`sage.{topology,homology}`: Modularization fixes #35581

mkoeppe · 2023-04-28T20:08:24Z

📚 Description

sage.topology is closely linked to functionality from sage.graphs. Doctests that either use methods or examples that require sage.graphs are marked # optional - sage.graphs; likewise for sage.groups (for multiplicative groups) and (less often) sage.combinat.
Doctests that use finite fields are marked as # optional - sage.rings.finite_rings because implementation classes of GF(...) depend on various libraries.
Doctests that compute homology are marked as # optional - sage.modules because sage.homology needs vector spaces. This functionality is not part of the distribution sagemath-categories but a higher up distribution (as of #35095, the distribution sagemath-polyhedra contains sage.modules, sage.matrix, sage.homology).
Doctests involving free resolutions are marked # optional - sage.libs.singular.

Some examples are read from data files; the corresponding tests are now marked # optional - pyparsing.

A sporadic use of a function from numpy has been replaced by an equivalent itertools function.

The correct placement of the # optional tags can be (and has been) tested using #35095.

While going through the doctests, I also reformatted some so that they can be read in our HTML documentation style (furo) without having to scroll horizontally.

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

…y itertools

…mology_modularization

src/sage/homology/chain_complex_morphism.py

src/sage/homology/free_resolution.py

src/sage/topology/cell_complex.py

kwankyu · 2023-05-24T03:34:13Z

src/sage/topology/filtered_simplicial_complex.py

@@ -552,12 +552,12 @@ def _remove_pivot_rows(self, s, simplices):
            sage: l = [([0], 0), ([1], 0), ([2], 1), ([3], 1), ([0, 1], 1), ([1, 2], 1),
            ....:      ([0, 3], 2), ([2, 3], 2), ([0, 2], 3), ([0, 1, 2], 4)]
            sage: X = FilteredSimplicialComplex(l)
-            sage: X._persistent_homology()
+            sage: X._persistent_homology()                                              # optional - sage.rings.finite_rings
            [[(0, 1), (1, 2), (0, +Infinity)], [(3, 4), (2, +Infinity)], []]


No sage.modules?

Thanks for catching this, I'll add it.

src/sage/topology/simplicial_complex.py

kwankyu · 2023-05-24T03:42:33Z

src/sage/topology/simplicial_complex.py

-            sage: C2.simplified()
+            sage: RP2 = simplicial_complexes.RealProjectiveSpace(2)                     # optional - sage.libs.pari
+            sage: C2 = RP2.fundamental_group(simplify=False); C2                        # optional - sage.graphs sage.groups sage.libs.pari
+            Finitely presented group < e0, e1, e2, e3, e4, e5, e6, e7, e8, e9 | e0, e3,


Does L4090 need sage.libs.pari? Or is it L4091?

Looks like a mistake. I have removed sage.libs.pari from all lines in this block

kwankyu · 2023-05-24T03:43:50Z

src/sage/topology/simplicial_complex.py

@@ -4252,27 +4260,28 @@ def automorphism_group(self):
        EXAMPLES::

            sage: S = simplicial_complexes.Simplex(3)
-            sage: S.automorphism_group().is_isomorphic(SymmetricGroup(4))
+            sage: S.automorphism_group().is_isomorphic(SymmetricGroup(4))           # optional - sage.graphs
            True



Is this sage.graphs or sage.groups?

both; I'll fix it

…ge.modules

kwankyu · 2023-05-24T03:55:01Z

src/sage/topology/simplicial_set_constructions.py

            {0: 0, 1: 0, 2: Z x Z, 3: Z}
-            sage: len(P.nondegenerate_simplices())


No sage.modules or sage.groups?

A lot of sage.modules are missing in this file. Adding now

I meant L1226.

src/sage/topology/simplicial_set_examples.py

kwankyu · 2023-05-24T04:01:28Z

src/sage/topology/simplicial_set_morphism.py

-            sage: susp_eta.mapping_cone().homology() == eta.mapping_cone().suspension().homology()
+            sage: mc_susp_eta = eta.suspension().mapping_cone()                         # optional - sage.graphs
+            sage: susp_mc_eta = eta.mapping_cone().suspension()                         # optional - sage.graphs
+            sage: mc_susp_eta.homology() == susp_mc_eta.homology()                      # optional - sage.graphs
            True


No sage.modules?

Thanks, added.

…s etc

…age.modules

…odules

…ge.rings.finite_rings

kwankyu · 2023-05-24T04:31:10Z

Though I looked through all changes, definitely I could not check everything. However, as I understand it, these optional tags are not harmful even they are misplaced, but could just be less useful to test distribution packages. Misplaced tags may be corrected when we start to test all distribution packages before Sage release. Am I right?

mkoeppe · 2023-05-24T04:37:44Z

as I understand it, these optional tags are not harmful even they are misplaced, but could just be less useful to test distribution packages. Misplaced tags may be corrected when we start to test all distribution packages before Sage release. Am I right?

Right. For testing the monolithic Sage library, there is no change at all. (The only thing that could go wrong is to misspell a # optional tag, which would silently disable the test.)
I am testing these annotations with sagemath-categories and sagemath-polyhedra from #35095. The goal there is to get most tests of these distributions to pass; the annotations do not have to be perfect for that.

src/sage/homology/algebraic_topological_model.py

src/sage/homology/graded_resolution.py

github-actions · 2023-05-24T20:57:57Z

Documentation preview for this PR (built with commit c4c593a) is ready! 🎉

kwankyu

Thanks.

mkoeppe · 2023-05-25T00:05:03Z

Thanks for the review!

mkoeppe added c: linear algebra c: algebraic topology t: refactoring labels Apr 28, 2023

mkoeppe self-assigned this Apr 28, 2023

mkoeppe added the s: needs review label Apr 28, 2023

Matthias Koeppe added 8 commits April 30, 2023 11:30

sage.homology: Add # optional

326078e

sage.topology: More # optional

6b5cd65

sage.homology: Modularization fixes for imports

acf3d47

sage.topology: Modularization fixes for imports

b9aa548

sage.topology: More # optional

a0398e9

src/sage/homology/homology_morphism.py: Replace use of numpy.cumsum b…

3a435fc

…y itertools

src/sage/categories/simplicial_sets.py: More # optional

f0e41e5

sage.{homology,topology}: Doctest cosmetics

7b24c69

mkoeppe force-pushed the sage_topology_homology_modularization branch from f806616 to 7b24c69 Compare April 30, 2023 18:30

Matthias Koeppe added 6 commits May 4, 2023 16:19

src/sage/features/standard.py: Add pyparsing

19083cd

sage.topology: Fix # optional

661ce3e

Merge remote-tracking branch 'upstream/develop' into sage_topology_ho…

d68dc8b

…mology_modularization

src/sage/topology/simplicial_complex.py: Add # optional

b8340ef

src/sage/topology/simplicial_set.py: Add # optional

983f464

Merge remote-tracking branch 'upstream/develop' into sage_topology_ho…

8a9620d

…mology_modularization

kwankyu reviewed May 24, 2023

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src/sage/homology/free_resolution.py: Use file-level # optional

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kwankyu reviewed May 24, 2023

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src/sage/topology/filtered_simplicial_complex.py: Add # optional - sa…

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…ge.modules

kwankyu reviewed May 24, 2023

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Matthias Koeppe added 6 commits May 23, 2023 21:08

src/sage/topology/simplicial_complex.py: Add # optional - sage.module…

33f30d6

…s etc

src/sage/topology/simplicial_complex.py: Remove unnecessary # optional

5f853b5

src/sage/topology/simplicial_set_constructions.py: Add # optional - s…

11fd1f7

…age.modules

src/sage/topology/simplicial_set_morphism.py: Add # optional - sage.m…

9dfc0c4

…odules

src/sage/topology/simplicial_complex_homset.py: Doctest cosmetics

f3eb176

src/sage/homology/algebraic_topological_model.py: Add # optional - sa…

170fab6

…ge.rings.finite_rings

src/sage/homology/chain_complex_homspace.py: Doctest cosmetics

0c97bcf

kwankyu reviewed May 24, 2023

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kwankyu reviewed May 24, 2023

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src/sage/homology/graded_resolution.py Outdated Show resolved Hide resolved

src/sage/homology/graded_resolution.py: Use file-level # optional

c4c593a

kwankyu approved these changes May 25, 2023

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kwankyu added s: positive review and removed s: needs review labels May 25, 2023

vbraun merged commit cb2f3c0 into sagemath:develop May 28, 2023

mkoeppe added this to the sage-10.1 milestone May 28, 2023

mkoeppe removed the s: positive review label May 28, 2023

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`sage.{topology,homology}`: Modularization fixes #35581

`sage.{topology,homology}`: Modularization fixes #35581

mkoeppe commented Apr 28, 2023 •

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		{0: 0, 1: 0, 2: Z x Z, 3: Z}
		sage: len(P.nondegenerate_simplices())

sage.{topology,homology}: Modularization fixes #35581

sage.{topology,homology}: Modularization fixes #35581

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mkoeppe commented Apr 28, 2023 • edited Loading

📚 Description

📝 Checklist

⌛ Dependencies

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mkoeppe commented May 25, 2023

`sage.{topology,homology}`: Modularization fixes #35581

`sage.{topology,homology}`: Modularization fixes #35581

mkoeppe commented Apr 28, 2023 •

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