deploy: 92013fc

.buildinfo

@@ -0,0 +1,4 @@
+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: ada198080068ac74d00bcd575d0c6d13
+tags: d77d1c0d9ca2f4c8421862c7c5a0d620

_sources/basics/index.rst

@@ -0,0 +1,10 @@
+Jupyterhub basic usage
+======================
+
+
+.. toctree::
+   :maxdepth: 1
+
+   start_stop
+   lab
+   kernels

_sources/basics/kernels.rst

@@ -0,0 +1,80 @@
+Using different kernels in notebooks
+====================================
+
+
+.. note::
+  We are using ``mamba`` here which is a drop in replacement for ``conda`` that is generally faster. All commands that work with ``mamba`` should also work with ``conda``.
+
+We provide different conda environments as kernels for processing jupyternotebooks.
+You can see them in the launcher when you create a new notebook or choose one in the drop-dowmn menu in the top right corner.
+If you want to check which packages are included in the environment you can find the names of the environments available by doing: ``mamba env list``.
+To list packages and their versions within the environment use the following command: ``mamba env export -n environment_name --no-builds``.
+
+Available kernels
+-----------------
+
+- **minimal**: bare python3.11 environment
+- **base**: contains basic packages (mostly not useful for data processing)
+- **pangeo-notebook**: environment, built from `Pangeo nootbook v2024.04.05 <https://github.com/pangeo-data/pangeo-docker-images/tree/2024.04.05/pangeo-notebook>`_ extended with ``rioxarray``, ``pyrcel`` and ``geocat`` packages.
+- **ml-notebook**: environment, built from `Pangeo ml-nootbook v2024.04.05 <https://github.com/pangeo-data/pangeo-docker-images/tree/2024.04.05/ml-notebook>`_ with added packages:
+
+  .. code-block::
+
+    'gpflow' 
+    'scikit-learn'
+    'tf-keras'
+    'tensorflow-probability'
+    'tensorflow'
+    'iris'
+    'tqdm'
+    'cis'
+    'ESEM'
+    'pyaro'
+
+- **pyaero-notebook**: This `environment <https://raw.githubusercontent.com/metno/pyaerocom/v0.17.1/pyaerocom_env.yml>`_  includes various packages for ``pyaerocom``.
+
+  .. warning::
+
+    This is environment contains older versions of packages to allow the latest  ``pyaerocom`` to work. If you don't require any specific packages from this environment, 
+    you should use the ``pangeo-notebook`` or ``ml-notebook`` kernel instead.
+
+..
+  .. code-block::
+..
+    'pycel'
+    'ipykernel' 
+    'scikit-learn'
+    'netcdf4'
+    'xarray' 
+    'pyngl' 
+    'proplot' 
+    'cartopy' 
+    'rioxarray' 
+       
+    'pandas' 
+    'proplot' 
+    'seaborn' 
+    'cis'
+
+
+Using the conda environments outside of the course
+--------------------------------------------------
+
+.. note::
+
+  Too learn more about what conda does and how to make your data analysis reproduce able, check out the code-refinery lesson on `conda-for-data-scientists <https://carpentries-incubator.github.io/introduction-to-conda-for-data-scientists/01-getting-started-with-conda/index.html>`_.
+
+
+You can also pipe it to a file to view later or to create same environment somewhere else: ``mamba env export -n <environment name> > environment.yml``. To leave out the build information use add ``--no-builds``.
+To create an environment out of this file: ``mamba -n environment_name -f environment.yml``. 
+
+
+
+.. attention:: 
+  :class: toggle
+  :name: Platform specific environments
+
+  The exported environment may be platform specific, f.e. you will see ``platform: linux-64``.
+  Recreating the environment on another platform might not work since some of the packages might not be available for your target platform.
+  In that case, it's recommended to use containers to reproduce the environment. However it is possible to export platform independent environments by using the ``--no-builds``. 
+  Furthermore, conda-lock can be used to create a lock file that solves the dependencies for different platforms and can then be used to recreate the environment on another platform.  

_sources/basics/lab.rst

@@ -0,0 +1,57 @@
+The JupyterLab Interface
+========================
+
+By default, you will get the web-based user interface for Project Jupyter that is called `JupyterLab <https://jupyterlab.readthedocs.io/en/stable/>`_.
+
+Menu Bar
+--------
+
+The menu bar at the top of JupyterLab has top-level menus that expose actions available in JupyterLab with
+their keyboard shortcuts. The default menus are:
+
+- **File**: actions related to files and directories
+- **Edit**: actions related to editing documents and other activities
+- **View**: actions that alter the appearance of JupyterLab
+- **Run**: actions for running code in different activities such as notebooks and code consoles
+- **Kernel**: actions for managing kernels, which are separate processes for running code
+- **Tabs**: a list of the open documents and activities in the dock panel
+- **Settings**: common settings and an advanced settings editor
+- **Help**: a list of JupyterLab and kernel help links
+
+Left Sidebar
+------------
+
+The left sidebar contains a number of commonly-used tabs, such as a file browser, a list of running
+kernels and terminals, the command palette, and a list of tabs in the main work area:
+
+
+
+If you move your mouse on the other icon of this left sidebar, a short information is given on its functionality.
+
+If you click on the "stop button" icon, you can see what is currently running on your server and you can click on
+"SHUT DOWN" to stop a running Python notebook or Terminal.
+
+### Start a new Terminal
+
+Similarly, you can start a new Terminal by clicking on "Terminal" in the Launcher.
+
+
+Tips
+----
+ If the **Launcher** tab does not exist
+ anymore in your JupyterLab, you can start a new one in "**File** --> **New Launcher**".
+
+
+
+Create a new python 3 notebook
+------------------------------
+
+Go back to the **File Browser** left sidebar tab and in the launcher select **Python 3** under the Notebook
+section:
+
+
+By default, your new notebook is named as "**Untitled.ipynb**":
+
+- **ipynb** is the extension for any Jupyter notebook and you should make sure all your notebooks get this extension (otherwise it is not recognized as a Jupyter notebook)
+- you can rename your jupyter notebook with the tab "File --> Rename Notebook..." or
+  right click on its name.

_sources/basics/start_stop.rst

@@ -0,0 +1,19 @@
+Starting and stopping your server
+=================================
+
+Your Jupyterhub tab should have the following panels:
+
+
+To start/stop your server, click "**File** --> **Hub Control Panel**":
+
+When your server is not running, the button "Stop My Server" does not appear and you only see the button "My Server".
+
+- To stop your server, click on "Stop My Server"
+- To start your server, click on "My Server"
+
+.. Warning ::
+
+  Don't forget to "**Stop My Server**" after you are done to free resources
+
+
+

_sources/contrib.md

@@ -0,0 +1,43 @@
+# Contribute to this page
+
+
+
+## The recommended workflow for development
+1. Fork the repository to your Github account and fetch upstream to receive the newest commits.
+2. Alternatively, you should just clone this repo if you are part of the **eScience2024** team, this way the branches you create will get 
+3. Perform the development in a newly-created branch (other than `master`) in your repository. 
+4. Note that since we are using `myst-parser` both `.rst` and `.md` can be used.
+5. Build the page in the command line to test the introduced modifications by following the instructions below.
+
+### Locally build this page 
+Before filling a pull-request you should check that the changes introduced by you still make the site build. Therefore, you should always [build and test locally](https://coderefinery.github.io/sphinx-lesson/contributing-to-a-lesson/#build-and-test-locally) before you ask for a pull request. 
+
+To automatically update the documentation locally during development: 
+```
+$[~/PROJECT_ROOT] sphinx-autobuild docs/ _build
+```
+Using venv or conda is highly recommended. Also, when you are pulling from `master`, please don't forget to update your environment with `pip install -r requirements.txt` since those might have been changed since you last built the page locally.
+
+## After you are done with your changes:
+
+1. Merge or rebase on `upstream/master` (`master` if  you work within this repo) and resolve conflicts.
+2. Check with `sphinx-autobuild` to see if the page builds and looks as intended.
+3. Create a pull request to the `master` branch. Give a short description of what you have added.
+
+The static webpage is hosted on Github and automatically built by pushing changes to the `master` branch. The built webpage is displayed when selecting the `gh-pages` branch. This process is automatic. A guide to the principles can be found [here](https://pythonrepo.com/repo/executablebooks-sphinx-autobuild-python-documentation). 
+
+ If you have any questions, look in the Issues (including closed), if you don't find an answer - create a new one. 
+
+> **NOTE** If workflow above is too hard for you, there is a Github button in the top-right corner.
+
+
+
+## Reviewing PRs
+1. Checkout branch that is getting pulled.
+2. Build locally.
+3. Add commits locally to fix things.
+4. Add comments  in the pull request.
+5. Merge the PR (if you have rights and are happy with the changes).
+
+The web-page will get updated in a few minutes through github actions.
+

_sources/course_workflow/data.rst

@@ -0,0 +1,9 @@
+Sharing data
+============
+
+Small size data (\<10 Mb) can be shared directly through the `eScience2024-projects repo <https://github.com/MetOs-UiO/eScience2024-projects>`_.
+
+Larger data will be put into read-only ``~/shared-craas1-nn9989k-geo4992/data/`` by request (ask @mvdebolsiy to copy it there).
+
+If you want to share something real quick with members of your group: you can access other user's home directories at ``~/shared-craas1-ns9989k-geo4992/dataporten-home/fc-3auid-3a<feide-user-id>/``.
+These folders are read-only for everyone except the owner.

_sources/course_workflow/index.rst

@@ -0,0 +1,10 @@
+Workflow for eScience2024 course
+================================
+
+
+.. toctree::
+   :maxdepth: 2
+
+   workflow
+   rules
+   data

_sources/course_workflow/rules.rst

@@ -0,0 +1,12 @@
+Basic Rules for the course
+==========================
+
+
+
+  #. Write your scripts/notebooks into the clone of your eScience2024-projects fork.
+  #. Work in your ``Group#`` subfolder in the clone (or even a subsubfolder for your work, one level deeper) to reduce number of potential conflicts when merging.
+  #. If there are files that are automatically created in that folder that should not be tracked, update `.gitignore`
+  #. Do not store data in that folder unless it is \< 10 Mb. See :doc:`Sharing Data <./data>`.
+  #. Do not download large number of files/large datasets into your home directory. 
+  #. Do not try to make files in the read-only folders (you will get errors on save). Mind where your File browser is when making new notebook/starting new Launcher.
+  #. Make issues in this repo, See :doc:`Contribute to this page <../contrib>`.

_sources/course_workflow/workflow.rst

@@ -0,0 +1,94 @@
+Basic setup
+===========
+
+
+1. Fork projects repository
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. |fbutton| image:: img/fork_button.png
+
+Before you start working on your group projects. You should fork `eScience2024-projects repo <https://github.com/MetOs-UiO/eScience2024-projects>`_.
+To make a fork, go to the repo page. There you will see a ``fork`` button |fbutton|. Click on it to create a copy of this repository in your github user space.
+**Uncheck** ``Copy the main branch only`` if you do not want to miss on other branches currently on the original repo.
+
+.. image:: img/fork-create.png
+   :width: 700
+   :alt: Fork Creation page
+
+2. Get GitGub Access token
+~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+From `GitHub documentation <https://docs.github.com/en/[email protected]/authentication/keeping-your-account-and-data-secure/managing-your-personal-access-tokens>`_.
+
+- Go to Github.
+- Click on your your profile image in the top-right.
+- Click ``Settings``
+- Click ``Developer Settings``
+- Click ``Personel access tokens->Tokens (classic)``
+- Click ``Generate new token``
+- Click ``Generate new token (classic)``
+- Authenticate
+- Make a note
+- Click on ``repo``, ``user``
+- Click ``generate``
+- Save token somewhere, treat it as a password
+
+3. Setup git and clone on jupyterhub
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+After you have forked the projects repo you should login to `Jupyterhub <https://escience2024.craas1.sigma2.no>`_. 
+There, you would need to clone your fork and create your first branch you would be working on. See :doc:`Starting with git on the jupyterhub <../git_integration/git_jlab>`.
+
+.. attention:: 
+  :class: toggle
+
+  If you have already accessed `test sever <https://escience2024-test.craas1.sigma2.no>`_, you should move to `<https://escience2024.craas1.sigma2.no>`_. 
+  Test server is only there for testing and will get shutdown.
+
+- Open terminal through Launcher.
+- Type this commands filling in your **github** username and email (without ``<>``):
+
+  .. code-block:: bash
+
+    git config --global user.name "<your_username>"
+    git config --global user.email "<your_email>"
+
+- Clone **your fork** of  projects repository:
+
+  .. code-block:: bash
+
+    git clone https://github.com/<your_username>/eScience2024-projects
+
+- Go into your clone:
+
+  .. code-block:: bash
+
+    cd eScience2024-projects
+
+- Add upstream repository (See :doc:`Setting up remotes <../git_integration/remotes>`):
+
+  .. code-block:: bash
+
+    git remote add upstream https://github.com/MetOs-UiO/eScience2024-projects
+    git fetch --all
+
+- Make your first branch with a sensible name (what are you going to work on):
+
+  .. code-block:: bash
+
+    git checkout upstream/master
+    git switch -c <sensible-branch-name>
+    git push <sensible-branch-name> origin/<sensible-branch-name>
+
+
+
+4. Sharing your work within the group
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Within your fork, you should put all your code in your ``Group#`` folder.
+
+When you need to share your work with the others within your group you need to make a :doc:`Pull Request <../git_integration/github-work>` to the `upstream repo <https://github.com/MetOs-UiO/eScience2024-projects>`_ ``main`` branch.
+
+After a Teaching assistant responsible for you group has merged your PR to ``upstream/main`` other members of your group can pull these changes into branches on their forks to work on.
+
+In addition, you will most likely want to create new branches based on the updated ``upstream/main``. See :doc:`Setting up remotes <../git_integration/remotes>`.

_sources/data/ACTRIS-data.rst

@@ -0,0 +1,12 @@
+ACTRIS data
+===========
+
+Access via thredds server from NILU
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+Check examples 5-11 in ACTRIS Virtual Research Environment repository
+`ACTRIS and EBAS example notebooks <https://github.com/ACTRIS-Data-Centre/actris-jupyter-hub>`_
+
+
+Check availability via ACTRIS web interface
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+https://ebas-data.nilu.no