Knowledge-Graph-Hub / kg-obo

A package to transform all OBO ontologies into KGX TSV format and OBO json, and put the transformed graph in KGhub
https://knowledge-graph-hub.github.io/kg-obo/getting_started.html
GNU General Public License v3.0
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Jenkins issues re: Python 3.9 #177

Closed caufieldjh closed 2 years ago

caufieldjh commented 2 years ago

After changing over the Jenkins build to a new Docker image with Python 3.9.14, builds fail with:

Error: Command '['/var/lib/jenkins/workspace/knowledge-graph-hub_kg-obo_main/gitrepo/venv/bin/python3.9', '-Im', 'ensurepip', '--upgrade', '--default-pip']' returned non-zero exit status 1.

Initially, this just seems like a missing venv installation, but after apt-get install python3.9-dev python3.9-venv the issue is still unresolved.

Running python3.9 -Im ensurepip --upgrade --default-pip on its own from within the Docker container completes as expected:

Looking in links: /tmp/tmpwwcx5m_0
Requirement already satisfied: setuptools in /usr/lib/python3/dist-packages (45.2.0)
Processing /tmp/tmpwwcx5m_0/setuptools-58.1.0-py3-none-any.whl
Requirement already satisfied: pip in /usr/local/lib/python3.9/dist-packages (22.2.2)
Installing collected packages: setuptools
  Attempting uninstall: setuptools
    Found existing installation: setuptools 45.2.0
    Uninstalling setuptools-45.2.0:
      Successfully uninstalled setuptools-45.2.0
Successfully installed setuptools-58.1.0
caufieldjh commented 2 years ago

Hrm, Jenkins wants to run venv from /var/lib/jenkins/workspace/knowledge-graph-hub_kg-obo_main/gitrepo/venv/bin/python3.9 so maybe that's the issue

caufieldjh commented 2 years ago

There's also the likely possibility that the Jenkins run is just using a cached Docker image rather than an updated one

caufieldjh commented 2 years ago

Fixes by #178