Dependencies not installed when installing v3.2.0 from PyPI

[hakonanes]

Hi all!

Installing diffpy.structure v3.2.0 from PyPI into a Python 3.11.9 environment with

pip install diffpy.structure

and running

>>> from diffpy.structure import loadStructure

raises

Traceback (most recent call last):
 File "<stdin>", line 1, in <module>
 File "/opt/homebrew/Caskroom/mambaforge/base/envs/diffpy/lib/python3.11/site-packages/diffpy/structure/__init__.py", line 40, in <module>
 from diffpy.structure.atom import Atom
 File "/opt/homebrew/Caskroom/mambaforge/base/envs/diffpy/lib/python3.11/site-packages/diffpy/structure/atom.py", line 20, in <module>
 import numpy
ModuleNotFoundError: No module named 'numpy'

Looking at my fresh environment

> pip list
Package Version
---------------- -------
diffpy.structure 3.2.0
pip 24.2
setuptools 72.2.0
wheel 0.44.0

🤔 ... it is rather bare. Should I not get the dependencies when installing from PyPI? This is what I'd expect. It seems to me like you can include NumPy and PyCIFRW as core dependencies in your pyproject.toml file?

As a maintainer of a package depending on diffpy.structure for CIF reading, this means that we now have to list PyCIFRW as a dependency when using diffpy.structure.parsers.p_cif, while before we only had to list diffpy.structure.

[sbillinge]

Thanks for this @hakonanes, they should install. We will take a look.

We have been restructuring our packages to make them consistent and have introduced some bugs out seems. Our apologies. Thanks for posting the bug.

[sbillinge]

We will try and push out a fix today.

[sbillinge]

closed by a related PR, but reopening because it is not tested.

[sbillinge]

@hakonanes I pushed a new release-candidate to pypi. Please can you test that it works for you? It is a pre-release so you will only get it if you pin the dependency to diffpy.structure==3.2.1rc1

If this works then I will make a full release of 3.2.1 which you would then get with pip install diffpy.structure as usual.

[hakonanes]

Hi @sbillinge and team, it works! Thanks for the speedy fixing :)

Extending my environment from above:

$ pip list
Package Version
---------------- -------
diffpy.structure 3.2.0
pip 24.2
setuptools 72.2.0
wheel 0.44.0

$ pip install diffpy.structure==3.2.1rc1
Collecting diffpy.structure==3.2.1rc1
 Downloading diffpy_structure-3.2.1rc1.tar.gz (98 kB)
 Installing build dependencies ... done
 Getting requirements to build wheel ... done
 Preparing metadata (pyproject.toml) ... done
Collecting numpy<2.0.0 (from diffpy.structure==3.2.1rc1)
 Using cached numpy-1.26.4-cp311-cp311-macosx_11_0_arm64.whl.metadata (114 kB)
Collecting pycifrw (from diffpy.structure==3.2.1rc1)
 Using cached PyCifRW-4.4.6-cp311-cp311-macosx_11_0_arm64.whl
Collecting ply (from pycifrw->diffpy.structure==3.2.1rc1)
 Using cached ply-3.11-py2.py3-none-any.whl.metadata (844 bytes)
Using cached numpy-1.26.4-cp311-cp311-macosx_11_0_arm64.whl (14.0 MB)
Using cached ply-3.11-py2.py3-none-any.whl (49 kB)
Building wheels for collected packages: diffpy.structure
 Building wheel for diffpy.structure (pyproject.toml) ... done
 Created wheel for diffpy.structure: filename=diffpy.structure-3.2.1rc1-py3-none-any.whl size=117000 sha256=6576bad2030cf77c434995c6ad0cd60d23d9581b8b8f07328d43f580c3a81657
 Stored in directory: /Users/hakon/Library/Caches/pip/wheels/0b/bc/54/c7ae5a7de90a8402f7b51677fbad2cb5327817e2e5b9853008
Successfully built diffpy.structure
Installing collected packages: ply, numpy, pycifrw, diffpy.structure
 Attempting uninstall: diffpy.structure
 Found existing installation: diffpy.structure 3.2.0
 Uninstalling diffpy.structure-3.2.0:
 Successfully uninstalled diffpy.structure-3.2.0
Successfully installed diffpy.structure-3.2.1rc1 numpy-1.26.4 ply-3.11 pycifrw-4.4.6

$ pip list
Package Version
---------------- --------
diffpy.structure 3.2.1rc1
numpy 1.26.4
pip 24.2
ply 3.11
PyCifRW 4.4.6
setuptools 72.2.0
wheel 0.44.0

[sbillinge]

I will make the full release now. It will be 3.2.1

[sbillinge]

closed by #98 and tested