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Could not install pySCTransform #13
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I would recommend creating a conda environment for pysctransform. The rest of the install instructions remain the same. |
I created a new conda env called pysct, and installed both scanpy (installed together with the creation of conda env) and louvain (conda install failed so I installed using pip install louvain after activating the pysct conda env). And did both pip install git+https://github.com/saketkc/pysctransform.git and. pip install git+https://github.com/saketkc/pysctransform.git --use-pep517. The message I got seems to be the same as before. Appreciate it if you could help me further. ---------message------------- Collecting git+https://github.com/saketkc/pysctransform.git × python setup.py bdist_wheel did not run successfully.
note: This error originates from a subprocess, and is likely not a problem with pip. × python setup.py clean did not run successfully.
note: This error originates from a subprocess, and is likely not a problem with pip. -------message end------------ -------new message------------ Collecting git+https://github.com/saketkc/pysctransform.git × pip subprocess to install backend dependencies did not run successfully.
note: This error originates from a subprocess, and is likely not a problem with pip. × pip subprocess to install backend dependencies did not run successfully. note: This error originates from a subprocess, and is likely not a problem with pip. -------message end------------ |
I was able to install this using conda: $ conda create -n pysct scipy numpy kdepy matplotlib
$ conda activate pysct
$ pip install git+https://github.com/saketkc/pysctransform.git --use-pep517 |
Description
Tried to install it but failed
What I Did
pip install git+https://github.com/saketkc/pysctransform.git
-----------messages start----------
Collecting git+https://github.com/saketkc/pysctransform.git
Cloning https://github.com/saketkc/pysctransform.git to /private/var/folders/5g/_ftzsf6n2695r2xbd78d0b4m0000gq/T/pip-req-build-5g2te194
Running command git clone --filter=blob:none --quiet https://github.com/saketkc/pysctransform.git /private/var/folders/5g/_ftzsf6n2695r2xbd78d0b4m0000gq/T/pip-req-build-5g2te194
Resolved https://github.com/saketkc/pysctransform.git to commit d14af48
Preparing metadata (setup.py) ... error
error: subprocess-exited-with-error
× python setup.py egg_info did not run successfully.
│ exit code: 1
╰─> [124 lines of output]
/Users/yuhoulin/anaconda3/envs/scanpy/lib/python3.11/site-packages/setuptools/init.py:84: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated.
!!
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.
-------------------message end-----------------
I then tried:
pip install git+https://github.com/saketkc/pysctransform.git --use-pep517
-------------------message start------------------
Collecting git+https://github.com/saketkc/pysctransform.git
Cloning https://github.com/saketkc/pysctransform.git to /private/var/folders/5g/_ftzsf6n2695r2xbd78d0b4m0000gq/T/pip-req-build-oy2horsc
Running command git clone --filter=blob:none --quiet https://github.com/saketkc/pysctransform.git /private/var/folders/5g/_ftzsf6n2695r2xbd78d0b4m0000gq/T/pip-req-build-oy2horsc
Resolved https://github.com/saketkc/pysctransform.git to commit d14af48
Installing build dependencies ... done
Getting requirements to build wheel ... done
Installing backend dependencies ... error
error: subprocess-exited-with-error
× pip subprocess to install backend dependencies did not run successfully.
│ exit code: 1
╰─> [115 lines of output]
Collecting KDEpy>=1.1.0
Using cached KDEpy-1.1.5-cp311-cp311-macosx_11_0_arm64.whl
Collecting patsy>=0.5.1
Using cached patsy-0.5.3-py2.py3-none-any.whl (233 kB)
Collecting pandas>=1.3.0
Obtaining dependency information for pandas>=1.3.0 from https://files.pythonhosted.org/packages/e5/cd/c941b51e95992968e3e8abc7180f33b952478abd6943062051517a808db7/pandas-2.1.0-cp311-cp311-macosx_11_0_arm64.whl.metadata
Using cached pandas-2.1.0-cp311-cp311-macosx_11_0_arm64.whl.metadata (18 kB)
Collecting matplotlib>=3.4.2
Obtaining dependency information for matplotlib>=3.4.2 from https://files.pythonhosted.org/packages/f6/22/9c31044ff7339c63727a135872e5cb59564f11625372a81c3eebf148f4af/matplotlib-3.7.2-cp311-cp311-macosx_11_0_arm64.whl.metadata
Using cached matplotlib-3.7.2-cp311-cp311-macosx_11_0_arm64.whl.metadata (5.6 kB)
Collecting numpy>=1.21.0
Obtaining dependency information for numpy>=1.21.0 from https://files.pythonhosted.org/packages/86/a1/b8ef999c32f26a97b5f714887e21f96c12ae99a38583a0a96e65283ac0a1/numpy-1.25.2-cp311-cp311-macosx_11_0_arm64.whl.metadata
Using cached numpy-1.25.2-cp311-cp311-macosx_11_0_arm64.whl.metadata (5.6 kB)
Collecting adjustText>=0.7.3
Using cached adjustText-0.8-py3-none-any.whl (9.1 kB)
Collecting scipy>=1.7.0
Obtaining dependency information for scipy>=1.7.0 from https://files.pythonhosted.org/packages/2a/12/62804d63514ecd9d2ecb73497c3e38094f9139bc60b0353b653253d106bb/scipy-1.11.2-cp311-cp311-macosx_12_0_arm64.whl.metadata
Using cached scipy-1.11.2-cp311-cp311-macosx_12_0_arm64.whl.metadata (146 kB)
Collecting scikit-learn>=0.24
Obtaining dependency information for scikit-learn>=0.24 from https://files.pythonhosted.org/packages/18/36/60b58b6199547b7b46be03e05508d053162fbce146639bfc65609fa49b23/scikit_learn-1.3.0-cp311-cp311-macosx_12_0_arm64.whl.metadata
Using cached scikit_learn-1.3.0-cp311-cp311-macosx_12_0_arm64.whl.metadata (11 kB)
Collecting tqdm>=4.61.2
Obtaining dependency information for tqdm>=4.61.2 from https://files.pythonhosted.org/packages/00/e5/f12a80907d0884e6dff9c16d0c0114d81b8cd07dc3ae54c5e962cc83037e/tqdm-4.66.1-py3-none-any.whl.metadata
Using cached tqdm-4.66.1-py3-none-any.whl.metadata (57 kB)
Collecting statsmodels>=0.12.2
Using cached statsmodels-0.14.0-cp311-cp311-macosx_11_0_arm64.whl (9.4 MB)
Collecting scanpy==1.7.2
Using cached scanpy-1.7.2-py3-none-any.whl (10.3 MB)
Collecting anndata>=0.7.4 (from scanpy==1.7.2)
Obtaining dependency information for anndata>=0.7.4 from https://files.pythonhosted.org/packages/a7/ee/767a05c299d95b438ef9c8ab6dbc15896cfb9121cf4327fe1da160a45343/anndata-0.9.2-py3-none-any.whl.metadata
Using cached anndata-0.9.2-py3-none-any.whl.metadata (6.1 kB)
Collecting seaborn (from scanpy==1.7.2)
Using cached seaborn-0.12.2-py3-none-any.whl (293 kB)
Collecting h5py>=2.10.0 (from scanpy==1.7.2)
Obtaining dependency information for h5py>=2.10.0 from https://files.pythonhosted.org/packages/37/82/859d9fc800a316e692bd040437d45613512b43d49fb0435c5bbab9e71511/h5py-3.9.0-cp311-cp311-macosx_11_0_arm64.whl.metadata
Using cached h5py-3.9.0-cp311-cp311-macosx_11_0_arm64.whl.metadata (2.5 kB)
Collecting tables (from scanpy==1.7.2)
Using cached tables-3.8.0.tar.gz (8.0 MB)
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'error'
error: subprocess-exited-with-error
note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error
× pip subprocess to install backend dependencies did not run successfully.
│ exit code: 1
╰─> See above for output.
note: This error originates from a subprocess, and is likely not a problem with pip.
-------------------message end-----------------
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