Merge pull request #17 from gavinmdouglas/2023.2

2023.2

Author: gavinmdouglas

README.md

@@ -1,4 +1,4 @@
 # q2-picrust2
-QIIME2 plugin for PICRUSt2
+QIIME 2 plugin for PICRUSt2
 
 For descriptions of how to install and run this plugin, see [here](https://github.com/picrust/picrust2/wiki/q2-picrust2-Tutorial/).

q2_picrust2/__init__.py

@@ -1,13 +1,4 @@
-# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2018, QIIME 2 development team.
-#
-# Distributed under the terms of the Modified BSD License.
-#
-# The full license is in the file LICENSE, distributed with this software.
-# ----------------------------------------------------------------------------
-
 from ._full_pipeline import full_pipeline
 from ._custom_tree_pipeline import custom_tree_pipeline
 
 __all__ = ['custom_tree_pipeline', 'full_pipeline']
-

q2_picrust2/_custom_tree_pipeline.py

@@ -78,7 +78,6 @@ def custom_tree_pipeline(table: biom.Table,
                               print_stdout=highly_verbose,
                               print_stderr=True)
 
-
         system_call_check(hsp_out_EC_cmd,
                           print_command=True,
                           print_stdout=highly_verbose,

q2_picrust2/_full_pipeline.py

@@ -1,6 +1,5 @@
 import biom
 from os import path
-import sys
 import pandas as pd
 from tempfile import TemporaryDirectory
 import picrust2.pipeline
@@ -36,7 +35,7 @@ def full_pipeline(table: biom.Table,
         seq_outfile = path.join(temp_dir, "seqs.fna")
 
         with open(seq_outfile, "w") as outfile_fh:
-            for seqname, sequence in seq.iteritems():
+            for seqname, sequence in seq.items():
                 print(">" + str(seqname) + "\n" + str(sequence),
                       file=outfile_fh)
 

q2_picrust2/plugin_setup.py

@@ -13,7 +13,7 @@
 
 plugin = Plugin(
     name='picrust2',
-    version="2021.11",
+    version="2023.2",
     website='https://github.com/gavinmdouglas/q2-picrust2',
     package='q2_picrust2',
     description=('This QIIME 2 plugin wraps the default 16S PICRUSt2 pipeline to run '
@@ -67,10 +67,10 @@
         'skip_minpath': ('Do not run MinPath to identify which pathways are '
                          'present as a first pass (on by default).'),
         'edge_exponent': ('Setting for maximum parisomony hidden-state '
-                         'prediction. Specifies weighting transition costs '
-                         'by the inverse length of edge lengths. If 0, then '
-                         'edge lengths do not influence predictions. Must be '
-                         'a non-negative real-valued number.'),
+                          'prediction. Specifies weighting transition costs '
+                          'by the inverse length of edge lengths. If 0, then '
+                          'edge lengths do not influence predictions. Must be '
+                          'a non-negative real-valued number.'),
         'no_gap_fill': ('Do not perform gap filling before predicting '
                         'pathway abundances (gap filling is on otherwise by '
                         'default).'),
@@ -133,10 +133,10 @@
         'skip_minpath': ('Do not run MinPath to identify which pathways are '
                          'present as a first pass (on by default).'),
         'edge_exponent': ('Setting for maximum parisomony hidden-state '
-                         'prediction. Specifies weighting transition costs '
-                         'by the inverse length of edge lengths. If 0, then '
-                         'edge lengths do not influence predictions. Must be '
-                         'a non-negative real-valued number.'),
+                          'prediction. Specifies weighting transition costs '
+                          'by the inverse length of edge lengths. If 0, then '
+                          'edge lengths do not influence predictions. Must be '
+                          'a non-negative real-valued number.'),
         'no_gap_fill': ('Do not perform gap filling before predicting '
                         'pathway abundances (gap filling is on otherwise by '
                         'default).'),

setup.py

@@ -2,7 +2,7 @@
 
 setup(
     name="q2-picrust2",
-    version="2021.11",
+    version="2023.2",
     packages=find_packages(),
     package_data={'q2_picrust2': ['citations.bib']},
     author="Gavin Douglas",