problem installing v1.2

hi i just tried the following manually:

ensured i was starting fresh

conda clean --all
pip cache purge

create a new environment

conda create --name test "python=3.10"
conda activate test

install palantir

pip install palantir

And this is what happened:

(test)jovyan@jupyter-zktuong:~$ pip install palantir
Collecting palantir
  Downloading palantir-1.2-py3-none-any.whl (27 kB)
Collecting numpy>=1.14.2
  Downloading numpy-1.24.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (17.3 MB)
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Collecting scikit-learn
  Downloading scikit_learn-1.2.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (9.6 MB)
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Collecting tables>=3.4.2
  Downloading tables-3.8.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (6.5 MB)
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Collecting seaborn>=0.8.1
  Downloading seaborn-0.12.2-py3-none-any.whl (293 kB)
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Collecting scanpy>=1.6.0
  Downloading scanpy-1.9.3-py3-none-any.whl (2.0 MB)
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Collecting pygam
  Downloading pygam-0.9.0-py3-none-any.whl (522 kB)
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Collecting joblib
  Downloading joblib-1.2.0-py3-none-any.whl (297 kB)
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Collecting pandas>=0.22.0
  Downloading pandas-1.5.3-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (12.1 MB)
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Collecting scipy>=1.3
  Downloading scipy-1.10.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (34.4 MB)
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Collecting tzlocal
  Downloading tzlocal-4.3-py3-none-any.whl (20 kB)
Collecting cmake
  Downloading cmake-3.26.0-py2.py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (24.0 MB)
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Collecting fcsparser>=0.1.2
  Downloading fcsparser-0.2.4-py3-none-any.whl (5.0 MB)
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Collecting PhenoGraph>=1.5.3
  Downloading PhenoGraph-1.5.7-py3-none-any.whl (159 kB)
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Collecting networkx>=2.1
  Downloading networkx-3.0-py3-none-any.whl (2.0 MB)
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Collecting Cython
  Downloading Cython-0.29.33-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_24_x86_64.whl (1.9 MB)
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Collecting matplotlib>=2.2.2
  Downloading matplotlib-3.7.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.6 MB)
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Requirement already satisfied: six in ./my-conda-envs/test/lib/python3.10/site-packages (from fcsparser>=0.1.2->palantir) (1.16.0)
Requirement already satisfied: setuptools in ./my-conda-envs/test/lib/python3.10/site-packages (from fcsparser>=0.1.2->palantir) (67.6.0)
Collecting pillow>=6.2.0
  Downloading Pillow-9.4.0-cp310-cp310-manylinux_2_28_x86_64.whl (3.4 MB)
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Collecting cycler>=0.10
  Downloading cycler-0.11.0-py3-none-any.whl (6.4 kB)
Requirement already satisfied: python-dateutil>=2.7 in ./my-conda-envs/test/lib/python3.10/site-packages (from matplotlib>=2.2.2->palantir) (2.8.2)
Requirement already satisfied: packaging>=20.0 in ./my-conda-envs/test/lib/python3.10/site-packages (from matplotlib>=2.2.2->palantir) (23.0)
Collecting pyparsing>=2.3.1
  Downloading pyparsing-3.0.9-py3-none-any.whl (98 kB)
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Collecting kiwisolver>=1.0.1
  Downloading kiwisolver-1.4.4-cp310-cp310-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (1.6 MB)
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Collecting contourpy>=1.0.1
  Downloading contourpy-1.0.7-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (300 kB)
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Collecting fonttools>=4.22.0
  Downloading fonttools-4.39.2-py3-none-any.whl (1.0 MB)
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Collecting pytz>=2020.1
  Downloading pytz-2022.7.1-py2.py3-none-any.whl (499 kB)
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Collecting leidenalg>=0.8.2
  Downloading leidenalg-0.9.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.3 MB)
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Requirement already satisfied: psutil>4 in ./my-conda-envs/test/lib/python3.10/site-packages (from PhenoGraph>=1.5.3->palantir) (5.9.4)
Collecting patsy
  Downloading patsy-0.5.3-py2.py3-none-any.whl (233 kB)
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Collecting anndata>=0.7.4
  Downloading anndata-0.8.0-py3-none-any.whl (96 kB)
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Collecting tqdm
  Downloading tqdm-4.65.0-py3-none-any.whl (77 kB)
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Collecting natsort
  Downloading natsort-8.3.1-py3-none-any.whl (38 kB)
Collecting session-info
  Downloading session_info-1.0.0.tar.gz (24 kB)
  Preparing metadata (setup.py) ... done
Collecting h5py>=3
  Downloading h5py-3.8.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.6 MB)
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Collecting numba>=0.41.0
  Downloading numba-0.56.4-cp310-cp310-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (3.5 MB)
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Collecting umap-learn>=0.3.10
  Downloading umap-learn-0.5.3.tar.gz (88 kB)
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  Preparing metadata (setup.py) ... done
Collecting statsmodels>=0.10.0rc2
  Downloading statsmodels-0.13.5-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (9.9 MB)
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Collecting threadpoolctl>=2.0.0
  Downloading threadpoolctl-3.1.0-py3-none-any.whl (14 kB)
Collecting numexpr>=2.6.2
  Downloading numexpr-2.8.4-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (381 kB)
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Collecting py-cpuinfo
  Downloading py_cpuinfo-9.0.0-py3-none-any.whl (22 kB)
Collecting blosc2~=2.0.0
  Downloading blosc2-2.0.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.9 MB)
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Collecting progressbar2<5.0.0,>=4.2.0
  Downloading progressbar2-4.2.0-py2.py3-none-any.whl (27 kB)
Collecting pytz-deprecation-shim
  Downloading pytz_deprecation_shim-0.1.0.post0-py2.py3-none-any.whl (15 kB)
Collecting msgpack
  Downloading msgpack-1.0.5-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (316 kB)
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Collecting igraph<0.11,>=0.10.0
  Downloading igraph-0.10.4-cp39-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.3 MB)
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Collecting llvmlite<0.40,>=0.39.0dev0
  Downloading llvmlite-0.39.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (34.6 MB)
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Collecting numba>=0.41.0
  Downloading numba-0.56.3-cp310-cp310-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (3.5 MB)
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  Downloading numba-0.56.2-cp310-cp310-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (3.5 MB)
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  Downloading numba-0.56.0-cp310-cp310-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (3.5 MB)
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  Downloading numba-0.55.2-cp310-cp310-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (3.4 MB)
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  Downloading numba-0.55.1-1-cp310-cp310-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (3.3 MB)
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Collecting llvmlite<0.39,>=0.38.0rc1
  Downloading llvmlite-0.38.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (34.5 MB)
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Collecting numba>=0.41.0
  Downloading numba-0.55.0-cp310-cp310-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (3.3 MB)
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  Downloading numba-0.51.2.tar.gz (2.1 MB)
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  Preparing metadata (setup.py) ... done
Collecting llvmlite<0.35,>=0.34.0.dev0
  Downloading llvmlite-0.34.0.tar.gz (107 kB)
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  Preparing metadata (setup.py) ... done
Collecting python-utils>=3.0.0
  Downloading python_utils-3.5.2-py2.py3-none-any.whl (24 kB)
Collecting pynndescent>=0.5
  Downloading pynndescent-0.5.8.tar.gz (1.1 MB)
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  Preparing metadata (setup.py) ... done
Collecting tzdata
  Downloading tzdata-2022.7-py2.py3-none-any.whl (340 kB)
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Collecting stdlib_list
  Downloading stdlib_list-0.8.0-py3-none-any.whl (63 kB)
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Collecting texttable>=1.6.2
  Downloading texttable-1.6.7-py2.py3-none-any.whl (10 kB)
Building wheels for collected packages: numba, umap-learn, session-info, llvmlite, pynndescent
  Building wheel for numba (setup.py) ... error
  error: subprocess-exited-with-error

  × python setup.py bdist_wheel did not run successfully.
  │ exit code: 1
  ╰─> [8 lines of output]
      Traceback (most recent call last):
        File "<string>", line 2, in <module>
        File "<pip-setuptools-caller>", line 34, in <module>
        File "/tmp/pip-install-6zouwcen/numba_3294b22b9dac4af6be0413468fd97588/setup.py", line 354, in <module>
          metadata['ext_modules'] = get_ext_modules()
        File "/tmp/pip-install-6zouwcen/numba_3294b22b9dac4af6be0413468fd97588/setup.py", line 87, in get_ext_modules
          import numpy.distutils.misc_util as np_misc
      ModuleNotFoundError: No module named 'numpy'
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for numba
  Running setup.py clean for numba
  error: subprocess-exited-with-error

  × python setup.py clean did not run successfully.
  │ exit code: 1
  ╰─> [8 lines of output]
      Traceback (most recent call last):
        File "<string>", line 2, in <module>
        File "<pip-setuptools-caller>", line 34, in <module>
        File "/tmp/pip-install-6zouwcen/numba_3294b22b9dac4af6be0413468fd97588/setup.py", line 354, in <module>
          metadata['ext_modules'] = get_ext_modules()
        File "/tmp/pip-install-6zouwcen/numba_3294b22b9dac4af6be0413468fd97588/setup.py", line 87, in get_ext_modules
          import numpy.distutils.misc_util as np_misc
      ModuleNotFoundError: No module named 'numpy'
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed cleaning build dir for numba
  Building wheel for umap-learn (setup.py) ... done
  Created wheel for umap-learn: filename=umap_learn-0.5.3-py3-none-any.whl size=82816 sha256=62b4ae7f1943097d7214539513a762123870baff3fc725ca88ea1f7d1876a18a
  Stored in directory: /home/jovyan/.cache/pip/wheels/a0/e8/c6/a37ea663620bd5200ea1ba0907ab3c217042c1d035ef606acc
  Building wheel for session-info (setup.py) ... done
  Created wheel for session-info: filename=session_info-1.0.0-py3-none-any.whl size=8026 sha256=5c0cfd7c28189d3d3fe972a9b8520cad99266551228d918437d6eee2fa4688c0
  Stored in directory: /home/jovyan/.cache/pip/wheels/6a/aa/b9/eb5d4031476ec10802795b97ccf937b9bd998d68a9b268765a
  Building wheel for llvmlite (setup.py) ... error
  error: subprocess-exited-with-error

  × python setup.py bdist_wheel did not run successfully.
  │ exit code: 1
  ╰─> [26 lines of output]
      running bdist_wheel
      /home/jovyan/my-conda-envs/test/bin/python3.1 /tmp/pip-install-6zouwcen/llvmlite_b86444259f7a45ebb3f94dd26342045d/ffi/build.py
      LLVM version... Traceback (most recent call last):
        File "/tmp/pip-install-6zouwcen/llvmlite_b86444259f7a45ebb3f94dd26342045d/ffi/build.py", line 105, in main_posix
          out = subprocess.check_output([llvm_config, '--version'])
        File "/home/jovyan/my-conda-envs/test/lib/python3.10/subprocess.py", line 421, in check_output
          return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
        File "/home/jovyan/my-conda-envs/test/lib/python3.10/subprocess.py", line 503, in run
          with Popen(*popenargs, **kwargs) as process:
        File "/home/jovyan/my-conda-envs/test/lib/python3.10/subprocess.py", line 971, in __init__
          self._execute_child(args, executable, preexec_fn, close_fds,
        File "/home/jovyan/my-conda-envs/test/lib/python3.10/subprocess.py", line 1847, in _execute_child
          raise child_exception_type(errno_num, err_msg, err_filename)
      FileNotFoundError: [Errno 2] No such file or directory: 'llvm-config'

      During handling of the above exception, another exception occurred:

      Traceback (most recent call last):
        File "/tmp/pip-install-6zouwcen/llvmlite_b86444259f7a45ebb3f94dd26342045d/ffi/build.py", line 191, in <module>
          main()
        File "/tmp/pip-install-6zouwcen/llvmlite_b86444259f7a45ebb3f94dd26342045d/ffi/build.py", line 181, in main
          main_posix('linux', '.so')
        File "/tmp/pip-install-6zouwcen/llvmlite_b86444259f7a45ebb3f94dd26342045d/ffi/build.py", line 107, in main_posix
          raise RuntimeError("%s failed executing, please point LLVM_CONFIG "
      RuntimeError: llvm-config failed executing, please point LLVM_CONFIG to the path for llvm-config
      error: command '/home/jovyan/my-conda-envs/test/bin/python3.1' failed with exit code 1
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for llvmlite
  Running setup.py clean for llvmlite
  Building wheel for pynndescent (setup.py) ... done
  Created wheel for pynndescent: filename=pynndescent-0.5.8-py3-none-any.whl size=55496 sha256=8a7e15d00e0f3953b38f35e4f71b0245d7776f1ec542eb47d360634e3408c2e8
  Stored in directory: /home/jovyan/.cache/pip/wheels/f8/5c/b4/a06301605095861524c1c7268a0d445b3a4c50292ce3bec24c
Successfully built umap-learn session-info pynndescent
Failed to build numba llvmlite
Installing collected packages: texttable, stdlib_list, pytz, py-cpuinfo, msgpack, cmake, tzdata, tqdm, threadpoolctl, session-info, python-utils, pyparsing, pillow, numpy, networkx, natsort, llvmlite, kiwisolver, joblib, igraph, fonttools, Cython, cycler, blosc2, scipy, pytz-deprecation-shim, progressbar2, patsy, pandas, numexpr, numba, leidenalg, h5py, contourpy, tzlocal, tables, statsmodels, scikit-learn, pygam, matplotlib, fcsparser, anndata, seaborn, pynndescent, PhenoGraph, umap-learn, scanpy, palantir
  Running setup.py install for llvmlite ... error
  error: subprocess-exited-with-error

  × Running setup.py install for llvmlite did not run successfully.
  │ exit code: 1
  ╰─> [31 lines of output]
      running install
      /home/jovyan/my-conda-envs/test/lib/python3.10/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
        warnings.warn(
      running build
      got version from file /tmp/pip-install-6zouwcen/llvmlite_b86444259f7a45ebb3f94dd26342045d/llvmlite/_version.py {'version': '0.34.0', 'full': 'c5889c9e98c6b19d5d85ebdd982d64a03931f8e2'}
      running build_ext
      /home/jovyan/my-conda-envs/test/bin/python3.1 /tmp/pip-install-6zouwcen/llvmlite_b86444259f7a45ebb3f94dd26342045d/ffi/build.py
      LLVM version... Traceback (most recent call last):
        File "/tmp/pip-install-6zouwcen/llvmlite_b86444259f7a45ebb3f94dd26342045d/ffi/build.py", line 105, in main_posix
          out = subprocess.check_output([llvm_config, '--version'])
        File "/home/jovyan/my-conda-envs/test/lib/python3.10/subprocess.py", line 421, in check_output
          return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
        File "/home/jovyan/my-conda-envs/test/lib/python3.10/subprocess.py", line 503, in run
          with Popen(*popenargs, **kwargs) as process:
        File "/home/jovyan/my-conda-envs/test/lib/python3.10/subprocess.py", line 971, in __init__
          self._execute_child(args, executable, preexec_fn, close_fds,
        File "/home/jovyan/my-conda-envs/test/lib/python3.10/subprocess.py", line 1847, in _execute_child
          raise child_exception_type(errno_num, err_msg, err_filename)
      FileNotFoundError: [Errno 2] No such file or directory: 'llvm-config'

      During handling of the above exception, another exception occurred:

      Traceback (most recent call last):
        File "/tmp/pip-install-6zouwcen/llvmlite_b86444259f7a45ebb3f94dd26342045d/ffi/build.py", line 191, in <module>
          main()
        File "/tmp/pip-install-6zouwcen/llvmlite_b86444259f7a45ebb3f94dd26342045d/ffi/build.py", line 181, in main
          main_posix('linux', '.so')
        File "/tmp/pip-install-6zouwcen/llvmlite_b86444259f7a45ebb3f94dd26342045d/ffi/build.py", line 107, in main_posix
          raise RuntimeError("%s failed executing, please point LLVM_CONFIG "
      RuntimeError: llvm-config failed executing, please point LLVM_CONFIG to the path for llvm-config
      error: command '/home/jovyan/my-conda-envs/test/bin/python3.1' failed with exit code 1
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
error: legacy-install-failure

× Encountered error while trying to install package.
╰─> llvmlite

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

My OS info:

(test)jovyan@jupyter-zktuong:~$ lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description:    Ubuntu 20.04.1 LTS
Release:        20.04
Codename:       focal

some update - i think the reason is the numpy/numba/llvm conflict caused in the numpy version required by pygam vs scanpy:

(test)jovyan@jupyter-zktuong:~$ pip install "numpy>=1.14.2"
Requirement already satisfied: numpy>=1.14.2 in ./my-conda-envs/test/lib/python3.10/site-packages (1.24.2)

(test)jovyan@jupyter-zktuong:~$ pip install "pandas>=0.22.0"
Collecting pandas>=0.22.0
  Using cached pandas-1.5.3-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (12.1 MB)
Requirement already satisfied: pytz>=2020.1 in ./my-conda-envs/test/lib/python3.10/site-packages (from pandas>=0.22.0) (2022.7.1)
Requirement already satisfied: numpy>=1.21.0 in ./my-conda-envs/test/lib/python3.10/site-packages (from pandas>=0.22.0) (1.24.2)
Requirement already satisfied: python-dateutil>=2.8.1 in ./my-conda-envs/test/lib/python3.10/site-packages (from pandas>=0.22.0) (2.8.2)
Requirement already satisfied: six>=1.5 in ./my-conda-envs/test/lib/python3.10/site-packages (from python-dateutil>=2.8.1->pandas>=0.22.0) (1.16.0)
Installing collected packages: pandas
Successfully installed pandas-1.5.3

(test)jovyan@jupyter-zktuong:~$ pip install "scipy>=1.3"
Requirement already satisfied: scipy>=1.3 in ./my-conda-envs/test/lib/python3.10/site-packages (1.10.1)
Requirement already satisfied: numpy<1.27.0,>=1.19.5 in ./my-conda-envs/test/lib/python3.10/site-packages (from scipy>=1.3) (1.24.2)

(test)jovyan@jupyter-zktuong:~$ pip install "networkx>=2.1"
Requirement already satisfied: networkx>=2.1 in ./my-conda-envs/test/lib/python3.10/site-packages (3.0)

(test)jovyan@jupyter-zktuong:~$ pip install "scikit-learn"
Requirement already satisfied: scikit-learn in ./my-conda-envs/test/lib/python3.10/site-packages (1.2.2)
Requirement already satisfied: numpy>=1.17.3 in ./my-conda-envs/test/lib/python3.10/site-packages (from scikit-learn) (1.24.2)
Requirement already satisfied: threadpoolctl>=2.0.0 in ./my-conda-envs/test/lib/python3.10/site-packages (from scikit-learn) (3.1.0)
Requirement already satisfied: joblib>=1.1.1 in ./my-conda-envs/test/lib/python3.10/site-packages (from scikit-learn) (1.2.0)
Requirement already satisfied: scipy>=1.3.2 in ./my-conda-envs/test/lib/python3.10/site-packages (from scikit-learn) (1.10.1)
(test)jovyan@jupyter-zktuong:~$ pip install "joblib"
Requirement already satisfied: joblib in ./my-conda-envs/test/lib/python3.10/site-packages (1.2.0)

(test)jovyan@jupyter-zktuong:~$ pip install "fcsparser>=0.1.2"
Collecting fcsparser>=0.1.2
  Using cached fcsparser-0.2.4-py3-none-any.whl (5.0 MB)
Requirement already satisfied: numpy in ./my-conda-envs/test/lib/python3.10/site-packages (from fcsparser>=0.1.2) (1.24.2)
Requirement already satisfied: setuptools in ./my-conda-envs/test/lib/python3.10/site-packages (from fcsparser>=0.1.2) (67.6.0)
Requirement already satisfied: pandas in ./my-conda-envs/test/lib/python3.10/site-packages (from fcsparser>=0.1.2) (1.5.3)
Requirement already satisfied: six in ./my-conda-envs/test/lib/python3.10/site-packages (from fcsparser>=0.1.2) (1.16.0)
Requirement already satisfied: pytz>=2020.1 in ./my-conda-envs/test/lib/python3.10/site-packages (from pandas->fcsparser>=0.1.2) (2022.7.1)
Requirement already satisfied: python-dateutil>=2.8.1 in ./my-conda-envs/test/lib/python3.10/site-packages (from pandas->fcsparser>=0.1.2) (2.8.2)
Installing collected packages: fcsparser
Successfully installed fcsparser-0.2.4

(test)jovyan@jupyter-zktuong:~$ pip install "PhenoGraph>=1.5.3"
Requirement already satisfied: PhenoGraph>=1.5.3 in ./my-conda-envs/test/lib/python3.10/site-packages (1.5.7)
Requirement already satisfied: scipy>=1.5.1 in ./my-conda-envs/test/lib/python3.10/site-packages (from PhenoGraph>=1.5.3) (1.10.1)
Requirement already satisfied: setuptools>=18.0.1 in ./my-conda-envs/test/lib/python3.10/site-packages (from PhenoGraph>=1.5.3) (67.6.0)
Requirement already satisfied: psutil>4 in ./my-conda-envs/test/lib/python3.10/site-packages (from PhenoGraph>=1.5.3) (5.9.4)
Requirement already satisfied: numpy>=1.12 in ./my-conda-envs/test/lib/python3.10/site-packages (from PhenoGraph>=1.5.3) (1.24.2)
Requirement already satisfied: scikit-learn>=0.17 in ./my-conda-envs/test/lib/python3.10/site-packages (from PhenoGraph>=1.5.3) (1.2.2)
Requirement already satisfied: leidenalg>=0.8.2 in ./my-conda-envs/test/lib/python3.10/site-packages (from PhenoGraph>=1.5.3) (0.9.1)
Requirement already satisfied: igraph<0.11,>=0.10.0 in ./my-conda-envs/test/lib/python3.10/site-packages (from leidenalg>=0.8.2->PhenoGraph>=1.5.3) (0.10.4)
Requirement already satisfied: threadpoolctl>=2.0.0 in ./my-conda-envs/test/lib/python3.10/site-packages (from scikit-learn>=0.17->PhenoGraph>=1.5.3) (3.1.0)
Requirement already satisfied: joblib>=1.1.1 in ./my-conda-envs/test/lib/python3.10/site-packages (from scikit-learn>=0.17->PhenoGraph>=1.5.3) (1.2.0)
Requirement already satisfied: texttable>=1.6.2 in ./my-conda-envs/test/lib/python3.10/site-packages (from igraph<0.11,>=0.10.0->leidenalg>=0.8.2->PhenoGraph>=1.5.3) (1.6.7)

(test)jovyan@jupyter-zktuong:~$ pip install "tables>=3.4.2"
Collecting tables>=3.4.2
  Using cached tables-3.8.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (6.5 MB)
Requirement already satisfied: cython>=0.29.21 in ./my-conda-envs/test/lib/python3.10/site-packages (from tables>=3.4.2) (0.29.33)
Requirement already satisfied: numpy>=1.19.0 in ./my-conda-envs/test/lib/python3.10/site-packages (from tables>=3.4.2) (1.24.2)
Requirement already satisfied: py-cpuinfo in ./my-conda-envs/test/lib/python3.10/site-packages (from tables>=3.4.2) (9.0.0)
Collecting blosc2~=2.0.0
  Using cached blosc2-2.0.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.9 MB)
Requirement already satisfied: numexpr>=2.6.2 in ./my-conda-envs/test/lib/python3.10/site-packages (from tables>=3.4.2) (2.8.4)
Requirement already satisfied: packaging in ./my-conda-envs/test/lib/python3.10/site-packages (from tables>=3.4.2) (23.0)
Requirement already satisfied: msgpack in ./my-conda-envs/test/lib/python3.10/site-packages (from blosc2~=2.0.0->tables>=3.4.2) (1.0.5)
Installing collected packages: blosc2, tables
Successfully installed blosc2-2.0.0 tables-3.8.0

(test)jovyan@jupyter-zktuong:~$ pip install "Cython"
Requirement already satisfied: Cython in ./my-conda-envs/test/lib/python3.10/site-packages (0.29.33)

(test)jovyan@jupyter-zktuong:~$ pip install "cmake"
Requirement already satisfied: cmake in ./my-conda-envs/test/lib/python3.10/site-packages (3.26.0)

(test)jovyan@jupyter-zktuong:~$ pip install "matplotlib>=2.2.2"
Collecting matplotlib>=2.2.2
  Using cached matplotlib-3.7.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.6 MB)
Collecting fonttools>=4.22.0
  Using cached fonttools-4.39.2-py3-none-any.whl (1.0 MB)
Requirement already satisfied: pyparsing>=2.3.1 in ./my-conda-envs/test/lib/python3.10/site-packages (from matplotlib>=2.2.2) (3.0.9)
Collecting kiwisolver>=1.0.1
  Using cached kiwisolver-1.4.4-cp310-cp310-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (1.6 MB)
Requirement already satisfied: packaging>=20.0 in ./my-conda-envs/test/lib/python3.10/site-packages (from matplotlib>=2.2.2) (23.0)
Collecting contourpy>=1.0.1
  Using cached contourpy-1.0.7-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (300 kB)
Requirement already satisfied: numpy>=1.20 in ./my-conda-envs/test/lib/python3.10/site-packages (from matplotlib>=2.2.2) (1.24.2)
Requirement already satisfied: python-dateutil>=2.7 in ./my-conda-envs/test/lib/python3.10/site-packages (from matplotlib>=2.2.2) (2.8.2)
Collecting cycler>=0.10
  Using cached cycler-0.11.0-py3-none-any.whl (6.4 kB)
Requirement already satisfied: pillow>=6.2.0 in ./my-conda-envs/test/lib/python3.10/site-packages (from matplotlib>=2.2.2) (9.4.0)
Requirement already satisfied: six>=1.5 in ./my-conda-envs/test/lib/python3.10/site-packages (from python-dateutil>=2.7->matplotlib>=2.2.2) (1.16.0)
Installing collected packages: kiwisolver, fonttools, cycler, contourpy, matplotlib
Successfully installed contourpy-1.0.7 cycler-0.11.0 fonttools-4.39.2 kiwisolver-1.4.4 matplotlib-3.7.1

(test)jovyan@jupyter-zktuong:~$ pip install "seaborn>=0.8.1"
Collecting seaborn>=0.8.1
  Using cached seaborn-0.12.2-py3-none-any.whl (293 kB)
Requirement already satisfied: pandas>=0.25 in ./my-conda-envs/test/lib/python3.10/site-packages (from seaborn>=0.8.1) (1.5.3)
Requirement already satisfied: matplotlib!=3.6.1,>=3.1 in ./my-conda-envs/test/lib/python3.10/site-packages (from seaborn>=0.8.1) (3.7.1)
Requirement already satisfied: numpy!=1.24.0,>=1.17 in ./my-conda-envs/test/lib/python3.10/site-packages (from seaborn>=0.8.1) (1.24.2)
Requirement already satisfied: fonttools>=4.22.0 in ./my-conda-envs/test/lib/python3.10/site-packages (from matplotlib!=3.6.1,>=3.1->seaborn>=0.8.1) (4.39.2)
Requirement already satisfied: pyparsing>=2.3.1 in ./my-conda-envs/test/lib/python3.10/site-packages (from matplotlib!=3.6.1,>=3.1->seaborn>=0.8.1) (3.0.9)
Requirement already satisfied: cycler>=0.10 in ./my-conda-envs/test/lib/python3.10/site-packages (from matplotlib!=3.6.1,>=3.1->seaborn>=0.8.1) (0.11.0)
Requirement already satisfied: packaging>=20.0 in ./my-conda-envs/test/lib/python3.10/site-packages (from matplotlib!=3.6.1,>=3.1->seaborn>=0.8.1) (23.0)
Requirement already satisfied: contourpy>=1.0.1 in ./my-conda-envs/test/lib/python3.10/site-packages (from matplotlib!=3.6.1,>=3.1->seaborn>=0.8.1) (1.0.7)
Requirement already satisfied: python-dateutil>=2.7 in ./my-conda-envs/test/lib/python3.10/site-packages (from matplotlib!=3.6.1,>=3.1->seaborn>=0.8.1) (2.8.2)
Requirement already satisfied: pillow>=6.2.0 in ./my-conda-envs/test/lib/python3.10/site-packages (from matplotlib!=3.6.1,>=3.1->seaborn>=0.8.1) (9.4.0)
Requirement already satisfied: kiwisolver>=1.0.1 in ./my-conda-envs/test/lib/python3.10/site-packages (from matplotlib!=3.6.1,>=3.1->seaborn>=0.8.1) (1.4.4)
Requirement already satisfied: pytz>=2020.1 in ./my-conda-envs/test/lib/python3.10/site-packages (from pandas>=0.25->seaborn>=0.8.1) (2022.7.1)
Requirement already satisfied: six>=1.5 in ./my-conda-envs/test/lib/python3.10/site-packages (from python-dateutil>=2.7->matplotlib!=3.6.1,>=3.1->seaborn>=0.8.1) (1.16.0)
Installing collected packages: seaborn
Successfully installed seaborn-0.12.2

(test)jovyan@jupyter-zktuong:~$ pip install "tzlocal"
Collecting tzlocal
  Using cached tzlocal-4.3-py3-none-any.whl (20 kB)
Requirement already satisfied: pytz-deprecation-shim in ./my-conda-envs/test/lib/python3.10/site-packages (from tzlocal) (0.1.0.post0)
Requirement already satisfied: tzdata in ./my-conda-envs/test/lib/python3.10/site-packages (from pytz-deprecation-shim->tzlocal) (2022.7)
Installing collected packages: tzlocal
Successfully installed tzlocal-4.3

(test)jovyan@jupyter-zktuong:~$ pip install "scanpy>=1.6.0"
Collecting scanpy>=1.6.0
  Using cached scanpy-1.9.3-py3-none-any.whl (2.0 MB)
Requirement already satisfied: seaborn in ./my-conda-envs/test/lib/python3.10/site-packages (from scanpy>=1.6.0) (0.12.2)
Collecting umap-learn>=0.3.10
  Using cached umap_learn-0.5.3-py3-none-any.whl
Requirement already satisfied: pandas>=1.0 in ./my-conda-envs/test/lib/python3.10/site-packages (from scanpy>=1.6.0) (1.5.3)
Requirement already satisfied: natsort in ./my-conda-envs/test/lib/python3.10/site-packages (from scanpy>=1.6.0) (8.3.1)
Collecting statsmodels>=0.10.0rc2
  Using cached statsmodels-0.13.5-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (9.9 MB)
Collecting h5py>=3
  Using cached h5py-3.8.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.6 MB)
Requirement already satisfied: patsy in ./my-conda-envs/test/lib/python3.10/site-packages (from scanpy>=1.6.0) (0.5.3)
Requirement already satisfied: session-info in ./my-conda-envs/test/lib/python3.10/site-packages (from scanpy>=1.6.0) (1.0.0)
Requirement already satisfied: networkx>=2.3 in ./my-conda-envs/test/lib/python3.10/site-packages (from scanpy>=1.6.0) (3.0)
Requirement already satisfied: numpy>=1.17.0 in ./my-conda-envs/test/lib/python3.10/site-packages (from scanpy>=1.6.0) (1.24.2)
Requirement already satisfied: scipy>=1.4 in ./my-conda-envs/test/lib/python3.10/site-packages (from scanpy>=1.6.0) (1.10.1)
Requirement already satisfied: packaging in ./my-conda-envs/test/lib/python3.10/site-packages (from scanpy>=1.6.0) (23.0)
Requirement already satisfied: matplotlib>=3.4 in ./my-conda-envs/test/lib/python3.10/site-packages (from scanpy>=1.6.0) (3.7.1)
Requirement already satisfied: scikit-learn>=0.22 in ./my-conda-envs/test/lib/python3.10/site-packages (from scanpy>=1.6.0) (1.2.2)
Requirement already satisfied: joblib in ./my-conda-envs/test/lib/python3.10/site-packages (from scanpy>=1.6.0) (1.2.0)
Requirement already satisfied: tqdm in ./my-conda-envs/test/lib/python3.10/site-packages (from scanpy>=1.6.0) (4.65.0)
Collecting anndata>=0.7.4
  Using cached anndata-0.8.0-py3-none-any.whl (96 kB)
Requirement already satisfied: numba>=0.41.0 in ./my-conda-envs/test/lib/python3.10/site-packages (from scanpy>=1.6.0) (0.56.4)
Requirement already satisfied: pillow>=6.2.0 in ./my-conda-envs/test/lib/python3.10/site-packages (from matplotlib>=3.4->scanpy>=1.6.0) (9.4.0)
Requirement already satisfied: pyparsing>=2.3.1 in ./my-conda-envs/test/lib/python3.10/site-packages (from matplotlib>=3.4->scanpy>=1.6.0) (3.0.9)
Requirement already satisfied: cycler>=0.10 in ./my-conda-envs/test/lib/python3.10/site-packages (from matplotlib>=3.4->scanpy>=1.6.0) (0.11.0)
Requirement already satisfied: contourpy>=1.0.1 in ./my-conda-envs/test/lib/python3.10/site-packages (from matplotlib>=3.4->scanpy>=1.6.0) (1.0.7)
Requirement already satisfied: python-dateutil>=2.7 in ./my-conda-envs/test/lib/python3.10/site-packages (from matplotlib>=3.4->scanpy>=1.6.0) (2.8.2)
Requirement already satisfied: kiwisolver>=1.0.1 in ./my-conda-envs/test/lib/python3.10/site-packages (from matplotlib>=3.4->scanpy>=1.6.0) (1.4.4)
Requirement already satisfied: fonttools>=4.22.0 in ./my-conda-envs/test/lib/python3.10/site-packages (from matplotlib>=3.4->scanpy>=1.6.0) (4.39.2)
Requirement already satisfied: setuptools in ./my-conda-envs/test/lib/python3.10/site-packages (from numba>=0.41.0->scanpy>=1.6.0) (67.6.0)
Requirement already satisfied: llvmlite<0.40,>=0.39.0dev0 in ./my-conda-envs/test/lib/python3.10/site-packages (from numba>=0.41.0->scanpy>=1.6.0) (0.39.1)
Collecting numpy>=1.17.0
  Using cached numpy-1.23.5-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (17.1 MB)
Requirement already satisfied: pytz>=2020.1 in ./my-conda-envs/test/lib/python3.10/site-packages (from pandas>=1.0->scanpy>=1.6.0) (2022.7.1)
Requirement already satisfied: threadpoolctl>=2.0.0 in ./my-conda-envs/test/lib/python3.10/site-packages (from scikit-learn>=0.22->scanpy>=1.6.0) (3.1.0)
Requirement already satisfied: six in ./my-conda-envs/test/lib/python3.10/site-packages (from patsy->scanpy>=1.6.0) (1.16.0)
Collecting pynndescent>=0.5
  Using cached pynndescent-0.5.8-py3-none-any.whl
Requirement already satisfied: stdlib-list in ./my-conda-envs/test/lib/python3.10/site-packages (from session-info->scanpy>=1.6.0) (0.8.0)
Installing collected packages: numpy, h5py, statsmodels, anndata, pynndescent, umap-learn, scanpy
  Attempting uninstall: numpy
    Found existing installation: numpy 1.24.2
    Uninstalling numpy-1.24.2:
      Successfully uninstalled numpy-1.24.2
ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
pygam 0.9.0 requires numpy<2.0.0,>=1.24.2, but you have numpy 1.23.5 which is incompatible.
Successfully installed anndata-0.8.0 h5py-3.8.0 numpy-1.23.5 pynndescent-0.5.8 scanpy-1.9.3 statsmodels-0.13.5 umap-learn-0.5.3

(test)jovyan@jupyter-zktuong:~$ pip install "pygam"
Requirement already satisfied: pygam in ./my-conda-envs/test/lib/python3.10/site-packages (0.9.0)
Requirement already satisfied: progressbar2<5.0.0,>=4.2.0 in ./my-conda-envs/test/lib/python3.10/site-packages (from pygam) (4.2.0)
Collecting numpy<2.0.0,>=1.24.2
  Using cached numpy-1.24.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (17.3 MB)
Requirement already satisfied: scipy<2.0.0,>=1.10.1 in ./my-conda-envs/test/lib/python3.10/site-packages (from pygam) (1.10.1)
Requirement already satisfied: python-utils>=3.0.0 in ./my-conda-envs/test/lib/python3.10/site-packages (from progressbar2<5.0.0,>=4.2.0->pygam) (3.5.2)
Installing collected packages: numpy
  Attempting uninstall: numpy
    Found existing installation: numpy 1.23.5
    Uninstalling numpy-1.23.5:
      Successfully uninstalled numpy-1.23.5
ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
numba 0.56.4 requires numpy<1.24,>=1.18, but you have numpy 1.24.2 which is incompatible.
Successfully installed numpy-1.24.2

dpeerlab / Palantir

problem installing v1.2 #102

ensured i was starting fresh

create a new environment

install palantir