(Please feel free to change forum section of this question if this one is not right and add appropriate tags.)
Since I got stuck on this problem, I am trying to take a look at what exactly is happening in the code level of QIIME2 - effectively meaning adding some state prints.
However, modifying /home/user/miniconda3/envs/qiime2-2018.8/bin/qiime
file does not have any actual impact on the behavior of QIIME2 or its execution.
For example, this is actual execution wrapper:
#!/home/krampl/miniconda3/envs/qiime2-2018.8/bin/python
# -*- coding: utf-8 -*-
import re
import sys
from q2cli.__main__ import qiime
if __name__ == '__main__':
sys.argv[0] = re.sub(r'(-script\.pyw?|\.exe)?$', '', sys.argv[0])
sys.exit(qiime())
Adding print('Hello World!')
after if
statement (or even before) does not change the behavior of QIIME2 (meaning there is no print to terminal).
Thinking there is rewritten somewhere standard output to something else beside terminal, I tried to write to a file instead with similar results - there was no file created, let alone written to it.
Even commenting out lines has no impact as can be seen from this example:
#!/home/krampl/miniconda3/envs/qiime2-2018.8/bin/python
# -*- coding: utf-8 -*-
import re
import sys
from q2cli.__main__ import qiime
#if __name__ == '__main__':
# sys.argv[0] = re.sub(r'(-script\.pyw?|\.exe)?$', '', sys.argv[0])
# sys.exit(qiime())
My questions are: Is this behavior caused by Conda itself and if it is not, how can I modify the code, so my changes will appear?
Steps taken:
$source activate qiime2-2018.8
$vim `which qiime` # can be replaced with actual path to execution wrapper file
# adding print('Hello World!') and saving
$qiime
OS: Ubuntu 16.04.1 LTS
conda version : 4.5.11
Qiime2 version: 2018.8