py310-scipy @1.9.3: _biasedurn.pyx:13:4: 'numpy/random.pxd' not found

[renzresearch]

I was installing py-scikit-image on Ventura. I got this:

Error: Failed to build py310-scipy: command execution failed
Error: See /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_python_py-scipy/py310-scipy/main.log for details.
Error: Follow https://guide.macports.org/#project.tickets if you believe there
is a bug.
Error: Processing of port py-scikit-image failed

The main.log is attached.

[renzresearch]

Log file

[michaelld (Michael Dickens)]

has duplicate #66335

[michaelld (Michael Dickens)]

For folks with this issue, what does the following return:

port contents py310-numpy | grep random | grep -v /tests/ | grep -v /_examples/ | grep -v \.so | grep -v /__pycache__/

Also: are you able to install py311-scipy? if it fails then attach the build log

[michaelld (Michael Dickens)]

Ignore that last query ... I haven't committed those changes for py311-scipy yet ... requires some other Py311 ports. Basically wondering if this issue is limited to Py310 or does it impact other versions of SciPy?

[coolstars21]

port contents py310-numpy | grep random | grep -v /tests/ | grep -v /_examples/ | grep -v \.so | grep -v /pycache/

/opt/local/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/numpy/core/include/numpy/random/bitgen.h /opt/local/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/numpy/core/include/numpy/random/distributions.h /opt/local/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/numpy/random/init.pxd /opt/local/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/numpy/random/init.py /opt/local/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/numpy/random/init.pyi /opt/local/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/numpy/random/_bounded_integers.pxd /opt/local/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/numpy/random/_common.pxd /opt/local/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/numpy/random/_generator.pyi /opt/local/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/numpy/random/_mt19937.pyi /opt/local/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/numpy/random/_pcg64.pyi /opt/local/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/numpy/random/_philox.pyi /opt/local/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/numpy/random/_pickle.py /opt/local/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/numpy/random/_sfc64.pyi /opt/local/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/numpy/random/bit_generator.pxd /opt/local/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/numpy/random/bit_generator.pyi /opt/local/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/numpy/random/c_distributions.pxd /opt/local/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/numpy/random/lib/libnpyrandom.a /opt/local/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/numpy/random/mtrand.pyi /opt/local/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/numpy/random/setup.py

[coolstars21]

I just tried to install py39-scipy and got an error as well. Log is attached.

Note that I have py27-scipy running, though.

[coolstars21]

Log file for py39-scipy

[michaelld (Michael Dickens)]

Thanks @coolstars21 . Py39-scipy shows the same issue. The port contents py310-numpy looks correct to me. What does the following return:

python3.10 -c "import numpy ; print(numpy.__version__)"

[coolstars21]

/opt/local/bin/python3.10 -c "import numpy ; print(numpy.version)"

1.23.5

[michaelld (Michael Dickens)]

OK; that's good. What about python3.10 -c "import numpy ; print(numpy.version)"

[coolstars21]

/opt/local/bin/python3.10 -c "import numpy ; print(numpy.version)"

<module 'numpy.version' from '/opt/local/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/numpy/version.py'>

[michaelld (Michael Dickens)]

OK that looks good too

[michaelld (Michael Dickens)]

I'll note that the ​MP builders succeed with `py310-numpy` for all OSX >= 10.7 ... but that there is no macOS 13 builder up yet. It builds for me on my macOS 13.1-beta Intel computer:

% mp_host_info
macOS 13.1 22C5050e
Xcode 14.1 14B47b
% port -v installed py310-scipy
The following ports are currently installed:
  py310-scipy @1.9.3_0+gfortran+openblas (active) requested_variants='' platform='darwin 22' archs='x86_64' date='2022-11-17T18:14:48-0500'

I don't have a macOS 13 ARM64 computer up right now, but at least one log shows building for Intel.

[michaelld (Michael Dickens)]

Comparing build logs (mine versus the one here), there are no real differences. Just for some reason it fails for folks here but it doesn't for me or the MP builders. So strange!

[adsche]

I get this as well (macOS Ventura 13.0.1, xcode 14.1, ARM64 (M2), python 3.10.9+lto+optimizations, py310-numpy @1.23.5_0+gfortran+openblas)

Numpy does indeed not contain the 'missing'(?) random.pxd file:

port contents py310-numpy | grep pxd
  /opt/local/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/numpy/__init__.cython-30.pxd
  /opt/local/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/numpy/__init__.pxd
  /opt/local/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/numpy/random/__init__.pxd
  /opt/local/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/numpy/random/_bounded_integers.pxd
  /opt/local/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/numpy/random/_common.pxd
  /opt/local/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/numpy/random/bit_generator.pxd
  /opt/local/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/numpy/random/c_distributions.pxd

Possibly same issue in the scipy tracker, attributed to a 'wrong'(?) cython being used? ​https://github.com/scipy/scipy/issues/17552

Anything I can do to help debug this?

[adsche]

Ok, wow, indeed, it picked up the wrong cython. sudo port select cython cython310 fixed it for me (it was cython39 before which I did not install nor select manually).

However, does the port maybe have to be fixed to use the correct one? Otherwise it would require manual intervention to have py39-scipy and py310-scipy installed at the same time, correct?

[kencu (Ken)]

this has installed for me with no problems twice now on an M1 running Ventura.

As Michael notes it builds for him on Intel as well, I'm going to call this fixed, therefore, or perhaps it was being caused by people having sudo port select'ed an older cython.

 % port -v installed py310-scipy
The following ports are currently installed:
  py310-scipy @1.9.3_0+gfortran+openblas requested_variants='' platform='darwin 22' archs='arm64' date='2022-12-29T13:31:38-0800'
  py310-scipy @1.10.0_0+gfortran+openblas (active) requested_variants='' platform='darwin 22' archs='arm64' date='2023-02-05T19:26:39-0800'

please reopen with new info if ongoing issues.