[Biopython-dev] Bug#746484: file not distributable

[Peter Cock]

Hi Andreas,

Are you specifically asking about Biopython 1.63 here? I think you
can reasonable exclude this DTD file (and any others under the
Bio/Entrez/DTD file). Biopython 1.63 will warn if they are missing
but attempt to download them automatically.

We're looking at dropping all the NCBI Entrez related DTD files,
since the next Biopython release (v1.64) will automatically download
AND cache them - see recent discussion, e.g.

http://lists.open-bio.org/pipermail/biopython-dev/2014-March/011205.html

We haven't actually removed the files on GitHub yet, but this
might be an incentive to do so.

Thanks,

Peter

On Wed, Apr 30, 2014 at 2:17 PM, Andreas Tille <tille at debian.org> wrote:
> Hello,
>
> our ftpmaster has detected an issue with one of the DTDs which are
> distributed with BioPython source.
>
> I can confirm that after applying the following patch
>
>
> --- a/Bio/Entrez/DTDs/modules.ent
> +++ b/Bio/Entrez/DTDs/modules.ent
> @@ -350,13 +350,6 @@ Version  Reason/Occasion
>  "mathmlsetup.ent"                                                    >
>
>
> -<!--                    MATHML 2.0 QUALIFIED NAMES                 -->
> -<!ENTITY % mathml-qname.mod
> -                        PUBLIC
> -"-//W3C//ENTITIES MathML 2.0 Qualified Names 1.0//EN"
> -"mathml/mathml2-qname-1.mod"                                         >
> -
> -
>  <!--                    MATHML 2.0 DTD                             -->
>  <!ENTITY % mathml.dtd   PUBLIC
>  "-//W3C//DTD MathML 2.0//EN"
>
>
> the file in question can be removed from the archive without breaking
> the build (including the test suite).  I would like to suggest to drop
> the file in question from your distribution tarball in case my analysis
> that it is not needed is correct.
>
> Kind regards
>
>          Andreas.
>
> On Wed, Apr 30, 2014 at 02:25:09PM +0200, Thorsten Alteholz wrote:
>> Package: python-biopython
>> Version: 1.63-2
>> Severity: serious
>> User: alteholz at debian.org
>> Usertags: ftp
>> X-Debbugs-CC: ftpmaster at ftp-master.debian.org
>> thanks
>>
>> Dear Maintainer,
>>
>> according to:
>>  http://www.w3.org/Consortium/Legal/2002/copyright-documents-20021231
>> the file
>>  biopython-1.63\Bio\Entrez\DTDs\mathml2-qname-1.mod
>> may not be modified and such this file is not distributable in main.
>>
>>   Thorsten
>>
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>>
>
> --
> http://fam-tille.de