Error when pip installing WFDB in colab

[briangow]

Currently we get the following error message when pip installing WFDB on colab:

!pip install wfdb
Collecting wfdb
  Downloading wfdb-3.4.1-py3-none-any.whl (137 kB)
     |████████████████████████████████| 137 kB 5.2 MB/s 
Requirement already satisfied: numpy>=1.10.1 in /usr/local/lib/python3.7/dist-packages (from wfdb) (1.21.6)
Requirement already satisfied: requests>=2.8.1 in /usr/local/lib/python3.7/dist-packages (from wfdb) (2.23.0)
Collecting matplotlib>=3.3.4
  Downloading matplotlib-3.5.2-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (11.2 MB)
     |████████████████████████████████| 11.2 MB 44.0 MB/s 
Requirement already satisfied: pandas>=0.17.0 in /usr/local/lib/python3.7/dist-packages (from wfdb) (1.3.5)
Requirement already satisfied: scipy>=0.17.0 in /usr/local/lib/python3.7/dist-packages (from wfdb) (1.4.1)
Requirement already satisfied: cycler>=0.10 in /usr/local/lib/python3.7/dist-packages (from matplotlib>=3.3.4->wfdb) (0.11.0)
Collecting fonttools>=4.22.0
  Downloading fonttools-4.33.3-py3-none-any.whl (930 kB)
     |████████████████████████████████| 930 kB 47.9 MB/s 
Requirement already satisfied: python-dateutil>=2.7 in /usr/local/lib/python3.7/dist-packages (from matplotlib>=3.3.4->wfdb) (2.8.2)
Requirement already satisfied: pillow>=6.2.0 in /usr/local/lib/python3.7/dist-packages (from matplotlib>=3.3.4->wfdb) (7.1.2)
Requirement already satisfied: kiwisolver>=1.0.1 in /usr/local/lib/python3.7/dist-packages (from matplotlib>=3.3.4->wfdb) (1.4.2)
Requirement already satisfied: pyparsing>=2.2.1 in /usr/local/lib/python3.7/dist-packages (from matplotlib>=3.3.4->wfdb) (3.0.8)
Requirement already satisfied: packaging>=20.0 in /usr/local/lib/python3.7/dist-packages (from matplotlib>=3.3.4->wfdb) (21.3)
Requirement already satisfied: typing-extensions in /usr/local/lib/python3.7/dist-packages (from kiwisolver>=1.0.1->matplotlib>=3.3.4->wfdb) (4.2.0)
Requirement already satisfied: pytz>=2017.3 in /usr/local/lib/python3.7/dist-packages (from pandas>=0.17.0->wfdb) (2022.1)
Requirement already satisfied: six>=1.5 in /usr/local/lib/python3.7/dist-packages (from python-dateutil>=2.7->matplotlib>=3.3.4->wfdb) (1.15.0)
Requirement already satisfied: certifi>=2017.4.17 in /usr/local/lib/python3.7/dist-packages (from requests>=2.8.1->wfdb) (2021.10.8)
Requirement already satisfied: chardet<4,>=3.0.2 in /usr/local/lib/python3.7/dist-packages (from requests>=2.8.1->wfdb) (3.0.4)
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>=2.8.1->wfdb) (1.24.3)
Requirement already satisfied: idna<3,>=2.5 in /usr/local/lib/python3.7/dist-packages (from requests>=2.8.1->wfdb) (2.10)
Installing collected packages: fonttools, matplotlib, wfdb
  Attempting uninstall: matplotlib
    Found existing installation: matplotlib 3.2.2
    Uninstalling matplotlib-3.2.2:
      Successfully uninstalled matplotlib-3.2.2
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.
albumentations 0.1.12 requires imgaug<0.2.7,>=0.2.5, but you have imgaug 0.2.9 which is incompatible.
Successfully installed fonttools-4.33.3 matplotlib-3.5.2 wfdb-3.4.1
WARNING: The following packages were previously imported in this runtime:
  [matplotlib,mpl_toolkits]
You must restart the runtime in order to use newly installed versions.

[bemoody]

Colab should update their stuff. But AFAIK, there shouldn't be any incompatibility with matplotlib 3.2.2, so we could probably relax that requirement in wfdb.

Is the issue just matplotlib or something else? Does the following work if you run it in a fresh notebook?

!pip install 'numpy>=1.10.1' 'scipy>=1.0.0' 'pandas>=1.0.0' 'requests>=2.8.1'

[tompollard]

Does the following work if you run it in a fresh notebook?

since i already had a notebook open, yes it does:

> !pip install 'numpy>=1.10.1' 'scipy>=1.0.0' 'pandas>=1.0.0' 'requests>=2.8.1'

Requirement already satisfied: numpy>=1.10.1 in /usr/local/lib/python3.7/dist-packages (1.21.6)
Requirement already satisfied: scipy>=1.0.0 in /usr/local/lib/python3.7/dist-packages (1.4.1)
Requirement already satisfied: pandas>=1.0.0 in /usr/local/lib/python3.7/dist-packages (1.3.5)
Requirement already satisfied: requests>=2.8.1 in /usr/local/lib/python3.7/dist-packages (2.23.0)
Requirement already satisfied: pytz>=2017.3 in /usr/local/lib/python3.7/dist-packages (from pandas>=1.0.0) (2022.1)
Requirement already satisfied: python-dateutil>=2.7.3 in /usr/local/lib/python3.7/dist-packages (from pandas>=1.0.0) (2.8.2)
Requirement already satisfied: certifi>=2017.4.17 in /usr/local/lib/python3.7/dist-packages (from requests>=2.8.1) (2021.10.8)
Requirement already satisfied: idna<3,>=2.5 in /usr/local/lib/python3.7/dist-packages (from requests>=2.8.1) (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>=2.8.1) (1.24.3)
Requirement already satisfied: chardet<4,>=3.0.2 in /usr/local/lib/python3.7/dist-packages (from requests>=2.8.1) (3.0.4)
Requirement already satisfied: six>=1.5 in /usr/local/lib/python3.7/dist-packages (from python-dateutil>=2.7.3->pandas>=1.0.0) (1.15.0)

[tompollard]

Simply attempting to update matplotlib to the latest version raises the same error in Colab:

!pip install --upgrade matplotlib

...

Requirement already satisfied: packaging>=20.0 in /usr/local/lib/python3.7/dist-packages (from matplotlib) (21.3)
Requirement already satisfied: typing-extensions in /usr/local/lib/python3.7/dist-packages (from kiwisolver>=1.0.1->matplotlib) (4.2.0)
Requirement already satisfied: six>=1.5 in /usr/local/lib/python3.7/dist-packages (from python-dateutil>=2.7->matplotlib) (1.15.0)
Installing collected packages: fonttools, matplotlib
  Attempting uninstall: matplotlib
    Found existing installation: matplotlib 3.2.2
    Uninstalling matplotlib-3.2.2:
      Successfully uninstalled matplotlib-3.2.2
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.
albumentations 0.1.12 requires imgaug<0.2.7,>=0.2.5, but you have imgaug 0.2.9 which is incompatible.
Successfully installed fonttools-4.33.3 matplotlib-3.5.2
WARNING: The following packages were previously imported in this runtime:
  [matplotlib,mpl_toolkits]
You must restart the runtime in order to use newly installed versions.

[tompollard]

Thanks to @bemoody's fix in https://github.com/MIT-LCP/wfdb-python/pull/377/files, the issue appears to be resolved.

Running the following command in Colab:

!pip install git+https://github.com/mit-lcp/wfdb-python.git@327501b08fc0a749ee6fa5f77a8995f91b84f435

...generates the following installation output:

...

Looking in indexes: https://pypi.org/simple, https://us-python.pkg.dev/colab-wheels/public/simple/
Collecting git+https://github.com/mit-lcp/wfdb-python.git@327501b08fc0a749ee6fa5f77a8995f91b84f435
  Cloning https://github.com/mit-lcp/wfdb-python.git (to revision 327501b08fc0a749ee6fa5f77a8995f91b84f435) to /tmp/pip-req-build-d96sca4p
  Running command git clone -q https://github.com/mit-lcp/wfdb-python.git /tmp/pip-req-build-d96sca4p
  Running command git rev-parse -q --verify 'sha^327501b08fc0a749ee6fa5f77a8995f91b84f435'
  Running command git fetch -q https://github.com/mit-lcp/wfdb-python.git 327501b08fc0a749ee6fa5f77a8995f91b84f435
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
    Preparing wheel metadata ... done
Requirement already satisfied: requests<3.0.0,>=2.8.1 in /usr/local/lib/python3.7/dist-packages (from wfdb==4.0.0a0) (2.23.0)
Requirement already satisfied: scipy<2.0.0,>=1.0.0 in /usr/local/lib/python3.7/dist-packages (from wfdb==4.0.0a0) (1.4.1)
Requirement already satisfied: pandas<2.0.0,>=1.0.0 in /usr/local/lib/python3.7/dist-packages (from wfdb==4.0.0a0) (1.3.5)
Requirement already satisfied: matplotlib<4.0.0,>=3.2.2 in /usr/local/lib/python3.7/dist-packages (from wfdb==4.0.0a0) (3.2.2)
Requirement already satisfied: numpy<2.0.0,>=1.10.1 in /usr/local/lib/python3.7/dist-packages (from wfdb==4.0.0a0) (1.21.6)
Requirement already satisfied: python-dateutil>=2.1 in /usr/local/lib/python3.7/dist-packages (from matplotlib<4.0.0,>=3.2.2->wfdb==4.0.0a0) (2.8.2)
Requirement already satisfied: kiwisolver>=1.0.1 in /usr/local/lib/python3.7/dist-packages (from matplotlib<4.0.0,>=3.2.2->wfdb==4.0.0a0) (1.4.2)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.7/dist-packages (from matplotlib<4.0.0,>=3.2.2->wfdb==4.0.0a0) (3.0.9)
Requirement already satisfied: cycler>=0.10 in /usr/local/lib/python3.7/dist-packages (from matplotlib<4.0.0,>=3.2.2->wfdb==4.0.0a0) (0.11.0)
Requirement already satisfied: typing-extensions in /usr/local/lib/python3.7/dist-packages (from kiwisolver>=1.0.1->matplotlib<4.0.0,>=3.2.2->wfdb==4.0.0a0) (4.2.0)
Requirement already satisfied: pytz>=2017.3 in /usr/local/lib/python3.7/dist-packages (from pandas<2.0.0,>=1.0.0->wfdb==4.0.0a0) (2022.1)
Requirement already satisfied: six>=1.5 in /usr/local/lib/python3.7/dist-packages (from python-dateutil>=2.1->matplotlib<4.0.0,>=3.2.2->wfdb==4.0.0a0) (1.15.0)
Requirement already satisfied: certifi>=2017.4.17 in /usr/local/lib/python3.7/dist-packages (from requests<3.0.0,>=2.8.1->wfdb==4.0.0a0) (2022.5.18.1)
Requirement already satisfied: idna<3,>=2.5 in /usr/local/lib/python3.7/dist-packages (from requests<3.0.0,>=2.8.1->wfdb==4.0.0a0) (2.10)
Requirement already satisfied: chardet<4,>=3.0.2 in /usr/local/lib/python3.7/dist-packages (from requests<3.0.0,>=2.8.1->wfdb==4.0.0a0) (3.0.4)
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<3.0.0,>=2.8.1->wfdb==4.0.0a0) (1.24.3)
Building wheels for collected packages: wfdb
  Building wheel for wfdb (PEP 517) ... done
  Created wheel for wfdb: filename=wfdb-4.0.0a0-py3-none-any.whl size=150758 sha256=35a0b30c35656c076546f5ee39c2d03db2ba4c44d2f30b8450c3b86388b865cd
  Stored in directory: /root/.cache/pip/wheels/31/6a/c1/2f929c3fce6d58310e1d77ff571303429df054912c4812ac09
Successfully built wfdb
Installing collected packages: wfdb
Successfully installed wfdb-4.0.0a0