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Dependencies are not resolved correctly when running the digits example on Google colab. #202

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bobturneruk opened this issue Aug 12, 2021 · 2 comments 路 Fixed by #208
Closed

Dependencies are not resolved correctly when running the digits example on Google colab. #202

bobturneruk opened this issue Aug 12, 2021 · 2 comments 路 Fixed by #208
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v0.1.0

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bobturneruk commented Aug 12, 2021 •
edited

馃悰 Bug

Dependencies are not resolved correctly when running the digits example on Google colab. Notebook otherwise runs fine.

To reproduce

Steps to reproduce the behavior:

  1. Navigate to https://colab.research.google.com/github/pykale/pykale/blob/main/examples/digits_dann_lightn/tutorial.ipynb and follow instructions in the notebook.

Or, code snippet to reproduce the behaviour

** Stack trace/error message **

Running on CoLab
Collecting pykale[extras]
  Cloning https://github.com/pykale/pykale.git to /tmp/pip-install-152ad5l4/pykale_674492876602436890922aa8e5d76e61
  Running command git clone -q https://github.com/pykale/pykale.git /tmp/pip-install-152ad5l4/pykale_674492876602436890922aa8e5d76e61
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
    Preparing wheel metadata ... done
WARNING: pykale 0.1.0rc2 does not provide the extra 'extras'
Requirement already satisfied: ipython in /usr/local/lib/python3.7/dist-packages (from pykale[extras]) (5.5.0)
Requirement already satisfied: numpy>=1.18.0 in /usr/local/lib/python3.7/dist-packages (from pykale[extras]) (1.19.5)
Collecting PyTDC
  Downloading PyTDC-0.2.0.tar.gz (73 kB)
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Collecting pytorch-memlab
  Downloading pytorch_memlab-0.2.3.tar.gz (21 kB)
Collecting scikit-learn>=0.23.2
  Downloading scikit_learn-0.24.2-cp37-cp37m-manylinux2010_x86_64.whl (22.3 MB)
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Requirement already satisfied: matplotlib in /usr/local/lib/python3.7/dist-packages (from pykale[extras]) (3.2.2)
Collecting tensorly>=0.5.1
  Downloading tensorly-0.6.0-py3-none-any.whl (160 kB)
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Requirement already satisfied: torchsummary>=1.5.0 in /usr/local/lib/python3.7/dist-packages (from pykale[extras]) (1.5.1)
Requirement already satisfied: Pillow in /usr/local/lib/python3.7/dist-packages (from pykale[extras]) (7.1.2)
Requirement already satisfied: torchvision in /usr/local/lib/python3.7/dist-packages (from pykale[extras]) (0.10.0+cu102)
Requirement already satisfied: scikit-image>=0.16.2 in /usr/local/lib/python3.7/dist-packages (from pykale[extras]) (0.16.2)
Requirement already satisfied: torch>=1.7.0 in /usr/local/lib/python3.7/dist-packages (from pykale[extras]) (1.9.0+cu102)
Collecting pytorch-lightning>=1.3.0
  Downloading pytorch_lightning-1.4.2-py3-none-any.whl (916 kB)
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Collecting scipy>=1.5.4
  Downloading scipy-1.7.1-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (28.5 MB)
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Requirement already satisfied: ipykernel in /usr/local/lib/python3.7/dist-packages (from pykale[extras]) (4.10.1)
Collecting yacs>=0.1.7
  Downloading yacs-0.1.8-py3-none-any.whl (14 kB)
Collecting future>=0.17.1
  Downloading future-0.18.2.tar.gz (829 kB)
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Collecting PyYAML>=5.1
  Downloading PyYAML-5.4.1-cp37-cp37m-manylinux1_x86_64.whl (636 kB)
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Collecting fsspec[http]!=2021.06.0,>=2021.05.0
  Downloading fsspec-2021.7.0-py3-none-any.whl (118 kB)
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Requirement already satisfied: tensorboard>=2.2.0 in /usr/local/lib/python3.7/dist-packages (from pytorch-lightning>=1.3.0->pykale[extras]) (2.5.0)
Collecting torchmetrics>=0.4.0
  Downloading torchmetrics-0.5.0-py3-none-any.whl (272 kB)
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Requirement already satisfied: packaging>=17.0 in /usr/local/lib/python3.7/dist-packages (from pytorch-lightning>=1.3.0->pykale[extras]) (21.0)
Collecting pyDeprecate==0.3.1
  Downloading pyDeprecate-0.3.1-py3-none-any.whl (10 kB)
Requirement already satisfied: typing-extensions in /usr/local/lib/python3.7/dist-packages (from pytorch-lightning>=1.3.0->pykale[extras]) (3.7.4.3)
Requirement already satisfied: tqdm>=4.41.0 in /usr/local/lib/python3.7/dist-packages (from pytorch-lightning>=1.3.0->pykale[extras]) (4.41.1)
Collecting aiohttp
  Downloading aiohttp-3.7.4.post0-cp37-cp37m-manylinux2014_x86_64.whl (1.3 MB)
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Requirement already satisfied: requests in /usr/local/lib/python3.7/dist-packages (from fsspec[http]!=2021.06.0,>=2021.05.0->pytorch-lightning>=1.3.0->pykale[extras]) (2.23.0)
Requirement already satisfied: pyparsing>=2.0.2 in /usr/local/lib/python3.7/dist-packages (from packaging>=17.0->pytorch-lightning>=1.3.0->pykale[extras]) (2.4.7)
Requirement already satisfied: PyWavelets>=0.4.0 in /usr/local/lib/python3.7/dist-packages (from scikit-image>=0.16.2->pykale[extras]) (1.1.1)
Requirement already satisfied: imageio>=2.3.0 in /usr/local/lib/python3.7/dist-packages (from scikit-image>=0.16.2->pykale[extras]) (2.4.1)
Requirement already satisfied: networkx>=2.0 in /usr/local/lib/python3.7/dist-packages (from scikit-image>=0.16.2->pykale[extras]) (2.5.1)
Requirement already satisfied: python-dateutil>=2.1 in /usr/local/lib/python3.7/dist-packages (from matplotlib->pykale[extras]) (2.8.1)
Requirement already satisfied: kiwisolver>=1.0.1 in /usr/local/lib/python3.7/dist-packages (from matplotlib->pykale[extras]) (1.3.1)
Requirement already satisfied: cycler>=0.10 in /usr/local/lib/python3.7/dist-packages (from matplotlib->pykale[extras]) (0.10.0)
Requirement already satisfied: six in /usr/local/lib/python3.7/dist-packages (from cycler>=0.10->matplotlib->pykale[extras]) (1.15.0)
Requirement already satisfied: decorator<5,>=4.3 in /usr/local/lib/python3.7/dist-packages (from networkx>=2.0->scikit-image>=0.16.2->pykale[extras]) (4.4.2)
Requirement already satisfied: joblib>=0.11 in /usr/local/lib/python3.7/dist-packages (from scikit-learn>=0.23.2->pykale[extras]) (1.0.1)
Collecting threadpoolctl>=2.0.0
  Downloading threadpoolctl-2.2.0-py3-none-any.whl (12 kB)
Requirement already satisfied: grpcio>=1.24.3 in /usr/local/lib/python3.7/dist-packages (from tensorboard>=2.2.0->pytorch-lightning>=1.3.0->pykale[extras]) (1.34.1)
Requirement already satisfied: setuptools>=41.0.0 in /usr/local/lib/python3.7/dist-packages (from tensorboard>=2.2.0->pytorch-lightning>=1.3.0->pykale[extras]) (57.2.0)
Requirement already satisfied: markdown>=2.6.8 in /usr/local/lib/python3.7/dist-packages (from tensorboard>=2.2.0->pytorch-lightning>=1.3.0->pykale[extras]) (3.3.4)
Requirement already satisfied: tensorboard-data-server<0.7.0,>=0.6.0 in /usr/local/lib/python3.7/dist-packages (from tensorboard>=2.2.0->pytorch-lightning>=1.3.0->pykale[extras]) (0.6.1)
Requirement already satisfied: wheel>=0.26 in /usr/local/lib/python3.7/dist-packages (from tensorboard>=2.2.0->pytorch-lightning>=1.3.0->pykale[extras]) (0.36.2)
Requirement already satisfied: protobuf>=3.6.0 in /usr/local/lib/python3.7/dist-packages (from tensorboard>=2.2.0->pytorch-lightning>=1.3.0->pykale[extras]) (3.17.3)
Requirement already satisfied: google-auth-oauthlib<0.5,>=0.4.1 in /usr/local/lib/python3.7/dist-packages (from tensorboard>=2.2.0->pytorch-lightning>=1.3.0->pykale[extras]) (0.4.4)
Requirement already satisfied: tensorboard-plugin-wit>=1.6.0 in /usr/local/lib/python3.7/dist-packages (from tensorboard>=2.2.0->pytorch-lightning>=1.3.0->pykale[extras]) (1.8.0)
Requirement already satisfied: google-auth<2,>=1.6.3 in /usr/local/lib/python3.7/dist-packages (from tensorboard>=2.2.0->pytorch-lightning>=1.3.0->pykale[extras]) (1.32.1)
Requirement already satisfied: werkzeug>=0.11.15 in /usr/local/lib/python3.7/dist-packages (from tensorboard>=2.2.0->pytorch-lightning>=1.3.0->pykale[extras]) (1.0.1)
Requirement already satisfied: absl-py>=0.4 in /usr/local/lib/python3.7/dist-packages (from tensorboard>=2.2.0->pytorch-lightning>=1.3.0->pykale[extras]) (0.12.0)
Requirement already satisfied: cachetools<5.0,>=2.0.0 in /usr/local/lib/python3.7/dist-packages (from google-auth<2,>=1.6.3->tensorboard>=2.2.0->pytorch-lightning>=1.3.0->pykale[extras]) (4.2.2)
Requirement already satisfied: rsa<5,>=3.1.4 in /usr/local/lib/python3.7/dist-packages (from google-auth<2,>=1.6.3->tensorboard>=2.2.0->pytorch-lightning>=1.3.0->pykale[extras]) (4.7.2)
Requirement already satisfied: pyasn1-modules>=0.2.1 in /usr/local/lib/python3.7/dist-packages (from google-auth<2,>=1.6.3->tensorboard>=2.2.0->pytorch-lightning>=1.3.0->pykale[extras]) (0.2.8)
Requirement already satisfied: requests-oauthlib>=0.7.0 in /usr/local/lib/python3.7/dist-packages (from google-auth-oauthlib<0.5,>=0.4.1->tensorboard>=2.2.0->pytorch-lightning>=1.3.0->pykale[extras]) (1.3.0)
Requirement already satisfied: importlib-metadata in /usr/local/lib/python3.7/dist-packages (from markdown>=2.6.8->tensorboard>=2.2.0->pytorch-lightning>=1.3.0->pykale[extras]) (4.6.1)
Requirement already satisfied: pyasn1<0.5.0,>=0.4.6 in /usr/local/lib/python3.7/dist-packages (from pyasn1-modules>=0.2.1->google-auth<2,>=1.6.3->tensorboard>=2.2.0->pytorch-lightning>=1.3.0->pykale[extras]) (0.4.8)
Requirement already satisfied: chardet<4,>=3.0.2 in /usr/local/lib/python3.7/dist-packages (from requests->fsspec[http]!=2021.06.0,>=2021.05.0->pytorch-lightning>=1.3.0->pykale[extras]) (3.0.4)
Requirement already satisfied: idna<3,>=2.5 in /usr/local/lib/python3.7/dist-packages (from requests->fsspec[http]!=2021.06.0,>=2021.05.0->pytorch-lightning>=1.3.0->pykale[extras]) (2.10)
Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /usr/local/lib/python3.7/dist-packages (from requests->fsspec[http]!=2021.06.0,>=2021.05.0->pytorch-lightning>=1.3.0->pykale[extras]) (1.24.3)
Requirement already satisfied: certifi>=2017.4.17 in /usr/local/lib/python3.7/dist-packages (from requests->fsspec[http]!=2021.06.0,>=2021.05.0->pytorch-lightning>=1.3.0->pykale[extras]) (2021.5.30)
Requirement already satisfied: oauthlib>=3.0.0 in /usr/local/lib/python3.7/dist-packages (from requests-oauthlib>=0.7.0->google-auth-oauthlib<0.5,>=0.4.1->tensorboard>=2.2.0->pytorch-lightning>=1.3.0->pykale[extras]) (3.1.1)
Collecting nose
  Downloading nose-1.3.7-py3-none-any.whl (154 kB)
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Requirement already satisfied: attrs>=17.3.0 in /usr/local/lib/python3.7/dist-packages (from aiohttp->fsspec[http]!=2021.06.0,>=2021.05.0->pytorch-lightning>=1.3.0->pykale[extras]) (21.2.0)
Collecting multidict<7.0,>=4.5
  Downloading multidict-5.1.0-cp37-cp37m-manylinux2014_x86_64.whl (142 kB)
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Collecting async-timeout<4.0,>=3.0
  Downloading async_timeout-3.0.1-py3-none-any.whl (8.2 kB)
Collecting yarl<2.0,>=1.0
  Downloading yarl-1.6.3-cp37-cp37m-manylinux2014_x86_64.whl (294 kB)
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Requirement already satisfied: zipp>=0.5 in /usr/local/lib/python3.7/dist-packages (from importlib-metadata->markdown>=2.6.8->tensorboard>=2.2.0->pytorch-lightning>=1.3.0->pykale[extras]) (3.5.0)
Requirement already satisfied: jupyter-client in /usr/local/lib/python3.7/dist-packages (from ipykernel->pykale[extras]) (5.3.5)
Requirement already satisfied: tornado>=4.0 in /usr/local/lib/python3.7/dist-packages (from ipykernel->pykale[extras]) (5.1.1)
Requirement already satisfied: traitlets>=4.1.0 in /usr/local/lib/python3.7/dist-packages (from ipykernel->pykale[extras]) (5.0.5)
Requirement already satisfied: pygments in /usr/local/lib/python3.7/dist-packages (from ipython->pykale[extras]) (2.6.1)
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Collecting fuzzywuzzy
  Downloading fuzzywuzzy-0.18.0-py2.py3-none-any.whl (18 kB)
Requirement already satisfied: pandas in /usr/local/lib/python3.7/dist-packages (from PyTDC->pykale[extras]) (1.1.5)
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Collecting calmsize
  Downloading calmsize-0.1.3.tar.gz (3.7 kB)
Building wheels for collected packages: pykale, future, PyTDC, pytorch-memlab, calmsize
  Building wheel for pykale (PEP 517) ... done
  Created wheel for pykale: filename=pykale-0.1.0rc2-py2.py3-none-any.whl size=133155 sha256=57c8de8e048d605ed228ee1502bcddb68a2403fe91214a10133229a808214ffd
  Stored in directory: /tmp/pip-ephem-wheel-cache-13m5rj5v/wheels/c1/55/38/ee279131d91650716ebcd64b3b7c9c3dd2a09359176663fabf
  Building wheel for future (setup.py) ... done
  Created wheel for future: filename=future-0.18.2-py3-none-any.whl size=491070 sha256=22406cefd7a6fef9bc2feef1d7ee86f1839ce1da36953c41f96e4f056503f15f
  Stored in directory: /root/.cache/pip/wheels/56/b0/fe/4410d17b32f1f0c3cf54cdfb2bc04d7b4b8f4ae377e2229ba0
  Building wheel for PyTDC (setup.py) ... done
  Created wheel for PyTDC: filename=PyTDC-0.2.0-py3-none-any.whl size=79519 sha256=607c9dcb8e1c7a367ad8ed9386b2ffa4474da298fd68ded326518c56ff661ec9
  Stored in directory: /root/.cache/pip/wheels/e5/e5/66/3dfd956e2e078a1ffda5819843469be9cad0a33dc2dfee5163
  Building wheel for pytorch-memlab (setup.py) ... done
  Created wheel for pytorch-memlab: filename=pytorch_memlab-0.2.3-py3-none-any.whl size=20196 sha256=9957b6a827c4e3d6c5bbd876e9fcd38767ca96b564fe7af9514c6f7b0bc10752
  Stored in directory: /root/.cache/pip/wheels/38/72/a9/b7c27b9cb14298e8b283eb8ded7c2fdc896e6b3609bd0af51a
  Building wheel for calmsize (setup.py) ... done
  Created wheel for calmsize: filename=calmsize-0.1.3-py3-none-any.whl size=2889 sha256=ed72ad96ddf15e1fbb1d7fd5caba2cba5e434d650d165005b130ed87214c218f
  Stored in directory: /root/.cache/pip/wheels/a3/92/5f/c4c4e3fa257084aecbdc44c0fe60bdef0cb870603f3642dd96
Successfully built pykale future PyTDC pytorch-memlab calmsize
Installing collected packages: multidict, yarl, async-timeout, threadpoolctl, scipy, fsspec, aiohttp, torchmetrics, scikit-learn, PyYAML, pyDeprecate, nose, fuzzywuzzy, future, calmsize, yacs, tensorly, pytorch-memlab, pytorch-lightning, PyTDC, pykale
  Attempting uninstall: scipy
    Found existing installation: scipy 1.4.1
    Uninstalling scipy-1.4.1:
      Successfully uninstalled scipy-1.4.1
  Attempting uninstall: scikit-learn
    Found existing installation: scikit-learn 0.22.2.post1
    Uninstalling scikit-learn-0.22.2.post1:
      Successfully uninstalled scikit-learn-0.22.2.post1
  Attempting uninstall: PyYAML
    Found existing installation: PyYAML 3.13
    Uninstalling PyYAML-3.13:
      Successfully uninstalled PyYAML-3.13
  Attempting uninstall: future
    Found existing installation: future 0.16.0
    Uninstalling future-0.16.0:
      Successfully uninstalled future-0.16.0
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.
albumentations 0.1.12 requires imgaug<0.2.7,>=0.2.5, but you have imgaug 0.2.9 which is incompatible.
Successfully installed PyTDC-0.2.0 PyYAML-5.4.1 aiohttp-3.7.4.post0 async-timeout-3.0.1 calmsize-0.1.3 fsspec-2021.7.0 future-0.18.2 fuzzywuzzy-0.18.0 multidict-5.1.0 nose-1.3.7 pyDeprecate-0.3.1 pykale-0.1.0rc2 pytorch-lightning-1.4.2 pytorch-memlab-0.2.3 scikit-learn-0.24.2 scipy-1.7.1 tensorly-0.6.0 threadpoolctl-2.2.0 torchmetrics-0.5.0 yacs-0.1.8 yarl-1.6.3
Cloning into 'pykale'...
remote: Enumerating objects: 8815, done.
remote: Counting objects: 100% (539/539), done.
remote: Compressing objects: 100% (347/347), done.
remote: Total 8815 (delta 349), reused 333 (delta 191), pack-reused 8276
Receiving objects: 100% (8815/8815), 15.13 MiB | 25.03 MiB/s, done.
Resolving deltas: 100% (6304/6304), done.
/content/pykale/examples/digits_dann_lightn

Expected Behaviour

No errors or warnings.

Environment

As per Google collab.

Additional context

The first warning acn be resolved by removing #egg=pykale[extras] from the pip install.
@bobturneruk bobturneruk added the bug Something isn't working label Aug 12, 2021
@github-actions github-actions bot added this to To do in v0.1.0 Aug 12, 2021
@bobturneruk bobturneruk changed the title [Bug] Dependencies are not resolved correctly when running the digits example on Google colab. Aug 12, 2021
@haipinglu
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haipinglu commented Aug 16, 2021 •
edited

#egg=pykale[extras] has been removed in #207

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Solution at https://stackoverflow.com/questions/62580797/in-colab-doing-image-data-augmentation-with-imgaug-is-not-working-as-intended

@haipinglu haipinglu mentioned this issue Aug 17, 2021
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v0.1.0 automation moved this from To do to Done Aug 18, 2021
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fix imgaug version error pykale/pykale
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