fixes for reading .pc planar code files #40068
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I tried on a fedora desktop with several optional packages and get plenty of failing doctests. A summary: Running doctests with ID 2025-05-08-19-24-04-d2bc28d7.
Git branch: blop
Git ref: 10.7.beta2-1-g76c30ff3134
Running with SAGE_LOCAL='/home/dcoudert/sage/local' and SAGE_VENV='/home/dcoudert/sage/local/var/lib/sage/venv-python3.12'
Using --optional=benzene,buckygen,csdp,dot2tex,fedora,glucose,pip,plantri,python_igraph,sage,sage_numerical_backends_cplex,sage_spkg,texttable
Features to be detected: 4ti2,SAGE_SRC,benzene,bliss,buckygen,conway_polynomials,coxeter3,csdp,cvxopt,cvxopt,database_cremona_ellcurve,database_cremona_mini_ellcurve,database_cubic_hecke,database_ellcurves,dat
abase_graphs,database_jones_numfield,database_knotinfo,dot2tex,dvipng,ecm,fpylll,fricas,gap_package_atlasrep,gap_package_design,gap_package_grape,gap_package_guava,gap_package_hap,gap_package_polenta,gap_packa
ge_polycyclic,gap_package_qpa,gap_package_quagroup,gfan,giac,glucose,graphviz,imagemagick,info,ipython,jmol,jupymake,jupyter_sphinx,kenzo,kissat,latte_int,lrcalc_python,lrslib,mathics,matroid_database,mcqd,mea
taxe,meson_editable,mpmath,msolve,nauty,networkx,numpy,palp,pandoc,pdf2svg,pdftocairo,pexpect,phitigra,pillow,plantri,polytopes_db,polytopes_db_4d,pplpy,primecountpy,ptyprocess,pycosat,pycryptosat,pynormaliz,p
yparsing,python_igraph,requests,rpy2,rubiks,sage.combinat,sage.geometry.polyhedron,sage.graphs,sage.groups,sage.libs.braiding,sage.libs.ecl,sage.libs.flint,sage.libs.gap,sage.libs.giac,sage.libs
8000
.homfly,sage.li
bs.linbox,sage.libs.m4ri,sage.libs.ntl,sage.libs.pari,sage.libs.singular,sage.misc.cython,sage.modular,sage.modules,sage.numerical.mip,sage.plot,sage.rings.complex_double,sage.rings.finite_rings,sage.rings.fun
ction_field,sage.rings.number_field,sage.rings.padics,sage.rings.polynomial.pbori,sage.rings.real_double,sage.rings.real_mpfr,sage.sat,sage.schemes,sage.symbolic,sage_numerical_backends_coin,sagemath_doc_html,
scipy,singular,sirocco,sloane_database,sphinx,symengine_py,sympy,tdlib,threejs,topcom
Doctesting 1 file.
sage -t --warn-long 5.0 --random-seed=86598867965644471363315214300576176590 src/sage/graphs/graph_generators.py
**********************************************************************
File "src/sage/graphs/graph_generators.py", line 1644, in sage.graphs.graph_generators.GraphGenerators.fullerenes
Failed example:
len(list(gen)) # optional - buckygen
Exception raised:
Traceback (most recent call last):
File "/home/dcoudert/sage/src/sage/doctest/forker.py", line 730, in _run
self.compile_and_execute(example, compiler, test.globs)
File "/home/dcoudert/sage/src/sage/doctest/forker.py", line 1154, in compile_and_execute
exec(compiled, globs)
File "<doctest sage.graphs.graph_generators.GraphGenerators.fullerenes[1]>", line 1, in <module>
len(list(gen)) # optional - buckygen
^^^^^^^^^
File "/home/dcoudert/sage/src/sage/graphs/graph_generators.py", line 1717, in fullerenes
yield from graphs._read_planar_code(sp.stdout, immutable=immutable)
File "/home/dcoudert/sage/src/sage/graphs/graph_generators.py", line 1557, in _read_planar_code
raise TypeError('not a binary file')
TypeError: not a binary file
**********************************************************************
...
...
**********************************************************************
File "src/sage/graphs/graph_generators.py", line 1754, in sage.graphs.graph_generators.GraphGenerators.fusenes
Failed example:
len(list(gen)) # optional - benzene
Exception raised:
Traceback (most recent call last):
File "/home/dcoudert/sage/src/sage/doctest/forker.py", line 730, in _run
self.compile_and_execute(example, compiler, test.globs)
File "/home/dcoudert/sage/src/sage/doctest/forker.py", line 1154, in compile_and_execute
exec(compiled, globs)
File "<doctest sage.graphs.graph_generators.GraphGenerators.fusenes[1]>", line 1, in <module>
len(list(gen)) # optional - benzene
^^^^^^^^^
File "/home/dcoudert/sage/src/sage/graphs/graph_generators.py", line 1808, in fusenes
yield from graphs._read_planar_code(sp.stdout, immutable=immutable)
File "/home/dcoudert/sage/src/sage/graphs/graph_generators.py", line 1557, in _read_planar_code
raise TypeError('not a binary file')
TypeError: not a binary file
**********************************************************************
...
...
**********************************************************************
File "src/sage/graphs/graph_generators.py", line 1946, in sage.graphs.graph_generators.GraphGenerators.plantri_gen
Failed example:
next(gen)
Exception raised:
Traceback (most recent call last):
File "/home/dcoudert/sage/src/sage/doctest/forker.py", line 730, in _run
self.compile_and_execute(example, compiler, test.globs)
File "/home/dcoudert/sage/src/sage/doctest/forker.py", line 1154, in compile_and_execute
exec(compiled, globs)
File "<doctest sage.graphs.graph_generators.GraphGenerators.plantri_gen[1]>", line 1, in <module>
next(gen)
File "/home/dcoudert/sage/src/sage/graphs/graph_generators.py", line 1997, in plantri_gen
yield from graphs._read_planar_code(sp.stdout, immutable=immutable)
File "/home/dcoudert/sage/src/sage/graphs/graph_generators.py", line 1557, in _read_planar_code
raise TypeError('not a binary file')
TypeError: not a binary file
**********************************************************************
... |
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ok, so we should be more permissive somhow.. |
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Voila une nouvelle tentative |
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I do not understand permissiveness. Allowing files in text mode leads to wrong results as soon as a graph contains 10 or more vertices (when charcode |
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dcoudert
suggested changes
May 9, 2025
There was a problem hiding this comment.
I still get a failing doctest.
sage -t --warn-long 5.0 --random-seed=315374832306038895147412932306415972585 src/sage/graphs/graph_generators.py
**********************************************************************
File "src/sage/graphs/graph_generators.py", line 1974, in sage.graphs.graph_generators.GraphGenerators.plantri_gen
Failed example:
list(graphs.plantri_gen("6 -c=3")) # optional - plantri
Expected:
Traceback (most recent call last):
...
AttributeError: invalid options '6 -c=3'
Got:
<BLANKLINE>
Traceback (most recent call last):
File "/home/dcoudert/sage/src/sage/doctest/forker.py", line 730, in _run
self.compile_and_execute(example, compiler, test.globs)
File "/home/dcoudert/sage/src/sage/doctest/forker.py", line 1154, in compile_and_execute
exec(compiled, globs)
File "<doctest sage.graphs.graph_generators.GraphGenerators.plantri_gen[6]>", line 1, in <module>
list(graphs.plantri_gen("6 -c=3")) # optional - plantri
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/dcoudert/sage/src/sage/graphs/graph_generators.py", line 1990, in plantri_gen
yield from graphs._read_planar_code(sp.stdout, immutable=immutable)
File "/home/dcoudert/sage/src/sage/graphs/graph_generators.py", line 1561, in _read_planar_code
raise TypeError('file has no valid planar code header')
TypeError: file has no valid planar code header
**********************************************************************
1 item had failures:
1 of 8 in sage.graphs.graph_generators.GraphGenerators.plantri_gen
[213 tests, 1 failure, 4.23s wall]
----------------------------------------------------------------------
sage -t --warn-long 5.0 --random-seed=315374832306038895147412932306415972585 src/sage/graphs/graph_generators.py # 1 doctest failed
dcoudert
approved these changes
May 10, 2025
There was a problem hiding this comment.
LGTM.
Note that I cannot reproduce the failing doctests of the CI Conda (macOS, Python 3.11, all):
https://github.com/sagemath/sage/actions/runs/14927882186/job/41936763451?pr=40068#step:12:1989 and
https://github.com/sagemath/sage/actions/runs/14927882186/job/41936763451?pr=40068#step:12:8357.
I tried on both macOS and fedora with Python 3.12. These errors seems independent from this PR.
vbraun
pushed a commit
to vbraun/sage
that referenced
this pull request
May 11, 2025
sagemathgh-40068: fixes for reading .pc planar code files fixes sagemath#40062 ### 📝 Checklist - [x] The title is concise and informative. - [x] The description explains in detail what this PR is about. - [x] I have linked a relevant issue or discussion. - [x] I have created tests covering the changes. - [x] I have updated the documentation and checked the documentation preview. URL: sagemath#40068 Reported by: Frédéric Chapoton Reviewer(s): David Coudert
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fixes #40062
📝 Checklist