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juliusbeezer : git   24

Inside eLife: Forking software used in eLife papers to GitHub | eLife
In line with eLife's aims to encourage more open and reproducible science, we have created a GitHub account to track new software or a new algorithm when they are central to the submission and to make sure that the right version of the code that was used within an article persists. When a paper is accepted in eLife, if the authors have included a link to code within GitHub, a copy of the authors' repository is "forked" (cloned) to the eLife GitHub account, with a clear link to the authors' original repository. This means that we can keep an archive of the version of the code that was issued at the point of publication and that the authors, as well as the community, can continue to build upon the work in their own repositories. If authors have used another version control system, a copy of the code will also be added into the eLife GitHub account.

Jan Willem de Gee (University Medical Center Hamburg-Eppendorf), one of the first eLife authors to have code included within eLife’s GitHub account, said: "I think it's really great the way eLife promotes accessibility, transparency and reproducibility; it was our pleasure to contribute."
sciencepublishing  code  coding  git 
april 2017 by juliusbeezer
Mango: Git completely decentralised — Medium
Git was ahead of its time. In the last 5 years decentralised storage and consensus systems (blockchains) have gained significant footing and we are able to accomplish the decentralisation goal of Git entirely. There is no need for central providers. There is no single point of failure.

Welcome Mango, which combines Ethereum with IPFS or Swarm as a backend for Git.
git  publishing 
july 2016 by juliusbeezer
The Plain Person’s Guide to Plain Text Social Science
I recommend you write prose and code using a good text editor; analyze quantitative data with R or Stata; minimize error by storing your work in a simple format (plain text is best), and make a habit of documenting what you’ve done. For data analysis, consider using a format like RMarkdown and tools like Knitr to make your work more easily reproducible for your future self. Use Pandoc to turn your plain-text documents into PDF, HTML, or Word files to share with others. Keep your projects in a version control system. Back everything up regularly. Make your computer work for you by automating as many of these steps as you can.

To help you get started, I provide a drop-in set of useful defaults to get started with Emacs (a powerful, free text-editor). I share some templates and style files that can get you quickly from plain text to various output formats. And I point to several alternatives, because no humane person should recommend Emacs without presenting some other options as well.
Two ongoing computing revolutions are tending to pull in opposite directions. On one side, the mobile, cloud-centered, touch-screen, phone-or-tablet model has brought powerful computing to more people than ever before. This revolution is the one everyone is talking about, because it is happening on a huge scale and is where all the money is. In practice it puts single-purpose applications in the foreground and hides from the user both the workings of the operating system and (especially) the structure of the file system where items are stored and moved around.

On the other side, open-source tools for plain-text coding, data analysis, and writing are also better and more accessible than they have ever been. This has happened on a smaller scale than the first revolution, of course. But still, these tools really have revolutionized the availability and practice of data analysis and scientific computing generally. They continue to do so, too, as people work to make them better at everything from slurping up data on the web to presenting it there. These tools mostly work by gluing together separate, specialized widgets into a reproducible workflow. They are “bitty” or granular because the process of data analysis is that way as well. They do much less to hide the operating system layer—instead they often directly mesh with it—and they also presuppose a working knowledge of the file system underpinning the organization of the things the researcher is using or creating, from data files to code to figures and final papers.
writing  tools  text_tools  sciencepublishing  scholarly  opensource  coding  git 
march 2016 by juliusbeezer
Upload files to your repositories · GitHub
You’ll soon be able to skip the command line and upload files directly to your repositories without having to leave the browser. Repository uploads will be rolling out over the next few days, so if you can’t upload yet, sit tight.
git  tools 
february 2016 by juliusbeezer
Ry’s Git Tutorial - RyPress
Ry’s Git Tutorial is a complete introduction to distributed version control with a focus on practical command line usage. We explain Git’s robust branching, merging, and collaboration capabilities from the ground up, so prior experience with centralized systems like SVN or CVS is not required.
git  tools 
november 2015 by juliusbeezer
Editors’ Choice: Introducing Git-Lit
One of the more interesting Git corpus projects I became aware of following this discussion is GITenberg. Led by Seth Woodworth, the project scrapes a text from Project Gutenberg, initializes a git repository for it, adds README and CONTRIBUTING files generated from the text’s metadata, and uploads the resulting repository to GitHub. They have gitified around 43,000 works this way. The project also converts Project Gutenberg vanilla plain text into ASCIIDOC—a good example of this is the GITenberg edition of The Adventures of Huckleberry Finn. This is an amazingly ambitious project that holds the promise of wide-ranging applications for editing, versioning, and disseminating literature.

One such application might lie with the 68,000 digital texts recently created by the British Library. James Baker, a digital curator of the British Library, left a comment on my original post, suggesting that the method I describe might be used to parse and post the Library’s texts. He sent me a few sample texts of the ALTO XML documents that the Stanford Literary Lab had used. I adapted some of the GITenberg code to read these texts, generate README files for them, and turn them into GitHub repositories. I’m provisionally calling this project Git-Lit.
digitalhumanities  corpus  git 
september 2015 by juliusbeezer
Frequently Yelled Statements |
"This is censorship!"

"No, it’s not. I’m not preventing you from speaking. I just don’t have to listen."

Twitter tool that widens out block to social media entourage of certain key accounts, with whitelist reinclusion on appeal.
twitter  attention  opensource  git 
july 2015 by juliusbeezer
Mercurial vs. Git vs. Bazaar: The aftermath | experimentalworks
About version control systems (including bazaar, 'bzr' to many)
"Over the last years, the version control system community has fought, what some people would call the “VCS war”...When in 2005 both Git and Mercurial were released and Bazaar followed shortly after, the fight who is the best system of the three started. While early Mercurial versions seemed to be much easier to use than Git, Git was already used in the Linux kernel and built up a strong opinion. Things were even till 2008 Github launched and changed the OpenSource world and is what people would consider Git’s “killer app”. Mercurial’s equivalent Bitbucket never reached the popularity of Github...In the end there isn’t much to say about Bazaar. It development slowly deceased and it’s been widely considered the big looser of the VCS wars. Bazaar is dead.
git  bzr 
may 2015 by juliusbeezer
The Fork Factor: an academic impact factor based on reuse. | Authorea
A versioning system, such as Authorea and GitHub, empowers forking of peer-reviewed research data, allowing a colleague of yours to further develop it in a new direction. Forking inherits the history of the work and preserves the value chain of science (i.e., who did what). In other words, forking in science means standing on the shoulder of giants (or soon to be giants) and is equivalent to citing someone else’s work but in a functional manner. Whether it is a “negative” result (we like to call it non-confirmatory result) or not, publishing your peer reviewed research in Authorea will promote forking of your data.
citation  git  sciencepublishing 
march 2015 by juliusbeezer
Jekyll • Simple, blog-aware, static sites
No more databases, comment moderation, or pesky updates to install—just your content.
cms  blogs  tools  software  web  cool  git 
february 2015 by juliusbeezer
About | SciGit Blog
SciGit is an online platform that helps scientists collaborate on documents easily. SciGit’s goals are to help scientists track changes made to their documents, not require any alteration of workflow or environment for it to be used, and provide easy to use publishing tools with peer review. SciGit provides three services:

A website where you can browse projects, including their history, team members, and files.
A desktop client that provides a simple, Dropbox-like interface where you drag and drop files into a folder to have them automatically cloud-synced.
A publishing service on the website with integrated crowdsourced peer review.
git  tools  text_tools  sciencepublishing 
january 2015 by juliusbeezer
Beginning Git and Github for Linux Users |
changes are checksummed, so you are assured of data integrity, and always being able to reverse changes.

Git is very fast, because your work is all done on your local PC and then pushed to a remote repository. This makes everything you do totally safe, because nothing affects the remote repo until you push changes to it. And even then you have one more failsafe: branches. Git's branching system is brilliant. Create a branch from your master branch, perform all manner of awful experiments, and then nuke it or push it upstream. When it's upstream other contributors can work on it, or you can create a pull request to have it reviewed, and then after it passes muster merge it into the master branch.

So what if, after all this caution, it still blows up the master branch? No worries, because you can revert your merge.
git  tools 
november 2014 by juliusbeezer by GITenberg
Serving books the way we serve code has its benefits. We can use Git and the Github Api, to do things like automatically generate epub and pdf files whenever there is a change stored in Git.
ebooks  git  tools 
november 2014 by juliusbeezer
Authorea | The Fork Factor: an academic impact factor based on reuse.
A versioning system, such as Authorea and GitHub, empowers forking of peer-reviewed research data, allowing a colleague of yours to further develop it in a new direction. Forking inherits the history of the work and preserves the value chain of science (i.e., who did what). In other words, forking in science means standing on the shoulder of giants (or soon to be giants) and is equivalent to citing someone else’s work but in a functional manner. Whether it is a “negative” result (we like to call it non-confirmatory result) or not, publishing your peer reviewed research in Authorea will promote forking of your data. (To learn how we plan to implement peer review in the system, please stay tuned for future posts on this blog.)
citation  git  sciencepublishing  scholarly 
october 2014 by juliusbeezer by GITenberg
$ git commit Alice-in-Wonderland.txt -m "Down the Rabbit Hole..."

Project GITenberg is a Free and Open, Collaborative, Trackable and Scriptable digital library. It leverages the power of the Git version control system and the collaborative potential of Github to make books more open.

Currently there are over 43,000 books in GITenberg.
ebooks  git  free 
september 2014 by juliusbeezer
pyradio player
handy commandline radio player. Fast!
radio  sound  python  freesoftware  git 
march 2014 by juliusbeezer
Using git in my writing workflow
Martin Eve shares his git setup for versioning docs
git  text_tools 
august 2013 by juliusbeezer
A Call for Scholarly Markdown | Gobbledygook
Blog post and productive discussion re: publishing tools for collaborative authoring, LaTeX/html/Word/Markdown/PDF. All a mess. All to play for.
scholarly  tools  git  sciencepublishing 
june 2013 by juliusbeezer
open science manuscripts and “web-native” scholarship | kay
further pushing the boundaries of review and scholarly publishing by further breaking apart and repackaging the components to arguably present something more useful, accessible and reproducible.
Carl has been thinking for a while on how to best package an open science manuscript for maximum reuse – doing some really cool things to help make his work accessible and reproducible that transcends current traditional publishing submission systems.
Now, not everything Carl has detailed here may resonate with those who are unfamiliar with GitHub (heck, I’m still learning), but I think he touches on some neat hacks on the system that I’d personally like to see taken further.
scholarly  sciencepublishing  git  openaccess  peerreview 
june 2013 by juliusbeezer
GitHub for Cats
Very basic starter guide for github
git  software  tools 
march 2013 by juliusbeezer
GitHub needs to take open source seriously | Open Source Software - InfoWorld
Apparently the kids are so post-FOSS, probably because they are just bored to death with the licensing wars.
git  freesoftware  dccomment 
november 2012 by juliusbeezer
Weekend Project: Using git to Manage Config Files |
Typically I use Dropbox to sync my files for work, but Dropbox isn't a good solution for files under /etc or .config type files under your home directory. You could whip up some hacks to compensate for this, but the other problem is that Dropbox isn't a good solution when you want to pull the config files onto a new machine — and only those files.
git  sysadmin  linux  mutt  et_cetera 
april 2011 by juliusbeezer

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