Re: [Python-Dev] Official citation for Python

2018-09-10 Thread Gerald Klix 
Wouldn't it make sense to ask the developers of the other Python 
implementations too?


Just my 0.02€,


Gerald



Am 09.09.2018 um 21:43 schrieb Jacqueline Kazil:

The PSF has received a few inquiries asking the question — “How do I cite
Python?”So, I am reaching out to you all to figure this out.

(For those that don’t know my background, I have been in academia for a bit
as a Ph.D student and have worked at the Library of Congress writing code
to process Marc records , among
other things.)

IMHO the citation for Python should be decided upon by the Python
developers and should live somewhere on the site.

Two questions to be answered…

1. What format should it take?
2. Where does it live on the site?

To help frame the first one, I quickly wrote this up —
https://docs.google.com/document/d/1R0mo8EYVIPNkmNBImpcZTbk0e78T2oU71ioX5NvVTvY/edit#

tldr; Summary of possibilities…

1. Article for one citation (1 DOI, generated by the publication)
2. No article (many DOIs — one for each major version through Zenodo
 (or similar service))

Discuss.

-Jackie

Jackie Kazil
Board of Directors, PSF



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Re: [Python-Dev] AES decryption/encryption support for zipfile

2018-09-10 Thread Gregory P. Smith 
On Wed, Sep 5, 2018 at 8:24 AM 大野隆弘  wrote:

> Sorry, allow me to ask one more thing.
> If I want to use AES in zipfile module, what the good way to implement?
>

If anyone wants to add support for additional zipfile encryption/decryption
methods, there are a few options:

(a) Fork the stdlib zipfile module and create one that supports the
additional features, posting it on PyPI.  That way it could have
dependencies on other third party libraries such as
https://cryptography.io/en/latest/.

(b) Figure out the set of hooks necessary for the zipfile module to support
pluggable encryption as an API so that external libraries could provide
encryption support to it.

(c) Write a library that wraps an existing third party zip file creation
tool or library instead of reusing the stdlib zipfile code.

Option (a) is probably easiest to start with... but creates a maintenance
burden of keeping that module up to date.

Option (b) will be more challenging, the zipfile API modifications and
their tests would need merging and would only show up in a future CPython
release (3.8 today).

Option (c) is entirely different, but would get you out of the business of
dealing with the zipfile spec itself.

Unstated option (n): write something entirely new not based on existing
code or tools.  An entirely different form of challenge.

In general the existing stdlib zipfile module code is not loved by any of
us who have had to work on it in the past decade, it is a hairy mess (but
does work, so it's got that going for it).  Granted, the zip format as a
specification vs the many implementations out there to be compatible with
is also what I'd call an underspecified mess...

-gps


> Thanks and Regards,
> -
> Takahiro Ono
>
> 2018年9月5日(水) 23:01 大野隆弘 :
>
>> Christian,  really appreciated the details. I understood.
>>
>> Is wrapper library like ssl module with openssl on platform also not good
>> idea?
>> My intention is not re-invention but single standard way as standard
>> library.
>>
>> If I can read past discussion somewhere, it's also appreciated
>>
>> Thanks and Regards,
>> Takahiro Ono
>>
>>
>>
>>
>> 2018年9月5日(水) 1:48 Christian Heimes :
>>
>>> On 2018-09-04 16:37, 大野隆弘 wrote:
>>> > Dear all,
>>> >
>>> > Have we tried cipher implementation includes AES as a standard library
>>> > in the past?
>>> > https://docs.python.org/3.6/library/crypto.html
>>> >
>>> > if possible I want to try to implement AES because famous 3rd party
>>> > library is not maintained and general cipher programs should be used
>>> for
>>> > multiple purpose.Though the implementation is tough,  I believe this
>>> > should be worth to it.
>>> > In my case, I want to use AES implementation for zipfile module.
>>>
>>> strong -1
>>>
>>> The Python standard library doesn't contain any encryption, signing, and
>>> other cryptographic algorithms for multiple reasons. The only exception
>>> from the rule are hashing algorithms and HMAC construct. There are legal
>>> implications like export restrictions. Crypto is just too hard to get
>>> right and we don't want to give the user additional rope. We already had
>>> a very lengthy and exhausting discussion for the secrets module. That
>>> module just provides a user-friendly interface to CPRNG.
>>>
>>> By the way, AES by itself is a useless to borderline dangerous
>>> algorithm. It must be embedded within additional layers like block mode,
>>> authenticated encryption / MAC, and more. There isn't a single correct
>>> answer for block mode and AD algorithm, too. It highly depends on the
>>> problem space. While GCM AEAD mode is good choice for network
>>> communication, it can be a pretty bad idea for persistent storage.
>>>
>>> There is one excellent Python library with high level and low level
>>> cryptographic algorithms: http://cryptography.readthedocs.io/ . It's t
>>>
>>> Regards,
>>> Christian
>>>
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Re: [Python-Dev] Official citation for Python

2018-09-10 Thread Brett Cannon 
On Sun, 9 Sep 2018 at 20:55 Terry Reedy  wrote:

> On 9/9/2018 11:39 PM, Jacqueline Kazil wrote:
> > Terry -- For clarification, the format question was not a style
> > question. It was a reference to the one versus many that I wrote in the
> > explainer.
>
> I don't know what you mean by this.
>
> > Yes... there are many prescribed formats already. That is the easy part.
>
> Different publications use different citation formats.  We cannot
> dictate which format an author or publication uses.  We could, and I
> think should, suggest the content of the different fields that go into
> the various formats.  And we could give examples of citing, say, the
> Reference Manual, in the most common formats.
>

What we can suggest, though, is what the information should be and that's
what Jackie is initially asking about, i.e. do we want a single reference
for the language that is version-agnostic or one for each Python release?

My vote is a single reference and leave it up to the person referencing to
clarify the version they are using. Seems the simplest to maintain
long-term.

-Brett


>
> > On Sun, Sep 9, 2018 at 11:33 PM Terry Reedy  > > wrote:
> >
> > On 9/9/2018 3:43 PM, Jacqueline Kazil wrote:
> >  > The PSF has received a few inquiries asking the
> question —
> >  > “How do I cite Python?”So, I am reaching out to you all to figure
> > this out.
> >  >
> >  > (For those that don’t know my background, I have been in academia
> > for a
> >  > bit as a Ph.D student and have worked at the Library of Congress
> > writing
> >  > code to process Marc records
> > ,
> >  > among other things.)
> >  >
> >  > IMHO the citation for Python should be decided upon by the Python
> >  > developers and should live somewhere on the site.
>
> The PSF is the publisher.  It seems that you might be more competent to
> make some of the decisions than are we developers, who have mostly left
> academia some time ago.
>
> >  > Two questions to be answered…
> >  >
> >  >  1. What format should it take?
> >
> > There are by now formats for citing web documents.  I presume style
> > guides now include such.  Try a current version of the Chicago
> > Manual of
> > Style.  (not sure of exact title).  I will ask a university professor
> > who should know more than I.
> >
> >  >  2. Where does it live on the site?
> >
> > On https://bugs.python.org/issue26597, I suggested the Copyright
> page.
>
> To make the answer more visible,
>
> > I now think a link to 'Citing these Documents' on
> > https://docs.python.org/3/
> > would be even better.
>
> tjr
>
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Re: [Python-Dev] Official citation for Python

2018-09-10 Thread Chris Barker via Python-Dev 
I"d like ot know what thee citations are expected to be used for?

i.e. -- usually, academic papers have a collection of citiations to
acknowledge where you got an idea, or fact, or  It serves both to
jusstify something and make it clear that it is not your own idea (i.e. not
pagerism).

in the enclosed doc, it says:

"""
*If someone publishes research, they will cite the exact major version that
was used, so if someone was trying to recreate the research they would be
able to do it.*
*"""*
That is about reproducible results, which is really a different thing than
the usual citations. In that case, you would want some way to identify the
actual source code (cPython version 3.6.4, and probably a url to the source
-- but how long might that last???) And you would need to post your own
source anyway.

Again, regular citation is about acknowledging the source of an idea or
fact, or something of that nature. I can imagine a paper about computer
language design or some such might need to reference Python -- in which
case it should reference the Language Reference, I suppose. Maybe we should
have a DOI for each version of the standard docs.

But "I wrote some code in Python to produce these statistics" -- does that
need a citation? If so, maybe that would take a different form.

Anyway, hard to make this decision without some idea how the citation is
intended to be used.

-CHB




On Mon, Sep 10, 2018 at 9:51 AM, Gerald Klix  wrote:

> Wouldn't it make sense to ask the developers of the other Python
> implementations too?
>
> Just my 0.02€,
>
>
> Gerald
>
>
>
> Am 09.09.2018 um 21:43 schrieb Jacqueline Kazil:
>
>> The PSF has received a few inquiries asking the question — “How do I cite
>> Python?”So, I am reaching out to you all to figure this out.
>>
>> (For those that don’t know my background, I have been in academia for a
>> bit
>> as a Ph.D student and have worked at the Library of Congress writing code
>> to process Marc records , among
>> other things.)
>>
>> IMHO the citation for Python should be decided upon by the Python
>> developers and should live somewhere on the site.
>>
>> Two questions to be answered…
>>
>> 1. What format should it take?
>> 2. Where does it live on the site?
>>
>> To help frame the first one, I quickly wrote this up —
>> https://docs.google.com/document/d/1R0mo8EYVIPNkmNBImpcZTbk0
>> e78T2oU71ioX5NvVTvY/edit#
>>
>> tldr; Summary of possibilities…
>>
>> 1. Article for one citation (1 DOI, generated by the publication)
>> 2. No article (many DOIs — one for each major version through Zenodo
>>  (or similar service))
>>
>> Discuss.
>>
>> -Jackie
>>
>> Jackie Kazil
>> Board of Directors, PSF
>>
>>
>>
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>> Unsubscribe: https://mail.python.org/mailman/options/python-dev/python.
>> 00%40klix.ch
>>
>
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> barker%40noaa.gov
>



-- 

Christopher Barker, Ph.D.
Oceanographer

Emergency Response Division
NOAA/NOS/OR&R(206) 526-6959   voice
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[Python-Dev] 3.7.1 and 3.6.7 Releases Coming Soon

2018-09-10 Thread Ned Deily 
I have updated the schedules for the next maintenance releases of Python 3.7.x 
and 3.6.x.  My original plan had been to get 3.7.1, the first 3.7 maintenance 
release, out by the end of July.  It was solely my fault that that did not 
happen so I hope you'll accept my apologies; I will try to not let it happen 
again.  I have now scheduled a 3.7.1 release candidate and rescheduled the 
3.6.7 release candidate for 2018-09-18, about a week from today, and 3.7.1 
final and 3.6.7 final for 2018-09-28.  That allows us to take advantage of 
fixes generated at the Core Developers sprint taking place this week.

Please review any open issues you are working on or are interested in and try 
to get them merged in to the 3.7 and/or 3.6 branches soon - by the beginning of 
next week at the latest.  As usual, if there are any issues you believe need to 
be addressed prior to these releases, please ensure there are open issues for 
them in the bug tracker (bugs.python.org) and that their priorities are set 
accordingly (e.g. "release blocker").

Thanks for your support!
--Ned

--
  Ned Deily
  n...@python.org -- []

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Re: [Python-Dev] Official citation for Python

2018-09-10 Thread Steven D'Aprano 
On Mon, Sep 10, 2018 at 09:25:29PM +0200, Chris Barker via Python-Dev wrote:
> I"d like ot know what thee citations are expected to be used for?
> 
> i.e. -- usually, academic papers have a collection of citiations to
> acknowledge where you got an idea, or fact, or  It serves both to
> jusstify something and make it clear that it is not your own idea (i.e. not
> pagerism).

[
> That is about reproducible results, which is really a different thing than
> the usual citations.

I don't think it is. I think you are seeing a distinction that is not 
there. If citations were just about acknowledgement, we could say "I got 
this idea from Bob" and be done with it. Citations are about identifying 
the *exact* source so that anyone can reproduce the given ideas by 
checking not just "Bob" but the specific page number of a specific 
edition of a specific work.

So the requirement for precision is no different between papers and 
software, and the academic standards for citing software already take 
that into account. There are challenges with software, to be sure -- 
code is much more ephemeral, there may be literally hundreds of 
authors, etc. But in principle, the kinds of information needed to 
cite a software package is known. The major citation styles already 
include this. When you are using a specific style, this page:

https://openresearchsoftware.metajnl.com/about/

suggests a few formats, depending on how you got access to the software.

The bottom line is, we don't have to guess what information to provide. 
People like Jacqueline can tell us what they need, and we'll just fill 
in the values.

The people citing Python know what information they need, we just have 
to help them get it. I think that the best way to do that is to provide 
the correct information in a single place, in a single, standard format, 
and let them choose the appropriate citation style for their 
publication.

Jackie, do I have that right?



-- 
Steve
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Re: [Python-Dev] Official citation for Python

2018-09-10 Thread Wes Turner 
I also see reproducibility and citation graphs as distinct concepts.

If it's reproducibility you're after, bibliographic citations are very
unlikely to enable someone else to assemble an identical build environment
from which the same conclusion should be repeatably derivable.

A ScholarlyArticle can be reproducible with no citations whatsoever.
A ScholarlyArticle may very likely have many citations and still be
woefully unreproducible.

This citation doesn't contain a URL, but still isn't quite useless (while
the paper is excellent); because there's at least a DOI string:

Sandve GK, Nekrutenko A, Taylor J, Hovig E (2013) Ten Simple Rules for
Reproducible Computational Research. PLoS Comput Biol 9(10): e1003285.
doi:10.1371/journal.pcbi.1003285

> Rule 3: Archive the Exact Versions of All External Programs Used

mybinder.org builds Jupyter containers from git repositories that contain
config files with repo2docker.

https://repo2docker.readthedocs.io/en/latest/config_files.html#configuration-files
"""
Dockerfile
environment.yml
requirements.txt
REQUIRE
install.R
apt.txt
setup.py
postBuild
runtime.txt
"""

Specifying the exact version of Python (and what package it was installed
from and/or what URL the source was obtained and built from) is no
substitute for hashes of the 'pinned' versions of said artifacts.

# includes the python version
$ conda env export -f environment.yml

# these do not include the python version
$ pip freeze -r requirements.txt --all
$ pipenv lock # > Pipfile.lock
$ pipenv sync # < Pipfile.lock

Uploading a built container or VM image to e.g. Docker Hub / GitLab
Container Registry / Vagrant Cloud is another way to ensure that research
findings are reproducible.
- Dockerfile, docker-compose.yml
- Vagrantfile

> Rule 4: Version Control All Custom Scripts

https://mozillascience.github.io/code-research-object/ (FigShare + GitHub
=> DOI citation URI)

https://guides.github.com/activities/citable-code/ (Zenodo + GitHub => DOI
citation URI)

...

Is it necessary to cite Python (or all packages) if you're not building a
derivative of Python or said packages?

It's definitely a good idea to "Archive the Exact Versions of All External
Programs Used"; but IDK that those are best represented with bibliographic
citations. Really, a link to the Homepage, Source, Docs, and Wikipedia page
are probably more helpful to a reviewer that's not familiar with and wants
to help support by linking dereferenceable URLs and https://5stardata.info.

While out of scope and OT, it's worth mentioning that search engines index
https://schema.org/Dataset metadata; which is helpful for data reuse and
autodiscovering requisite premises for the argument presented in a
https://schema.org/ScholarlyArticle .

A citation for each MAJ.MIN.PATCH revision of CPython (and/or other
excellent packages) might be a bit much.

On Monday, September 10, 2018, Steven D'Aprano  wrote:

> On Mon, Sep 10, 2018 at 09:25:29PM +0200, Chris Barker via Python-Dev
> wrote:
> > I"d like ot know what thee citations are expected to be used for?
> >
> > i.e. -- usually, academic papers have a collection of citiations to
> > acknowledge where you got an idea, or fact, or  It serves both to
> > jusstify something and make it clear that it is not your own idea (i.e.
> not
> > pagerism).
>
> [
> > That is about reproducible results, which is really a different thing
> than
> > the usual citations.
>
> I don't think it is. I think you are seeing a distinction that is not
> there. If citations were just about acknowledgement, we could say "I got
> this idea from Bob" and be done with it. Citations are about identifying
> the *exact* source so that anyone can reproduce the given ideas by
> checking not just "Bob" but the specific page number of a specific
> edition of a specific work.
>
> So the requirement for precision is no different between papers and
> software, and the academic standards for citing software already take
> that into account. There are challenges with software, to be sure --
> code is much more ephemeral, there may be literally hundreds of
> authors, etc. But in principle, the kinds of information needed to
> cite a software package is known. The major citation styles already
> include this. When you are using a specific style, this page:
>
> https://openresearchsoftware.metajnl.com/about/
>
> suggests a few formats, depending on how you got access to the software.
>
> The bottom line is, we don't have to guess what information to provide.
> People like Jacqueline can tell us what they need, and we'll just fill
> in the values.
>
> The people citing Python know what information they need, we just have
> to help them get it. I think that the best way to do that is to provide
> the correct information in a single place, in a single, standard format,
> and let them choose the appropriate citation style for their
> publication.
>
> Jackie, do I have that right?
>
>
>
> --
> Steve
> ___
>