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Installing dependencies: issue with molecule-tda #277

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Andrew-S-Rosen opened this issue Aug 4, 2022 · 15 comments
Open

Installing dependencies: issue with molecule-tda #277

Andrew-S-Rosen opened this issue Aug 4, 2022 · 15 comments

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@Andrew-S-Rosen
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Andrew-S-Rosen commented Aug 4, 2022 •
edited
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Hey Kevin,

I'm trying to install mofdscribe and all the dependencies. I'm having some trouble installing molecule-tda. I cloned the repo and pip install .'d it and got back the following. This is on WSL with Python 3.8. I'm not too familiar with poetry so am still trying to figure this one out.

Processing /mnt/c/Users/asros/github/molecule-tda
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... error
  error: subprocess-exited-with-error

  × Preparing metadata (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> [16 lines of output]
      Traceback (most recent call last):
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 363, in <module>
          main()
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 345, in main
          json_out['return_val'] = hook(**hook_input['kwargs'])
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 164, in prepare_metadata_for_build_wheel
          return hook(metadata_directory, config_settings)
        File "/tmp/pip-build-env-gobwb3l6/overlay/lib/python3.8/site-packages/poetry/core/masonry/api.py", line 44, in prepare_metadata_for_build_wheel
          builder = WheelBuilder(poetry)
        File "/tmp/pip-build-env-gobwb3l6/overlay/lib/python3.8/site-packages/poetry/core/masonry/builders/wheel.py", line 58, in __init__
          super(WheelBuilder, self).__init__(poetry, executable=executable)
        File "/tmp/pip-build-env-gobwb3l6/overlay/lib/python3.8/site-packages/poetry/core/masonry/builders/builder.py", line 85, in __init__
          self._module = Module(
        File "/tmp/pip-build-env-gobwb3l6/overlay/lib/python3.8/site-packages/poetry/core/masonry/utils/module.py", line 63, in __init__
          raise ModuleOrPackageNotFound(
      poetry.core.masonry.utils.module.ModuleOrPackageNotFound: No file/folder found for package molecule-tda
      [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.
@kjappelbaum
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Thanks for the feedback and sorry for the issues. Installation is indeed still a big issue as I'm waiting for a couple of PRs to be merged (e.g., #2, #202).

Currently, you need to go via the "refactor" branch on my fork for moltda:

mofdscribe/README.md

Lines 59 to 73 in 3a8ab66

To install in development mode, use the following:
```bash
$ git clone git+https://github.com/kjappelbaum/mofdscribe.git
$ cd mofdscribe
$ pip install -e .
```
if you want to use all utilities, you can use the `all` extra: `pip install -e ".[all]"`
We depend on many other external tools. Currently, you need to manually install (due to pending merges for conda-recipies):
- `conda install -c conda-forge raspa2 zeopp-lsmo`
- `moltda` from my refactor branch https://github.com/kjappelbaum/molecule-tda/tree/refactor
- `moffragmentor` from my private repository https://github.com/kjappelbaum/moffragmentor (which additionally requires `conda install -c conda-forge openbabel`)

(Unfortunately, I ran out of CI time this month and hence the actions are failing)

@Andrew-S-Rosen
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Ah, my mistake! I misread the instructions. For some reason, I thought you meant your fork was a refactor of the original. Oops...! Thanks!

@kjappelbaum
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In this case I should probably rewrite to make it clearer ;) Thx!

@Andrew-S-Rosen
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In hindsight, you were pretty clear. I just am over-eager in forking everything and then forked main by default instead. 😅

@Andrew-S-Rosen
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Andrew-S-Rosen commented Aug 4, 2022 •
edited
Loading

Closed this prematurely. I did pip install git+https://github.com/kjappelbaum/molecule-tda.git@refactor and got the following. I can try in a "genuine" Linux environment.

  Building wheel for diode (setup.py) ... error
  ERROR: Command errored out with exit status 1:
   command: /home/arosen/anaconda3/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-ge_8qp0t/diode_8aabb942e15f43dcbc868c8ea98ab730/setup.py'"'"'; __file__='"'"'/tmp/pip-install-ge_8qp0t/diode_8aabb942e15f43dcbc868c8ea98ab730/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-ruapmvlm
       cwd: /tmp/pip-install-ge_8qp0t/diode_8aabb942e15f43dcbc868c8ea98ab730/
  Complete output (79 lines):
  running bdist_wheel
  running build
  running build_py
  package init file 'bindings/python/__init__.py' not found (or not a regular file)
  running build_ext
  -- The C compiler identification is GNU 9.3.0
  -- The CXX compiler identification is GNU 9.3.0
  -- Check for working C compiler: /usr/bin/cc
  -- Check for working C compiler: /usr/bin/cc -- works
  -- Detecting C compiler ABI info
  -- Detecting C compiler ABI info - done
  -- Detecting C compile features
  -- Detecting C compile features - done
  -- Check for working CXX compiler: /usr/bin/c++
  -- Check for working CXX compiler: /usr/bin/c++ -- works
  -- Detecting CXX compiler ABI info
  -- Detecting CXX compiler ABI info - done
  -- Detecting CXX compile features
  -- Detecting CXX compile features - done
  CMake Warning at CMakeLists.txt:12 (find_package):
    By not providing "FindCGAL.cmake" in CMAKE_MODULE_PATH this project has
    asked CMake to find a package configuration file provided by "CGAL", but
    CMake did not find one.

    Could not find a package configuration file provided by "CGAL" with any of
    the following names:

      CGALConfig.cmake
      cgal-config.cmake

    Add the installation prefix of "CGAL" to CMAKE_PREFIX_PATH or set
    "CGAL_DIR" to a directory containing one of the above files.  If "CGAL"
    provides a separate development package or SDK, be sure it has been
    installed.


  CMake Error at CMakeLists.txt:13 (include):
    include called with wrong number of arguments.  include() only takes one
    file.


  -- pybind11 v2.6.2 dev1
  -- Found PythonInterp: /home/arosen/anaconda3/bin/python (found version "3.8.12")
  -- Found PythonLibs: /home/arosen/anaconda3/lib/libpython3.8.so
  -- Performing Test HAS_FLTO
  -- Performing Test HAS_FLTO - Success
  -- Configuring incomplete, errors occurred!
  See also "/tmp/pip-install-ge_8qp0t/diode_8aabb942e15f43dcbc868c8ea98ab730/build/temp.linux-x86_64-3.8/CMakeFiles/CMakeOutput.log".
  Traceback (most recent call last):
    File "<string>", line 1, in <module>
    File "/tmp/pip-install-ge_8qp0t/diode_8aabb942e15f43dcbc868c8ea98ab730/setup.py", line 60, in <module>
      setup(
    File "/home/arosen/anaconda3/lib/python3.8/site-packages/setuptools/__init__.py", line 153, in setup
      return distutils.core.setup(**attrs)
    File "/home/arosen/anaconda3/lib/python3.8/distutils/core.py", line 148, in setup
      dist.run_commands()
    File "/home/arosen/anaconda3/lib/python3.8/distutils/dist.py", line 966, in run_commands
      self.run_command(cmd)
    File "/home/arosen/anaconda3/lib/python3.8/distutils/dist.py", line 985, in run_command
      cmd_obj.run()
    File "/home/arosen/anaconda3/lib/python3.8/site-packages/wheel/bdist_wheel.py", line 299, in run
      self.run_command('build')
    File "/home/arosen/anaconda3/lib/python3.8/distutils/cmd.py", line 313, in run_command
      self.distribution.run_command(command)
    File "/home/arosen/anaconda3/lib/python3.8/distutils/dist.py", line 985, in run_command
      cmd_obj.run()
    File "/home/arosen/anaconda3/lib/python3.8/distutils/command/build.py", line 135, in run
      self.run_command(cmd_name)
    File "/home/arosen/anaconda3/lib/python3.8/distutils/cmd.py", line 313, in run_command
      self.distribution.run_command(command)
    File "/home/arosen/anaconda3/lib/python3.8/distutils/dist.py", line 985, in run_command
      cmd_obj.run()
    File "/tmp/pip-install-ge_8qp0t/diode_8aabb942e15f43dcbc868c8ea98ab730/setup.py", line 32, in run
      self.build_extension(ext)
    File "/tmp/pip-install-ge_8qp0t/diode_8aabb942e15f43dcbc868c8ea98ab730/setup.py", line 57, in build_extension
      subprocess.check_call(['cmake', ext.sourcedir] + cmake_args, cwd=self.build_temp, env=env)
    File "/home/arosen/anaconda3/lib/python3.8/subprocess.py", line 364, in check_call
      raise CalledProcessError(retcode, cmd)
  subprocess.CalledProcessError: Command '['cmake', '/tmp/pip-install-ge_8qp0t/diode_8aabb942e15f43dcbc868c8ea98ab730', '-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=/tmp/pip-install-ge_8qp0t/diode_8aabb942e15f43dcbc868c8ea98ab730/build/lib.linux-x86_64-3.8', '-DPYTHON_EXECUTABLE=/home/arosen/anaconda3/bin/python', '-Dbuild_examples=OFF', '-DCMAKE_BUILD_TYPE=Release']' returned non-zero exit status 1.
  ----------------------------------------
  ERROR: Failed building wheel for diode
  Running setup.py clean for diode
  Building wheel for dionysus (setup.py) ... error
  ERROR: Command errored out with exit status 1:
   command: /home/arosen/anaconda3/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-ge_8qp0t/dionysus_27ada80b946349d2951108aa99ef32a6/setup.py'"'"'; __file__='"'"'/tmp/pip-install-ge_8qp0t/dionysus_27ada80b946349d2951108aa99ef32a6/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-kx2w3_ch
       cwd: /tmp/pip-install-ge_8qp0t/dionysus_27ada80b946349d2951108aa99ef32a6/
  Complete output (77 lines):
  /home/arosen/anaconda3/lib/python3.8/site-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead
    warnings.warn(
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build/lib.linux-x86_64-3.8
  creating build/lib.linux-x86_64-3.8/dionysus
  copying bindings/python/dionysus/_version.py -> build/lib.linux-x86_64-3.8/dionysus
  copying bindings/python/dionysus/__init__.py -> build/lib.linux-x86_64-3.8/dionysus
  copying bindings/python/dionysus/plot.py -> build/lib.linux-x86_64-3.8/dionysus
  running build_ext
  -- The C compiler identification is GNU 9.3.0
  -- The CXX compiler identification is GNU 9.3.0
  -- Check for working C compiler: /usr/bin/cc
  -- Check for working C compiler: /usr/bin/cc -- works
  -- Detecting C compiler ABI info
  -- Detecting C compiler ABI info - done
  -- Detecting C compile features
  -- Detecting C compile features - done
  -- Check for working CXX compiler: /usr/bin/c++
  -- Check for working CXX compiler: /usr/bin/c++ -- works
  -- Detecting CXX compiler ABI info
  -- Detecting CXX compiler ABI info - done
  -- Detecting CXX compile features
  -- Detecting CXX compile features - done
  -- Could NOT find Boost (missing: Boost_INCLUDE_DIR)
  -- pybind11 v2.6.2 dev1
  -- Found PythonInterp: /home/arosen/anaconda3/bin/python (found version "3.8.12")
  -- Found PythonLibs: /home/arosen/anaconda3/lib/libpython3.8.so
  -- Performing Test HAS_FLTO
  -- Performing Test HAS_FLTO - Success
  CMake Error: The following variables are used in this project, but they are set to NOTFOUND.
  Please set them or make sure they are set and tested correctly in the CMake files:
  Boost_INCLUDE_DIR (ADVANCED)
     used as include directory in directory /tmp/pip-install-ge_8qp0t/dionysus_27ada80b946349d2951108aa99ef32a6
     used as include directory in directory /tmp/pip-install-ge_8qp0t/dionysus_27ada80b946349d2951108aa99ef32a6
     used as include directory in directory /tmp/pip-install-ge_8qp0t/dionysus_27ada80b946349d2951108aa99ef32a6/bindings/python
     used as include directory in directory /tmp/pip-install-ge_8qp0t/dionysus_27ada80b946349d2951108aa99ef32a6/bindings/python
     used as include directory in directory /tmp/pip-install-ge_8qp0t/dionysus_27ada80b946349d2951108aa99ef32a6/bindings/python
     used as include directory in directory /tmp/pip-install-ge_8qp0t/dionysus_27ada80b946349d2951108aa99ef32a6/bindings/python
     used as include directory in directory /tmp/pip-install-ge_8qp0t/dionysus_27ada80b946349d2951108aa99ef32a6/bindings/python/pybind11
     used as include directory in directory /tmp/pip-install-ge_8qp0t/dionysus_27ada80b946349d2951108aa99ef32a6/bindings/python/pybind11

  -- Configuring incomplete, errors occurred!
  See also "/tmp/pip-install-ge_8qp0t/dionysus_27ada80b946349d2951108aa99ef32a6/build/temp.linux-x86_64-3.8/CMakeFiles/CMakeOutput.log".
  Traceback (most recent call last):
    File "<string>", line 1, in <module>
    File "/tmp/pip-install-ge_8qp0t/dionysus_27ada80b946349d2951108aa99ef32a6/setup.py", line 67, in <module>
      setup(
    File "/home/arosen/anaconda3/lib/python3.8/site-packages/setuptools/__init__.py", line 153, in setup
      return distutils.core.setup(**attrs)
    File "/home/arosen/anaconda3/lib/python3.8/distutils/core.py", line 148, in setup
      dist.run_commands()
    File "/home/arosen/anaconda3/lib/python3.8/distutils/dist.py", line 966, in run_commands
      self.run_command(cmd)
    File "/home/arosen/anaconda3/lib/python3.8/distutils/dist.py", line 985, in run_command
      cmd_obj.run()
    File "/home/arosen/anaconda3/lib/python3.8/site-packages/wheel/bdist_wheel.py", line 299, in run
      self.run_command('build')
    File "/home/arosen/anaconda3/lib/python3.8/distutils/cmd.py", line 313, in run_command
      self.distribution.run_command(command)
    File "/home/arosen/anaconda3/lib/python3.8/distutils/dist.py", line 985, in run_command
      cmd_obj.run()
    File "/home/arosen/anaconda3/lib/python3.8/distutils/command/build.py", line 135, in run
      self.run_command(cmd_name)
    File "/home/arosen/anaconda3/lib/python3.8/distutils/cmd.py", line 313, in run_command
      self.distribution.run_command(command)
    File "/home/arosen/anaconda3/lib/python3.8/distutils/dist.py", line 985, in run_command
      cmd_obj.run()
    File "/tmp/pip-install-ge_8qp0t/dionysus_27ada80b946349d2951108aa99ef32a6/setup.py", line 39, in run
      self.build_extension(ext)
    File "/tmp/pip-install-ge_8qp0t/dionysus_27ada80b946349d2951108aa99ef32a6/setup.py", line 64, in build_extension
      subprocess.check_call(['cmake', ext.sourcedir] + cmake_args, cwd=self.build_temp, env=env)
    File "/home/arosen/anaconda3/lib/python3.8/subprocess.py", line 364, in check_call
      raise CalledProcessError(retcode, cmd)
  subprocess.CalledProcessError: Command '['cmake', '/tmp/pip-install-ge_8qp0t/dionysus_27ada80b946349d2951108aa99ef32a6', '-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=/tmp/pip-install-ge_8qp0t/dionysus_27ada80b946349d2951108aa99ef32a6/build/lib.linux-x86_64-3.8', '-DPYTHON_EXECUTABLE=/home/arosen/anaconda3/bin/python', '-Dbuild_examples=OFF', '-DCMAKE_BUILD_TYPE=Release']' returned non-zero exit status 1.
  ----------------------------------------
  ERROR: Failed building wheel for dionysus
  Running setup.py clean for dionysus
  Building wheel for pyclustering (setup.py) ... done
  Created wheel for pyclustering: filename=pyclustering-0.10.1.2-py3-none-any.whl size=2395121 sha256=a22b7350cd7eb6d1dde3d472af001a48b27c0f93f64ee8a8bb0aabca199f25fe
  Stored in directory: /home/arosen/.cache/pip/wheels/dc/25/8b/072b221a5cff4f04e7999d39ca1b6cb5dad702cc3e1da951d4
Successfully built moltda pyclustering
Failed to build diode dionysus
Installing collected packages: pyclustering, loguru, dionysus, diode, moltda
    Running setup.py install for dionysus ... /
error
    ERROR: Command errored out with exit status 1:
     command: /home/arosen/anaconda3/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-ge_8qp0t/dionysus_27ada80b946349d2951108aa99ef32a6/setup.py'"'"'; __file__='"'"'/tmp/pip-install-ge_8qp0t/dionysus_27ada80b946349d2951108aa99ef32a6/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-p5rrc2c3/install-record.txt --single-version-externally-managed --compile --install-headers /home/arosen/anaconda3/include/python3.8/dionysus
         cwd: /tmp/pip-install-ge_8qp0t/dionysus_27ada80b946349d2951108aa99ef32a6/
    Complete output (79 lines):
    /home/arosen/anaconda3/lib/python3.8/site-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead
      warnings.warn(
    running install
    running build
    running build_py
    creating build
    creating build/lib.linux-x86_64-3.8
    creating build/lib.linux-x86_64-3.8/dionysus
    copying bindings/python/dionysus/_version.py -> build/lib.linux-x86_64-3.8/dionysus    copying bindings/python/dionysus/__init__.py -> build/lib.linux-x86_64-3.8/dionysus    copying bindings/python/dionysus/plot.py -> build/lib.linux-x86_64-3.8/dionysus
    running build_ext
    -- The C compiler identification is GNU 9.3.0
    -- The CXX compiler identification is GNU 9.3.0
    -- Check for working C compiler: /usr/bin/cc
    -- Check for working C compiler: /usr/bin/cc -- works
    -- Detecting C compiler ABI info
    -- Detecting C compiler ABI info - done
    -- Detecting C compile features
    -- Detecting C compile features - done
    -- Check for working CXX compiler: /usr/bin/c++
    -- Check for working CXX compiler: /usr/bin/c++ -- works
    -- Detecting CXX compiler ABI info
    -- Detecting CXX compiler ABI info - done
    -- Detecting CXX compile features
    -- Detecting CXX compile features - done
    -- Could NOT find Boost (missing: Boost_INCLUDE_DIR)
    -- pybind11 v2.6.2 dev1
    -- Found PythonInterp: /home/arosen/anaconda3/bin/python (found version "3.8.12")
    -- Found PythonLibs: /home/arosen/anaconda3/lib/libpython3.8.so
    -- Performing Test HAS_FLTO
    -- Performing Test HAS_FLTO - Success
    CMake Error: The following variables are used in this project, but they are set to NOTFOUND.
    Please set them or make sure they are set and tested correctly in the CMake files:
    Boost_INCLUDE_DIR (ADVANCED)
       used as include directory in directory /tmp/pip-install-ge_8qp0t/dionysus_27ada80b946349d2951108aa99ef32a6
       used as include directory in directory /tmp/pip-install-ge_8qp0t/dionysus_27ada80b946349d2951108aa99ef32a6
       used as include directory in directory /tmp/pip-install-ge_8qp0t/dionysus_27ada80b946349d2951108aa99ef32a6/bindings/python
       used as include directory in directory /tmp/pip-install-ge_8qp0t/dionysus_27ada80b946349d2951108aa99ef32a6/bindings/python
       used as include directory in directory /tmp/pip-install-ge_8qp0t/dionysus_27ada80b946349d2951108aa99ef32a6/bindings/python
       used as include directory in directory /tmp/pip-install-ge_8qp0t/dionysus_27ada80b946349d2951108aa99ef32a6/bindings/python
       used as include directory in directory /tmp/pip-install-ge_8qp0t/dionysus_27ada80b946349d2951108aa99ef32a6/bindings/python/pybind11
       used as include directory in directory /tmp/pip-install-ge_8qp0t/dionysus_27ada80b946349d2951108aa99ef32a6/bindings/python/pybind11

    -- Configuring incomplete, errors occurred!
    See also "/tmp/pip-install-ge_8qp0t/dionysus_27ada80b946349d2951108aa99ef32a6/build/temp.linux-x86_64-3.8/CMakeFiles/CMakeOutput.log".
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-install-ge_8qp0t/dionysus_27ada80b946349d2951108aa99ef32a6/setup.py", line 67, in <module>
        setup(
      File "/home/arosen/anaconda3/lib/python3.8/site-packages/setuptools/__init__.py", line 153, in setup
        return distutils.core.setup(**attrs)
      File "/home/arosen/anaconda3/lib/python3.8/distutils/core.py", line 148, in setup        dist.run_commands()
      File "/home/arosen/anaconda3/lib/python3.8/distutils/dist.py", line 966, in run_commands
        self.run_command(cmd)
      File "/home/arosen/anaconda3/lib/python3.8/distutils/dist.py", line 985, in run_command
        cmd_obj.run()
      File "/home/arosen/anaconda3/lib/python3.8/site-packages/setuptools/command/install.py", line 61, in run
        return orig.install.run(self)
      File "/home/arosen/anaconda3/lib/python3.8/distutils/command/install.py", line 545, in run
        self.run_command('build')
      File "/home/arosen/anaconda3/lib/python3.8/distutils/cmd.py", line 313, in run_command
        self.distribution.run_command(command)
      File "/home/arosen/anaconda3/lib/python3.8/distutils/dist.py", line 985, in run_command
        cmd_obj.run()
      File "/home/arosen/anaconda3/lib/python3.8/distutils/command/build.py", line 135, in run
        self.run_command(cmd_name)
      File "/home/arosen/anaconda3/lib/python3.8/distutils/cmd.py", line 313, in run_command
        self.distribution.run_command(command)
      File "/home/arosen/anaconda3/lib/python3.8/distutils/dist.py", line 985, in run_command
        cmd_obj.run()
      File "/tmp/pip-install-ge_8qp0t/dionysus_27ada80b946349d2951108aa99ef32a6/setup.py", line 39, in run
        self.build_extension(ext)
      File "/tmp/pip-install-ge_8qp0t/dionysus_27ada80b946349d2951108aa99ef32a6/setup.py", line 64, in build_extension
        subprocess.check_call(['cmake', ext.sourcedir] + cmake_args, cwd=self.build_temp, env=env)
      File "/home/arosen/anaconda3/lib/python3.8/subprocess.py", line 364, in check_call
        raise CalledProcessError(retcode, cmd)
    subprocess.CalledProcessError: Command '['cmake', '/tmp/pip-install-ge_8qp0t/dionysus_27ada80b946349d2951108aa99ef32a6', '-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=/tmp/pip-install-ge_8qp0t/dionysus_27ada80b946349d2951108aa99ef32a6/build/lib.linux-x86_64-3.8', '-DPYTHON_EXECUTABLE=/home/arosen/anaconda3/bin/python', '-Dbuild_examples=OFF', '-DCMAKE_BUILD_TYPE=Release']' returned non-zero exit status 1.
    ----------------------------------------
ERROR: Command errored out with exit status 1: /home/arosen/anaconda3/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-ge_8qp0t/dionysus_27ada80b946349d2951108aa99ef32a6/setup.py'"'"'; __file__='"'"'/tmp/pip-install-ge_8qp0t/dionysus_27ada80b946349d2951108aa99ef32a6/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-p5rrc2c3/install-record.txt --single-version-externally-managed --compile --install-headers /home/arosen/anaconda3/include/python3.8/dionysus Check the logs for full command output.

@Andrew-S-Rosen Andrew-S-Rosen reopened this Aug 4, 2022
@kjappelbaum
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So sorry for the issues!

I'm pretty sure it is that you're missing cgal (https://anaconda.org/conda-forge/cgal).

Really need to get those conda things merged ....!

kjappelbaum added a commit that referenced this issue Aug 4, 2022
@kjappelbaum
docs: add note about cgal
1f2a88d 
#277
@Andrew-S-Rosen
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Contributor Author

It's all good! That's part of the process :)

Maybe one step closer? This is what I get after installing cgal.

  Building wheel for moltda (pyproject.toml) ... done
  Created wheel for moltda: filename=moltda-0.1.0-py3-none-any.whl size=13408 sha256=4613b83eda8286064a82c3ad61db38695a34354d5b662053cf96fcb0573e6f5c
  Stored in directory: /tmp/pip-ephem-wheel-cache-bscgb819/wheels/56/ad/4d/0b01b700f5fca1d6afe91ca074648eb8758068e41b6906e989
  Building wheel for diode (setup.py) ... error
  error: subprocess-exited-with-error

  × python setup.py bdist_wheel did not run successfully.
  │ exit code: 1
  ╰─> [83 lines of output]
      running bdist_wheel
      running build
      running build_py
      running build_ext
      -- The C compiler identification is GNU 9.3.0
      -- The CXX compiler identification is GNU 9.3.0
      -- Check for working C compiler: /usr/bin/cc
      -- Check for working C compiler: /usr/bin/cc -- works
      -- Detecting C compiler ABI info
      -- Detecting C compiler ABI info - done
      -- Detecting C compile features
      -- Detecting C compile features - done
      -- Check for working CXX compiler: /usr/bin/c++
      -- Check for working CXX compiler: /usr/bin/c++ -- works
      -- Detecting CXX compiler ABI info
      -- Detecting CXX compiler ABI info - done
      -- Detecting CXX compile features
      -- Detecting CXX compile features - done
      CMake Warning at /home/arosen/anaconda3/envs/mofs/lib/cmake/CGAL/CGALConfig.cmake:92 (message):
        CGAL_DATA_DIR cannot be deduced, set the variable CGAL_DATA_DIR to set the
        default value of CGAL::data_file_path()
      Call Stack (most recent call first):
        CMakeLists.txt:12 (find_package)


      -- Using header-only CGAL
      -- Targetting Unix Makefiles
      -- Using /usr/bin/c++ compiler.
      CMake Error at /usr/share/cmake-3.16/Modules/FindPackageHandleStandardArgs.cmake:146 (message):
        Could NOT find GMP (missing: GMP_LIBRARIES GMP_INCLUDE_DIR)
      Call Stack (most recent call first):
        /usr/share/cmake-3.16/Modules/FindPackageHandleStandardArgs.cmake:393 (_FPHSA_FAILURE_MESSAGE)
        /home/arosen/anaconda3/envs/mofs/lib/cmake/CGAL/FindGMP.cmake:68 (find_package_handle_standard_args)
        /home/arosen/anaconda3/envs/mofs/lib/cmake/CGAL/CGAL_SetupGMP.cmake:24 (find_package)
        /home/arosen/anaconda3/envs/mofs/lib/cmake/CGAL/CGAL_SetupCGALDependencies.cmake:36 (include)
        /home/arosen/anaconda3/envs/mofs/lib/cmake/CGAL/CGALConfig.cmake:153 (include)
        CMakeLists.txt:12 (find_package)


      -- Configuring incomplete, errors occurred!
      See also "/tmp/pip-install-v179ph49/diode_bdaea3c89eb44d1fb097ff3914376931/build/temp.linux-x86_64-cpython-38/CMakeFiles/CMakeOutput.log".
      Traceback (most recent call last):
        File "<string>", line 2, in <module>
        File "<pip-setuptools-caller>", line 34, in <module>
        File "/tmp/pip-install-v179ph49/diode_bdaea3c89eb44d1fb097ff3914376931/setup.py", line 60, in <module>
          setup(
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/site-packages/setuptools/__init__.py", line 87, in setup
          return distutils.core.setup(**attrs)
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/site-packages/setuptools/_distutils/core.py", line 185, in setup
          return run_commands(dist)
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/site-packages/setuptools/_distutils/core.py", line 201, in run_commands
          dist.run_commands()
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/site-packages/setuptools/_distutils/dist.py", line 973, in run_commands
          self.run_command(cmd)
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/site-packages/setuptools/dist.py", line 1217, in run_command
          super().run_command(command)
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/site-packages/setuptools/_distutils/dist.py", line 992, in run_command
          cmd_obj.run()
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/site-packages/wheel/bdist_wheel.py", line 299, in run
          self.run_command('build')
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/site-packages/setuptools/_distutils/cmd.py", line 319, in run_command
          self.distribution.run_command(command)
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/site-packages/setuptools/dist.py", line 1217, in run_command
          super().run_command(command)
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/site-packages/setuptools/_distutils/dist.py", line 992, in run_command
          cmd_obj.run()
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/site-packages/setuptools/command/build.py", line 24, in run
          super().run()
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/site-packages/setuptools/_distutils/command/build.py", line 132, in run
          self.run_command(cmd_name)
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/site-packages/setuptools/_distutils/cmd.py", line 319, in run_command
          self.distribution.run_command(command)
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/site-packages/setuptools/dist.py", line 1217, in run_command
          super().run_command(command)
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/site-packages/setuptools/_distutils/dist.py", line 992, in run_command
          cmd_obj.run()
        File "/tmp/pip-install-v179ph49/diode_bdaea3c89eb44d1fb097ff3914376931/setup.py", line 32, in run
          self.build_extension(ext)
        File "/tmp/pip-install-v179ph49/diode_bdaea3c89eb44d1fb097ff3914376931/setup.py", line 57, in build_extension
          subprocess.check_call(['cmake', ext.sourcedir] + cmake_args, cwd=self.build_temp, env=env)
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/subprocess.py", line 364, in check_call
          raise CalledProcessError(retcode, cmd)
      subprocess.CalledProcessError: Command '['cmake', '/tmp/pip-install-v179ph49/diode_bdaea3c89eb44d1fb097ff3914376931', '-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=/tmp/pip-install-v179ph49/diode_bdaea3c89eb44d1fb097ff3914376931/build/lib.linux-x86_64-cpython-38', '-DPYTHON_EXECUTABLE=/home/arosen/anaconda3/envs/mofs/bin/python3.8', '-Dbuild_examples=OFF', '-DCMAKE_BUILD_TYPE=Release']' 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: Failed building wheel for diode
  Running setup.py clean for diode
Successfully built moltda
Failed to build diode
Installing collected packages: dionysus, diode, threadpoolctl, scikit-learn, pyclustering, moltda
  Running setup.py install for diode ... error
  error: subprocess-exited-with-error

  × Running setup.py install for diode did not run successfully.
  │ exit code: 1
  ╰─> [87 lines of output]
      running install
      /home/arosen/anaconda3/envs/mofs/lib/python3.8/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
      running build_py
      running build_ext
      -- The C compiler identification is GNU 9.3.0
      -- The CXX compiler identification is GNU 9.3.0
      -- Check for working C compiler: /usr/bin/cc
      -- Check for working C compiler: /usr/bin/cc -- works
      -- Detecting C compiler ABI info
      -- Detecting C compiler ABI info - done
      -- Detecting C compile features
      -- Detecting C compile features - done
      -- Check for working CXX compiler: /usr/bin/c++
      -- Check for working CXX compiler: /usr/bin/c++ -- works
      -- Detecting CXX compiler ABI info
      -- Detecting CXX compiler ABI info - done
      -- Detecting CXX compile features
      -- Detecting CXX compile features - done
      CMake Warning at /home/arosen/anaconda3/envs/mofs/lib/cmake/CGAL/CGALConfig.cmake:92 (message):
        CGAL_DATA_DIR cannot be deduced, set the variable CGAL_DATA_DIR to set the
        default value of CGAL::data_file_path()
      Call Stack (most recent call first):
        CMakeLists.txt:12 (find_package)


      -- Using header-only CGAL
      -- Targetting Unix Makefiles
      -- Using /usr/bin/c++ compiler.
      CMake Error at /usr/share/cmake-3.16/Modules/FindPackageHandleStandardArgs.cmake:146 (message):
        Could NOT find GMP (missing: GMP_LIBRARIES GMP_INCLUDE_DIR)
      Call Stack (most recent call first):
        /usr/share/cmake-3.16/Modules/FindPackageHandleStandardArgs.cmake:393 (_FPHSA_FAILURE_MESSAGE)
        /home/arosen/anaconda3/envs/mofs/lib/cmake/CGAL/FindGMP.cmake:68 (find_package_handle_standard_args)
        /home/arosen/anaconda3/envs/mofs/lib/cmake/CGAL/CGAL_SetupGMP.cmake:24 (find_package)
        /home/arosen/anaconda3/envs/mofs/lib/cmake/CGAL/CGAL_SetupCGALDependencies.cmake:36 (include)
        /home/arosen/anaconda3/envs/mofs/lib/cmake/CGAL/CGALConfig.cmake:153 (include)
        CMakeLists.txt:12 (find_package)


      -- Configuring incomplete, errors occurred!
      See also "/tmp/pip-install-v179ph49/diode_bdaea3c89eb44d1fb097ff3914376931/build/temp.linux-x86_64-cpython-38/CMakeFiles/CMakeOutput.log".
      Traceback (most recent call last):
        File "<string>", line 2, in <module>
        File "<pip-setuptools-caller>", line 34, in <module>
        File "/tmp/pip-install-v179ph49/diode_bdaea3c89eb44d1fb097ff3914376931/setup.py", line 60, in <module>
          setup(
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/site-packages/setuptools/__init__.py", line 87, in setup
          return distutils.core.setup(**attrs)
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/site-packages/setuptools/_distutils/core.py", line 185, in setup
          return run_commands(dist)
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/site-packages/setuptools/_distutils/core.py", line 201, in run_commands
          dist.run_commands()
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/site-packages/setuptools/_distutils/dist.py", line 973, in run_commands
          self.run_command(cmd)
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/site-packages/setuptools/dist.py", line 1217, in run_command
          super().run_command(command)
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/site-packages/setuptools/_distutils/dist.py", line 992, in run_command
          cmd_obj.run()
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/site-packages/setuptools/command/install.py", line 68, in run
          return orig.install.run(self)
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/site-packages/setuptools/_distutils/command/install.py", line 698, in run
          self.run_command('build')
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/site-packages/setuptools/_distutils/cmd.py", line 319, in run_command
          self.distribution.run_command(command)
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/site-packages/setuptools/dist.py", line 1217, in run_command
          super().run_command(command)
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/site-packages/setuptools/_distutils/dist.py", line 992, in run_command
          cmd_obj.run()
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/site-packages/setuptools/command/build.py", line 24, in run
          super().run()
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/site-packages/setuptools/_distutils/command/build.py", line 132, in run
          self.run_command(cmd_name)
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/site-packages/setuptools/_distutils/cmd.py", line 319, in run_command
          self.distribution.run_command(command)
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/site-packages/setuptools/dist.py", line 1217, in run_command
          super().run_command(command)
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/site-packages/setuptools/_distutils/dist.py", line 992, in run_command
          cmd_obj.run()
        File "/tmp/pip-install-v179ph49/diode_bdaea3c89eb44d1fb097ff3914376931/setup.py", line 32, in run
          self.build_extension(ext)
        File "/tmp/pip-install-v179ph49/diode_bdaea3c89eb44d1fb097ff3914376931/setup.py", line 57, in build_extension
          subprocess.check_call(['cmake', ext.sourcedir] + cmake_args, cwd=self.build_temp, env=env)
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/subprocess.py", line 364, in check_call
          raise CalledProcessError(retcode, cmd)
      subprocess.CalledProcessError: Command '['cmake', '/tmp/pip-install-v179ph49/diode_bdaea3c89eb44d1fb097ff3914376931', '-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=/tmp/pip-install-v179ph49/diode_bdaea3c89eb44d1fb097ff3914376931/build/lib.linux-x86_64-cpython-38', '-DPYTHON_EXECUTABLE=/home/arosen/anaconda3/envs/mofs/bin/python3.8', '-Dbuild_examples=OFF', '-DCMAKE_BUILD_TYPE=Release']' 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: legacy-install-failure

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

@kjappelbaum
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Owner

Now it seems to be https://anaconda.org/anaconda/gmp

Bought some CI time and will fix the actions later today when I'm in the office.

Do you mind if I ask what OS you are using? (I used clean conda envs on a bunch of UNIX machines and I didn't need to do many extra steps, would be good to know why you have a harder time)

@Andrew-S-Rosen
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Contributor Author

Andrew-S-Rosen commented Aug 4, 2022 •
edited
Loading

Thanks! I still got the error below. I'm using the Windows Subsystem for Linux rather than "real" Linux, so that may be a root cause of the problem (it's Ubuntu 20.04.3 LTS on a Windows 11 machine; a clean Conda environment with Python 3.8). I'll try a typical Linux environment shortly so I'm not wasting your time with debugging. Hopefully that'll go smoother.

  Building wheel for diode (setup.py) ... error
  error: subprocess-exited-with-error

  × python setup.py bdist_wheel did not run successfully.
  │ exit code: 1
  ╰─> [83 lines of output]
      running bdist_wheel
      running build
      running build_py
      running build_ext
      -- The C compiler identification is GNU 9.3.0
      -- The CXX compiler identification is GNU 9.3.0
      -- Check for working C compiler: /usr/bin/cc
      -- Check for working C compiler: /usr/bin/cc -- works
      -- Detecting C compiler ABI info
      -- Detecting C compiler ABI info - done
      -- Detecting C compile features
      -- Detecting C compile features - done
      -- Check for working CXX compiler: /usr/bin/c++
      -- Check for working CXX compiler: /usr/bin/c++ -- works
      -- Detecting CXX compiler ABI info
      -- Detecting CXX compiler ABI info - done
      -- Detecting CXX compile features
      -- Detecting CXX compile features - done
      CMake Warning at /home/arosen/anaconda3/envs/mofs/lib/cmake/CGAL/CGALConfig.cmake:92 (message):
        CGAL_DATA_DIR cannot be deduced, set the variable CGAL_DATA_DIR to set the
        default value of CGAL::data_file_path()
      Call Stack (most recent call first):
        CMakeLists.txt:12 (find_package)


      -- Using header-only CGAL
      -- Targetting Unix Makefiles
      -- Using /usr/bin/c++ compiler.
      CMake Error at /usr/share/cmake-3.16/Modules/FindPackageHandleStandardArgs.cmake:146 (message):
        Could NOT find GMP (missing: GMP_LIBRARIES GMP_INCLUDE_DIR)
      Call Stack (most recent call first):
        /usr/share/cmake-3.16/Modules/FindPackageHandleStandardArgs.cmake:393 (_FPHSA_FAILURE_MESSAGE)
        /home/arosen/anaconda3/envs/mofs/lib/cmake/CGAL/FindGMP.cmake:68 (find_package_handle_standard_args)
        /home/arosen/anaconda3/envs/mofs/lib/cmake/CGAL/CGAL_SetupGMP.cmake:24 (find_package)
        /home/arosen/anaconda3/envs/mofs/lib/cmake/CGAL/CGAL_SetupCGALDependencies.cmake:36 (include)
        /home/arosen/anaconda3/envs/mofs/lib/cmake/CGAL/CGALConfig.cmake:153 (include)
        CMakeLists.txt:12 (find_package)


      -- Configuring incomplete, errors occurred!
      See also "/tmp/pip-install-fqlqjpow/diode_251e51ecb23646faba75e8ae36767fcb/build/temp.linux-x86_64-cpython-38/CMakeFiles/CMakeOutput.log".
      Traceback (most recent call last):
        File "<string>", line 2, in <module>
        File "<pip-setuptools-caller>", line 34, in <module>
        File "/tmp/pip-install-fqlqjpow/diode_251e51ecb23646faba75e8ae36767fcb/setup.py", line 60, in <module>
          setup(
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/site-packages/setuptools/__init__.py", line 87, in setup
          return distutils.core.setup(**attrs)
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/site-packages/setuptools/_distutils/core.py", line 185, in setup
          return run_commands(dist)
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/site-packages/setuptools/_distutils/core.py", line 201, in run_commands
          dist.run_commands()
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/site-packages/setuptools/_distutils/dist.py", line 973, in run_commands
          self.run_command(cmd)
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/site-packages/setuptools/dist.py", line 1217, in run_command
          super().run_command(command)
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/site-packages/setuptools/_distutils/dist.py", line 992, in run_command
          cmd_obj.run()
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/site-packages/wheel/bdist_wheel.py", line 299, in run
          self.run_command('build')
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/site-packages/setuptools/_distutils/cmd.py", line 319, in run_command
          self.distribution.run_command(command)
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/site-packages/setuptools/dist.py", line 1217, in run_command
          super().run_command(command)
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/site-packages/setuptools/_distutils/dist.py", line 992, in run_command
          cmd_obj.run()
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/site-packages/setuptools/command/build.py", line 24, in run
          super().run()
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/site-packages/setuptools/_distutils/command/build.py", line 132, in run
          self.run_command(cmd_name)
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/site-packages/setuptools/_distutils/cmd.py", line 319, in run_command
          self.distribution.run_command(command)
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/site-packages/setuptools/dist.py", line 1217, in run_command
          super().run_command(command)
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/site-packages/setuptools/_distutils/dist.py", line 992, in run_command
          cmd_obj.run()
        File "/tmp/pip-install-fqlqjpow/diode_251e51ecb23646faba75e8ae36767fcb/setup.py", line 32, in run
          self.build_extension(ext)
        File "/tmp/pip-install-fqlqjpow/diode_251e51ecb23646faba75e8ae36767fcb/setup.py", line 57, in build_extension
          subprocess.check_call(['cmake', ext.sourcedir] + cmake_args, cwd=self.build_temp, env=env)
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/subprocess.py", line 364, in check_call
          raise CalledProcessError(retcode, cmd)
      subprocess.CalledProcessError: Command '['cmake', '/tmp/pip-install-fqlqjpow/diode_251e51ecb23646faba75e8ae36767fcb', '-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=/tmp/pip-install-fqlqjpow/diode_251e51ecb23646faba75e8ae36767fcb/build/lib.linux-x86_64-cpython-38', '-DPYTHON_EXECUTABLE=/home/arosen/anaconda3/envs/mofs/bin/python3.8', '-Dbuild_examples=OFF', '-DCMAKE_BUILD_TYPE=Release']' 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: Failed building wheel for diode
  Running setup.py clean for diode
Successfully built moltda
Failed to build diode
Installing collected packages: diode, threadpoolctl, scikit-learn, pyclustering, moltda
  Running setup.py install for diode ... error
  error: subprocess-exited-with-error

  × Running setup.py install for diode did not run successfully.
  │ exit code: 1
  ╰─> [87 lines of output]
      running install
      /home/arosen/anaconda3/envs/mofs/lib/python3.8/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
      running build_py
      running build_ext
      -- The C compiler identification is GNU 9.3.0
      -- The CXX compiler identification is GNU 9.3.0
      -- Check for working C compiler: /usr/bin/cc
      -- Check for working C compiler: /usr/bin/cc -- works
      -- Detecting C compiler ABI info
      -- Detecting C compiler ABI info - done
      -- Detecting C compile features
      -- Detecting C compile features - done
      -- Check for working CXX compiler: /usr/bin/c++
      -- Check for working CXX compiler: /usr/bin/c++ -- works
      -- Detecting CXX compiler ABI info
      -- Detecting CXX compiler ABI info - done
      -- Detecting CXX compile features
      -- Detecting CXX compile features - done
      CMake Warning at /home/arosen/anaconda3/envs/mofs/lib/cmake/CGAL/CGALConfig.cmake:92 (message):
        CGAL_DATA_DIR cannot be deduced, set the variable CGAL_DATA_DIR to set the
        default value of CGAL::data_file_path()
      Call Stack (most recent call first):
        CMakeLists.txt:12 (find_package)


      -- Using header-only CGAL
      -- Targetting Unix Makefiles
      -- Using /usr/bin/c++ compiler.
      CMake Error at /usr/share/cmake-3.16/Modules/FindPackageHandleStandardArgs.cmake:146 (message):
        Could NOT find GMP (missing: GMP_LIBRARIES GMP_INCLUDE_DIR)
      Call Stack (most recent call first):
        /usr/share/cmake-3.16/Modules/FindPackageHandleStandardArgs.cmake:393 (_FPHSA_FAILURE_MESSAGE)
        /home/arosen/anaconda3/envs/mofs/lib/cmake/CGAL/FindGMP.cmake:68 (find_package_handle_standard_args)
        /home/arosen/anaconda3/envs/mofs/lib/cmake/CGAL/CGAL_SetupGMP.cmake:24 (find_package)
        /home/arosen/anaconda3/envs/mofs/lib/cmake/CGAL/CGAL_SetupCGALDependencies.cmake:36 (include)
        /home/arosen/anaconda3/envs/mofs/lib/cmake/CGAL/CGALConfig.cmake:153 (include)
        CMakeLists.txt:12 (find_package)


      -- Configuring incomplete, errors occurred!
      See also "/tmp/pip-install-fqlqjpow/diode_251e51ecb23646faba75e8ae36767fcb/build/temp.linux-x86_64-cpython-38/CMakeFiles/CMakeOutput.log".
      Traceback (most recent call last):
        File "<string>", line 2, in <module>
        File "<pip-setuptools-caller>", line 34, in <module>
        File "/tmp/pip-install-fqlqjpow/diode_251e51ecb23646faba75e8ae36767fcb/setup.py", line 60, in <module>
          setup(
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/site-packages/setuptools/__init__.py", line 87, in setup
          return distutils.core.setup(**attrs)
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/site-packages/setuptools/_distutils/core.py", line 185, in setup
          return run_commands(dist)
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/site-packages/setuptools/_distutils/core.py", line 201, in run_commands
          dist.run_commands()
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/site-packages/setuptools/_distutils/dist.py", line 973, in run_commands
          self.run_command(cmd)
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/site-packages/setuptools/dist.py", line 1217, in run_command
          super().run_command(command)
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/site-packages/setuptools/_distutils/dist.py", line 992, in run_command
          cmd_obj.run()
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/site-packages/setuptools/command/install.py", line 68, in run
          return orig.install.run(self)
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/site-packages/setuptools/_distutils/command/install.py", line 698, in run
          self.run_command('build')
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/site-packages/setuptools/_distutils/cmd.py", line 319, in run_command
          self.distribution.run_command(command)
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/site-packages/setuptools/dist.py", line 1217, in run_command
          super().run_command(command)
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/site-packages/setuptools/_distutils/dist.py", line 992, in run_command
          cmd_obj.run()
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/site-packages/setuptools/command/build.py", line 24, in run
          super().run()
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/site-packages/setuptools/_distutils/command/build.py", line 132, in run
          self.run_command(cmd_name)
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/site-packages/setuptools/_distutils/cmd.py", line 319, in run_command
          self.distribution.run_command(command)
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/site-packages/setuptools/dist.py", line 1217, in run_command
          super().run_command(command)
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/site-packages/setuptools/_distutils/dist.py", line 992, in run_command
          cmd_obj.run()
        File "/tmp/pip-install-fqlqjpow/diode_251e51ecb23646faba75e8ae36767fcb/setup.py", line 32, in run
          self.build_extension(ext)
        File "/tmp/pip-install-fqlqjpow/diode_251e51ecb23646faba75e8ae36767fcb/setup.py", line 57, in build_extension
          subprocess.check_call(['cmake', ext.sourcedir] + cmake_args, cwd=self.build_temp, env=env)
        File "/home/arosen/anaconda3/envs/mofs/lib/python3.8/subprocess.py", line 364, in check_call
          raise CalledProcessError(retcode, cmd)
      subprocess.CalledProcessError: Command '['cmake', '/tmp/pip-install-fqlqjpow/diode_251e51ecb23646faba75e8ae36767fcb', '-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=/tmp/pip-install-fqlqjpow/diode_251e51ecb23646faba75e8ae36767fcb/build/lib.linux-x86_64-cpython-38', '-DPYTHON_EXECUTABLE=/home/arosen/anaconda3/envs/mofs/bin/python3.8', '-Dbuild_examples=OFF', '-DCMAKE_BUILD_TYPE=Release']' 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: legacy-install-failure

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

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

@kjappelbaum
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Nono, really good to know! I think WSL is common and I do not have access so I'm happy that you're the guinea pig! 🧪

@kjappelbaum kjappelbaum mentioned this issue Aug 4, 2022
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2 tasks
@kjappelbaum
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it is a bit hacky, but if you run

mofdscribe/.github/workflows/tests.yml

Lines 60 to 61 in 1f2a88d

sudo apt-get install libcgal-dev -y & conda install raspa2 zeopp-lsmo cgal boost -c conda-forge -y
pip install pytest & pip install git+https://github.com/kjappelbaum/molecule-tda.git@refactor

does this lead you anywhere?

@Andrew-S-Rosen
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Success! The key was sudo apt-get install libcgal-dev.

@kjappelbaum
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shall we close this issue? I think the installation is a bit simpler now, even though it still requires manually conda installs to have the full functionality

@Andrew-S-Rosen
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Yes, close!

@kjappelbaum kjappelbaum reopened this Sep 12, 2022
@kjappelbaum
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kjappelbaum commented Sep 12, 2022 •
edited
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reopening as @sauradeep93 reported issues on Mac. It is interesting that the conda-installed cgal seems not to work.

kjappelbaum added a commit that referenced this issue Sep 12, 2022
@kjappelbaum
docs: add cgal note (#277)
b3650ca 
[skip ci]
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@Andrew-S-Rosen @kjappelbaum