Merge pull request #285 from picrust/v2.5.1

v2.5.1
picrust · Oct 31, 2022 · 98f1113 · 98f1113
2 parents 90ff3d9 + 3d229dd
commit 98f1113
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Showing 24 changed files with 32 additions and 27 deletions.
diff --git a/picrust2/__init__.py b/picrust2/__init__.py
@@ -4,4 +4,4 @@
 __copyright__ = "Copyright 2018-2022, PICRUSt Project"
 __license__ = "GPL"
 __url__ = "https://github.com/picrust/picrust2"
-__version__ = "2.5.0"
+__version__ = "2.5.1"
diff --git a/picrust2/default.py b/picrust2/default.py
@@ -2,7 +2,7 @@
 
 __copyright__ = "Copyright 2018-2022, The PICRUSt Project"
 __license__ = "GPL"
-__version__ = "2.5.0"
+__version__ = "2.5.1"
 
 from os import path
 

diff --git a/picrust2/metagenome_pipeline.py b/picrust2/metagenome_pipeline.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 
 __license__ = "GPL"
-__version__ = "2.5.0"
+__version__ = "2.5.1"
 
 import sys
 import pandas as pd
@@ -338,7 +338,7 @@ def metagenome_contributions(func_abun, sample_abun, rare_seqs=[],
             func_abun_subset_melt['taxon_rel_function_abun'] = func_abun_subset_melt['genome_function_count'] * func_abun_subset_melt['taxon_rel_abun']
 
             func_abun_subset_melt['norm_taxon_function_contrib'] = func_abun_subset_melt['taxon_function_abun'] / \
-                                                                   func_abun_subset_melt.groupby("function").sum()["taxon_function_abun"][func_abun_subset_melt["function"]].to_numpy()
+                                                                   func_abun_subset_melt.groupby("function").sum(numeric_only = True)["taxon_function_abun"][func_abun_subset_melt["function"]].to_numpy()
 
         # Collapse sequences identified as "rare" to the same category.
         rare_seqs = [r for r in rare_seqs if r in func_abun_subset_melt['taxon'].to_list()]

diff --git a/picrust2/pathway_pipeline.py b/picrust2/pathway_pipeline.py
@@ -2,7 +2,7 @@
 
 __copyright__ = "Copyright 2018-2022, The PICRUSt Project"
 __license__ = "GPL"
-__version__ = "2.5.0"
+__version__ = "2.5.1"
 
 import sys
 from collections import defaultdict
@@ -498,6 +498,8 @@ def pathway_pipeline(inputfile,
             path_abun_unstrat_by_seq = contrib_to_unstrat(contrib_table=path_abun_strat,
                                                           sample_order=list(path_abun_unstrat.columns.values))
 
+        path_abun_unstrat_by_seq.index.name = 'pathway'
+
     # Check if an abundance table is empty, which can happen when very few gene
     # families are input.
     if len(path_abun_unstrat.index) == 0:
@@ -530,7 +532,7 @@ def prep_pathway_df_out(in_tab, strat_index=False, num_digits=4):
 
         if not in_tab_df.empty:
             # Split stratified index into 2 new columns.
-            split_df = pd.DataFrame.from_records(list(in_tab_df.index.str.split('\\|\\|\\|', 1)), columns=['pathway', 'sequence'])
+            split_df = pd.DataFrame.from_records(list(in_tab_df.index.str.split(pat = '\\|\\|\\|', n = 1)), columns=['pathway', 'sequence'])
             in_tab_df.reset_index(inplace=True)
             in_tab_df[['pathway', 'sequence']] = split_df
 
@@ -540,6 +542,9 @@ def prep_pathway_df_out(in_tab, strat_index=False, num_digits=4):
         # Add these columns to be first.
         in_tab_df = in_tab_df[['pathway', 'sequence'] + orig_col]
 
+    else:
+        in_tab_df.index.name = 'pathway'
+
     return(in_tab_df)
 
 

diff --git a/picrust2/pipeline.py b/picrust2/pipeline.py
@@ -2,7 +2,7 @@
 
 __copyright__ = "Copyright 2018-2022, The PICRUSt Project"
 __license__ = "GPL"
-__version__ = "2.5.0"
+__version__ = "2.5.1"
 
 from os import path
 import sys

diff --git a/picrust2/place_seqs.py b/picrust2/place_seqs.py
@@ -2,7 +2,7 @@
 
 __copyright__ = "Copyright 2018-2022, The PICRUSt Project"
 __license__ = "GPL"
-__version__ = "2.5.0"
+__version__ = "2.5.1"
 
 import sys
 from os import path, chdir, getcwd

diff --git a/picrust2/util.py b/picrust2/util.py
@@ -2,7 +2,7 @@
 
 __copyright__ = "Copyright 2018-2022, The PICRUSt Project"
 __license__ = "GPL"
-__version__ = "2.5.0"
+__version__ = "2.5.1"
 
 from os import makedirs, chmod
 from os.path import abspath, dirname, isdir, join, exists, splitext
@@ -544,7 +544,7 @@ def convert_humann2_to_picrust2(infiles, outfile, stratified):
 
         original_col = list(humann2_combined.columns)
 
-        split_df = pd.DataFrame.from_records(list(humann2_combined.index.str.split('\\|', 1)), columns=[first_col, 'sequence'])
+        split_df = pd.DataFrame.from_records(list(humann2_combined.index.str.split(pat = '\\|', n = 1)), columns=[first_col, 'sequence'])
 
         humann2_combined.reset_index(inplace=True)
 

diff --git a/picrust2/wrap_hsp.py b/picrust2/wrap_hsp.py
@@ -2,7 +2,7 @@
 
 __copyright__ = "Copyright 2018-2022, The PICRUSt Project"
 __license__ = "GPL"
-__version__ = "2.5.0"
+__version__ = "2.5.1"
 
 from os import path
 import sys

diff --git a/scripts/add_descriptions.py b/scripts/add_descriptions.py
@@ -2,7 +2,7 @@
 
 __copyright__ = "Copyright 2018-2022, The PICRUSt Project"
 __license__ = "GPL"
-__version__ = "2.5.0"
+__version__ = "2.5.1"
 
 import argparse
 from picrust2.default import default_map

diff --git a/scripts/convert_table.py b/scripts/convert_table.py
@@ -2,7 +2,7 @@
 
 __copyright__ = "Copyright 2018-2022, The PICRUSt Project"
 __license__ = "GPL"
-__version__ = "2.5.0"
+__version__ = "2.5.1"
 
 import argparse
 from picrust2.util import (check_files_exist, contrib_to_legacy,

diff --git a/scripts/hsp.py b/scripts/hsp.py
@@ -2,7 +2,7 @@
 
 __copyright__ = "Copyright 2018-2022, The PICRUSt Project"
 __license__ = "GPL"
-__version__ = "2.5.0"
+__version__ = "2.5.1"
 
 import argparse
 from picrust2.wrap_hsp import castor_hsp_workflow

diff --git a/scripts/metagenome_pipeline.py b/scripts/metagenome_pipeline.py
@@ -2,7 +2,7 @@
 
 __copyright__ = "Copyright 2018-2022, The PICRUSt Project"
 __license__ = "GPL"
-__version__ = "2.5.0"
+__version__ = "2.5.1"
 
 import argparse
 from os import path

diff --git a/scripts/pathway_pipeline.py b/scripts/pathway_pipeline.py
@@ -2,7 +2,7 @@
 
 __copyright__ = "Copyright 2018-2022, The PICRUSt Project"
 __license__ = "GPL"
-__version__ = "2.5.0"
+__version__ = "2.5.1"
 
 import argparse
 from picrust2.pathway_pipeline import pathway_pipeline

diff --git a/scripts/picrust2_pipeline.py b/scripts/picrust2_pipeline.py
@@ -2,7 +2,7 @@
 
 __copyright__ = "Copyright 2018-2022, The PICRUSt Project"
 __license__ = "GPL"
-__version__ = "2.5.0"
+__version__ = "2.5.1"
 
 import argparse
 from os import path

diff --git a/scripts/place_seqs.py b/scripts/place_seqs.py
@@ -2,7 +2,7 @@
 
 __copyright__ = "Copyright 2018-2022, The PICRUSt Project"
 __license__ = "GPL"
-__version__ = "2.5.0"
+__version__ = "2.5.1"
 
 import argparse
 from picrust2.place_seqs import place_seqs_pipeline

diff --git a/scripts/print_picrust2_config.py b/scripts/print_picrust2_config.py
@@ -2,7 +2,7 @@
 
 __copyright__ = "Copyright 2018-2022, The PICRUSt Project"
 __license__ = "GPL"
-__version__ = "2.5.0"
+__version__ = "2.5.1"
 
 from sys import platform, version as python_version, executable
 

diff --git a/scripts/shuffle_predictions.py b/scripts/shuffle_predictions.py
@@ -2,7 +2,7 @@
 
 __copyright__ = "Copyright 2018-2022, The PICRUSt Project"
 __license__ = "GPL"
-__version__ = "2.5.0"
+__version__ = "2.5.1"
 
 import argparse
 from picrust2.util import check_files_exist, shuffle_predictions

diff --git a/setup.py b/setup.py
@@ -5,7 +5,7 @@
 
 __copyright__ = "Copyright 2018-2022, The PICRUSt Project"
 __license__ = "GPL"
-__version__ = "2.5.0"
+__version__ = "2.5.1"
 __maintainer__ = "Gavin Douglas"
 
 long_description = ("Please visit the google group if you have questions: "

diff --git a/tests/test_hsp.py b/tests/test_hsp.py
@@ -2,7 +2,7 @@
 
 __copyright__ = "Copyright 2018-2022, The PICRUSt Project"
 __license__ = "GPL"
-__version__ = "2.5.0"
+__version__ = "2.5.1"
 
 import unittest
 from os import path

diff --git a/tests/test_metagenome_pipeline.py b/tests/test_metagenome_pipeline.py
@@ -2,7 +2,7 @@
 
 __copyright__ = "Copyright 2018-2022, The PICRUSt Project"
 __license__ = "GPL"
-__version__ = "2.5.0"
+__version__ = "2.5.1"
 
 import unittest
 from os import path

diff --git a/tests/test_pathway_pipeline.py b/tests/test_pathway_pipeline.py
@@ -2,7 +2,7 @@
 
 __copyright__ = "Copyright 2018-2022, The PICRUSt Project"
 __license__ = "GPL"
-__version__ = "2.5.0"
+__version__ = "2.5.1"
 
 import unittest
 import pandas as pd

diff --git a/tests/test_place_seqs.py b/tests/test_place_seqs.py
@@ -2,7 +2,7 @@
 
 __copyright__ = "Copyright 2018-2022, The PICRUSt Project"
 __license__ = "GPL"
-__version__ = "2.5.0"
+__version__ = "2.5.1"
 
 import unittest
 import gzip

diff --git a/tests/test_util.py b/tests/test_util.py
@@ -2,7 +2,7 @@
 
 __copyright__ = "Copyright 2018-2022, The PICRUSt Project"
 __license__ = "GPL"
-__version__ = "2.5.0"
+__version__ = "2.5.1"
 
 import unittest
 from os import path

diff --git a/tests/test_workflow.py b/tests/test_workflow.py
@@ -2,7 +2,7 @@
 
 __copyright__ = "Copyright 2018-2022, The PICRUSt Project"
 __license__ = "GPL"
-__version__ = "2.5.0"
+__version__ = "2.5.1"
 
 import unittest
 from os import path