Update after NCBI Taxonomy change and upgrade to 2024

Pelomonas genus is now fully equivalent to Roseateles On branch master modified: README.md modified: rcf modified: recentrifuge/__init__.py modified: recentrifuge/config.py modified: recentrifuge/krona.js modified: recentrifuge/test/TEST.rcf.xlsx modified: refasplit modified: remock modified: retaxdump modified: retest modified: rextraccnt modified: rextract modified: setup.py
khyox · Jan 9, 2024 · 01a06e2 · 01a06e2
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diff --git a/README.md b/README.md
@@ -5,8 +5,8 @@
 
 
 ____
-[![Retest](https://github.com/khyox/Recentrifuge/actions/workflows/retest.yaml/badge.svg?branch=v1.13.0)](https://github.com/khyox/recentrifuge/actions/workflows/retest.yaml)
-[![](https://img.shields.io/maintenance/yes/2023.svg)](http://www.recentrifuge.org)
+[![Retest](https://github.com/khyox/Recentrifuge/actions/workflows/retest.yaml/badge.svg?branch=v1.13.1)](https://github.com/khyox/recentrifuge/actions/workflows/retest.yaml)
+[![](https://img.shields.io/maintenance/yes/2024.svg)](http://www.recentrifuge.org)
 [![](https://img.shields.io/github/languages/top/khyox/recentrifuge.svg)](https://pypi.org/project/recentrifuge/)
 [![](https://img.shields.io/pypi/pyversions/recentrifuge.svg)](https://pypi.org/project/recentrifuge/)
 [![](https://img.shields.io/pypi/v/recentrifuge.svg)](https://pypi.org/project/recentrifuge/)

diff --git a/rcf b/rcf
@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 #
-#     Copyright (C) 2017–2023, Jose Manuel Martí Martínez
+#     Copyright (C) 2017–2024, Jose Manuel Martí Martínez
 #
 #     This program is free software: you can redistribute it and/or modify
 #     it under the terms of the GNU Affero General Public License as

diff --git a/recentrifuge/__init__.py b/recentrifuge/__init__.py
@@ -1,5 +1,5 @@
 #
-#     Copyright (C) 2017–2023, Jose Manuel Martí Martínez
+#     Copyright (C) 2017–2024, Jose Manuel Martí Martínez
 #
 #     With the single exception of the file krona.js, which has embedded
 #     its own free software licence, you can redistribute Recentrifuge
@@ -28,13 +28,13 @@
            'ontology', 'params', 'stats', 'taxclass', 'mock',
            '__author__', '__date__', '__version__']
 __author__ = 'Jose Manuel Martí'
-__copyright__ = 'Copyright (C) 2017–2023 Jose Manuel Marti Martinez'
+__copyright__ = 'Copyright (C) 2017–2024 Jose Manuel Marti Martinez'
 __license__ = 'GNU Affero General Public License Version 3'
 __email__ = 'jse.mnl **AT** gmail.com'
 __maintainer__ = 'Jose Manuel Marti'
 __status__ = 'Production/Stable'
-__date__ = 'Dec 2023'
-__version__ = '1.13.0'
+__date__ = 'Jan 2024'
+__version__ = '1.13.1'
 
 import sys
 from Bio import SeqIO

diff --git a/recentrifuge/config.py b/recentrifuge/config.py
@@ -10,7 +10,7 @@
 # Licence notice
 LICENSE = ('''
 
-    Copyright (C) 2017–2022, Jose Manuel Martí Martínez
+    Copyright (C) 2017–2024, Jose Manuel Martí Martínez
     
     This program is free software: you can redistribute it and/or modify
     it under the terms of the GNU Affero General Public License as

diff --git a/recentrifuge/krona.js b/recentrifuge/krona.js
@@ -73,7 +73,7 @@
 // 
 //----------------------------------------------------------------------------
 //
-// Copyright (C) 2017-2023 Jose Manuel Martí Martínez, for the changes in
+// Copyright (C) 2017-2024 Jose Manuel Martí Martínez, for the changes in
 // this file from the Krona Javascript 2.0 release.
 //
 // Redistribution and use in source and binary forms, with or without

diff --git a/recentrifuge/test/TEST.rcf.xlsx b/recentrifuge/test/TEST.rcf.xlsx
diff --git a/refasplit b/refasplit
@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 #
-#     Copyright (C) 2017–2023, Jose Manuel Martí Martínez
+#     Copyright (C) 2017–2024, Jose Manuel Martí Martínez
 #
 #     This program is free software: you can redistribute it and/or modify
 #     it under the terms of the GNU Affero General Public License as

diff --git a/remock b/remock
@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 #
-#     Copyright (C) 2017–2023, Jose Manuel Martí Martínez
+#     Copyright (C) 2017–2024, Jose Manuel Martí Martínez
 #
 #     This program is free software: you can redistribute it and/or modify
 #     it under the terms of the GNU Affero General Public License as

diff --git a/retaxdump b/retaxdump
@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 #
-#     Copyright (C) 2017–2023, Jose Manuel Martí Martínez
+#     Copyright (C) 2017–2024, Jose Manuel Martí Martínez
 #
 #     This program is free software: you can redistribute it and/or modify
 #     it under the terms of the GNU Affero General Public License as

diff --git a/retest b/retest
@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 #
-#     Copyright (C) 2017–2023 Jose Manuel Martí Martínez
+#     Copyright (C) 2017–2024 Jose Manuel Martí Martínez
 #
 #     This program is free software: you can redistribute it and/or modify
 #     it under the terms of the GNU Affero General Public License as

diff --git a/rextraccnt b/rextraccnt
@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 #
-#     Copyright (C) 2017–2023, Jose Manuel Martí Martínez
+#     Copyright (C) 2017–2024, Jose Manuel Martí Martínez
 #
 #     This program is free software: you can redistribute it and/or modify
 #     it under the terms of the GNU Affero General Public License as

diff --git a/rextract b/rextract
@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 #
-#     Copyright (C) 2017–2023, Jose Manuel Martí Martínez
+#     Copyright (C) 2017–2024, Jose Manuel Martí Martínez
 #
 #     This program is free software: you can redistribute it and/or modify
 #     it under the terms of the GNU Affero General Public License as

diff --git a/setup.py b/setup.py
@@ -2,7 +2,7 @@
 
 setup(
     name='recentrifuge',
-    version='1.13.0',
+    version='1.13.1',
     packages=['recentrifuge'],
     url='http://www.recentrifuge.org',
     license='AGPL except krona.js, with its own license by BNBI',
@@ -12,7 +12,7 @@
     long_description="""
 **Robust comparative analysis and contamination removal for metagenomics**
 
-[![Retest](https://github.com/khyox/Recentrifuge/actions/workflows/retest.yaml/badge.svg?branch=v1.13.0)](https://github.com/khyox/recentrifuge/actions/workflows/retest.yaml)
+[![Retest](https://github.com/khyox/Recentrifuge/actions/workflows/retest.yaml/badge.svg?branch=v1.13.1)](https://github.com/khyox/recentrifuge/actions/workflows/retest.yaml)
 
 With Recentrifuge, researchers can interactively explore what organisms are in their samples and at which level of confidence, thus enabling a robust comparative analysis of multiple samples in any metagenomic study.