oscar-franzen / adobo

functions and algorithms for single cell RNA-seq analyses
GNU General Public License v3.0
11 stars 5 forks source link

from scipy.stats import median_absolute_deviation as mad #3

Open zhangdudu0 opened 1 year ago

zhangdudu0 commented 1 year ago

>>> import adobo Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/software/adobo/adobo/__init__.py", line 19, in <module> from . import preproc File "/software/adobo/adobo/preproc.py", line 28, in <module> from scipy.stats import median_absolute_deviation as mad ImportError: cannot import name 'median_absolute_deviation' from 'scipy.stats' (/usr/local/lib/python3.8/site-packages/scipy/stats/__init__.py)

zhangdudu0 commented 1 year ago
[root@hxh adobo]# pip install adobo --user
Looking in indexes: https://mirrors.aliyun.com/pypi/simple
Collecting adobo
  Downloading https://mirrors.aliyun.com/pypi/packages/89/b9/1a756a25eda9c73d7a927c652ff35cb45cef909b8a0dc64eb6ede1c47f65/adobo-0.2.57.tar.gz (33.1 MB)
     ━━━━╺━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.6/33.1 MB 464.2 kB/s eta 0:01:04
ERROR: Operation cancelled by user
[root@hxh adobo]# pip install adobo --user -i http://pypi.douban.com/simple/ --trusted-host pypi.douban.com
Looking in indexes: http://pypi.douban.com/simple/
Collecting adobo
  Downloading http://pypi.doubanio.com/packages/89/b9/1a756a25eda9c73d7a927c652ff35cb45cef909b8a0dc64eb6ede1c47f65/adobo-0.2.57.tar.gz (33.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 33.1/33.1 MB 1.6 MB/s eta 0:00:00
  Preparing metadata (setup.py) ... done
Requirement already satisfied: pandas>=0.25.0 in /usr/local/lib/python3.8/site-packages (from adobo) (1.5.2)
Requirement already satisfied: numpy>=1.17.0 in /usr/local/lib/python3.8/site-packages (from adobo) (1.23.5)
Requirement already satisfied: scikit-learn>=0.21.3 in /usr/local/lib/python3.8/site-packages (from adobo) (1.1.3)
Collecting leidenalg>=0.7.0
  Downloading http://pypi.doubanio.com/packages/35/22/363be33229521ed02e66e3bd1c9287792344501d8c6311231e8cd985de3e/leidenalg-0.9.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.3 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.3/1.3 MB 18.2 MB/s eta 0:00:00
Collecting python-igraph>=0.7.1
  Downloading http://pypi.doubanio.com/packages/d0/93/c5b48fe8fa3d95c61d80754ac6138ad385bbbb6e3b90a1f6a86706efba9f/python-igraph-0.10.2.tar.gz (9.5 kB)
  Preparing metadata (setup.py) ... done
Requirement already satisfied: scipy>=1.3.0 in /usr/local/lib/python3.8/site-packages (from adobo) (1.9.3)
Collecting umap-learn>=0.3.9
  Downloading http://pypi.doubanio.com/packages/e1/eb/dca6cfd872e8542fb57dd56ff2d5d67baed270aee6db739c6414d8d5b3b5/umap-learn-0.5.3.tar.gz (88 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 88.2/88.2 kB 259.4 MB/s eta 0:00:00
  Preparing metadata (setup.py) ... done
Collecting statsmodels>=0.10.1
  Downloading http://pypi.doubanio.com/packages/60/de/7cd008964ff647cdb6266079b0fc3029d220b546b6f8727866bef63b18e1/statsmodels-0.13.5-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (9.9 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 9.9/9.9 MB 48.2 MB/s eta 0:00:00
Requirement already satisfied: matplotlib>=3.1.1 in /usr/local/lib/python3.8/site-packages (from adobo) (3.6.2)
Collecting seaborn>=0.9.0
  Downloading http://pypi.doubanio.com/packages/77/18/7354cb68dd7906d5a3118e0ed3e30c37502f9e6253139ecfcf4fa33af210/seaborn-0.12.1-py3-none-any.whl (288 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 288.2/288.2 kB 244.0 MB/s eta 0:00:00
Requirement already satisfied: psutil>=5.4.2 in /usr/local/lib/python3.8/site-packages (from adobo) (5.9.4)
Requirement already satisfied: datatable>=0.9.0 in /usr/local/lib/python3.8/site-packages (from adobo) (1.0.0)
Collecting fa2
  Downloading http://pypi.doubanio.com/packages/48/d1/aa67d917628d29b83f3413790155da575865f3eab8b6e577c5871ef987d8/fa2-0.3.5.tar.gz (435 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 435.4/435.4 kB 323.2 MB/s eta 0:00:00
  Preparing metadata (setup.py) ... done
Collecting networkx>=2.3
  Downloading http://pypi.doubanio.com/packages/42/31/d2f89f1ae42718f8c8a9e440ebe38d7d5fe1e0d9eb9178ce779e365b3ab0/networkx-2.8.8-py3-none-any.whl (2.0 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.0/2.0 MB 53.9 MB/s eta 0:00:00
Collecting patsy>=0.5.1
  Downloading http://pypi.doubanio.com/packages/2a/e4/b3263b0e353f2be7b14f044d57874490c9cef1798a435f038683acea5c98/patsy-0.5.3-py2.py3-none-any.whl (233 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 233.8/233.8 kB 338.0 MB/s eta 0:00:00
Collecting mplcursors>=0.3
  Downloading http://pypi.doubanio.com/packages/03/ec/f28dd523e8397ae8c55878b802380aae7bfd65448f17e5c2b30927fe6575/mplcursors-0.5.2.tar.gz (89 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 89.0/89.0 kB 255.8 MB/s eta 0:00:00
  Preparing metadata (setup.py) ... error
  error: subprocess-exited-with-error

  × python setup.py egg_info did not run successfully.
  │ exit code: 1
  ╰─> [39 lines of output]
      /usr/local/lib/python3.8/site-packages/setuptools/dist.py:642: UserWarning: Usage of dash-separated 'index-url' will not be supported in future versions. Please use the underscore name 'index_url' instead
        warnings.warn(
      WARNING: The wheel package is not available.
      WARNING: The repository located at mirrors.cloud.aliyuncs.com is not a trusted or secure host and is being ignored. If this repository is available via HTTPS we recommend you use HTTPS instead, otherwise you may silence this warning and allow it anyway with '--trusted-host mirrors.cloud.aliyuncs.com'.
      ERROR: Could not find a version that satisfies the requirement setuptools_scm (from versions: none)
      ERROR: No matching distribution found for setuptools_scm
      Traceback (most recent call last):
        File "/usr/local/lib/python3.8/site-packages/setuptools/installer.py", line 75, in fetch_build_egg
          subprocess.check_call(cmd)
        File "/usr/local/lib/python3.8/subprocess.py", line 364, in check_call
          raise CalledProcessError(retcode, cmd)
      subprocess.CalledProcessError: Command '['/usr/bin/python', '-m', 'pip', '--disable-pip-version-check', 'wheel', '--no-deps', '-w', '/tmp/tmpun8zcs_u', '--quiet', '--index-url', 'http://mirrors.cloud.aliyuncs.com/pypi/simple/', 'setuptools_scm']' returned non-zero exit status 1.

      The above exception was the direct cause of the following exception:

      Traceback (most recent call last):
        File "<string>", line 2, in <module>
        File "<pip-setuptools-caller>", line 34, in <module>
        File "/tmp/pip-install-0o_r3283/mplcursors_1b447c0fa1ed4ffb97d6dfb4682ab39a/setup.py", line 7, in <module>
          setup(
        File "/tmp/pip-install-0o_r3283/mplcursors_1b447c0fa1ed4ffb97d6dfb4682ab39a/setupext.py", line 50, in setup
          setuptools.setup(**kwargs)
        File "/usr/local/lib/python3.8/site-packages/setuptools/__init__.py", line 152, in setup
          _install_setup_requires(attrs)
        File "/usr/local/lib/python3.8/site-packages/setuptools/__init__.py", line 147, in _install_setup_requires
          dist.fetch_build_eggs(dist.setup_requires)
        File "/usr/local/lib/python3.8/site-packages/setuptools/dist.py", line 721, in fetch_build_eggs
          resolved_dists = pkg_resources.working_set.resolve(
        File "/usr/local/lib/python3.8/site-packages/pkg_resources/__init__.py", line 766, in resolve
          dist = best[req.key] = env.best_match(
        File "/usr/local/lib/python3.8/site-packages/pkg_resources/__init__.py", line 1051, in best_match
          return self.obtain(req, installer)
        File "/usr/local/lib/python3.8/site-packages/pkg_resources/__init__.py", line 1063, in obtain
          return installer(requirement)
        File "/usr/local/lib/python3.8/site-packages/setuptools/dist.py", line 780, in fetch_build_egg
          return fetch_build_egg(self, req)
        File "/usr/local/lib/python3.8/site-packages/setuptools/installer.py", line 77, in fetch_build_egg
          raise DistutilsError(str(e)) from e
      distutils.errors.DistutilsError: Command '['/usr/bin/python', '-m', 'pip', '--disable-pip-version-check', 'wheel', '--no-deps', '-w', '/tmp/tmpun8zcs_u', '--quiet', '--index-url', 'http://mirrors.cloud.aliyuncs.com/pypi/simple/', 'setuptools_scm']' returned non-zero exit status 1.
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.
hint: See above for details.