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Incompatible with NumPy 2 #102

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njzjz opened this issue Jun 24, 2024 · 0 comments · Fixed by #101
Closed

Incompatible with NumPy 2 #102

njzjz opened this issue Jun 24, 2024 · 0 comments · Fixed by #101

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@njzjz
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njzjz commented Jun 24, 2024

Importing rdkit with numpy 2.0.0 will throw the following errors:

A module that was compiled using NumPy 1.x cannot be run in
NumPy 2.0.0 as it may crash. To support both 1.x and 2.x
versions of NumPy, modules must be compiled with NumPy 2.0.
Some module may need to rebuild instead e.g. with 'pybind11>=2.12'.

If you are a user of the module, the easiest solution will be to
downgrade to 'numpy<2' or try to upgrade the affected module.
We expect that some modules will need time to support NumPy 2.

Traceback (most recent call last):  File "/usr/lib/python3.10/runpy.py", line 196, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "/usr/lib/python3.10/runpy.py", line 86, in _run_code
    exec(code, run_globals)
  File "/usr/local/lib/python3.10/dist-packages/colab_kernel_launcher.py", line 37, in <module>
    ColabKernelApp.launch_instance()
  File "/usr/local/lib/python3.10/dist-packages/traitlets/config/application.py", line 992, in launch_instance
    app.start()
  File "/usr/local/lib/python3.10/dist-packages/ipykernel/kernelapp.py", line 619, in start
    self.io_loop.start()
  File "/usr/local/lib/python3.10/dist-packages/tornado/platform/asyncio.py", line 195, in start
    self.asyncio_loop.run_forever()
  File "/usr/lib/python3.10/asyncio/base_events.py", line 603, in run_forever
    self._run_once()
  File "/usr/lib/python3.10/asyncio/base_events.py", line 1909, in _run_once
    handle._run()
  File "/usr/lib/python3.10/asyncio/events.py", line 80, in _run
    self._context.run(self._callback, *self._args)
  File "/usr/local/lib/python3.10/dist-packages/tornado/ioloop.py", line 685, in <lambda>
    lambda f: self._run_callback(functools.partial(callback, future))
  File "/usr/local/lib/python3.10/dist-packages/tornado/ioloop.py", line 738, in _run_callback
    ret = callback()
  File "/usr/local/lib/python3.10/dist-packages/tornado/gen.py", line 825, in inner
    self.ctx_run(self.run)
  File "/usr/local/lib/python3.10/dist-packages/tornado/gen.py", line 786, in run
    yielded = self.gen.send(value)
  File "/usr/local/lib/python3.10/dist-packages/ipykernel/kernelbase.py", line 361, in process_one
    yield gen.maybe_future(dispatch(*args))
  File "/usr/local/lib/python3.10/dist-packages/tornado/gen.py", line 234, in wrapper
    yielded = ctx_run(next, result)
  File "/usr/local/lib/python3.10/dist-packages/ipykernel/kernelbase.py", line 261, in dispatch_shell
    yield gen.maybe_future(handler(stream, idents, msg))
  File "/usr/local/lib/python3.10/dist-packages/tornado/gen.py", line 234, in wrapper
    yielded = ctx_run(next, result)
  File "/usr/local/lib/python3.10/dist-packages/ipykernel/kernelbase.py", line 539, in execute_request
    self.do_execute(
  File "/usr/local/lib/python3.10/dist-packages/tornado/gen.py", line 234, in wrapper
    yielded = ctx_run(next, result)
  File "/usr/local/lib/python3.10/dist-packages/ipykernel/ipkernel.py", line 302, in do_execute
    res = shell.run_cell(code, store_history=store_history, silent=silent)
  File "/usr/local/lib/python3.10/dist-packages/ipykernel/zmqshell.py", line 539, in run_cell
    return super(ZMQInteractiveShell, self).run_cell(*args, **kwargs)
  File "/usr/local/lib/python3.10/dist-packages/IPython/core/interactiveshell.py", line 2975, in run_cell
    result = self._run_cell(
  File "/usr/local/lib/python3.10/dist-packages/IPython/core/interactiveshell.py", line 3030, in _run_cell
    return runner(coro)
  File "/usr/local/lib/python3.10/dist-packages/IPython/core/async_helpers.py", line 78, in _pseudo_sync_runner
    coro.send(None)
  File "/usr/local/lib/python3.10/dist-packages/IPython/core/interactiveshell.py", line 3257, in run_cell_async
    has_raised = await self.run_ast_nodes(code_ast.body, cell_name,
  File "/usr/local/lib/python3.10/dist-packages/IPython/core/interactiveshell.py", line 3473, in run_ast_nodes
    if (await self.run_code(code, result,  async_=asy)):
  File "/usr/local/lib/python3.10/dist-packages/IPython/core/interactiveshell.py", line 3553, in run_code
    exec(code_obj, self.user_global_ns, self.user_ns)
  File "<ipython-input-1-0f218e1a7d3d>", line 1, in <cell line: 1>
    import rdkit.Chem as Chem
  File "/usr/local/lib/python3.10/dist-packages/rdkit/__init__.py", line 23, in <module>
    from rdkit.Chem.Draw import IPythonConsole
  File "/usr/local/lib/python3.10/dist-packages/rdkit/Chem/__init__.py", line 15, in <module>
    from rdkit import DataStructs, RDConfig, rdBase
  File "/usr/local/lib/python3.10/dist-packages/rdkit/DataStructs/__init__.py", line 13, in <module>
    from rdkit.DataStructs import cDataStructs
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
AttributeError: _ARRAY_API not found

See https://gist.github.com/njzjz/4b299ce4f38ff304051ec38c0f49f3ba for details.

See https://numpy.org/devdocs/dev/depending_on_numpy.html, numpy>=2.0.0rc1 should be used in the build dependency.

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