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* adding logo

* update logo and some minor edits

* update syles

* update submission guidelines

* adding pip

* completed how to cite

* update bibliography instructions

* adding submission guidelines

* updates

* adding SEA Logo

* update submission guidelines

* update template
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negin513 committed Apr 30, 2024
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91 changes: 67 additions & 24 deletions notebooks/notebook-template.ipynb
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"cell_type": "markdown",
"metadata": {},
"source": [
"You can use LaTeX syntax for equations in your documents. Math can be displayed either using $$ symbols to wrap the equation or by using the \\begin{equation} to start an equation block. Please see the examples below: \n",
"\n",
"Example 1: \n",
"### Math and Equations\n",
" \n",
"Equations can be included in your notebooks by either using `$$` symbols to wrap the equation or by using the `\\begin{equation}` to start an equation/math block. Please see the examples below: \n",
"\n",
"Example 1: Using `$$`\n",

"\n",
"$$\n",
"x = \\frac{-b \\pm \\sqrt{b^2 - 4ac}}{2a}\n",
"$$\n",
"\n",
"\n",
"For example, here is an example of a cross-product, which we can reference later in the docs. \n",
"You can use LaTeX syntax for equations in your documents. For example, here is an example of a cross-product:\n",
"\n",
"Example 1: \n",
"Example 2: \n",
"\n",
"\\begin{equation}\n",
"\\label{matrix}\n",

"\\mathbf{u} \\times \\mathbf{v}=\\left|\\begin{array}{ll}u_{2} & u_{3} \\\\ v_{2} & v_{3}\\end{array}\\right| \\mathbf{i}+\\left|\\begin{array}{ll}u_{3} & u_{1} \\\\ v_{3} & v_{1}\\end{array}\\right| \\mathbf{j}+\\left|\\begin{array}{ll}u_{1} & u_{2} \\\\ v_{1} & v_{2}\\end{array}\\right| \\mathbf{k}\n",
"\\end{equation}\n",
"\n",
"\n",
"Using the `$$` syntax, we can also use `\\label{label-name}` to add a label to the equation, which we can reference later. For example, here is the example1 equation with a label:\n",
"Using the `\\begin{equation}` syntax, we can also use `\\label{label-name}` to add a label to the equation, which we can reference later.\n",
"\n",
"using the `$$` syntax, one can easily reference the equation too. For example here is the equation 1 with a label added that can be referenced:\n",
"\n",
"$$\n",
"x = \\frac{-b \\pm \\sqrt{b^2 - 4ac}}{2a}\n",
"$$ (my_label)\n",
"\n",
"\n",
"#### Linking to equations\n",
"\n",
"You can easily link to these equations using `{eq}label` syntax. For example:\n",
"\n",
"$$ \\label{one-liner} Ax=b $$\n"
"- A link to example 2 equation : {eq}`matrix`\n",
"- A link to example 3 equation : {eq}`my_label`"
]
},
{
Expand All @@ -79,22 +97,29 @@
"### Cross-Referencing \n",
"MyST has support for figures, images and rich cross-references to preview the figures when you hover over a reference.\n",
"\n",
"To reference a figure in your notebook, first add the figure with a `label` or a `name`. Next use the label to reference it. \n",
"\n",
"🛠 Double click the next cell to see the MyST `{figure}` syntax.\n",
"\n",
"```{figure} https://artsourceinternational.com/wp-content/uploads/2018/04/P-1984-1.jpg\n",
":label: my-fig\n",
":label: mountain-fig\n",
":align: center\n",
"\n",
"My **bold** mountain 🏔🚠.\n",
"```\n",
"\n",
"Check out [](#my-fig)!!"
"Check out how we referenced [](#mountain-fig)!!\n",
"\n",
":::{seealso}\n",
"To see more examples on cross-referencing figures, please see [this page](https://jupyterbook.org/en/stable/content/references.html#reference-figures).\n",
":::"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [

"### Code Block Outputs\n",
"\n",
"Jupyter Book will also embed your code blocks and output in your book. For example, here’s some sample Matplotlib code:"
Expand Down Expand Up @@ -179,7 +204,8 @@
"\n",
"### Feature: Inline variable evaluation (eval)💪\n",
"\n",
"There are a few other nifty things that you can do with MyST Markdown below. You can also see all of the live demos in the documentation at <https://mystmd.org/guide>. \n",
"There are a few other nifty things that you can do with MyST Markdown below.\n",

"\n",
"\n",
"You can use the `{eval}` role to evaluate variables directly inside of your markdown cells, including widgets, sparklines and other variables.\n",
Expand All @@ -189,29 +215,43 @@
},
{
"cell_type": "code",
"execution_count": 8,
"execution_count": null,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"array([ 3.21268345, 4.27245096, 5.4818639 , 6.64996325, 7.18688751,\n",
" 8.82407456, 9.21284497, 10.32676994, 11.3190472 , 12.19617186])"
]
},
"execution_count": 8,
"metadata": {},
"output_type": "execute_result"
}
],
"outputs": [],

"source": [
"monthly_mean = np.median(data, axis=0)\n",
"monthly_mean"
]
},
{
"cell_type": "markdown",
"metadata": {},
"metadata": {
"user_expressions": [
{
"expression": "np.max(data, axis=0)",
"result": {
"ename": "NameError",
"evalue": "name 'np' is not defined",
"status": "error",
"traceback": [
"\u001b[0;31mNameError\u001b[0m\u001b[0;31m:\u001b[0m name 'np' is not defined\n"
]
}
},
{
"expression": "monthly_mean",
"result": {
"ename": "NameError",
"evalue": "name 'monthly_mean' is not defined",
"status": "error",
"traceback": [
"\u001b[0;31mNameError\u001b[0m\u001b[0;31m:\u001b[0m name 'monthly_mean' is not defined\n"
]
}
}
]
},
"source": [
"The maximum temperature each month is {eval}`np.max(data, axis=0)` and average temperature is {eval}`monthly_mean`.\n",
"\n",
Expand All @@ -233,6 +273,9 @@
"source": [
"## References\n",
"\n",
"Using the following syntax will automatically create the bibliography from the `references.bib` file. \n",
"\n",

" ```{bibliography}\n",
" ```"
]
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20 changes: 12 additions & 8 deletions submission-guidelines.md
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2. **Name your Repository**: Name your repository using the following naming convention: `SEA-ISS-2024-<paper-title>`. For example, if your paper title is "My Awesome Paper", your repository name should be `SEA-ISS-2024-My-Awesome-Paper`.

```{note}
For your submissions, please use the following naming convention for your paper repository: `SEA-ISS-2024-<paper-title>`. For example, if your paper title is "My Awesome Paper", your repository name should be `SEA-ISS-2024-My-Awesome-Paper`.
```


3. **Activate GitHub Pages**: Once you created your repository, go to the settings of your repository, scroll down to the "Pages" section, and under "Build and deployment" choose Source: "GitHub Actions". This will allow you to view your Jupyter Book online.
This will be automatically triggered when you push your changes to your repository. Once you activate this, you can view your Jupyter Book by clicking on the link provided in the "Pages" section of your repository settings.

Expand All @@ -27,7 +32,6 @@ This will be automatically triggered when you push your changes to your reposito
└── notebook2.ipynb
```


This framework supports [the MyST Markdown language](https://jupyterbook.org/en/stable/reference/glossary.html#term-MyST) in Markdown and notebook documents. This allows users to write rich, publication-quality markup in their documents.

7. **Update the Table of Contents**: Update the `toc.yml` file to include the notebooks you've added.
Expand All @@ -38,6 +42,7 @@ This will be automatically triggered when you push your changes to your reposito

10. **Check your Jupyter Book**: Once you've pushed your changes, check that your Jupyter Book is building correctly. You can check the status of your Jupyter Book by clicking on the "Actions" tab of your repository.


```{tip}
**Citations and Bibliography**: For adding citations to your paper and referencing others, please see our detailed guidelines [here](notebooks/notebook-example2_references.md). In short, after adding your references to your `references.bib` file, you can add the citation to your paper using the `{cite}[authoryearkey]` syntax.
```
Expand All @@ -51,6 +56,8 @@ This will be automatically triggered when you push your changes to your reposito
* Navigate to the settings of your paper repository, scroll down to the Danger Zone, and click "Transfer" .
* Select or type "UCAR-SEA" to transfer the repository to the conference organizers. This step will make your paper public and allow the conference organizers to review your paper.



### Make Zenodo DOI for your paper

12. **Make Zenodo DOI for your paper:** Once you've completed the steps above, you can make Zenodo DOI for your paper:
Expand All @@ -60,6 +67,7 @@ This will be automatically triggered when you push your changes to your reposito
* You need to first create a new release for your paper repository. Click on "Create a new release" and add the version number of your paper. For example, if this is the first version of your paper, you can add "v1.0.0" as the version number.
* Once you've created a new release, you can go back to the "New Upload" page and select the version of your paper and create a new DOI for your paper.


13. **Update the DOI badge**: Once you've created a new DOI for your paper, you can update the DOI badge in the README.md file of your paper repository with the new DOI.

## Configure Binder for your paper:
Expand All @@ -69,18 +77,14 @@ This will be automatically triggered when you push your changes to your reposito
* For those who would like their papers to be easily launched in an executable environment based upon the specifications in the repository, you can update the Binder badge in the README.md to appropriately reflect your repository name and path to your notebooks. You can find more information about how this works on the [My Binder website](https://mybinder.org/).
* If your notebooks are not interative or you would rather not include this feature, simply remove the line for the Binder badge in the README.md file.


-----------------


```{tip}
You can submit your paper as one notebook or split it up to multiple notebooks and markdown files. Please see the [example paper1](notebooks/notebook-template) and [example paper2](notebooks/notebook-example2_part1) for examples of how to structure your paper.
```

```{note}
For your submissions, please use the following naming convention for your paper repository: `SEA-ISS-2024-<paper-title>`. For example, if your paper title is "My Awesome Paper", your repository name should be `SEA-ISS-2024-My-Awesome-Paper`.
```




```{note}
Please reach out to the conference organizers or open an issue or a discussion in this repository if you have any questions or need help with your submission.
```

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