diff --git a/.nojekyll b/.nojekyll index 102ffe35..67f095b8 100644 --- a/.nojekyll +++ b/.nojekyll @@ -1 +1 @@ -a417f2da \ No newline at end of file +8504c46c \ No newline at end of file diff --git a/develop/03_DOD.html b/develop/03_DOD.html index d3885aeb..dbdd388e 100644 --- a/develop/03_DOD.html +++ b/develop/03_DOD.html @@ -955,23 +955,23 @@

Naming conventions

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- diff --git a/develop/05_VC.html b/develop/05_VC.html index 672ce4dd..1cdef34b 100644 --- a/develop/05_VC.html +++ b/develop/05_VC.html @@ -337,7 +337,7 @@

Version control

if you’re interested in delving deeper, explore our course on Git and GitHub.

Alternatively, here are some examples and online resources to expand your understanding:

diff --git a/develop/examples/NGS_metadata.html b/develop/examples/NGS_metadata.html index 32735c45..09d59988 100644 --- a/develop/examples/NGS_metadata.html +++ b/develop/examples/NGS_metadata.html @@ -266,23 +266,23 @@

Sample metadata fie
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- @@ -851,23 +851,23 @@

Project metadata f
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- @@ -1345,23 +1345,23 @@

Assay metadata field
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- @@ -1949,23 +1949,23 @@

Assay metadata field
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- diff --git a/develop/practical_workshop.html b/develop/practical_workshop.html index 6df90548..4108abb8 100644 --- a/develop/practical_workshop.html +++ b/develop/practical_workshop.html @@ -545,23 +545,23 @@

Assay metadata field
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- @@ -1151,23 +1151,23 @@

Project metadata f
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- @@ -1761,23 +1761,23 @@

Suggestions for N
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- diff --git a/search.json b/search.json index 319328d0..6742195e 100644 --- a/search.json +++ b/search.json @@ -453,7 +453,7 @@ "href": "develop/05_VC.html", "title": "5. Data Analysis with Version Control", "section": "", - "text": "Course Overview\n\n\n\n⏰ Time Estimation: X minutes\n💬 Learning Objectives:\n\nVersion control essentials and practices\nGit and Github repositories\nCreate repositories\nGitHub page to showcase your data analysis reports\n\n\n\nThis lesson introduces version control with Git and Github and its significance in research. You will gain the ability to create Git repositories, and skills to build GitHub pages for showcasing data analysis.\n\n\nVersion control systematically tracks project changes, documenting alterations for understanding project evolution. It holds significant importance in research data management, software development, and data analysis, offering numerous advantages.\n\n\n\n\n\n\nAdvantages of using version control\n\n\n\n\nDocument Progress: Detailed change history aids understanding of project development and modifications.\nEnsure Data Integrity: Prevents accidental data loss or corruption, with each change tracked for easy recovery.\nFacilitate Collaboration: Enables seamless collaboration among team members, allowing multiple individuals to work concurrently without conflicts.\nReproducibility: Preserves project state for accurate validation and analysis.\nBranching and Experimentation: Allows the creation of alternative project versions for experimentation, without altering the main branch.\nGlobal Accessibility: Platforms like GitHub provide visibility for sharing, feedback, and contribution to open science.\n\n\n\n\n\n\n\n\n\nTake our course on Git & Github\n\n\n\nif you’re interested in delving deeper, explore our course on Git and GitHub.\nAlternatively, here are some examples and online resources to expand your understanding:\n\n[Git and GitHub online resources] https://docs.github.com/en/get-started/start-your-journey/git-and-github-learning-resources\nGitHub documentation\nGit documentation\n\n\n\n\n\nGit is a widely adopted version control system that empowers developers and researchers to efficiently manage their project’s history, collaborate seamlessly, track changes, and ensure data integrity. Git operates on core principles and mechanisms:\n\nLocal Repository: Each user maintains a local repository on their computer, storing the complete project history for independent work.\nSnapshots, Not Files: Git captures snapshots of the entire project at different points instead of tracking individual file changes, ensuring data consistency.\nCommits: Users create ‘commits’ as snapshots of the project at specific moments, recording changes made to files along with explanatory commit messages.\nBranching: Git supports branching, enabling users to create separate lines of development for new features or bug fixes without affecting the main branch.\nMerging: Changes from one branch can be merged into another, facilitating the incorporation of new features or bug fixes back into the main project with a smooth merging process.\nDistributed Architecture: Git’s distributed nature means each user’s local repository is a complete copy of the project, enabling offline work and ensuring data redundancy.\nRemote Repositories: Users can connect and synchronize their local repositories with remote repositories hosted on platforms like GitHub, facilitating collaboration and project sharing.\nPush and Pull: Users ‘push’ their local changes to a remote repository to share with others and ‘pull’ changes made by others into their local repository to stay updated.\nConflict Resolution: Git provides tools to resolve conflicts manually in cases of conflicting changes, ensuring data integrity during collaboration.\nVersioning and Tagging: Git offers versioning and tagging capabilities, allowing users to mark specific points in history such as major releases or significant milestones.\n\n\n\n\nIn addition to exploring Git, we will also explore GitHub, a collaborative platform for hosting Git repositories. GitHub enhances Git’s capabilities by offering features like issue tracking, security measures to protect repositories, and GitHub Pages for creating project websites. Additionally, GitHub provides the option to set repositories as private until you are ready to share your work publicly.\n\n\n\n\n\n\nAlternatives flows for collaborative projects\n\n\n\n\nGitLab\nBitBucket We will focus on GitHub for the remainder of this lesson due to its widespread usage and compatibility.\n\n\n\n\n\n\n\n\n\nWarning\n\n\n\nWe will discuss repositories for archiving experimental or large datasets in lesson 7.\n\n\n\n\nMoving from Git to GitHub involves transitioning from a local version control setup to a remote hosting platform. You will need a GitHub account for the exercise in this section.\n\n\n\n\n\n\nCreate a GitHub account\n\n\n\n\nIf you don’t have a GitHub account yet, click here.\nInstall Git from Git webpage\n\n\n\nYou have two options when it comes to creating a repository for your project. First, you can start from scratch by creating a new repository and adding files to it as your project progresses. Alternatively, if you already have an existing folder structure for your project, you can initialize a repository directly from that folder. It is crucial to initiate version control in the early stages of a project to facilitate easy tracking of changes and effective management of the project’s version history from the beginning.\n\n\nIf you completed all the exercises in lesson 3, you should have a project data structure prepared. Otherwise, consider using one of your existing projects or creating a small toy example for practice using cookiecutter (see practical_workshop).\n\n\n\n\n\n\nGithub documentation link\n\n\n\n\nAdding locally hosted code to Github\n\n\n\n\n\n\n\n\n\nExercise 1: initialize a repository from an existing folder:\n\n\n\n\n\n\n\n\nFirst, initialize the repository using the command git init. This command is run only once, even in collaborative projects (git init).\nOnce the repository is initialized, create a remote repository on GitHub.\nAdd the remote URL to your local git repository using git remote add origin <URL>`. This associates the remote URL with the name “origin”.\nEnsure you have at least one commit in your history by staging existing files with git add and then creating a snapshot, known as committing, with git commit.\nFinally, push your local commits to the remote repository and establish a tracking relationship using git push -u origin master.\n\n\n\n\n\n\n\n\n\nAlternatively to converting folders to repositories, you can create a new repository remotely, and then clone (git clone) it locally. Here, git init is not needed. You can move the files into the repository locally (git add, git commit, and git push). If you are creating a collaborative repository, you can now share it with your colleagues.\n\n\n\n\n\n\nTips to write good commit messages\n\n\n\nWrite useful and clear Git commits. Check out this post for tips.\n\n\n\n\n\n\n\nAfter setting up your repository on GitHub, take advantage of the opportunity to enhance it by adding your data analysis reports. Whether they are in Jupyter Notebooks, Rmarkdowns, or HTML reports, you can showcase them on a GitHub Page.\nOnce you have created your repository (and put it in GitHub), you have now the opportunity to add your data analysis reports that you created, in either Jupyter Notebooks, Rmarkdowns, or HTML reports, in a GitHub Page website. Creating a GitHub page is very simple, and we recommend that you follow the nice tutorial that GitHub has put for you.\nFor simplicity, we recommend using Quarto or MkDocs. Visit their websites and follow the instructions to get started.\n\n\n\n\n\n\nTutorial links\n\n\n\n\nGet started in quarto: https://quarto.org/docs/get-started/. We recommend using the VS code tool, if you do, follow this tutorial.\nMkDocs materials to further customize MkDocs websites.\n\n\n\n\n\n\nWe provide an example of setting up Git, MkDocs, and a GitHub account, enabling you to replicate the process independently! (see Exercise 5 in the practical material)\n\n\n\n\nIn this lesson, we explored version control and utilized Git and GitHub to establish data analysis repositories from our Project folders. Additionally, we delved into creating a GitHub organization and leveraging GitHub Pages to showcase data analysis scripts and notebooks publicly. Remember to complete the corresponding exercise from the practical workshop to reinforce your knowledge.\n\n\n\nVersion Control and Code Repository Link.", + "text": "Course Overview\n\n\n\n⏰ Time Estimation: X minutes\n💬 Learning Objectives:\n\nVersion control essentials and practices\nGit and Github repositories\nCreate repositories\nGitHub page to showcase your data analysis reports\n\n\n\nThis lesson introduces version control with Git and Github and its significance in research. You will gain the ability to create Git repositories, and skills to build GitHub pages for showcasing data analysis.\n\n\nVersion control systematically tracks project changes, documenting alterations for understanding project evolution. It holds significant importance in research data management, software development, and data analysis, offering numerous advantages.\n\n\n\n\n\n\nAdvantages of using version control\n\n\n\n\nDocument Progress: Detailed change history aids understanding of project development and modifications.\nEnsure Data Integrity: Prevents accidental data loss or corruption, with each change tracked for easy recovery.\nFacilitate Collaboration: Enables seamless collaboration among team members, allowing multiple individuals to work concurrently without conflicts.\nReproducibility: Preserves project state for accurate validation and analysis.\nBranching and Experimentation: Allows the creation of alternative project versions for experimentation, without altering the main branch.\nGlobal Accessibility: Platforms like GitHub provide visibility for sharing, feedback, and contribution to open science.\n\n\n\n\n\n\n\n\n\nTake our course on Git & Github\n\n\n\nif you’re interested in delving deeper, explore our course on Git and GitHub.\nAlternatively, here are some examples and online resources to expand your understanding:\n\nGit and GitHub online resources\nGitHub documentation\nGit documentation\n\n\n\n\n\nGit is a widely adopted version control system that empowers developers and researchers to efficiently manage their project’s history, collaborate seamlessly, track changes, and ensure data integrity. Git operates on core principles and mechanisms:\n\nLocal Repository: Each user maintains a local repository on their computer, storing the complete project history for independent work.\nSnapshots, Not Files: Git captures snapshots of the entire project at different points instead of tracking individual file changes, ensuring data consistency.\nCommits: Users create ‘commits’ as snapshots of the project at specific moments, recording changes made to files along with explanatory commit messages.\nBranching: Git supports branching, enabling users to create separate lines of development for new features or bug fixes without affecting the main branch.\nMerging: Changes from one branch can be merged into another, facilitating the incorporation of new features or bug fixes back into the main project with a smooth merging process.\nDistributed Architecture: Git’s distributed nature means each user’s local repository is a complete copy of the project, enabling offline work and ensuring data redundancy.\nRemote Repositories: Users can connect and synchronize their local repositories with remote repositories hosted on platforms like GitHub, facilitating collaboration and project sharing.\nPush and Pull: Users ‘push’ their local changes to a remote repository to share with others and ‘pull’ changes made by others into their local repository to stay updated.\nConflict Resolution: Git provides tools to resolve conflicts manually in cases of conflicting changes, ensuring data integrity during collaboration.\nVersioning and Tagging: Git offers versioning and tagging capabilities, allowing users to mark specific points in history such as major releases or significant milestones.\n\n\n\n\nIn addition to exploring Git, we will also explore GitHub, a collaborative platform for hosting Git repositories. GitHub enhances Git’s capabilities by offering features like issue tracking, security measures to protect repositories, and GitHub Pages for creating project websites. Additionally, GitHub provides the option to set repositories as private until you are ready to share your work publicly.\n\n\n\n\n\n\nAlternatives flows for collaborative projects\n\n\n\n\nGitLab\nBitBucket We will focus on GitHub for the remainder of this lesson due to its widespread usage and compatibility.\n\n\n\n\n\n\n\n\n\nWarning\n\n\n\nWe will discuss repositories for archiving experimental or large datasets in lesson 7.\n\n\n\n\nMoving from Git to GitHub involves transitioning from a local version control setup to a remote hosting platform. You will need a GitHub account for the exercise in this section.\n\n\n\n\n\n\nCreate a GitHub account\n\n\n\n\nIf you don’t have a GitHub account yet, click here.\nInstall Git from Git webpage\n\n\n\nYou have two options when it comes to creating a repository for your project. First, you can start from scratch by creating a new repository and adding files to it as your project progresses. Alternatively, if you already have an existing folder structure for your project, you can initialize a repository directly from that folder. It is crucial to initiate version control in the early stages of a project to facilitate easy tracking of changes and effective management of the project’s version history from the beginning.\n\n\nIf you completed all the exercises in lesson 3, you should have a project data structure prepared. Otherwise, consider using one of your existing projects or creating a small toy example for practice using cookiecutter (see practical_workshop).\n\n\n\n\n\n\nGithub documentation link\n\n\n\n\nAdding locally hosted code to Github\n\n\n\n\n\n\n\n\n\nExercise 1: initialize a repository from an existing folder:\n\n\n\n\n\n\n\n\nFirst, initialize the repository using the command git init. This command is run only once, even in collaborative projects (git init).\nOnce the repository is initialized, create a remote repository on GitHub.\nAdd the remote URL to your local git repository using git remote add origin <URL>`. This associates the remote URL with the name “origin”.\nEnsure you have at least one commit in your history by staging existing files with git add and then creating a snapshot, known as committing, with git commit.\nFinally, push your local commits to the remote repository and establish a tracking relationship using git push -u origin master.\n\n\n\n\n\n\n\n\n\nAlternatively to converting folders to repositories, you can create a new repository remotely, and then clone (git clone) it locally. Here, git init is not needed. You can move the files into the repository locally (git add, git commit, and git push). If you are creating a collaborative repository, you can now share it with your colleagues.\n\n\n\n\n\n\nTips to write good commit messages\n\n\n\nWrite useful and clear Git commits. Check out this post for tips.\n\n\n\n\n\n\n\nAfter setting up your repository on GitHub, take advantage of the opportunity to enhance it by adding your data analysis reports. Whether they are in Jupyter Notebooks, Rmarkdowns, or HTML reports, you can showcase them on a GitHub Page.\nOnce you have created your repository (and put it in GitHub), you have now the opportunity to add your data analysis reports that you created, in either Jupyter Notebooks, Rmarkdowns, or HTML reports, in a GitHub Page website. Creating a GitHub page is very simple, and we recommend that you follow the nice tutorial that GitHub has put for you.\nFor simplicity, we recommend using Quarto or MkDocs. Visit their websites and follow the instructions to get started.\n\n\n\n\n\n\nTutorial links\n\n\n\n\nGet started in quarto: https://quarto.org/docs/get-started/. We recommend using the VS code tool, if you do, follow this tutorial.\nMkDocs materials to further customize MkDocs websites.\n\n\n\n\n\n\nWe provide an example of setting up Git, MkDocs, and a GitHub account, enabling you to replicate the process independently! (see Exercise 5 in the practical material)\n\n\n\n\nIn this lesson, we explored version control and utilized Git and GitHub to establish data analysis repositories from our Project folders. Additionally, we delved into creating a GitHub organization and leveraging GitHub Pages to showcase data analysis scripts and notebooks publicly. Remember to complete the corresponding exercise from the practical workshop to reinforce your knowledge.\n\n\n\nVersion Control and Code Repository Link.", "crumbs": [ "Course material", "Key practices", @@ -465,7 +465,7 @@ "href": "develop/05_VC.html#version-control", "title": "5. Data Analysis with Version Control", "section": "", - "text": "Version control systematically tracks project changes, documenting alterations for understanding project evolution. It holds significant importance in research data management, software development, and data analysis, offering numerous advantages.\n\n\n\n\n\n\nAdvantages of using version control\n\n\n\n\nDocument Progress: Detailed change history aids understanding of project development and modifications.\nEnsure Data Integrity: Prevents accidental data loss or corruption, with each change tracked for easy recovery.\nFacilitate Collaboration: Enables seamless collaboration among team members, allowing multiple individuals to work concurrently without conflicts.\nReproducibility: Preserves project state for accurate validation and analysis.\nBranching and Experimentation: Allows the creation of alternative project versions for experimentation, without altering the main branch.\nGlobal Accessibility: Platforms like GitHub provide visibility for sharing, feedback, and contribution to open science.\n\n\n\n\n\n\n\n\n\nTake our course on Git & Github\n\n\n\nif you’re interested in delving deeper, explore our course on Git and GitHub.\nAlternatively, here are some examples and online resources to expand your understanding:\n\n[Git and GitHub online resources] https://docs.github.com/en/get-started/start-your-journey/git-and-github-learning-resources\nGitHub documentation\nGit documentation\n\n\n\n\n\nGit is a widely adopted version control system that empowers developers and researchers to efficiently manage their project’s history, collaborate seamlessly, track changes, and ensure data integrity. Git operates on core principles and mechanisms:\n\nLocal Repository: Each user maintains a local repository on their computer, storing the complete project history for independent work.\nSnapshots, Not Files: Git captures snapshots of the entire project at different points instead of tracking individual file changes, ensuring data consistency.\nCommits: Users create ‘commits’ as snapshots of the project at specific moments, recording changes made to files along with explanatory commit messages.\nBranching: Git supports branching, enabling users to create separate lines of development for new features or bug fixes without affecting the main branch.\nMerging: Changes from one branch can be merged into another, facilitating the incorporation of new features or bug fixes back into the main project with a smooth merging process.\nDistributed Architecture: Git’s distributed nature means each user’s local repository is a complete copy of the project, enabling offline work and ensuring data redundancy.\nRemote Repositories: Users can connect and synchronize their local repositories with remote repositories hosted on platforms like GitHub, facilitating collaboration and project sharing.\nPush and Pull: Users ‘push’ their local changes to a remote repository to share with others and ‘pull’ changes made by others into their local repository to stay updated.\nConflict Resolution: Git provides tools to resolve conflicts manually in cases of conflicting changes, ensuring data integrity during collaboration.\nVersioning and Tagging: Git offers versioning and tagging capabilities, allowing users to mark specific points in history such as major releases or significant milestones.\n\n\n\n\nIn addition to exploring Git, we will also explore GitHub, a collaborative platform for hosting Git repositories. GitHub enhances Git’s capabilities by offering features like issue tracking, security measures to protect repositories, and GitHub Pages for creating project websites. Additionally, GitHub provides the option to set repositories as private until you are ready to share your work publicly.\n\n\n\n\n\n\nAlternatives flows for collaborative projects\n\n\n\n\nGitLab\nBitBucket We will focus on GitHub for the remainder of this lesson due to its widespread usage and compatibility.\n\n\n\n\n\n\n\n\n\nWarning\n\n\n\nWe will discuss repositories for archiving experimental or large datasets in lesson 7.\n\n\n\n\nMoving from Git to GitHub involves transitioning from a local version control setup to a remote hosting platform. You will need a GitHub account for the exercise in this section.\n\n\n\n\n\n\nCreate a GitHub account\n\n\n\n\nIf you don’t have a GitHub account yet, click here.\nInstall Git from Git webpage\n\n\n\nYou have two options when it comes to creating a repository for your project. First, you can start from scratch by creating a new repository and adding files to it as your project progresses. Alternatively, if you already have an existing folder structure for your project, you can initialize a repository directly from that folder. It is crucial to initiate version control in the early stages of a project to facilitate easy tracking of changes and effective management of the project’s version history from the beginning.\n\n\nIf you completed all the exercises in lesson 3, you should have a project data structure prepared. Otherwise, consider using one of your existing projects or creating a small toy example for practice using cookiecutter (see practical_workshop).\n\n\n\n\n\n\nGithub documentation link\n\n\n\n\nAdding locally hosted code to Github\n\n\n\n\n\n\n\n\n\nExercise 1: initialize a repository from an existing folder:\n\n\n\n\n\n\n\n\nFirst, initialize the repository using the command git init. This command is run only once, even in collaborative projects (git init).\nOnce the repository is initialized, create a remote repository on GitHub.\nAdd the remote URL to your local git repository using git remote add origin <URL>`. This associates the remote URL with the name “origin”.\nEnsure you have at least one commit in your history by staging existing files with git add and then creating a snapshot, known as committing, with git commit.\nFinally, push your local commits to the remote repository and establish a tracking relationship using git push -u origin master.\n\n\n\n\n\n\n\n\n\nAlternatively to converting folders to repositories, you can create a new repository remotely, and then clone (git clone) it locally. Here, git init is not needed. You can move the files into the repository locally (git add, git commit, and git push). If you are creating a collaborative repository, you can now share it with your colleagues.\n\n\n\n\n\n\nTips to write good commit messages\n\n\n\nWrite useful and clear Git commits. Check out this post for tips.\n\n\n\n\n\n\n\nAfter setting up your repository on GitHub, take advantage of the opportunity to enhance it by adding your data analysis reports. Whether they are in Jupyter Notebooks, Rmarkdowns, or HTML reports, you can showcase them on a GitHub Page.\nOnce you have created your repository (and put it in GitHub), you have now the opportunity to add your data analysis reports that you created, in either Jupyter Notebooks, Rmarkdowns, or HTML reports, in a GitHub Page website. Creating a GitHub page is very simple, and we recommend that you follow the nice tutorial that GitHub has put for you.\nFor simplicity, we recommend using Quarto or MkDocs. Visit their websites and follow the instructions to get started.\n\n\n\n\n\n\nTutorial links\n\n\n\n\nGet started in quarto: https://quarto.org/docs/get-started/. We recommend using the VS code tool, if you do, follow this tutorial.\nMkDocs materials to further customize MkDocs websites.\n\n\n\n\n\n\nWe provide an example of setting up Git, MkDocs, and a GitHub account, enabling you to replicate the process independently! (see Exercise 5 in the practical material)", + "text": "Version control systematically tracks project changes, documenting alterations for understanding project evolution. It holds significant importance in research data management, software development, and data analysis, offering numerous advantages.\n\n\n\n\n\n\nAdvantages of using version control\n\n\n\n\nDocument Progress: Detailed change history aids understanding of project development and modifications.\nEnsure Data Integrity: Prevents accidental data loss or corruption, with each change tracked for easy recovery.\nFacilitate Collaboration: Enables seamless collaboration among team members, allowing multiple individuals to work concurrently without conflicts.\nReproducibility: Preserves project state for accurate validation and analysis.\nBranching and Experimentation: Allows the creation of alternative project versions for experimentation, without altering the main branch.\nGlobal Accessibility: Platforms like GitHub provide visibility for sharing, feedback, and contribution to open science.\n\n\n\n\n\n\n\n\n\nTake our course on Git & Github\n\n\n\nif you’re interested in delving deeper, explore our course on Git and GitHub.\nAlternatively, here are some examples and online resources to expand your understanding:\n\nGit and GitHub online resources\nGitHub documentation\nGit documentation\n\n\n\n\n\nGit is a widely adopted version control system that empowers developers and researchers to efficiently manage their project’s history, collaborate seamlessly, track changes, and ensure data integrity. Git operates on core principles and mechanisms:\n\nLocal Repository: Each user maintains a local repository on their computer, storing the complete project history for independent work.\nSnapshots, Not Files: Git captures snapshots of the entire project at different points instead of tracking individual file changes, ensuring data consistency.\nCommits: Users create ‘commits’ as snapshots of the project at specific moments, recording changes made to files along with explanatory commit messages.\nBranching: Git supports branching, enabling users to create separate lines of development for new features or bug fixes without affecting the main branch.\nMerging: Changes from one branch can be merged into another, facilitating the incorporation of new features or bug fixes back into the main project with a smooth merging process.\nDistributed Architecture: Git’s distributed nature means each user’s local repository is a complete copy of the project, enabling offline work and ensuring data redundancy.\nRemote Repositories: Users can connect and synchronize their local repositories with remote repositories hosted on platforms like GitHub, facilitating collaboration and project sharing.\nPush and Pull: Users ‘push’ their local changes to a remote repository to share with others and ‘pull’ changes made by others into their local repository to stay updated.\nConflict Resolution: Git provides tools to resolve conflicts manually in cases of conflicting changes, ensuring data integrity during collaboration.\nVersioning and Tagging: Git offers versioning and tagging capabilities, allowing users to mark specific points in history such as major releases or significant milestones.\n\n\n\n\nIn addition to exploring Git, we will also explore GitHub, a collaborative platform for hosting Git repositories. GitHub enhances Git’s capabilities by offering features like issue tracking, security measures to protect repositories, and GitHub Pages for creating project websites. Additionally, GitHub provides the option to set repositories as private until you are ready to share your work publicly.\n\n\n\n\n\n\nAlternatives flows for collaborative projects\n\n\n\n\nGitLab\nBitBucket We will focus on GitHub for the remainder of this lesson due to its widespread usage and compatibility.\n\n\n\n\n\n\n\n\n\nWarning\n\n\n\nWe will discuss repositories for archiving experimental or large datasets in lesson 7.\n\n\n\n\nMoving from Git to GitHub involves transitioning from a local version control setup to a remote hosting platform. You will need a GitHub account for the exercise in this section.\n\n\n\n\n\n\nCreate a GitHub account\n\n\n\n\nIf you don’t have a GitHub account yet, click here.\nInstall Git from Git webpage\n\n\n\nYou have two options when it comes to creating a repository for your project. First, you can start from scratch by creating a new repository and adding files to it as your project progresses. Alternatively, if you already have an existing folder structure for your project, you can initialize a repository directly from that folder. It is crucial to initiate version control in the early stages of a project to facilitate easy tracking of changes and effective management of the project’s version history from the beginning.\n\n\nIf you completed all the exercises in lesson 3, you should have a project data structure prepared. Otherwise, consider using one of your existing projects or creating a small toy example for practice using cookiecutter (see practical_workshop).\n\n\n\n\n\n\nGithub documentation link\n\n\n\n\nAdding locally hosted code to Github\n\n\n\n\n\n\n\n\n\nExercise 1: initialize a repository from an existing folder:\n\n\n\n\n\n\n\n\nFirst, initialize the repository using the command git init. This command is run only once, even in collaborative projects (git init).\nOnce the repository is initialized, create a remote repository on GitHub.\nAdd the remote URL to your local git repository using git remote add origin <URL>`. This associates the remote URL with the name “origin”.\nEnsure you have at least one commit in your history by staging existing files with git add and then creating a snapshot, known as committing, with git commit.\nFinally, push your local commits to the remote repository and establish a tracking relationship using git push -u origin master.\n\n\n\n\n\n\n\n\n\nAlternatively to converting folders to repositories, you can create a new repository remotely, and then clone (git clone) it locally. Here, git init is not needed. You can move the files into the repository locally (git add, git commit, and git push). If you are creating a collaborative repository, you can now share it with your colleagues.\n\n\n\n\n\n\nTips to write good commit messages\n\n\n\nWrite useful and clear Git commits. Check out this post for tips.\n\n\n\n\n\n\n\nAfter setting up your repository on GitHub, take advantage of the opportunity to enhance it by adding your data analysis reports. Whether they are in Jupyter Notebooks, Rmarkdowns, or HTML reports, you can showcase them on a GitHub Page.\nOnce you have created your repository (and put it in GitHub), you have now the opportunity to add your data analysis reports that you created, in either Jupyter Notebooks, Rmarkdowns, or HTML reports, in a GitHub Page website. Creating a GitHub page is very simple, and we recommend that you follow the nice tutorial that GitHub has put for you.\nFor simplicity, we recommend using Quarto or MkDocs. Visit their websites and follow the instructions to get started.\n\n\n\n\n\n\nTutorial links\n\n\n\n\nGet started in quarto: https://quarto.org/docs/get-started/. We recommend using the VS code tool, if you do, follow this tutorial.\nMkDocs materials to further customize MkDocs websites.\n\n\n\n\n\n\nWe provide an example of setting up Git, MkDocs, and a GitHub account, enabling you to replicate the process independently! 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