Add style guide / reference for `# optional - sage....` doctest tags, extend `sage -t` and `sage -fixdoctests` for modularization tasks #35749

mkoeppe · 2023-06-09T16:40:57Z

📚 Description

Fixing the handling of file-level # optional tags.
Some files were not being doctested; fixing the recently introduced errors in doctests.
Implementing block-scoped tags (originally done in PR Implement persistent optional tag #35779, merged here)
Expanding the documentation on the # optional / # needs tags used for modularization purposes, with examples.
Adding features sage.modular, sage.numerical.mip, sage.rings.complex_double, sage.sat
The tools sage -t and sage --fixdoctests receive some new options for modularization tasks (see added documentation):
```
$ make pypi-wheels
$ make SAGE_CHECK=yes sagemath-modules
$ ./sage --fixdoctests --distribution sagemath-modules \
    src/sage/combinat/root_system/root_lattice_realization_algebras.py
```
(example uses 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)
Suppressing # optional/# needs of present features in the help system
.

Motivated by the sage-devel thread https://groups.google.com/g/sage-devel/c/utA0N1it0Eo (2023-06)

📝 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

Depends on sage.features: Declare features as "standard" explicitly #35820 (merged here)
Vote at https://groups.google.com/g/sage-devel/c/8KZNRBs6F6U (result: https://groups.google.com/g/sage-devel/c/MtS2u3VbJEo)

…agemath-...

…g doctests, # optional

mkoeppe · 2023-06-16T14:52:31Z

(the doctest failure in ell_rational_field is unrelated)

### 📚 Description  Packages such as **sagemath-categories** are currently mixed with optional SPKGs in the reference guide. We separate them out as a separate category. We also move the section on `Feature`s right next to the package list. #35749 and follow-ups will interlink these sections. Preview: - https://deploy-preview-35734--sagemath- tobias.netlify.app/reference/spkg/index.html#packages-of-the- modularized-sage-library - https://deploy-preview-35734--sagemath- tobias.netlify.app/reference/spkg/index.html#runtime-detectable- features-and-conditional-doctests   - Part of #29705  ### 📝 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   URL: #35734 Reported by: Matthias Köppe Reviewer(s): Kwankyu Lee, Matthias Köppe

SageMath version 10.1.beta4, Release Date: 2023-06-21

kwankyu · 2023-07-12T02:21:21Z

As this PR is motivated by the sage-devel discussion started by @tscrim, I invite him to review this PR once more.

If there's no comment from him for a couple of days, I will set it positive review.

…#35749

mkoeppe · 2023-07-14T16:08:53Z

Thank you!

vbraun · 2023-07-19T08:57:24Z

Doctests fail because now the previously-skipped broken files are picked up

sage -t --long --random-seed=286735480429121101562228604801325644303 sage/schemes/elliptic_curves/heegner.py  # 4 doctests failed
sage -t --long --random-seed=286735480429121101562228604801325644303 sage/schemes/elliptic_curves/hom_frobenius.py  # 2 doctests failed

kwankyu · 2023-07-19T09:12:18Z

From sage-release

That's already fixed in #35749, which is why that PR is marked critical.

We didn't fix the failures. Just that @mkoeppe mentioned that they are not related with this PR. According to @vbraun, indeed they are.

kwankyu · 2023-07-19T10:25:02Z

They all look easy to fix. All the doctests rely on arbitrary choice between $P$ and $-P$ which are points of an elliptic curve whose $x$-coordinates are the same. I am 100% sure about the doctests in age/schemes/elliptic_curves/hom_frobenius.py and 80% sure about the doctests in sage/schemes/elliptic_curves/heegner.py. Needs a look from an expert @yyyyx4.

kwankyu · 2023-07-19T12:50:15Z

We may fix them in the style

--- a/src/sage/schemes/elliptic_curves/heegner.py
+++ b/src/sage/schemes/elliptic_curves/heegner.py
@@ -47,8 +47,8 @@ We find some Mordell-Weil generators in the rank 1 case using Heegner points::
     sage: E = EllipticCurve('43a'); P = E.heegner_point(-7)
     sage: P.x_poly_exact()
     x
-    sage: P.point_exact()
-    (0 : 0 : 1)
+    sage: p = P.point_exact(); p == E(0,0,1) or -p == E(0,0,1)
+    True
 
     sage: E = EllipticCurve('997a')
     sage: E.rank()

kwankyu · 2023-07-19T13:42:26Z

Please merge #35966 here for test.

github-actions · 2023-07-19T17:30:33Z

Documentation preview for this PR (built with commit 44549f6; changes) is ready! 🎉

… imports    ### 📚 Description  - Many `# optional` are removed because small prime finite fields no longer need to be marked `# optional/needs sage.rings.finite_rings` since #35847 - Other `# optional` are replaced by codeblock-scoped `# needs` tags - Remaining `# optional` with standard features are replaced by `# needs` - Some import fixes needed for separate testing of **sagemath-modules** or **sagemath-graphs**[modules] from #35095   This is: - done with the help of `sage -fixdoctests` from #35749 - Part of: #29705 - Cherry-picked from: #35095  ### 📝 Checklist  - [x] The title is concise, informative, and self-explanatory. - [x] The description explains in detail what this PR is about. - [x] I have linked a relevant issue or discussion. - [ ] I have created tests covering the changes. - [ ] I have updated the documentation accordingly. ### ⌛ Dependencies   URL: #35919 Reported by: Matthias Köppe Reviewer(s): David Coudert, Matthias Köppe

…s, update `# needs`   - `# optional` with standard features are replaced by `# needs` - Some import fixes needed for separate testing of **sagemath-graphs** from #35095   This is: - done with the help of `sage -fixdoctests` from #35749 - Part of: #29705 - Cherry-picked from: #35095 ### 📝 Checklist     - [x] The title is concise, informative, and self-explanatory. - [x] The description explains in detail what this PR is about. - [x] I have linked a relevant issue or discussion. - [ ] I have created tests covering the changes. - [ ] I have updated the documentation accordingly. ### ⌛ Dependencies   URL: #35951 Reported by: Matthias Köppe Reviewer(s): David Coudert

…eds`   - Many `# optional` are removed because small prime finite fields no longer need to be marked `# optional/needs sage.rings.finite_rings` since #35847 - Other `# optional` are replaced by codeblock-scoped `# needs` tags - Remaining `# optional` with standard features are replaced by `# needs` - Some import fixes needed for separate testing of **sagemath-graphs** from #35095   This is: - done with the help of `sage -fixdoctests` from #35749 - Part of: #29705 - Cherry-picked from: #35095    ### 📝 Checklist     - [x] The title is concise, informative, and self-explanatory. - [x] The description explains in detail what this PR is about. - [x] I have linked a relevant issue or discussion. - [ ] I have created tests covering the changes. - [ ] I have updated the documentation accordingly. ### ⌛ Dependencies   URL: #35943 Reported by: Matthias Köppe Reviewer(s): David Coudert, Matthias Köppe

- Many `# optional` are removed because small prime finite fields no longer need to be marked `# optional/needs sage.rings.finite_rings` since #35847 - Other `# optional` are replaced by codeblock-scoped `# needs` tags - Remaining `# optional` with standard features are replaced by `# needs` - Some import fixes needed for separate testing of **sagemath-graphs** from #35095   This is: - done with the help of `sage -fixdoctests` from #35749 - Part of: #29705 - Cherry-picked from: #35095 ### 📝 Checklist     - [x] The title is concise, informative, and self-explanatory. - [x] The description explains in detail what this PR is about. - [x] I have linked a relevant issue or discussion. - [ ] I have created tests covering the changes. - [ ] I have updated the documentation accordingly. ### ⌛ Dependencies   URL: #35957 Reported by: Matthias Köppe Reviewer(s): David Coudert, Matthias Köppe

…#35749

src/sage/features/sagemath.py: Expand documentation on # optional - s…

664c56c

…agemath-...

mkoeppe added the c: documentation label Jun 9, 2023

mkoeppe self-assigned this Jun 9, 2023

src/doc/en/developer/coding_basics.rst: Add style guide for formattin…

d7ecd4d

…g doctests, # optional

mkoeppe changed the title ~~Expand documentation on # optional - sagemath-... (modularization)~~ Add style guide and reference for # optional - sagemath-... doctest annotations (for modularization) Jun 9, 2023

Matthias Koeppe added 5 commits June 9, 2023 13:15

src/sage/features/sagemath.py: Fix markup, expand examples

e7173cd

src/sage/features/sagemath.py: Add module-level doc

3aacb73

Fix markup

bfb9a52

src/sage/features/sagemath.py: Expand on sage.graphs

4b69756

Expand on sage.graphs, sage.modules

d46fb19

mkoeppe added the s: needs review label Jun 10, 2023

Matthias Koeppe added 4 commits June 10, 2023 12:07

src/doc/en/developer/coding_basics.rst: Fix doctest output

5dc088f

Fix markup

1ad2776

src/doc/en/developer/coding_basics.rst: Fix doctest

eef016f

Merge branch 'develop' into feature_definitions

74b98cf

mkoeppe requested review from tobiasdiez and dcoudert June 13, 2023 16:07

mkoeppe changed the title ~~Add style guide and reference for # optional - sagemath-... doctest annotations (for modularization)~~ Add style guide and reference for # optional - sage.... doctest annotations (for modularization) Jun 16, 2023

kwankyu added 2 commits June 16, 2023 19:46

Add persistent optional tag

2440c0b

Fix a typo

647380c

kwankyu added 6 commits June 17, 2023 09:39

Allow needs for optional

2bd55ab

Block ends with a blank line

9485097

Use needs in the doctest

6dd4afd

Remove redundant backslash

f7152bd

Use formal needs:

87f5e15

Revert to needs revising the doctest

bdc4232

mkoeppe changed the title ~~Add style guide and reference for # optional - sage.... doctest annotations (for modularization)~~ Add style guide and reference for # optional - sage.... doctest annotations, extend sage -fixdoctests for modularization Jun 23, 2023

Merge tag '10.1.beta4' into feature_definitions

0596705

SageMath version 10.1.beta4, Release Date: 2023-06-21

mkoeppe added a commit to mkoeppe/sage that referenced this pull request Jul 12, 2023

'./sage -fixdoctests --only-tags' for files conflicting with sagemath…

f6a4067

…#35749

mkoeppe added a commit to mkoeppe/sage that referenced this pull request Jul 12, 2023

Do not use block # optional until sagemath#35749 is merged

8feae19

mkoeppe added a commit to mkoeppe/sage that referenced this pull request Jul 13, 2023

Do not use block # optional until sagemath#35749 is merged

e7bc5db

kwankyu added s: positive review and removed s: needs review labels Jul 14, 2023

jhpalmieri added the c: doctest framework label Jul 19, 2023

vbraun added the s: needs work label Jul 19, 2023

Fix random doctests in elliptic curves

6b5b82c

kwankyu mentioned this pull request Jul 19, 2023

Fix random doctest failures in elliptic curves #35966

Closed

5 tasks

Merge branch 'fix-doctests-elliptic-curves' into feature_definitions

44549f6

mkoeppe removed the s: needs work label Jul 19, 2023

tornaria mentioned this pull request Jul 21, 2023

Move hilbert_numerator test to its proper place #35977

Merged

jhpalmieri mentioned this pull request Jul 27, 2023

Deprecate sorting by default in connected component methods for graphs #35891

Merged

5 tasks

vbraun merged commit f2abd5a into sagemath:develop Jul 30, 2023

github-actions bot removed the s: positive review label Jul 30, 2023

mkoeppe deleted the feature_definitions branch July 30, 2023 17:24

mkoeppe added this to the sage-10.1 milestone Jul 30, 2023

mkoeppe added a commit to mkoeppe/sage that referenced this pull request Aug 2, 2023

'./sage -fixdoctests --only-tags' for files conflicting with sagemath…

cd752ff

…#35749

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Add style guide / reference for `# optional - sage....` doctest tags, extend `sage -t` and `sage -fixdoctests` for modularization tasks #35749

Add style guide / reference for `# optional - sage....` doctest tags, extend `sage -t` and `sage -fixdoctests` for modularization tasks #35749

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Add style guide / reference for # optional - sage.... doctest tags, extend sage -t and sage -fixdoctests for modularization tasks #35749

Add style guide / reference for # optional - sage.... doctest tags, extend sage -t and sage -fixdoctests for modularization tasks #35749

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mkoeppe commented Jun 9, 2023 • edited Loading

📚 Description

📝 Checklist

⌛ Dependencies

mkoeppe commented Jun 16, 2023

kwankyu commented Jul 12, 2023

mkoeppe commented Jul 14, 2023

vbraun commented Jul 19, 2023

kwankyu commented Jul 19, 2023

kwankyu commented Jul 19, 2023

kwankyu commented Jul 19, 2023

kwankyu commented Jul 19, 2023

github-actions bot commented Jul 19, 2023

Add style guide / reference for `# optional - sage....` doctest tags, extend `sage -t` and `sage -fixdoctests` for modularization tasks #35749

Add style guide / reference for `# optional - sage....` doctest tags, extend `sage -t` and `sage -fixdoctests` for modularization tasks #35749

mkoeppe commented Jun 9, 2023 •

edited

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