New modularized distributions sagemath-{flint,gap,giac,homfly,ntl,pari} by mkoeppe · Pull Request #35663 · sagemath/sage

mkoeppe · 2023-05-22T00:53:25Z

📚 Description

We add new distributions that ship the Cython modules depending on a specific library.

To test: make pypi-wheels.
(This is also automatically run as part of the Build&Test workflow.)

Goals of this PR:

wheels for the distributions are separately buildable
disjointness of the wheels

Non-goals:

disjointness of source distributions (currently we ship, but do not install, duplicate copies of pxd files)
separately testable (this depends on Modularization of sagelib: Distributions sagemath-{brial,combinat,eclib,flint,gap,giac,glpk,graphs,groups,homfly,lcalc,libbraiding,libecm,linbox,modules,mpmath,ntl,pari,plot,polyhedra,schemes,singular,standard-no-symbolics,symbolics} #35095, which enlarges sagemath-categories)

This PR:

Resolves Distributions sagemath-{flint-arb,homfly,giac,gap}, add "sage_setup: distribution" to Cython modules #30666

Part of:

Meta-ticket: Modularize sagelib into separate distributions (pip-installable packages) sagemath-... for Sage 10.x #29705

📝 Checklist

The title is concise, informative, and self-explanatory.
The description explains in detail what this PR is about.
I have linked a relevant issue or discussion.
I have created tests covering the changes.
I have updated the documentation accordingly.

⌛ Dependencies

…jects spkg-install

…t from sage.libs.flint (only used by doctesting helper functions)

mkoeppe · 2023-06-13T04:45:56Z

Is this WIP?

Ready for review now.

dimpase · 2023-06-13T15:40:45Z

Are these 60 commits makes sense, or they better be squashed?

How does one install, say sagemath-flint ? Is it in the docs?

mkoeppe · 2023-06-13T15:50:28Z

You do "make sagemath_flint", as with any other package.
(It only builds the wheel -- installing it into the Sage venv makes no sense because it duplicates parts of the monolithic Sage library.)

Testing is documented in https://doc.sagemath.org/html/en/developer/packaging_sage_library.html#testing-the-distribution-in-virtual-environments-with-tox

dimpase · 2023-06-13T16:20:01Z

I am getting

...
[sagemath_objects-10.1.beta3] ERROR: Could not find a version that satisfies the requirement sage-setup~=10.1b3
[sagemath_objects-10.1.beta3] ERROR: No matching distribution found for sage-setup~=10.1b3
[sagemath_objects-10.1.beta3]
...

while running make sagemath_flint

mkoeppe · 2023-06-13T16:21:16Z

Try make wheels first.

mkoeppe · 2023-06-13T16:25:03Z

(That's documented in the current beta's documentation: https://sagemath-tobias.netlify.app/developer/packaging_sage_library.html#testing-the-distribution-in-virtual-environments-with-tox)

dimpase · 2023-06-13T16:41:02Z

why doesn't the target sagemath_flint depend on wheels ?

dimpase · 2023-06-13T16:43:00Z

make wheels errors out with

[sagemath_flint-10.0] gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-rpath-link,/home/dimpase/work/software/sage/local/lib -L/home/dimpase/work/software/sage/local/lib -Wl,-rpath,/home/dimpase/work/software/sage/local/lib -Wl,-rpath-link,/home/dimpase/work/software/sage/local/lib -L/home/dimpase/work/software/sage/local/lib -Wl,-rpath,/home/dimpase/work/software/sage/local/lib -g -O2 build/temp.linux-x86_64-cpython-39/build/cythonized/sage/rings/polynomial/polynomial_complex_arb.o -L/usr/lib -lflint -larb -lgmp -o build/lib.linux-x86_64-cpython-39/sage/rings/polynomial/polynomial_complex_arb.cpython-39-x86_64-linux-gnu.so -lpari
[sagemath_flint-10.0] /usr/bin/ld: cannot find -larb
[sagemath_flint-10.0] collect2: error: ld returned 1 exit status
[sagemath_flint-10.0] error: command '/usr/bin/gcc' failed with exit code 1
[sagemath_flint-10.0] 
[sagemath_flint-10.0] ERROR Backend subprocess exited when trying to invoke build_wheel

dimpase · 2023-06-13T16:51:50Z

The latter is most probably related to the fact that it's Debian, with SAGE_ARB_LIBRARY="flint-arb", not SAGE_ARB_LIBRARY="arb"

mkoeppe · 2023-06-13T16:58:40Z

Try with this commit. (Need to re-run bootstrap.)

mkoeppe · 2023-06-13T17:54:35Z

why doesn't the target sagemath_flint depend on wheels ?

That's a long story; there's something that I need to redesign in the relation between editable installations and normal installations. That work is best done as part of a switch of the editable installs to using PEP-660 editable wheels (#34209)

…ution'

…e_setup__distribution__directives_to_all_cython_modules_needing_external_libraries

…yproject.toml.m4

…lint,ntl,pari} for now to suppress warning

…rectives_to_all_cython_modules_needing_external_libraries SageMath version 10.1.beta8, Release Date: 2023-07-30

…ctives_to_all_cython_modules_needing_external_libraries SageMath version 10.1.rc0, Release Date: 2023-08-13

github-actions · 2023-08-13T18:30:41Z

Documentation preview for this PR (built with commit 0dd0300; changes) is ready! 🎉

mkoeppe · 2023-09-19T19:38:50Z

This has been merged into #35095

Matthias Koeppe added 30 commits December 2, 2022 16:49

Mark files # sage_setup: distribution = sagemath-flint-arb

619c8c8

Mark files # sage_setup: distribution = sagemath-homfly

71b5921

Mark files # sage_setup: distribution = sagemath-giac

fe08ab2

Mark files # sage_setup: distribution = sagemath-gap

640aa74

Do not mark *.h files with # sage-setup: distribution

d1ef655

pkgs/sagemath-gap, build/pkgs/sagemath_gap: New

8c46aab

pkgs/sagemath-homfly, build/pkgs/sagemath_homfly: New

6db9b01

build/pkgs/sagemath_{gap,homfly}/spkg-install: Symlink to sagemath_ob…

390ebb8

…jects spkg-install

pkgs/sagemath-gap/MANIFEST.in: Add VERSION.txt

9f26fb8

src/sage/libs/gap: Add # sage_setup: distribution to more files

13f030c

Add src/sage/**/all__sagemath_gap.py

a73b489

pkgs/sagemath-gap: WIP setup.py

30112b2

src/sage/groups/perm_gps/partn_ref/data_structures.pyx: Remove cimpor…

cae814a

…t from sage.libs.flint (only used by doctesting helper functions)

Add src/sage/**/all__sagemath_gap.py

5fda124

Add src/sage/**/all__sagemath_gap.py

a2feea0

pkgs/sagemath-gap/tox.ini: New

665d01c

pkgs/sagemath-gap/MANIFEST.in: Add deps for sage/coding/codecan

963fa77

pkgs/sagemath-gap: Update description

96b863c

build/pkgs/sagemath_gap/dependencies: Update

b73a929

pkgs/sagemath-homfly: Fix up

fc91135

pkgs/sagemath-environment: Add sage.misc.package_dir properly

0869a7f

.gitignore: Ignore generated files

31b08a1

pkgs/sagemath-flint-arb: New

961fb3f

pkgs/sagemath-giac: New

45cce7b

Fixup

47a2519

Add tox.ini

513fc3f

Makefile: Add to PYPI_WHEEL_PACKAGES

0f198ca

Remove copy-pasted conda.txt files

133e5b8

src/sage/sets/disjoint_set.pyx: Remove obsolete -*- coding -*- line

4c8f5b5

pkgs/sagemath-flint-arb: Update description

2be77af

Matthias Koeppe added 4 commits June 12, 2023 14:40

pkgs/sagemath-ntl: Fix up

bf20fd5

pkgs/sagemath-ntl: Exclude totallyreal

83dbfe0

build/pkgs/sagemath_ntl/dependencies: Add ntl

73b9b4d

pkgs/sagemath-standard/setup.py: Add sagemath-pari

6d0447a

pkgs/sagemath-flint: Add sage-conf as build dependency

b8fed5e

Matthias Koeppe added 11 commits June 15, 2023 12:27

build/pkgs/sagemath_ntl/install-requires.txt: Fixup

e0d1220

pkgs/sagemath-gap: Fixups

11491c2

src/sage/graphs/spanning_tree.pyx: Remove faulty 'sage_setup: distrib…

a97f975

…ution'

pkgs/sagemath-gap: Add sage.interfaces.gap*

011decd

Merge remote-tracking branch 'upstream/develop' into t/30666/add__sag…

5ef0c13

…e_setup__distribution__directives_to_all_cython_modules_needing_external_libraries

bootstrap: Write m4/sage_spkg_versions_toml.m4 and use it in pkgs/*/p…

7dfaf07

…yproject.toml.m4

Use m4/setup_cfg_metadata.m4 in setup.cfg files to reduce boilerplate

703dfc5

pkgs/sagemath-{flint,gap,giac,homfly,pari}: Update from sagemath#35095

abcee7e

src/sage/features/sagemath.py: Remove spkg from features sage.libs.{f…

da3510a

…lint,ntl,pari} for now to suppress warning

Merge tag '10.1.beta8' into t/30666/add__sage_setup__distribution__di…

7a19835

…rectives_to_all_cython_modules_needing_external_libraries SageMath version 10.1.beta8, Release Date: 2023-07-30

Merge tag '10.1.rc0' into t/30666/add__sage_setup__distribution__dire…

0dd0300

…ctives_to_all_cython_modules_needing_external_libraries SageMath version 10.1.rc0, Release Date: 2023-08-13

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📚 Description

📝 Checklist

⌛ Dependencies

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