renamed the python package from kalign to kalign-python

Author: TimoLassmann

CMakeLists.txt

@@ -13,7 +13,7 @@ include(GenerateExportHeader)
 
 set(KALIGN_LIBRARY_VERSION_MAJOR 3)
 set(KALIGN_LIBRARY_VERSION_MINOR 4)
-set(KALIGN_LIBRARY_VERSION_PATCH 7)
+set(KALIGN_LIBRARY_VERSION_PATCH 8)
 set(KALIGN_LIBRARY_VERSION_STRING ${KALIGN_LIBRARY_VERSION_MAJOR}.${KALIGN_LIBRARY_VERSION_MINOR}.${KALIGN_LIBRARY_VERSION_PATCH})
 
 

ChangeLog

@@ -1,22 +1,22 @@
-2024-04-24  Timo Lassmann  <timo.lassmann@telethonkids.org.au>
+2024-04-24  Timo Lassmann  <timolassmann@icloud.com>
 
 	* version 3.4.1
 	- Fixed an issue when kalign is given hundreds of identical sequences.
 	- added build.zig
 
-2023-12-10  Timo Lassmann  <timo.lassmann@telethonkids.org.au>
+2023-12-10  Timo Lassmann  <timolassmann@icloud.com>
 
 	* version 3.4.0
 	- Added a simple sequence simulator for testing
 	- Fixed an issue where alignments would be slighly different
 	depending on the number of threads used.
 
-2022-11-05  Timo Lassmann  <timo.lassmann@telethonkids.org.au>
+2022-11-05  Timo Lassmann  <timolassmann@icloud.com>
 
 	* version 3.3.5
 	- Added a check to find and remove sequences of length 0.
 
-2022-10-28  Timo Lassmann  <timo.lassmann@telethonkids.org.au>
+2022-10-28  Timo Lassmann  <timolassmann@icloud.com>
 
 	* version 3.3.4 - Cmake and more
 	- switched to cmake
@@ -30,7 +30,7 @@
 	3) alignment types giving users more control over alignment parameters.
 	4) multi-threading
 
-2022-03-21  Timo Lassmann  <timo.lassmann@telethonkids.org.au>
+2022-03-21  Timo Lassmann  <timolassmann@icloud.com>
 
 	* version 3.3.2 - Bug Fix
 	There was a bug in building a guide tree from highly similar sequences. The fix
@@ -40,7 +40,7 @@
 	In addition Kalign now compiles on Apple's M1 chip and possibly on other ARM architectures
 	as well (although I did not test the latter).
 
-2021-04-16  Timo Lassmann  <timo.lassmann@telethonkids.org.au>
+2021-04-16  Timo Lassmann  <timolassmann@icloud.com>
 
 	* version 3.3.1 - Bug Fix
 	The previous version kalign checked the top 50 sequences in inputs to determine
@@ -62,7 +62,7 @@
 	[Date Time] : WARNING : align the sequences.                         (rwalign.c line 517)
 	[Date Time] : WARNING : -------------------------------------------- (rwalign.c line 518)
 
-2020-11-06  Timo Lassmann  <timo.lassmann@telethonkids.org.au>
+2020-11-06  Timo Lassmann  <timolassmann@icloud.com>
 
 	* version 3.3 - Threading and more
 	- Kalign now runs pairwise distance estimation, guide tree building and alignments in parallel.
@@ -73,7 +73,7 @@
 
 
 
-2020-09-24  Timo Lassmann  <timo.lassmann@telethonkids.org.au>
+2020-09-24  Timo Lassmann  <timolassmann@icloud.com>
 
 	* version 3.2.7 - Development version
 	- dynamic programming in now more modular.
@@ -87,13 +87,13 @@
 
 	with the empirically derived gap penalties.
 
-2020-04-22  Timo Lassmann  <timo.lassmann@telethonkids.org.au>
+2020-04-22  Timo Lassmann  <timolassmann@icloud.com>
 
 	* version 3.2.5
 	- Bug fix: when given long output named the first lines in msf
 	output could be truncated.
 
-2020-04-01  Timo Lassmann  <timo.lassmann@telethonkids.org.au>
+2020-04-01  Timo Lassmann  <timolassmann@icloud.com>
 
 	* version 3.2.4
 	- Fixed issue relating to stdin input on clusters.

pyproject.toml

@@ -7,17 +7,17 @@ requires = [
 build-backend = "scikit_build_core.build"
 
 [project]
-name = "kalign"
-version = "3.4.7"
+name = "kalign-python"
+version = "3.4.8"
 description = "Python wrapper for the Kalign multiple sequence alignment engine"
 readme = "README-python.md"
 license = "GPL-3.0-or-later"
 license-files = ["COPYING"]
 authors = [
-    {name = "Timo Lassmann", email = "timo.lassmann@telethonkids.org.au"}
+    {name = "Timo Lassmann", email = "timolassmann@icloud.com"}
 ]
 maintainers = [
-    {name = "Timo Lassmann", email = "timo.lassmann@telethonkids.org.au"}
+    {name = "Timo Lassmann", email = "timolassmann@icloud.com"}
 ]
 keywords = [
     "bioinformatics",

python-kalign/__init__.py

@@ -18,17 +18,13 @@ class AlignedSequences(NamedTuple):
     sequences: List[str]
 
 
-from . import _core, io, utils
+from importlib.metadata import version
 
-try:
-    from importlib.metadata import PackageNotFoundError
-    from importlib.metadata import version as _dist_version
+from . import _core, io, utils
 
-    __version__ = _dist_version("kalign")
-except Exception:
-    __version__ = "3.4.7"
+__version__ = version("kalign-python")
 __author__ = "Timo Lassmann"
-__email__ = "timo.lassmann@telethonkids.org.au"
+__email__ = "timolassmann@icloud.com"
 
 # Re-export constants for convenience
 DNA = _core.DNA

scripts/balibase_test.org

@@ -1,6 +1,6 @@
 #+TITLE:  Test kalign on BAliBASE
 #+AUTHOR: Timo Lassmann 
-#+EMAIL:  timo.lassmann@telethonkids.org.au
+#+EMAIL:  timolassmann@icloud.com
 #+DATE:   2019-04-23
 #+LATEX_CLASS: report
 #+OPTIONS:  toc:nil

scripts/benchmark.org

@@ -1,6 +1,6 @@
 #+TITLE:  Benchmark of MSA algorithms
 #+AUTHOR: Timo Lassmann
-#+EMAIL:  timo.lassmann@telethonkids.org.au
+#+EMAIL:  timolassmann@icloud.com
 #+DATE:   2019-09-27
 #+LATEX_CLASS: report
 #+OPTIONS:  toc:nil

scripts/bralibase.org

@@ -1,6 +1,6 @@
 #+TITLE:  Test kalign on BAliBASE 
 #+AUTHOR: Timo Lassmann
-#+EMAIL:  timo.lassmann@telethonkids.org.au
+#+EMAIL:  timolassmann@icloud.com
 #+DATE:   2019-04-23
 #+LATEX_CLASS: report
 #+OPTIONS:  toc:nil