Opened 10 years ago
Closed 2 years ago
#10501 closed task (fixed)
Deprecate adjoint in favor of adjugate
Reported by:  rbeezer  Owned by:  jason, was 

Priority:  minor  Milestone:  sage8.7 
Component:  linear algebra  Keywords:  notation, linear algebra, adjugate, matrices, determinants 
Cc:  was, mvngu, kohel, tornaria, mjo  Merged in:  
Authors:  Kwankyu Lee  Reviewers:  Darij Grinberg 
Report Upstream:  N/A  Work issues:  
Branch:  bf44252 (Commits, GitHub, GitLab)  Commit:  bf44252756d2f663acc479c1a345c1913716a1f6 
Dependencies:  Stopgaps: 
Description (last modified by )
Matrix methods named adjoint
and _adjoint
are renamed adjugate
and _adjugate
and replacements are added that raise deprecation warnings.
This is part of the program at #10465.
Attachments (1)
Change History (33)
Changed 10 years ago by
comment:1 Changed 10 years ago by
 Cc was mvngu kohel tornaria added
 Status changed from new to needs_review
comment:2 followup: ↓ 3 Changed 10 years ago by
 Status changed from needs_review to needs_work
I already stated some objections to this on the mailing list, but I'll repeat:
On deprecating "adjoint" meaning "matrix of cofactors"
 it's standard terminology and has meant this in sage for long
 "adjugate" is newer and (IMO) less standard terminology  in particular it has no obvious translations
On using "adjoint" meaning "conjugate transpose"
 "conjugate transpose" is easy to say, and it's really what is meant
 the "adjoint operator" for a matrix seems illdefined, because a matrix is not an operator but only a representation of an operator in some basis.
Moreover, if there are two colliding usages of the name "adjoint", I would find it more reasonable to keep the usage that is already traditional in Sage.
The usage of "adjoint" is ubiquitous in relation to quadratic forms afaict (and, as John Cremona pointed out, is where the term originates with Gauss on ternary quadratic forms)
Reference for "Adjoint of a matrix":
Bourbaki, Elements, book 2, chapter III, section 11, exercise 9:
The adjoint of a square matrix X of order n over A is the matrix X = (det (A'")) of minors of A" of order n — 1.
(Note that the term also shows at the index of terminology of the book)
PS: searching for
"The adjoint of a square matrix" bourbaki
in books.google.com, yields the above passage.
comment:3 in reply to: ↑ 2 Changed 10 years ago by
Replying to tornaria:
Hi Gonzalo,
I certainly read your postings to the mailing list carefully and appreciated the points you raised. However, I had not realized you were so opposed to the change.
After some discussion, I asked 'Is there any objection to deprecating the current .adjoint() function (which returns a matrix of cofactors) and renaming it as the "adjugate"?'
It was not meant to be an official vote, but I got +1 replies from Grout, Cremona, Loeffler and Stein. Dima P and Karl Crisman had earlier voiced support. There were no objections stated once I asked the question carefully. So I have been proceeding on the assumption that there was strong support.
I do not believe I changed any of the names of the commands for quadratic forms, though I can see that causing confusion if the adjoint of a matrix becomes the conjugate transpose.
I have written a patch (#10471) with the conjugate_transpose()
, which I find a really clumsy command, but workable in the interim. William has suggested a more general adjoint
function, which I would need to think about some more, but maybe that does not help with any of your objections (sounds like maybe that is worse in your view).
I have twice now taught a "matrix analysis" course and it seems to me that adjoint gets used regularly (but maybe not consistently) for the conjugate transpose. I am in the middle of making a major push to add significant amount of Sage code to my introductory linear algebra text, which is going very nicely. But I need to also fix my "complex inner product" since I defined it with the conjugation on the "wrong" half. So I would really like to keep Sage, my text, and the word "adjoint" all consistent with each other when I get to that point in a few weeks.
Do you have some suggestions for a way forward?
Thanks, Rob
comment:4 Changed 8 years ago by
 Cc mjo added
+1 from me. I hit this today, and just checked a handful of books:
 Atkinson, An Introduction to Numerical Analysis, 1989. Section 7.1.
 Axler, Linear Algebra Done Right, 1997. Ch. 6.
 Marcus & Minc, Introduction to Linear Algebra, 1988. Section 1.4.
 Meyer, Matrix Analysis and Applied Linear Algebra, 2000. Section 3.2.
 Rudin, Functional Analysis, 1991. Chapter 4.
 Shilov, Linear Algebra, 1977. Section 7.6.
All of which use the "new" meaning. In the interest of fairness, I also found,
 Edwards, Elementary Linear Algebra, 2000. Section 3.4.
Which uses the cofactor definition.
comment:5 followup: ↓ 6 Changed 8 years ago by
Hmm. Given two completely different uses of the word "adjoint" in this situation, I wonder if the right solution is to avoid it completely (with a deprecation warning for a while). If we use the "new" meaning, there will still be people who type A.adjoint()
expecting the old meaning, and vice versa. Something like A.conjugate_transpose()
can be found by tab completion; is that good enough? Is A.adjugate()
the right name for the other version?
comment:6 in reply to: ↑ 5 ; followup: ↓ 7 Changed 8 years ago by
Replying to jhpalmieri:
Hmm. Given two completely different uses of the word "adjoint" in this situation, I wonder if the right solution is to avoid it completely (with a deprecation warning for a while). If we use the "new" meaning, there will still be people who type
A.adjoint()
expecting the old meaning, and vice versa. Something likeA.conjugate_transpose()
can be found by tab completion; is that good enough? IsA.adjugate()
the right name for the other version?
Did someone seriously implement m.conjugate_transpose()
as a shortcut for m.conjugate().transpose()
? =)
I never thought to look for another method, I just did the operations individually.
From what I understand, the terms "adjoint" and "adjunct" come from higher algebra, most of which is over my head. If that's the case, books written after e.g. category theory became popular will probably gravitate towards the new terminology. Although it does suck to have to deprecate adjoint
, give it a new name, and then give something else the old name.
Most of us have access to math departments; maybe we could do a survey of people working in linear algebra? If the result is overwhelming, rename it.
comment:7 in reply to: ↑ 6 ; followup: ↓ 8 Changed 8 years ago by
Replying to mjo:
Did someone seriously implement
m.conjugate_transpose()
as a shortcut form.conjugate().transpose()
? =)
Yep, that was me. ;) But the BDFL suggested it. Required reading:
https://groups.google.com/forum/?fromgroups=#!topic/sagedevel/YjImMWVVwo4
You will see a lot of support for changes. You'll see one conscientious objector. I dropped it. If someone else wants to carry the torch, I'll have their back.
Rob
comment:8 in reply to: ↑ 7 ; followup: ↓ 9 Changed 8 years ago by
Did someone seriously implement
m.conjugate_transpose()
as a shortcut form.conjugate().transpose()
? =)
It's not as bad as you think, because tabcompletion doesn't work on m.conjugate()
, though it would be awesome if Sage could magically know that...
Rob, so what does the latest version of your book do?
comment:9 in reply to: ↑ 8 Changed 8 years ago by
Replying to kcrisman:
Rob, so what does the latest version of your book do?
conjugatetranspose has always been called "adjoint," in line with my experience teaching numerical linear algebra. I even have my inner product conjugating the correct vector now. ;)
See: http://linear.ups.edu/html/sectionMO.html#subsectionAM
I almost never have need to reference the matrix of cofactors (proposed as adjugate here), but do use it one exercise about building a matrix inverse this way.
See: Exercise PDM.T20 in http://linear.ups.edu/html/sectionPDM.html
Rob
comment:10 Changed 8 years ago by
 Milestone changed from sage5.11 to sage5.12
comment:11 Changed 7 years ago by
 Milestone changed from sage6.1 to sage6.2
comment:12 Changed 7 years ago by
 Milestone changed from sage6.2 to sage6.3
comment:13 Changed 7 years ago by
 Milestone changed from sage6.3 to sage6.4
comment:14 Changed 3 years ago by
 Branch set to u/klee/10501
 Commit set to 0669f64d384d8b42838d590a41a6bf9fcb115979
 Milestone changed from sage6.4 to sage8.4
 Priority changed from major to minor
 Status changed from needs_work to needs_review
I want to revive this ticket. So here is the needed patch.
One thing not found in Rob's original patch is alias adjoint_classical
of adjugate
. The alias is used in quadratic form code in Sage.
New commits:
0669f64  Deprecate adjoint for adjugate and adjoint_classical

comment:15 Changed 3 years ago by
 Description modified (diff)
comment:16 Changed 3 years ago by
 Commit changed from 0669f64d384d8b42838d590a41a6bf9fcb115979 to 43ab6df581d54a2d627c030443a9320c6a7dee8e
comment:17 Changed 3 years ago by
 Commit changed from 43ab6df581d54a2d627c030443a9320c6a7dee8e to 08eee094dd63965b8aadf3a38b2f3fe620910a9b
Branch pushed to git repo; I updated commit sha1. New commits:
08eee09  import deprecated_function_alias on global level to avoid crash

comment:18 Changed 3 years ago by
 Commit changed from 08eee094dd63965b8aadf3a38b2f3fe620910a9b to d1bbfb1bd29c9cfb688d24d9a71e92ce98148513
Branch pushed to git repo; I updated commit sha1. New commits:
d1bbfb1  change more adjoint to adjugate

comment:19 Changed 3 years ago by
 Commit changed from d1bbfb1bd29c9cfb688d24d9a71e92ce98148513 to 2f1597566c868739e748599aa5e8b2c2eb59775e
Branch pushed to git repo; I updated commit sha1. New commits:
2f15975  fix neglected doctest failures

comment:20 Changed 3 years ago by
 Milestone changed from sage8.4 to sage8.5
comment:21 Changed 2 years ago by
 Branch changed from u/klee/10501 to public/ticket/10501
 Commit changed from 2f1597566c868739e748599aa5e8b2c2eb59775e to b4994c43854ebbece7186b7b7b5cd132873f9939
 Keywords notation linear algebra adjugate matrices determinants added
I wholeheartedly agree with "adjugate". When I see "adjoint", I look up the definition. When I see "adjugate", I immediately know what is meant.
Pushed a little commit to improve the documentation. IMHO, this is an easy ticket to review: just run all doctests. If they work, then it's fine.
New commits:
64b9491  Merge branch 'u/klee/10501' of git://trac.sagemath.org/sage into adj

b4994c4  actually define the adjugate in the doc

comment:22 Changed 2 years ago by
 Commit changed from b4994c43854ebbece7186b7b7b5cd132873f9939 to 356285df8e0ede0f6d2ccc02559744004528b744
Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:
356285d  Deprecate adjoint for adjugate and adjoint_classical

comment:23 Changed 2 years ago by
Squashed and rebased to sage 8.6. In addition, refined some docstrings and comments.
comment:24 followup: ↓ 25 Changed 2 years ago by
If klee and darij are both agreed that each other's respective contributions are sufficient, then you can jointly set to positive review (sometimes Authors are 1, 2 and Reviewers are 2, 1).
I do wonder whether some of the py3 things like
 raise TypeError("Oops! The matrix must have " + str(n) + " rows. =(") + raise TypeError("the matrix must have {} rows".format(n))
are necessary on this ticket, since it makes it a little more of a patch bomb.
Also, don't we typically test deprecations (and then remove when deprecation is done)?
comment:25 in reply to: ↑ 24 ; followup: ↓ 26 Changed 2 years ago by
Replying to kcrisman:
If klee and darij are both agreed that each other's respective contributions are sufficient, then you can jointly set to positive review (sometimes Authors are 1, 2 and Reviewers are 2, 1).
Positive review on his part of the code. It is up to him to put his name to the Author field.
I do wonder whether some of the py3 things like
 raise TypeError("Oops! The matrix must have " + str(n) + " rows. =(") + raise TypeError("the matrix must have {} rows".format(n))are necessary on this ticket, since it makes it a little more of a patch bomb.
Not necessary. But I think we don't need to freak away from making small improvements unrelated with the main issue of the ticket. Do we?
Or do you regard the small changes as no improvements?
Also, don't we typically test deprecations (and then remove when deprecation is done)?
I didn't know. I don't know.
comment:26 in reply to: ↑ 25 Changed 2 years ago by
Or do you regard the small changes as no improvements?
No, it's just that it causes more opportunities for clashes with other tickets.
Also, don't we typically test deprecations (and then remove when deprecation is done)?
I didn't know. I don't know.
For one of many examples, see (at least right now correct link) this spot
sage: x, y, z = var('x, y, z') sage: S = CoordinatePatch((x, y, z)); S doctest:...: DeprecationWarning: Use Manifold instead. See http://trac.sagemath.org/24444 for details. Open subset of R^3 with coordinates x, y, z
I guess this should be done for positive review.
comment:27 Changed 2 years ago by
Sorry, I don't have time for this :/
I could reread the rebased branch once the stress from the semester start has subsided, but I'm generally extremely short on time until September or so(?). Sorry.
comment:28 Changed 2 years ago by
 Commit changed from 356285df8e0ede0f6d2ccc02559744004528b744 to bf44252756d2f663acc479c1a345c1913716a1f6
Branch pushed to git repo; I updated commit sha1. New commits:
bf44252  Add a test for deprecation

comment:29 Changed 2 years ago by
Anything else to do?
comment:30 Changed 2 years ago by
 Milestone changed from sage8.5 to sage8.7
 Reviewers set to Darij Grinberg
The new version looks good to me. If complete doctests pass (anyone please check), please make this a positive_review.
(I should not be listed as author; my changes were trivial.)
comment:31 Changed 2 years ago by
 Status changed from needs_review to positive_review
comment:32 Changed 2 years ago by
 Branch changed from public/ticket/10501 to bf44252756d2f663acc479c1a345c1913716a1f6
 Resolution set to fixed
 Status changed from positive_review to closed
Three files caused doctest errors on a full run with only the necessary changes in sage/matrix. I've made changes in these other places to fix those failures, and the affected files now pass their tests. I'm running the full suite right now.
I've cc'ed folks who I think might be able to doublecheck that no complications have crept in. If you want to sneak a quick look at the patch, here's a quick guide:
Minh, David: sage/crypto/classical.py, inverse_key() for a Hill Cryptosystem
Gonzalo: sage/quadratic_forms/quadratic_form_ternary_Tornaria.py, adjoints of a form
William: sage/quadratic_forms/quadratic_form.py, adjoint_primitive()