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book/computers.md

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A computer can be broken down into a number of components, for example: hardware, software and peripherals, as illustrated in the figure below.
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```{figure} computers/figures/typical.svg
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```{figure} https://files.mude.citg.tudelft.nl/typical.svg
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name: computer_typical
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As far as this book is concerned, the _application software_ is where our true interest lies, as it is here where we will be writing programs to solve our problems of interest and collaborate with others. This is where our everyday software tools for scientific computing are categorized, for example, Python, VS Code, Matlab, our web browsers (e.g., Chrome) and much more software! As illustrated in the following figure, "we want to be" working at a relatively high level of application software (e.g., writing Python code to conduct analysis and make interesting visualizations) such that we don't have to worry about which OS we are working on. This is both to allow us to focus on our work, as well as collaborate others.
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```{figure} computers/figures/apps.svg
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```{figure} https://files.mude.citg.tudelft.nl/apps.svg
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width: 80%
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name: computer_applications

book/environments.md

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The purpose of environments and environment managers is to allow an arbitrary software project to be used on an arbitrary computer, regardless of operating system (although one should note that some OS-specific software is required, for example the environment manager itself). This is illustrated schematically in the following figure.
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```{figure} environments/figures/simple.svg
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```{figure} https://files.mude.citg.tudelft.nl/simple.svg
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Environments and environment managers make it very easy to share projects between collaborators without the need to make computer-specific versions that are compatible with a wide variety of hardware and operating systems. This is illustrated schematically in the following figure, where multiple environment managers can be used to run projects on different computers. Depending on the requirements of a project or computer, a wide number of environment managers could be considered by the user.
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```{figure} environments/figures/complex.svg
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```{figure} https://files.mude.citg.tudelft.nl/complex.svg
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book/install/common/env_vars_windows.md

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````{tip}
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Keep in mind that the Windows OS allows you to set environment variables for a specific _user_ as well as for the _system_ (all users). It is important to note which environment variable you should set for a given activity, as choosing the wrong one can have unintended consequences (or lead to much frustration!). The difference can be seen in the example here:
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```{figure} figures/environment_var_system_user.png
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```{figure} https://files.mude.citg.tudelft.nl/environment_var_system_user.png
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name: environment_var_system_user
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The easiest way to find the appropriate setting window is by typing the first letters of "environment" in the Windows toolbar. The first three letters are usually enough to cause several relevant options to appear; select _Edit environment variables for your account_ and see the figure below for an illustration:
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```{figure} figures/environment_var_search.png
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```{figure} https://files.mude.citg.tudelft.nl/environment_var_search.png
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To set the right variable, pay particular attention to the descriptions provided in the environment variable window, as it is easy to miss; the right location is illustrated clearly in the following figure:
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```{figure} figures/environment_var_miniconda_not_system.png
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```{figure} https://files.mude.citg.tudelft.nl/environment_var_miniconda_not_system.png
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Once you have identified the proper (user) window, look for the `PATH` variable, select it, then click the "Edit..." button. If the variable value is empty, you will probably see a window similar to that in the following figure; enter (paste) the path of the folder (directory) you wish to add to the path in the field "Variable value" then click "OK." Note that you can browse for the file and folder of interest via the settings window if you did not already copy the path via the File Explorer or a CLI.
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```{figure} figures/environment_var_miniconda.png
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```{figure} https://files.mude.citg.tudelft.nl/environment_var_miniconda.png
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name: environment_var_miniconda
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If there are already values set for the `PATH` variable then the "Edit..." button will probably show a window like that in the following figure. In this case, you can add a new path via the "New" button; paste the path in an open row of the list. Note that you can browse for the file and folder of interest via the settings window if you did not already copy the path via the File Explorer or a CLI.
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```{figure} figures/environment_var_PATH_examples.png
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```{figure} https://files.mude.citg.tudelft.nl/environment_var_PATH_examples.png
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The following figure illustrates exactly where you should paste your desired folder (directory) path after clicking the "New" button:
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```{figure} figures/environment_var_PATH_new.png
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```{figure} https://files.mude.citg.tudelft.nl/environment_var_PATH_new.png
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book/install/common/hidden.md

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Settings for hidden files and folders can be found directly via the Windows File Explorer. First find the "options" or "settings" configuration window (sometimes pressing the `ALT` button toggles the menubar on and off):
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```{figure} figures/hidden_windows_1.png
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```{figure} https://files.mude.citg.tudelft.nl/hidden_windows_1.png
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Then navigate to the proper location in the "View" tab of the Folder Options window:
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```{figure} figures/hidden_windows_2.png
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```{figure} https://files.mude.citg.tudelft.nl/hidden_windows_2.png
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book/install/git/intro.md

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Console example in {numref}`setup1_2`:
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```{figure} https://files.mude.citg.tudelft.nl/setup1.png
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book/install/python/miniconda.md

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Note that depending on your Windows settings `CTRL+V` does not always work; you may need to use the menu bar of the terminal window or right-click and select paste. In addition, the paste feature typically works one line at a time, therefore after the first line is executed (download) you may need to hit enter once or twice to complete the last lines, as they may not execute automatically.
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```{figure} figures/miniconda_install.png
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```{figure} https://files.mude.citg.tudelft.nl/miniconda_install.png
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Open the Windows tool bar and begin typing "Anaconda". You should soon see two options appear: "Anaconda Prompt" and "Anaconda PowerShell Prompt." There two versions are based on the two primary CLI's on Windows: Command Prompt and PowerShell. Unless you are an experienced PowerShell user, we recommend using the Command Prompt version: Anaconda Prompt (see figure below):
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```{figure} figures/anaconda_prompt_open_windows.png
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```{figure} https://files.mude.citg.tudelft.nl/anaconda_prompt_open_windows.png
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book/version_control/version_control.md

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What you have been doing is called version control. Version control systems start with a base version of the document and then record changes you make each step of the way. You can think of it as a recording of your progress: you can rewind to start at the base document and play back each change you made, eventually arriving at your most recent version, as shown in figure {numref}`intro1`:
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Once you think of changes as separate from the document itself, you can then think about "playing back" different sets of changes on the base document, resulting in different versions of that document. For example, two users can make independent sets of changes on the same document, resulting in 2 independent versions ({numref}`intro2`).
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Unless multiple users make changes to the same section of the document - a conflict - you can incorporate two sets of changes into the same base document ({numref}`intro3`).
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```{figure} https://files.mude.citg.tudelft.nl/intro3.png
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book/workflows/git/branch_merge.md

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The graph below shows the commit history of a repo with two commits:
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![Commit graph of our repository](./images/branch1.png)
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![Commit graph of our repository](https://files.mude.citg.tudelft.nl/branch1.png)
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The main advantage of version control is that it allows developers to work together in parallel. During projects, you will be working on "feature" branches and separating the work to review and merge it later. A common graphical structure of commits is shown below, where we have developers working on 3 separate branches and merging their work when necessary. This separation offers flexibility, parallelization of work, and offers more control over the development process.
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![Commit graph of a sample repository](./images/branch2.png)
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![Commit graph of a sample repository](https://files.mude.citg.tudelft.nl/branch2.png)
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## Creating a branch
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First, let us check on what branch we are currently at. On GitHub, navigate to your repository and click on the "Branch: main" dropdown to see the list of branches. The branch with a checkmark is your current branch.
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![Check existing branches](./images/branch3.png)
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![Check existing branches](https://files.mude.citg.tudelft.nl/branch3.png)
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Let us create a new branch from `main` on GitHub, which we will call `first-branch`. Click on the "Branch: main" dropdown, type `first-branch` in the text box, and click "Create branch: first-branch from main".
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![Moving to branch `first-branch`](./images/branch4.png)
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![Moving to branch `first-branch`](https://files.mude.citg.tudelft.nl/branch4.png)
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Let us modify our `README.md` file again and add a sentence to the first line of it. Navigate to the `README.md` file, click the pencil icon to edit it, and add your content to the first line:
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![Committing new changes](./images/branch5.png)
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![Committing new changes](https://files.mude.citg.tudelft.nl/branch5.png)
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## Merging branches / pull requests
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We can merge the `main` branch into `first-branch` by creating a pull request. On GitHub, go to the "Pull requests" tab, click "New pull request", select `first-branch` as the base branch and `main` as the compare branch, and click "Create pull request". We can check (as shown below) that there are no conflicts and then we click "Merge pull request" to merge `main` into `first-branch`.
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![Pull request](./images/branch6.png)
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![Pull request](https://files.mude.citg.tudelft.nl/branch6.png)
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We can now inspect the README.md again with the new changes. The progress of the other branch (`main`) has been moved to `first-branch` as seen below.
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![New commits graph](./images/branch7.png)
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![New commits graph](https://files.mude.citg.tudelft.nl/branch7.png)
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We will now return to `main` and merge `first-branch` into it with another pull request. Follow the same steps as before, but this time select `first-branch` as the compare branch and `main` as the base branch.
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![Merging `first-branch` into `main`](./images/branch10.png)
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![Merging `first-branch` into `main`](https://files.mude.citg.tudelft.nl/branch10.png)
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## Deleting branches
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Branch `first-branch` has lived its use, so we can delete it as we do not plan on making new changes to it. This will not remove any of the commits made on it. It will only remove the pointer itself. Do this from the pull request page by clicking "Delete branch".
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![Deleting a branch](./images/branch12.png)
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![Deleting a branch](https://files.mude.citg.tudelft.nl/branch12.png)
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## Branches locally
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book/workflows/git/cloning.md

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Upon opening VS Code, we see that the first thing that is needed is to clone a repository ({numref}`clone1_VSC`). First, we have to get the address from our GitHub account.
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Now you are ready to click the "Clone Repository" option in the Source Control tab of VS Code ({numref}`clone1`). Paste the address you copied from GitHub into the top bar and press 'enter' (as shown in {numref}`clone4_VSC`). Then select the folder or location on your local machine where you would like the _local repository_ to be stored ({numref}`clone5_VSC`).
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```{figure} https://files.mude.citg.tudelft.nl/clone4.png
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```{figure} https://files.mude.citg.tudelft.nl/clone5.png
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If you were successful in cloning the repository, you will see something similar to {numref}`clone7` and you can choose to open your _local repository_. Now we are ready to work on the files and preserve the changes by making our first local **commit**!
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```{figure} https://files.mude.citg.tudelft.nl/clone7.png
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