Merge pull request #9 from csdms/mdpiper/version-control

Create version control lessons

lessons/git/README.md

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+index.md

lessons/git/configuring-git.md

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+![ESPIn logo](../../media/ESPIn.png)
+
+# Configuring git
+
+When using `git` for the first time on a computer,
+some setup is required.
+Start by opening a terminal
+(your preferred terminal app on Linux or macOS;
+the Git Bash Shell on Windows).
+
+Make sure `git` is installed and in the application search path:
+```
+$ git --version
+```
+
+Configure `git` on your machine with the following commands:
+```
+$ git config --global user.name "[your name]"
+$ git config --global user.email "[your email address]"
+```
+Substitute your name and email address in the brackets above.
+This information is used by `git`,
+as well as GitHub and other `git`-based services.
+(A quick reminder,
+if you haven't already done so,
+please [sign up](https://github.com/signup) for an account on GitHub.)
+
+You can also set the default editor used with `git`:
+```
+$ git config --global core.editor "nano -w"
+```
+We'll use `nano` by default,
+but if you prefer a different editor,
+the Software Carpentry [lesson](https://swcarpentry.github.io/git-novice/02-setup/index.html)
+on version control has a summary table
+with configuration commands for various editors.
+
+Check the configuration you set:
+```
+$ git config --list
+```
+
+
+## Command structure
+
+Note that the syntax for using `git` is slightly different than what we saw
+for the commands in the [shell lesson](../shell/index.md).
+`git` uses *subcommands*.
+All calls to `git` look like `git [subcommand] [options]`.
+This is a not uncommon syntax for shell commands.
+We'll see other software (e.g., `conda`) that uses a similar subcommand syntax.
+
+
+## Getting help with git
+
+`git` provides several ways to get help.
+Get help on the `git` command itself:
+```
+$ git --help
+```
+The output from this command shows the most common subcommands.
+Get help on a specific subcommand with:
+```
+git [subcommand] --help
+```
+replacing the brackets with the subcommand;
+e.g., `git config --help` will provide detailed information
+on all of the options for the `config` subcommand.
+
+To see a list of all subcommands, try:
+```
+$ git --help -a
+```
+
+`git` also has a (very long) `man` page:
+```
+man git 
+```
+
+Finally,
+the full [git documentation](https://git-scm.com/docs) is available online.
+
+
+## Summary
+
+`git`:
+
+* needs to be configured on a computer before it's used
+* uses subcommands
+* provides several ways to get help
+
+___
+
+[Introduction to version control](./index.md) |
+Previous: [index](./index.md) |
+Next: [Version control in a single-user project](./git-single-user-project.md)

lessons/git/git-collaborative-project.md

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+![ESPIn logo](../../media/ESPIn.png)
+
+# Version control in a collaborative project
+
+In this section,
+we'll work through an example that broadly demonstrates
+how to use version control for a collaborative project.
+Imagine, for instance,
+using version control to back up and track
+your thesis, a class project, or a journal article<sup>[1](#git-fn1)</sup>.
+This is where GitHub is powerful.
+
+
+## Fork a repository on GitHub
+
+We'll start by *forking* a repository on GitHub.
+A fork is a copy of a repository placed under your GitHub account.
+Forks are used for repositories where you don't have write access
+(meaning you can view files, but not change them).
+Note that forking is a GitHub, not a `git`, concept.
+
+Let's use the ESPIn course repository as an example.
+(We've held off on doing this earlier
+because this is the proper way to do it.)
+
+
+1. Go to the [ESPIn repository](https://github.com) on GitHub.
+1. From the top right of the repository page, select the *Fork* button--you'll
+   be asked where to create the fork; select your GitHub account.
+
+After the fork is created,
+the path to the repository on GitHub will read
+**[username]/espin** instead of **csdms/espin**,
+where **[username]** is your GitHub username,
+indicating your ownership of this copy of the repository.
+
+
+## Clone the repository
+
+The forked repository lives on GitHub.
+To work with it,
+you have to clone it to your computer.
+
+On your computer, open a terminal and change to your **Desktop** directory:
+```
+$ cd ~/Desktop
+```
+
+Now clone the fork from GitHub.
+```
+$ git clone https://github.com/[username]/espin
+```
+where the bracketed text should be replaced with your GitHub username.
+
+The repository is cloned into the directory **espin**.
+Change to it and view its contents:
+```
+$ cd espin
+$ pwd
+/Users/mpiper/Desktop/espin
+$ ls
+LICENSE          data             lessons
+README.md        environment.yaml media
+```
+
+
+## Make a branch
+
+Next,
+to prepare for making changes to the repository,
+let's make a new branch.
+Recall a branch is an alternate timeline for the history of a repository.
+Branches are used in a collaborative project to propose changes.
+
+The syntax for creating a branch is `git branch [branchname]`.
+It's a convention to use imperative case for the branch name,
+and to prepend your GitHub username.
+Looking ahead,
+let's name this branch `change-colormap`.
+If your GitHub username is `@mdpiper`,
+this would be:
+```
+$ git branch mdpiper/change-colormap
+```
+
+Although we've created a new branch,
+our *current branch*,
+the one accepting changes,
+is still the default `main` branch,
+as we can see with `git status`:
+```
+$ $ git status
+On branch main
+Your branch is up to date with 'origin/main'.
+
+nothing to commit, working tree clean
+```
+
+Alternately,
+we can use the `git branch` command to see the current and available branches:
+```
+$ git branch
+* main
+  mdpiper/change-colormap
+```
+Here, the current branch is marked with an asterisk.
+
+To change the current branch,
+use the `git checkout` subcommand
+(again, for a hypothetical user `@mdpiper` (red panda)):
+```
+$ git checkout mdpiper/change-colormap
+Switched to branch 'mdpiper/change-colormap'
+```
+You can verify that the new branch is current with `git status` or `git branch`.
+
+
+## Modify a file in the repository
+
+As we did in the previous example,
+let's change the colormap in the sample Python script;
+however, this time we'll do so in your fork of the ESPIn repository.
+
+Use your text editor to open the Python script:
+```
+$ nano ./lessons/se/boulder_dem.py
+```
+and recall that we'd like to change the colormap from "jet" to "viridis"
+on line 21 of the file, like so:
+```python
+elev = ax.imshow(data, cmap="viridis")
+```
+Once you've made the change, save the file and exit the editor.
+
+Using `git status`, we can see that the file has been modified.
+```
+$ git status
+On branch mdpiper/change-colormap
+Changes not staged for commit:
+  (use "git add <file>..." to update what will be committed)
+  (use "git checkout -- <file>..." to discard changes in working directory)
+
+	modified:   lessons/se/boulder_dem.py
+
+no changes added to commit (use "git add" and/or "git commit -a")
+```
+
+Commit the change to the branch
+(noting that we're again skipping the staging step):
+```
+$ git commit lessons/se/boulder_dem.py -m "Use viridis colormap for display"
+[mdpiper/change-colormap 5b0d87c] Use viridis colormap for display
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+```
+
+
+## Push changes to GitHub
+
+Now that we've made a change to the local copy of the fork,
+let's push the change back to the remote:
+```
+$ git push origin mdpiper/change-colormap
+Counting objects: 10, done.
+Delta compression using up to 4 threads.
+Compressing objects: 100% (10/10), done.
+Writing objects: 100% (10/10), 91.63 KiB | 45.81 MiB/s, done.
+Total 10 (delta 6), reused 1 (delta 0)
+remote: Resolving deltas: 100% (6/6), completed with 4 local objects.
+remote:
+remote: Create a pull request for 'mdpiper/change-colormap' on GitHub by visiting:
+remote:      https://github.com/mdpiper/espin/pull/new/mdpiper/change-colormap
+remote:
+To https://github.com/mdpiper/espin.git
+ * [new branch]      mdpiper/change-colormap -> mdpiper/change-colormap
+```
+Note that the output from `git push` is more verbose
+that in the previous, single-user, example;
+it includes a link to create a *pull request* on GitHub.
+Copy/paste this link into your browser
+and we'll create a pull request next.
+
+
+## Create a pull request
+
+A *pull request* is a GitHub feature
+that allows you to argue why the changes that you've pushed to a repository
+deserve to be included in that repository.
+In a pull request,
+you have to make a case to the owner of the repository
+that your code improves on theirs.
+
+A pull request includes a title, a body,
+and, optionally, a comment thread.
+The title should be as brief, yet descriptive, as possible,
+and written as an imperative.
+The body is used to explain your changes
+and to argue for their inclusion in the repository.
+To help make the text more descriptive,
+the body is written in [Markdown](https://docs.github.com/en/github/writing-on-github/basic-writing-and-formatting-syntax),
+a simple markup language.
+In the body,
+you can also `@` other GitHub users (e.g., `@BCampforts`)
+to include them on the pull request.
+The comment thread is used to discuss the merits of the pull request.
+
+GitHub provides [much more information](https://docs.github.com/en/github/collaborating-with-issues-and-pull-requests/about-pull-requests)
+on pull requests.
+
+Argue well, and your contribution may be accepted by the repository owner!
+
+
+## Summary
+
+The power of GitHub lies in its streamlined support for collaborative development.
+GitHub has rewritten the rules for open source software development,
+and this has diffused into the modern practice of science,
+For example,
+all CSDMS products are open source.
+If you find a problem in our software, documentation,
+Jupyter Notebooks, etc.,
+please fix it and send us pull request!
+You'll get credit for your contribution.
+
+
+This table summarizes `git` and GitHub concepts covered in this section:
+
+| Concept      | Description
+| ------------ | -----------
+| fork         | a repository copied from elsewhere on GitHub that exists under your GitHub account
+| current branch | the active repository branch accepting changes
+| pull request | A process for explaining changes pushed to a repository
+
+This table summarizes the `git` subcommands used in this section:
+
+| Subcommand | Description
+| ---------- | -----------
+| branch     | create a branch of a repository
+| checkout   | set a branch as the current branch in a repository
+
+
+<a name="git-fn1">1</a>: Yes, that was on purpose.
+
+___
+
+[Introduction to version control](./index.md) |
+Previous: [Version control in a single-user project](./git-single-user-project.md)