From 2e7773a355a1ce07336faa5ecc1683df1ebd4056 Mon Sep 17 00:00:00 2001 From: Aitor Blanco Date: Tue, 17 Jan 2023 17:29:05 +0100 Subject: [PATCH] Upgrades to version 4.0.4 --- CHANGELOG.md | 9 +++++++++ metaphlan/metaphlan.py | 4 ++-- metaphlan/strainphlan.py | 4 ++-- metaphlan/utils/add_metadata_tree.py | 4 ++-- metaphlan/utils/consensus_markers.py | 4 ++-- metaphlan/utils/database_controller.py | 4 ++-- metaphlan/utils/external_exec.py | 4 ++-- metaphlan/utils/extract_markers.py | 4 ++-- metaphlan/utils/parallelisation.py | 4 ++-- metaphlan/utils/phylophlan_controller.py | 4 ++-- metaphlan/utils/plot_tree_graphlan.py | 4 ++-- metaphlan/utils/sample2markers.py | 4 ++-- metaphlan/utils/sgb_to_gtdb_profile.py | 4 ++-- metaphlan/utils/strain_transmission.py | 4 ++-- metaphlan/utils/util_fun.py | 4 ++-- setup.py | 2 +- 16 files changed, 38 insertions(+), 29 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 5320055..8cdcadc 100755 --- 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 + +
+ ## 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 index a175b9b..3e89335 100755 --- a/metaphlan/metaphlan.py +++ b/metaphlan/metaphlan.py @@ -4,8 +4,8 @@ 'Nicola Segata (nicola.segata@unitn.it), ' 'Duy Tin Truong, ' 'Francesco Asnicar (f.asnicar@unitn.it)') -__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 index 1d0321e..aa5fa6c 100755 --- a/metaphlan/strainphlan.py +++ b/metaphlan/strainphlan.py @@ -4,8 +4,8 @@ 'Francesco Asnicar (f.asnicar@unitn.it), ' 'Moreno Zolfo (moreno.zolfo@unitn.it), ' 'Francesco Beghini (francesco.beghini@unitn.it)') -__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 index 54535fe..879936e 100755 --- 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 (duytin.truong@unitn.it), ' 'Aitor Blanco Miguez (aitor.blancomiguez@unitn.it)') -__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 index c04fedc..d04b8ba 100644 --- a/metaphlan/utils/consensus_markers.py +++ b/metaphlan/utils/consensus_markers.py @@ -1,6 +1,6 @@ __author__ = 'Aitor Blanco Miguez (aitor.blancomiguez@unitn.it)' -__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 index 3292f75..8e3ccd6 100644 --- a/metaphlan/utils/database_controller.py +++ b/metaphlan/utils/database_controller.py @@ -1,6 +1,6 @@ __author__ = 'Aitor Blanco Miguez (aitor.blancomiguez@unitn.it)' -__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 index a6be10c..e8e249a 100755 --- a/metaphlan/utils/external_exec.py +++ b/metaphlan/utils/external_exec.py @@ -3,8 +3,8 @@ 'Francesco Asnicar (f.asnicar@unitn.it), ' 'Moreno Zolfo (moreno.zolfo@unitn.it), ' 'Francesco Beghini (francesco.beghini@unitn.it)') -__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 index 3aedc9d..03f72d2 100755 --- a/metaphlan/utils/extract_markers.py +++ b/metaphlan/utils/extract_markers.py @@ -1,8 +1,8 @@ #!/usr/bin/env python __author__ = ('Aitor Blanco Miguez (aitor.blancomiguez@unitn.it), ' 'Francesco Beghini (francesco.beghini@unitn.it)') -__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 index 622becb..7575fca 100755 --- a/metaphlan/utils/parallelisation.py +++ b/metaphlan/utils/parallelisation.py @@ -3,8 +3,8 @@ 'Francesco Asnicar (f.asnicar@unitn.it), ' 'Moreno Zolfo (moreno.zolfo@unitn.it), ' 'Francesco Beghini (francesco.beghini@unitn.it)') -__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 index 6448fb3..303029b 100644 --- a/metaphlan/utils/phylophlan_controller.py +++ b/metaphlan/utils/phylophlan_controller.py @@ -1,6 +1,6 @@ __author__ = 'Aitor Blanco Miguez (aitor.blancomiguez@unitn.it' -__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 index 41bc3a5..7c3a26a 100755 --- 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 (duytin.truong@unitn.it), ' 'Aitor Blanco Miguez (aitor.blancomiguez@unitn.it)') -__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 index 7e86d43..440ebbd 100755 --- a/metaphlan/utils/sample2markers.py +++ b/metaphlan/utils/sample2markers.py @@ -5,8 +5,8 @@ 'Francesco Asnicar (f.asnicar@unitn.it), ' 'Moreno Zolfo (moreno.zolfo@unitn.it), ' 'Francesco Beghini (francesco.beghini@unitn.it)') -__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 index 110094d..1978aa1 100755 --- 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 (aitor.blancomiguez@unitn.it' -__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 index 66df15f..d11bf1f 100755 --- a/metaphlan/utils/strain_transmission.py +++ b/metaphlan/utils/strain_transmission.py @@ -1,8 +1,8 @@ #!/usr/bin/env python __author__ = ('Aitor Blanco (aitor.blancomiguez@unitn.it), ' 'Mireia Valles-Colomer (mireia.vallescolomer@unitn.it)') -__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 index 29bc1eb..b8511ea 100755 --- a/metaphlan/utils/util_fun.py +++ b/metaphlan/utils/util_fun.py @@ -3,8 +3,8 @@ 'Francesco Asnicar (f.asnicar@unitn.it), ' 'Moreno Zolfo (moreno.zolfo@unitn.it), ' 'Francesco Beghini (francesco.beghini@unitn.it)') -__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 index 8a05559..222f7d6 100755 --- 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='aitor.blancomiguez@unitn.it', url='http://github.com/biobakery/MetaPhlAn/',