.trestle.trestle as tres
  #import flye.trestle.graph_resolver as tres_graph
@@ -35,10 +39,10 @@ Last-Update: Fri, 02 Feb 2024 10:40:30 +0100
 -from flye.six.moves import range
 +from six.moves import range
  
- logger = logging.getLogger()
- 
---- a/flye/polishing/alignment.py
-+++ b/flye/polishing/alignment.py
+ if sys.version_info[0] == 2:
+     raise Exception("Python 2 is unsupported")
+--- flye.orig/flye/polishing/alignment.py
++++ flye/flye/polishing/alignment.py
 @@ -18,8 +18,8 @@
  import flye.utils.fasta_parser as fp
  from flye.utils.utils import which, get_median
@@ -50,8 +54,8 @@ Last-Update: Fri, 02 Feb 2024 10:40:30 +0100
  
  
  logger = logging.getLogger()
---- a/flye/polishing/bubbles.py
-+++ b/flye/polishing/bubbles.py
+--- flye.orig/flye/polishing/bubbles.py
++++ flye/flye/polishing/bubbles.py
 @@ -10,7 +10,7 @@
  from __future__ import division
  import logging
@@ -70,8 +74,8 @@ Last-Update: Fri, 02 Feb 2024 10:40:30 +0100
  
  
  logger = logging.getLogger()
---- a/flye/polishing/consensus.py
-+++ b/flye/polishing/consensus.py
+--- flye.orig/flye/polishing/consensus.py
++++ flye/flye/polishing/consensus.py
 @@ -10,8 +10,8 @@
  from __future__ import division
  import logging
@@ -92,8 +96,8 @@ Last-Update: Fri, 02 Feb 2024 10:40:30 +0100
  
  logger = logging.getLogger()
  
---- a/flye/polishing/polish.py
-+++ b/flye/polishing/polish.py
+--- flye.orig/flye/polishing/polish.py
++++ flye/flye/polishing/polish.py
 @@ -21,8 +21,8 @@
  import flye.utils.fasta_parser as fp
  from flye.utils.utils import which
@@ -105,8 +109,8 @@ Last-Update: Fri, 02 Feb 2024 10:40:30 +0100
  
  
  POLISH_BIN = "flye-modules"
---- a/flye/short_plasmids/circular_sequences.py
-+++ b/flye/short_plasmids/circular_sequences.py
+--- flye.orig/flye/short_plasmids/circular_sequences.py
++++ flye/flye/short_plasmids/circular_sequences.py
 @@ -9,8 +9,8 @@
  import flye.utils.fasta_parser as fp
  from flye.utils.sam_parser import read_paf, read_paf_grouped
@@ -118,8 +122,8 @@ Last-Update: Fri, 02 Feb 2024 10:40:30 +0100
  
  logger = logging.getLogger()
  
---- a/flye/short_plasmids/unmapped_reads.py
-+++ b/flye/short_plasmids/unmapped_reads.py
+--- flye.orig/flye/short_plasmids/unmapped_reads.py
++++ flye/flye/short_plasmids/unmapped_reads.py
 @@ -9,8 +9,8 @@
  from flye.utils.sam_parser import read_paf_grouped
  import logging
@@ -131,8 +135,8 @@ Last-Update: Fri, 02 Feb 2024 10:40:30 +0100
  
  logger = logging.getLogger()
  
---- a/flye/short_plasmids/utils.py
-+++ b/flye/short_plasmids/utils.py
+--- flye.orig/flye/short_plasmids/utils.py
++++ flye/flye/short_plasmids/utils.py
 @@ -2,7 +2,7 @@
  #This file is a part of Flye program.
  #Released under the BSD license (see LICENSE file)
@@ -142,8 +146,8 @@ Last-Update: Fri, 02 Feb 2024 10:40:30 +0100
  
  def find_connected_components(graph):
      def dfs(start_vertex, connected_components_counter):
---- a/flye/trestle/divergence.py
-+++ b/flye/trestle/divergence.py
+--- flye.orig/flye/trestle/divergence.py
++++ flye/flye/trestle/divergence.py
 @@ -12,7 +12,7 @@
  from __future__ import division
  import logging
@@ -162,8 +166,8 @@ Last-Update: Fri, 02 Feb 2024 10:40:30 +0100
  
  logger = logging.getLogger()
  
---- a/flye/trestle/graph_resolver.py
-+++ b/flye/trestle/graph_resolver.py
+--- flye.orig/flye/trestle/graph_resolver.py
++++ flye/flye/trestle/graph_resolver.py
 @@ -13,8 +13,8 @@
  
  import flye.utils.fasta_parser as fp
@@ -175,8 +179,8 @@ Last-Update: Fri, 02 Feb 2024 10:40:30 +0100
  
  logger = logging.getLogger()
  
---- a/flye/trestle/trestle.py
-+++ b/flye/trestle/trestle.py
+--- flye.orig/flye/trestle/trestle.py
++++ flye/flye/trestle/trestle.py
 @@ -25,8 +25,8 @@
  
  import flye.trestle.divergence as div
@@ -188,8 +192,8 @@ Last-Update: Fri, 02 Feb 2024 10:40:30 +0100
  
  logger = logging.getLogger()
  
---- a/flye/utils/fasta_parser.py
-+++ b/flye/utils/fasta_parser.py
+--- flye.orig/flye/utils/fasta_parser.py
++++ flye/flye/utils/fasta_parser.py
 @@ -23,7 +23,7 @@
      _STR = bytes.decode
      _BYTES = str.encode
@@ -199,8 +203,8 @@ Last-Update: Fri, 02 Feb 2024 10:40:30 +0100
  
  
  logger = logging.getLogger()
---- a/flye/utils/sam_parser.py
-+++ b/flye/utils/sam_parser.py
+--- flye.orig/flye/utils/sam_parser.py
++++ flye/flye/utils/sam_parser.py
 @@ -32,8 +32,8 @@
      _STR = bytes.decode
      _BYTES = str.encode


=====================================
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/-/compare/8bddd17f26b33c0c81ce847fdea6fe088fed0ca4...77d0e909a7f9f48b6a7e79b36b7c489e84715d70

-- 
View it on GitLab: https://salsa.debian.org/med-team/flye/-/compare/8bddd17f26b33c0c81ce847fdea6fe088fed0ca4...77d0e909a7f9f48b6a7e79b36b7c489e84715d70
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