How do I know what passagemath packages to install?

General
1

I did pip install passagemath-graphs and when I then run

from sage.all__sagemath_graphs import *

g = Graph({
    0: [1, 2],
    1: [0, 2],
    2: [0, 1, 3],
    3: [2]
})

aut = g.automorphism_group()
print(aut.order())

I get ModuleNotFoundError: No module named 'sage.groups.perm_gps.permgroup'

This code works when I do pip install passsagemath-standard.

Is this intended behavior? If yes, is there a way to automatically determine which additional pip install’s I have to do? I am trying to minimize the amount of installed packages (that is, avoid installing passsagemath-standard).

2

Great question. Several complementary answers:

1 Like
3

I’ve added a bit of documentation in passagemath-graphs: Define extra "groups", document extras by mkoeppe · Pull Request #1027 · passagemath/passagemath · GitHub; comments very welcome

4

Thanks a lot from this prompt answer, and great to see this getting more user friendly. Great!

So, if I understand correctly, pip install passagemath-graphs[groups] should work for this example. However, it doesn’t for me. I also tried pip install passagemath-graphs[groups, test].

I get:

  File "sage/groups/perm_gps/permgroup_element.pyx", line 137, in init sage.groups.perm_gps.permgroup_element
ImportError: cannot import name libgap

This is the list of passagemath packages that are installed now:

passagemath-categories  10.5.42
passagemath-environment 10.5.42
passagemath-gap         10.5.42
passagemath-graphs      10.5.42
passagemath-groups      10.5.42
passagemath-modules     10.5.42
passagemath-nauty       10.5.42
passagemath-objects     10.5.42
passagemath-repl        10.5.42
5

It will in the next release, after passagemath-graphs: Define extra "groups" by mkoeppe · Pull Request #1027 · passagemath/passagemath · GitHub is merged!

6

Confirmed; I’ll post a workaround.

7

This works with the current release; note the extra import.

$ pipx run --pip-args="--prefer-binary" --spec "passagemath-graphs[gap,test]" python
Python 3.11.8 (main, Feb  6 2024, 21:21:21) [Clang 15.0.0 (clang-1500.1.0.2.5)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> from sage.all__sagemath_graphs import *
>>> from sage.all__sagemath_gap import *
>>> g = Graph({
...     0: [1, 2],
...     1: [0, 2],
...     2: [0, 1, 3],
...     3: [2]
... })
>>> aut = g.automorphism_group()
>>> print(aut.order())
2
1 Like
8

Thanks a lot!

Strange (to me) that the extra import is not needed if I install ‘passagemath-standard’.

9

Thanks for the report. Well, these effects of import cycles in the Sage library are quite complex.

10

More specifically, the main purpose of modules such as sage.all__sagemath_graphs is to set up the global namespace for the purpose of doctesting; these modules use try…except to load sage.all__... packages of various relevant extras. When passagemath-standard is installed, this can lead to the preloading of sage.all__sagemath_gap.

11

Thanks for clarifying. So sage.all__sagemath_graphs finds some package X installed by passagemath-standard, which gets imported, which in turn imports sage.all__sagemath_gap.

I am grateful you are embarking on the huge task of disentangling Sage. I guess this issue of required imports depending on what is installed just means this disentangling is not yet fully complete.

EDIT: Ah, I see that this is exactly what PR 1027 resolves for this case.

12

Yes, there’s some remaining technical debt from 20 years of monolithic development, even after 5 years of modularization work.

13

Release passagemath-10.5.43 · passagemath/passagemath · GitHub is out, and pip install passagemath-graphs[groups] now works

14

pip install passagemath-graphs[groups] now works

The original example doesn’t yet work for me. I get
ModuleNotFoundError: No module named 'sage.misc.sage_eval'

This is the output of pip list

Package                 Version
----------------------- -------
cysignals               1.12.3
Cython                  3.1.2
gmpy2                   2.2.1
memory_allocator        0.1.4
mpmath                  1.3.0
passagemath-categories  10.5.43
passagemath-environment 10.5.43
passagemath-gap         10.5.43
passagemath-graphs      10.5.43
passagemath-groups      10.5.43
passagemath-modules     10.5.43
passagemath-nauty       10.5.43
passagemath-objects     10.5.43
pip                     23.0.1
setuptools              65.5.0

Only after manually installing passagemath-repl it works.

15

Thanks for testing! I was just fighting against similar sage_eval-related issues, I’ll investigate.
Edit: I’ve opened Eliminate use of `sage_eval` · Issue #1041 · passagemath/passagemath · GitHub

1 Like