Hi Kingsley, On Sun, Dec 10, 2023 at 12:55:43PM -0800, Kingsley G. Morse Jr. wrote: > Hi Rebecca, Julian and all science minded pythonistas of debian, great and > small! > > I like your correspondence about upgrading from > version 1.5 of pandas to 2.1. > > It's open, scientific and explores the ideal of > proceeding wisely in a matter of public interest. > > My humble thoughts are: > > 1.) Rebecca: *Why* did you write that you'd like > to move forward with the pandas 1.5 -> 2.1 > transition? What's your reason?
A thought from me on this: pandas 2.1 has many improvements over pandas 1.5. And increasingly, other packages will be requiring these new features. So why would one not want to move forward with it? > 2.) What may be the advantage of migrating to > version 3.0 of Cython? It is compatible with Python 3.12, whereas the current version of Cython in Debian (0.29.x) is not really. (For example, it has an "import imp" in it, and this breaks with Python 3.12, which has removed this deprecated module.) As Cython 0.29.x is no longer maintained upstream, having been superseded by Cython 3.x after many years of development, our options are to either continue to patch Cython 0.29.x within Debian to keep it working with Python 3.12 or to upgrade to Cython 3.x. As there is also software which now depends on Cython 3.x to build, the former option seems unappealing. (At best, we might wish to keep the cython-legacy package around for building packages which can't yet use Cython 3.x, but that should be a short-term thing, not a long-term one.) > 3.) The following one-liner suggests 44 debian > packages might be affected by the breaks > Rebecca said would be caused by pandas 2.x: > > $ for s in augur cnvkit dyda emperor esda mirtop pymatgen pyranges > python-anndata python-biom-format python-cooler python-nanoget python-skbio > python-ulmo q2-quality-control q2-demux q2-taxa q2-types q2templates > sklearn-pandas ; do apt-cache search "$s" ; done | less This does not seem like a particularly helpful one-liner; it picks up packages such as python3-dyda-pipeline-config which are not in the original list. Instead, you perhaps want to count the number of packages depending on these packages. But what Rebecca is looking at (I think) is how many packages would need fixing by the pandas upgrade. (But it is probably worse than this: I'm guessing these are only the packages which fail to build with pandas 2.x or whose autopkgtest fails with pandas 2.x. But there may well be other breakage caused by the upgrade which is not detectable in this way. That is an issue which will have to be handled by individual packages as they are discovered, and the timing of the pandas upgrade is not related to this problem.) > 4.) The break that worries me the most is > sklearn-pandas, because it seems to me that > sklearn is > > popular and > > fundamental. It seems that sklearn-pandas is abandoned; there were just two commits in 2022, and prior to that was May 2021. There has been no activity since. If someone is willing to patch it for Pandas 2.x, great (perhaps you might help the maintainer to do this?), otherwise it might have to drop out of Debian. Best wishes, Julian
