Python 2.7 End-of-Life

[tomkinsc]

Now that we have reached 2020, Python 2.7 is officially deprecated. The language will not see future maintenance or security patches. Consequently, as discussed in the first core meeting of the year:

• bioconda now discourages contribution of Python 2.7 packages to the channel
• In the very near future, Python 2.7 builds will be disabled unless explicitly enabled on a per-package basis by including a conda_build_config.yaml file. A description of how to do this will be added to the bioconda documentation.
• Where possible, existing packages relying on Python 2.7 should be converted to support Python 3—ideally upstream in their origin repositories, but via 2to3 and/or manual patching in bioconda where necessary.
• Existing packages already built using Python 2.7 will continue to be hosted on anaconda.org and will continue to be available for installation until a decision has been made to remove them.

To get the ball rolling on updates to packages, here is a list of bioconda packages currently pinning to Python 2.7 (or <3):
bioconda_py27_packages_as_of_2019-01-06_names_only.txt
bioconda_py27_packages_as_of_2019-01-06_matches.txt

[marcelm]

The _names_only.txt lists 261 affected packages, but it appears to (thankfully) contain a couple of false positives. For example, it includes tiddit, but the tiddit recipe does not actually pin to Python 2.7. Perhaps the script that was run was a bit over-eager and it’s actually not as bad?

Some old versions of recipes such as pysam/pysam/0.7.7, pysam/0.8.3 and pysam/0.9.1 could also be left out because the main/current recipe does not require Python 2.7.