caplter-research-protocols

Repository of CAP LTER field and lab protocols for long-term monitoring projects

How to make updates to protocols using GitKraken:

1. GitKraken will recognize every file that has had a change. Select each pending file that is ready to upload by clicking "Stage file". If every file is ready to upload, select "Stage all changes".

Figure 1. Selecting files to upload.

2. Add a Commit Message describing the changes made. Click "Stage files/changes to commit" to finalize changes.

Figure 2. Staging/committing files, with Commit Message.

3. A new branch will appear with your changes. Currently, those changes reside locally, and are not yet online. To merge your changes with the online CAP repository, click "Push".

Figure 3. Pushing local branch online to origin.

4. To verify your changes have successfully been uploaded, a notification should appear in the corner of your screen saying "Pushed Successfully". Additionally, there should only be one branch present in Gitkraken, with both the "origin" and "local" icons.

Figure 4. Pushed Successfully. Red arrow: both "origin" and "local" icons.

Github Markdown Cheat Sheet:

Use these tips to help you make edits to the Markdown files. For more Markdown tips, check out this link.

Bold/Italic

Surround text with two asterisks or underscores to make it **bold**.

Surround text with two asterisks to make it bold.

Surround text with one asterisk to make it _italic_.

Surround text with one asterisk to make it italic.

Combine the two for _**bold italic**_.

Combine the two for bold italic.

Lists

1. Use this syntax for a numbered list.
2. Second item.
2. Number order doesn't matter.
   1. Use three leading spaces to add a nested list.
   2. Like this.
4. Back to the list.

1. Use this syntax for a numbered list.
2. Second item.
3. Number order doesn't matter.
   1. Use three leading spaces to add a nested list.
   2. Like this.
4. Back to the list.

* Use this syntax for a bulleted list.
* Asterisks, pluses, and dashes can be used as bullets.
+ Github will group different bullets into different lists.
+ Notice the spacing above.
   + Use three leading spaces to add a nested list.
+ Back to the list.

• Use this syntax for a bulleted list.
• Asterisks, pluses, and dashes can be used as bullets.

• Github will group different bullets into different lists.
• Notice the spacing above.
  • Use three leading spaces to add a nested list.
• Back to the list.

Links (and Line Breaks)

Use the following syntax to insert links.

[Link 1: Inline-style link](https://www.google.com)   <- three trailing spaces
[Link 2: Inline-style link w/ title](https://www.google.com "Google")

Link 3, the URL itself: https://www.google.com

Link 1: Inline-style link
Link 2: Inline-style link w/ title

Link 3, the URL itself: https://www.google.com

Note that the first two links are grouped together in the same paragraph, while the third link begins a separate paragraph. This is due to the number of newlines between each link. Between Link 1 and Link 2, there is only one newline, while between Link 2 and Link 3, there are 2 newlines.

If you want to separate two lines within the same paragraph (using only 1 newline), add three trailing spaces to the end of the first line. Otherwise, Github will not separate them.

Example:

These lines have no trailing spaces.
Github won't separate them.

These lines have three trailing spaces.   <- three trailing spaces
This will be written as a new line in the same paragraph.

These lines have no trailing spaces. Github won't separate them.

These lines have three trailing spaces.
This will be written as a new line in the same paragraph.

Images

Use the following syntax to insert an image.

![alt text](LINK "Title Text")

The link can either be a web link or a relative path to an image in the Github repository. Links are cap-sensitive.

![alt text](https://www.allaboutbirds.org/guide/assets/photo/67385731-480px.jpg "Example")

![alt text](ADP/Images/ADP_Sample_Processing_Fig1.PNG "ADP Sample Processing")

Subscript/Superscript

To write text in subscript, surround it with the <sub>html sub tag</sub>.

To write text in subscript, surround it with the _{html sub tag}.

For superscript, surround the text with the <sup>html sup tag</sup>.

For superscript, surround the text with the ^{html sup tag}.

H<sub>2</sub>O
e=mc<sup>2</sup>

H₂O
e=mc²

Symbols

You can insert symbols in Github Markdown using character entities. To do this, use the following syntax: an ampersand, the character entity code, and a semicolon. Here are some of the most common ones used in the protocols; for a more extensive list, see this link.

±
Δ
θ
μ
π
≥
≤
→

±
Δ
θ
μ
π
≥
≤
→

Headers

# Use one pound sign for the title heading at the top of each protocol. (Header 1)
## Use two pound signs for each main heading in the protocols. (Header 2)
### Use three pound signs for subheadings. (Header 3)

Header 1

Header 2

Header 3