From 7cd94baf6a0842c8a5afae06ac45581d92804f70 Mon Sep 17 00:00:00 2001 From: Liz Gehret Date: Mon, 13 Jan 2025 12:21:05 -0700 Subject: [PATCH 1/2] REF: import util from framework --- q2_composition/_ancombc.py | 15 +-------------- 1 file changed, 1 insertion(+), 14 deletions(-) diff --git a/q2_composition/_ancombc.py b/q2_composition/_ancombc.py index c92bdb5..ac7c72a 100644 --- a/q2_composition/_ancombc.py +++ b/q2_composition/_ancombc.py @@ -14,24 +14,11 @@ import qiime2 from qiime2.metadata import NumericMetadataColumn, CategoricalMetadataColumn +from qiime2.sdk.util import run_commands from ._format import DataLoafPackageDirFmt -def run_commands(cmds, verbose=True): - if verbose: - print('Running external command line application(s). This may print' - ' messages to stdout and/or stderr.') - print('The command(s) being run are below. These commands cannot be' - ' manually re-run as they will depend on temporary files that no' - ' longer exist.') - for cmd in cmds: - if verbose: - print('\nCommand:', end=' ') - print(' '.join(cmd), end='\n\n') - subprocess.run(cmd, check=True) - - def ancombc(table: pd.DataFrame, metadata: qiime2.Metadata, formula: str, p_adj_method: str = 'holm', prv_cut: float = 0.1, lib_cut: int = 0, reference_levels: str = None, From a4654b975be536d32d9a0816bcc3ed21721aaeec Mon Sep 17 00:00:00 2001 From: Liz Gehret Date: Thu, 6 Feb 2025 11:23:21 -0700 Subject: [PATCH 2/2] moved location for helper --- q2_composition/_ancombc.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/q2_composition/_ancombc.py b/q2_composition/_ancombc.py index ac7c72a..c6661fa 100644 --- a/q2_composition/_ancombc.py +++ b/q2_composition/_ancombc.py @@ -14,7 +14,7 @@ import qiime2 from qiime2.metadata import NumericMetadataColumn, CategoricalMetadataColumn -from qiime2.sdk.util import run_commands +from qiime2.plugin.util import run_commands from ._format import DataLoafPackageDirFmt