In installed the tool via command line (conda) using the instructions on Github. Then trying to replicate the demo code, I get the following error about a deprecated attribute for module 'numpy':
Traceback (most recent call last):
File "/Users/valizad2/miniconda/envs/st2/bin/sourcetracker2", line 8, in <module>
sys.exit(cli())
File "/Users/valizad2/miniconda/envs/st2/lib/python3.8/site-packages/click/core.py", line 1157, in __call__
return self.main(*args, **kwargs)
File "/Users/valizad2/miniconda/envs/st2/lib/python3.8/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
File "/Users/valizad2/miniconda/envs/st2/lib/python3.8/site-packages/click/core.py", line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/Users/valizad2/miniconda/envs/st2/lib/python3.8/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/Users/valizad2/miniconda/envs/st2/lib/python3.8/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
File "/Users/valizad2/miniconda/envs/st2/lib/python3.8/site-packages/sourcetracker/_cli/gibbs.py", line 214, in gibbs
f(sample)
File "/Users/valizad2/miniconda/envs/st2/lib/python3.8/site-packages/sourcetracker/_sourcetracker.py", line 822, in _cli_sink_source_prediction_runner
results = gibbs_sampler(cp, sink_data, restarts, draws_per_restart, burnin,
File "/Users/valizad2/miniconda/envs/st2/lib/python3.8/site-packages/sourcetracker/_sourcetracker.py", line 530, in gibbs_sampler
order = np.arange(sink_sum, dtype=np.int)
File "/Users/valizad2/miniconda/envs/st2/lib/python3.8/site-packages/numpy/__init__.py", line 305, in __getattr__
raise AttributeError(__former_attrs__[attr])
AttributeError: module 'numpy' has no attribute 'int'.
`np.int` was a deprecated alias for the builtin `int`. To avoid this error in existing code, use `int` by itself. Doing this will not modify any behavior and is safe. When replacing `np.int`, you may wish to use e.g. `np.int64` or `np.int32` to specify the precision. If you wish to review your current use, check the release note link for additional information.
The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at:
https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
In installed the tool via command line (conda) using the instructions on Github. Then trying to replicate the demo code, I get the following error about a deprecated attribute for module 'numpy':
sourcetracker2 gibbs -i otu_table.biom -m map.txt -o example1/