With 9.2.beta4,

{{{
sage -t --optional=sage,internet src/sage/combinat/designs/bibd.py
}}}

gives

{{{
sage -t --long src/sage/combinat/designs/bibd.py
**********************************************************************
File "src/sage/combinat/designs/bibd.py", line 109, in
sage.combinat.designs.bibd.balanced_incomplete_block_design
Failed example:
    B                                                              #
optional - internet
Expected:
    Incidence structure with 66 points and 143 blocks
Got:
    (66,6,1)-Balanced Incomplete Block Design
**********************************************************************
File "src/sage/combinat/designs/bibd.py", line 113, in
sage.combinat.designs.bibd.balanced_incomplete_block_design
Failed example:
    designs.balanced_incomplete_block_design(66, 6, 1, use_LJCR=True)  #
optional - internet
Expected:
    Incidence structure with 66 points and 143 blocks
Got:
    (66,6,1)-Balanced Incomplete Block Design
**********************************************************************
1 item had failures:
   2 of  26 in
sage.combinat.designs.bibd.balanced_incomplete_block_design
    0 tests not run because we ran out of time
    [120 tests, 2 failures, 5.32 s]
}}}

URL: https://trac.sagemath.org/30131
Reported by: slabbe
Ticket author(s): Frédéric Chapoton
Reviewer(s): Sébastien Labbé, Dima Pasechnik

and use {{{_richcmp_}}} instead

So far, this remains used only in complex MPC and Integer classes.

URL: https://trac.sagemath.org/30130
Reported by: chapoton
Ticket author(s): Frédéric Chapoton
Reviewer(s): Travis Scrimshaw

`[ -n "$SAGE_ROOT/" ]` is always true because of the trailing slash.
This causes two test failures on distro packages.

URL: https://trac.sagemath.org/30129
Reported by: arojas
Ticket author(s): Antonio Rojas
Reviewer(s): Matthias Koeppe

The sage-env script is run under `/bin/sh` but contains bashisms:

{{{
SAGE_SCRIPTS_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
}}}

This causes a build failure when `/bin/sh` is not bash:

{{{
cd '/home/mjo/src/sage.git/build/pkgs/sage_conf' && .
'/home/mjo/src/sage.git/src/bin/sage-env' && .
'/home/mjo/src/sage.git/build/bin/sage-build-env-config' && sage-logger
-p '/home/mjo/src/sage.git/build/pkgs/sage_conf/spkg-install'
'/home/mjo/src/sage.git/logs/pkgs/sage_conf-none.log'
/bin/sh: 123: /home/mjo/src/sage.git/src/bin/sage-env: Bad substitution
Error: SAGE_SCRIPTS_DIR is set to a bad value:
SAGE_SCRIPTS_DIR=/home/mjo/src/sage.git/build/pkgs/sage_conf
You must correct it or erase it and rerun this script
make[3]: *** [Makefile:2022:
/home/mjo/src/sage.git/local/var/lib/sage/installed/sage_conf-none]
Error 1
}}}

The comment at the top of sage-env about using bash features should be
removed afterwards. For bonus points, it would be nice if we could add a
non-bash shell to one of the CI runs.

URL: https://trac.sagemath.org/30128
Reported by: mjo
Ticket author(s): Michael Orlitzky
Reviewer(s): Matthias Koeppe

There is the category of `Graphs` and there is an axiom 'Connected'
(used in `Manifolds`), but so far there is no category of connected
graphs. They would be metric spaces... if edge weights are positive.

URL: https://trac.sagemath.org/30126
Reported by: mkoeppe
Ticket author(s): Travis Scrimshaw
Reviewer(s): Matthias Koeppe

Follow-up from #30106, where the following was observed:
{{{
sage: var('ξ')._maxima_()
....:
<repr(<sage.interfaces.maxima_lib.MaximaLibElement at 0x32c1d4828>)
failed: RuntimeError: ECL says: Cannot coerce string $_SAGE_VAR_ξ to a
base-string>
}}}
The above error is due to a bug in ECL 16.1.2 and 20.4.24:
{{{
> (princ-to-string 'ξ)
"Ξ"
> (setf local-table (copy-readtable nil))
> (setf (readtable-case local-table) :invert)
:INVERT
> (let ((*readtable* local-table) (*print-case* :upcase)) (princ-to-
string 'ξ))
Cannot coerce string Ξ to a base-string
}}}
The above code is from Maxima's `PRINT-INVERT-CASE` function in
commac.lisp.

Upstream issue: https://gitlab.com/embeddable-common-
lisp/ecl/-/issues/602

URL: https://trac.sagemath.org/30122
Reported by: mkoeppe
Ticket author(s): Matthias Koeppe
Reviewer(s): Markus Wageringel

These packages are long gone, yet
{{{
grep -R KASH src/doc
grep -R Macaulay src/doc
}}}
return hits such as
`Macaulay and KASH are Sage packages` etc.

URL: https://trac.sagemath.org/30109
Reported by: dimpase
Ticket author(s): John Palmieri
Reviewer(s): Matthias Koeppe

As a follow-up to #29278, #29280: If we use Unicode variable names in
`SR`, declaring a domain gives an error:
{{{
sage: SR.var('π', domain='real')
RuntimeError: ECL says: THROW: The catch MACSYMA-QUIT is undefined.
SystemError: <built-in method var of sage.symbolic.ring.SymbolicRing
object at 0x334506908> returned a result with an error set
}}}

This comes from our ECL interface:
{{{
sage: from sage.libs.ecl import *
sage: u_symbol = EclObject('🔥')
sage: u_symbol
<repr(<sage.libs.ecl.EclObject at 0x337e7b3c8>) failed:
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x94 in position 2:
invalid start byte>
sage: u_symbol.python()
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x94 in position 2:
invalid start byte
}}}

Also note:
{{{
sage: b_symbol = EclObject(bytes([166]))
sage: b_symbol
<repr(<sage.libs.ecl.EclObject at 0x337e7b058>) failed:
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xa6 in position 0:
invalid start byte>
}}}

URL: https://trac.sagemath.org/30106
Reported by: mkoeppe
Ticket author(s): Matthias Koeppe
Reviewer(s): Markus Wageringel

We added methods to generate the extended Kasami codes and the Kasami
codes.
For a definition of those codes see the book "Distance-Regular Graphs"
by Brouwer et. al.

URL: https://trac.sagemath.org/30085
Reported by: gh-Ivo-Maffei
Ticket author(s): Ivo Maffei
Reviewer(s): Dima Pasechnik

Trac #29922: sage.doctest: Make imports more specific; make global environment for tests customizable

We prepare the Sage doctesting module for running in environments where
`sage.all` is not available (#29705).

1. An explicit import in `sage.doctest.parsing`:
{{{
# We need to import from sage.all to avoid circular imports.
from sage.all import RealIntervalField
RIFtol = RealIntervalField(1044)
}}}

2. We make the global environment for tests customizable in
`sage.doctest.forker`: in `init_sage`:
{{{
    import sage.repl.ipython_kernel.all_jupyter
}}}
   and again in `DocTestTask._run`:
{{{
            # Import Jupyter globals to doctest the Jupyter
            # implementation of widgets and interacts
            import sage.repl.ipython_kernel.all_jupyter as sage_all
}}}
   ... which is
{{{
"""
All imports for Jupyter
"""

from sage.all_cmdline import *

from .widgets_sagenb import (input_box, text_control, slider,
        range_slider, checkbox, selector, input_grid, color_selector)
from .interact import interact
}}}

   This is exposed by the new `sage-runtest` option `--environment`.

   For example, #29865 defines modules such as `sage.all__sage_objects`.
We would invoke `sage -t --environment=sage.all__sage_objects` to test
against this global environment.

3. We ignore errors importing `sage.interfaces`.

URL: https://trac.sagemath.org/29922
Reported by: mkoeppe
Ticket author(s): Matthias Koeppe
Reviewer(s): Jonathan Kliem

We add a method that tests `is_combinatorially_isomorphic`.

URL: https://trac.sagemath.org/29908
Reported by: gh-kliem
Ticket author(s): Jonathan Kliem
Reviewer(s): Matthias Koeppe

Trac #29901: .github/workflows/: Test all optional packages, add workflow for testing all experimental packages

Follow up from #29341.

URL: https://trac.sagemath.org/29901
Reported by: mkoeppe
Ticket author(s): Matthias Koeppe
Reviewer(s): Jonathan Kliem

The new dilation with #29200 discovered two bugs:

{{{
sage: 2*Polyhedron([[]], backend='cdd')
...
TypeError ...
}}}

and

{{{
sage: K.<sqrt2> = QuadraticField(2)
sage: sqrt2*Polyhedron(backend='normaliz')
...
AttributeError
}}}

The underlying errors are the following:

{{{
sage: from sage.geometry.polyhedron.backend_cdd import Polyhedron_QQ_cdd
sage: from sage.geometry.polyhedron.parent import Polyhedra_QQ_cdd
sage: parent = Polyhedra_QQ_cdd(QQ, 0, 'cdd')
sage: p = Polyhedron_QQ_cdd(parent, [iter([]), iter([]), iter([])],
None)
Traceback (most recent call last):
...
TypeError: can't multiply sequence by non-int of type 'NoneType'

sage: Polyhedron(ieqs=[], ambient_dim=5, backend='cdd')
Traceback (most recent call last):
...
TypeError: unsupported operand type(s) for -=: 'NoneType' and 'int'

sage: from sage.geometry.polyhedron.parent import Polyhedra_RDF_cdd
sage: from sage.geometry.polyhedron.backend_cdd import
Polyhedron_RDF_cdd
sage: parent = Polyhedra_RDF_cdd(RDF, 1, 'cdd')
sage: Vrep = [[], [], [[1.0]]]
sage: Hrep = [[], []]
sage: p = Polyhedron_RDF_cdd(parent, Vrep, Hrep,
....:                        Vrep_minimal=True, Hrep_minimal=True)
Traceback (most recent call last):
...
TypeError: unsupported operand type(s) for -=: 'NoneType' and 'int'
}}}

There are two tiny fixes to it:
- Make sure to tell the empty polyhedron appart at
`Polyhedron_base.__init__`.
- Add a trivial inequality for initialization of the universe polyhedron
with backend `cdd`.

We add doctests for each fix. Note that also #29907 will indirectly test
this.

URL: https://trac.sagemath.org/29899
Reported by: gh-kliem
Ticket author(s): Jonathan Kliem
Reviewer(s): Matthias Koeppe

... from a forgotten branch on #16351 ...

URL: https://trac.sagemath.org/29882
Reported by: mkoeppe
Ticket author(s): Florent Hivert, Sébastien Labbé
Reviewer(s): Travis Scrimshaw

We upgrade Cython to 0.29.21

(https://github.com/cython/cython/blob/master/CHANGES.rst#02921-2020-07-
09)

This is supposed to fix many bugs compared to our current 0.29.17, but a
bug reported with the new version (https://groups.google.com/g/sage-
devel/c/ij0ulNf7ZuI/m/qF0AlS9IBgAJ):
{{{
$sage -c 1+1
SageMath version 9.1, Release Date: 2020-05-20
Traceback (most recent call last):
  File "/home/conda/feedstock_root/build_artifacts/sagelib_1592119926566
/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_p
lacehold_placehold_placehold_placehold_placehold_placehold_placehold_pla
cehold_placehold_placehold_placehold_placehol/bin/sage-eval", line 4, in
<module>
    from sage.all import *
  File "/home/conda/feedstock_root/build_artifacts/sagelib_1592119926566
/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_p
lacehold_placehold_placehold_placehold_placehold_placehold_placehold_pla
cehold_placehold_placehold_placehold_placehol/lib/python3.6/site-
packages/sage/all.py", line 117, in <module>
    import sage.misc.lazy_import
  File "sage/misc/lazy_import.pyx", line 1, in init
sage.misc.lazy_import (build/cythonized/sage/misc/lazy_import.c:10174)
AttributeError: type object 'sage.misc.lazy_import.LazyImport' has no
attribute '__div__'
}}}

Previous update:
 - #29480 - Upgrade Cython to 0.29.17 (merged in 9.2.beta1)

URL: https://trac.sagemath.org/29861
Reported by: mkoeppe
Ticket author(s): Matthias Koeppe
Reviewer(s): Dima Pasechnik

This ticket adds an spkg-configure.m4 for zn_poly, in order to use it
from a system package if possible (see #27330).

Nothing special with this one: Sage builds without any problem with this
system package.

URL: https://trac.sagemath.org/29649
Reported by: gh-thierry-FreeBSD
Ticket author(s): Thierry Thomas, Dima Pasechnik
Reviewer(s): Matthias Koeppe

The pushout of two algebraic number fields with a coerce embedding in
`AA` (the real algebraic fields) is implemented as being `AA`. As a
consequence, it is possible to add elements from different number fields
{{{
sage: K.<a> = NumberField(x^3 - 2, embedding=AA(2)**(1/3))
sage: L.<b> = NumberField(x^2 - 3, embedding=AA(3)**(1/2))
sage: a + b
2.991971857463751?
}}}
Though, the pushout is not implemented for fields with coerce embedding
in `QQbar` (algebraic field).
{{{
sage: K.<a> = NumberField(x^3 - 2, embedding=QQbar(2)**(1/3) *
QQbar.zeta(3))
sage: L.<b> = NumberField(x^3 - 3, embedding=QQbar(3)**(1/3) *
QQbar.zeta(3)**2)
sage: a + b
Traceback (most recent call last):
...
TypeError: unsupported operand parent(s) for +
}}}
This ticket implements it.

URL: https://trac.sagemath.org/28778
Reported by: gh-kliem
Ticket author(s): Jonathan Kliem
Reviewer(s): Vincent Delecroix, Matthias Koeppe

#29766, #29441, and #29497 introduce build dependencies for packages
that are only active when `SAGE_CHECK` is not `no`.

But whether a package needs its check-dependencies depends on both
`SAGE_CHECK_PACKAGES` and `SAGE_CHECK`.

In this ticket, we move the handling of `SAGE_CHECK_PACKAGES` from
`sage-spkg` to the Makefile.

This allows packages to conditionalize dependencies based on the new
makefile variables `SAGE_CHECK_symengine_py` (for #29497) etc.

URL: https://trac.sagemath.org/30118
Reported by: mkoeppe
Ticket author(s): Matthias Koeppe
Reviewer(s): Dima Pasechnik

#29673 (spkg-configure.m4 for sympow) accepts broken `sympow` versions
on various systems, as noted on #29673, #3360

URL: https://trac.sagemath.org/30147
Reported by: mkoeppe
Ticket author(s): Dima Pasechnik
Reviewer(s): Matthias Koeppe

(from https://groups.google.com/d/msg/sage-
devel/OXOmOjlYQLo/7gOLtzsJCQAJ)

We already reject gcc 10, but if gfortran is installed separately, we
also have to check that version.

We also check for `gfortran-9` first, and on `homebrew`, we recommend
installing it via `brew install gcc@9`.

URL: https://trac.sagemath.org/30067
Reported by: mkoeppe
Ticket author(s): Matthias Koeppe
Reviewer(s): Dima Pasechnik

This ticket makes
{{{
sage -t --long --random-seed=n src/sage/graphs/
}}}
pass for different values `n` than just `0`.

URL: https://trac.sagemath.org/29965
Reported by: gh-kliem
Ticket author(s): Jonathan Kliem
Reviewer(s): David Coudert

Merge tag '9.2.beta5' into t/30118/handle_sage_check_packages_in_build_make_makefile_in__not_sage_spkg

SageMath version 9.2.beta5, Release Date: 2020-07-12

We introduce an option for doctests `--random-seed` that defaults to `0`
for now:

{{{
sage -t --long src/sage/all.py
...
Doctesting 1 file.
sage -t --long --random-seed=0 src/sage/all.py
    [16 tests, 0.73 s]
----------------------------------------------------------------------
All tests passed!
----------------------------------------------------------------------
Total time for all tests: 0.8 seconds
    cpu time: 0.7 seconds
    cumulative wall time: 0.7 seconds
}}}

This allows specifying, which random seed shall be used for the
doctests.

URL: https://trac.sagemath.org/29962
Reported by: gh-kliem
Ticket author(s): Jonathan Kliem
Reviewer(s): Markus Wageringel, Matthias Koeppe

We add a method that checks gale transforms and it's inverse.

We also fix two `# long time` flags for the snub cube:
- one is missing spaces,
- the other test certainly doesn't take 30 seconds anymore (I need about
2).

URL: https://trac.sagemath.org/29918
Reported by: gh-kliem
Ticket author(s): Jonathan Kliem
Reviewer(s): Matthias Koeppe

This ticket aims to implement diameter computation method for weighted
and unweighted undirected graphs, as given in
[http://arxiv.org/abs/1803.04660]

URL: https://trac.sagemath.org/29744
Reported by: gh-vipul79321
Ticket author(s): Vipul Gupta
Reviewer(s): David Coudert

We implement the fraction field of Ore polynomial rings.

The elements of the fraction field are represented by fractions of the
form `denom^(-1) * num`.

URL: https://trac.sagemath.org/29678
Reported by: caruso
Ticket author(s): Xavier Caruso
Reviewer(s): Travis Scrimshaw

This ticket changes `SAGE_ROOT`, so that it is always the absolute
physical path, i.e. symbolic links are resolved.

-----

As reported on [https://groups.google.com/d/msg/sage-
release/kU5M1QVuQQY/4ClWRtgMBAAJ sage-release], when building Sage
9.1.beta9 from a path that is a symbolic link, the following test in
`src/sage/env.py` fails:

{{{
    sage: env = {k:v for (k,v) in os.environ.items() if not
k.startswith("SAGE_")}
    sage: from subprocess import check_output
    sage: cmd = "from sage.all import SAGE_ROOT, SAGE_LOCAL;
print((SAGE_ROOT, SAGE_LOCAL))"
    sage: out = check_output([sys.executable, "-c", cmd],
env=env).decode().strip()   # long time
    sage: out == repr((SAGE_ROOT, SAGE_LOCAL))
# long time
}}}

The problem is that the left path in `out` is the symbolic link to
Sage's root directory, whereas `SAGE_ROOT` is the absolute path without
symbolic link.

URL: https://trac.sagemath.org/29446
Reported by: gh-mwageringel
Ticket author(s): Markus Wageringel
Reviewer(s): Matthias Koeppe

This ticket adds some code based on the tiling solver class and dancing
links solver to find a surrounding of a polyomino with copies of itself.
An example is below:

{{{
sage: from sage.combinat.tiling import Polyomino
sage: H = Polyomino([(-1, 1), (-1, 4), (-1, 7), (0, 0), (0, 1), (0, 2),
....: (0, 3), (0, 4), (0, 5), (0, 6), (0, 7), (0, 8), (1, 1), (1, 2),
....: (1, 3), (1, 4), (1, 5), (1, 6), (1, 7), (1, 8), (2, 0), (2, 2),
....: (2, 3), (2, 5), (2, 6), (2, 8)])
sage: H.show2d()
}}}

[[Image(H.png)]]

{{{
sage: %time solution = H.self_surrounding(10, ncpus=8)
CPU times: user 1.69 s, sys: 1.08 s, total: 2.77 s
Wall time: 3.85 s
sage: G = sum([p.show2d() for p in solution], Graphics())
sage: G
}}}

[[Image(G.png)]]

See: https://en.wikipedia.org/wiki/Heesch%27s_problem

URL: https://trac.sagemath.org/29160
Reported by: slabbe
Ticket author(s): Sébastien Labbé
Reviewer(s): Travis Scrimshaw, Frédéric Chapoton

This ticket adds three methods to graphs to compute three variations  of
the Cheeger constant:

- the "transition isoperimetric number" (`cheeger_constant`)
- the edge isoperimetric number (`edge_isoperimetric_number`)
- the vertex isoperimetric number or magnifying constant
(`vertex_isoperimetric_number`)

Note that the implemented Cheeger constant is also the **conductance**
of the simple random walk on the graph.

URL: https://trac.sagemath.org/21942
Reported by: pelegm
Ticket author(s): Vincent Delecroix, David  Coudert
Reviewer(s): Peleg Michaeli, Frédéric Chapoton

`make dist` is currently broken.

https://github.com/mkoeppe/sage/runs/848070855
{{{
Finished cloning Sage sources
make[1]: Entering directory '/home/runner/work/sage/sage/build/make'
env SAGE_INSTALL_FETCH_ONLY=yes make -B SAGERUNTIME= \
        alabaster appnope arb babel bleach boost_cropped brial bzip2
cddlib c....
...
cd '/home/runner/work/sage/sage/build/pkgs/sage_conf' && .
'/home/runner/work/sage/sage/src/bin/sage-env' && .
'/home/runner/work/sage/sage/build/bin/sage-build-env-config' && sage-
logger -p '/home/runner/work/sage/sage/build/pkgs/sage_conf/spkg-
install' '/home/runner/work/sage/sage/logs/pkgs/sage_conf-none.log'
[sage_conf-none] Installing
[sage_conf-none] Error: Tried to use Sage's Python which was not yet
installed.
[sage_conf-none] If this was called from an spkg-install script for
another
[sage_conf-none] package you should add $(PYTHON) as a dependency in
[sage_conf-none] build/pkgs/<pkg>/dependencies
[sage_conf-none] Error: could not determine package name
[sage_conf-none] *******************************************************
*************************
[sage_conf-none] Error installing
[sage_conf-none] *
}}}

On this ticket we fix it and add a test run to GH Actions so that it
does not get broken again.

Related:
 - #29896 - make download

URL: https://trac.sagemath.org/30088
Reported by: mkoeppe
Ticket author(s): Matthias Koeppe
Reviewer(s): Michael Orlitzky, John Palmieri