[Bioc-devel] Switch to SSH protocol for git clone instructions on package landing pages?

[Shepherd, Lori]

I made updates to the landing pages to have both commands.

For example:


Source Repository: git clone https://git.bioconductor.org/packages/bsseq
Source Repository (Developer Access): git clone git at git.bioconductor.org:packages/bsseq

We didn't want simply Source Repository (https) and Source Repository (ssh) as with our experience with users, the naive user doesn't know the difference between ssh and https and as Nitesh pointed out only developers of the package will have RW access via ssh.

If you think something else is more appropriate please let me know and I can make further changes.  The website should reflect the new landing pages within the hour.



Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Kasper Daniel Hansen <kasperdanielhansen at gmail.com>
Sent: Monday, May 7, 2018 4:56:43 AM
To: Morgan, Martin
Cc: bioc-devel at r-project.org
Subject: Re: [Bioc-devel] Switch to SSH protocol for git clone instructions on package landing pages?

I think I am formulating myself pretty badly.

If I want to get the Bioconductor git address for a package I gott o (say)
  https://www.bioconductor.org/packages/bsseq

At the bottom of this page, under the heading "Package Archive" I see the
source repository (The Bioconductor git pointer, which is different from
our devel repos on Github).  This is currently

    Source Repository: git clone https://git.bioconductor.org/packages/bsseq

I am lazy.  I like cut'and'paste.  I would like this to be changed to

    Source Repository (https): git clone
https://git.bioconductor.org/packages/bsseq
    Source Repository (ssh): git clone git at git.bioconductor.org:
packages/bsseq

This is a small thing, but there are subtle differences wrt : and / in the
way the two protocols are written.  On Github there is a drop-down menu
giving me the choice of how to clone the repos, which I find very useful.

Best,
Kasper







On Mon, May 7, 2018 at 12:22 AM, Martin Morgan <
martin.morgan at roswellpark.org> wrote:

>
>
> On 04/30/2018 08:17 AM, Kasper Daniel Hansen wrote:
>
>> Still, it is convenient for some of us to have copy+paste code on the
>> landing page.  How about having both https and ssh?
>>
>
> Supporting https:// would require account and password management. I
> guess we have moved closer to that than originally anticipated, but we were
> trying to avoid getting involved in that. Also, we had not anticipated that
> some organizations would block ssh activity. At the moment and for the
> foreseeable future, https is read-only.
>
> Martin
>
>
>
>> On Sun, Apr 29, 2018 at 8:57 AM, Peter Hickey <peter.hickey at gmail.com>
>> wrote:
>>
>> Ah, thanks both Joris and Nitesh. I didn't appreciate that SSH access is
>>> limited to those with a public key registered on the git server.
>>>
>>> On Sun, 29 Apr 2018 at 11:50 Turaga, Nitesh <
>>> Nitesh.Turaga at roswellpark.org
>>>
>>>>
>>>> wrote:
>>>
>>> Hi Pete,
>>>>
>>>> For developers there is no reason not to use the SSH protocol. But there
>>>> are many people who�d like to clone the repo and look at it on their
>>>>
>>> local
>>>
>>>> machine.
>>>>
>>>> Take for example packages which are not maintained on both the
>>>> bioconductor server and Github. For these packages, a good way for users
>>>>
>>> to
>>>
>>>> browse the source code on their local machine is using the HTTPS
>>>>
>>> protocol,
>>>
>>>> since they will not have access to download it via SSH ( you need
>>>> permissions to do this).
>>>>
>>>> We always advocate developers to only use SSH though. For everyone else,
>>>> HTTPS is the best option.
>>>>
>>>> Best,
>>>>
>>>> Nitesh
>>>>
>>>> On Apr 29, 2018, at 10:03 AM, Peter Hickey <peter.hickey at gmail.com>
>>>>>
>>>> wrote:
>>>>
>>>>>
>>>>> The one-liner on the package landing page describing how to check out
>>>>> a package from the git repo uses HTTPS rather than ssh, e.g.:
>>>>>
>>>>> # From https://bioconductor.org/packages/bsseq/
>>>>> git clone https://git.bioconductor.org/packages/bsseq
>>>>>
>>>>> However, as a developer we should be using the SSH protocol
>>>>> (https://bioconductor.org/developers/how-to/git/faq/).
>>>>>
>>>>> Is there any reason not to use the SSH protocol (i.e. git clone
>>>>> git at git.bioconductor.org:packages/bsseq) in the instructions given on
>>>>> the landing page? It seems to me an unnecessary source of friction,
>>>>> particularly for new developers who will end up with the dreaded
>>>>> "fatal: remote error: FATAL: W any packages/myPackage nobody DENIED by
>>>>> fallthru (or you mis-spelled the reponame)" error message if they
>>>>> don't know to switch protocols
>>>>> (https://bioconductor.org/developers/how-to/git/faq/)
>>>>>
>>>>> Cheers,
>>>>> Pete
>>>>>
>>>>> _______________________________________________
>>>>> Bioc-devel at r-project.org mailing list
>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>>
>>>>
>>>>
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