meta-ticket: failing internet/optional doctests

[seblabbe]

This meta-ticket lists tickets opened for failing doctests involving internet, optional and/or external packages as discovered by running:

sage -tp --optional=sage,optional,external --all

Many issues are related to internet (running them is activated by the tag external in the above command) which can be specifically tested with the following command:

sage -tp --optional=sage,internet --all

Tickets

Still open tickets:

• 1 internet doctest failing in repl/interpreter.py #34683 1 internet doctest failing in repl/interpreter.py
• 1 internet doctest failing in src/sage/tests/cmdline.py - ore_algebra version #31475 1 internet doctest failing in src/sage/tests/cmdline.py - ore_algebra version
• Fix failing doctests in groups/perm_gps/permgroup.py #32294 Fix failing doctests with optional package gap_packages
• sage --ipynb2rst is broken due to changes in nbconvert #32697 1 pandoc optional doctest failing in src/sage/tests/cmdline.py

Failing doctests maybe related to the presence of an optional package:

• 1 doctest failing in combinat/designs/incidence_structures.py #32053 1 doctest failing in combinat/designs/incidence_structures.py

Fixed in 9.8:

• 2 doctests failures with external software octave #34607 2 doctests failures with external software octave
• 5 internet doctests failing in oeis #34609 5 internet doctests failing in oeis
• 1 internet doctest failing in graphs/isgci.py #34612 1 internet doctest failing in graphs/isgci.py
• Fix error in sage.misc.latex.view doctest #34594: fix failure in latex.py: latex plus latex_package_tkz_graph
• Fix findstat internet tests #34595: find findstat internet failures
• 1 internet doctest failing in src/sage/misc/package.py #32051 1 internet doctest failing in src/sage/misc/package.py
• doctests failures in sage/graphs when using COIN solver #30635 doctests failures in sage/graphs when using COIN solver
• 5 doctests failing related to external program octave #33093 5 doctests failing related to external program octave

Fixed in 9.7:

• 1 doctest failing in oeis.py #33943 1 doctest failing in oeis.py

Fixed in 9.6:

• warnings to ignore are not ignored when a doctest is tagged with # tol #33588 15 GLPK doctests failing because "Long-step dual simplex will be used" gets printed
• fix some optional u-prefix doctests #33179 fix some optional internet u-prefix doctests in oeis, findstat, matematica

Fixed in 9.5:

• Fix installation of cryptominisat and pycryptosat #33162 Fix installation of cryptominisat and pycryptosat + doctests failings in 6 files
• 9 internet doctests failing in src/sage/databases/findstat.py #32694 9 internet doctests failing in src/sage/databases/findstat.py
• 2 glucose doctests failing in sage/sat/solvers/dimacs.py #32740 2 glucose doctests failing in sage/sat/solvers/dimacs.py
• 1 fricas optional doctest failing in interfaces/fricas.py #32886 1 fricas optional doctest failing in interfaces/fricas.py
• sage --standard, sage --optional and sage --experimental are broken #32885 9 internet doctests failing in tests/cmdline.py - AttributeError: can't set attribute
• 1 internet doctest failing in src/sage/finance/stock.py #32696 1 internet doctest failing in src/sage/finance/stock.py
• 5 internet doctests failing in src/sage/databases/oeis.py #32695 5 internet doctests failing in src/sage/databases/oeis.py
• 1 internet failing doctest in src/sage/calculus/calculus.py #32693 1 internet failing doctest in src/sage/calculus/calculus.py
• 2 internet doctest failing in oeis.py #32050 2 internet doctest failing in oeis.py
• Fix polytopes_db_4d optional doctest #32290 Fix polytopes_db_4d optional doctest

Fixed in 9.4:

• 5 failing doctests in src/sage/graphs #32052 5 failing doctests in src/sage/graphs (duplicate of doctests failures in sage/graphs when using COIN solver #30635)
• regression: conversion of Mathematica's Sqrt to Sage fails #31756 regression: conversion of Mathematica's Sqrt to Sage fails
• 1 internet doctests failing in symbolic/integration/external.py #31865 1 internet doctests failing in symbolic/integration/external.py
• 3 internet doctests failing in oeis.py #31866 3 internet doctests failing in oeis.py

Fixed in 9.3:

• 2 internet doctests failing in findstat.py #31054 2 internet doctests failing in findstat.py
• 2 internet doctests failing in findstat.py and oeis.py #31023 2 internet doctests failing in findstat.py and oeis.py
• findstat error handling #30630 internet findstat error handling
• sympow gives "RuntimeError: failed to compute analytic rank" doctest failures #30633 sympow gives "RuntimeError: failed to compute analytic rank" doctest failures
• failing doctest with optional tag octave #30636 failing doctest with optional tag octave
• doctest failing in designs/incidence_structures.py #30637 doctest failing in designs/incidence_structures.py

Fixed in 9.2:

• few easy internet doctests failures to fix #30632 few easy internet doctests failures to fix
• failing internet doctests using mathematica free #30634 failing internet doctests using mathematica free
• internet doctest failing in arith/misc.py #30638 internet doctest failing in arith/misc.py
• 17 internet doctest failing in findstat.py #28864 internet doctests failing in findstat.py
• 2 internet doctests failing in bibd.py #30131 2 internet doctests failing in bibd.py
• 1 internet doctest failing in oeis.py (cross_references) #30138 1 internet doctest failing in oeis.py (cross_references)
• 1 internet doctest failing in combinat/species/library.py + combinat/tutorial.py #30020 3 internet oeis doctests failing in combinat
• 1 internet doctest failing in combinat/quickref.py #30019 1 internet doctest failing in combinat/quickref.py
• 1 optional internet oeis doctest failing (busy beaver ordering) #29787 1 optional internet oeis doctest failing (busy beaver ordering)
• Memory error with graphs generators: JankoKharaghaniGraph and SquaredSkewHadamardMatrixGraph #25465 2 doctests failed in smallgraphs.py (a duplicate was 2 doctests failed in smallgraphs.py #28865)

Fixed in 9.1:

• internet test in OEIS failing #29579 1 internet test failing in OEIS
• failing internet test integration #29578 1 internet test failing in symbolic/integration/external.py
• doctest killed due to abort in geometry/polyhedron/base.py #28866 doctest killed due to abort in geometry/polyhedron/base.py
• 7 imagemagick failing doctest in plot/animate.py #28868 7 imagemagick failing doctests in plot/animate.py
• 1 optional internet oeis doctest failing in combinat/tutorial.py #29237 1 optional internet oeis doctest failing in combinat/tutorial.py
• Latte test failure #29300 Latte test failure
• 1 imagemagick failing doctest in misc/latex.py #28867 1 imagemagick failing doctest in misc/latex.py
• 1 internet doctest failing in repl/load.py #29047 1 internet doctest failing in repl/load.py
• 1 doctest failing in src/sage/databases/oeis.py with tag internet #29048 1 internet doctest failing in src/sage/databases/oeis.py

Fixed in 9.0:

• 5 cplex doctests failed in cplex_backend.pyx #28708 5 cplex doctests failed in cplex_backend.pyx

• Fixing missing optional flag in base_QQ.py #28700 missing latte_int optional tag in three doctests (a duplicate ticket was missing latte optional tag in three doctests #28697)

• 5 internet doctests failing in findstat.py #27838 5 (now 8) internet doctests failing in findstat.py

• py3: fix doctests with cbc #28689 fix doctests with cbc

• py3: fix doctests with gurobi #28756 py3: fix doctests with gurobi

• py3: dot2tex + graphviz doctests failures #28759 py3: dot2tex + graphviz doctests failures

• py3: internet str vs bytes doctests failures #28760 py3: imagemagick,internet,latex str vs bytes doctests failures

• py3: further fixes for misc #28761 py3: further fixes for misc relative to internet doctests failures

• DIMACS solver not workng with Python3 (7 glucose optional doctests failed) #28763 7 glucose optional doctests failed in sat/solvers/dimacs.py

• 2 internet doctest failed in hadamard_matrix.py #28764 2 internet doctest failed in hadamard_matrix.py

• 2 doctests failed in cmdline.py related to rst2ipynb #28762 2 doctests failed in cmdline.py related to rst2ipynb

• failing internet doctest in repl/load.py #28808 failing internet in repl/load.py

• 1 doctest failed in thematic_tutorials/linear_programming.rst #28863 1 doctest failed in thematic_tutorials/linear_programming.rst because of CPLEX
  Fixed in 8.9:

• 1 doctest failing in src/sage/databases/oeis.py with tag internet #28455 1 doctest failing in src/sage/databases/oeis.py with tag internet

• 1 internet doctest failing in oeis.py (Avogadro's) #28127 1 internet doctest failing in oeis.py (Avogadro's)

• py3: fix str vs bytes issues with gurobi #28206 py3: fix str vs bytes issues with gurobi

Fixed in 8.8:

• 2 failing trivial internet doctests related to oeis #27872 2 failing trivial internet doctests related to oeis
• covering_design.py & design_catalog.py: Fix AttributeError #27821 failing internet doctests in sage/combinat/designs (again)
• 6 doctests failed in src/sage/databases/oeis.py with tag internet #27783 6 doctests internet failed in databases/oeis.py
• 1 pynormaliz doctest failing in src/sage/geometry/polyhedron/backend_normaliz.py #27782 1 pynormaliz doctest failing in geometry/polyhedron/backend_normaliz.py
• 2 doctests failing in src/sage/misc/package.py when --optional=sage,internet #27781 2 internet doctests failing in misc/package.py
• py3: combinat/designs: bytes-like object is required, not 'str' #26592 3+2 failing internet doctests in sage/combinat/designs

Fixed in 8.7:

• 2 internet doctest failing in misc/persist.pyx #25614 2 failing internet doctests in sage/misc/persist.pyx
• MR8: fix doctest for an updated OEIS sequence #27361 oeis.py related to internet
• fix doctest in graph_latex #27249 fix doctest in graph_latex related to dot2tex and graphviz
• failing internet doctest in sage/repl/load.py #25535 1 failing internet doctest in sage/repl/load.py
• 1 optional doctest failing in cmdline.py related to pandoc #27172 1 optional doctest failing in cmdline.py related to pandoc
• 5 internet doctests failing in findstat.py #26997 5 internet doctests failing in findstat.py
• 1 optional gurobi doctest failing #26999 1 optional gurobi doctest failing

Fixed in 8.6:

• 1 internet doctest failing in combinat/tutorial.py #26921 1 internet doctest failing in combinat/tutorial.py
• Few failing internet doctests in mma_free_integrator #25501 3+1 internet failing doctests in sage/symbolic/integration/external.py and internal.py, because of mma_free_integrator is broken, thus also fixing Let Mathematica free integration work with definite integrals #14764
• 2 failing doctests in sql_db.py #26920 -> graph canonical labels and doctest failures in databases/sql_db.py #26994 (2 failing doctests in sql_db.py because of optional pkg bliss)

Fixed in 8.5:

• 20 internet doctests failed in sage/finance/stock.py #25473 20 failing internet doctests in finance/stock.py
• 3 other internet doctests failing in findstat.py #26348 3 other internet doctests failures in findstat.py
• failing optional internet doctests in sage/combinat/designs #26502 3+2 failing internet doctests in sage/combinat/designs
• Remove ellipsis in one findstat doctest #26728: Remove ellipsis in one findstat doctest

Fixed in 8.4:

• 1 internet doctest failing in databases/findstat.py #25773 (1 more internet in findstat)
• 3 other internet doctests failing in oeis.py #26125 (3 more internet in oeis)
• I/O operation on closed file when sage -t --optional=sage,external --logfile is_provided.log #25378 (I/O on closed file error when running doctest with external packages)
• clean deprecation warning in doctests for paths.py + animate.py #26347 (animate.py and paths.py related to external ffmpeg and imagemagick)

Fixed in 8.3:

• OEIS update (database format change, new entries, incorrect warning handling) #25471 (oeis)
• 18 internet doctests failed in databases/findstat.py #25472 (findstat)
• Few internet doctests failed in 6 files #25474 (6 files)
• 2 internet failing doctests in coding/databases.py #25534 (coding/databases.py)
• src/sage/plot/animate.py: UnicodeDecodeError in doctesting framework #25416 (failures in animate.py related to external package imagemagick)
• doctest failures related to automorphism groups of edge-labelled graphs #25399 (failures related to optional package bliss)

Closed as invalid because not always reproducible:

• 1 internet doctest failing in combinat/designs/ext_rep.py #25615 1 internet doctest failing in sage/combinat/designs/ext_rep.py

Reports

Many of the above tickets originated in reports of failing doctests
on the sage-release mailing list, after the release announcement for
various development versions of Sage. See for instance:

• sage-release thread for Sage 8.3.beta6
• sage-release thread for Sage 8.3.beta3

and more can be found by
searching for "internet" on sage-release.

CC: @slel @vinklein @sagetrac-tmonteil

Component: doctest coverage

Keywords: meta-ticket, internet, optional doctests, thursdaysbdx

Issue created by migration from https://trac.sagemath.org/ticket/25536

[seblabbe]

comment:1

I fixed #25474. I am clueless for the others.

[seblabbe]

comment:2

added persist.pyx

[slel]

comment:15

See also

• Remove ellipsis in one findstat doctest #26728: Remove ellipsis in one findstat doctest

[seblabbe]

comment:108

tickets merged in 9.5.beta9

[seblabbe]

comment:112

one ticket merged in 9.6

[seblabbe]

comment:114

ticket fixed in 9.6

[seblabbe]

comment:123

tickets merged in 9.8.beta1

[seblabbe]

comment:124

tickets merged in 9.8.beta2