nanoporetech/pod5-file-format

Can't install on arm

Psy-Fer opened this issue · 4 comments

Psy-Fer commented

Hello,

I have a workflow that does a test for our blue-crab builds (pod5<->slow5 conversion tool), and it is failing on the arm build.

Here is the error when installing pod5 from a requirements.txt file

Installed /usr/local/lib/python3.8/dist-packages/pytz-2023.3.post1-py3.8.egg
Searching for pyarrow~=14.0.0
Reading https://pypi.org/simple/pyarrow/
Downloading https://files.pythonhosted.org/packages/51/95/3f051619192aff9cae4694d245f337500e0b88ad346ccaeeed803f4f5158/pyarrow-14.0.1-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl#sha256=450e4605e3c20e558485f9161a79280a61c55efe585d51513c014de9ae8d393f
Best match: pyarrow 14.0.1
Processing pyarrow-14.0.1-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl
Installing pyarrow-14.0.1-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl to /usr/local/lib/python3.8/dist-packages
Adding pyarrow 14.0.1 to easy-install.pth file

Installed /usr/local/lib/python3.8/dist-packages/pyarrow-14.0.1-py3.8-linux-aarch64.egg
Searching for polars~=0.19
Reading https://pypi.org/simple/polars/
Downloading https://files.pythonhosted.org/packages/b2/34/3a35406a2aa2c6ed0f905805d780c4e3521f961e91cb7be8bfcb75d30964/polars-0.19.19.tar.gz#sha256=3e904d197aabf36e37fda263470eaf51ec92fb865cdea4f93947713480199303
Best match: polars 0.19.19
Processing polars-0.19.19.tar.gz
error: Couldn't find a setup script in /tmp/easy_install-0brr715i/polars-0.19.19.tar.gz

Seems like the issue is installing polars which is required by pod5 (we don't use it in any of our libs).

Not sure if you can see this, but it's the github actions with the failure
https://github.com/Psy-Fer/blue-crab/actions/runs/7111154691/job/19358754834

Everything else built fine.

Any ideas?

Thanks
James

HalfPhoton commented

Hi @Psy-Fer,
We're looking into this issue and will get back to you with updates.

Best regards,
Rich

Psy-Fer commented

Appreciate it :)

HalfPhoton commented

Hi James,
It looks like your build pipeline is sufficiently outdated it's starting to break down.

To fix add the following to your build workflows:

# This upgrades your pip from 20.0.2 (2020) to most recent.
pip install --upgrade pip

# Install your own package with:
pip install .

# Like this
  arm64:
    name: pyslow5 ubuntu arm
    runs-on: ubuntu-latest
    steps:
    - run: docker run --rm --privileged multiarch/qemu-user-static:register --reset
    - uses: docker://multiarch/ubuntu-core:arm64-focal
      with:
        args: 'uname -a'
    - uses: actions/checkout@v1
    - uses: docker://multiarch/ubuntu-core:arm64-focal
      with:
        args: >
          bash -c "apt-get update &&
          apt-get install -y zlib1g-dev gcc make python3 python3-pip git wget &&
  >>      pip install --upgrade pip &&
          pip3 install setuptools cython numpy &&
          ldd --version && gcc --version && python3 --version &&
          git clone -b dev https://github.com/hasindu2008/slow5lib && cd slow5lib && python3 setup.py install && cd .. &&
  >>      pip install . && 
          blue-crab --help && test/test.sh"

I hope this has been helpful. It might also be worthwhile maintaining the other build workflows while your there. 👍

Kind regards,
Rich

HalfPhoton commented

Closing as resolved as this is not a POD5 issue.

  • 😄1