Closed awlange closed 1 month ago
peastman
commented
1 month ago PDBFixer is pure Python. It isn't compiled at all, and shouldn't care which version of numpy you have.
The real issue comes from OpenMM. It has a compiled Python module, which limits binary compatibility. If you install it with conda, it will guarantee that compatible versions of packages are installed. We're currently working on support for installation with pip, but we're not quite there yet.
awlange
commented
1 month ago Righto, can use the conda install in a separate environment. I was initially attempting to avoid using conda to install in order to avoid mixing pip and conda in the environment I was using. So, that's why I went the route of trying to install. Hope to see that pip/pypi package soon!
Agreed that it looks like OpenMM being the ultimate culprit. Here is my full stack trace (at bottom), where I can see the call in OpenMM as the issue. It seems the upstream dependency on OpenMM numpy version is implicit for PDBFixer.
It's a-okay by me that this PR is not merged. I just figured out how to make this work for my case, and I thought it might be a simple quick fix that is useful for others.
/Users/adrianlange/programming/copy2/pdbfixer/venv/lib/python3.12/site-packages/OpenMM-8.1.1-py3.12-macosx-14.0-arm64.egg/openmm/__init__.py:16: SyntaxWarning: invalid escape sequence '\p'
os.environ['PATH'] = '%(lib)s;%(lib)s\plugins;%(path)s' % {
/Users/adrianlange/programming/copy2/pdbfixer/venv/lib/python3.12/site-packages/OpenMM-8.1.1-py3.12-macosx-14.0-arm64.egg/openmm/openmm.py:10518: SyntaxWarning: invalid escape sequence '\S'
match = re.search("<([^?]\S*)", inputString)
/Users/adrianlange/programming/copy2/pdbfixer/venv/lib/python3.12/site-packages/OpenMM-8.1.1-py3.12-macosx-14.0-arm64.egg/openmm/app/internal/pdbstructure.py:1071: SyntaxWarning: invalid escape sequence '\.'
if not re.match("pdb.%2s.\.ent\.gz" % subdir , pdb_file):
/Users/adrianlange/programming/copy2/pdbfixer/venv/lib/python3.12/site-packages/OpenMM-8.1.1-py3.12-macosx-14.0-arm64.egg/openmm/app/internal/pdbstructure.py:1082: SyntaxWarning: invalid escape sequence '\.'
if not re.match("pdb.%2s.\.ent\.gz" % subdir , pdb_file):
A module that was compiled using NumPy 1.x cannot be run in
NumPy 2.0.0rc2 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 "/Users/adrianlange/programming/copy2/pdbfixer/venv/bin/pdbfixer", line 33, in <module>
sys.exit(load_entry_point('pdbfixer==1.9.0', 'console_scripts', 'pdbfixer')())
File "/Users/adrianlange/programming/copy2/pdbfixer/venv/bin/pdbfixer", line 25, in importlib_load_entry_point
return next(matches).load()
File "/opt/homebrew/Cellar/python@3.12/3.12.3/Frameworks/Python.framework/Versions/3.12/lib/python3.12/importlib/metadata/__init__.py", line 205, in load
module = import_module(match.group('module'))
File "/opt/homebrew/Cellar/python@3.12/3.12.3/Frameworks/Python.framework/Versions/3.12/lib/python3.12/importlib/__init__.py", line 90, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "/Users/adrianlange/programming/copy2/pdbfixer/venv/lib/python3.12/site-packages/pdbfixer-1.9.0-py3.12.egg/pdbfixer/__init__.py", line 2, in <module>
from .pdbfixer import PDBFixer
File "/Users/adrianlange/programming/copy2/pdbfixer/venv/lib/python3.12/site-packages/pdbfixer-1.9.0-py3.12.egg/pdbfixer/pdbfixer.py", line 36, in <module>
import openmm.app as app
File "/Users/adrianlange/programming/copy2/pdbfixer/venv/lib/python3.12/site-packages/OpenMM-8.1.1-py3.12-macosx-14.0-arm64.egg/openmm/app/__init__.py", line 17, in <module>
from .xtcfile import XTCFile
File "/Users/adrianlange/programming/copy2/pdbfixer/venv/lib/python3.12/site-packages/OpenMM-8.1.1-py3.12-macosx-14.0-arm64.egg/openmm/app/xtcfile.py", line 6, in <module>
from openmm.app.internal.xtc_utils import (
Traceback (most recent call last):
File "/Users/adrianlange/programming/copy2/pdbfixer/venv/bin/pdbfixer", line 33, in <module>
sys.exit(load_entry_point('pdbfixer==1.9.0', 'console_scripts', 'pdbfixer')())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/adrianlange/programming/copy2/pdbfixer/venv/bin/pdbfixer", line 25, in importlib_load_entry_point
return next(matches).load()
^^^^^^^^^^^^^^^^^^^^
File "/opt/homebrew/Cellar/python@3.12/3.12.3/Frameworks/Python.framework/Versions/3.12/lib/python3.12/importlib/metadata/__init__.py", line 205, in load
module = import_module(match.group('module'))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/homebrew/Cellar/python@3.12/3.12.3/Frameworks/Python.framework/Versions/3.12/lib/python3.12/importlib/__init__.py", line 90, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "<frozen importlib._bootstrap>", line 1387, in _gcd_import
File "<frozen importlib._bootstrap>", line 1360, in _find_and_load
File "<frozen importlib._bootstrap>", line 1310, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 488, in _call_with_frames_removed
File "<frozen importlib._bootstrap>", line 1387, in _gcd_import
File "<frozen importlib._bootstrap>", line 1360, in _find_and_load
File "<frozen importlib._bootstrap>", line 1331, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 935, in _load_unlocked
File "<frozen importlib._bootstrap_external>", line 995, in exec_module
File "<frozen importlib._bootstrap>", line 488, in _call_with_frames_removed
File "/Users/adrianlange/programming/copy2/pdbfixer/venv/lib/python3.12/site-packages/pdbfixer-1.9.0-py3.12.egg/pdbfixer/__init__.py", line 2, in <module>
from .pdbfixer import PDBFixer
File "/Users/adrianlange/programming/copy2/pdbfixer/venv/lib/python3.12/site-packages/pdbfixer-1.9.0-py3.12.egg/pdbfixer/pdbfixer.py", line 36, in <module>
import openmm.app as app
File "/Users/adrianlange/programming/copy2/pdbfixer/venv/lib/python3.12/site-packages/OpenMM-8.1.1-py3.12-macosx-14.0-arm64.egg/openmm/app/__init__.py", line 17, in <module>
from .xtcfile import XTCFile
File "/Users/adrianlange/programming/copy2/pdbfixer/venv/lib/python3.12/site-packages/OpenMM-8.1.1-py3.12-macosx-14.0-arm64.egg/openmm/app/xtcfile.py", line 6, in <module>
from openmm.app.internal.xtc_utils import (
File "openmm/app/internal/xtc_utils/xtc.pyx", line 1, in init openmm.app.internal.xtc_utils
ImportError: numpy.core.multiarray failed to import (auto-generated because you didn't call 'numpy.import_array()' after cimporting numpy; use '<void>numpy._import_array' to disable if you are certain you don't need it).Yeah, mixing pip and conda can be awkward. We'll hopefully have a better solution for it soon.
TL;DR Small bug fix for
numpy < 2version cap.I encountered an error when attempting to perform a local installation of
pdbfixeron macOS Sonoma 14.1, Apple M3 Max with python 3.12.3.After creating a clean virtual environment and
pip install setuptools, I ranpython setup.py install. The installation appears to successfully complete, however when calling the CLI executablepdbfixer, the following (abbreviated) error message is displayed:This error is preventing successful execution of
pdbfixer.Looking at
setup.py, I see that the version fornumpyis not specified, in which case I believe the installation will attempt to use the latest available version. According to the release history ofnumpy, the latest version is nownumpy 2.0.0rc2. I believe this was the root cause of the error.To help, I simply added a version cap in
setup.pyfornumpy < 2. Then, re-installing succeeds, and the CLIpdbfixercommand works as expected.