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Installation of newer bknn 1.6.0 package (att @ktpolanski) conflicts with numpy installation for scanpy 1.9.8:
The following packages are incompatible
├─ bbknn 1.6.0** is installable with the potential options
│ ├─ bbknn 1.6.0 would require
│ │ └─ numpy >=1.26.2,<2.0a0 with the potential options
│ │ ├─ numpy [1.21.3|1.21.4|...|1.26.4] would require
│ │ │ ├─ python >=3.10,<3.11.0a0 , which can be installed;
│ │ │ └─ python_abi 3.10.* *_cp310, which can be installed;
│ │ ├─ numpy [1.23.4|1.23.5|...|1.26.4] would require
│ │ │ ├─ python >=3.11,<3.12.0a0 , which can be installed;
│ │ │ └─ python_abi 3.11.* *_cp311, which can be installed;
│ │ ├─ numpy [1.26.2|1.26.3|1.26.4] would require
│ │ │ └─ python_abi 3.12.* *_cp312, which can be installed;
│ │ ├─ numpy [1.26.2|1.26.3|1.26.4], which can be installed;
│ │ ├─ numpy [1.26.2|1.26.3] would require
│ │ │ └─ pypy3.9 >=7.3.13 , which can be installed;
│ │ └─ numpy 1.26.4 would require
│ │ └─ pypy3.9 >=7.3.15 , which can be installed;
│ ├─ bbknn 1.6.0 would require
│ │ ├─ python >=3.10,<3.11.0a0 , which can be installed;
│ │ └─ python_abi 3.10.* *_cp310, which can be installed;
│ └─ bbknn 1.6.0 would require
│ ├─ python >=3.8,<3.9.0a0 , which can be installed;
│ └─ python_abi 3.8.* *_cp38, which can be installed;
├─ numpy >=1.17.3,<1.25.0 is installable with the potential options
│ ├─ numpy [1.21.3|1.21.4|...|1.26.4], which can be installed (as previously explained);
│ ├─ numpy [1.23.4|1.23.5|...|1.26.4], which can be installed (as previously explained);
│ ├─ numpy [1.17.3|1.17.4|...|1.24.4] conflicts with any installable versions previously reported;
│ ├─ numpy [1.17.3|1.17.5|1.18.1] would require
│ │ └─ python >=3.6,<3.7.0a0 , which can be installed;
│ ├─ numpy [1.17.3|1.17.5|1.18.1] would require
│ │ └─ python >=3.7,<3.8.0a0 , which can be installed;
│ ├─ numpy [1.17.3|1.17.5|1.18.1] would require
│ │ └─ python >=3.8,<3.9.0a0 , which can be installed;
│ ├─ numpy [1.17.5|1.18.1|...|1.19.5] would require
│ │ ├─ python >=3.6,<3.7.0a0 , which can be installed;
│ │ └─ python_abi 3.6.* *_cp36m, which can be installed;
│ ├─ numpy [1.17.5|1.18.1|...|1.21.6] would require
│ │ ├─ python >=3.7,<3.8.0a0 , which can be installed;
│ │ └─ python_abi 3.7.* *_cp37m, which can be installed;
│ ├─ numpy [1.17.5|1.18.1|...|1.24.4] would require
│ │ ├─ python >=3.8,<3.9.0a0 , which can be installed;
│ │ └─ python_abi 3.8.* *_cp38, which can be installed;
│ ├─ numpy [1.18.1|1.18.4|...|1.19.5] would require
│ │ └─ python_abi 3.6 *_pypy36_pp73, which can be installed;
│ ├─ numpy [1.19.5|1.20.0|...|1.21.5] would require
│ │ └─ python_abi 3.7 *_pypy37_pp73, which can be installed;
│ ├─ numpy [1.19.5|1.20.3|...|1.24.1] would require
│ │ └─ python_abi 3.8 *_pypy38_pp73, which can be installed;
│ ├─ numpy [1.19.5|1.20.3|...|1.24.1] would require
│ │ └─ python_abi 3.9 *_pypy39_pp73, which can be installed;
│ ├─ numpy [1.24.2|1.24.3|1.24.4] would require
│ │ └─ pypy3.8 >=7.3.11 , which can be installed;
│ ├─ numpy [1.24.2|1.24.3|1.24.4] would require
│ │ └─ pypy3.9 >=7.3.11 , which can be installed;
│ ├─ numpy 1.23.3 would require
│ │ └─ numpy-base 1.23.3 py310h375b286_0, which does not exist (perhaps a missing channel);
│ └─ numpy 1.23.3 would require
│ └─ numpy-base 1.23.3 py310h8e6c178_0, which does not exist (perhaps a missing channel);
└─ python 3.9** is not installable because it conflicts with any installable versions previously reported.
Pinning numpy to those versions is required or otherwise we get the following runtime error when running our tests:
# (in test file scanpy-scripts-tests.bats, line 677)
# `run rm -f $bbknn_obj && eval "$scanpy integrate bbknn $bbknn_opt $louvain_obj $bbknn_obj"' failed
# /home/runner/micromamba-root/envs/scanpy-scripts/lib/python3.9/site-packages/scipy/__init__.py:146: UserWarning: A NumPy version >=1.17.3 and <1.25.0 is required for this version of SciPy (detected version 1.26.4
# warnings.warn(f"A NumPy version >={np_minversion} and <{np_maxversion}"
# computing batch balanced neighbors
# Traceback (most recent call last):
# File "/home/runner/micromamba-root/envs/scanpy-scripts/bin/scanpy-cli", line 8, in <module>
# sys.exit(cli())
# File "/home/runner/micromamba-root/envs/scanpy-scripts/lib/python3.9/site-packages/click/core.py", line 829, in __call__
# return self.main(*args, **kwargs)
# File "/home/runner/micromamba-root/envs/scanpy-scripts/lib/python3.9/site-packages/click/core.py", line 782, in main
# rv = self.invoke(ctx)
# File "/home/runner/micromamba-root/envs/scanpy-scripts/lib/python3.9/site-packages/click/core.py", line 12, in invoke
# return _process_result(sub_ctx.command.invoke(sub_ctx))
# File "/home/runner/micromamba-root/envs/scanpy-scripts/lib/python3.9/site-packages/click/core.py", line 1259, in invoke
# return _process_result(sub_ctx.command.invoke(sub_ctx))
# File "/home/runner/micromamba-root/envs/scanpy-scripts/lib/python3.9/site-packages/click/core.py", line 1066, in invoke
# return ctx.invoke(self.callback, **ctx.params)
# File "/home/runner/micromamba-root/envs/scanpy-scripts/lib/python3.9/site-packages/click/core.py", line , in invoke
# return callback(*args, **kwargs)
# File "/home/runner/micromamba-root/envs/scanpy-scripts/lib/python3.9/site-packages/scanpy_scripts/cmd_utils.py", line 49, in cmd
# func(adata, **kwargs)
# File "/home/runner/micromamba-root/envs/scanpy-scripts/lib/python3.9/site-packages/scanpy_scripts/lib/_bbknn.py", line 24, in bbknn
# sce.pp.bbknn(adata, batch_key=key, **kwargs)
# File "/home/runner/micromamba-root/envs/scanpy-scripts/lib/python3.9/site-packages/scanpy/external/pp/_bbknn.py", line 134, in bbknn
# return bbknn(
# File "/home/runner/micromamba-root/envs/scanpy-scripts/lib/python3.9/site-packages/bbknn/__init__.py", line 108, in bbknn
# bbknn_out = matrix.bbknn(pca=pca, batch_list=batch_list, scanpy_logging=True, **kwargs)
# File "/home/runner/micromamba-root/envs/scanpy-scripts/lib/python3.9/site-packages/bbknn/matrix.py", line 350, in bbknn
# params['n_pcs'] = np.min([params['n_pcs'], pca.shape[1]])
# File "/home/runner/micromamba-root/envs/scanpy-scripts/lib/python3.9/site-packages/numpy/core/fromnumeric.py", line 2953, in min
# return _wrapreduction(a, np.minimum, 'min', axis, None, out,
# File "/home/runner/micromamba-root/envs/scanpy-scripts/lib/python3.9/site-packages/numpy/core/fromnumeric.py", line 88, in _wrapreduction
# return ufunc.reduce(obj, axis, dtype, out, **passkwargs)
# TypeError: '<=' not supported between instances of 'NoneType' and 'int'
Not sure what might be forcing that scipy version.
The text was updated successfully, but these errors were encountered:
Installation of newer bknn 1.6.0 package (att @ktpolanski) conflicts with numpy installation for scanpy 1.9.8:
Pinning numpy to those versions is required or otherwise we get the following runtime error when running our tests:
Not sure what might be forcing that scipy version.
The text was updated successfully, but these errors were encountered: