Update Dockerfile - Fixes pandas installation
#1169
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# Problem I realized because of an error with `nf-synapse` that the newer versions of the `synapseclient` docker container do not have `pandas` installed properly. # Solution This issue was caused by mixing `apt-get` installing `python3-pandas` with a base Python image. The issue being that Python packages installed via `apt-get` don't automatically integrate with the Python environment from the Docker base image. Fortunately we have a `pandas` extra built into `setup.cfg`, so I switched to installing it that way. # Testing Built the container locally, started up a Python terminal inside of it, and ran `import pandas`. If you do this with `sagebionetworks/synapsepythonclient:v4.7.0` you get an import error.
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Problem
I realized because of an error encountered by an
nf-synapseuser that the newer versions of thesynapseclientdocker container do not havepandasinstalled properly.Solution
This issue was caused by mixing
apt-getinstallingpython3-pandaswith a base Python image. The problem being that Python packages installed viaapt-getdon't automatically integrate with the Python environment from the Docker base image. Fortunately we have apandasextra built intosetup.cfg, so I switched to installing it that way.Testing
Built the container locally, started up a Python terminal inside of it, and ran
import pandas. If you do this withsagebionetworks/synapsepythonclient:v4.7.0you get an import error.