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34 changes: 34 additions & 0 deletions ch-git.md
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git remote set-head origin -a
```

GitHub Personal Access Token (PAT)
------------------------------------

The tokens have two purposes that we encounter regularly.

### Pushing to any repo or reading from a private repo

...especially on Linux machines that don't have [GitHub Desktop](https://desktop.github.com/).

{TODO: write this section}

### Using the [remotes](https://remotes.r-lib.org/) package

If you are using the [remotes](https://remotes.r-lib.org/) with a line like
`remotes::install_github("Melinae/TabularManifest")` or `remotes::install_github("tidyverse/ggplot2")`,
you may encounter this error:

```
Using GitHub PAT from the git credential store.
Error: Failed to install 'unknown package' from GitHub:
HTTP error 401.
Bad credentials
```

If so,
1. Create a classic personal access token at <https://github.com/settings/tokens>.
(Make sure you're logged in.)
We suggest creating one per machine, so you don't have to juggle them between computers.
1. Maybe name it "ouhsc-desktop" or "home-laptop" (obligatory reminder to never store PHI on a personal machine).
Copy the new token to your clipboard.
1. Then use the [gitcreds](https://gitcreds.r-lib.org/) package by running, `gitcreds::gitcreds_set()`.
Then select to add/replace the token with the value that you just copied to your clipboard.
1. Rerun the `remotes::install_github()`.

Repo Style
------------------------------------

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<meta name="twitter:description" content="The page you requested cannot be found (perhaps it was moved or renamed). You may want to try searching to find the page's new location, or use the table of contents to find the page you are...">
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<footer class="bg-primary text-light mt-5"><div class="container"><div class="row">

<div class="col-12 col-md-6 mt-3">
<p>"<strong>Collaborative Data Science Practices</strong>" was written by Will Beasley. It was last built on 2024-07-08.</p>
<p>"<strong>Collaborative Data Science Practices</strong>" was written by Will Beasley. It was last built on 2024-08-26.</p>
</div>

<div class="col-12 col-md-6 mt-3">
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<meta name="twitter:description" content="The authors thank all our colleagues for the discussions and experiences about data science that lead to this book. At OUHSC, this includes @adrose, @aggie-dbc, @ARPeters, @Ashley-Jorgensen,...">
<!-- JS --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://kit.fontawesome.com/6ecbd6c532.js" crossorigin="anonymous"></script><script src="libs/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
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div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
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<footer class="bg-primary text-light mt-5"><div class="container"><div class="row">

<div class="col-12 col-md-6 mt-3">
<p>"<strong>Collaborative Data Science Practices</strong>" was written by Will Beasley. It was last built on 2024-07-08.</p>
<p>"<strong>Collaborative Data Science Practices</strong>" was written by Will Beasley. It was last built on 2024-08-26.</p>
</div>

<div class="col-12 col-md-6 mt-3">
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<meta name="twitter:description" content="3.1 Encapsulation 3.2 Leverage team member’s strengths &amp; avoid weaknesses 3.2.1 Focused code files 3.2.2 Metadata for content experts 3.3 Scales 3.3.1 Single source &amp; single analysis ...">
<!-- JS --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://kit.fontawesome.com/6ecbd6c532.js" crossorigin="anonymous"></script><script src="libs/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
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div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
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<footer class="bg-primary text-light mt-5"><div class="container"><div class="row">

<div class="col-12 col-md-6 mt-3">
<p>"<strong>Collaborative Data Science Practices</strong>" was written by Will Beasley. It was last built on 2024-07-08.</p>
<p>"<strong>Collaborative Data Science Practices</strong>" was written by Will Beasley. It was last built on 2024-08-26.</p>
</div>

<div class="col-12 col-md-6 mt-3">
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<meta name="twitter:description" content="Automation is an important prerequisite of reproducibility. 10.1 Mediator A nontrivial project usually has multiple stages in its pipeline. Instead of a human deciding when to execute which...">
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div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
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<footer class="bg-primary text-light mt-5"><div class="container"><div class="row">

<div class="col-12 col-md-6 mt-3">
<p>"<strong>Collaborative Data Science Practices</strong>" was written by Will Beasley. It was last built on 2024-07-08.</p>
<p>"<strong>Collaborative Data Science Practices</strong>" was written by Will Beasley. It was last built on 2024-08-26.</p>
</div>

<div class="col-12 col-md-6 mt-3">
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git remote set-head origin -a
```

GitHub Personal Access Token (PAT)
------------------------------------

The tokens have two purposes that we encounter regularly.

### Pushing to any repo or reading from a private repo

...especially on Linux machines that don't have [GitHub Desktop](https://desktop.github.com/).

{TODO: write this section}

### Using the [remotes](https://remotes.r-lib.org/) package

If you are using the [remotes](https://remotes.r-lib.org/) with a line like
`remotes::install_github("Melinae/TabularManifest")` or `remotes::install_github("tidyverse/ggplot2")`,
you may encounter this error:

```
Using GitHub PAT from the git credential store.
Error: Failed to install 'unknown package' from GitHub:
HTTP error 401.
Bad credentials
```

If so,
1. Create a classic personal access token at <https://github.com/settings/tokens>.
(Make sure you're logged in.)
We suggest creating one per machine, so you don't have to juggle them between computers.
1. Maybe name it "ouhsc-desktop" or "home-laptop" (obligatory reminder to never store PHI on a personal machine).
Copy the new token to your clipboard.
1. Then use the [gitcreds](https://gitcreds.r-lib.org/) package by running, `gitcreds::gitcreds_set()`.
Then select to add/replace the token with the value that you just copied to your clipboard.
1. Rerun the `remotes::install_github()`.

Repo Style
------------------------------------

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<meta name="twitter:description" content="2.1 Simplify 2.1.1 Data Types Use the simplest data type reasonable. A simpler data type is less likely contain unintended values. As we have seen, a string variable called gender can...">
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div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
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<footer class="bg-primary text-light mt-5"><div class="container"><div class="row">

<div class="col-12 col-md-6 mt-3">
<p>"<strong>Collaborative Data Science Practices</strong>" was written by Will Beasley. It was last built on 2024-07-08.</p>
<p>"<strong>Collaborative Data Science Practices</strong>" was written by Will Beasley. It was last built on 2024-08-26.</p>
</div>

<div class="col-12 col-md-6 mt-3">
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<meta name="twitter:description" content="12.1 Social Contract Issues Organized Commits &amp; Coherent Diffs Branch &amp; Merge Strategy 12.2 Code Reviews Daily Reviews of PRs Periodic Reviews of Files 12.3 Remote Headset &amp; sharing screens ...">
<!-- JS --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://kit.fontawesome.com/6ecbd6c532.js" crossorigin="anonymous"></script><script src="libs/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
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div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
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<footer class="bg-primary text-light mt-5"><div class="container"><div class="row">

<div class="col-12 col-md-6 mt-3">
<p>"<strong>Collaborative Data Science Practices</strong>" was written by Will Beasley. It was last built on 2024-07-08.</p>
<p>"<strong>Collaborative Data Science Practices</strong>" was written by Will Beasley. It was last built on 2024-08-26.</p>
</div>

<div class="col-12 col-md-6 mt-3">
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