caporaso-lab / sourcetracker2

SourceTracker2
BSD 3-Clause "New" or "Revised" License
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Demo doesn't work #162

Open NeginValizadegan opened 4 months ago

NeginValizadegan commented 4 months ago

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/

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
gene-knight9 commented 3 months ago

You can re-download the Sourcetracker2 package on GitHub to fix the problem.【pip install https://github.com/biota/sourcetracker2/archive/master.zip