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62 changes: 41 additions & 21 deletions _sources/git.rst.txt
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GIT tips
========

Getting Started with Git and GitHub
-----------------------------------
If you are new to Git and GitHub, this page helps you getting started by explaining
how to make some modification to a repository. The explaining assumes that you
are trying to modify this website, but it should work for most repositories.

1. Set Up Your SSH Key
______________________

To securely connect with GitHub, you'll need to add your SSH key to your GitHub account. Here you can find how to `add your public key <https://docs.github.com/en/authentication/connecting-to-github-with-ssh/adding-a-new-ssh-key-to-your-github-account>`_ .
To securely connect with GitHub, you'll need to add your SSH key to your GitHub
account. |public_key|, you can find how to add your public key to your account.

.. |public_key| raw:: html

<a href="https://docs.github.com/en/authentication/connecting-to-github-with-ssh/adding-a-new-ssh-key-to-your-github-account" target="_blank">here</a>

2. Clone a GitHub Repository
____________________________

Navigate to the directory where you want to download the repository, then use the :code:`git clone` command:
If you are not a member of the `psm-compute` organization, fork
the repository (i.e. create a duplicate of the repository in your own GitHub account),
then clone it (see below).

If you are a member, natigate to the |repository|, click on `Code`, then copy
the `SSH` link and clone the repository using :code:`git clone` :

.. |repository| raw:: html

<a href="https://github.com/psm-compute/psm-compute.github.io" target="_blank">here</a>

.. code:: bash
git clone [email protected]:psm-compute/psm-compute.github.io.git
This command will create a copy of the repository in your specified directory.
This command will create a local copy of the repository on your computer.

3. Check the Status of Your Repository
______________________________________

After cloning, it's a good practice to check the status of your repository to see if there are any changes:
From you computer, when you start making modifications to the files, it's a
you can check the status of your repository to see if there are any changes:

.. code:: bash
Expand All @@ -34,18 +50,23 @@ After cloning, it's a good practice to check the status of your repository to se
4. Create and Switch to a New Branch
____________________________________

To make changes without affecting the main branch, create a new branch and switch to it. Let's make a test updating `README.md` file.
To make changes without affecting the main branch, create a new branch:

.. code:: bash
git branch update_readme
git checkout update_readme
and then, switch to the new branch:

.. code:: bash
git checkout update_readme
5. Edit Files and Stage Changes
_______________________________

Make the necessary edits to your files. For example, to edit the `README.md` file, use a text editor like `vi`:
Make the necessary edits to the files. For example, to edit the `README.md` file,
use a text editor like `vi`:

.. code:: bash
Expand All @@ -70,15 +91,16 @@ Commit your changes with a descriptive message:

.. code:: bash
git commit -m "Test change README.md"
git commit -m "Modified the README.md file"
Next, push your changes to GitHub. If it's the first time you're pushing from this branch, you'll need to set the upstream branch:
Next, push your changes to GitHub:

.. code:: bash
git push
If you encounter an error, you'll typically need to set the upstream for the branch:
If it's the first time you're pushing from this branch, you'll need to set the
upstream branch:

.. code:: bash
Expand All @@ -87,19 +109,17 @@ If you encounter an error, you'll typically need to set the upstream for the bra
7. Create a Pull Request
________________________

Finally, open your web browser and navigate to the GitHub page for this project:

`<https://github.com/psm-compute/psm-compute.github.io>`_

After pushing your changes, you should see a message indicating the recent pushes. Click on **"Compare & pull request"**.

On the right side of the page, select your reviewers, and add a description if needed. This will create a pull request for your changes to be reviewed and merged.

Finally, open your web browser and navigate to the GitHub repository (|repository|):
After pushing your changes, you should see a message indicating the recent
pushes. Click on **"Compare & pull request"**. On the right side of the page,
select your reviewers, and add a description if needed. This will create a pull
request for your changes to be reviewed and merged.

8. Delete the Branch Locally (Optional)
_______________________________________

If you no longer need the branch locally, you can delete it:
Once your changes are merged with the main branch, and if you no longer need the
branch locally, you can delete it:

.. code:: bash
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35 changes: 17 additions & 18 deletions _sources/oar.rst.txt
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OAR tips
========

This page collect some tips for running jobs using the OAR system of |GRICAD|.
Feel free to add your own tricks to the list, or signal us any error.

|GRICAD|
This page collect some tips and tricks for managing jobs using the OAR system of |GRICAD|.

.. |GRICAD| raw:: html

<a href="https://gricad-doc.univ-grenoble-alpes.fr/hpc/joblaunch/job_management/" target="_blank">GRICAD</a>

Cancel All Your Jobs at Once
----------------------------

Cancel all your jobs at once by typing:

.. code:: bash
oarstat -u username | awk '{print $1}' | xargs -n 1 oardel
where username should be replaced by your ID.

Submit Jobs with Dependencies
-----------------------------

You can submit jobs with dependencies using the following example. Assume you have two job scripts, `job1.sh` and `job2.sh`, that you wish to submit:
You can submit jobs with dependencies using the following example. Assuming that
you have two job scripts, `job1.sh` and `job2.sh`, and that you wish to submit
`job2.sh` `after` `job1.sh` is done.

1. Submit `job1.sh` and capture its job ID:

Expand All @@ -38,6 +26,17 @@ You can submit jobs with dependencies using the following example. Assume you ha
oarsub -S ./job2.sh -a $job1_id
In this example, `job2.sh` will automatically wait for `job1.sh` to complete
before starting, using the job ID captured in `job1_id`.
In this example, `job2.sh` will wait for `job1.sh` to complete
before starting, using the job ID (`job1_id`).

Cancel All Your Jobs at Once
----------------------------

You can cancel all your jobs at once by typing:

.. code:: bash
oarstat -u username | awk '{print $1}' | xargs -n 1 oardel
where username should be replaced by your ID.

68 changes: 39 additions & 29 deletions git.html
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<main role="main" id="main">
<section id="git-tips">
<span id="id1"></span><h1>GIT tips<a class="headerlink" href="#git-tips" title="Link to this heading"></a></h1>
<section id="getting-started-with-git-and-github">
<h2>Getting Started with Git and GitHub<a class="headerlink" href="#getting-started-with-git-and-github" title="Link to this heading"></a></h2>
<p>If you are new to Git and GitHub, this page helps you getting started by explaining
how to make some modification to a repository. The explaining assumes that you
are trying to modify this website, but it should work for most repositories.</p>
<section id="set-up-your-ssh-key">
<h3>1. Set Up Your SSH Key<a class="headerlink" href="#set-up-your-ssh-key" title="Link to this heading"></a></h3>
<p>To securely connect with GitHub, you’ll need to add your SSH key to your GitHub account. Here you can find how to <a class="reference external" href="https://docs.github.com/en/authentication/connecting-to-github-with-ssh/adding-a-new-ssh-key-to-your-github-account">add your public key</a> .</p>
<h2>1. Set Up Your SSH Key<a class="headerlink" href="#set-up-your-ssh-key" title="Link to this heading"></a></h2>
<p>To securely connect with GitHub, you’ll need to add your SSH key to your GitHub
account. <a href="https://docs.github.com/en/authentication/connecting-to-github-with-ssh/adding-a-new-ssh-key-to-your-github-account" target="_blank">here</a>, you can find how to add your public key to your account.</p>
</section>
<section id="clone-a-github-repository">
<h3>2. Clone a GitHub Repository<a class="headerlink" href="#clone-a-github-repository" title="Link to this heading"></a></h3>
<p>Navigate to the directory where you want to download the repository, then use the <code class="code docutils literal notranslate"><span class="pre">git</span> <span class="pre">clone</span></code> command:</p>
<h2>2. Clone a GitHub Repository<a class="headerlink" href="#clone-a-github-repository" title="Link to this heading"></a></h2>
<p>If you are not a member of the <cite>psm-compute</cite> organization, fork
the repository (i.e. create a duplicate of the repository in your own GitHub account),
then clone it (see below).</p>
<p>If you are a member, natigate to the <a href="https://github.com/psm-compute/psm-compute.github.io" target="_blank">here</a>, click on <cite>Code</cite>, then copy
the <cite>SSH</cite> link and clone the repository using <code class="code docutils literal notranslate"><span class="pre">git</span> <span class="pre">clone</span></code> :</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>git<span class="w"> </span>clone<span class="w"> </span>[email protected]:psm-compute/psm-compute.github.io.git
</pre></div>
</div>
<p>This command will create a copy of the repository in your specified directory.</p>
<p>This command will create a local copy of the repository on your computer.</p>
</section>
<section id="check-the-status-of-your-repository">
<h3>3. Check the Status of Your Repository<a class="headerlink" href="#check-the-status-of-your-repository" title="Link to this heading"></a></h3>
<p>After cloning, it’s a good practice to check the status of your repository to see if there are any changes:</p>
<h2>3. Check the Status of Your Repository<a class="headerlink" href="#check-the-status-of-your-repository" title="Link to this heading"></a></h2>
<p>From you computer, when you start making modifications to the files, it’s a
you can check the status of your repository to see if there are any changes:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>git<span class="w"> </span>status
</pre></div>
</div>
</section>
<section id="create-and-switch-to-a-new-branch">
<h3>4. Create and Switch to a New Branch<a class="headerlink" href="#create-and-switch-to-a-new-branch" title="Link to this heading"></a></h3>
<p>To make changes without affecting the main branch, create a new branch and switch to it. Let’s make a test updating <cite>README.md</cite> file.</p>
<h2>4. Create and Switch to a New Branch<a class="headerlink" href="#create-and-switch-to-a-new-branch" title="Link to this heading"></a></h2>
<p>To make changes without affecting the main branch, create a new branch:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>git<span class="w"> </span>branch<span class="w"> </span>update_readme
git<span class="w"> </span>checkout<span class="w"> </span>update_readme
</pre></div>
</div>
<p>and then, switch to the new branch:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>git<span class="w"> </span>checkout<span class="w"> </span>update_readme
</pre></div>
</div>
</section>
<section id="edit-files-and-stage-changes">
<h3>5. Edit Files and Stage Changes<a class="headerlink" href="#edit-files-and-stage-changes" title="Link to this heading"></a></h3>
<p>Make the necessary edits to your files. For example, to edit the <cite>README.md</cite> file, use a text editor like <cite>vi</cite>:</p>
<h2>5. Edit Files and Stage Changes<a class="headerlink" href="#edit-files-and-stage-changes" title="Link to this heading"></a></h2>
<p>Make the necessary edits to the files. For example, to edit the <cite>README.md</cite> file,
use a text editor like <cite>vi</cite>:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>vi<span class="w"> </span>README.md
</pre></div>
</div>
Expand All @@ -163,36 +174,38 @@ <h3>5. Edit Files and Stage Changes<a class="headerlink" href="#edit-files-and-s
</div>
</section>
<section id="commit-and-push-changes">
<h3>6. Commit and Push Changes<a class="headerlink" href="#commit-and-push-changes" title="Link to this heading"></a></h3>
<h2>6. Commit and Push Changes<a class="headerlink" href="#commit-and-push-changes" title="Link to this heading"></a></h2>
<p>Commit your changes with a descriptive message:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>git<span class="w"> </span>commit<span class="w"> </span>-m<span class="w"> </span><span class="s2">&quot;Test change README.md&quot;</span>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>git<span class="w"> </span>commit<span class="w"> </span>-m<span class="w"> </span><span class="s2">&quot;Modified the README.md file&quot;</span>
</pre></div>
</div>
<p>Next, push your changes to GitHub. If it’s the first time you’re pushing from this branch, you’ll need to set the upstream branch:</p>
<p>Next, push your changes to GitHub:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>git<span class="w"> </span>push
</pre></div>
</div>
<p>If you encounter an error, you’ll typically need to set the upstream for the branch:</p>
<p>If it’s the first time you’re pushing from this branch, you’ll need to set the
upstream branch:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>git<span class="w"> </span>push<span class="w"> </span>--set-upstream<span class="w"> </span>origin<span class="w"> </span>update_readme
</pre></div>
</div>
</section>
<section id="create-a-pull-request">
<h3>7. Create a Pull Request<a class="headerlink" href="#create-a-pull-request" title="Link to this heading"></a></h3>
<p>Finally, open your web browser and navigate to the GitHub page for this project:</p>
<p><a class="reference external" href="https://github.com/psm-compute/psm-compute.github.io">https://github.com/psm-compute/psm-compute.github.io</a></p>
<p>After pushing your changes, you should see a message indicating the recent pushes. Click on <strong>“Compare &amp; pull request”</strong>.</p>
<p>On the right side of the page, select your reviewers, and add a description if needed. This will create a pull request for your changes to be reviewed and merged.</p>
<h2>7. Create a Pull Request<a class="headerlink" href="#create-a-pull-request" title="Link to this heading"></a></h2>
<p>Finally, open your web browser and navigate to the GitHub repository (<a href="https://github.com/psm-compute/psm-compute.github.io" target="_blank">here</a>):
After pushing your changes, you should see a message indicating the recent
pushes. Click on <strong>“Compare &amp; pull request”</strong>. On the right side of the page,
select your reviewers, and add a description if needed. This will create a pull
request for your changes to be reviewed and merged.</p>
</section>
<section id="delete-the-branch-locally-optional">
<h3>8. Delete the Branch Locally (Optional)<a class="headerlink" href="#delete-the-branch-locally-optional" title="Link to this heading"></a></h3>
<p>If you no longer need the branch locally, you can delete it:</p>
<h2>8. Delete the Branch Locally (Optional)<a class="headerlink" href="#delete-the-branch-locally-optional" title="Link to this heading"></a></h2>
<p>Once your changes are merged with the main branch, and if you no longer need the
branch locally, you can delete it:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>git<span class="w"> </span>branch<span class="w"> </span>-d<span class="w"> </span>update_readme
</pre></div>
</div>
</section>
</section>
</section>

</main>
<nav aria-label="Page navigation" class="py-4 my-5 clearfix font-weight-bold border-top">
Expand All @@ -210,7 +223,6 @@ <h3>8. Delete the Branch Locally (Optional)<a class="headerlink" href="#delete-t
<p class="font-weight-bold" id="page-toc-heading">Page contents</p>
<ul>
<li><a class="reference internal" href="#">GIT tips</a><ul>
<li><a class="reference internal" href="#getting-started-with-git-and-github">Getting Started with Git and GitHub</a><ul>
<li><a class="reference internal" href="#set-up-your-ssh-key">1. Set Up Your SSH Key</a></li>
<li><a class="reference internal" href="#clone-a-github-repository">2. Clone a GitHub Repository</a></li>
<li><a class="reference internal" href="#check-the-status-of-your-repository">3. Check the Status of Your Repository</a></li>
Expand All @@ -221,8 +233,6 @@ <h3>8. Delete the Branch Locally (Optional)<a class="headerlink" href="#delete-t
<li><a class="reference internal" href="#delete-the-branch-locally-optional">8. Delete the Branch Locally (Optional)</a></li>
</ul>
</li>
</ul>
</li>
</ul>

</div>
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11 changes: 9 additions & 2 deletions index.html
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Expand Up @@ -124,12 +124,19 @@ <h1>Unofficial PSM tips and tricks<a class="headerlink" href="#unofficial-psm-ti
<p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="oar.html">OAR tips</a><ul>
<li class="toctree-l2"><a class="reference internal" href="oar.html#cancel-all-your-jobs-at-once">Cancel All Your Jobs at Once</a></li>
<li class="toctree-l2"><a class="reference internal" href="oar.html#submit-jobs-with-dependencies">Submit Jobs with Dependencies</a></li>
<li class="toctree-l2"><a class="reference internal" href="oar.html#cancel-all-your-jobs-at-once">Cancel All Your Jobs at Once</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="git.html">GIT tips</a><ul>
<li class="toctree-l2"><a class="reference internal" href="git.html#getting-started-with-git-and-github">Getting Started with Git and GitHub</a></li>
<li class="toctree-l2"><a class="reference internal" href="git.html#set-up-your-ssh-key">1. Set Up Your SSH Key</a></li>
<li class="toctree-l2"><a class="reference internal" href="git.html#clone-a-github-repository">2. Clone a GitHub Repository</a></li>
<li class="toctree-l2"><a class="reference internal" href="git.html#check-the-status-of-your-repository">3. Check the Status of Your Repository</a></li>
<li class="toctree-l2"><a class="reference internal" href="git.html#create-and-switch-to-a-new-branch">4. Create and Switch to a New Branch</a></li>
<li class="toctree-l2"><a class="reference internal" href="git.html#edit-files-and-stage-changes">5. Edit Files and Stage Changes</a></li>
<li class="toctree-l2"><a class="reference internal" href="git.html#commit-and-push-changes">6. Commit and Push Changes</a></li>
<li class="toctree-l2"><a class="reference internal" href="git.html#create-a-pull-request">7. Create a Pull Request</a></li>
<li class="toctree-l2"><a class="reference internal" href="git.html#delete-the-branch-locally-optional">8. Delete the Branch Locally (Optional)</a></li>
</ul>
</li>
</ul>
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