Re: [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 
g...@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  on behalf of Kasper Daniel 
Hansen 
Sent: Monday, May 7, 2018 4:56:43 AM
To: Morgan, Martin
Cc: bioc-devel@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 g...@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.mor...@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 
>> 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.tur...@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 
>
 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
> g...@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@r-project.org mailing list
> 

Re: [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 g...@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.mor...@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 
>> 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.tur...@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 
>
 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
> g...@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@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>



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

[Martin Morgan]

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 
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 

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
g...@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

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

[Turaga, Nitesh]

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  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
> g...@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@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel



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

[Peter Hickey]

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 
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 
> 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
> > g...@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@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
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Re: [Bioc-devel] Switch to SSH protocol for git clone instructions on package landing pages?

[Joris Meys]

Using SSH will only work when they have a public key on the git server
registered. Otherwise they will get the dreaded "Please make sure you have
the correct access rights and the repository exists" error message. The
same happens when I forget to add the correct key to my pageant. In my
humble opinion it doesn't pay off to make it more difficult for general
users to download the source code in order to make the process more simple
for your developers.

Cheers
Joris

On Sun, Apr 29, 2018 at 4:03 PM, Peter Hickey 
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
> g...@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@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>



-- 
Joris Meys
Statistical consultant

Department of Data Analysis and Mathematical Modelling
Ghent University
Coupure Links 653, B-9000 Gent (Belgium)


tel: +32 (0)9 264 61 79
---
Biowiskundedagen 2017-2018
http://www.biowiskundedagen.ugent.be/

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

[Peter Hickey]

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
g...@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

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