Pip install order on Renku using the Dockerfile


I ran into the following issue when trying to install the “biogeme” package in a Renku project but I also found a workaround. However, I am wondering whether this issue arises due to the Renku specific way of installing packages via the Dockerfile or because the biogeme package metadata hasn’t been correctly specified ?

It looks to me like they haven’t made a release with the correct build environment configuration. If I install from source it does what you expect:

$ pip install git+https://github.com/michelbierlaire/biogeme

Collecting git+https://github.com/michelbierlaire/biogeme
  Cloning https://github.com/michelbierlaire/biogeme to /private/var/folders/99/jng0jljd13db0h4jwbwtx4mh0000gn/T/pip-req-build-b_9y1swd
  Running command git clone --filter=blob:none --quiet https://github.com/michelbierlaire/biogeme /private/var/folders/99/jng0jljd13db0h4jwbwtx4mh0000gn/T/pip-req-build-b_9y1swd
  Resolved https://github.com/michelbierlaire/biogeme to commit 1bbb553215ebcd438e1371604e561c36448b0c92
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting tqdm>=4.64.1
  Using cached tqdm-4.64.1-py2.py3-none-any.whl (78 kB)
Collecting cython>=0.29.16
  Using cached Cython-0.29.33-py2.py3-none-any.whl (987 kB)
Collecting scipy>=1.7.3
  Using cached scipy-1.10.0-cp39-cp39-macosx_12_0_arm64.whl (28.9 MB)
Collecting tomlkit>=0.11.5
  Using cached tomlkit-0.11.6-py3-none-any.whl (35 kB)
Collecting pandas>=1.3.5
  Downloading pandas-1.5.3-cp39-cp39-macosx_11_0_arm64.whl (11.0 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.0/11.0 MB 11.1 MB/s eta 0:00:00
Collecting numpy>=1.20.3
  Using cached numpy-1.24.2-cp39-cp39-macosx_11_0_arm64.whl (13.9 MB)
Collecting python-dateutil>=2.8.1
  Using cached python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB)
Collecting pytz>=2020.1
  Using cached pytz-2022.7.1-py2.py3-none-any.whl (499 kB)
Collecting six>=1.5
  Using cached six-1.16.0-py2.py3-none-any.whl (11 kB)
Building wheels for collected packages: biogeme
  Building wheel for biogeme (pyproject.toml) ... done
  Created wheel for biogeme: filename=biogeme-3.2.11-cp39-cp39-macosx_11_0_arm64.whl size=413075 sha256=a39aac3fe5fad26bdcb2cbb536121c763153ee5a7b7c677c5ecf36c456a40348
  Stored in directory: /private/var/folders/99/jng0jljd13db0h4jwbwtx4mh0000gn/T/pip-ephem-wheel-cache-twiu7536/wheels/35/6f/19/60eb6521f86f108e68b79e36695fa7114d808166a925848e86
Successfully built biogeme
Installing collected packages: pytz, tqdm, tomlkit, six, numpy, cython, scipy, python-dateutil, pandas, biogeme
Successfully installed biogeme-3.2.11 cython-0.29.33 numpy-1.24.2 pandas-1.5.3 python-dateutil-2.8.2 pytz-2022.7.1 scipy-1.10.0 six-1.16.0 tomlkit-0.11.6 tqdm-4.64.1

1 Like

Thanks for your feedback @rrrrrok !

No problem - now just pester them to make a new release :wink: