By the way, regarding sphinx plugin, have a look at this: http://sphinxcontrib-bibtex.readthedocs.org/en/latest/quickstart.html#minimal-example
and this: http://sphinxcontrib-bibtex.readthedocs.org/en/latest/related.html sphinxcontrib-bibtex lets you can create "local bibliographies" which will bypass the need for parsing the documentation. Mainak On Sun, Aug 30, 2015 at 6:46 AM, Joel Nothman <joel.noth...@gmail.com> wrote: > A "Cite me with duecredit" sash on the opposite corner to "Fork me on > github"? ;) > > On 30 August 2015 at 14:36, Mathieu Blondel <math...@mblondel.org> wrote: > >> >> >> On Sun, Aug 30, 2015 at 7:27 AM, Yaroslav Halchenko <s...@onerussian.com> >> wrote: >> >>> >>> As long as installation is straightforward, I think it should be a minor >>> hurdle. It will be by default (Recommends) installed with scikit-learn, >>> pymvpa, >>> and any other related package I am maintaining in Debian/Ubuntu. It is >>> already >>> available from pypi although installation there could be a bit >>> problematic due >>> to external depends indeed. We will look into minimizing possibility for >>> issues and will also look into packaging within conda universe. Happen >>> it is a >>> no brainer to have it installed -- installation of an external tool, >>> especially >>> if recommended by the project, should not be a big issue. >>> >> >> Even if installation is easy, people also have to know that the project >> even exists. >> >> > For this reason, I think the ideal >>> > solution should be web based. This could for example take the form >>> of a >>> > sphinx plugin for easily integrating with the project's >>> documentation. We >>> > could maintain a BibTeX file and reference BibTeX entries from >>> within the >>> > documentation. The sphinx plugin would make it easier to find >>> relevant >>> > citations from various places in the documentation (class >>> reference, user >>> > guide). >>> >>> Although sound idea on its own, even if complementary to duecredit, it >>> IMHO would not be as "productive". Sure thing some determined users >>> will look up references for pieces they used, but not exhaustively and >>> not for core functions which they might have not even knew have called >>> (indirectly). >>> >> >> Indeed, both approaches are complementary. Even if duecredit succeeds, I >> think it would still be nice to make it easier to find relevant citations >> from the online documentation. Ideally, the citation annotations would be >> reused by both duecredit and the sphinx plugin. >> >> >>> That is exactly what duecredit tries to address -- automate that >>> collection of references. >>> >> >> We also need to give an idea to users as to *why* they should cite a >> certain paper. For example, cite paper [...] because it is the solver used >> by LinearSVC(dual=True) for solving the SVM dual objective. >> >> >>> >>> > One difficulty, though, is that the relevant citations in >>> scikit-learn >>> > estimators often depends on constructor options. For example, in >>> > LinearSVC, the paper to cite is not the same whether we use >>> dual=True or >>> > dual=False, penalty="l1" or penalty="l2", etc. >>> >>> That is already partially handled, e.g. >>> >>> >>> https://github.com/duecredit/duecredit/blob/master/duecredit/injections/mod_scipy.py#L134 >>> injector.add('scipy.cluster.hierarchy', 'linkage', BibTeX(""" >>> @article{ward1963hierarchical, >>> title={Hierarchical grouping to optimize an objective function}, >>> author={Ward Jr, Joe H}, >>> journal={Journal of the American statistical association}, >>> volume={58}, >>> number={301}, >>> pages={236--244}, >>> year={1963}, >>> publisher={Taylor \& Francis} >>> }"""), >>> conditions={(1, 'method'): {'ward'}}, >>> description="Ward hierarchical clustering", >>> min_version='0.4.3', >>> tags=['reference']) >>> >>> says to reference that publication only if method='ward' to the linkage >>> call. >>> Similarly I can decorate __init__. But thus partially -- since I don't >>> want to >>> cite merely if __init__ was called, I would like to cite only if actual >>> computation has happened, so it should also be conditioned on some >>> methods of >>> the class being called... We will look into supporting that. >>> >> >> Ideally the citation annotations should be as concise as possible. For >> the BibTeX part, I would prefer to reference an external BibTeX file. For >> example, the file could sit next to __ini__.py at the project root. >> >> Mathieu >> >> >> ------------------------------------------------------------------------------ >> >> _______________________________________________ >> Scikit-learn-general mailing list >> Scikit-learn-general@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/scikit-learn-general >> >> > > > ------------------------------------------------------------------------------ > > _______________________________________________ > Scikit-learn-general mailing list > Scikit-learn-general@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/scikit-learn-general > >
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