Meta-ticket: Create upstream repositories, pip-installable packages for database packages

[tobiasdiez]

The Sage distribution contains a number of "database packages", many of which do not seem to have a "real upstream" (or installation procedures other than our scripts in build/pkgs).

We transform them into pip-installable packages and publish them to PyPI so that they can be installed using standard Python tools (and become Python dependencies of sagelib) and then discovered by libraries using standard Python facilities.

Role model: https://pypi.org/project/database-knotinfo/

For those that do not have a real upstream, we create separate git repositories in github.com/sagemath/ to serve as new upstream.

List of packages/tickets:

Architecture independent:

• database_stein_watkins (New upstream for database_stein_watkins #33881)
• combinatorial_designs (single text file MOLS_table.txt), 8 kB, https://repology.org/project/sagemath-combinatorial-designs/versions
• graphs (graphs.db, brouwer_srg_database.json, smallgraphs.txt, isgci_sage.xml), 336 kB; the SPKG.rst explains: The code used to parse the data from Andries E. Brouwer's website is available at https://github.com/nathanncohen/strongly_regular_graphs_database
• polytopes_db (various files), 41 kB
• polytopes_db_4d (various files), 878 MB

Prepared files:

• conway_polynomials (Upstream Python distribution package for conway_polynomials #32747, Update to new conway-polynomials python package #36765)
• elliptic_curves

New data sources:

• Interface to the KnotInfo and LinkInfo databases #30352 Interface to the KnotInfo and LinkInfo databases
• database_graver_ppi - https://www.math.ucdavis.edu/~mkoeppe/art/ppi/index.html
• https://mathdb.mathhub.info/
• https://swmath.org/

Related (other stuff written by the Sage distribution into $SAGE_SHARE):

• Meta-ticket: Use system Jupyter notebook / JupyterLab #30306 - jupyter notebook related things
• Meta-ticket: Sage docbuild #20080 - documentation
• sage.combinat.cluster_algebra_quiver: Use sage.feature to define database file system location #30885 - sage.features

Techniques:

• importlib.resources - would help making a distribution zip_safe (sage.repl: Replace use of SAGE_EXTCODE by importlib.resources #31306)
• could consider advertise install location using a pkgconfig file: #30787 comment:24
• Reduce local duplication of large database package when venvs are in use: https://pypi.org/project/pydupes/ (similar to rdfind)
• Avoid duplicate installation by using PEP 660 editable wheels. Use a build backend that supports it: flit, pdm, hatchling, poetry, not setuptools. https://discuss.python.org/t/pep-660-and-setuptools/14855
• However there are implementation restrictions in the interaction of editable wheels and implicit namespace packages

CC: @mkoeppe @jhpalmieri @kiwifb @isuruf @antonio-rojas @dimpase @slel @tobihan @jamesjer @soehms @videlec @williamstein @roed314

Component: build

Keywords: sd111

Issue created by migration from https://trac.sagemath.org/ticket/30914

[mkoeppe]

comment:1

Which files, specifically?

[mkoeppe]

comment:2

If you are talking about database packages such as build/pkgs/conway_polynomials, in particular those that do not seem to have a "real upstream" (or installation procedures other than our scripts in build/pkgs), then yes, I agree that a possible direction would be to create pip-installable packages for them and to publish them to PyPI. They should be maintained outside of the source tree, each in a separate git repository.

[mkoeppe]

comment:3

If this is what you had in mind, let's transform this ticket into a meta-ticket and get the downstream packagers of Sage on board -- they may have insights on the upstream status of some of these packages, which we may have forgotten about.

[kiwifb]

comment:4

Yes, a confirmation of which bits would be nice. If @mkoeppe is right you are talking about

• combinatorial_designs
• conway_polynomials
• elliptic_curves
• graphs
• polytopes_db
• plus some other optional packages
  They are indeed static but come in two flavors.

Architecture independent:

• combinatorial_designs
• graphs
• polytopes_db
  which are really file copying.

Prepared files

• conway_polynomials
• elliptic_curves
  where the files are processed before install with some python code that may be depending on python or some other software.

conway_polynomials uses pickle.dump which could pose problems across python versions?

elliptic_curves is put into a SQL database with sqlite, this should be a stable format. Don't know if that's portable between, say, x86_64 and ppc64le?

[mkoeppe]

comment:5

OK, I've taken the liberty to rewrite the ticket description

[mkoeppe]

comment:6

Replying to @kiwifb:

Prepared files

• conway_polynomials
• elliptic_curves
  where the files are processed before install with some python code that may be depending on python or some other software.

conway_polynomials uses pickle.dump which could pose problems across python versions?

elliptic_curves is put into a SQL database with sqlite, this should be a stable format. Don't know if that's portable between, say, x86_64 and ppc64le?

For these ones, we should make the actual source distribution architecture-independent.
The architecture-dependent products could be built during setup.py - and published as wheels.

[mkoeppe]

comment:7

For example database_stein_watkins_mini's SPKG.rst lists http://modular.math.washington.edu/papers/stein-watkins/ as upstream or source, which is defunct

[mkoeppe]

comment:8

One thing that may need discussion is that for huge databases, one may want to avoid installing multiple copies

[slel]

comment:10

Replying to @mkoeppe:

For example database_stein_watkins_mini's SPKG.rst lists http://modular.math.washington.edu/papers/stein-watkins/ as upstream or source, which is defunct

It's at https://wstein.org/papers/stein-watkins/

[tobiasdiez]

comment:11

Replying to @kiwifb:

Yes, a confirmation of which bits would be nice. If @mkoeppe is right you are talking about ...

Yes, that's exactly what I meant! Thanks everybody for their input, that's already way better than what I've imagined originally.

[mkoeppe]

Changed keywords from none to sd111

[mkoeppe]

comment:21

Sage development has entered the release candidate phase for 9.3. Setting a new milestone for this ticket based on a cursory review of ticket status, priority, and last modification date.

[mkoeppe]

comment:24

For #32432 (sagemath-polyhedra), pip-installable polytopes_db, polytopes_db_4d would be good

[mkoeppe]

comment:35

Replying to @slel:

Replying to @mkoeppe:

For example database_stein_watkins_mini's SPKG.rst lists http://modular.math.washington.edu/papers/stein-watkins/ as upstream or source, which is defunct

It's at https://wstein.org/papers/stein-watkins/

The link "Click here for the database" (https://wstein.org/ecdb) and "Our database" (https://wstein.org/papers/stein-watkins/ecdb) are both broken

[orlitzky]

Can I have a new sagemath/ repo for https://github.com/orlitzky/mols-handbook-data please? This is the old combinatorial_designs data.

[orlitzky]

For #32432 (sagemath-polyhedra), pip-installable polytopes_db, polytopes_db_4d would be good

This one is going to be annoying because the interface to it relies on the nonstandard PALP executable names. PALP now has an upstream repository at https://gitlab.com/stringstuwien/PALP, but I've been waiting for my first easy PR to get merged before I proceed with the makefile changes needed to build all of the extra executables.

[orlitzky]

PALP upstream now supports the names used in the polytope databases. One less blocker.