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

[Kasper Daniel Hansen]

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
>>>>>
>>>>
>>>>
>>>>
>>>> This email message may contain legally privileged and/or confidential
>>>> information.  If you are not the intended recipient(s), or the employee
>>>>
>>> or
>>>
>>>> agent responsible for the delivery of this message to the intended
>>>> recipient(s), you are hereby notified that any disclosure, copying,
>>>> distribution, or use of this email message is prohibited.  If you have
>>>> received this message in error, please notify the sender immediately by
>>>> e-mail and delete this email message from your computer. Thank you.
>>>>
>>>
>>>          [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
>>> Bioc-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>>
>>         [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>>
>
> This email message may contain legally privileged and/or confidential
> information.  If you are not the intended recipient(s), or the employee or
> agent responsible for the delivery of this message to the intended
> recipient(s), you are hereby notified that any disclosure, copying,
> distribution, or use of this email message is prohibited.  If you have
> received this message in error, please notify the sender immediately by
> e-mail and delete this email message from your computer. Thank you.
>

	[[alternative HTML version deleted]]