Using graphein 1.7.7 in colab #424
Description
Describe the bug
Using graphein in colab:
When graphin is installed in colab environment , numpy gets downgraded when using pip install graphein in colab. Then from graphein.protein.config import ProteinGraphConfig fails with this message:
ValueError Traceback (most recent call last)
[<ipython-input-2-427fb779643b>](https://localhost:8080/#) in <cell line: 0>()
----> 1 from graphein.protein.config import ProteinGraphConfig
2
3 config = ProteinGraphConfig()
4 config.dict()
8 frames
[/usr/local/lib/python3.11/dist-packages/numpy/random/_pickle.py](https://localhost:8080/#) in <module>
----> 1 from .mtrand import RandomState
2 from ._philox import Philox
3 from ._pcg64 import PCG64, PCG64DXSM
4 from ._sfc64 import SFC64
5
numpy/random/mtrand.pyx in init numpy.random.mtrand()
ValueError: numpy.dtype size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject
To Reproduce
This is the output of running !pip install graphein:
Collecting graphein
Downloading graphein-1.7.7-py3-none-any.whl.metadata (19 kB)
Requirement already satisfied: pandas in /usr/local/lib/python3.11/dist-packages (from graphein) (2.2.2)
Collecting biopandas>=0.5.1 (from graphein)
Downloading biopandas-0.5.1-py3-none-any.whl.metadata (1.6 kB)
Collecting biopython (from graphein)
Downloading biopython-1.85-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (13 kB)
Collecting bioservices>=1.10.0 (from graphein)
Downloading bioservices-1.12.1-py3-none-any.whl.metadata (19 kB)
Collecting cpdb-protein==0.2.0 (from graphein)
Downloading cpdb-protein-0.2.0.tar.gz (68 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 68.6/68.6 kB 4.6 MB/s eta 0:00:00
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... done
Requirement already satisfied: cython in /usr/local/lib/python3.11/dist-packages (from graphein) (3.0.12)
Collecting deepdiff (from graphein)
Downloading deepdiff-8.4.2-py3-none-any.whl.metadata (7.1 kB)
Collecting loguru (from graphein)
Downloading loguru-0.7.3-py3-none-any.whl.metadata (22 kB)
Collecting looseversion (from graphein)
Downloading looseversion-1.3.0-py2.py3-none-any.whl.metadata (4.6 kB)
Requirement already satisfied: matplotlib>=3.4.3 in /usr/local/lib/python3.11/dist-packages (from graphein) (3.10.0)
Requirement already satisfied: multipledispatch in /usr/local/lib/python3.11/dist-packages (from graphein) (1.0.0)
Requirement already satisfied: networkx in /usr/local/lib/python3.11/dist-packages (from graphein) (3.4.2)
Collecting numpy<2 (from graphein)
Downloading numpy-1.26.4-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (61 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 61.0/61.0 kB 4.3 MB/s eta 0:00:00
Requirement already satisfied: plotly in /usr/local/lib/python3.11/dist-packages (from graphein) (5.24.1)
Requirement already satisfied: pydantic in /usr/local/lib/python3.11/dist-packages (from graphein) (2.11.3)
Requirement already satisfied: rich in /usr/local/lib/python3.11/dist-packages (from graphein) (13.9.4)
Collecting rich-click (from graphein)
Downloading rich_click-1.8.8-py3-none-any.whl.metadata (7.9 kB)
Requirement already satisfied: seaborn in /usr/local/lib/python3.11/dist-packages (from graphein) (0.13.2)
Requirement already satisfied: pyyaml!=5.4.0,!=5.4.1,!=6.0.0 in /usr/local/lib/python3.11/dist-packages (from graphein) (6.0.2)
Requirement already satisfied: scikit-learn in /usr/local/lib/python3.11/dist-packages (from graphein) (1.6.1)
Requirement already satisfied: scipy>=1.8 in /usr/local/lib/python3.11/dist-packages (from graphein) (1.14.1)
Requirement already satisfied: tqdm in /usr/local/lib/python3.11/dist-packages (from graphein) (4.67.1)
Collecting wget (from graphein)
Downloading wget-3.2.zip (10 kB)
Preparing metadata (setup.py) ... done
Requirement already satisfied: xarray in /usr/local/lib/python3.11/dist-packages (from graphein) (2025.1.2)
Collecting jaxtyping (from graphein)
Downloading jaxtyping-0.3.1-py3-none-any.whl.metadata (7.0 kB)
Collecting mmtf-python==1.1.3 (from biopandas>=0.5.1->graphein)
Downloading mmtf_python-1.1.3-py2.py3-none-any.whl.metadata (1.2 kB)
Collecting looseversion (from graphein)
Downloading looseversion-1.1.2-py3-none-any.whl.metadata (4.6 kB)
Requirement already satisfied: setuptools in /usr/local/lib/python3.11/dist-packages (from biopandas>=0.5.1->graphein) (75.2.0)
Requirement already satisfied: msgpack>=1.0.0 in /usr/local/lib/python3.11/dist-packages (from mmtf-python==1.1.3->biopandas>=0.5.1->graphein) (1.1.0)
Collecting appdirs<2.0.0,>=1.4.4 (from bioservices>=1.10.0->graphein)
Downloading appdirs-1.4.4-py2.py3-none-any.whl.metadata (9.0 kB)
Requirement already satisfied: beautifulsoup4<5.0.0,>=4.12.3 in /usr/local/lib/python3.11/dist-packages (from bioservices>=1.10.0->graphein) (4.13.4)
Requirement already satisfied: click<9.0.0,>=8.1.8 in /usr/local/lib/python3.11/dist-packages (from bioservices>=1.10.0->graphein) (8.1.8)
Collecting colorlog<7.0.0,>=6.9.0 (from bioservices>=1.10.0->graphein)
Downloading colorlog-6.9.0-py3-none-any.whl.metadata (10 kB)
Collecting easydev<0.14.0,>=0.13.3 (from bioservices>=1.10.0->graphein)
Downloading easydev-0.13.3-py3-none-any.whl.metadata (4.0 kB)
Collecting grequests<0.8.0,>=0.7.0 (from bioservices>=1.10.0->graphein)
Downloading grequests-0.7.0-py2.py3-none-any.whl.metadata (1.3 kB)
Requirement already satisfied: lxml<6.0.0,>=5.3.0 in /usr/local/lib/python3.11/dist-packages (from bioservices>=1.10.0->graphein) (5.3.2)
Requirement already satisfied: requests<3.0.0,>=2.32.3 in /usr/local/lib/python3.11/dist-packages (from bioservices>=1.10.0->graphein) (2.32.3)
Collecting requests-cache<2.0.0,>=1.2.1 (from bioservices>=1.10.0->graphein)
Downloading requests_cache-1.2.1-py3-none-any.whl.metadata (9.9 kB)
Collecting suds-community<2.0.0,>=1.2.0 (from bioservices>=1.10.0->graphein)
Downloading suds_community-1.2.0-py3-none-any.whl.metadata (1.6 kB)
Requirement already satisfied: wrapt<2.0.0,>=1.17.2 in /usr/local/lib/python3.11/dist-packages (from bioservices>=1.10.0->graphein) (1.17.2)
Collecting xmltodict<0.15.0,>=0.14.2 (from bioservices>=1.10.0->graphein)
Downloading xmltodict-0.14.2-py2.py3-none-any.whl.metadata (8.0 kB)
Requirement already satisfied: contourpy>=1.0.1 in /usr/local/lib/python3.11/dist-packages (from matplotlib>=3.4.3->graphein) (1.3.2)
Requirement already satisfied: cycler>=0.10 in /usr/local/lib/python3.11/dist-packages (from matplotlib>=3.4.3->graphein) (0.12.1)
Requirement already satisfied: fonttools>=4.22.0 in /usr/local/lib/python3.11/dist-packages (from matplotlib>=3.4.3->graphein) (4.57.0)
Requirement already satisfied: kiwisolver>=1.3.1 in /usr/local/lib/python3.11/dist-packages (from matplotlib>=3.4.3->graphein) (1.4.8)
Requirement already satisfied: packaging>=20.0 in /usr/local/lib/python3.11/dist-packages (from matplotlib>=3.4.3->graphein) (24.2)
Requirement already satisfied: pillow>=8 in /usr/local/lib/python3.11/dist-packages (from matplotlib>=3.4.3->graphein) (11.1.0)
Requirement already satisfied: pyparsing>=2.3.1 in /usr/local/lib/python3.11/dist-packages (from matplotlib>=3.4.3->graphein) (3.2.3)
Requirement already satisfied: python-dateutil>=2.7 in /usr/local/lib/python3.11/dist-packages (from matplotlib>=3.4.3->graphein) (2.8.2)
Requirement already satisfied: pytz>=2020.1 in /usr/local/lib/python3.11/dist-packages (from pandas->graphein) (2025.2)
Requirement already satisfied: tzdata>=2022.7 in /usr/local/lib/python3.11/dist-packages (from pandas->graphein) (2025.2)
Requirement already satisfied: typing_extensions>=4 in /usr/local/lib/python3.11/dist-packages (from rich-click->graphein) (4.13.2)
Requirement already satisfied: markdown-it-py>=2.2.0 in /usr/local/lib/python3.11/dist-packages (from rich->graphein) (3.0.0)
Requirement already satisfied: pygments<3.0.0,>=2.13.0 in /usr/local/lib/python3.11/dist-packages (from rich->graphein) (2.18.0)
Collecting orderly-set<6,>=5.3.0 (from deepdiff->graphein)
Downloading orderly_set-5.4.0-py3-none-any.whl.metadata (6.2 kB)
Collecting wadler-lindig>=0.1.3 (from jaxtyping->graphein)
Downloading wadler_lindig-0.1.5-py3-none-any.whl.metadata (17 kB)
Requirement already satisfied: tenacity>=6.2.0 in /usr/local/lib/python3.11/dist-packages (from plotly->graphein) (9.1.2)
Requirement already satisfied: annotated-types>=0.6.0 in /usr/local/lib/python3.11/dist-packages (from pydantic->graphein) (0.7.0)
Requirement already satisfied: pydantic-core==2.33.1 in /usr/local/lib/python3.11/dist-packages (from pydantic->graphein) (2.33.1)
Requirement already satisfied: typing-inspection>=0.4.0 in /usr/local/lib/python3.11/dist-packages (from pydantic->graphein) (0.4.0)
Requirement already satisfied: joblib>=1.2.0 in /usr/local/lib/python3.11/dist-packages (from scikit-learn->graphein) (1.4.2)
Requirement already satisfied: threadpoolctl>=3.1.0 in /usr/local/lib/python3.11/dist-packages (from scikit-learn->graphein) (3.6.0)
Requirement already satisfied: soupsieve>1.2 in /usr/local/lib/python3.11/dist-packages (from beautifulsoup4<5.0.0,>=4.12.3->bioservices>=1.10.0->graphein) (2.6)
Collecting colorama<0.5.0,>=0.4.6 (from easydev<0.14.0,>=0.13.3->bioservices>=1.10.0->graphein)
Downloading colorama-0.4.6-py2.py3-none-any.whl.metadata (17 kB)
Collecting line-profiler<5.0.0,>=4.1.2 (from easydev<0.14.0,>=0.13.3->bioservices>=1.10.0->graphein)
Downloading line_profiler-4.2.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (34 kB)
Requirement already satisfied: pexpect<5.0.0,>=4.9.0 in /usr/local/lib/python3.11/dist-packages (from easydev<0.14.0,>=0.13.3->bioservices>=1.10.0->graphein) (4.9.0)
Requirement already satisfied: platformdirs<5.0.0,>=4.2.0 in /usr/local/lib/python3.11/dist-packages (from easydev<0.14.0,>=0.13.3->bioservices>=1.10.0->graphein) (4.3.7)
Collecting gevent (from grequests<0.8.0,>=0.7.0->bioservices>=1.10.0->graphein)
Downloading gevent-25.4.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (13 kB)
Requirement already satisfied: mdurl~=0.1 in /usr/local/lib/python3.11/dist-packages (from markdown-it-py>=2.2.0->rich->graphein) (0.1.2)
Requirement already satisfied: six>=1.5 in /usr/local/lib/python3.11/dist-packages (from python-dateutil>=2.7->matplotlib>=3.4.3->graphein) (1.17.0)
Requirement already satisfied: charset-normalizer<4,>=2 in /usr/local/lib/python3.11/dist-packages (from requests<3.0.0,>=2.32.3->bioservices>=1.10.0->graphein) (3.4.1)
Requirement already satisfied: idna<4,>=2.5 in /usr/local/lib/python3.11/dist-packages (from requests<3.0.0,>=2.32.3->bioservices>=1.10.0->graphein) (3.10)
Requirement already satisfied: urllib3<3,>=1.21.1 in /usr/local/lib/python3.11/dist-packages (from requests<3.0.0,>=2.32.3->bioservices>=1.10.0->graphein) (2.3.0)
Requirement already satisfied: certifi>=2017.4.17 in /usr/local/lib/python3.11/dist-packages (from requests<3.0.0,>=2.32.3->bioservices>=1.10.0->graphein) (2025.1.31)
Requirement already satisfied: attrs>=21.2 in /usr/local/lib/python3.11/dist-packages (from requests-cache<2.0.0,>=1.2.1->bioservices>=1.10.0->graphein) (25.3.0)
Collecting cattrs>=22.2 (from requests-cache<2.0.0,>=1.2.1->bioservices>=1.10.0->graphein)
Downloading cattrs-24.1.3-py3-none-any.whl.metadata (8.4 kB)
Collecting url-normalize>=1.4 (from requests-cache<2.0.0,>=1.2.1->bioservices>=1.10.0->graphein)
Downloading url_normalize-2.2.0-py3-none-any.whl.metadata (4.9 kB)
Requirement already satisfied: ptyprocess>=0.5 in /usr/local/lib/python3.11/dist-packages (from pexpect<5.0.0,>=4.9.0->easydev<0.14.0,>=0.13.3->bioservices>=1.10.0->graphein) (0.7.0)
Requirement already satisfied: greenlet>=3.2.0 in /usr/local/lib/python3.11/dist-packages (from gevent->grequests<0.8.0,>=0.7.0->bioservices>=1.10.0->graphein) (3.2.0)
Collecting zope.event (from gevent->grequests<0.8.0,>=0.7.0->bioservices>=1.10.0->graphein)
Downloading zope.event-5.0-py3-none-any.whl.metadata (4.4 kB)
Collecting zope.interface (from gevent->grequests<0.8.0,>=0.7.0->bioservices>=1.10.0->graphein)
Downloading zope.interface-7.2-cp311-cp311-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (44 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 44.4/44.4 kB 3.3 MB/s eta 0:00:00
Downloading graphein-1.7.7-py3-none-any.whl (316 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 316.0/316.0 kB 20.3 MB/s eta 0:00:00
Downloading biopandas-0.5.1-py3-none-any.whl (68 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 68.3/68.3 kB 5.2 MB/s eta 0:00:00
Downloading looseversion-1.1.2-py3-none-any.whl (8.1 kB)
Downloading mmtf_python-1.1.3-py2.py3-none-any.whl (25 kB)
Downloading bioservices-1.12.1-py3-none-any.whl (258 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 258.0/258.0 kB 18.1 MB/s eta 0:00:00
Downloading numpy-1.26.4-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (18.3 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 18.3/18.3 MB 34.6 MB/s eta 0:00:00
Downloading rich_click-1.8.8-py3-none-any.whl (35 kB)
Downloading biopython-1.85-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.3 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.3/3.3 MB 83.3 MB/s eta 0:00:00
Downloading deepdiff-8.4.2-py3-none-any.whl (87 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 87.6/87.6 kB 6.9 MB/s eta 0:00:00
Downloading jaxtyping-0.3.1-py3-none-any.whl (55 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 55.3/55.3 kB 4.1 MB/s eta 0:00:00
Downloading loguru-0.7.3-py3-none-any.whl (61 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 61.6/61.6 kB 4.4 MB/s eta 0:00:00
Downloading appdirs-1.4.4-py2.py3-none-any.whl (9.6 kB)
Downloading colorlog-6.9.0-py3-none-any.whl (11 kB)
Downloading easydev-0.13.3-py3-none-any.whl (57 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 57.0/57.0 kB 4.3 MB/s eta 0:00:00
Downloading grequests-0.7.0-py2.py3-none-any.whl (5.7 kB)
Downloading orderly_set-5.4.0-py3-none-any.whl (12 kB)
Downloading requests_cache-1.2.1-py3-none-any.whl (61 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 61.4/61.4 kB 4.6 MB/s eta 0:00:00
Downloading suds_community-1.2.0-py3-none-any.whl (145 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 145.3/145.3 kB 9.7 MB/s eta 0:00:00
Downloading wadler_lindig-0.1.5-py3-none-any.whl (20 kB)
Downloading xmltodict-0.14.2-py2.py3-none-any.whl (10.0 kB)
Downloading cattrs-24.1.3-py3-none-any.whl (66 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 66.5/66.5 kB 5.0 MB/s eta 0:00:00
Downloading colorama-0.4.6-py2.py3-none-any.whl (25 kB)
Downloading line_profiler-4.2.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (750 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 750.2/750.2 kB 41.1 MB/s eta 0:00:00
Downloading url_normalize-2.2.0-py3-none-any.whl (14 kB)
Downloading gevent-25.4.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (2.1 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.1/2.1 MB 72.6 MB/s eta 0:00:00
Downloading zope.event-5.0-py3-none-any.whl (6.8 kB)
Downloading zope.interface-7.2-cp311-cp311-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (259 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 259.8/259.8 kB 19.0 MB/s eta 0:00:00
Building wheels for collected packages: cpdb-protein, wget
Building wheel for cpdb-protein (pyproject.toml) ... done
Created wheel for cpdb-protein: filename=cpdb_protein-0.2.0-cp311-cp311-linux_x86_64.whl size=245145 sha256=7fa9a4cce0b449aff467480b36f30845326704306419e0d3f0b1f4999537cbfd
Stored in directory: /root/.cache/pip/wheels/9d/0a/be/785478cf0a0939ea190abc78a86ba920af4b262047130b47cc
Building wheel for wget (setup.py) ... done
Created wheel for wget: filename=wget-3.2-py3-none-any.whl size=9655 sha256=004a627ab1f04484d7df3648b99f4020dc9d4e97b1d7743d6a1485261256b582
Stored in directory: /root/.cache/pip/wheels/40/b3/0f/a40dbd1c6861731779f62cc4babcb234387e11d697df70ee97
Successfully built cpdb-protein wget
Installing collected packages: wget, appdirs, zope.interface, zope.event, xmltodict, wadler-lindig, url-normalize, suds-community, orderly-set, numpy, mmtf-python, looseversion, loguru, line-profiler, colorlog, colorama, cattrs, requests-cache, jaxtyping, gevent, easydev, deepdiff, biopython, rich-click, grequests, cpdb-protein, biopandas, bioservices, graphein
Attempting uninstall: numpy
Found existing installation: numpy 2.0.2
Uninstalling numpy-2.0.2:
Successfully uninstalled numpy-2.0.2
ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
thinc 8.3.6 requires numpy<3.0.0,>=2.0.0, but you have numpy 1.26.4 which is incompatible.
Successfully installed appdirs-1.4.4 biopandas-0.5.1 biopython-1.85 bioservices-1.12.1 cattrs-24.1.3 colorama-0.4.6 colorlog-6.9.0 cpdb-protein-0.2.0 deepdiff-8.4.2 easydev-0.13.3 gevent-25.4.1 graphein-1.7.7 grequests-0.7.0 jaxtyping-0.3.1 line-profiler-4.2.0 loguru-0.7.3 looseversion-1.1.2 mmtf-python-1.1.3 numpy-1.26.4 orderly-set-5.4.0 requests-cache-1.2.1 rich-click-1.8.8 suds-community-1.2.0 url-normalize-2.2.0 wadler-lindig-0.1.5 wget-3.2 xmltodict-0.14.2 zope.event-5.0 zope.interface-7.2
Desktop (please complete the following information):
- OS: in Colab
- Python Version: Python 3.11.12
- Graphein Version [e.g. 22] & how it was installed: graphein-1.7.7 installed using pip in colab