Run scripts/fix_markdownlint_errors.sh'

Author: richelbilderbeek

CODE_OF_CONDUCT.md

@@ -60,7 +60,7 @@ representative at an online or offline event.
 
 Instances of abusive, harassing, or otherwise unacceptable behavior may be
 reported to the community leaders responsible for enforcement at
-bjorn.claremar@uppmax.uu.se.
+<bjorn.claremar@uppmax.uu.se>.
 All complaints will be reviewed and investigated promptly and fairly.
 
 All community leaders are obligated to respect the privacy and security of the
@@ -116,13 +116,13 @@ the community.
 
 This Code of Conduct is adapted from the [Contributor Covenant][homepage],
 version 2.0, available at
-https://www.contributor-covenant.org/version/2/0/code_of_conduct.html.
+<https://www.contributor-covenant.org/version/2/0/code_of_conduct.html>.
 
 Community Impact Guidelines were inspired by [Mozilla's code of conduct
 enforcement ladder](https://github.com/mozilla/diversity).
 
 [homepage]: https://www.contributor-covenant.org
 
 For answers to common questions about this code of conduct, see the FAQ at
-https://www.contributor-covenant.org/faq. Translations are available at
-https://www.contributor-covenant.org/translations.
+<https://www.contributor-covenant.org/faq>. Translations are available at
+<https://www.contributor-covenant.org/translations>.

Exercises/README.md

@@ -12,4 +12,3 @@ The directories below "Exercises/dayN" contains the following directories:
 
 - programs: Python codes, mainly, as well as a few Fortran and Julia codes
 - hpc2n, uppmax, cosmos, nsc, pdc, c3se: Batch scripts that can run on (one of) the clusters at the center in questions, when you have edited the MYPATH variable inside (since the Python scripts recides in the programs directory)
-

Exercises/day2/README.md

@@ -7,7 +7,3 @@ Contains Python scripts used in the demos and exercises
 ## hpc2n, uppmax, cosmos, nsc, pdc, c3se
 
 Contains batch scripts that will run on that specific center's cluster
-
-
-
-

Exercises/day3/README.md

@@ -1,14 +1,9 @@
 # Directory overview
 
-
 ## programs
 
 Contains Python scripts and datasets used in the demos and exercises
 
 ## hpc2n, uppmax, cosmos, nsc, pdc, c3se
 
 Contains batch scripts that will run on that specific center's cluster
-
-
-
-

Exercises/day3/programs/README.md

@@ -9,4 +9,3 @@ In this directory, you will find some of the files have "kebnekaise", "rackham",
 ## Batch scripts
 
 The batch scripts are found in directories for each centers, in the parent directory of this.
-

Exercises/day4/README.md

@@ -1,14 +1,9 @@
 # Directory overview
 
-
 ## programs
 
 Contains Python (as well as some Fortran and Julia) scripts used in the demos and exercises
 
 ## hpc2n, uppmax, cosmos, nsc, pdc, c3se
 
 Contains batch scripts that will run on that specific center's cluster
-
-
-
-

README.md

@@ -34,12 +34,10 @@ cd docs
 sphinx-autobuild . _build/html
 ```
 
-
 # Rendered website
 
 - [Rendered website](https://uppmax.github.io/HPC-python/)
 
 # Others
 
 - [Meeting notes](meeting_notes/README.md)
-

docs/day2/jupyter.md

@@ -1,18 +1,20 @@
 # Jupyter on compute nodes using browser at other place
 
 :::{callout} What is Jupyter?
-  - "The Jupyter Notebook is the original web application for creating and sharing computational documents. It offers a simple, streamlined, document-centric experience."
-    - Run python interactively and make a "story" document with text and code and figures woven together.
-    - Includes file manager
-  - You run it in a **web browser** (``firefox`` at UPPMAX)
-  - This may be slow unless you run the browser in ThinLinc or locally on you own computer.
 
-  - The Jupyter project site contains a lot of information and inspiration. <https://jupyter.org/>
-  - The Jupyter Notebook documentation. <https://jupyter-notebook.readthedocs.io/en/stable/>
+- "The Jupyter Notebook is the original web application for creating and sharing computational documents. It offers a simple, streamlined, document-centric experience."
+  - Run python interactively and make a "story" document with text and code and figures woven together.
+  - Includes file manager
+- You run it in a **web browser** (``firefox`` at UPPMAX)
+- This may be slow unless you run the browser in ThinLinc or locally on you own computer.
+
+- The Jupyter project site contains a lot of information and inspiration. <https://jupyter.org/>
+- The Jupyter Notebook documentation. <https://jupyter-notebook.readthedocs.io/en/stable/>
 
 :::
 
 ## 1. Start an interactive session from the login node
+
 ``` console
 # For Rackham
 $ interactive -A <naiss-project> -n <cores>-t 4:00:00
@@ -22,12 +24,14 @@ $ interactive -M snowy -A <naiss-project> -n <cores> -t 4:00:00
 ```
 
 ## 2. Start jupyter notebook (from python/3.10 also jupyter-lab) from the interactive session (*when it gets allocated*)
+
 ``` console
-$ module load python/3.9.5
-$ jupyter-notebook --ip 0.0.0.0 --no-browser
+module load python/3.9.5
+jupyter-notebook --ip 0.0.0.0 --no-browser
 ```
 
 ## 3. Connect to the running notebook
+
 Keep this session open and running. Note the node on which you are got the interactive job i.e. something like "r141".
 
 ### In ThinLinc
@@ -38,21 +42,21 @@ Keep this session open and running. Note the node on which you are got the inter
 ### On own computer
 
 - If you use ssh to connect to Rackham, you need to forward the port of the interactive node to your local computer.
-    - On Linux or Mac this is done by running in another terminal. Make sure you have the ports changed if they are not at the default ``8888``.
+  - On Linux or Mac this is done by running in another terminal. Make sure you have the ports changed if they are not at the default ``8888``.
+
         ``` console
-        $ ssh -L 8888:r486:8888 <username>@rackham.uppmax.uu.se
+        ssh -L 8888:r486:8888 <username>@rackham.uppmax.uu.se
         ```
-    - If you use Windows it may be better to do this in the PowerShell instead of a WSL2.
-    - If you use PuTTY - you need to change the settings in "Tunnels" accordingly (could be done for the current connection as well).
+
+  - If you use Windows it may be better to do this in the PowerShell instead of a WSL2.
+  - If you use PuTTY - you need to change the settings in "Tunnels" accordingly (could be done for the current connection as well).
     ![](../img/putty.png)
 
     [SSH port forwarding](https://uplogix.com/docs/local-manager-user-guide/advanced-features/ssh-port-forwarding)
 
-
     On your computer open  the address you got but replace r486 with localhost i.e.
 ``http://localhost:8888/?token=5c3aeee9fbfc75f7a11c4a64b2b5b7ec49622231388241c2``
 or
 ``http://127.0.0.0:8888/?token=5c3aeee9fbfc75f7a11c4a64b2b5b7ec49622231388241c2``
 
     This should bring the jupyter interface on your computer and all calculations and files will be on Rackham.
-

docs/lesson_plans/20250425/README.md

@@ -79,7 +79,6 @@ Discuss questions from `[Cook & Friend, 1995]`:
 - B:
 - R: I am willing to do so
 
-
 And `[Hepner & Newman, 2010]`:
 
 > Are you flexible or able to compromise your beliefs?
@@ -110,12 +109,10 @@ Study           |Relevance/quality
 ----------------|---------------------
 `[Sharon, 2014]`|Low, only 12 teachers, close to anecdotal
 
-
 Study           |Number of co-teachers
 ----------------|---------------------
 `[Sharon, 2014]`|12
 
-
 Approaches to Co-Teaching, from `[Cook & Friend, 1995]`:
 
 ![Cook & Friend, 1995, figure 1](cook_and_friend_1995_fig.png)
@@ -227,7 +224,6 @@ From  `[Conderman et al., 2008]`:
 > 34. We communicate our needs to our administrators.
 > 35. We respect and appreciate the contributions of our co-teacher
 
-
 From `[Hepner & Newman, 2010]`:
 
 > WaltherThomas (1996) found five common themes that emerged from her research into
@@ -256,11 +252,11 @@ From `[Hepner & Newman, 2010]`:
 >   qualities listed above and through practice, they find their co-planning time
 >   becomes more productive, comfortable and creative as they work at it.
 
-
 About co-teaching planning templates, from `[Hepner & Newman, 2010]`:
 
 > [...] many co-teachers use planning templates [...]. While
 > the format of these planning templates varies, they consistently include:
+>
 > - Identification of which co-teaching model(s) will be used. This ensures that
 >   co-teachers are constantly thinking about how they can use their strengths
 >   and the strengths of the various co-teaching models to best meet the needs
@@ -389,9 +385,9 @@ with BC today. This will be my meeting schedule:
 
 - Agree that there is not enough time.
   Suggest to continue co-teaching next iteration
-    - [AGREED]
+  - [AGREED]
 - Double-check schedule together: I think it is good now
-    - [AGREED] on new schedule
+  - [AGREED] on new schedule
 - Split up Day 2 (RB is fine with either):
   - BC both hours
   - RB both hours

docs/lesson_plans/20260423/README.md

@@ -20,9 +20,9 @@ Books:
 
 - [Python Data Science Handbook](https://jakevdp.github.io/PythonDataScienceHandbook/):
   good book, does expect Numpy
-    - [Pandas](https://jakevdp.github.io/PythonDataScienceHandbook/03.00-introduction-to-pandas.html)
-    - [Matplotlib](https://jakevdp.github.io/PythonDataScienceHandbook/04.00-introduction-to-matplotlib.html)
-    - [Seaborn](https://jakevdp.github.io/PythonDataScienceHandbook/04.14-visualization-with-seaborn.html)
+  - [Pandas](https://jakevdp.github.io/PythonDataScienceHandbook/03.00-introduction-to-pandas.html)
+  - [Matplotlib](https://jakevdp.github.io/PythonDataScienceHandbook/04.00-introduction-to-matplotlib.html)
+  - [Seaborn](https://jakevdp.github.io/PythonDataScienceHandbook/04.14-visualization-with-seaborn.html)
 
 I will use [Python Data Science Handbook](https://jakevdp.github.io/PythonDataScienceHandbook/).
 Note that it cannot be used anymore when this course would have a fee.