On 04/19/2018 06:29 PM, Leonardo Collado Torres wrote: Hi Valerie,
Thanks for the reply and the doc changes ^^. I added a few short replies below. Best, Leo On Thu, Apr 19, 2018 at 4:49 PM, Obenchain, Valerie <valerie.obench...@roswellpark.org><mailto:valerie.obench...@roswellpark.org> wrote: Hi Leo, Great feedback, thanks. On 04/19/2018 08:04 AM, Leonardo Collado Torres wrote: This looks great Valerie, congrats to all of those involved in making the web app! I hope that it leads to less questions/confusion. Here are some minor comments, mostly about including some links/docs. * Under the which packages we have access to, I noticed that it's not showing the experimental data packages. I guess that's because they are not in git yet (right?). All software, data experiment and workflow packages are in git. You should be able to see all associated with your account. One of the goals of the app was to make package access more transparent which could help explain why a `push` or `fetch` failed. We match your email to the username we have in the gitolite packages.conf file. When I search packages.conf I see your username on these packages: ~/git.bioconductor.org/admin/gitolite-admin >grep -B 1 'master.*collado-torres' conf/packages.conf repo packages/sva RW master = j.leek l.collado-torres -- repo packages/derfinder RW master = l.collado-torres -- repo packages/derfinderHelper RW master = l.collado-torres -- repo packages/derfinderPlot RW master = l.collado-torres -- repo packages/regionReport RW master = l.collado-torres -- repo packages/recount RW master = l.collado-torres -- repo packages/recountWorkflow RW master = l.collado-torres If there is a package missing that you should have access to let us know. Also let me know if this differs from the list you saw when you were logged in. This matches what I saw when I logged in. The only data package I've contributed to Bioc is derfinderData. We haven't had to make any changes to it in a long time as you can see at https://github.com/leekgroup/derfinderData. I don't know if that played a role in the package not showing up on m list. My email is there on the DESCRIPTION file though https://github.com/leekgroup/derfinderData/blob/master/DESCRIPTION#L7. You're right, not all experimental data packages show up in this list because they aren't all in the packages.conf config file. The reason is historical. When we first started the experimental data packages we viewed them as static or at least changing very little. SVN write access wasn't given unless the maintainer explicitly requested it. When we transitioned from SVN to Git, only packages with write access by a specific maintainer were transferred to the config file. After the next release we'll go through the data packages and make sure they're all in packages.conf with write access by the maintainer in DESCRIPTION. * Under add an ssh key, the second option mentions "username.keys files in your GitHub account". I hadn't heard about this before. Is that file made automatically by editing https://github.com/settings/keys? If there's a website that describes this in more detail, I suggest including a link to it. Yes, this is the standard keys file and is edited through github account settings. A link has been added to the github HOWTO page: https://help.github.com/articles/adding-a-new-ssh-key-to-your-github-account/ I like the change, it's much clearer! * I've seen several emails where Nitesh and others ask developers to check their SSH key using ssh -T g...@git.bioconductor.org<mailto:g...@git.bioconductor.org>, so maybe adding a reminder there would be good. Actually, maybe just include a link to http://bioconductor.org/developers/how-to/git/faq/ from this new site. By the way, that last link is not directly available from http://bioconductor.org/developers/ (I think), I had to go to http://bioconductor.org/developers/how-to/git/ then "See other frequently asked questions." I've added a link to the FAQ. Nice! By the way, I just noticed a typo on http://bioconductor.org/developers/how-to/git/faq/ bullet 17: git clone g...@git.bioconductor.org:packagse/<mailto:g...@git.bioconductor.org:packagse/><myPackage> packagse -> packages Fixed (may take 20 minutes to propagate). Since the FAQ is specific to version control it probably still belongs under developers -> Git Source Control. Maybe we could change the title from 'See other frequently asked questions' to just 'FAQ' or something more obvious. Ok! To me it's really the "Git / ssh Bioc FAQ". I'll pass that on, thanks. Val * Typo: "Which packages do I have acces to?" --> access Fixed. Valerie Best, Leo On Wed, Apr 18, 2018 at 12:53 PM, Obenchain, Valerie <valerie.obench...@roswellpark.org><mailto:valerie.obench...@roswellpark.org> wrote: My last email didn't make it through to the list - trying again ... The Web App for managing SSH keys is now available at https://git.bioconductor.org/BiocCredentials/ Accounts have been created for all package maintainers. Note the central identifier, i.e., how you login is your email. This email was taken from the DESCRIPTION of your package or the Google Sheet if you registered a key there. When you first visit the App you'll need to activate your account. An activation link will be sent to your email. Once your account is activated you can login. Trying to login without activation will lead to an error. Let us know if you have any questions or problems. This email message may contain legally privileged and/or confidential information. 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