Upgrades to version 4.0.4

biobakery · Jan 17, 2023 · 2e7773a · 2e7773a
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,3 +1,12 @@
+## Version 4.0.4 (Jan 17nd, 2023)
+### Changed features
+* [MetaPhlAn] Download of the pre-computed Bowtie2 database is now the default option during installation
+* [StrainPhlAn] Improved StrainPhlAn's sample2makers.py script performance and speed
+### Fixes
+* [StrainPhlAn] Fixes error when using --abs_n_samples_threshold in the PhyloPhlAn call
+
+<br/>
+
 ## Version 4.0.3 (Oct 24nd, 2022)
 ### Changed features
 * [MetaPhlAn] Removal of the NCBI taxID from the merged profiles produced by the `merge_metaphlan_profiles.py` script

diff --git a/metaphlan/metaphlan.py b/metaphlan/metaphlan.py
@@ -4,8 +4,8 @@
               'Nicola Segata ([email protected]), '
               'Duy Tin Truong, '
               'Francesco Asnicar ([email protected])')
-__version__ = '4.0.3'
-__date__ = '24 Oct 2022'
+__version__ = '4.0.4'
+__date__ = '17 Jan 2023'
 
 import sys
 try:

diff --git a/metaphlan/strainphlan.py b/metaphlan/strainphlan.py
@@ -4,8 +4,8 @@
               'Francesco Asnicar ([email protected]), '
               'Moreno Zolfo ([email protected]), '
               'Francesco Beghini ([email protected])')
-__version__ = '4.0.3'
-__date__ = '24 Oct 2022'
+__version__ = '4.0.4'
+__date__ = '17 Jan 2023'
 
 
 import argparse as ap

diff --git a/metaphlan/utils/add_metadata_tree.py b/metaphlan/utils/add_metadata_tree.py
@@ -1,8 +1,8 @@
 #!/usr/bin/env python
 __author__ = ('Duy Tin Truong ([email protected]), '
               'Aitor Blanco Miguez ([email protected])')
-__version__ = '4.0.3'
-__date__    = '24 Oct 2022'
+__version__ = '4.0.4'
+__date__    = '17 Jan 2023'
 
 import argparse as ap
 import pandas

diff --git a/metaphlan/utils/consensus_markers.py b/metaphlan/utils/consensus_markers.py
@@ -1,6 +1,6 @@
 __author__ = 'Aitor Blanco Miguez ([email protected])'
-__version__ = '4.0.3'
-__date__ = '24 Oct 2022'
+__version__ = '4.0.4'
+__date__ = '17 Jan 2023'
 
 
 import os

diff --git a/metaphlan/utils/database_controller.py b/metaphlan/utils/database_controller.py
@@ -1,6 +1,6 @@
 __author__ = 'Aitor Blanco Miguez ([email protected])'
-__version__ = '4.0.3'
-__date__ = '24 Oct 2022'
+__version__ = '4.0.4'
+__date__ = '17 Jan 2023'
 
 
 import os

diff --git a/metaphlan/utils/external_exec.py b/metaphlan/utils/external_exec.py
@@ -3,8 +3,8 @@
               'Francesco Asnicar ([email protected]), '
               'Moreno Zolfo ([email protected]), '
               'Francesco Beghini ([email protected])')
-__version__ = '4.0.3'
-__date__ = '24 Oct 2022'
+__version__ = '4.0.4'
+__date__ = '17 Jan 2023'
 
 
 import os

diff --git a/metaphlan/utils/extract_markers.py b/metaphlan/utils/extract_markers.py
@@ -1,8 +1,8 @@
 #!/usr/bin/env python
 __author__ = ('Aitor Blanco Miguez ([email protected]), '
               'Francesco Beghini ([email protected])')
-__version__ = '4.0.3'
-__date__ = '24 Oct 2022'
+__version__ = '4.0.4'
+__date__ = '17 Jan 2023'
 
 
 import os

diff --git a/metaphlan/utils/parallelisation.py b/metaphlan/utils/parallelisation.py
@@ -3,8 +3,8 @@
               'Francesco Asnicar ([email protected]), '
               'Moreno Zolfo ([email protected]), '
               'Francesco Beghini ([email protected])')
-__version__ = '4.0.3'
-__date__ = '24 Oct 2022'
+__version__ = '4.0.4'
+__date__ = '17 Jan 2023'
 
 
 from typing import Iterable, Callable, Any

diff --git a/metaphlan/utils/phylophlan_controller.py b/metaphlan/utils/phylophlan_controller.py
@@ -1,6 +1,6 @@
 __author__ = 'Aitor Blanco Miguez ([email protected]'
-__version__ = '4.0.3'
-__date__ = '24 Oct 2022'
+__version__ = '4.0.4'
+__date__ = '17 Jan 2023'
 
 
 import os

diff --git a/metaphlan/utils/plot_tree_graphlan.py b/metaphlan/utils/plot_tree_graphlan.py
@@ -1,8 +1,8 @@
 #!/usr/bin/env python
 __author__ = ('Duy Tin Truong ([email protected]), '
               'Aitor Blanco Miguez ([email protected])')
-__version__ = '4.0.3'
-__date__    = '24 Oct 2022'
+__version__ = '4.0.4'
+__date__    = '17 Jan 2023'
 
 import argparse as ap
 import dendropy

diff --git a/metaphlan/utils/sample2markers.py b/metaphlan/utils/sample2markers.py
@@ -5,8 +5,8 @@
               'Francesco Asnicar ([email protected]), '
               'Moreno Zolfo ([email protected]), '
               'Francesco Beghini ([email protected])')
-__version__ = '4.0.3'
-__date__ = '24 Oct 2022'
+__version__ = '4.0.4'
+__date__ = '17 Jan 2023'
 
 
 

diff --git a/metaphlan/utils/sgb_to_gtdb_profile.py b/metaphlan/utils/sgb_to_gtdb_profile.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 __author__ = 'Aitor Blanco ([email protected]'
-__version__ = '4.0.3'
-__date__ = '24 Oct 2022'
+__version__ = '4.0.4'
+__date__ = '17 Jan 2023'
 
 import os
 import time

diff --git a/metaphlan/utils/strain_transmission.py b/metaphlan/utils/strain_transmission.py
@@ -1,8 +1,8 @@
 #!/usr/bin/env python
 __author__ = ('Aitor Blanco ([email protected]), '
               'Mireia Valles-Colomer ([email protected])')
-__version__ = '4.0.3'
-__date__ = '24 Oct 2022'
+__version__ = '4.0.4'
+__date__ = '17 Jan 2023'
 
 
 import os

diff --git a/metaphlan/utils/util_fun.py b/metaphlan/utils/util_fun.py
@@ -3,8 +3,8 @@
               'Francesco Asnicar ([email protected]), '
               'Moreno Zolfo ([email protected]), '
               'Francesco Beghini ([email protected])')
-__version__ = '4.0.3'
-__date__ = '24 Oct 2022'
+__version__ = '4.0.4'
+__date__ = '17 Jan 2023'
 
 
 import os

diff --git a/setup.py b/setup.py
@@ -14,7 +14,7 @@
 
 setuptools.setup(
     name='MetaPhlAn',
-    version='4.0.3',
+    version='4.0.4',
     author='Aitor Blanco-Miguez',
     author_email='[email protected]',
     url='http://github.com/biobakery/MetaPhlAn/',