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Fix missing create_graph.c in source distribution #201

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merged 1 commit into from
Sep 12, 2024
Merged

Fix missing create_graph.c in source distribution #201

merged 1 commit into from
Sep 12, 2024

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DanielYang59
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@DanielYang59 DanielYang59 commented Sep 12, 2024 •
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Summary

  • Fix missing create_graph.c in source distribution

I believe this really fixes #160 where create_graph.c is missing from sdist, in other words, sdist should be installable alone, and wheels should not replace sdist.

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DanielYang59 commented Sep 12, 2024 •
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@janosh Perhaps you could review this, and after this I would be able to run workflows :)

@BowenD-UCB BowenD-UCB enabled auto-merge (squash) September 12, 2024 03:58
@DanielYang59
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DanielYang59 commented Sep 12, 2024 •
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one way to get around the need to manually approve CI runs on every commit would be to merge a small PR instantly.

@janosh This PR should do this job, but looks like you have to "force merge" it. I believe test failure is not related to this PR and they're just revealed after you turned off fail-fast :)

Also I confirm locally the new sdist works just fine

* Creating isolated environment: venv+pip...
* Installing packages in isolated environment:
  - Cython
  - setuptools>=65,<70
  - wheel
* Getting build dependencies for sdist...
* Installing packages in isolated environment:
  - Cython
* Building sdist...
running sdist
running egg_info
creating chgnet.egg-info
writing chgnet.egg-info/PKG-INFO
writing dependency_links to chgnet.egg-info/dependency_links.txt
writing requirements to chgnet.egg-info/requires.txt
writing top-level names to chgnet.egg-info/top_level.txt
writing manifest file 'chgnet.egg-info/SOURCES.txt'
reading manifest file 'chgnet.egg-info/SOURCES.txt'
adding license file 'LICENSE'
writing manifest file 'chgnet.egg-info/SOURCES.txt'
running check
creating chgnet-0.3.8
creating chgnet-0.3.8/chgnet
creating chgnet-0.3.8/chgnet.egg-info
creating chgnet-0.3.8/chgnet/data
creating chgnet-0.3.8/chgnet/graph
creating chgnet-0.3.8/chgnet/graph/fast_converter_libraries
creating chgnet-0.3.8/chgnet/model
creating chgnet-0.3.8/chgnet/pretrained
creating chgnet-0.3.8/chgnet/pretrained/0.2.0
creating chgnet-0.3.8/chgnet/pretrained/0.3.0
creating chgnet-0.3.8/chgnet/trainer
creating chgnet-0.3.8/chgnet/utils
creating chgnet-0.3.8/tests
copying files to chgnet-0.3.8...
copying LICENSE -> chgnet-0.3.8
copying README.md -> chgnet-0.3.8
copying pyproject.toml -> chgnet-0.3.8
copying setup.py -> chgnet-0.3.8
copying chgnet/__init__.py -> chgnet-0.3.8/chgnet
copying chgnet/py.typed -> chgnet-0.3.8/chgnet
copying chgnet.egg-info/PKG-INFO -> chgnet-0.3.8/chgnet.egg-info
copying chgnet.egg-info/SOURCES.txt -> chgnet-0.3.8/chgnet.egg-info
copying chgnet.egg-info/dependency_links.txt -> chgnet-0.3.8/chgnet.egg-info
copying chgnet.egg-info/requires.txt -> chgnet-0.3.8/chgnet.egg-info
copying chgnet.egg-info/top_level.txt -> chgnet-0.3.8/chgnet.egg-info
copying chgnet/data/__init__.py -> chgnet-0.3.8/chgnet/data
copying chgnet/data/dataset.py -> chgnet-0.3.8/chgnet/data
copying chgnet/graph/__init__.py -> chgnet-0.3.8/chgnet/graph
copying chgnet/graph/converter.py -> chgnet-0.3.8/chgnet/graph
copying chgnet/graph/crystalgraph.py -> chgnet-0.3.8/chgnet/graph
copying chgnet/graph/cygraph.pyx -> chgnet-0.3.8/chgnet/graph
copying chgnet/graph/graph.py -> chgnet-0.3.8/chgnet/graph
copying chgnet/graph/fast_converter_libraries/create_graph.c -> chgnet-0.3.8/chgnet/graph/fast_converter_libraries
copying chgnet/graph/fast_converter_libraries/uthash.h -> chgnet-0.3.8/chgnet/graph/fast_converter_libraries
copying chgnet/model/__init__.py -> chgnet-0.3.8/chgnet/model
copying chgnet/model/basis.py -> chgnet-0.3.8/chgnet/model
copying chgnet/model/composition_model.py -> chgnet-0.3.8/chgnet/model
copying chgnet/model/dynamics.py -> chgnet-0.3.8/chgnet/model
copying chgnet/model/encoders.py -> chgnet-0.3.8/chgnet/model
copying chgnet/model/functions.py -> chgnet-0.3.8/chgnet/model
copying chgnet/model/layers.py -> chgnet-0.3.8/chgnet/model
copying chgnet/model/model.py -> chgnet-0.3.8/chgnet/model
copying chgnet/pretrained/0.2.0/README.md -> chgnet-0.3.8/chgnet/pretrained/0.2.0
copying chgnet/pretrained/0.2.0/chgnet_0.2.0_e30f77s348m32.pth.tar -> chgnet-0.3.8/chgnet/pretrained/0.2.0
copying chgnet/pretrained/0.3.0/README.md -> chgnet-0.3.8/chgnet/pretrained/0.3.0
copying chgnet/pretrained/0.3.0/chgnet_0.3.0_e29f68s314m37.pth.tar -> chgnet-0.3.8/chgnet/pretrained/0.3.0
copying chgnet/trainer/__init__.py -> chgnet-0.3.8/chgnet/trainer
copying chgnet/trainer/trainer.py -> chgnet-0.3.8/chgnet/trainer
copying chgnet/utils/__init__.py -> chgnet-0.3.8/chgnet/utils
copying chgnet/utils/common_utils.py -> chgnet-0.3.8/chgnet/utils
copying chgnet/utils/vasp_utils.py -> chgnet-0.3.8/chgnet/utils
copying tests/test_converter.py -> chgnet-0.3.8/tests
copying tests/test_crystal_graph.py -> chgnet-0.3.8/tests
copying tests/test_dataset.py -> chgnet-0.3.8/tests
copying tests/test_encoders.py -> chgnet-0.3.8/tests
copying tests/test_graph.py -> chgnet-0.3.8/tests
copying tests/test_md.py -> chgnet-0.3.8/tests
copying tests/test_model.py -> chgnet-0.3.8/tests
copying tests/test_relaxation.py -> chgnet-0.3.8/tests
copying tests/test_trainer.py -> chgnet-0.3.8/tests
copying tests/test_utils.py -> chgnet-0.3.8/tests
copying tests/test_vasp_utils.py -> chgnet-0.3.8/tests
copying chgnet.egg-info/SOURCES.txt -> chgnet-0.3.8/chgnet.egg-info
Writing chgnet-0.3.8/setup.cfg
Creating tar archive
removing 'chgnet-0.3.8' (and everything under it)
Successfully built chgnet-0.3.8.tar.gz
(venv) yang@Yang-MacBook chgnet % pip install dist/chgnet-0.3.8.tar.gz 
Looking in indexes: https://pypi.tuna.tsinghua.edu.cn/simple
Processing ./dist/chgnet-0.3.8.tar.gz
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Requirement already satisfied: ase>=3.23.0 in ./venv/lib/python3.12/site-packages (from chgnet==0.3.8) (3.23.0)
Requirement already satisfied: cython>=3 in ./venv/lib/python3.12/site-packages (from chgnet==0.3.8) (3.0.10)
Requirement already satisfied: numpy<2,>=1.26 in ./venv/lib/python3.12/site-packages (from chgnet==0.3.8) (1.26.4)
Requirement already satisfied: nvidia-ml-py3>=7.352.0 in ./venv/lib/python3.12/site-packages (from chgnet==0.3.8) (7.352.0)
Requirement already satisfied: pymatgen>=2023.10.11 in ./venv/lib/python3.12/site-packages (from chgnet==0.3.8) (2024.8.9)
Requirement already satisfied: torch>=1.11.0 in ./venv/lib/python3.12/site-packages (from chgnet==0.3.8) (2.5.0.dev20240808)
Requirement already satisfied: typing-extensions>=4.12 in ./venv/lib/python3.12/site-packages (from chgnet==0.3.8) (4.12.2)
Requirement already satisfied: scipy>=1.6.0 in ./venv/lib/python3.12/site-packages (from ase>=3.23.0->chgnet==0.3.8) (1.14.0)
Requirement already satisfied: matplotlib>=3.3.4 in ./venv/lib/python3.12/site-packages (from ase>=3.23.0->chgnet==0.3.8) (3.9.0)
Requirement already satisfied: joblib>=1 in ./venv/lib/python3.12/site-packages (from pymatgen>=2023.10.11->chgnet==0.3.8) (1.4.2)
Requirement already satisfied: monty>=2024.7.29 in ./venv/lib/python3.12/site-packages (from pymatgen>=2023.10.11->chgnet==0.3.8) (2024.7.30)
Requirement already satisfied: networkx>=2.2 in ./venv/lib/python3.12/site-packages (from pymatgen>=2023.10.11->chgnet==0.3.8) (3.3)
Requirement already satisfied: palettable>=3.3.3 in ./venv/lib/python3.12/site-packages (from pymatgen>=2023.10.11->chgnet==0.3.8) (3.3.3)
Requirement already satisfied: pandas>=2 in ./venv/lib/python3.12/site-packages (from pymatgen>=2023.10.11->chgnet==0.3.8) (2.2.2)
Requirement already satisfied: plotly>=4.5.0 in ./venv/lib/python3.12/site-packages (from pymatgen>=2023.10.11->chgnet==0.3.8) (5.23.0)
Requirement already satisfied: pybtex>=0.24.0 in ./venv/lib/python3.12/site-packages (from pymatgen>=2023.10.11->chgnet==0.3.8) (0.24.0)
Requirement already satisfied: requests>=2.32 in ./venv/lib/python3.12/site-packages (from pymatgen>=2023.10.11->chgnet==0.3.8) (2.32.3)
Requirement already satisfied: ruamel.yaml>=0.17.0 in ./venv/lib/python3.12/site-packages (from pymatgen>=2023.10.11->chgnet==0.3.8) (0.18.6)
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Requirement already satisfied: tqdm>=4.60 in ./venv/lib/python3.12/site-packages (from pymatgen>=2023.10.11->chgnet==0.3.8) (4.66.5)
Requirement already satisfied: uncertainties>=3.1.4 in ./venv/lib/python3.12/site-packages (from pymatgen>=2023.10.11->chgnet==0.3.8) (3.2.2)
Requirement already satisfied: filelock in ./venv/lib/python3.12/site-packages (from torch>=1.11.0->chgnet==0.3.8) (3.15.4)
Requirement already satisfied: jinja2 in ./venv/lib/python3.12/site-packages (from torch>=1.11.0->chgnet==0.3.8) (3.1.4)
Requirement already satisfied: fsspec in ./venv/lib/python3.12/site-packages (from torch>=1.11.0->chgnet==0.3.8) (2024.6.1)
Requirement already satisfied: setuptools in ./venv/lib/python3.12/site-packages (from torch>=1.11.0->chgnet==0.3.8) (74.1.2)
Requirement already satisfied: contourpy>=1.0.1 in ./venv/lib/python3.12/site-packages (from matplotlib>=3.3.4->ase>=3.23.0->chgnet==0.3.8) (1.2.1)
Requirement already satisfied: cycler>=0.10 in ./venv/lib/python3.12/site-packages (from matplotlib>=3.3.4->ase>=3.23.0->chgnet==0.3.8) (0.12.1)
Requirement already satisfied: fonttools>=4.22.0 in ./venv/lib/python3.12/site-packages (from matplotlib>=3.3.4->ase>=3.23.0->chgnet==0.3.8) (4.53.1)
Requirement already satisfied: kiwisolver>=1.3.1 in ./venv/lib/python3.12/site-packages (from matplotlib>=3.3.4->ase>=3.23.0->chgnet==0.3.8) (1.4.5)
Requirement already satisfied: packaging>=20.0 in ./venv/lib/python3.12/site-packages (from matplotlib>=3.3.4->ase>=3.23.0->chgnet==0.3.8) (24.1)
Requirement already satisfied: pillow>=8 in ./venv/lib/python3.12/site-packages (from matplotlib>=3.3.4->ase>=3.23.0->chgnet==0.3.8) (10.4.0)
Requirement already satisfied: pyparsing>=2.3.1 in ./venv/lib/python3.12/site-packages (from matplotlib>=3.3.4->ase>=3.23.0->chgnet==0.3.8) (3.1.2)
Requirement already satisfied: python-dateutil>=2.7 in ./venv/lib/python3.12/site-packages (from matplotlib>=3.3.4->ase>=3.23.0->chgnet==0.3.8) (2.9.0.post0)
Requirement already satisfied: pytz>=2020.1 in ./venv/lib/python3.12/site-packages (from pandas>=2->pymatgen>=2023.10.11->chgnet==0.3.8) (2024.1)
Requirement already satisfied: tzdata>=2022.7 in ./venv/lib/python3.12/site-packages (from pandas>=2->pymatgen>=2023.10.11->chgnet==0.3.8) (2024.1)
Requirement already satisfied: tenacity>=6.2.0 in ./venv/lib/python3.12/site-packages (from plotly>=4.5.0->pymatgen>=2023.10.11->chgnet==0.3.8) (9.0.0)
Requirement already satisfied: PyYAML>=3.01 in ./venv/lib/python3.12/site-packages (from pybtex>=0.24.0->pymatgen>=2023.10.11->chgnet==0.3.8) (6.0.1)
Requirement already satisfied: latexcodec>=1.0.4 in ./venv/lib/python3.12/site-packages (from pybtex>=0.24.0->pymatgen>=2023.10.11->chgnet==0.3.8) (3.0.0)
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Requirement already satisfied: idna<4,>=2.5 in ./venv/lib/python3.12/site-packages (from requests>=2.32->pymatgen>=2023.10.11->chgnet==0.3.8) (3.7)
Requirement already satisfied: urllib3<3,>=1.21.1 in ./venv/lib/python3.12/site-packages (from requests>=2.32->pymatgen>=2023.10.11->chgnet==0.3.8) (2.2.2)
Requirement already satisfied: certifi>=2017.4.17 in ./venv/lib/python3.12/site-packages (from requests>=2.32->pymatgen>=2023.10.11->chgnet==0.3.8) (2024.7.4)
Requirement already satisfied: ruamel.yaml.clib>=0.2.7 in ./venv/lib/python3.12/site-packages (from ruamel.yaml>=0.17.0->pymatgen>=2023.10.11->chgnet==0.3.8) (0.2.8)
Requirement already satisfied: mpmath<1.4,>=1.1.0 in ./venv/lib/python3.12/site-packages (from sympy>=1.2->pymatgen>=2023.10.11->chgnet==0.3.8) (1.3.0)
Requirement already satisfied: MarkupSafe>=2.0 in ./venv/lib/python3.12/site-packages (from jinja2->torch>=1.11.0->chgnet==0.3.8) (2.1.5)
Building wheels for collected packages: chgnet
  Building wheel for chgnet (pyproject.toml) ... done
  Created wheel for chgnet: filename=chgnet-0.3.8-cp312-cp312-macosx_14_0_arm64.whl size=8825899 sha256=20afb98b3fd6ad8e07226a5f2ec7b56f2bda061d2a80a6dc4f36db6d76905d17
  Stored in directory: /Users/yang/Library/Caches/pip/wheels/d8/28/da/b2de38ad4cc189e3f099b41f163c5806b31e4d3e6d54bcc05a
Successfully built chgnet
Installing collected packages: chgnet
  Attempting uninstall: chgnet
    Found existing installation: chgnet 0.3.8
    Uninstalling chgnet-0.3.8:
      Successfully uninstalled chgnet-0.3.8
Successfully installed chgnet-0.3.8

@janosh janosh added pkg Package fix Bug fix PRs labels Sep 12, 2024
@janosh janosh merged commit fbfe69c into CederGroupHub:main Sep 12, 2024
4 of 10 checks passed
@DanielYang59 DanielYang59 deleted the fix-sdist branch September 12, 2024 11:45
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@janosh janosh janosh approved these changes

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[Bug]: pip install chgnet failed
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