Re: Worth packaging bio_assembly_refinement?
Hi Afif, first of all thanks for looking at Circlator, which was on my list as well :) >> I'm looking into packaging Circlator, which depends on the Sanger >> program bio_assembly_refinement. Looking into it, I'm wondering whether >> this is a tool that will just get folded into circlator eventually. Do >> you think it's worth packaging it separately? > > I should add that the alternative would be to bundle it into the > circlator package as a multi-orig tarball. The question is better > rephrased as whether it's worth packaging bio_assembly_refinement > /separately/. Yes, I noticed the dependency on bio_assembly_refinement as well and I was’t sure what part of it is really needed, since it’s description sounded a bit similar to Circlator itself. I didn’t have the time yet to look into it in more detail yet. I have cc’d Martin Hunt, the Circlator author, and Nishadi de Silva, the bio_assembly_refinement author, on this email and they might be able to say more. Many thanks, Sascha
Re: RFS: python-typing
On Mon, Mar 07, 2016 at 06:33:24PM +0100, Michael Crusoe wrote: > Thanks! > > git+ssh://git.debian.org/git/debian-med/python-typing.git As you wrote in the ITP, are you still interested in this? FYI, I'm a supporter of starting dropping python2 bits when possible; removing py2 will be painful enough also without more new packages... -- regards, Mattia Rizzolo GPG Key: 66AE 2B4A FCCF 3F52 DA18 4D18 4B04 3FCD B944 4540 .''`. more about me: http://mapreri.org : :' : Launchpad user: https://launchpad.net/~mapreri `. `'` Debian QA page: https://qa.debian.org/developer.php?login=mattia `- signature.asc Description: PGP signature
Bug#817056: ITP: python-typing -- Type Hints for Python
See https://www.python.org/dev/peps/pep-0484/#suggested-syntax-for-python-2-7-and-straddling-code Pe 8 mar. 2016 06:24, "Brian May"a scris: > "Michael R. Crusoe" writes: > > > This is a backport of the standard library typing module to Python > > versions older than 3.5. > > Not sure what the point of this is; doesn't typing hinting require PEP > 3107, which isn't in Python 2.x? > -- > Brian May >
Re: Worth packaging bio_assembly_refinement?
On الإثنين 7 آذار 2016 21:48, Afif Elghraoui wrote: > Hi, Sascha, > I'm looking into packaging Circlator, which depends on the Sanger > program bio_assembly_refinement. Looking into it, I'm wondering whether > this is a tool that will just get folded into circlator eventually. Do > you think it's worth packaging it separately? > I should add that the alternative would be to bundle it into the circlator package as a multi-orig tarball. The question is better rephrased as whether it's worth packaging bio_assembly_refinement /separately/. Thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name
Worth packaging bio_assembly_refinement?
Hi, Sascha, I'm looking into packaging Circlator, which depends on the Sanger program bio_assembly_refinement. Looking into it, I'm wondering whether this is a tool that will just get folded into circlator eventually. Do you think it's worth packaging it separately? Thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name
Bug#817056: ITP: python-typing -- Type Hints for Python
"Michael R. Crusoe"writes: > This is a backport of the standard library typing module to Python > versions older than 3.5. Not sure what the point of this is; doesn't typing hinting require PEP 3107, which isn't in Python 2.x? -- Brian May
Re: Can "PDB" license be considered free ?
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On Mon, Mar 07, 2016 at 04:38:55PM -0600, Don Armstrong wrote: > On Mon, 07 Mar 2016, Peter Rice wrote: > > The conclusion was that scientific data (SwissProt, PDB, etc.) are > > scientific facts and it is not reasonable to require permission to > > change them. > > This isn't true; there are loads of reasons to change sequences and > structural models of proteins. Protein sequences are just based on > references which have inaccuracies and do not represent ancestral > sequences or the true variation present in real populations; in my lab > we modify UniProt sequences and redistribute those modifications in > publications all of the time. Note that this text only says that if you modify things, you're required to change the name. In other words, they are protecting the terminology, so when you use a certain code, everyone is always talking about the same thing. This is a very reasonable thing to require; without it, the database would be much less useful. > All of that said, because PDB and UniProt files are not works of > authorship, they likely do not qualify for copyright protection in the > US, so the licensing terms can largely be ignored. However, that may not > be true of other jurisdictions. The text that was quoted doesn't really talk about IP; it just says that it isn't about that: as a user, you must find the license and abide by it. This is annoying (because it means you must find those licenses before you know if you can use the data), but I don't blame them. On the other hand, if you are correct (I have no idea about this data) that it is not copyrightable, then you also don't need a license, so that solves that problem. The question would probably have been better asked on -legal though, so I'm sending it there. For those reading there without seeing the thread before, it starts here: https://lists.debian.org/debian-devel/2016/03/msg00091.html Thanks, Bas -BEGIN PGP SIGNATURE- Version: GnuPG v1 iQIcBAEBAgAGBQJW3kjSAAoJEJzRfVgHwHE6vUIP/2c9sCzBFH7L2muFotxeDFnB 9A3TRZbTfRX05Ik9FZyFSZr/zE/XEHA/aMogvEu1sB3Z1XpyEEx5Q+kvDiB4lqL7 6h5g5LTXWKIzdPDNciwCMSVqpBtPfuOJ11qEGPRZbsPVfXLjoSh+bjarSmYltun+ TlcpkOwcpSuevJI+BVxDKz5L59DcNqp/0Dh8kj2ek+dzDWmOiyJ1azqx6DptR3KB uZ0gKi7LRsOjy6f6Q/bKs5Ym0it4CoVIBYuABAxFV6YsoP7qeUQqhd9gWqw9jAuV 6JTxnyLBwEZHJ640PAvTl/Q7W7+LL3aRQvqwCUfLUKtvAVywR5mBzTn5DrY0r8SO ms0bftWq2DFezqctn8WYMvseIjkq4k2/Bt2e59dIi8d8ytj79dE5+raYl/cYYNUt 71shP7r+41zRb23ZguRVHcpOIBMu5UlhHpXR8PWhUhDF4mhnPDBXZGmvrZTTgVjy iOHC3g7EtFg5NZTdMeeKs7NyKtT9ZLLDbwqiVmKSTPgIGywSyVLpR2X+5S0pek3C ybtvSBifRQd8m/nhveQiQFAhNIpJHjFimdzTObKonKVAGAhag4TlvO9dak921CZK TWii3txJnPmTMAaR/LGY8VjlcJjwN3J1UZTvB/0HTVGnLEUjSxtN0f6BQo1KXVSV TDvMAD6wYUfdt9Ik9krj =bzir -END PGP SIGNATURE-
Re: Can "PDB" license be considered free ?
On Mon, 07 Mar 2016, Peter Rice wrote: > We had this discussion some years back about SwissProt protein > sequence entries included as test data in EMBOSS. We also have PDB > files in the EMBOSS test data. > > The conclusion was that scientific data (SwissProt, PDB, etc.) are > scientific facts and it is not reasonable to require permission to > change them. This isn't true; there are loads of reasons to change sequences and structural models of proteins. Protein sequences are just based on references which have inaccuracies and do not represent ancestral sequences or the true variation present in real populations; in my lab we modify UniProt sequences and redistribute those modifications in publications all of the time. PDB files are also just the current model of a particular crystallization of a particular set of molecules. It's pretty standard practice to modify them using simulations to account for different binding partners and assemblies. [I've published the PDB files containing these modifications, for example.] All of that said, because PDB and UniProt files are not works of authorship, they likely do not qualify for copyright protection in the US, so the licensing terms can largely be ignored. However, that may not be true of other jurisdictions. -- Don Armstrong http://www.donarmstrong.com It is easier to build strong children than to repair broken men. -- Frederick Douglass
Bug#817056: ITP: python-typing -- Type Hints for Python
That was my plan. Though I just realized that I don't need this if I switch to building only the Python 3 version of schema-salad-tool so I am likely to close this ITP. The package is at git+ssh://git.debian.org/git/debian-med/python-typing.git if anyone is interested. On Mon, Mar 7, 2016 at 7:38 PM, Scott Kittermanwrote: > On Monday, March 07, 2016 09:01:30 AM Michael R. Crusoe wrote: > > Package: wnpp > > Severity: wishlist > > Owner: Debian Med team > > > > * Package name: python-typing > > Version : 3.5.0.1 > > Upstream Author : Guido van Rossum, Jukka Lehtosalo, Łukasz Langa > > * URL : > > https://docs.python.org/3.5/library/typing.html * License : > Python > > 2.0 > > Programming Lang: Python > > Description : Type Hints for Python > > > > This is a backport of the standard library typing module to Python > > versions older than 3.5. > > > > Typing defines a standard notation for Python function and variable > > type annotations. The notation can be used for documenting code in a > > concise, standard format, and it has been designed to also be used by > > static and runtime type checkers, static analyzers, IDEs and other > > tools. > > > > This is a new dependency for python-schema-salad, and will be for any > other > > Py2/Py3 package that contains typing hints. It will be maintained by the > > Debian-Med team but I'm happy to hand it over to other interested > parties. > > Please only package this for python(2). We are in the process of dropping > python3.4, so a python3 package isn't needed. > > Scott K > -- Michael R. Crusoe CWL Community Engineer cru...@ucdavis.edu Common Workflow Language projectUniversity of California, Davis https://impactstory.org/MichaelRCrusoe http://twitter.com/biocrusoe
Re: Can "PDB" license be considered free ?
Hi, > * The user assumes all responsibility for insuring that intellectual > property claims associated with any data set deposited in the PDB > archive are honored. It should be understood that the PDB data files > do not contain any information on intellectual property claims with > the exception in some cases of a reference for a patent involving the > structure. I.e. on one hand the user would have to hunt down the IP information to see whether she can use the pdb files at all, and on the other had, there seem to be parts that are covered by patents for which a user would probably need to acquire an additional license. Would this not conflict with the DFSG 7? "The rights attached to the program must apply to all to whom the program is redistributed without the need for execution of an additional license by those parties." Best, Gert https://www.debian.org/social_contract
Re: Can "PDB" license be considered free ?
Hi Riley, On 07/03/2016 19:20, Riley Baird wrote: The distribution of modified PDB data including the records HEADER, CAVEAT, REVDAT, SPRSDE, DBREF, SEQADV, and MODRES in PDB format and their mmCIF and XML equivalents is not allowed. I'm not sure what the PDB format is, so I might be wrong, but my intuition is that trying to stop people from distributing data in a certain file format would be non-free. We had this discussion some years back about SwissProt protein sequence entries included as test data in EMBOSS. We also have PDB files in the EMBOSS test data. The conclusion was that scientific data (SwissProt, PDB, etc.) are scientific facts and it is not reasonable to require permission to change them. The license says you may not alter the entries in the PDB database (text file) and redistribute it in any of its original formats - because PDB releases must only come from the curators of the database. It may help to consider an equivalent in another field. Imagine an open source package that included a copy of the Declaration of Independence. It would not be reasonable to insist on permission to change the text, for example to add a phrase from Animal Farm ... "but some are more equal than others" Hope that helps, Peter Rice
Re: Can "PDB" license be considered free ?
> The distribution of modified PDB data including the records HEADER, CAVEAT, > REVDAT, SPRSDE, DBREF, SEQADV, and MODRES in PDB format and their mmCIF and > XML equivalents is not allowed. I'm not sure what the PDB format is, so I might be wrong, but my intuition is that trying to stop people from distributing data in a certain file format would be non-free. pgpMKPjhDxFW5.pgp Description: PGP signature
Bug#817056: ITP: python-typing -- Type Hints for Python
On Monday, March 07, 2016 09:01:30 AM Michael R. Crusoe wrote: > Package: wnpp > Severity: wishlist > Owner: Debian Med team> > * Package name: python-typing > Version : 3.5.0.1 > Upstream Author : Guido van Rossum, Jukka Lehtosalo, Łukasz Langa > * URL : > https://docs.python.org/3.5/library/typing.html * License : Python > 2.0 > Programming Lang: Python > Description : Type Hints for Python > > This is a backport of the standard library typing module to Python > versions older than 3.5. > > Typing defines a standard notation for Python function and variable > type annotations. The notation can be used for documenting code in a > concise, standard format, and it has been designed to also be used by > static and runtime type checkers, static analyzers, IDEs and other > tools. > > This is a new dependency for python-schema-salad, and will be for any other > Py2/Py3 package that contains typing hints. It will be maintained by the > Debian-Med team but I'm happy to hand it over to other interested parties. Please only package this for python(2). We are in the process of dropping python3.4, so a python3 package isn't needed. Scott K
Re: Can "PDB" license be considered free ?
Alex Mestiashviliwrites: > I am going to package a software with pdb files in the test suite and > I wonder if the license below can be considered free. For reference in the discussion and for later reference, it helps to have the license text directly in a message. > ftp://ftp.wwpdb.org/pub/pdb/advisory.txt At the time of this message, that URL responds with the following text: = ADVISORY NOTICE FOR USE OF THE PDB ARCHIVE By using the materials available in this archive, the user agrees to abide by the following conditions: * The archival data files in the PDB archive are made freely available to all users. Data files within the archive may be redistributed in original form without restriction. Redistribution of modified data files using the same file name as is on the FTP server is prohibited. The rules for file names are detailed at http://www.wwpdb.org/wwpdb_charter.html. * Data files containing PDB content may incorporate the PDB 4-letter entry name (e.g. 1ABC) in standard PDB records only if they are exactly the same as what is residing in the PDB archive. This does not prevent databases from including PDB entry_id's as cross-references where it is clear that they refer to the PDB archive. PDB records refer to the standard PDB format. The distribution of modified PDB data including the records HEADER, CAVEAT, REVDAT, SPRSDE, DBREF, SEQADV, and MODRES in PDB format and their mmCIF and XML equivalents is not allowed. * The user assumes all responsibility for insuring that intellectual property claims associated with any data set deposited in the PDB archive are honored. It should be understood that the PDB data files do not contain any information on intellectual property claims with the exception in some cases of a reference for a patent involving the structure. * Any opinion, findings, and conclusions expressed in the PDB archive by the authors/contributors do not necessarily reflect the views of the wwPDB. * The data in the PDB archive are provided on an "as is" basis. The wwPDB nor its comprising institutions cannot be held liable to any party for direct, indirect, special, incidental, or consequential damages, including lost profits, arising from the use of PDB materials. * Resources on this site are provided without warranty of any kind, either expressed or implied. This includes but is not limited to merchantability or fitness for a particular purpose. The institutions managing this site make no representation that these resources will not infringe any patent or other proprietary right. = -- \ “Facts do not cease to exist because they are ignored.” —Aldous | `\Huxley | _o__) | Ben Finney
Can "PDB" license be considered free ?
Hi All, I am going to package a software with pdb files in the test suite and I wonder if the license below can be considered free. ftp://ftp.wwpdb.org/pub/pdb/advisory.txt http://www.rcsb.org/pdb/static.do?p=general_information/about_pdb/policies_references.html Thank you, Alex
RFS: python-typing
Thanks! git+ssh://git.debian.org/git/debian-med/python-typing.git -- Michael R. Crusoe
Bug#817056: ITP: python-typing -- Type Hints for Python
Package: wnpp Severity: wishlist Owner: Debian Med team* Package name: python-typing Version : 3.5.0.1 Upstream Author : Guido van Rossum, Jukka Lehtosalo, Łukasz Langa * URL : https://docs.python.org/3.5/library/typing.html * License : Python 2.0 Programming Lang: Python Description : Type Hints for Python This is a backport of the standard library typing module to Python versions older than 3.5. Typing defines a standard notation for Python function and variable type annotations. The notation can be used for documenting code in a concise, standard format, and it has been designed to also be used by static and runtime type checkers, static analyzers, IDEs and other tools. This is a new dependency for python-schema-salad, and will be for any other Py2/Py3 package that contains typing hints. It will be maintained by the Debian-Med team but I'm happy to hand it over to other interested parties.
Re: bamtools_2.4.0+dfsg-4_amd64.changes REJECTED
Thanks! On Mon, Mar 7, 2016 at 8:26 AM Mattia Rizzolowrote: > uploaded. > > On Mon, Mar 7, 2016 at 6:55 AM Michael Crusoe > wrote: > >> My apologies; I've updated Git >> >> On Sun, Mar 6, 2016 at 10:50 AM, Afif Elghraoui >> wrote: >> >>> Hi, Michael, >>> >>> On السبت 5 آذار 2016 11:22, Michael R. Crusoe wrote: >>> Can I get bamtools 2.4.0+dfsg-4 sponsored? I split the library documentation into a separate package so I can't upload on my own. >>> I don't see the latest changes in git. Could you push what you have? >>> >>> Thanks and regards >>> Afif >>> >>> -- >>> Afif Elghraoui | عفيف الغراوي >>> http://afif.ghraoui.name >>> >>> >>