Merge pull request #232 from monicagiraldochica/create_advanceGitGuide

advanced github guide

Author: monicagiraldochica

docs/_static/img/GitHubAdvGuide_enblPgs.png

@@ -90,7 +90,7 @@ Most applications do not use more than one CPU core. Single-thread jobs that req
 
 #### Multi-thread
 
-A multi-thread application is able to use multiple cores on a single server by spawning multiple threads from a single process. Each thread uses one CPU core, and all share memory. For a multi-thread application, we can use a single task, and specify multiple cpus per task.
+A multi-thread application is able to use multiple cores on a single server by spawning multiple threads from a single process. Each thread uses one CPU core, and all share memory. For a multi-thread application, we can use a single task, and specify multiple CPUs per task.
 
 ```txt
 #SBATCH --ntasks=1
@@ -166,7 +166,7 @@ Job scheduling policies include resource limits on partitions and QOS's, and a f
 
 ### Fairshare
 
-Fairshare is a scheduler algorithm that manages job priority, based on a comparison of all cluster utilization, to promote equal use the cluster. Fairshare tracks daily usage and uses data from the previous 7 days to adjust job priority. The effect of fairshare data is reduced each day using a decay factor. In practice, when a user increases their cluster utilization, their job priority is lowered compared to other users.
+Fairshare is a scheduler algorithm that manages job priority, based on a comparison of all cluster utilization, to promote equal use of the cluster. Fairshare tracks daily usage and uses data from the previous 7 days to adjust job priority. The effect of fairshare data is reduced each day using a decay factor. In practice, when a user increases their cluster utilization, their job priority is lowered compared to other users.
 
 Fairshare effectively allows infrequent users a fair chance to run their jobs on the cluster among the many jobs of more frequent users.
 

docs/_static/img/GitHubAdvGuide_img1.png

@@ -1,10 +1,10 @@
-# How to use Jupyter Notebook in the cluster
+# Jupyter Notebook
 
 ## Connect to OnDemand
 
 In our cluster, **Jupyter can only be run through OnDemand**. To connect to Open OnDemand, please follow our [Connecting Guide](../cluster/access/ondemand.md).
 
-## Open the Jupyter Notebook App inside OnDemand
+## Open the Jupyter Notebook
 
 To open Jupyter Notebook, please follow the instructions in our [Open OnDemand Guide](../cluster/access/ondemand.md#jupyter-notebook-example).
 
@@ -19,7 +19,7 @@ pip install matplotlib --user
 
 **You will need to restart your Kernel** in Jupyter Notebook to capture the changes. In the top menu, click Kernel and then Restart Kernel.
 
-## Activate a python environment
+## Activate python environment
 
 If you have installed a Python environment in your home directory, you can use it inside Jupyter Notebook. Go to the Terminal and login to the cluster. Then, run the following commands, replacing `myenv` by the name of your python environment. This name should be unique, if another Kernel with the same name exists, it will be replaced. If you get a `No module named ipykernel` error message, install ipykernel in the python environment, like so:
 
@@ -39,7 +39,7 @@ deactivate
 
 Now you can open a new or an existing Jupyter Notebook. In the upper menu, click on Kernel, then Change Kernel, and select "Python (myenv)". Now Jupyter Notebook will use your selected Python environment. You may need to restart the kernel to use updated packages.
 
-## Activate a conda environment
+## Activate conda environment
 
 If you have a Conda environment in your home directory, you can use it inside Jupyter Notebook. Go to the Terminal and login to the cluster. Then, run the following commands, replacing `mycondaenv` by the name of your conda environment. This name should be unique, if another Kernel with the same name exists, it will be replaced. The last step, deactivating your conda environment, is important. Otherwise, you will have problems opening Jupyter Notebook.
 
@@ -127,11 +127,11 @@ IPython magic commands provide shortcuts for common tasks. To see the list of al
 | `%time` | Print the execution time of a line. |
 | `%who` | See list of environment variables. |
 
-### Executing shell commands
+### Shell commands
 
 As we saw in the table above, you can execute a cell as Bash instead of Python using the `%%bash` magic command. But you can also execute a single line as bash by preceding the line with `!`.
 
-If the current Kernel is from a [Conda environment](#activate-a-conda-environment), you might get `command not found` errors when trying to run binaries included in your conda environment. This is because the command is not available in the default shell environment used by Jupyter Notebook. Jupyter Notebook will not automatically activate your Conda environment when using shell commands with `!`. In order to do that you would have to add the following code to a cell and then execute it:
+If the current Kernel is from a [Conda environment](#activate-conda-environment), you might get `command not found` errors when trying to run binaries included in your conda environment. This is because the command is not available in the default shell environment used by Jupyter Notebook. Jupyter Notebook will not automatically activate your Conda environment when using shell commands with `!`. In order to do that you would have to add the following code to a cell and then execute it:
 
 ```python
 import os
@@ -148,11 +148,11 @@ myfiles = !ls
 print(myfiles[2])
 ```
 
-### Writing cells using Markdown
+### Markdown cells
 
 You can run cells as Markdown using the magic command shown in the table above `%%markdown` or selecting Markdown as the language of the current cell. [The Markdown Guide](https://www.markdownguide.org/getting-started/){:target="_blank"} is a great place to start learning Markdown.
 
-### Use Latex to display formulas
+### Latex formulas
 
 You can use Latex to display formulas within Markdown cells. To display Latex code within the current line, surround your expression with a dollar sign on each side. For example: `$x2+y2=8$`. To display the formula in a separate line, wrap it with two dollar signs before and after the Latex code.
 
@@ -164,7 +164,7 @@ Will generate the following output when run:
 
 ![Latex example output](LatexExampleOutput.png)
 
-### Display media inside your notebook
+### Display media
 
 You can display different type of media in your Jupyter Notebook, including images, audio, video or PDF files.
 

docs/_static/img/branches.png

@@ -8,7 +8,9 @@ Bash and Python are among the most commonly used programming languages in data s
 
 [Python guide](https://www.w3schools.com/python/){:target="_blank"}: This guide provides everything you need to know to become a Python programmer capable of analyzing, manipulating, and visualizing large datasets. Key topics widely used in data science are covered, including modules such as NumPy, pandas, SciPy, Django, and the Matplotlib library. You'll also find information on machine learning, working with databases, and much more.
 
-[Markdown Guide](https://www.markdownguide.org/getting-started/){:target="_blank"}: This is a comprehensive guide that covers everything from how does it work and its most common applications to explanations of basic and extended syntax and some useful hacks.
+[Markdown guide](https://www.markdownguide.org/getting-started/){:target="_blank"}: This is a comprehensive guide that covers everything from how does it work and its most common applications to explanations of basic and extended syntax and some useful hacks.
+
+[HTML guide](https://www.w3schools.com/Html/){:target="_blank"}: In this tutorial you will find anything you need about html. It is targeted to programmers with any level of experience as it covers a very wide range of topics.
 
 ## Tools
 
@@ -26,7 +28,9 @@ An IDE, or Integrated Development Environment, is an application for software de
 
 The most commonly used version control tools by software developers are Git and GitHub. They can be used in research to organize and share scripts, recover from accidental loss of data, create excellent documentation on your projects, showcase your work, and keep track of changes in your code. It is important to note that Git and GitHub are different things even though they work hand by hand. On one hand, Git is a version control tool that can be used outside Github and allows you to track changes in files. On the other hand, GitHub is a web-based platform that hosts repositories and uses Git.
 
-[Our Git and GitHub Guide](../software/git.md): This complete guide will take you through the steps on how to configure git, create a new repository and host it on GitHub, as well as creating and managing branches and merging changes with your main remote branch.
+[Our Beginners Git and GitHub Guide](../software/git.md): This guide will take you through the steps on how to configure git, create a new repository and host it on GitHub. It is a good place to start if you have no experience with git.
+
+[Our Advanced Git and GitHub Guide](../software/advanced_git.md): This guide covers how to create a GitHub page, use branches to edit your documentation and collaborate with others, and how to resolve merge conflicts and other issues.
 
 ### Time Management Tools