Organizing the e directory by MichaelABurr · Pull Request #4347 · Macaulay2/M2

MichaelABurr · 2026-05-21T19:33:49Z

These are the changes from the Macaulay2 workshop in Atlanta containing the changes to the locations of the files in the e-directory of Macaulay2.

…ine development work.

RingElem wraps (Ring*, ring_elem) with stack allocation and value-returning operators, replacing verbose RingElement pointer code in tests. Includes fromString via BasicPolyListParser. Also adds Monoid::variableNames(). I am using claude code opus 4.6 to help do this, in part to learn how to use claude effectively.

…g camel case instead of snake case for method names

…imple QuotientRingTest

Mburr group4 sagbi.hpp

First commit of a file that Mike gave us

Changed comments in NAG to use doxygen style

…r-group3

This reverts commit 766650f.

Remove printf call from PolyParser

Restructure engine file layout

mikestillman · 2026-05-22T12:23:22Z

+    $<BUILD_INTERFACE:${CMAKE_SOURCE_DIR}/Macaulay2/e/CoefficientRings>
+    $<BUILD_INTERFACE:${CMAKE_SOURCE_DIR}/Macaulay2/e/matrices>
+    $<BUILD_INTERFACE:${CMAKE_SOURCE_DIR}/Macaulay2/e/Rings>
    $<BUILD_INTERFACE:${CMAKE_SOURCE_DIR}/Macaulay2/c> # need scc-core.h


Is this supposed to be rings, not Rings? Why are these here in the d directory, but only these?

I think that these should be removed (but we'll need to check after making this change). I believe that they were added as a work-around so that the full paths didn't need to be added, but we decided against that approach. It looks like we forgot to delete these after that decision.

mikestillman · 2026-05-25T15:02:34Z

@@ -8,13 +8,13 @@
 #include <mpfi.h>
 #include "interface/random.h"
 #include "interface/gmp-util.h"


We might need to move these 2 files out of interface/. But that should be done after this PR.

mikestillman · 2026-05-25T15:10:50Z

 #include <vector>
-// g++ franzi-brp.cpp franzi-brp-test.cpp -o franzi-brp-test
+// g++ -I. computations/BRP.cpp computations/BRP-test.cpp -o BRP-test



Did anyone test this line?

mikestillman · 2026-05-25T15:15:22Z

 // Copyright 1998  Michael E. Stillman

-#include "LLL.hpp"
+#include "computations/LLL.hpp"


This is a comment, that might affect many files, including some (or many) before this PR. If a .hpp file is in the same directory as the .cpp file (as here), should it be, e.g., #include "LLL.hpp", or #include "computations/LLL.hpp". I'm not sure which is best. I have had trouble with CLion not being able to find header files, but that has largely been fixed by using compile_commands.json.

mikestillman · 2026-05-25T15:34:51Z

 #include "MonomialTypes.hpp"
-#include "PolynomialStream.hpp"
+#include "../unused/PolynomialStream.hpp"



Hmm, if it is pointed to, is it unused? Potentially! This is fine though, just a comment.

mikestillman · 2026-05-25T15:49:01Z


 #include "monideal-minprimes.hpp"
-#include "text-io.hpp"
+#include "../text-io.hpp"


This seems to be against the convention that files included are given paths off of e (if they are in this tree)?

mikestillman · 2026-05-25T15:50:01Z

-#include "debug.hpp"
-#include "monoid.hpp"
-#include "text-io.hpp"
+#include "../ExponentList.hpp"


Same comment here. What do we want to do about .. in include files here?

mikestillman · 2026-05-25T15:59:30Z

@@ -453,7 +453,7 @@ const RingElement *towerExtendedGCD(const RingElement *F,
 // top level translation to polynomials in other rings //
 /////////////////////////////////////////////////////////

-#include "polyring.hpp"
+#include "rings/polyring.hpp"


This is a double include, ok I guess, and it predates this PR.

mikestillman · 2026-05-25T18:05:52Z

+M2_arrayint arr = stdvector_to_M2_arrayint(std::vector<int>{2, 3, 5});
+```
+
+## Building and Running Tests


This part is specific to me. We should fix this, but we can do so after this is merged, I believe.

mikestillman · 2026-05-25T20:10:58Z

 BasicPoly parseBasicPoly(std::string poly, std::vector<std::string> varnames)
 {
-  std::string_view str { poly};
+  std::string_view str {poly};


Are the (correctness of the )changes in this file tested?

(Answering my own question!) Yes, I see that there is a new unit test file with a good set of tests.

mikestillman · 2026-05-25T20:16:06Z

@@ -0,0 +1,120 @@
+// Copyright 2026, The Macaulay2 Authors.
+//
+// RingElem: A lightweight value-semantics wrapper around (const Ring*, ring_elem).


I know I wrote this, but it was done with Claude's help. I can imagine changing this doc, but perhaps we do that separately to this PR?

mikestillman · 2026-05-25T20:18:29Z

@@ -0,0 +1,66 @@
+// Copyright 2026, The Macaulay2 Authors.


This code is ok for now, but should be revisited when we are looking more specifically at the unit tests. (I know: I think I wrote it, or the first version of it).

mikestillman

Most of this PR involves name changes. Some involves doxygen doc, and some involve unit tests, and some involve removing complex.{c,h} files.

The refactoring group in Atlanta did a good job here, thanks!

Here are a few comments, to keep in mind going forward:

We want to be consistent with header file names: I've seen ../, but also just the name (where .. refers to e.)
there appears to be a file in unused which is begin used?
there are a few things flagged in comments. We should pay attention to these when we meet.
We should make a file in the issues directory (?) with a set of guidelines for naming of files here, how to do headers (as above), and maybe set up github to automatically format c++ code using .clang-tidy.

mikestillman · 2026-05-26T01:12:09Z

I forgot that this is still a draft PR though!

mikestillman and others added 30 commits February 22, 2026 20:36

adding in code for testing weyl algebras, also CLAUDE.md file for eng…

2b3de4d

…ine development work.

switch RingElem class to use mRing, mValue as member fields, and usin…

478ce0c

…g camel case instead of snake case for method names

add idealFromStrings, computeGB, simpleQuotientRing utilities and a s…

79c0eef

…imple QuotientRingTest

EliminationTemplates v1

a4d3cc9

merge in main

c1c7fea

some requested fixes

5195c5d

more fixes

7da035d

more fixes

66e78d0

documentation + fixes

8a9dcd1

documentation + fixes

b7898f8

update list of distributed packgaes

babece6

move files, fix warnings

d54306e

typo

1af67b2

Minor addition to util functions

d84f473

First commit of a file that Mike gave us

63aeaa3

Changed comments to use doxygen style

bf80699

updating sagbi.hpp doxygen

22b9779

merge michael

74579de

Merge branch 'unit-testing' of github.com:mikestillman/M2

6a699f6

Merge pull request #12 from timduff35/mburr-group3

5e44ec2

Mburr group4 sagbi.hpp

Merge pull request #8 from dswinarski/Group2

cb44e47

First commit of a file that Mike gave us

Merge pull request #10 from haackett/Group4

56fe2c1

Changed comments in NAG to use doxygen style

Merge branch 'Group2' of https://github.com/MichaelABurr/M2 into mbur…

d42105b

…r-group3

Moving files in e directory. Moved schur2.hpp and schur2.cpp into Schur/

c98799e

mike clusters

766650f

Revert "mike clusters"

8866857

This reverts commit 766650f.

Moving all three pairs of schur files from e to e/Schur/

ee41aa3

moved arings files into basic-rings directory

86b1c07

add rings directory

ae612ba

MichaelABurr and others added 13 commits May 20, 2026 22:49

Merge pull request #44 from haackett/poly-parsing

90c0fab

Remove printf call from PolyParser

move schreyer resolutions

733355b

monomial -> monomials

a56ffff

Restructure engine file layout

4767f07

Merge pull request #45 from andrew-tawfeek/matrix-only-clean

565c3d3

Restructure engine file layout

Fix matrix header dependency path

f9a86e2

Restructure engine file layout

4b6b730

fix pluralization in schreyer-resolutions/ and monomials/

80ae380

Restructure engine file layout

0182f8d

Merged

9eff6ee

Merge branch 'timduff35-mburr-group3' into Subdirectories

7bcd079

Merged

cd4f6bf

Merge branch 'andrew-tawfeek-matrix-only-clean' into Subdirectories

961d7a0

mikestillman reviewed May 22, 2026

View reviewed changes

d-torrance added the Engine Macaulay2/e label May 22, 2026

This was referenced May 24, 2026

Fix for the d interface problem in Issue 1984 #4361

Open

fix lift from fraction field to base/coefficient ring (#3896) #4270

Open

mikestillman reviewed May 25, 2026

View reviewed changes

mikestillman approved these changes May 25, 2026

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MichaelABurr commented May 21, 2026

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mikestillman commented May 26, 2026

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