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Published February 11, 2020 | Version v0.16
Software Open

cfe-lab/Kive: Python 3

Creators

  • 1. BC Centre for Excellence in HIV/AIDS

Description

The main change is #721 updating to Python 3. Other changes include:

  • #785, #786, and #782 improve error handling when launching Slurm jobs.
  • #774 and #793 fix permissions bugs.
  • #833 removes PostgreSQL 9 left by the previous release.

See the milestone for a complete list.

Config Changes
  • Install Python 3.6 and switch Apache to launch it.

    sudo systemctl stop httpd
    sudo yum install centos-release-scl
    sudo yum install python36 python36-devel rh-python36-mod_wsgi
    sudo cp /opt/rh/httpd24/root/usr/lib64/httpd/modules/mod_rh-python36-wsgi.so /lib64/httpd/modules
    sudo cp /opt/rh/httpd24/root/etc/httpd/conf.modules.d/10-rh-python36-wsgi.conf /etc/httpd/conf.modules.d
    sudo mv /opt/venv_kive /opt/py27_venv_kive
    sudo python3.6 -m venv /opt/venv_kive
    sudo /opt/venv_kive/bin/python -m pip install --upgrade pip
    sudo /opt/venv_kive/bin/python -m pip install -r requirements.txt
    sudo sed -ie 's/python2.7/python3.6/' /etc/httpd/conf.d/001-kive.conf
    sudo systemctl start httpd
    
  • Add KIVE_SLURM_PATH entry to /etc/sysconfig/httpd.

  • Remove Python 2's .pyc files with find . -name '*.pyc' -delete.
  • Remove PostgreSQL 9 with sudo yum remove postgresql-libs. That will take the other packages that depend on it.
  • The Python packages in Kive's virtual environment should already be up to date, because you just installed them. That should include the switch to psycopg2-binary.

Files

cfe-lab/Kive-v0.16.zip

Files (27.8 MB)

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