Code and data management with Git. Department of Human Genetics Center for Human and Clinical Genetics

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1 Code and data management with Git Introduction to Version Control Mihai Lefter Department of Human Genetics Center for Human and Clinical Genetics

2 Course Outline Introduction Git basics Practical 1 The git commit graph Practical 2 Lunch break Colaboration: remote repositories Practical 3 1/29 Code and data management with Git

3 Introduction Outline What is version control? Definition General features Step by step example Distributed repositories Why to use/not use version control? Git Web-based remotes GitLab vs GitHub 2/29 Code and data management with Git

4 Definition The management of changes to documents, computer programs, large web sites, and other collections of information. Wikipedia A system that records changes to a file or set of files over time so that you can recall specific versions later. 3/29 Code and data management with Git

5 General features Keep track of your files in an orderly manner. Hide old versions. Easily access old versions. Check the differences between current and older versions. Enables collaboration. Record who made changes and when. 4/29 Code and data management with Git

6 Step by step run_tool.sh #! /bin/bash tool src target -ratio 100 5/29 Code and data management with Git

7 Step by step Initialize VCS Commit the file Commit id (generated by git) 1d438b8 Add script run_tool.sh #! /bin/bash tool src target -ratio 100 Commit message (specified by the user) 6/29 Code and data management with Git

8 Step by step Edit the existing file run_tool.sh #! /bin/bash tool src target -ratio 100 -config settings.json 1d438b8 H settings.json { "ratio": 100 } Create new file 7/29 Code and data management with Git

9 Step by step Commit Commit id (generated by git) run_tool.sh #! /bin/bash tool src target -config settings.json 2f5458a Make script configurable. Commit message (specified by the user) settings.json { "ratio": 100 } 1d438b8 8/29 Code and data management with Git

10 Step by step Repository 2f5458a H my_project.vcs run_script.sh settings.sh 1d438b8 9/29 Code and data management with Git

11 Step by step Repository 12f82a1 H my_project.vcs license.txt README.md run_script.sh notes.md settings.sh 2f5458a Time 1d438b8 10/29 Code and data management with Git

12 Step by step 7a45299 H settings.json 7a f82a { "ratio": 100, "gentrap": { "expression_measures": [ "fragments_per_gene", "cufflinks_strict" ], "call_variants": false, "aligner": "gsnap", "gsnap": { "exe": "/usr/local/bin/gsnap", "npaths": 1, "threads": 8 } } } Time 1d438b8 11/29 Code and data management with Git

13 Step by step 7a45299 H 12f82a1 settings.json V1 Time 1d438b { "ratio": 100, "gentrap": { "expression_measures": [ "fragments_per_gene", "cufflinks_strict" ], "strand_protocol": "dutp", "call_variants": false } } 12/29 Code and data management with Git

14 Step by step 7a45299 H 12f82a1 vs settings.json 7 additions and 2 deletions... 5 "fragments_per_gene", 6 "cufflinks_strict" 7 ], - "strand_protocol": "dutp", - "call_variants": false 8 + "call_variants": false, 9 + "aligner": "gsnap", 10 + "gsnap": { 11 + "exe": "/usr/local/bin/gsnap", 12 + "npaths": 1, 13 + "threads": } 15 } 16 }... Time 1d438b8 13/29 Code and data management with Git

15 Step by step Retrieve Initialize previous VCS file version 33e9cd8 H 7a f82a1 settings.json Time 14/29 Code and data management with Git

16 Step by step 33e9cd8 H 7a45299 Rollback entire project 12f82a1 H Time 15/29 Code and data management with Git

17 Local repository file Working copy 16/29 Code and data management with Git

18 Distributed repositories Server Server file Working copy file Working copy file Working copy file Working copy 17/29 Code and data management with Git

19 Distributed repositories Server Server Remote for all other repositories Computer A Computer D file Working copy file Working copy Remote for repositories on computer B and D. file Working copy Computer B file Working copy Computer C 18/29 Code and data management with Git

20 Why should I use it? For a single user: Revert files to a previous state. Revert the entire project back to a previous state. Review changes made over time. Backup. 19/29 Code and data management with Git

21 Why should I use it? For a single user: Revert files to a previous state. Revert the entire project back to a previous state. Review changes made over time. Backup. For multiple users: A reliable way to share files between people/computers. Allow multiple people working on the same project at the same time. Conflict resolution. See who made which changes at which time. 19/29 Code and data management with Git

22 Why should I not use it? I have my own system. 20/29 Code and data management with Git

23 Why should I not use it? I have my own system. my_project backup old backup old working working.thisone working old second.version old 20/29 Code and data management with Git

24 Why should I not use it? A list of common excuses: I have my own system. It is too much work. I am the only one working on this project. This code will not be used by anyone else. The bugs can be tracked forever.... my_project backup old backup old working working.thisone working old second.version old 21/29 Code and data management with Git

25 Why should I not use it? A list of common excuses: I have my own system. It is too much work. I am the only one working on this project. This code will not be used by anyone else. The bugs can be tracked forever.... Eventually leading to: I m too busy rewriting the code I accidentally deleted. 22/29 Code and data management with Git

26 Git The name Git (n): A person who is deemed to be despicable or contemptible. WordNet. I m an egotistical bastard, and I name all my projects after myself. First Linux, now git. Linus Torvalds. 23/29 Code and data management with Git

27 Git History Designed to replace the commercial package BitKeeper. Speed. Simple design. Strong support for non-linear development Thousands of parallel branches. Fully distributed. Able to handle large projects like the Linux kernel efficiently. 24/29 Code and data management with Git

28 Git Installation Linux sudo apt-get install git (Ubuntu) sudo yum install git (Fedora) Windows git-scm.com/download/win Mac git-scm.com/mac Once installed you can check Git version: git --version 25/29 Code and data management with Git

29 Remotes Web-based Server Central Server Repository Wrappers for the server repository: - GitHub - BitBucket - GitLab /29 Code and data management with Git

30 Remotes Web-based Server Central Repository Labels Milestones Projects Issues Groups To-Dos Wiki Members 27/29 Code and data management with Git

31 Remotes Web-based GitHub: Free for public repositories. Paid for private ones. Hosting provided for free. GitLab: Self hosting - own installation. No hosting provided. Basic features for free. Paid advanced ones. 28/29 Code and data management with Git

32 Acknowledgements Martijn Vermaat Wibowo Arindrarto Szymon Kie lbasa Jeroen Laros

Overview. 1. Install git and create a Github account 2. What is git? 3. How does git work? 4. What is GitHub? 5. Quick example using git and GitHub

Overview. 1. Install git and create a Github account 2. What is git? 3. How does git work? 4. What is GitHub? 5. Quick example using git and GitHub Git 101: Overview 1. Install git and create a Github account 2. What is git? 3. How does git work? 4. What is GitHub? 5. Quick example using git and GitHub Github icon 1 Install git and a create GitHub