`sage.features`: Add `sage.libs.singular`, features for standard Python packages #35237

mkoeppe · 2023-03-06T00:18:51Z

📚 Description

This is for the modularization effort, in particular:

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

We also add missing copyright headers and update existing copyrights in sage.features.

📝 Checklist

I have made sure that the title is self-explanatory and the description concisely explains the PR.
I have linked an issue or discussion.
I have created tests covering the changes.
I have updated the documentation accordingly.

⌛ Dependencies

codecov-commenter · 2023-03-06T01:47:35Z

Codecov Report

Patch coverage: 98.07% and project coverage change: +0.01 🎉

Comparison is base (52a81cb) 88.57% compared to head (2f0583c) 88.58%.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop   #35237      +/-   ##
===========================================
+ Coverage    88.57%   88.58%   +0.01%     
===========================================
  Files         2140     2141       +1     
  Lines       397273   397416     +143     
===========================================
+ Hits        351891   352061     +170     
+ Misses       45382    45355      -27

Impacted Files	Coverage Δ
src/sage/features/__init__.py	`95.18% <ø> (ø)`
src/sage/features/all.py	`100.00% <ø> (ø)`
src/sage/features/bliss.py	`100.00% <ø> (ø)`
src/sage/features/cddlib.py	`100.00% <ø> (ø)`
src/sage/features/csdp.py	`40.74% <ø> (ø)`
src/sage/features/cython.py	`100.00% <ø> (ø)`
src/sage/features/databases.py	`96.15% <ø> (-0.15%)`	⬇️
src/sage/features/dvipng.py	`100.00% <ø> (ø)`
src/sage/features/ffmpeg.py	`22.58% <ø> (-2.42%)`	⬇️
src/sage/features/gfan.py	`100.00% <ø> (ø)`
... and 124 more

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kwankyu · 2023-03-07T08:47:45Z

LGTM.

But why these feature files lack the usual heading of sage files?

…date=format:%Y FILE | sort -k2"

kwankyu · 2023-03-08T02:00:22Z

Thanks. I am waiting for B&T for sanity.

github-actions · 2023-03-08T03:20:49Z

Documentation preview for this PR is ready! 🎉
Built with commit: 2f0583c

mkoeppe · 2023-03-08T06:32:24Z

Thank you!

vbraun · 2023-03-27T23:06:23Z

sage -t --long --warn-long 39.2 --random-seed=123 src/sage/interfaces/r.py
**********************************************************************
File "src/sage/interfaces/r.py", line 697, in sage.interfaces.r.R.__reduce__
Failed example:
    rlr, t = r.__reduce__()  # optional - rpy2
Exception raised:
    Traceback (most recent call last):
      File "/home/release/Sage/src/sage/doctest/forker.py", line 695, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/home/release/Sage/src/sage/doctest/forker.py", line 1093, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.interfaces.r.R.__reduce__[0]>", line 1, in <module>
        rlr, t = r.__reduce__()  # optional - rpy2
                 ^^^^^^^^^^^^^^
      File "/home/release/Sage/local/var/lib/sage/venv-python3.11.1/lib/python3.11/copyreg.py", line 76, in _reduce_ex
        raise TypeError(f"cannot pickle {cls.__name__!r} object")
    TypeError: cannot pickle 'LazyImport' object
**********************************************************************

mkoeppe · 2023-03-27T23:44:34Z

~~I don't think this is related to the changes here.~~

~~Perhaps you installed R on a test machine and this is the first time that rpy2 tests are tested?~~

mkoeppe · 2023-03-30T12:04:27Z

Doctest failures because deprecation warnings for the same lazy_import are now issued separately for each doctest.

mkoeppe · 2023-03-30T15:55:46Z

I have deferred the work to fix the rpy2 test failures to #35396.

As a quick fix for this PR, 9990302 just removes the rpy2 feature detection again.

### 📚 Description - We split out `.derivations` (which uses modules) from `.maps` (which doesn't). - We separate the implementation of rational function fields (which do not need Singular for Gröbner basis calculations) from the implementation of more complicated function fields (which do). - We move some imports into methods. This is for modularization purposes: - Part of #29705    ### 📝 Checklist    - [x] I have made sure that the title is self-explanatory and the description concisely explains the PR. - [ ] I have linked an issue or discussion. - [ ] I have created tests covering the changes. - [ ] I have updated the documentation accordingly. ### ⌛ Dependencies   - Depends on #35237 (for the feature `sage.libs.singular`) - Depends on #35119 (to preempt merge conflicts) URL: #35230 Reported by: Matthias Köppe Reviewer(s): Kwankyu Lee, Matthias Köppe

…tion  ### 📚 Description    These tags make it possible/meaningful to doctest `sage.graphs` even when some "standard" packages (`networkx`, `numpy`, the modularized distribution packaging providing `sage.groups`) are not installed. - Part of #29705 - Split out from #34998 ### 📝 Checklist    - [x] I have made sure that the title is self-explanatory and the description concisely explains the PR. - [x] I have linked an issue or discussion. - [ ] I have created tests covering the changes. - [ ] I have updated the documentation accordingly. ### ⌛ Dependencies   This is just one commit on top of: - #35237 URL: #35266 Reported by: Matthias Köppe Reviewer(s): David Coudert, Dima Pasechnik, Matthias Köppe

…ags for modularization  ### 📚 Description    Adding tags that make it possible/meaningful to doctest `sage.manifolds`, `sage.tensor` even when some "standard" packages (`pplpy`, the modularized distribution packaging providing `sage.symbolic` and `sage.manifolds`) are not installed. Also taking care of `sage.geometry.riemannian_manifolds`. - Part of #29705 - Split out from #34998 ### 📝 Checklist    - [x] I have made sure that the title is self-explanatory and the description concisely explains the PR. - [x] I have linked an issue or discussion. - [ ] I have created tests covering the changes. - [ ] I have updated the documentation accordingly. ### ⌛ Dependencies   This is just two commits on top of: - #35237 URL: #35267 Reported by: Matthias Köppe Reviewer(s): Eric Gourgoulhon

### 📚 Description  As a follow-up on: - sagemath#35237 we make `rpy2` a dynamically detected feature, enabling the automatic run of doctests tagged `# optional - rpy2`; we use a file-level doctest tag for the `r.py` file. We also update the spkg documentation for sagemath#35347   Resolves sagemath#35347  ### 📝 Checklist  - [x] The title is concise, informative, and self-explanatory. - [x] 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  - Depends on sagemath#35237  URL: sagemath#35396 Reported by: Matthias Köppe Reviewer(s): Kwankyu Lee, Matthias Köppe

Matthias Koeppe added 4 commits March 5, 2023 15:04

sage.features: Add 'sage.libs.singular'

b7a0325

sage.features: Add 'sage.libs.singular' (fixup)

6557578

src/sage/features/singular.py: Fix up doctest

8f05e2c

sage.features.standard: New

ebac0f2

mkoeppe added the t: refactoring label Mar 6, 2023

mkoeppe self-assigned this Mar 6, 2023

Matthias Koeppe added 2 commits March 5, 2023 21:44

src/sage/features/standard.py: Fix up, rename features to match spkgs

a9fc02e

src/sage/features/standard.py: Fix up

2fafd82

mkoeppe added the s: needs review label Mar 6, 2023

Matthias Koeppe added 2 commits March 7, 2023 12:55

src/sage/features: Add/update copyright according to "git blame -w --…

86a2c57

…date=format:%Y FILE | sort -k2"

sage.features: Add feature sage.libs.gap

2f0583c

kwankyu approved these changes Mar 8, 2023

View reviewed changes

kwankyu added s: positive review and removed s: needs review labels Mar 8, 2023

vbraun removed the s: positive review label Mar 27, 2023

mkoeppe added the s: needs work label Mar 29, 2023

mkoeppe changed the title ~~sage.features: Add sage.libs.singular, features for standard Python packages~~ sage.features: Add sage.libs.singular, features for standard Python packages, activate/fix rpy2 tests Mar 29, 2023

mkoeppe added s: needs review and removed s: needs work labels Mar 29, 2023

mkoeppe requested a review from jhpalmieri March 29, 2023 23:57

mkoeppe added s: needs work and removed s: needs review labels Mar 30, 2023

Matthias Koeppe added 2 commits March 30, 2023 08:46

Merge remote-tracking branch 'upstream/develop' into features

a25f3d9

src/sage/features/standard.py: Remove rpy2 feature for now

9990302

mkoeppe force-pushed the features branch from 68bb5f1 to 9990302 Compare March 30, 2023 15:47

mkoeppe added s: positive review and removed s: needs work labels Mar 30, 2023

mkoeppe changed the title ~~sage.features: Add sage.libs.singular, features for standard Python packages, activate/fix rpy2 tests~~ sage.features: Add sage.libs.singular, features for standard Python packages Mar 30, 2023

vbraun merged commit c9daf36 into sagemath:develop Apr 1, 2023

mkoeppe added this to the sage-10.0 milestone Apr 1, 2023

mkoeppe removed the s: positive review label Apr 1, 2023

mkoeppe deleted the features branch April 15, 2023 23:20

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`sage.features`: Add `sage.libs.singular`, features for standard Python packages #35237

`sage.features`: Add `sage.libs.singular`, features for standard Python packages #35237

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sage.features: Add sage.libs.singular, features for standard Python packages #35237

sage.features: Add sage.libs.singular, features for standard Python packages #35237

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📚 Description

📝 Checklist

⌛ Dependencies

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mkoeppe commented Mar 30, 2023

`sage.features`: Add `sage.libs.singular`, features for standard Python packages #35237

`sage.features`: Add `sage.libs.singular`, features for standard Python packages #35237

mkoeppe commented Mar 6, 2023 •

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