Bug#1042704: qutip: FTBFS with Sphinx 7.1, docutils 0.20: TypeError: not all arguments converted during string formatting
Lucas Nussbaum
lucas at debian.org
Sun Jul 30 19:26:39 BST 2023
Source: qutip
Version: 4.7.1-2
Severity: important
Tags: ftbfs
User: python-modules-team at lists.alioth.debian.org
Usertags: sphinx7.1
Hi,
qutip fails to build with Sphinx 7.1 and docutils 0.20, both of which
are currently available in experimental.
Relevant part (hopefully):
> make[2]: Entering directory '/<<PKGBUILDDIR>>/doc'
> sphinx-build -b html -d /<<PKGBUILDDIR>>/.pybuild/doc/doctrees . /<<PKGBUILDDIR>>/.pybuild/doc/html
> Running Sphinx v7.1.1
> /<<PKGBUILDDIR>>/doc/conf.py:84: UserWarning: The documentation source and imported qutip package are not from the same source folder. This may result in the documentation containing text from different sources. Documentation source: '/<<PKGBUILDDIR>>'. Qutip package source: '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_qutip/build'.
> warnings.warn(
> WARNING: Invalid configuration value found: 'language = None'. Update your configuration to a valid language code. Falling back to 'en' (English).
> /usr/lib/python3/dist-packages/sphinx_gallery/sphinx_compatibility.py:71: RemovedInSphinx80Warning: The alias 'sphinx.util.status_iterator' is deprecated, use 'sphinx.util.display.status_iterator' instead. Check CHANGES for Sphinx API modifications.
> status_iterator = sphinx.util.status_iterator
> Calibrating OpenMP threshold...
> making output directory... done
> checking bibtex cache... out of date
> parsing bibtex file /<<PKGBUILDDIR>>/doc/guide/heom/heom.bib... parsed 3 entries
> [autosummary] generating autosummary for: apidoc/apidoc.rst, apidoc/classes.rst, apidoc/functions.rst, biblio.rst, changelog.rst, contributors.rst, copyright.rst, development/contributing.rst, development/development.rst, development/docs.rst, ..., guide/heom/bosonic.rst, guide/heom/fermionic.rst, guide/heom/history.rst, guide/heom/intro.rst, guide/heom/references.rst, guide/qip/qip-basics.rst, guide/qip/qip-processor.rst, guide/qip/qip-simulator.rst, index.rst, installation.rst
> Failed to import qutip.fortran.mcsolve_f90.
> Possible hints:
> * AttributeError: module 'qutip' has no attribute 'fortran'
> * ModuleNotFoundError: No module named 'qutip.fortran'
> generating gallery...
> Using Sphinx-Gallery to convert rst text blocks to markdown for .ipynb files.
> generating gallery for gallery/build...
> [2Kgenerating gallery for gallery/build/qip... [ 33%] plot_qip_intro_processor.py
> [2Kgenerating gallery for gallery/build/qip... [ 67%] plot_qip_relaxation.py
> [2Kgenerating gallery for gallery/build/qip... [100%] plot_qip_amplitude_noise.py
>
> computation time summary:
> - gallery/src/qip/plot_qip_intro_processor.py: 0.22 sec 0.0 MB
> - gallery/src/qip/plot_qip_relaxation.py: 0.13 sec 0.0 MB
> - gallery/src/qip/plot_qip_amplitude_noise.py: 0.12 sec 0.0 MB
> building [mo]: targets for 0 po files that are out of date
> writing output...
> building [html]: targets for 59 source files that are out of date
> updating environment: [new config] 64 added, 0 changed, 0 removed
> [2Kreading sources... [ 2%] apidoc/apidoc
> [2Kreading sources... [ 3%] apidoc/classes
> /usr/lib/python3/dist-packages/numpydoc/docscrape.py:460: UserWarning: potentially wrong underline length...
> Parameters
> ----------- in
> Calculates a matrix element.
> ... in the docstring of matrix_element in /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_qutip/build/qutip/qobj.py.
> warn(msg)
> /usr/lib/python3/dist-packages/numpydoc/docscrape.py:460: UserWarning: potentially wrong underline length...
> Parameters
> ----------- in
> Overlap between two state vectors or two operators.
> ... in the docstring of overlap in /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_qutip/build/qutip/qobj.py.
> warn(msg)
> /usr/lib/python3/dist-packages/numpydoc/docscrape.py:460: UserWarning: potentially wrong underline length...
> Returns
> ---------- in
> Returns the lattice Hamiltonian for the instance of Lattice1d.
> ... in the docstring of Hamiltonian in /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_qutip/build/qutip/lattice.py.
> warn(msg)
> /usr/lib/python3/dist-packages/numpydoc/docscrape.py:460: UserWarning: potentially wrong underline length...
> Parameters
> ------- in
> Returns a single particle wavefunction ket with the particle localized
> at a specified dof at a specified site of a specified cell.... in the docstring of basis in /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_qutip/build/qutip/lattice.py.
> warn(msg)
> /usr/lib/python3/dist-packages/numpydoc/docscrape.py:460: UserWarning: potentially wrong underline length...
> Returns
> ---------- in
> Returns a single particle wavefunction ket with the particle localized
> at a specified dof at a specified site of a specified cell.... in the docstring of basis in /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_qutip/build/qutip/lattice.py.
> warn(msg)
> /usr/lib/python3/dist-packages/numpydoc/docscrape.py:460: UserWarning: potentially wrong underline length...
> Parameters
> ------- in
> A function that returns an operator matrix that applies op to all the
> cells in the 1d lattice... in the docstring of distribute_operator in /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_qutip/build/qutip/lattice.py.
> warn(msg)
> /usr/lib/python3/dist-packages/numpydoc/docscrape.py:460: UserWarning: potentially wrong underline length...
> Returns
> ---------- in
> A function that returns an operator matrix that applies op to all the
> cells in the 1d lattice... in the docstring of distribute_operator in /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_qutip/build/qutip/lattice.py.
> warn(msg)
> /usr/lib/python3/dist-packages/numpydoc/docscrape.py:460: UserWarning: potentially wrong underline length...
> Returns
> ---------- in
> Return list of output states.
> ... in the docstring of get_final_states in /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_qutip/build/qutip/qip/circuit.py.
> warn(msg)
> [2Kreading sources... [ 5%] apidoc/functions
> /usr/lib/python3/dist-packages/numpydoc/docscrape.py:460: UserWarning: potentially wrong underline length...
> Examples
> --------- in
> Single-mode displacement operator.
> ... in the docstring of displace in /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_qutip/build/qutip/operators.py.
> warn(msg)
> /usr/lib/python3/dist-packages/numpydoc/docscrape.py:460: UserWarning: potentially wrong underline length...
> Raises
> ------- in
> Creates a random Nx1 sparse ket vector.
> ... in the docstring of rand_ket in /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_qutip/build/qutip/random_objects.py.
> warn(msg)
> /usr/lib/python3/dist-packages/numpydoc/docscrape.py:460: UserWarning: potentially wrong underline length...
> Raises
> ------- in
> Returns a Haar random pure state of dimension ``dim`` by
> applying a Haar random unitary to a fixed pure state.... in the docstring of rand_ket_haar in /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_qutip/build/qutip/random_objects.py.
> warn(msg)
> /usr/lib/python3/dist-packages/numpydoc/docscrape.py:460: UserWarning: potentially wrong underline length...
> Returns
> -------- in
> Operators for a three level system (qutrit)
> ... in the docstring of three_level_ops in /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_qutip/build/qutip/three_level_atom.py.
> warn(msg)
> /usr/lib/python3/dist-packages/numpydoc/docscrape.py:460: UserWarning: potentially wrong underline length...
> Returns
> -------- in
> Superoperator formed from pre-multiplication by operator A.
> ... in the docstring of spre in /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_qutip/build/qutip/superoperator.py.
> warn(msg)
> /usr/lib/python3/dist-packages/numpydoc/docscrape.py:460: UserWarning: potentially wrong underline length...
> Returns
> -------- in
> Superoperator formed from pre-multiplication by operator A and post-
> multiplication of operator B.... in the docstring of sprepost in /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_qutip/build/qutip/superoperator.py.
> warn(msg)
> /usr/lib/python3/dist-packages/numpydoc/docscrape.py:460: UserWarning: potentially wrong underline length...
> Returns
> -------- in
> Husimi-Q function of a given state vector or density matrix at phase-space
> points ``0.5 * g * (xvec + i*yvec)``.... in the docstring of qfunc in /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_qutip/build/qutip/wigner.py.
> warn(msg)
> /usr/lib/python3/dist-packages/numpydoc/docscrape.py:460: UserWarning: potentially wrong underline length...
> Returns :
> ------- in
> Draw a histogram for the matrix M, with the given x and y labels and title.
> ... in the docstring of matrix_histogram in /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_qutip/build/qutip/visualization.py.
> warn(msg)
> /usr/lib/python3/dist-packages/numpydoc/docscrape.py:460: UserWarning: potentially wrong underline length...
> Notes
> ------ in
> Plots a coloured Bloch sphere.
> ... in the docstring of plot_wigner_sphere in /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_qutip/build/qutip/visualization.py.
> warn(msg)
> /usr/lib/python3/dist-packages/numpydoc/docscrape.py:460: UserWarning: potentially wrong underline length...
> Returns
> ---------- in
> Function to define initial state of the qubits.
> ... in the docstring of qubit_states in /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_qutip/build/qutip/qip/qubits.py.
> warn(msg)
> /usr/lib/python3/dist-packages/numpydoc/docscrape.py:460: UserWarning: potentially wrong underline length...
> Returns
> -------- in
> Parallel execution of a mapping of `values` to the function `task`. This
> is functionally equivalent to::... in the docstring of parallel_map in /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_qutip/build/qutip/parallel.py.
> warn(msg)
> /usr/lib/python3/dist-packages/numpydoc/docscrape.py:460: UserWarning: potentially wrong underline length...
> Returns
> -------- in
> Serial mapping function with the same call signature as parallel_map, for
> easy switching between serial and parallel execution. This... in the docstring of serial_map in /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_qutip/build/qutip/parallel.py.
> warn(msg)
> /usr/lib/python3/dist-packages/numpydoc/docscrape.py:460: UserWarning: potentially wrong underline length...
> Returns
> -------- in
> Call the function ``task`` for each value in ``values`` using a cluster
> of IPython engines. The function ``task`` should have the signature... in the docstring of parallel_map in /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_qutip/build/qutip/ipynbtools.py.
> warn(msg)
> /usr/lib/python3/dist-packages/numpydoc/docscrape.py:460: UserWarning: potentially wrong underline length...
> Returns
> -------- in
> Call the function ``tast`` for each value in ``task_vec`` using a cluster
> of IPython engines. The function ``task`` should have the signature... in the docstring of parfor in /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_qutip/build/qutip/ipynbtools.py.
> warn(msg)
> /usr/lib/python3/dist-packages/numpydoc/docscrape.py:460: UserWarning: potentially wrong underline length...
> Returns
> -------- in
> Print an HTML-formatted table with version numbers for QuTiP and its
> dependencies. Use it in a IPython notebook to show which versions of... in the docstring of version_table in /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_qutip/build/qutip/ipynbtools.py.
> warn(msg)
> /usr/lib/python3/dist-packages/numpydoc/docscrape.py:460: UserWarning: potentially wrong underline length...
> Returns
> -------- in
> Simultaneous diagonalization of commuting Hermitian matrices.
> ... in the docstring of simdiag in /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_qutip/build/qutip/simdiag.py.
> warn(msg)
> [2Kreading sources... [ 6%] biblio
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_qutip/build/qutip/rhs_generate.py:docstring of qutip.rhs_generate.rhs_clear:7: CRITICAL: Unexpected section title or transition.
>
> ****
>
> Exception occurred:
> File "/usr/lib/python3/dist-packages/sphinx/ext/extlinks.py", line 103, in role
> title = caption % part
> ~~~~~~~~^~~~~~
> TypeError: not all arguments converted during string formatting
> The full traceback has been saved in /tmp/sphinx-err-slf0csvz.log, if you want to report the issue to the developers.
> Please also report this if it was a user error, so that a better error message can be provided next time.
> A bug report can be filed in the tracker at <https://github.com/sphinx-doc/sphinx/issues>. Thanks!
> make[2]: *** [Makefile:45: html] Error 2
The full build log is available from:
http://qa-logs.debian.net/2023/07/30/exp/qutip_4.7.1-2_unstable_sphinx-exp.log
Please see [1] for Sphinx changelog and [2] for Docutils changelog.
Also see [3] for the list of deprecated/removed APIs in Sphinx and possible
alternatives to them.
Some notable changes in Sphinx 6 and Sphinx 7:
- Sphinx no longer includes jquery.js and underscore.js by default.
Please use python3-sphinxcontrib.jquery package if you are using a custom
template and it still needs jquery.
- The setup.py build_sphinx command was removed. Please instead call
sphinx-build or "python3 -m sphinx" directly.
- For packages using the extlinks extension, the caption should contain
exactly one "%s" placeholder (if caption is not None).
In case you have questions, please Cc sphinx at packages.debian.org on reply.
[1]: https://www.sphinx-doc.org/en/master/changes.html
[2]: https://repo.or.cz/docutils.git/blob/refs/tags/docutils-0.20.1:/RELEASE-NOTES.txt
[3]: https://www.sphinx-doc.org/en/master/extdev/deprecated.html#dev-deprecated-apis
All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=sphinx7.1;users=python-modules-team@lists.alioth.debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=sphinx7.1&fusertaguser=python-modules-team@lists.alioth.debian.org&allbugs=1&cseverity=1&ctags=1&caffected=1#results
If you reassign this bug to another package, please marking it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects
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