You almost certainly have something out of sync here, either a PYTHONPATH
env var is set, or you are operating on the wrong conda env. Check this out:
#!/Users/matthew/.conda/envs/q2dev/bin/python
# -*- coding: utf-8 -*-
import re
import sys
from q2cli.__main__ import qiime
print('Hello World')
if __name__ == '__main__':
sys.argv[0] = re.sub(r'(-script\.pyw?|\.exe)?$', '', sys.argv[0])
sys.exit(qiime())
qiime frag2 74f1e04
Hello World
Usage: qiime [OPTIONS] COMMAND [ARGS]...
QIIME 2 command-line interface (q2cli)
--------------------------------------
To get help with QIIME 2, visit https://qiime2.org.
To enable tab completion in Bash, run the following command or add it to
your .bashrc/.bash_profile:
source tab-qiime
To enable tab completion in ZSH, run the following commands or add them to
your .zshrc:
autoload bashcompinit && bashcompinit && source tab-qiime
Options:
--version Show the version and exit.
--help Show this message and exit.
Commands:
info Display information about current deployment.
tools Tools for working with QIIME 2 files.
dev Utilities for developers and advanced users.
alignment Plugin for generating and manipulating alignments.
composition Plugin for compositional data analysis.
cutadapt Plugin for removing adapter sequences, primers, and
other unwanted sequence from sequence data.
dada2 Plugin for sequence quality control with DADA2.
deblur Plugin for sequence quality control with Deblur.
demux Plugin for demultiplexing & viewing sequence quality.
diversity Plugin for exploring community diversity.
emperor Plugin for ordination plotting with Emperor.
feature-classifier Plugin for taxonomic classification.
feature-table Plugin for working with sample by feature tables.
gneiss Plugin for building compositional models.
longitudinal Plugin for paired sample and time series analyses.
metadata Plugin for working with Metadata.
phylogeny Plugin for generating and manipulating phylogenies.
quality-control Plugin for quality control of feature and sequence data.
quality-filter Plugin for PHRED-based filtering and trimming.
sample-classifier Plugin for machine learning prediction of sample
metadata.
taxa Plugin for working with feature taxonomy annotations.
vsearch Plugin for clustering and dereplicating with vsearch.
As a general note, this is probably not the best way to go about making changes to anything in QIIME 2 — this platform is not a collection of scripts, like QIIME 1, rather it is a framework + interfaces (q2cli for example) + plugins, all of which are independent software packages.
I suspect that the problem you are seeing here is related to the import issue you reported earlier, so let’s keep the discussion there for now. Thanks!