[Biopython] Progress toward BSD license for BioPython?

[Peter Cock]

One of the scripts gives this output:

$ python license_report.py
...
[x] Bio done
[x] Bio/Affy done
[x] Bio/Align done
[x] Bio/AlignIO done
[x] Bio/Alphabet done
[x] Bio/Application done
[ ] Bio/Blast 5 of 6 files (83.3%) done
[ ] Bio/CAPS 1 files
[ ] Bio/Cluster 1 files
[ ] Bio/Compass 1 files
[ ] Bio/Crystal 1 files
[x] Bio/Data done
[x] Bio/Emboss done
[ ] Bio/Entrez 2 files
[ ] Bio/ExPASy 6 files
[ ] Bio/FSSP 1 of 3 files (33.3%) done
[ ] Bio/GenBank 4 files
[ ] Bio/Geo 2 files
[x] Bio/Graphics done
[ ] Bio/HMM 1 of 5 files (20.0%) done
[ ] Bio/KDTree 2 files
[ ] Bio/KEGG 9 files
[ ] Bio/Medline 1 files
[ ] Bio/NMR 3 files
[ ] Bio/Nexus 5 files
[ ] Bio/PDB 3 of 33 files (9.1%) done
[ ] Bio/Pathway 4 files
[ ] Bio/Phylo 29 files
[ ] Bio/PopGen 3 of 7 files (42.9%) done
[ ] Bio/Restriction 4 files
[x] Bio/SCOP done
[ ] Bio/SVDSuperimposer 1 files
[ ] Bio/SearchIO 31 of 32 files (96.9%) done
[ ] Bio/SeqIO 14 of 19 files (73.7%) done
[x] Bio/SeqUtils done
[ ] Bio/Sequencing 7 files
[ ] Bio/Statistics 1 of 2 files (50.0%) done
[ ] Bio/SubsMat 3 files
[ ] Bio/SwissProt 1 of 2 files (50.0%) done
[x] Bio/TogoWS done
[x] Bio/UniGene done
[x] Bio/UniProt done
[x] Bio/Wise done
[x] Bio/_py3k done
[ ] Bio/codonalign 5 files
[ ] Bio/motifs 4 of 15 files (26.7%) done
[x] Bio/phenotype done
[x] BioSQL done
Overall files: 150 old, 166 new (52.4%), 1 other, 317 in total
Overall LOC: 85950 old, 65841 new (43.3%), 148 other, 151939 in total

e.g. Looking at Bio/GenBank as an example, two of the files look OK
(so I could change them given a quiet moment) but we're missing five
names on Scanner and __init__.py right now (which might be a case
of tracking down their existing consent, or mean sending out emails).

Peter


On Tue, Aug 13, 2019 at 4:05 PM Peter Cock <p.j.a.cock at googlemail.com> wrote:
>
> Hello Brook,
>
> We're over half way in terms of the Bio/ and BioSQL/ files,
> I have been prioritising that over Tests/ etc),  see slide 6
> on the "Biopython Project Update 2019" talk recently in
> Basel
>
> https://doi.org/10.7490/f1000research.1117119.1
>
> Main issue:
>
> https://github.com/biopython/biopython/issues/898
>
> Currently open sub-issues include:
>
> https://github.com/biopython/biopython/issues/1878
> https://github.com/biopython/biopython/issues/1610
>
> I have some semi-automated scripts with associated data files
> mapping emails (GDPR sensitive data so I'm not sharing that
> openly) to GitHub accounts to a URL for their consent which
> have helped a lot with this (but still need to review the commit
> comments as especially in the CVS days commits were often
> done on a contributor's behalf).
>
> There are several former contributors we're not yet been
> able to contact about this... e.g. for Bio.PDB.
>
> Peter
>
> On Tue, Aug 13, 2019 at 3:55 PM Brook Milligan <brook at nmsu.edu> wrote:
> >
> > I understand that BioPython is moving toward relicensing everything under the BSD license.  What is the current status of that effort?  When is it likely to be completed?
> >
> > Cheers,
> > Brook
> >
> >
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