Bug#997772: python-cogent: FTBFS: You must configure the bibtex_bibfiles setting
Hi Andreas
On Wednesday, 3 November 2021 19:00:05 AEDT Andreas Tille wrote:
[...]
> File "/usr/lib/python3/dist-packages/setuptools/dist.py", line 182, in
> write_pkg_file license = rfc822_escape(self.get_license())
> File "/usr/lib/python3.9/distutils/util.py", line 476, in rfc822_escape
> lines = header.split('\n')
> AttributeError: 'list' object has no attribute 'split'
looking at setup.py, it has
license=["BSD"],
https://salsa.debian.org/med-team/python-cogent/-/blob/master/setup.py#L62
while the documentation for the setup() function indicates that licence should
be a string. That would certainly be consistent with the exception that is
raised with the output of get_license().
https://packaging.python.org/guides/distributing-packages-using-setuptools/
#license
I've not checked that this is indeed the problem, but patching setup.py to
have instead
license="BSD",
would be the next thing I'd try.
Incidentally, I see that upstream for cogent has ripped out setup.py entirely
and now has a flit based build system which will require a few changes to the
packaging in the future.
cheers
Stuart
--
Stuart Prescotthttp://www.nanonanonano.net/ stu...@nanonanonano.net
Debian Developer http://www.debian.org/ stu...@debian.org
GPG fingerprint90E2 D2C1 AD14 6A1B 7EBB 891D BBC1 7EBB 1396 F2F7
Bug#997772: python-cogent: FTBFS: You must configure the bibtex_bibfiles setting
On 11/3/21 1:30 PM, Andreas Tille wrote: Control: tags -1 pending Hi Stuart, Am Wed, Nov 03, 2021 at 09:43:40AM +1100 schrieb Stuart Prescott: Extension error: You must configure the bibtex_bibfiles setting make[2]: *** [Makefile:40: html] Error 2 this is sphinxcontrib-bibtex saying that you need to add the following to doc/conf.py: bibtex_bibfiles = "path/to/references.bib" However I can't see a .bib file anywhere in the source. I also can't see any code in the rst files or the docstrings that would actually use sphinxcontrib- bibtex so I'm not sure how this extension is actually used in these documents. Perhaps it isn't actually needed at all. Thanks for the good hint which helped me over this issue[1]. Unfortunately now dh_auto_install has an issue that did not occured before: [...] Pushed to salsa, and now it works as it should. I leave the onus of checking and uploading onto you. Regards, Nilesh OpenPGP_signature Description: OpenPGP digital signature
Bug#997772: python-cogent: FTBFS: You must configure the bibtex_bibfiles setting
Control: tags -1 pending
Hi Stuart,
Am Wed, Nov 03, 2021 at 09:43:40AM +1100 schrieb Stuart Prescott:
> > > > Extension error:
> > > > You must configure the bibtex_bibfiles setting
> > > > make[2]: *** [Makefile:40: html] Error 2
>
> this is sphinxcontrib-bibtex saying that you need to add the following to
> doc/conf.py:
>
> bibtex_bibfiles = "path/to/references.bib"
>
> However I can't see a .bib file anywhere in the source. I also can't see any
> code in the rst files or the docstrings that would actually use sphinxcontrib-
> bibtex so I'm not sure how this extension is actually used in these
> documents.
> Perhaps it isn't actually needed at all.
Thanks for the good hint which helped me over this issue[1]. Unfortunately
now dh_auto_install has an issue that did not occured before:
dh_auto_install -O--buildsystem=pybuild
I: pybuild base:232: /usr/bin/python3 setup.py install --root
/build/python-cogent-2021.5.7a+dfsg/debian/python3-cogent3
/usr/lib/python3/dist-packages/setuptools/dist.py:487: UserWarning: Normalizing
'2021.5.7a' to '2021.5.7a0'
warnings.warn(tmpl.format(**locals()))
running install
running build
running build_py
running install_lib
creating /build/python-cogent-2021.5.7a+dfsg/debian/python3-cogent3
creating /build/python-cogent-2021.5.7a+dfsg/debian/python3-cogent3/usr
...
byte-compiling
/build/python-cogent-2021.5.7a+dfsg/debian/python3-cogent3/usr/lib/python3.9/dist-packages/cogent3/phylo/least_squares.py
to least_squares.cpython-39.pyc
running install_egg_info
running egg_info
creating src/cogent3.egg-info
writing src/cogent3.egg-info/PKG-INFO
Traceback (most recent call last):
File "/build/python-cogent-2021.5.7a+dfsg/setup.py", line 52, in
setup(
File "/usr/lib/python3/dist-packages/setuptools/__init__.py", line 153, in
setup
return distutils.core.setup(**attrs)
File "/usr/lib/python3.9/distutils/core.py", line 148, in setup
dist.run_commands()
File "/usr/lib/python3.9/distutils/dist.py", line 966, in run_commands
self.run_command(cmd)
File "/usr/lib/python3.9/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/usr/lib/python3/dist-packages/setuptools/command/install.py", line 61,
in run
return orig.install.run(self)
File "/usr/lib/python3.9/distutils/command/install.py", line 602, in run
self.run_command(cmd_name)
File "/usr/lib/python3.9/distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/usr/lib/python3.9/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/usr/lib/python3/dist-packages/setuptools/command/install_egg_info.py",
line 51, in run
self.run_command('egg_info')
File "/usr/lib/python3.9/distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/usr/lib/python3.9/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/usr/lib/python3/dist-packages/setuptools/command/egg_info.py", line
292, in run
writer(self, ep.name, os.path.join(self.egg_info, ep.name))
File "/usr/lib/python3/dist-packages/setuptools/command/egg_info.py", line
635, in write_pkg_info
metadata.write_pkg_info(cmd.egg_info)
File "/usr/lib/python3.9/distutils/dist.py", line 1117, in write_pkg_info
self.write_pkg_file(pkg_info)
File "/usr/lib/python3/dist-packages/setuptools/dist.py", line 182, in
write_pkg_file
license = rfc822_escape(self.get_license())
File "/usr/lib/python3.9/distutils/util.py", line 476, in rfc822_escape
lines = header.split('\n')
AttributeError: 'list' object has no attribute 'split'
E: pybuild pybuild:354: install: plugin distutils failed with: exit code=1:
/usr/bin/python3 setup.py install --root
/build/python-cogent-2021.5.7a+dfsg/debian/python3-cogent3
dh_auto_install: error: pybuild --install -i python{version} -p 3.9 --dest-dir
/build/python-cogent-2021.5.7a\+dfsg/debian/tmp returned exit code 13
Any idea what might be wrong here?
Kind regards
Andreas.
[1]
https://salsa.debian.org/med-team/python-cogent/-/commit/43aa41a0fbce1643211bd69ec6ecaca209397753
--
http://fam-tille.de
Bug#997772: python-cogent: FTBFS: You must configure the bibtex_bibfiles setting
Hi Andreas > > > Extension error: > > > You must configure the bibtex_bibfiles setting > > > make[2]: *** [Makefile:40: html] Error 2 this is sphinxcontrib-bibtex saying that you need to add the following to doc/conf.py: bibtex_bibfiles = "path/to/references.bib" However I can't see a .bib file anywhere in the source. I also can't see any code in the rst files or the docstrings that would actually use sphinxcontrib- bibtex so I'm not sure how this extension is actually used in these documents. Perhaps it isn't actually needed at all. cheers Stuart -- Stuart Prescotthttp://www.nanonanonano.net/ stu...@nanonanonano.net Debian Developer http://www.debian.org/ stu...@debian.org GPG fingerprint90E2 D2C1 AD14 6A1B 7EBB 891D BBC1 7EBB 1396 F2F7
Bug#997772: python-cogent: FTBFS: You must configure the bibtex_bibfiles setting
Control: tags -1 help Control: tags -1 upstream Control: forwarded -1 https://github.com/cogent3/cogent3/issues/977 Hi, I wonder whether someone on the Python list might come up with some help Am Sun, Oct 24, 2021 at 01:57:39PM +0200 schrieb Lucas Nussbaum: > Source: python-cogent > Version: 2021.5.7a+dfsg-2 > ... > > make[2]: Entering directory '/<>/doc' > > sphinx-build -b html -d _build/doctrees . _build/html > > Running Sphinx v4.2.0 > > making output directory... done > > WARNING: html_static_path entry '_static' does not exist > > WARNING: The config value `today' has type `date', defaults to `str'. > > > > Extension error: > > You must configure the bibtex_bibfiles setting > > make[2]: *** [Makefile:40: html] Error 2 I suspect that this issue is caused by the Sphinx version bump. When looking at other places where this error was discussed[1], the recommendation is to use sphinxcontrib-bibtex<2.0.0 to requirements.txt which is no real option in the our packaging case. Any help how to adapt the code to python3-sphinxcontrib.bibtex 2.4.1 would be appreciated. Kind regards Andreas. [1] https://github.com/executablebooks/jupyter-book/issues/1137 -- http://fam-tille.de
Bug#997772: python-cogent: FTBFS: You must configure the bibtex_bibfiles setting
Source: python-cogent Version: 2021.5.7a+dfsg-2 Severity: serious Justification: FTBFS Tags: bookworm sid ftbfs User: lu...@debian.org Usertags: ftbfs-20211023 ftbfs-bookworm Hi, During a rebuild of all packages in sid, your package failed to build on amd64. Relevant part (hopefully): > make[2]: Entering directory '/<>/doc' > sphinx-build -b html -d _build/doctrees . _build/html > Running Sphinx v4.2.0 > making output directory... done > WARNING: html_static_path entry '_static' does not exist > WARNING: The config value `today' has type `date', defaults to `str'. > > Extension error: > You must configure the bibtex_bibfiles setting > make[2]: *** [Makefile:40: html] Error 2 The full build log is available from: http://qa-logs.debian.net/2021/10/23/python-cogent_2021.5.7a+dfsg-2_unstable.log A list of current common problems and possible solutions is available at http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute! 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 If you fail to reproduce this, please provide a build log and diff it with mine so that we can identify if something relevant changed in the meantime.
