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A high performance mapping class to construct ElM2D plots from large datasets of inorganic compositions.

License: GNU General Public License v3.0

Python 100.00%

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surgearrester sparks-baird

elm2d's Issues

Issues with running on Spyder 5.0.5

Works fine in Juptyer notebook. Spyder is having issues. Can you reproduce this behavior? Or does it work fine in Spyder for you? It's via its own anaconda environment.

    exitcode = _main(fd)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\spawn.py", line 114, in _main
    prepare(preparation_data)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\spawn.py", line 225, in prepare
    _fixup_main_from_path(data['init_main_from_path'])
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\spawn.py", line 277, in _fixup_main_from_path
    run_name="__mp_main__")
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\runpy.py", line 263, in run_path
    pkg_name=pkg_name, script_name=fname)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\runpy.py", line 96, in _run_module_code
    mod_name, mod_spec, pkg_name, script_name)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "C:\Users\sterg\Documents\GitHub\sparks-baird\ElM2D-test\test.py", line 21, in <module>
    embedding = mapper.fit_transform(df["formula"])
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\site-packages\ElM2D\ElM2D.py", line 188, in fit_transform
    self.fit(X)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\site-packages\ElM2D\ElM2D.py", line 176, in fit
    dist_vec = self._process_list(X, n_proc=self.n_proc)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\site-packages\ElM2D\ElM2D.py", line 384, in _process_list
    process_pool = Pool(n_proc)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\context.py", line 119, in Pool
    context=self.get_context())
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\pool.py", line 176, in __init__
    self._repopulate_pool()
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\pool.py", line 241, in _repopulate_pool
    w.start()
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\process.py", line 112, in start
    self._popen = self._Popen(self)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\context.py", line 322, in _Popen
    return Popen(process_obj)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\popen_spawn_win32.py", line 46, in __init__
    prep_data = spawn.get_preparation_data(process_obj._name)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\spawn.py", line 143, in get_preparation_data
    _check_not_importing_main()
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\spawn.py", line 136, in _check_not_importing_main
    is not going to be frozen to produce an executable.''')
RuntimeError: 
        An attempt has been made to start a new process before the
        current process has finished its bootstrapping phase.

        This probably means that you are not using fork to start your
        child processes and you have forgotten to use the proper idiom
        in the main module:

            if __name__ == '__main__':
                freeze_support()
                ...

        The "freeze_support()" line can be omitted if the program
        is not going to be frozen to produce an executable.
100%|##########| 100/100 [00:20<00:00,  4.79it/s]
 95%|#########5| 95/100 [00:19<00:00,  5.26it/s]s]
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\spawn.py", line 105, in spawn_main
    exitcode = _main(fd)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\spawn.py", line 114, in _main
    prepare(preparation_data)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\spawn.py", line 225, in prepare
    _fixup_main_from_path(data['init_main_from_path'])
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\spawn.py", line 277, in _fixup_main_from_path
    run_name="__mp_main__")
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\runpy.py", line 263, in run_path
    pkg_name=pkg_name, script_name=fname)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\runpy.py", line 96, in _run_module_code
    mod_name, mod_spec, pkg_name, script_name)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "C:\Users\sterg\Documents\GitHub\sparks-baird\ElM2D-test\test.py", line 21, in <module>
    embedding = mapper.fit_transform(df["formula"])
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\site-packages\ElM2D\ElM2D.py", line 188, in fit_transform
    self.fit(X)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\site-packages\ElM2D\ElM2D.py", line 176, in fit
    dist_vec = self._process_list(X, n_proc=self.n_proc)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\site-packages\ElM2D\ElM2D.py", line 384, in _process_list
    process_pool = Pool(n_proc)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\context.py", line 119, in Pool
    context=self.get_context())
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\pool.py", line 176, in __init__
    self._repopulate_pool()
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\pool.py", line 241, in _repopulate_pool
    w.start()
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\process.py", line 112, in start
    self._popen = self._Popen(self)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\context.py", line 322, in _Popen
    return Popen(process_obj)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\popen_spawn_win32.py", line 46, in __init__
    prep_data = spawn.get_preparation_data(process_obj._name)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\spawn.py", line 143, in get_preparation_data
    _check_not_importing_main()
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\spawn.py", line 136, in _check_not_importing_main
    is not going to be frozen to produce an executable.''')
RuntimeError: 
        An attempt has been made to start a new process before the
        current process has finished its bootstrapping phase.

        This probably means that you are not using fork to start your
        child processes and you have forgotten to use the proper idiom
        in the main module:

            if __name__ == '__main__':
                freeze_support()
                ...

        The "freeze_support()" line can be omitted if the program
        is not going to be frozen to produce an executable.
100%|##########| 100/100 [00:20<00:00,  4.84it/s]
100%|##########| 100/100 [00:20<00:00,  4.88it/s]]
100%|##########| 99/99 [00:00<00:00, 49639.70it/s]
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\spawn.py", line 105, in spawn_main
    exitcode = _main(fd)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\spawn.py", line 114, in _main
    prepare(preparation_data)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\spawn.py", line 225, in prepare
    _fixup_main_from_path(data['init_main_from_path'])
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\spawn.py", line 277, in _fixup_main_from_path
    run_name="__mp_main__")
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\runpy.py", line 263, in run_path
    pkg_name=pkg_name, script_name=fname)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\runpy.py", line 96, in _run_module_code
    mod_name, mod_spec, pkg_name, script_name)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "C:\Users\sterg\Documents\GitHub\sparks-baird\ElM2D-test\test.py", line 21, in <module>
    embedding = mapper.fit_transform(df["formula"])
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\site-packages\ElM2D\ElM2D.py", line 188, in fit_transform
    self.fit(X)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\site-packages\ElM2D\ElM2D.py", line 176, in fit
    dist_vec = self._process_list(X, n_proc=self.n_proc)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\site-packages\ElM2D\ElM2D.py", line 384, in _process_list
    process_pool = Pool(n_proc)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\context.py", line 119, in Pool
    context=self.get_context())
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\pool.py", line 176, in __init__
    self._repopulate_pool()
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\pool.py", line 241, in _repopulate_pool
    w.start()
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\process.py", line 112, in start
    self._popen = self._Popen(self)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\context.py", line 322, in _Popen
    return Popen(process_obj)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\popen_spawn_win32.py", line 46, in __init__
    prep_data = spawn.get_preparation_data(process_obj._name)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\spawn.py", line 143, in get_preparation_data
    _check_not_importing_main()
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\spawn.py", line 136, in _check_not_importing_main
    is not going to be frozen to produce an executable.''')
RuntimeError: 
        An attempt has been made to start a new process before the
        current process has finished its bootstrapping phase.

        This probably means that you are not using fork to start your
        child processes and you have forgotten to use the proper idiom
        in the main module:

            if __name__ == '__main__':
                freeze_support()
                ...

        The "freeze_support()" line can be omitted if the program
        is not going to be frozen to produce an executable.

Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\spawn.py", line 105, in spawn_main
    exitcode = _main(fd)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\spawn.py", line 114, in _main
    prepare(preparation_data)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\spawn.py", line 225, in prepare
    _fixup_main_from_path(data['init_main_from_path'])
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\spawn.py", line 277, in _fixup_main_from_path
    run_name="__mp_main__")
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\runpy.py", line 263, in run_path
    pkg_name=pkg_name, script_name=fname)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\runpy.py", line 96, in _run_module_code
    mod_name, mod_spec, pkg_name, script_name)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "C:\Users\sterg\Documents\GitHub\sparks-baird\ElM2D-test\test.py", line 21, in <module>
    embedding = mapper.fit_transform(df["formula"])
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\site-packages\ElM2D\ElM2D.py", line 188, in fit_transform
    self.fit(X)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\site-packages\ElM2D\ElM2D.py", line 176, in fit
    dist_vec = self._process_list(X, n_proc=self.n_proc)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\site-packages\ElM2D\ElM2D.py", line 384, in _process_list
    process_pool = Pool(n_proc)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\context.py", line 119, in Pool
    context=self.get_context())
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\pool.py", line 176, in __init__
    self._repopulate_pool()
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\pool.py", line 241, in _repopulate_pool
    w.start()
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\process.py", line 112, in start
    self._popen = self._Popen(self)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\context.py", line 322, in _Popen
    return Popen(process_obj)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\popen_spawn_win32.py", line 46, in __init__
    prep_data = spawn.get_preparation_data(process_obj._name)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\spawn.py", line 143, in get_preparation_data
    _check_not_importing_main()
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\spawn.py", line 136, in _check_not_importing_main
    is not going to be frozen to produce an executable.''')
RuntimeError: 
        An attempt has been made to start a new process before the
        current process has finished its bootstrapping phase.

        This probably means that you are not using fork to start your
        child processes and you have forgotten to use the proper idiom
        in the main module:

            if __name__ == '__main__':
                freeze_support()
                ...

        The "freeze_support()" line can be omitted if the program
        is not going to be frozen to produce an executable.
100%|##########| 100/100 [00:20<00:00,  4.87it/s]
100%|##########| 99/99 [00:00<00:00, 49830.32it/s]
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\spawn.py", line 105, in spawn_main
    exitcode = _main(fd)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\spawn.py", line 114, in _main
    prepare(preparation_data)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\spawn.py", line 225, in prepare
    _fixup_main_from_path(data['init_main_from_path'])
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\spawn.py", line 277, in _fixup_main_from_path
    run_name="__mp_main__")
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\runpy.py", line 263, in run_path
    pkg_name=pkg_name, script_name=fname)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\runpy.py", line 96, in _run_module_code
    mod_name, mod_spec, pkg_name, script_name)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "C:\Users\sterg\Documents\GitHub\sparks-baird\ElM2D-test\test.py", line 21, in <module>
    embedding = mapper.fit_transform(df["formula"])
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\site-packages\ElM2D\ElM2D.py", line 188, in fit_transform
    self.fit(X)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\site-packages\ElM2D\ElM2D.py", line 176, in fit
    dist_vec = self._process_list(X, n_proc=self.n_proc)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\site-packages\ElM2D\ElM2D.py", line 384, in _process_list
    process_pool = Pool(n_proc)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\context.py", line 119, in Pool
    context=self.get_context())
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\pool.py", line 176, in __init__
    self._repopulate_pool()
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\pool.py", line 241, in _repopulate_pool
    w.start()
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\process.py", line 112, in start
    self._popen = self._Popen(self)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\context.py", line 322, in _Popen
    return Popen(process_obj)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\popen_spawn_win32.py", line 46, in __init__
    prep_data = spawn.get_preparation_data(process_obj._name)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\spawn.py", line 143, in get_preparation_data
    _check_not_importing_main()
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\spawn.py", line 136, in _check_not_importing_main
    is not going to be frozen to produce an executable.''')
RuntimeError: 
        An attempt has been made to start a new process before the
        current process has finished its bootstrapping phase.

        This probably means that you are not using fork to start your
        child processes and you have forgotten to use the proper idiom
        in the main module:

            if __name__ == '__main__':
                freeze_support()
                ...

        The "freeze_support()" line can be omitted if the program
        is not going to be frozen to produce an executable.
100%|##########| 100/100 [00:20<00:00,  4.87it/s]
100%|##########| 100/100 [00:20<00:00,  4.79it/s]]
100%|##########| 100/100 [00:20<00:00,  4.78it/s]]
100%|##########| 99/99 [00:00<00:00, 49627.84it/s]
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\spawn.py", line 105, in spawn_main
    exitcode = _main(fd)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\spawn.py", line 114, in _main
    prepare(preparation_data)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\spawn.py", line 225, in prepare
    _fixup_main_from_path(data['init_main_from_path'])
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\spawn.py", line 277, in _fixup_main_from_path
    run_name="__mp_main__")
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\runpy.py", line 263, in run_path
    pkg_name=pkg_name, script_name=fname)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\runpy.py", line 96, in _run_module_code
    mod_name, mod_spec, pkg_name, script_name)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "C:\Users\sterg\Documents\GitHub\sparks-baird\ElM2D-test\test.py", line 21, in <module>
    embedding = mapper.fit_transform(df["formula"])
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\site-packages\ElM2D\ElM2D.py", line 188, in fit_transform
    self.fit(X)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\site-packages\ElM2D\ElM2D.py", line 176, in fit
    dist_vec = self._process_list(X, n_proc=self.n_proc)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\site-packages\ElM2D\ElM2D.py", line 384, in _process_list
    process_pool = Pool(n_proc)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\context.py", line 119, in Pool
    context=self.get_context())
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\pool.py", line 176, in __init__
    self._repopulate_pool()
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\pool.py", line 241, in _repopulate_pool
    w.start()
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\process.py", line 112, in start
    self._popen = self._Popen(self)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\context.py", line 322, in _Popen
    return Popen(process_obj)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\popen_spawn_win32.py", line 46, in __init__
    prep_data = spawn.get_preparation_data(process_obj._name)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\spawn.py", line 143, in get_preparation_data
    _check_not_importing_main()
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\spawn.py", line 136, in _check_not_importing_main
    is not going to be frozen to produce an executable.''')
RuntimeError: 
        An attempt has been made to start a new process before the
        current process has finished its bootstrapping phase.

        This probably means that you are not using fork to start your
        child processes and you have forgotten to use the proper idiom
        in the main module:

            if __name__ == '__main__':
                freeze_support()
                ...

        The "freeze_support()" line can be omitted if the program
        is not going to be frozen to produce an executable.

Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\spawn.py", line 105, in spawn_main
    exitcode = _main(fd)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\spawn.py", line 114, in _main
    prepare(preparation_data)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\spawn.py", line 225, in prepare
    _fixup_main_from_path(data['init_main_from_path'])
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\spawn.py", line 277, in _fixup_main_from_path
    run_name="__mp_main__")
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\runpy.py", line 263, in run_path
    pkg_name=pkg_name, script_name=fname)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\runpy.py", line 96, in _run_module_code
    mod_name, mod_spec, pkg_name, script_name)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "C:\Users\sterg\Documents\GitHub\sparks-baird\ElM2D-test\test.py", line 21, in <module>
    embedding = mapper.fit_transform(df["formula"])
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\site-packages\ElM2D\ElM2D.py", line 188, in fit_transform
    self.fit(X)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\site-packages\ElM2D\ElM2D.py", line 176, in fit
    dist_vec = self._process_list(X, n_proc=self.n_proc)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\site-packages\ElM2D\ElM2D.py", line 384, in _process_list
    process_pool = Pool(n_proc)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\context.py", line 119, in Pool
    context=self.get_context())
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\pool.py", line 176, in __init__
    self._repopulate_pool()
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\pool.py", line 241, in _repopulate_pool
    w.start()
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\process.py", line 112, in start
    self._popen = self._Popen(self)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\context.py", line 322, in _Popen
    return Popen(process_obj)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\popen_spawn_win32.py", line 46, in __init__
    prep_data = spawn.get_preparation_data(process_obj._name)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\spawn.py", line 143, in get_preparation_data
    _check_not_importing_main()
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\spawn.py", line 136, in _check_not_importing_main
    is not going to be frozen to produce an executable.''')
RuntimeError: 
        An attempt has been made to start a new process before the
        current process has finished its bootstrapping phase.

        This probably means that you are not using fork to start your
        child processes and you have forgotten to use the proper idiom
        in the main module:

            if __name__ == '__main__':
                freeze_support()
                ...

        The "freeze_support()" line can be omitted if the program
        is not going to be frozen to produce an executable.

Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\spawn.py", line 105, in spawn_main
    exitcode = _main(fd)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\spawn.py", line 114, in _main
    prepare(preparation_data)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\spawn.py", line 225, in prepare
    _fixup_main_from_path(data['init_main_from_path'])
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\spawn.py", line 277, in _fixup_main_from_path
    run_name="__mp_main__")
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\runpy.py", line 263, in run_path
    pkg_name=pkg_name, script_name=fname)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\runpy.py", line 96, in _run_module_code
    mod_name, mod_spec, pkg_name, script_name)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "C:\Users\sterg\Documents\GitHub\sparks-baird\ElM2D-test\test.py", line 21, in <module>
    embedding = mapper.fit_transform(df["formula"])
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\site-packages\ElM2D\ElM2D.py", line 188, in fit_transform
    self.fit(X)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\site-packages\ElM2D\ElM2D.py", line 176, in fit
    dist_vec = self._process_list(X, n_proc=self.n_proc)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\site-packages\ElM2D\ElM2D.py", line 384, in _process_list
    process_pool = Pool(n_proc)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\context.py", line 119, in Pool
    context=self.get_context())
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\pool.py", line 176, in __init__
    self._repopulate_pool()
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\pool.py", line 241, in _repopulate_pool
    w.start()
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\process.py", line 112, in start
    self._popen = self._Popen(self)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\context.py", line 322, in _Popen
    return Popen(process_obj)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\popen_spawn_win32.py", line 46, in __init__
    prep_data = spawn.get_preparation_data(process_obj._name)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\spawn.py", line 143, in get_preparation_data
    _check_not_importing_main()
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\spawn.py", line 136, in _check_not_importing_main
    is not going to be frozen to produce an executable.''')
RuntimeError: 
        An attempt has been made to start a new process before the
        current process has finished its bootstrapping phase.

        This probably means that you are not using fork to start your
        child processes and you have forgotten to use the proper idiom
        in the main module:

            if __name__ == '__main__':
                freeze_support()
                ...

        The "freeze_support()" line can be omitted if the program
        is not going to be frozen to produce an executable.
100%|##########| 100/100 [00:20<00:00,  4.86it/s]
100%|##########| 99/99 [00:00<00:00, 99220.09it/s]
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\spawn.py", line 105, in spawn_main
    exitcode = _main(fd)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\spawn.py", line 114, in _main
    prepare(preparation_data)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\spawn.py", line 225, in prepare
    _fixup_main_from_path(data['init_main_from_path'])
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\spawn.py", line 277, in _fixup_main_from_path
    run_name="__mp_main__")
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\runpy.py", line 263, in run_path
    pkg_name=pkg_name, script_name=fname)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\runpy.py", line 96, in _run_module_code
    mod_name, mod_spec, pkg_name, script_name)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "C:\Users\sterg\Documents\GitHub\sparks-baird\ElM2D-test\test.py", line 21, in <module>
    embedding = mapper.fit_transform(df["formula"])
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\site-packages\ElM2D\ElM2D.py", line 188, in fit_transform
    self.fit(X)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\site-packages\ElM2D\ElM2D.py", line 176, in fit
    dist_vec = self._process_list(X, n_proc=self.n_proc)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\site-packages\ElM2D\ElM2D.py", line 384, in _process_list
    process_pool = Pool(n_proc)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\context.py", line 119, in Pool
    context=self.get_context())
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\pool.py", line 176, in __init__
    self._repopulate_pool()
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\pool.py", line 241, in _repopulate_pool
    w.start()
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\process.py", line 112, in start
    self._popen = self._Popen(self)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\context.py", line 322, in _Popen
    return Popen(process_obj)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\popen_spawn_win32.py", line 46, in __init__
    prep_data = spawn.get_preparation_data(process_obj._name)
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\spawn.py", line 143, in get_preparation_data
    _check_not_importing_main()
  File "C:\Users\sterg\anaconda3\envs\ElM2D\lib\multiprocessing\spawn.py", line 136, in _check_not_importing_main
    is not going to be frozen to produce an executable.''')
RuntimeError: 
        An attempt has been made to start a new process before the
        current process has finished its bootstrapping phase.

        This probably means that you are not using fork to start your
        child processes and you have forgotten to use the proper idiom
        in the main module:

            if __name__ == '__main__':
                freeze_support()
                ...

        The "freeze_support()" line can be omitted if the program
        is not going to be frozen to produce an executable.
 52%|#####2    | 52/100 [00:11<00:10,  4.75it/s]

RuntimeError: An attempt has been made to start a new process before the current process has finished its bootstrapping phase.

Hey!
I encountered an error while fitting an ElM2D object and I really can't wrap my mind around it.
The problem appears when I launch the .fit (or .fit_transform) method with the following code (copypasted from the docs):

mapper = ElM2D()
mapper.fit(df['framework_formula'])
print(mapper.dm)
print(len(mapper.dm))

I get a very long terminal response; as following.

Fitting mod_petti kernel matrix
Constructing distances
Parsing Formula
100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 63/63 [00:00<00:00, 8667.34it/s] 
Constructing joint compositional pairings
100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 62/62 [00:00<00:00, 62227.05it/s] 
Creating Process Pool
Scattering compositions between processes and computing distances
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "C:\Users\anton\anaconda3\envs\elm2d-3\lib\multiprocessing\spawn.py", line 105, in spawn_main
    exitcode = _main(fd)
  File "C:\Users\anton\anaconda3\envs\elm2d-3\lib\multiprocessing\spawn.py", line 114, in _main
    prepare(preparation_data)
  File "C:\Users\anton\anaconda3\envs\elm2d-3\lib\multiprocessing\spawn.py", line 225, in prepare
    _fixup_main_from_path(data['init_main_from_path'])
  File "C:\Users\anton\anaconda3\envs\elm2d-3\lib\multiprocessing\spawn.py", line 277, in _fixup_main_from_path
    run_name="__mp_main__")
  File "C:\Users\anton\anaconda3\envs\elm2d-3\lib\runpy.py", line 263, in run_path
    pkg_name=pkg_name, script_name=fname)
  File "C:\Users\anton\anaconda3\envs\elm2d-3\lib\runpy.py", line 96, in _run_module_code
    mod_name, mod_spec, pkg_name, script_name)
  File "C:\Users\anton\anaconda3\envs\elm2d-3\lib\runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "c:\Users\anton\Documents\Python Scripts\MP_visual\elm2d.py", line 54, in <module>
    mapper.fit(df['framework_formula'])
  File "C:\Users\anton\anaconda3\envs\elm2d-3\lib\site-packages\ElM2D\ElM2D.py", line 193, in fit
    dist_vec = self._process_list(X, n_proc=self.n_proc)
  File "C:\Users\anton\anaconda3\envs\elm2d-3\lib\site-packages\ElM2D\ElM2D.py", line 421, in _process_list
    scores = process_map(self._pool_ElMD, pool_list, chunksize=self.chunksize)
  File "C:\Users\anton\anaconda3\envs\elm2d-3\lib\site-packages\tqdm\contrib\concurrent.py", line 130, in process_map
    return _executor_map(ProcessPoolExecutor, fn, *iterables, **tqdm_kwargs)
  File "C:\Users\anton\anaconda3\envs\elm2d-3\lib\site-packages\tqdm\contrib\concurrent.py", line 76, in _executor_map
    return list(tqdm_class(ex.map(fn, *iterables, **map_args), **kwargs))
  File "C:\Users\anton\anaconda3\envs\elm2d-3\lib\concurrent\futures\process.py", line 671, in map
    timeout=timeout)
  File "C:\Users\anton\anaconda3\envs\elm2d-3\lib\concurrent\futures\_base.py", line 587, in map
    fs = [self.submit(fn, *args) for args in zip(*iterables)]
  File "C:\Users\anton\anaconda3\envs\elm2d-3\lib\concurrent\futures\_base.py", line 587, in <listcomp>
    fs = [self.submit(fn, *args) for args in zip(*iterables)]
  File "C:\Users\anton\anaconda3\envs\elm2d-3\lib\concurrent\futures\process.py", line 641, in submit
    self._start_queue_management_thread()
  File "C:\Users\anton\anaconda3\envs\elm2d-3\lib\concurrent\futures\process.py", line 583, in _start_queue_management_thread
    self._adjust_process_count()
  File "C:\Users\anton\anaconda3\envs\elm2d-3\lib\concurrent\futures\process.py", line 607, in _adjust_process_count
    p.start()
  File "C:\Users\anton\anaconda3\envs\elm2d-3\lib\multiprocessing\process.py", line 112, in start
    self._popen = self._Popen(self)
  File "C:\Users\anton\anaconda3\envs\elm2d-3\lib\multiprocessing\context.py", line 322, in _Popen
    return Popen(process_obj)
  File "C:\Users\anton\anaconda3\envs\elm2d-3\lib\multiprocessing\popen_spawn_win32.py", line 46, in __init__
    prep_data = spawn.get_preparation_data(process_obj._name)
  File "C:\Users\anton\anaconda3\envs\elm2d-3\lib\multiprocessing\spawn.py", line 143, in get_preparation_data
    _check_not_importing_main()
  File "C:\Users\anton\anaconda3\envs\elm2d-3\lib\multiprocessing\spawn.py", line 136, in _check_not_importing_main
    is not going to be frozen to produce an executable.''')
RuntimeError:
        An attempt has been made to start a new process before the
        current process has finished its bootstrapping phase.

        This probably means that you are not using fork to start your
        child processes and you have forgotten to use the proper idiom
        in the main module:

            if __name__ == '__main__':
                freeze_support()
                ...

        The "freeze_support()" line can be omitted if the program
        is not going to be frozen to produce an executable.
  0%|                                                                                                                                                                            | 0/62 [00:24<?, ?it/s]

The RuntimeError's message is quite obscure to me. Any idea about what is going on?
I should also mention that the method started behaving like this after having worked for some hours.

Build:
new conda environment with python 3.7.11.
Packages installed: elmd 0.4.25, elm2d 0.4.1, ipykernel, numba 0.55.1, scikit-learn 1.0.2, seaborn 0.11.2, pandas 1.3.4, plotly 5.1.0, numpy 1.21.5 (all pip-installed)

Any help would be much appreciated, thank you!

Run ElM2D on GPU

Hi!
This may be a trivial question, but I was wondering: how can I run the fit_transform method on my GPU? The goal is to speed up the calculation.
I'm not an expert in the use of numba, so feel free to add any detail that you deem relevant!

Possible inconsistency between distance computations of various versions

This is a bit hard for me to check since I'm not sure what ElM2D versions corresponded with what ElMD versions, and randomly guessing can lead to a decent amount of refactoring. However, in one of my test files from a forked and heavily modified repo, I get the following output, which used to evaluate just fine with the 1e-3 absolute tolerance.

test_ElM2D.py

pytest

Not equal to tolerance rtol=1e-07, atol=0.001
wasserstein did not match network simplex.
Mismatched elements: 49996 / 250000 (20%)
Max absolute difference: 71.999967
Max relative difference: 183.
 x: array([[ 0.      , 82.      , 42.      , ..., 53.      , 53.333333,
        71.666667],
       [82.      ,  0.      , 40.      , ..., 29.      , 28.666667,...
 y: array([[ 0.      , 82.      , 42.      , ..., 53.      , 53.33328 ,
        71.666595],
       [82.      ,  0.      , 40.      , ..., 29.      , 28.666638,...

It's possible it's an issue on my side, but it seems like it might have to do with some of the changes in ElMD or ElM2D. Is there a pairwise distance matrix you especially trust that could be used directly in a unit test? If so, could you share it?

The RMSE is 6.33, so it doesn't seem to be just a matter of increasing the tolerance. Any other thoughts?

Input/Output files

formulae

stable-mp-500.csv

`500x500` distance matrices

mat_discover_ElM2D.csv
ElM2D_0-4-0_ElMD_0-4-3.csv

How do you feel about black code style?

Spyder allows for automatic black formatting - and I'm wondering if you're OK with me submitting a pull request that's had this auto-formatting applied to ElM2D.py.

Suggestions for development workflow

I'm trying to add a function for which I plan to submit a pull request, but I'm having some trouble with the workflow for developing. For example, I can use pip install -e . after cloning, or python setup.py install, etc. but I've been running into odd errors like the computation seeming to stall out. I was wondering what your workflow is and what you would suggest.

Numba needs NumPy 1.20 or less (import umap)

Traceback (most recent call last):
  File "c:\Users\sterg\.vscode\extensions\ms-python.python-2021.9.1230869389\pythonFiles\lib\python\debugpy\_vendored\pydevd\_pydevd_bundle\pydevd_vars.py", line 419, in evaluate_expression
    compiled = compile(_expression_to_evaluate(expression), '<string>', 'eval')
  File "<string>", line 1
    import umap
    ^
SyntaxError: invalid syntax

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "C:\Users\sterg\Anaconda3\envs\elm2d_\lib\site-packages\umap\__init__.py", line 2, in <module>
    from .umap_ import UMAP
  File "C:\Users\sterg\Anaconda3\envs\elm2d_\lib\site-packages\umap\umap_.py", line 28, in <module>
    import numba
  File "C:\Users\sterg\Anaconda3\envs\elm2d_\lib\site-packages\numba\__init__.py", line 198, in <module>
    _ensure_critical_deps()
  File "C:\Users\sterg\Anaconda3\envs\elm2d_\lib\site-packages\numba\__init__.py", line 138, in _ensure_critical_deps
    raise ImportError("Numba needs NumPy 1.20 or less")
ImportError: Numba needs NumPy 1.20 or less

Exception has occurred: TypeError       (note: full exception trace is shown but execution is paused at: test_dm_close)
EMD() takes 3 positional arguments but 4 were given
  File "C:\Users\sterg\Documents\GitHub\scratch\discover-size-check\mat_discover\ElM2D\test_ElM2D.py", line 67, in test_dm_close (Current frame)
    mapper2.fit(sub_formulas)

Version info:

ElM2D==0.4.0
ElMD==0.4.7

Featurizing seems rather slow

Does it have to do with chunksize=1?

ElM2D/ElM2D/ElM2D.py

Lines 435 to 444 in 7c82fdc

    
           def featurize(self, compositions, how="mean"): 
        
               elmd_obj = ElMD(metric=self.metric) 
        
               # if type(elmd_obj.periodic_tab[self.metric]["H"]) is int: 
        
               #     vectors = np.ndarray((len(compositions), len(elmd_obj.periodic_tab[self.metric]))) 
        
               # else: 
        
               #     vectors = np.ndarray((len(compositions), len(elmd_obj.periodic_tab[self.metric]["H"]))) 
        
               print(f"Constructing compositionally weighted {self.metric} feature vectors for each composition") 
        
               vectors = process_map(self._pool_featurize, compositions, chunksize=1)

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	def featurize(self, compositions, how="mean"):
	elmd_obj = ElMD(metric=self.metric)

	# if type(elmd_obj.periodic_tab[self.metric]["H"]) is int:
	# vectors = np.ndarray((len(compositions), len(elmd_obj.periodic_tab[self.metric])))
	# else:
	# vectors = np.ndarray((len(compositions), len(elmd_obj.periodic_tab[self.metric]["H"])))

	print(f"Constructing compositionally weighted {self.metric} feature vectors for each composition")
	vectors = process_map(self._pool_featurize, compositions, chunksize=1)