Git - computational workshop on version control

![Solo Manzanita_SRUK LOGO OFICIAL](https://hackmd.io/_uploads/ryASgZlnp.jpg) # Git and GitHub ## Computational workshop on version control Diego Alonso Álvarez and Sandra Álvarez Carretero --- ## Tips and instructions 1. Code along - you will learn more! :computer: 2. Ask questions - any time! :question: 3. Follow on the resources (see next page) :books: --- ## Resources - [Fundamentals of Git/GitHub](https://imperialcollegelondon.github.io/introductory_grad_school_git_course/) - [Further Git/GitHub for collaboration](https://imperialcollegelondon.github.io/intermediate_grad_school_git_course/) - [Referencing and citing content](https://docs.github.com/en/repositories/archiving-a-github-repository/referencing-and-citing-content) --- ## Outline - What is version control and why does it matter? - The publication workflow - Fundamentals of `git` - Sharing code/data in GitHub - Make your work citable - Other applications using GitHub --- ## What is version control and why does it matter? ----  ### What is version control? - A system for managing your work (not necessarily just code) which records snapshots of the current state of a set of files - Provides a historical record for your project - Reports “diffs” that describe the file changes between snapshots ----  ### What can go wrong without version control? | A library | Some code that uses it | |-----------|------------------------| | mylib-1.2.4_18.tgz | code_CP_10.8.07.tgz | | mylib-1.2.4_27.tgz | code_CP_17.5.07.tgz | | mylib-1.2.4_29.tgz | code_CP_23.8.07_final.tgz | - Lots of manual work to manage these files - Names are uninformative - Which versions are compatible with each other? - Difficult to find changes between versions ----  ### What can help version control with? - Mistakes happen - diagnose and fix them - Working on different things - Collaboration - Reproducibility --- ## The publication workflow How do we ensure that our code/data is **findable**? -- [**The FAIR Guiding Principles for scientific data management and stewardship**. Sci Data 3, 160018 (2016)](https://doi.org/10.1038/sdata.2016.18) -- [**Introducing the FAIR Principles for research software**. Sci Data 9, 622 (2022)](https://doi.org/10.1038/s41597-022-01710-x) ---- `commit` :arrow_forward: `tag` :arrow_forward: Release :arrow_forward: DOI ---- `dkfo344` :arrow_forward: `v0.2.5` :arrow_forward: `v0.2.5` + metadata :arrow_forward: 10.5281/zenodo.1185315 ---- `git` :arrow_forward: `git` :arrow_forward: GitHub :arrow_forward: Zenodo ---- | Concept | Looks like | Handled by | | -------- | -------- | -------- | | commit | dkfo344 | git | | tag | v0.2.5 | git | | Release | v0.2.5 + metadata | GitHub | | DOI | 10.5281/zenodo.1185315 | Zenodo | ---- ### A case study [Solcore](https://github.com/qpv-research-group/solcore5) --- ## Fundamentals of `git` ----  ### Configuring git ```bash $ git config --global user.name "FIRST_NAME LAST_NAME" $ git config --global user.email "email@example.com" ``` - info added to each `commit` (what?) - accountability (blame!) - finding who to ask for help ---- ### This is what will be going on <img src="https://imperialcollegelondon.github.io/introductory_grad_school_git_course/fig/git_areas.png" alt="image" width="700" height="auto"> Using `git` is like taking a plane... 🤔 ----  ### Initialising a repository Normal directory → version controlled one! - Running: ```bash $ git init ``` - Results in: ```output Initialized empty Git repository in /your/directory/.git ``` Ready to do version control! ----  ### Getting information ```bash $ git status ``` Information of files modified and staged for commit, among other. ```bash $ git log $ git log --one-line ``` Information about the history of the repository. ----  ### In more detail: `git add` ```bash $ git add file1 file2... ``` - Adds modified files/folders in your working directory to the **staging area**. - Only the staging area is committed to history. - It is an **explicit process**. - To remove things from the staging area: ```bash $ git restore --staged file1 file2 ``` ----  ### In more detail: `git commit` ```bash $ git commit -m "Some short message about the commit." ``` - Adds the staging area to the **history**. - Contains the changes made since previous point. - Create a commit id - or commit hash. - It is an **explicit process**. - To undo the last commit (safe way): ```bash $ git reset --soft HEAD^ ``` ---- ### Now this makes sense, right? <img src="https://imperialcollegelondon.github.io/introductory_grad_school_git_course/fig/git_areas.png" alt="image" width="700" height="auto"> Right?? 🤨 --- --- ### Wrap up - TBC --- ### Thank you! ![SRUK LOGO OFICIAL](https://hackmd.io/_uploads/HJ9zMZe3p.jpg) [www.sruk.org.uk](https://www.sruk.org.uk)

{"title":"Git - computational workshop on version control ","breaks":true,"description":"Version control might be an alien concept for many people, but it is indeed at the heart of reproducible research, fundamental in software development and, ultimately, enables a good practice to keep your data organised. It becomes even more relevant when multiple researchers collaborate on a particular project and it is necessary to know who changed what, when they did that, and, potentially, to be able to easily revert those changes. When developing software (e.g., just a small script to process your data, a more serious application for your research team, or a professional-level program), not using some form of version control is just unthinkable. \n\nAs a continuation of the SRUK/CERU Research Computing Workshop series, we will focus on teaching the basics of the main tool used for version control: Git. In addition, you will learn how to use GitHub, an online repository with which you can collaboratively work on a project while keeping all the benefits of version control.","showTags":"true","image":"https://hackmd.io/_uploads/HkE3wGesa.jpg","contributors":"[{\"id\":\"78c365e8-c501-47e6-ba3b-ef7939b5e127\",\"add\":7483,\"del\":4371}]","slideOptions":"{\"transition\":\"fade\",\"theme\":\"white\",\"parallaxBackgroundImage\":\"https://hackmd.io/_uploads/r1eUkWghp.jpg\"}"}