[RFC PATCH 00/10] Add sagemath.

Hello Guix!

This series adds SageMath. Everything compiles just fine and even the

Jupyter notebook interface works, but there is still much work to do. So

far, I have only added the minimal set of inputs required for the build

to succeed. Tests and documentations are still missing.

vicvbcun (10):

gnu: edge-addition-planarity-suite: Update to 3.0.2.0.

gnu: gap: Update to 4.11.1.

gnu: Remove ecl-16.

gnu: cliquer: Update to 1.22.

gnu: lcalc: Update to 2.0.5.

gnu: ntl: Update to 11.5.1.

gnu: eclib: Update to 20220621.

gnu: Add python-memory-allocator.

gnu: Add python-pplpy.

gnu: Add sagemath.

gnu/local.mk | 4 -

gnu/packages/algebra.scm | 19 +-

gnu/packages/graph.scm | 4 +-

.../patches/lcalc-default-parameters-1.patch | 26 --

.../patches/lcalc-default-parameters-2.patch | 58 ----

gnu/packages/patches/lcalc-lcommon-h.patch | 13 -

.../patches/lcalc-using-namespace-std.patch | 43 ---

gnu/packages/sagemath.scm | 267 ++++++++++++------

8 files changed, 194 insertions(+), 240 deletions(-)

delete mode 100644 gnu/packages/patches/lcalc-default-parameters-1.patch

delete mode 100644 gnu/packages/patches/lcalc-default-parameters-2.patch

delete mode 100644 gnu/packages/patches/lcalc-lcommon-h.patch

delete mode 100644 gnu/packages/patches/lcalc-using-namespace-std.patch

base-commit: f6904c0b19c2fcca41bbf1400c738bd833fec9a8

--

2.37.0

---

gnu/packages/graph.scm | 4 ++--

1 file changed, 2 insertions(+), 2 deletions(-)

[install]: install missing config.h header

---

gnu/packages/algebra.scm | 9 +++++----

1 file changed, 5 insertions(+), 4 deletions(-)

---

gnu/packages/sagemath.scm | 21 ---------------------

1 file changed, 21 deletions(-)

---

gnu/packages/algebra.scm | 6 +++---

1 file changed, 3 insertions(+), 3 deletions(-)

---

gnu/packages/algebra.scm | 4 ++--

1 file changed, 2 insertions(+), 2 deletions(-)

---

gnu/packages/sagemath.scm | 27 +++++++++++++++++++++++++++

1 file changed, 27 insertions(+)

---

gnu/packages/sagemath.scm | 17 +++++++++++++++++

1 file changed, 17 insertions(+)

gnu/packages/patches/lcalc-default-parameters-2.patch,

gnu/packages/patches/lcalc-lcommon-h.patch,

gnu/packages/patches/lcalc-using-namespace-std.patch: Delete files.

---

gnu/local.mk | 4 --

.../patches/lcalc-default-parameters-1.patch | 26 -------

.../patches/lcalc-default-parameters-2.patch | 58 ---------------

gnu/packages/patches/lcalc-lcommon-h.patch | 13 ----

.../patches/lcalc-using-namespace-std.patch | 43 -----------

gnu/packages/sagemath.scm | 71 ++++++-------------

6 files changed, 20 insertions(+), 195 deletions(-)

delete mode 100644 gnu/packages/patches/lcalc-default-parameters-1.patch

delete mode 100644 gnu/packages/patches/lcalc-default-parameters-2.patch

delete mode 100644 gnu/packages/patches/lcalc-lcommon-h.patch

delete mode 100644 gnu/packages/patches/lcalc-using-namespace-std.patch

---

Notes:

- I'm not sure about native inputs vs. inputs here.

- There is a broken symlink in share/jupyter/kernels/sagemath/doc is

currently a broken symlink. We should probably remove it and add it

into the documentation output.

- bin/ is currently full of random stuff, we probably only need a few

things.

gnu/packages/sagemath.scm | 106 ++++++++++++++++++++++++++++++++++++++

1 file changed, 106 insertions(+)

Switch to an autotoolized fork.

---

gnu/packages/sagemath.scm | 25 ++++++++++++-------------

1 file changed, 12 insertions(+), 13 deletions(-)

Hello!

vicvbcun <guix@ikherbers.com> skribis:

This looks great already! To make sure things don’t stall, we could

apply the patch series piecemeal, starting with the dependencies that

you think are ready, and leaving more time to polish the ‘sagemath’

package.

WDYT?

Regarding SageMath, my understanding is that it bundles lots of things.

In Guix, we’d like to make sure we do not use the bundled packages,

unless we practically can’t avoid it. To do that, the best option is to

remove “third-party” (or similar) directories right in the ‘snippet’ of

the ‘sagemath’ package. Could you give that a try?

Then, as you note, we’d rather run tests to make sure the package works

as intended.

Cc’ing Andreas, who I think is quite familiar with Sage.

Ludo’.

Hello,

On 2022-08-01T11:24:31+0200, Ludovic Courtès wrote:

Sounds like a good idea. The updates all seem fine to me (except gap)

and other than perhaps a better description for python-memory-allocator

I don't think there is much left to do for the other ones.

As for gap, I took another stab at it and it now builds reproducibly for

me. I also removed all the trailing #t's and changed the phases to use a

gexp.

By the way, the gap definition contains a snippet that deletes many gap

packages over concerns due to missing explicit licenses. However in a

cursory look at the tarball, I can see many LICENSE/COPYING files so

that may have changed.

If I understand the Sage build system correctly, missing dependencies

are automatically retrieved and build only when using the provided

Makefile. As is, the package definition builds and installs only the

python library part using setup.py. Thus a missing dependency probably

leads to a runtime error, though I haven't checked this.

I will try to see if I can get tests to work, though probably as

separate "package" like nixpkgs does[0], to avoid rebuilding sagemath so

often :).

As for sagemath itself, I will have a look at what exactly we need in

bin/.

[0]:

Remove logs that are not reproducible.

[source]<snippet>: Remove trailing #t.

[arguments]<#:phases>: Remove trailing #t, use gexps.

[install]: Install missing config.h header.

---

gnu/packages/algebra.scm | 181 +++++++++++++++++++--------------------

1 file changed, 90 insertions(+), 91 deletions(-)

On 2022-07-23T21:59:07+0200, vicvbcun wrote:

Well, I spoke to soon. As it turns out, the `sage' command I invoked to

test things a bit wound up using the sage installed by pacman, so no

wonder it worked perfectly. Nonetheless, I got some things working in a

guix shell container (so hopefully this wont happen again) with the help

of wrap-program and a few more dependencies.

I will try to post something that actually works a bit soon.

---

gnu/packages/graph.scm | 4 ++--

1 file changed, 2 insertions(+), 2 deletions(-)

---

gnu/packages/sagemath.scm | 134 ++++++++++++++++++++++++++++++++++++++

1 file changed, 134 insertions(+)

---

gnu/packages/sagemath.scm | 18 ++++++++++++++++++

1 file changed, 18 insertions(+)

---

gnu/packages/sagemath.scm | 21 +++++++++++++++++++++

1 file changed, 21 insertions(+)

Hello guix!

This is a second try, hopefully this time without silly errors.

The packaging of sagemath is for now structured as follows:

- `sagemath-just-build' builds everything using the minimal set of

dependecies to avoid rebuilding where possible. As runtime

dependencies are missing, this is useless on its own.

- `sagemath-with-dependencies' adds all remaining dependencies as

propagated-inputs. This should work, if we set a few additional

environment variables.

- `sagemath-tests' simply runs the tests.

If I interpret the output correctly, these are the tests that are still

failing:

Some of these seem harmless, others seem more concerning (including

segmentation faults), some due to still missing dependencies.

Some Notes:

- We need to set some environment variables, so that sage can find all

dependencies (see `sagemath-tests'). I suppose we could wrap the

`sage' command, but this would of course add them as dependencies.

- For the `sagemath-data-*' packages, I couldn't find explicit Licenses.

In Sage's COPYING.txt it just says "None (database)" for license.

- How should we handle test failures? Given errors such as the ones

below, it seems delusional to expect every test to succeed.

- `python-cython' is build-time dependency but may be needed at runtime.

This could cause issues when cross-compiling, right? I think its path

is only in the wrappers in bin/*.

vicvbcun (29):

gnu: Remove ecl-16.

gnu: edge-addition-planarity-suite: Update to 3.0.2.0.

gnu: gap: Update to 4.11.1.

gnu: cliquer: Update to 1.22.

gnu: lcalc: Update to 2.0.5.

gnu: ntl: Update to 11.5.1.

gnu: eclib: Update to 20220621.

gnu: lrcalc: Update to 2.1.

gnu: maxima: Update to 5.46.0.

gnu: python-sympy: Update to 1.10.1.

gnu: cddlib: Update to 0.94m.

gnu: Add python-memory-allocator.

gnu: Add python-pplpy.

gnu: Add primecount.

gnu: Add python-primecountpy.

gnu: Add python-lrcalc.

gnu: Add palp.

gnu: Add gfan.

gnu: Add flintqs.

gnu: Add tachyon.

gnu: Add sagemath-data-conway-polynomials.

gnu: Add sagemath-data-elliptic-curves.

gnu: Add sagemath-data-combinatorial-designs.

gnu: Add sagemath-data-graphs.

gnu: Add sagemath-data-poytopes-db.

gnu: Add pari-galdata.

gnu: Add sagemath-just-build.

gnu: Add sagemath-with-dependencies.

gnu: Add sagemath-tests.

gnu/local.mk | 9 +-

gnu/packages/algebra.scm | 203 +++--

gnu/packages/graph.scm | 4 +-

gnu/packages/maths.scm | 31 +-

.../ecl-16-format-directive-limit.patch | 83 --

.../ecl-16-ignore-stderr-write-error.patch | 17 -

gnu/packages/patches/ecl-16-libffi.patch | 16 -

.../patches/lcalc-default-parameters-1.patch | 26 -

.../patches/lcalc-default-parameters-2.patch | 58 --

gnu/packages/patches/lcalc-lcommon-h.patch | 13 -

.../patches/lcalc-using-namespace-std.patch | 43 -

gnu/packages/patches/lrcalc-includes.patch | 92 ---

gnu/packages/patches/tachyon-make-arch.patch | 13 +

gnu/packages/python-xyz.scm | 4 +-

gnu/packages/sagemath.scm | 780 ++++++++++++++++--

15 files changed, 833 insertions(+), 559 deletions(-)

delete mode 100644 gnu/packages/patches/ecl-16-format-directive-limit.patch

delete mode 100644 gnu/packages/patches/ecl-16-ignore-stderr-write-error.patch

delete mode 100644 gnu/packages/patches/ecl-16-libffi.patch

delete mode 100644 gnu/packages/patches/lcalc-default-parameters-1.patch

delete mode 100644 gnu/packages/patches/lcalc-default-parameters-2.patch

delete mode 100644 gnu/packages/patches/lcalc-lcommon-h.patch

delete mode 100644 gnu/packages/patches/lcalc-using-namespace-std.patch

delete mode 100644 gnu/packages/patches/lrcalc-includes.patch

create mode 100644 gnu/packages/patches/tachyon-make-arch.patch

base-commit: f6904c0b19c2fcca41bbf1400c738bd833fec9a8

--

2.37.0

---

gnu/packages/sagemath.scm | 48 +++++++++++++++++++++++++++++++++++++++

1 file changed, 48 insertions(+)

---

gnu/local.mk | 1 +

gnu/packages/patches/tachyon-make-arch.patch | 13 ++++++

gnu/packages/sagemath.scm | 48 ++++++++++++++++++++

3 files changed, 62 insertions(+)

create mode 100644 gnu/packages/patches/tachyon-make-arch.patch

---

gnu/packages/sagemath.scm | 21 +++++++++++++++++++++

1 file changed, 21 insertions(+)

---

gnu/packages/sagemath.scm | 27 +++++++++++++++++++++++++++

1 file changed, 27 insertions(+)

---

gnu/packages/sagemath.scm | 28 ++++++++++++++++++++++++++++

1 file changed, 28 insertions(+)

[source]: Remove patch.

---

gnu/local.mk | 1 -

gnu/packages/algebra.scm | 12 +--

gnu/packages/patches/lrcalc-includes.patch | 92 ----------------------

3 files changed, 2 insertions(+), 103 deletions(-)

delete mode 100644 gnu/packages/patches/lrcalc-includes.patch

---

gnu/packages/sagemath.scm | 27 +++++++++++++++++++++++++++

1 file changed, 27 insertions(+)

gnu/packages/patches/ecl-16-ignore-stderr-write-error.patch,

gnu/packages/patches/ecl-16-libffi.patch: Delete files.

---

gnu/local.mk | 3 -

.../ecl-16-format-directive-limit.patch | 83 -------------------

.../ecl-16-ignore-stderr-write-error.patch | 17 ----

gnu/packages/patches/ecl-16-libffi.patch | 16 ----

gnu/packages/sagemath.scm | 21 -----

5 files changed, 140 deletions(-)

delete mode 100644 gnu/packages/patches/ecl-16-format-directive-limit.patch

delete mode 100644 gnu/packages/patches/ecl-16-ignore-stderr-write-error.patch

delete mode 100644 gnu/packages/patches/ecl-16-libffi.patch

Switch to an autotoolized fork.

---

gnu/packages/sagemath.scm | 25 ++++++++++++-------------

1 file changed, 12 insertions(+), 13 deletions(-)

gnu/packages/patches/lcalc-default-parameters-2.patch,

gnu/packages/patches/lcalc-lcommon-h.patch,

gnu/packages/patches/lcalc-using-namespace-std.patch: Delete files.

---

gnu/local.mk | 4 --

.../patches/lcalc-default-parameters-1.patch | 26 -------

.../patches/lcalc-default-parameters-2.patch | 58 ---------------

gnu/packages/patches/lcalc-lcommon-h.patch | 13 ----

.../patches/lcalc-using-namespace-std.patch | 43 -----------

gnu/packages/sagemath.scm | 71 ++++++-------------

6 files changed, 20 insertions(+), 195 deletions(-)

delete mode 100644 gnu/packages/patches/lcalc-default-parameters-1.patch

delete mode 100644 gnu/packages/patches/lcalc-default-parameters-2.patch

delete mode 100644 gnu/packages/patches/lcalc-lcommon-h.patch

delete mode 100644 gnu/packages/patches/lcalc-using-namespace-std.patch

---

gnu/packages/sagemath.scm | 24 ++++++++++++++++++++++++

1 file changed, 24 insertions(+)

---

gnu/packages/sagemath.scm | 45 +++++++++++++++++++++++++++++++++++++++

1 file changed, 45 insertions(+)

---

gnu/packages/sagemath.scm | 20 ++++++++++++++++++++

1 file changed, 20 insertions(+)

[install]: install maxima.fas.

---

gnu/packages/maths.scm | 12 +++++++++---

1 file changed, 9 insertions(+), 3 deletions(-)

---

gnu/packages/python-xyz.scm | 4 ++--

1 file changed, 2 insertions(+), 2 deletions(-)

---

gnu/packages/sagemath.scm | 51 +++++++++++++++++++++++++++++++++++++++

1 file changed, 51 insertions(+)

---

gnu/packages/sagemath.scm | 22 ++++++++++++++++++++++

1 file changed, 22 insertions(+)

---

gnu/packages/algebra.scm | 6 +++---

1 file changed, 3 insertions(+), 3 deletions(-)

---

gnu/packages/sagemath.scm | 62 +++++++++++++++++++++++++++++++++++++++

1 file changed, 62 insertions(+)

---

gnu/packages/sagemath.scm | 23 +++++++++++++++++++++++

1 file changed, 23 insertions(+)

Remove logs that are not reproducible.

[source]<snippet>: Remove trailing #t.

[arguments]<#:phases>: Remove trailing #t, use gexps.

[install]: Install missing config.h header.

---

gnu/packages/algebra.scm | 181 +++++++++++++++++++--------------------

1 file changed, 90 insertions(+), 91 deletions(-)

---

gnu/packages/algebra.scm | 4 ++--

1 file changed, 2 insertions(+), 2 deletions(-)

---

gnu/packages/maths.scm | 19 ++++++++++++++-----

1 file changed, 14 insertions(+), 5 deletions(-)

---

gnu/packages/sagemath.scm | 27 +++++++++++++++++++++++++++

1 file changed, 27 insertions(+)

---

gnu/packages/sagemath.scm | 17 +++++++++++++++++

1 file changed, 17 insertions(+)

Hello,

On 2022-08-08T16:40:37+0200, Andreas Enge wrote:

Great! But note that I just sent an updated series with minor touch ups :).

The `upstream' directory only seems to exist in the published tarball.

So this should be no problem if we build from git.

I'll take a look!

Too late (for the most part) :).

Hello,

Am Mon, Aug 08, 2022 at 06:20:22PM +0200 schrieb guix@ikherbers.com:

thanks for the update! I just pushed an update of maxima (and wxmaxima), but

without your addition of ecl. Is there a good reason for this? In any case,

this should be done in a separate commit, since it is not required for the

update. For the record, I also tried to compile with gcl, but this still

failed.

Ah, interesting. Which one should we do? I personally tend to prefer tarballs

(as the official distribution mechanism of the project). Recently there has

been a preference in the Guix project for git repositories when autotools

are involved, as they make it possible to recreate the configure scripts

from their source. But since this is not the case here, the argument does

not hold.

Andreas

On Tue Aug 9, 2022 at 11:47 AM BST, Andreas Enge wrote:

I think it does sometimes hold even for projects that don't use autotools,

especially older ones: they sometimes work under the assumption that users

do not generally care about generated files in their release source, but

don't want to put generated files in their development repository.

This, of course, is why the autotools generated files problem exists in the

first place; autoconf was, after all, designed so that users didn't have to

have it installed to build a package, in a world where compiling from release

tarballs was the usual way to get new software.

-- (

I pushed your patch updating cddlib with a small change to include the

version number in the docdir, so that it coincides with the place where the

GNU build system stores the COPYING file.

Thanks,

Andreas

On 2022-08-09T12:47:27+0200, Andreas Enge wrote:

SageMath requires the FASL library? (I only know scheme) `maxima.fas'.

But it is only built when using ecl (See upstream here [0]). I don't

know if we need both sbcl and ecl. Arch uses both and puts the

lib/.../binary-* directories in separate packages[1], so maybe we could

use different outputs? Anyway, I have attached an rebased commit that

adds ecl.

The sage tarball is 1.35 GiB while the repository is only about 440 MiB.

That seems quite convincing on its own.

[0]:

[1]:

From cb877ee5091d801e08654ac55adaab1b5edfec91 Mon Sep 17 00:00:00 2001

Message-Id: <cb877ee5091d801e08654ac55adaab1b5edfec91.1660051561.git.guix@ikherbers.com>

The eventual sagemath package requires maxima.fas, which is only build with

ecl.

[configure-flags]: Build with ecl.

[install]: Install maxima.fas.

---

gnu/packages/maths.scm | 8 +++++++-

1 file changed, 7 insertions(+), 1 deletion(-)

On 09-08-2022 12:47, Andreas Enge wrote:

I am not aware of such a preference, do you have a source?

Switching to git repositories in one method to build from source, but

there exist other methods too that keep the official distribution

method, e.g. (for-each delete-file '("configure" ...)) in a snippet.

It's a method to a goal, but not a goal on itself as far as I'm aware.

Greetings,

Maxime.

Am Tue, Aug 09, 2022 at 11:32:56PM +0200 schrieb Maxime Devos:

No, it was just an impression I got from discussions on the mailing list.

So I am unsure if there is an official position, and do not know what

to do here...

Andreas

Hello,

I just pushed your update to python-sympy, after trying to recompile all its

dependents and verifying that they mostly do not become broken.

Andreas

Hello,

Am Wed, Aug 03, 2022 at 11:21:43AM +0200 schrieb guix@ikherbers.com:

today I looked at gap. Since there were many whitespace changes, I found

it a bit difficult to review, and copied only the most relevant/easiest

parts of your commit. In particular I did not move to gexps, which could

be done in a separate patch. So far I also did not apply the part for

making the build reproducible, which could be done in yet another patch.

Yes, there is an ongoing effort in GAP to clarify the license situation,

with apparently a lot of progress in this release. I have added (hopefully)

all packages with a free license and which do not require additional inputs.

We could go further; for instance add ZeroQMInterface (which requires

zeromq) and dependent packages, CddInterface (which I suppose requires

cddlib) and then NConvex, but I am a bit weary of adding dependencies,

even more so since we do not seem to have GAP users in Guix who could

give us feedback. It would be more motivating with users who confirm that

the packages do not only load, but actually work as expected...

Andreas

Hello,

I now pushed your updates to packages.

Concerning the new additions, please try to add a description that is a bit

longer than the synopsys and consists of complete sentences (which can be

a challenge if the project homepage is too scarce, I can lend a hand).

And it would be better to add the packages to different modules; many of

them are added now with the aim of getting Sage, but are independent.

So I would add primecount and gfan to algebra, palp to maths,

python-lrcalc, python-primecountpy and python-pplpy to the same module as

their "base packages", and python-memory-allocator probably to

python-xyz. I would suggest to keep in sagemath.scm only the packages for

which Sage has become upstream, such as flintqs.

For tachyon, you use a patch and a phase; would only the latter not be

enough? At worst by using substitute* on the Makefile? See the recent

discussion on patches vs. phases.

I did not yet have a look at the sagemath-... packages. And for

pari-galdata, I wonder if there is not a better way so that it can also

be used by the pari-gp package. The problem with pari-gp is that it

cannot handle a search path with multiple directories, but that all data

files need to be put into the same place. And all data files add up

to about 200MB. One solution would be to add by default only the smaller

data files galpol (10MB), nftables (8MB), galdata (52kB!) and nflistdata

(4MNB). Actually, galdata is so small that we might just add it by default

to pari-gp. It is not a perfect solution, but would improve the package

at almost no cost, and apparently be useful for Sage.

Andreas

Am Tue, Aug 09, 2022 at 03:40:53PM +0200 schrieb vicvbcun:

Okay, thanks!

I do not use maxima (so it would be nice to get input from someone who

does). To me it looks as if the different base lisps are more or less

exchangeable for the goal of getting a running binary. So maybe it would

be enough to build only the ecl version?

The latest change was to switch from gcl to sbcl, in a commit by Guillaume,

since maxima stopped building with the former; how about switching to ecl?

Andreas

Hello Guix!

Disclaimer: To prevent this from beeing delayed yet another week, I have

decided to sent this as is. Hence this may not be very coherent.

This finally is an updated third version. Allmost all tests[0] in

`sagemath-testsuite' succed without any issues[1] (See the log below for

the remaining failures and the comments in the `sagemath' patch).

However two issues remain: `sage/env.py' and

`sage/interacts/test_jupyter.rst'. Maybe updating `python-pkgconfig' and

`python-ipywidgets' solve these but someone braver than I currently am

would have to try :).

Other remaining problems:

- I'm not sure about the licenses of the`sagemath-data-*' packages.

-- `sagemath-data-combinatorial-designs' Supposedly in the public

domain, see also the notes attached to the patch.

-- `sagemath-data-polytopes-db'

SageMath's `COPYING.txt' claims that this has no license as it is a

database. However the `SPKG.rst' for `polytopes_db' claims GPL.

-- `sagemath-data-graphs'

SageMath's `COPYING.txt' claims that this has no license as it is a

database. `smallgraphs.txt' and`isgci_sage.xml' seem to be taken from

data [2] which has a CC-BY-SA 3.0 icon/button in the footer if you

click on one of the articles.

-- `sagemath-data-conway-polynomials'

SageMath's `COPYING.txt' claims that this has no license as it is a

database.

-- `sagemath-data-elliptic-curves'

The file `allcurves.00000-09999' is taken from [4] which contains an

Artistic License 2.0.

If I interpret it correctly, Debian distributes

`combinatorial-designs' as public domain and the rest of them as

GPLv2 or later (see [4], [5], [6], [7], [8]).

- Not all package descriptions are great. For `gfan' in particular I

know to little algebraic geometry to decide what information from the

website would be relevant.

- Currently SageMath is split into two packages:

`python-sagemath-standard' provides the actual content but is not

tested; `sagemath' runs the testsuite and only provides a symlink to

the `sage' executable. This is similar to how NixOS does it. Upsides

to this approach are that one can compile everything and run the tests

independently from each other (the former takes for me ~18 minutes,

the latter ~24 minutes I think), preventing uneccessary work. Also, as

there are many propagated packages, this makes sure everything is

setup correctly.

- I gave up rebuilding all the dependent packages when `gnuradio' filled

my `/tmp' tmpfs and building `python-graph-tool' consumed all my RAM

- Package the documentation

- Package SageTeX

- The transitive closure of is huge: `guix size python-sagemath-standard'

reports 5002.1 MiB. It also propagates many packages.

- `zn-poly' was presumably added a long time ago as a dependency for

SageMath but is not used anymore and seems pretty dead.

- `pynac' was merged into SageMath[9]

How do we/I proceed?

- We would need a decision on what to do with the `sagemath-data-*'

packages regarding the licenses.

- I would need feedback whether the current split into the

`python-sagemath-standard' and `sagemath' packages would be

acceptable.

- The package additions (but not `sagemath-data-*') could be fine modulo

issues with the descriptions.

- The other patches (i.e. gap, maxima, pari-gp, singular) should be

fine.

A couple of the patches also have some notes attached.

0: SageMath also has tests marked as optional or taking a long time. The

tests run by default should hopefully be enough to catch all packaging

errors.

1: I see coredumps during some of the tests (for `python', `mwrank' from

`eclib', `ecl', `gentourng' from `nauty') but these don't seem to effect

the result ¯\_(?)_/¯. At least the ones for mwrank (in

`src/sage/interfaces/mwrank.py') can also be seen for sage as packaged

by Arch Linux (eclib 20230424) and NixOS (eclib 20221012), for the

others I haven't found the relevant tests.

2: https://graphclasses.org/

3: https://github.com/JohnCremona/ecdata

4: https://salsa.debian.org/science-team/sagemath-database-combinatorial-designs/-/blob/master/debian/copyright

5: https://salsa.debian.org/science-team/sagemath-database-elliptic-curves/-/blob/master/debian/copyright

6: https://salsa.debian.org/science-team/sagemath-database-graphs/-/blob/master/debian/copyright

7: https://salsa.debian.org/science-team/sagemath-database-polytopes/-/blob/master/debian/copyright

8: https://salsa.debian.org/science-team/sagemath-database-conway-polynomials/-/blob/master/debian/copyright

9: https://github.com/pynac/pynac/commit/2a0d97bada891cbcaad950672143542a32ba2834

Lastly, this is the log of the tests that currently fail:

sage -t --random-seed=81087110751557935317942447629980408147 sage/misc/sage_ostools.pyx

**********************************************************************

File "sage/misc/sage_ostools.pyx", line 35, in sage.misc.sage_ostools.have_program

Failed example:

have_program('sh', '/bin')

Expected:

True

Got:

False

**********************************************************************

1 item had failures:

1 of 7 in sage.misc.sage_ostools.have_program

[41 tests, 1 failure, 0.05 s]

sage -t --random-seed=81087110751557935317942447629980408147 sage/interfaces/gap_workspace.py

**********************************************************************

File "sage/interfaces/gap_workspace.py", line 56, in sage.interfaces.gap_workspace.gap_workspace_file

Failed example:

name1 = Popen([sys.executable, '-c', cmd], stdout=PIPE).communicate()[0]

Expected nothing

Got:

Traceback (most recent call last):

File "<string>", line 1, in <module>

File "/tmp/guix-build-sagemath-10.0.drv-0/source/src/sage/all.py", line 62, in <module>

from .all__sagemath_repl import * # includes .all__sagemath_objects, .all__sagemath_environment

File "/tmp/guix-build-sagemath-10.0.drv-0/source/src/sage/all__sagemath_repl.py", line 83, in <module>

from .all__sagemath_objects import *

File "/tmp/guix-build-sagemath-10.0.drv-0/source/src/sage/all__sagemath_objects.py", line 16, in <module>

from sage.misc.all__sagemath_objects import *

File "/tmp/guix-build-sagemath-10.0.drv-0/source/src/sage/misc/all__sagemath_objects.py", line 3, in <module>

import sage.structure.all # to break a cyclic import

File "/tmp/guix-build-sagemath-10.0.drv-0/source/src/sage/structure/__init__.py", line 2, in <module>

import sage.structure.element

ModuleNotFoundError: No module named 'sage.structure.element'

**********************************************************************

File "sage/interfaces/gap_workspace.py", line 57, in sage.interfaces.gap_workspace.gap_workspace_file

Failed example:

name2 = Popen([sys.executable, '-c', cmd], stdout=PIPE).communicate()[0]

Expected nothing

Got:

Traceback (most recent call last):

File "<string>", line 1, in <module>

File "/tmp/guix-build-sagemath-10.0.drv-0/source/src/sage/all.py", line 62, in <module>

from .all__sagemath_repl import * # includes .all__sagemath_objects, .all__sagemath_environment

File "/tmp/guix-build-sagemath-10.0.drv-0/source/src/sage/all__sagemath_repl.py", line 83, in <module>

from .all__sagemath_objects import *

File "/tmp/guix-build-sagemath-10.0.drv-0/source/src/sage/all__sagemath_objects.py", line 16, in <module>

from sage.misc.all__sagemath_objects import *

File "/tmp/guix-build-sagemath-10.0.drv-0/source/src/sage/misc/all__sagemath_objects.py", line 3, in <module>

import sage.structure.all # to break a cyclic import

File "/tmp/guix-build-sagemath-10.0.drv-0/source/src/sage/structure/__init__.py", line 2, in <module>

import sage.structure.element

ModuleNotFoundError: No module named 'sage.structure.element'

**********************************************************************

1 item had failures:

2 of 12 in sage.interfaces.gap_workspace.gap_workspace_file

[14 tests, 2 failures, 0.68 s]

sage -t --random-seed=81087110751557935317942447629980408147 sage/repl/ipython_kernel/kernel.py

**********************************************************************

File "sage/repl/ipython_kernel/kernel.py", line 47, in sage.repl.ipython_kernel.kernel.SageKernel.__init__

Failed example:

from sage.repl.ipython_kernel.kernel import SageKernel

Expected nothing

Got:

doctest:warning

File "/gnu/store/vmqp0r0w4ky8w6978kn6sgm8fl91i2lj-python-sagemath-standard-10.0/bin/sage-runtests", line 154, in <module>

err = DC.run()

File "/gnu/store/vmqp0r0w4ky8w6978kn6sgm8fl91i2lj-python-sagemath-standard-10.0/lib/python3.10/site-packages/sage/doctest/control.py", line 1385, in run

self.run_doctests()

File "/gnu/store/vmqp0r0w4ky8w6978kn6sgm8fl91i2lj-python-sagemath-standard-10.0/lib/python3.10/site-packages/sage/doctest/control.py", line 1060, in run_doctests

self.dispatcher.dispatch()

File "/gnu/store/vmqp0r0w4ky8w6978kn6sgm8fl91i2lj-python-sagemath-standard-10.0/lib/python3.10/site-packages/sage/doctest/forker.py", line 2017, in dispatch

self.parallel_dispatch()

File "/gnu/store/vmqp0r0w4ky8w6978kn6sgm8fl91i2lj-python-sagemath-standard-10.0/lib/python3.10/site-packages/sage/doctest/forker.py", line 1912, in parallel_dispatch

w.start() # This might take some time

File "/gnu/store/vmqp0r0w4ky8w6978kn6sgm8fl91i2lj-python-sagemath-standard-10.0/lib/python3.10/site-packages/sage/doctest/forker.py", line 2186, in start

super().start()

File "/gnu/store/kj6wzba6p192baizq99b489rs8bynpn7-python-3.10.7/lib/python3.10/multiprocessing/process.py", line 121, in start

self._popen = self._Popen(self)

File "/gnu/store/kj6wzba6p192baizq99b489rs8bynpn7-python-3.10.7/lib/python3.10/multiprocessing/context.py", line 224, in _Popen

return _default_context.get_context().Process._Popen(process_obj)

File "/gnu/store/kj6wzba6p192baizq99b489rs8bynpn7-python-3.10.7/lib/python3.10/multiprocessing/context.py", line 281, in _Popen

return Popen(process_obj)

File "/gnu/store/kj6wzba6p192baizq99b489rs8bynpn7-python-3.10.7/lib/python3.10/multiprocessing/popen_fork.py", line 19, in __init__

self._launch(process_obj)

File "/gnu/store/kj6wzba6p192baizq99b489rs8bynpn7-python-3.10.7/lib/python3.10/multiprocessing/popen_fork.py", line 71, in _launch

code = process_obj._bootstrap(parent_sentinel=child_r)

File "/gnu/store/kj6wzba6p192baizq99b489rs8bynpn7-python-3.10.7/lib/python3.10/multiprocessing/process.py", line 314, in _bootstrap

self.run()

File "/gnu/store/vmqp0r0w4ky8w6978kn6sgm8fl91i2lj-python-sagemath-standard-10.0/lib/python3.10/site-packages/sage/doctest/forker.py", line 2158, in run

task(self.options, self.outtmpfile, msgpipe, self.result_queue)

File "/gnu/store/vmqp0r0w4ky8w6978kn6sgm8fl91i2lj-python-sagemath-standard-10.0/lib/python3.10/site-packages/sage/doctest/forker.py", line 2488, in __call__

doctests, extras = self._run(runner, options, results)

File "/gnu/store/vmqp0r0w4ky8w6978kn6sgm8fl91i2lj-python-sagemath-standard-10.0/lib/python3.10/site-packages/sage/doctest/forker.py", line 2540, in _run

result = runner.run(test)

File "/gnu/store/vmqp0r0w4ky8w6978kn6sgm8fl91i2lj-python-sagemath-standard-10.0/lib/python3.10/site-packages/sage/doctest/forker.py", line 866, in run

return self._run(test, compileflags, out)

File "/gnu/store/vmqp0r0w4ky8w6978kn6sgm8fl91i2lj-python-sagemath-standard-10.0/lib/python3.10/site-packages/sage/doctest/forker.py", line 695, in _run

self.compile_and_execute(example, compiler, test.globs)

File "/gnu/store/vmqp0r0w4ky8w6978kn6sgm8fl91i2lj-python-sagemath-standard-10.0/lib/python3.10/site-packages/sage/doctest/forker.py", line 1093, in compile_and_execute

exec(compiled, globs)

File "<doctest sage.repl.ipython_kernel.kernel.SageKernel.__init__[0]>", line 1, in <module>

from sage.repl.ipython_kernel.kernel import SageKernel

File "<frozen importlib._bootstrap>", line 1027, in _find_and_load

File "<frozen importlib._bootstrap>", line 1006, in _find_and_load_unlocked

File "<frozen importlib._bootstrap>", line 688, in _load_unlocked

File "<frozen importlib._bootstrap_external>", line 883, in exec_module

File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed

File "/gnu/store/vmqp0r0w4ky8w6978kn6sgm8fl91i2lj-python-sagemath-standard-10.0/lib/python3.10/site-packages/sage/repl/ipython_kernel/kernel.py", line 19, in <module>

from ipykernel.ipkernel import IPythonKernel

File "<frozen importlib._bootstrap>", line 1027, in _find_and_load

File "<frozen importlib._bootstrap>", line 1006, in _find_and_load_unlocked

File "<frozen importlib._bootstrap>", line 688, in _load_unlocked

File "<frozen importlib._bootstrap_external>", line 883, in exec_module

File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed

File "/gnu/store/d5883jyf46l3h4h3rc0d7ramgy47pab6-python-ipykernel-6.13.0/lib/python3.10/site-packages/ipykernel/ipkernel.py", line 19, in <module>

from .debugger import Debugger, _is_debugpy_available

File "<frozen importlib._bootstrap>", line 1027, in _find_and_load

File "<frozen importlib._bootstrap>", line 1006, in _find_and_load_unlocked

File "<frozen importlib._bootstrap>", line 688, in _load_unlocked

File "<frozen importlib._bootstrap_external>", line 883, in exec_module

File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed

File "/gnu/store/d5883jyf46l3h4h3rc0d7ramgy47pab6-python-ipykernel-6.13.0/lib/python3.10/site-packages/ipykernel/debugger.py", line 22, in <module>

from debugpy.server import api # noqa

File "<frozen importlib._bootstrap>", line 1027, in _find_and_load

File "<frozen importlib._bootstrap>", line 1006, in _find_and_load_unlocked

File "<frozen importlib._bootstrap>", line 688, in _load_unlocked

File "<frozen importlib._bootstrap_external>", line 883, in exec_module

File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed

File "/gnu/store/78bgdvac53aw2zhn1cq2jmsj78bwx2ln-python-debugpy-1.6.0/lib/python3.10/site-packages/debugpy/server/__init__.py", line 40, in <module>

import pydevd # noqa

File "<frozen importlib._bootstrap>", line 1027, in _find_and_load

File "<frozen importlib._bootstrap>", line 1006, in _find_and_load_unlocked

File "<frozen importlib._bootstrap>", line 688, in _load_unlocked

File "<frozen importlib._bootstrap_external>", line 883, in exec_module

File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed

File "/gnu/store/dnd753b65xbv3smqsnxvpl72lnnzlnll-python-pydevd-2.8.0-0.47e2984/lib/python3.10/site-packages/pydevd.py", line 41, in <module>

from _pydevd_bundle import pydevd_extension_utils, pydevd_frame_utils

File "<frozen importlib._bootstrap>", line 1078, in _handle_fromlist

File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed

File "<frozen importlib._bootstrap>", line 1027, in _find_and_load

File "<frozen importlib._bootstrap>", line 1006, in _find_and_load_unlocked

File "<frozen importlib._bootstrap>", line 688, in _load_unlocked

File "<frozen importlib._bootstrap_external>", line 883, in exec_module

File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed

File "/gnu/store/dnd753b65xbv3smqsnxvpl72lnnzlnll-python-pydevd-2.8.0-0.47e2984/lib/python3.10/site-packages/_pydevd_bundle/pydevd_extension_utils.py", line 5, in <module>

import pydevd_plugins.extensions as extensions

File "<frozen importlib._bootstrap>", line 1027, in _find_and_load

File "<frozen importlib._bootstrap>", line 1006, in _find_and_load_unlocked

File "<frozen importlib._bootstrap>", line 688, in _load_unlocked

File "<frozen importlib._bootstrap_external>", line 883, in exec_module

File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed

File "/gnu/store/dnd753b65xbv3smqsnxvpl72lnnzlnll-python-pydevd-2.8.0-0.47e2984/lib/python3.10/site-packages/pydevd_plugins/extensions/__init__.py", line 4, in <module>

__import__('pkg_resources').declare_namespace(__name__)

File "/gnu/store/06cjgrygh79bxbsr0x44ryx1wy1pwvh4-python-setuptools-67.6.1/lib/python3.10/site-packages/pkg_resources/__init__.py", line 2338, in declare_namespace

warnings.warn(msg, DeprecationWarning, stacklevel=2)

File "/gnu/store/kj6wzba6p192baizq99b489rs8bynpn7-python-3.10.7/lib/python3.10/warnings.py", line 109, in _showwarnmsg

sw(msg.message, msg.category, msg.filename, msg.lineno,

:

DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('pydevd_plugins.extensions')`.

Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages

doctest:warning

File "/gnu/store/vmqp0r0w4ky8w6978kn6sgm8fl91i2lj-python-sagemath-standard-10.0/bin/sage-runtests", line 154, in <module>

err = DC.run()

File "/gnu/store/vmqp0r0w4ky8w6978kn6sgm8fl91i2lj-python-sagemath-standard-10.0/lib/python3.10/site-packages/sage/doctest/control.py", line 1385, in run

self.run_doctests()

File "/gnu/store/vmqp0r0w4ky8w6978kn6sgm8fl91i2lj-python-sagemath-standard-10.0/lib/python3.10/site-packages/sage/doctest/control.py", line 1060, in run_doctests

self.dispatcher.dispatch()

File "/gnu/store/vmqp0r0w4ky8w6978kn6sgm8fl91i2lj-python-sagemath-standard-10.0/lib/python3.10/site-packages/sage/doctest/forker.py", line 2017, in dispatch

self.parallel_dispatch()

File "/gnu/store/vmqp0r0w4ky8w6978kn6sgm8fl91i2lj-python-sagemath-standard-10.0/lib/python3.10/site-packages/sage/doctest/forker.py", line 1912, in parallel_dispatch

w.start() # This might take some time

File "/gnu/store/vmqp0r0w4ky8w6978kn6sgm8fl91i2lj-python-sagemath-standard-10.0/lib/python3.10/site-packages/sage/doctest/forker.py", line 2186, in start

super().start()

File "/gnu/store/kj6wzba6p192baizq99b489rs8bynpn7-python-3.10.7/lib/python3.10/multiprocessing/process.py", line 121, in start

self._popen = self._Popen(self)

File "/gnu/store/kj6wzba6p192baizq99b489rs8bynpn7-python-3.10.7/lib/python3.10/multiprocessing/context.py", line 224, in _Popen

return _default_context.get_context().Process._Popen(process_obj)

File "/gnu/store/kj6wzba6p192baizq99b489rs8bynpn7-python-3.10.7/lib/python3.10/multiprocessing/context.py", line 281, in _Popen

return Popen(process_obj)

File "/gnu/store/kj6wzba6p192baizq99b489rs8bynpn7-python-3.10.7/lib/python3.10/multiprocessing/popen_fork.py", line 19, in __init__

self._launch(process_obj)

File "/gnu/store/kj6wzba6p192baizq99b489rs8bynpn7-python-3.10.7/lib/python3.10/multiprocessing/popen_fork.py", line 71, in _launch

code = process_obj._bootstrap(parent_sentinel=child_r)

File "/gnu/store/kj6wzba6p192baizq99b489rs8bynpn7-python-3.10.7/lib/python3.10/multiprocessing/process.py", line 314, in _bootstrap

self.run()

File "/gnu/store/vmqp0r0w4ky8w6978kn6sgm8fl91i2lj-python-sagemath-standard-10.0/lib/python3.10/site-packages/sage/doctest/forker.py", line 2158, in run

task(self.options, self.outtmpfile, msgpipe, self.result_queue)

File "/gnu/store/vmqp0r0w4ky8w6978kn6sgm8fl91i2lj-python-sagemath-standard-10.0/lib/python3.10/site-packages/sage/doctest/forker.py", line 2488, in __call__

doctests, extras = self._run(runner, options, results)

File "/gnu/store/vmqp0r0w4ky8w6978kn6sgm8fl91i2lj

---

Notes:

Previous versions of this commit had `python-cython' as `propagated-input'.

gnu/packages/python-xyz.scm | 20 ++++++++++++++++++++

1 file changed, 20 insertions(+)

[native-inputs]: Add autoconf and gdb.

[arguments]<#:tests?>: Run tests.

[arguments]<#:phases>: Remove phase 'configure, add phase

'set-shell-for-configure-script, add phase 'fix-testgdb.py.

---

gnu/packages/python-xyz.scm | 34 +++++++++++++++++++---------------

1 file changed, 19 insertions(+), 15 deletions(-)

---

gnu/packages/algebra.scm | 26 ++++++++++++++++++++++++++

1 file changed, 26 insertions(+)

---

Notes:

Prevent cycle (gnu packages sagemath) -> (gnu packages multiprecision) -> (gnu packages sagemath)

gnu/packages/multiprecision.scm | 28 +++++++++++++++++++++++++++-

gnu/packages/sagemath.scm | 25 -------------------------

2 files changed, 27 insertions(+), 26 deletions(-)

---

gnu/packages/algebra.scm | 20 ++++++++++++++++++++

1 file changed, 20 insertions(+)

---

gnu/packages/sagemath.scm | 23 +++++++++++++----------

1 file changed, 13 insertions(+), 10 deletions(-)

---

gnu/packages/sagemath.scm | 44 +++++++++++++++++++++++++++++++++++++++

1 file changed, 44 insertions(+)

---

Notes:

smallgraphs.txt, isgci_sage.xml: The website (graphclasses.org) has an CC-BY-SA 3.0 icon/button in footer

gnu/packages/sagemath.scm | 23 +++++++++++++++++++++++

1 file changed, 23 insertions(+)

---

gnu/packages/sagemath.scm | 47 +++++++++++++++++++++++++++++++++++++++

1 file changed, 47 insertions(+)

---

gnu/packages/sagemath.scm | 20 ++++++++++++++++++++

1 file changed, 20 insertions(+)

---

gnu/packages/algebra.scm | 19 +++++++++----------

1 file changed, 9 insertions(+), 10 deletions(-)

(pari-gp)[arguments]<#:phases>: Add phase "install-galdata".

---

Notes:

PARI/GP supports only a single load path.

Multiple packages should work in a profile, as they get symlinked in a single folder.

gnu/packages/algebra.scm | 16 +++++++++++++++-

1 file changed, 15 insertions(+), 1 deletion(-)

---

gnu/packages/maths.scm | 20 ++++++++++++++++++++

1 file changed, 20 insertions(+)

---

gnu/packages/algebra.scm | 24 ++++++++++++++++++++++++

1 file changed, 24 insertions(+)

The tomlib package depends on atlasrep.

---

gnu/packages/algebra.scm | 1 +

1 file changed, 1 insertion(+)

---

guix/download.scm | 37 ++++++++++++++++++++++++++++++++++++-

1 file changed, 36 insertions(+), 1 deletion(-)

---

Notes:

For license:

https://github.com/sagemath/sage/issues/16541#issuecomment-1417604644

https://github.com/sagemath/sage/issues/16541#issuecomment-1417604646

https://github.com/sagemath/sage/commit/e282f17bd361245dc899a4e56fede2d52f0efdba

gnu/packages/sagemath.scm | 28 ++++++++++++++++++++++++++++

1 file changed, 28 insertions(+)