Add Oriented Matroids Package #38024

thecaligarmo · 2024-05-18T20:00:44Z

This pull request merges the Oriented Matroids package that I developed (see https://github.com/thecaligarmo/oriented_matroids) into Sage so that others may develop directly into it rather than relying solely on myself.

This package should resolve ticket #18703 and in addition, my package should be removed from #31164 as this pull request will put Oriented Matroids directly into Sage rather than requiring a package.

If there are any changes needing to be made, just let me know and we can go from there.

📝 Checklist

The title is concise and informative.
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 and checked the documentation preview.

⌛ Dependencies

thecaligarmo · 2024-05-18T21:09:59Z

The Build & Test action seems to be failing, but I can't figure out why. It's stating it's not a git repository, when it clearly is. Not sure how to fix it.

github-actions · 2024-05-18T21:30:50Z

Documentation preview for this PR (built with commit 46c149c; changes) is ready! 🎉
This preview will update shortly after each push to this PR.

gmou3 · 2024-05-19T13:59:32Z

The Build & Test action seems to be failing, but I can't figure out why. It's stating it's not a git repository, when it clearly is. Not sure how to fix it.

Don't worry about that, it is some error of the tester.

SageMath version 10.4.beta7, Release Date: 2024-05-25

src/sage/matroids/all.py

gmou3 · 2024-05-28T15:42:55Z

src/sage/matroids/oriented_matroids/abstract_oriented_matroid.py

+        """
+        if hasattr(self, "_circuits"):
+            return self._circuits
+        raise NotImplementedError("Circuits not implemented")


I would recommend all Error messages to start uncapitalized and end without a dot.

gmou3 · 2024-05-28T15:43:34Z

src/sage/matroids/oriented_matroids/abstract_oriented_matroid.py

+            \mathcal{C} / A = \left\{ X\mid_{E \backslash A} : X \in \mathcal{C} \text{ and} A \subseteq X^0 \right\}
+
+        """
+        # sage: from sage.matroids.oriented_matroids.oriented_matroid import OrientedMatroid


Do something with this commented code?

gmou3 · 2024-05-28T15:44:47Z

src/sage/matroids/oriented_matroids/catalog.py

+
+AUTHORS:
+
+- Aram Dermenjian (): initial version


Need to add date or complete/delete file.

Co-authored-by: gmou3 <[email protected]>

thecaligarmo · 2024-07-02T17:41:48Z

@gmou3 I've gone ahead and fixed the things you wanted.

gmou3 · 2024-07-04T04:29:25Z

Thanks. I had opened a PR a while ago with some formatting recommendations. Please have a look and merge or close it please.

Some formatting recommendations

thecaligarmo · 2024-07-04T11:45:00Z

I hadn't noticed the pull request for some reason. I've added your changes as well and double checked things work nicely. Thanks for that.

thecaligarmo · 2024-10-05T20:36:53Z

Ok, I've gone ahead and altered the code to use a class instead of a constructor. We'll make a different PR for doing the same to Matroids (Which I believe should be done as well)

gmou3 · 2024-10-06T11:31:51Z

I can implement the corresponding changes for Matroid after the present PR is finalized and merged.
So feel free to diverge if it produces some improvement.

gmou3 · 2024-10-28T13:27:44Z

Have the desired changes been implemented according to @tscrim?

thecaligarmo · 2024-10-28T21:33:08Z

Have the desired changes been implemented according to @tscrim?

Yes. I think all the changes desired by @tscrim have been implemented. Unless I missed something or if there are new ones?

gmou3

Ok then, it also looks good to me.

Let's leave further work for future PRs.

tscrim

There are many things that need to be done before this can be included. Some of them are very important (all methods need doctests, even hidden and abstract ones); some of them are more minor (doc formatting I saw from checking the compiled doc); some are not necessary but trying to make the code within Sage more uniform.

src/sage/matroids/oriented_matroids/signed_subset_element.py

tscrim · 2024-11-01T01:02:15Z

src/sage/matroids/oriented_matroids/oriented_matroid.py

+        """
+        Return the dual oriented matroid.
+
+        EXAMPLES::


Suggested change

"""

Return the dual oriented matroid.

EXAMPLES::

"""

Return the dual oriented matroid.

EXAMPLES::

You should add an example for the case when there is no dual. If no such case exists, then this should be an @abstract_method (perhaps with optional=True).

Turns out that dual is not actually implemented yet. I had missed that an (incorrect) doctest was written by one of my mentees. I'll go ahead and fix this and see about adding code for making a dual.

tscrim · 2024-11-01T01:02:38Z

src/sage/matroids/oriented_matroids/oriented_matroid.py

+        r"""
+        Return the underlying matroid.
+        """
+        pass


Suggested change

pass

Abstract methods also still need a doctest (from one of the concrete implementations).

Is there a reason we're removing pass here? I guess I'm not understanding when it should be used if it's not used in these circumstances?

The docstring actually does the same job as pass, but by not having it, it suggests there is no implementation (rather than pass which would simply do nothing).

src/sage/matroids/oriented_matroids/oriented_matroid.py

When certificate is set to `True`, the method `is_valid` returns a tuple of a boolean and a dictionary. The dictionary provides some more information in case the matroid is not valid. Examples: ``` sage: M = matroids.catalog.Fano() sage: M.is_valid() True sage: M.is_valid(certificate=True) (True, {}) sage: C = [[1, 2, 3], [3, 4, 5]] sage: M = Matroid(circuits=C) sage: M.is_valid() False sage: M.is_valid(certificate=True) (False, {'circuit 1': frozenset({3, 4, 5}), 'circuit 2': frozenset({1, 2, 3}), 'element': 3, 'error': 'elimination axiom failed'}) ``` To be done constistently with sagemath#38024. URL: sagemath#38711 Reported by: gmou3 Reviewer(s): Travis Scrimshaw

Co-authored-by: Travis Scrimshaw <[email protected]>

Forgot to add a few code suggestions. Co-authored-by: Travis Scrimshaw <[email protected]>

thecaligarmo · 2024-11-09T17:08:05Z

@tscrim I'm trying to do TestSuite(E).run() on a SignedSubsetElement, but it keeps failing. From what I can tell, it's because of the following:

sage: from sage.matroids.oriented_matroids.oriented_matroid import OrientedMatroid
sage: from sage.matroids.oriented_matroids.signed_subset_element import SignedSubsetElement
sage: from sage.cpython.type import can_assign_class
sage: M = OrientedMatroid([[1],[-1]], key='circuit');
sage: E = SignedSubsetElement(M,data = (0,))
sage: can_assign_class(E)
True
sage: TestSuite(E).run()
Failure in _test_category:
Traceback (most recent call last):
  File "/sage/sagedev/src/sage/misc/sage_unittest.py", line 298, in run
    test_method(tester=tester)
  File "sage/structure/element.pyx", line 720, in sage.structure.element.Element._test_category
    tester.assertTrue(isinstance(self, self.parent().category().element_class))
  File "/usr/lib/python3.10/unittest/case.py", line 687, in assertTrue
    raise self.failureException(msg)
AssertionError: False is not true
------------------------------------------------------------
The following tests failed: _test_category

The isinstance(self, self.parent().category().element_class) line only runs if can_assign_class is true, but since that function is written in cython, I don't necessarily know what's happening to fix this. Do you know what this does or how to fix this?

To make life easier, here's the source for can_assign_class:

cpdef bint can_assign_class(obj) noexcept:
    """
    Can we assign ``obj.__class__``?

    Note that Python 3.5 has experimented with allowing assigning
    ``__class__`` in more cases but this was mostly reverted. In this
    function, we apply the Python 2.7 semantics.

    EXAMPLES::

        sage: class X: pass
        sage: from sage.cpython.type import can_assign_class
        sage: can_assign_class(X())
        True
        sage: class Y(int): pass
        sage: from sage.cpython.type import can_assign_class
        sage: can_assign_class(Y())
        True
        sage: can_assign_class(1)
        False
    """
    cdef PyTypeObject* tp = Py_TYPE(obj)
    if tp is PyInstance_Type:
        return True
    return (tp.tp_flags & Py_TPFLAGS_HEAPTYPE) != 0

tscrim · 2024-11-09T23:42:37Z

@tscrim I'm trying to do TestSuite(E).run() on a SignedSubsetElement, but it keeps failing.

It’s failing as it should because it doesn’t have a proper parent set. From what I can quickly see, it isn’t being used as an element in a set but a more generic helper object. So I would remove the inheritance from Element and instead derive from SageObject. It’s possible I missed something in its usage from a quick skim of the code.

Add Oriented Matroids Package

57ac44c

github-actions bot added the v: large label May 18, 2024

gmou3 added t: feature c: matroid theory labels May 19, 2024

tscrim added t: enhancement s: needs review and removed v: large s: needs review labels May 20, 2024

gmou3 added 2 commits May 28, 2024 14:32

Merge tag '10.4.beta7' into oriented_matroids

59fe83d

SageMath version 10.4.beta7, Release Date: 2024-05-25

Some formatting recommendations

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gmou3 reviewed May 28, 2024

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gmou3 suggested changes May 28, 2024

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Merge remote-tracking branch 'sagemath/develop' into oriented_matroids

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vbraun force-pushed the develop branch from eba5e19 to e5f42fa Compare June 3, 2024 22:15

Merge branch 'develop' into oriented_matroids

b9cefa8

github-actions bot added the v: large label Jun 17, 2024

fchapoton and others added 4 commits June 17, 2024 14:54

Update src/sage/matroids/all.py

ffbe028

Co-authored-by: gmou3 <[email protected]>

Merge branch 'develop' into oriented_matroids

00cff53

Remove catalog from oriented matroids (unused), update error messages

5ffcd32

Fix doctest

da8ef8f

github-actions bot added the s: needs review label Jul 2, 2024

thecaligarmo and others added 3 commits July 4, 2024 12:39

Merge branch 'oriented_matroids' into oriented_matroids

01ea791

Merge pull request #1 from gmou3/oriented_matroids

c13eaf9

Some formatting recommendations

Fix test error

1b1a269

Fix code style

2b46653

gmou3 approved these changes Oct 31, 2024

View reviewed changes

gmou3 added s: positive review and removed s: needs review labels Oct 31, 2024

tscrim requested changes Nov 1, 2024

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tscrim added s: needs work and removed s: positive review v: large labels Nov 1, 2024

gmou3 mentioned this pull request Nov 2, 2024

Move matroid constructor #38906

Open

Apply suggestions from code review

f5316f3

Co-authored-by: Travis Scrimshaw <[email protected]>

github-actions bot added s: needs review and removed s: needs work labels Nov 9, 2024

thecaligarmo and others added 8 commits November 9, 2024 00:49

Update src/sage/matroids/oriented_matroids/signed_subset_element.py

53ac251

Co-authored-by: Travis Scrimshaw <[email protected]>

Update src/sage/matroids/oriented_matroids/signed_subset_element.py

d9a3d83

Co-authored-by: Travis Scrimshaw <[email protected]>

Update src/sage/matroids/oriented_matroids/signed_subset_element.py

287f250

Co-authored-by: Travis Scrimshaw <[email protected]>

Update src/sage/matroids/oriented_matroids/signed_subset_element.py

6461e1a

Co-authored-by: Travis Scrimshaw <[email protected]>

Apply suggestions from code review

cb9c8e5

Forgot to add a few code suggestions. Co-authored-by: Travis Scrimshaw <[email protected]>

Merge branch 'develop' into oriented_matroids

1f57f5c

Doc changes

605a320

Doctest fixes and a minor bug fix

7fcd02b

thecaligarmo added 3 commits November 9, 2024 12:08

Fix doctests and remove signed subset testsuite

5a60b5f

Update certificates to be dicts

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Add some tests

46c149c

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Add Oriented Matroids Package #38024

Add Oriented Matroids Package #38024

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Add Oriented Matroids Package #38024

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Add Oriented Matroids Package #38024

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thecaligarmo commented May 18, 2024

📝 Checklist

⌛ Dependencies

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