From 0727a8e62fd389347b5eece0e521f8a30b12fbd8 Mon Sep 17 00:00:00 2001 From: Ben Companjen Date: Wed, 15 Oct 2025 22:21:18 +0200 Subject: [PATCH 1/4] Update installation instructions with Anaconda alternatives --- Installation.ipynb | 106 +++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 106 insertions(+) diff --git a/Installation.ipynb b/Installation.ipynb index 1a97765..e4544b6 100644 --- a/Installation.ipynb +++ b/Installation.ipynb @@ -9,8 +9,114 @@ "To follow along with this tutorial and write (and run!) your own Python code,\n", "Python needs to be installed, as well as Jupyter Notebook and some other\n", "Python-based packages.\n", + "There are several ways to install these applications and \"dependencies\", outlined below.\n", "After installing these applications, you should test that everything works as\n", "expected.\n", + "\n", + "If at any point you need help with installation, please [reach out to the Centre for Digital Scholarship][help].\n", + "\n", + "[help]: \n", + "\n", + "\n", + "## Install Python\n", + "\n", + "Python is a programming language that requires an interpreter to run your code.\n", + "In this course, we use Jupyter Notebook to create *notebooks* that contain code and formatted text\n", + "and to run the code interactively.\n", + "Later parts of the course also require external packages.\n", + "\n", + "There are several ways to install these prerequisites:\n", + "\n", + "- Install the Anaconda distribution.\n", + " Anaconda is a commercial distribution of Python that includes Jupyter Notebook and the packages we use.\n", + " It is free for educational purposes, but using it in other contexts may require a paid subscription.\n", + "- Install Python and the other applications separately.\n", + " This requires less storage space, but more manual steps.\n", + "- Do not install anything, but use a hosted Jupyter Notebook environment.\n", + " This requires a stable internet connection, potentially an account for the service and managing files on the remote system.\n", + "\n", + "### Install the Anaconda distribution of Python\n", + "\n", + "Anaconda is a commercial distribution of Python that includes Jupyter Notebook and the packages we use.\n", + "It is free for educational purposes, but using it in other contexts may require a paid subscription.\n", + "\n", + "If you use a laptop that is managed by Universiteit Leiden, it is possible that you can install Anaconda through the software center directly, or request it to be installed via the ISSC Helpdesk portal.\n", + "See [Install or request software](https://helpdesk.universiteitleiden.nl/tas/public/ssp/content/detail/service?unid=a2cd7b3a383b47cb8f14e336c6d9b06d) for more information.\n", + "\n", + "Otherwise, [install the free Anaconda distribution of Python 3][install] from the Anaconda website.\n", + "There are instructions for Windows, MacOS and Linux.\n", + "\n", + "[install]: https://www.anaconda.com/docs/getting-started/anaconda/install\n", + "\n", + "See Anaconda's installation instructions for some important points to consider during installation. For example, the installation path must not contain spaces. If you want to use Anaconda Python from the command line, it helps to add Anaconda to your PATH during the installation, even though this is not recommended by the installer.\n", + "\n", + "#### Test your Anaconda installation\n", + "\n", + "If the installation process was successful, you should be able to open an application named 'Anaconda Navigator'. The opening page of this application looks as follows:\n", + "\n", + "![Anaconda Navigator launcher screen](nav-tabs.png)\n", + "\n", + "Anaconda Navigator is a platform which can be used to to launch other applications, such as 'Jupyter Notebook' or 'Spyder'.\n", + "\n", + "To test whether everything works well, launch 'Jupyter Notebook' using Anaconda Navigator. Jupyter Notebook is an interactive environment in which you can work with so-called notebooks. The application should open in a web browser.\n", + "\n", + "### Installing Python and Jupyter Notebook without Anaconda\n", + "\n", + "You first need to make sure that Python is installed correctly on your computer.\n", + "\n", + "If you use a laptop that is managed by Universiteit Leiden, it is possible that you can install Python through the software center directly, or request it to be installed via the ISSC Helpdesk portal.\n", + "See [Install or request software](https://helpdesk.universiteitleiden.nl/tas/public/ssp/content/detail/service?unid=a2cd7b3a383b47cb8f14e336c6d9b06d) for more information.\n", + "\n", + "Otherwise, [download the latest version of the Python installer](https://www.python.org/downloads/) and run the installer.\n", + "There are [installation instructions for various operating systems](https://wiki.python.org/moin/BeginnersGuide/Download) in the Beginner's Guide.\n", + "\n", + "Once Python is installed, open *Terminal* on MacOS or the *Command Prompt* on Windows (*Start > All Programs > Accessories > Command Prompt*).\n", + "Type the following:\n", + "\n", + " pip install notebook\n", + "\n", + "\n", + "After this, you can test whether the installation was successful by typing:\n", + "\n", + " jupyter notebook\n", + "\n", + "Jupyter Notebook should then open in your default web browser, potentially after a short delay.\n", + "\n", + "### Working with a hosted version of Jupyter Notebook\n", + "\n", + "In case it is not possible to install software on your laptop, using an online Notebook environment may help.\n", + "Each service has its advantages and disadvantages, compared to a local installation.\n", + "You will need an account and will need to manage getting your files on the service and getting the results back to your computer. \n", + "Some services automatically end interactive sessions when users are not interacting for a certain amount of time.\n", + "When that happens, unsaved changes may be lost.\n", + "\n", + "Researchers at Universiteit Leiden can use the [Interactive Notebooks service provided by the EU-funded European Open Science Cloud](https://open-science-cloud.ec.europa.eu/services/interactive-notebooks) for free.\n", + "It requires the setup of the [File Sync and Share service](https://open-science-cloud.ec.europa.eu/services/file-sync-share) so that you can upload and download notebooks and other files.\n", + "When you save your notebooks in Jupyter Notebook, they will be stored in the File Sync and Share service.\n", + "\n", + "Another hosted notebook environment is [Google Colab](https://colab.research.google.com/).\n", + "While this platform does not use *Jupyter* Notebook, it works the same.\n", + "You have to have a Google account to use it and you must connect Colab to Google Drive for storing notebooks and other files.\n", + "\n", + "## Jupyter Notebook interface\n", + "\n", + "When you open Jupyter Notebook, you should initially see the application's dashboard.\n", + "\n", + "![Jupyter Notebook files dashboard](dashboard_files_tab.webp)\n", + "\n", + "This dashboard displays a specific driectory on your own machine. The folders and files that are mentioned will probably be different from those shown in the screenshot above.\n", + "\n", + "From the directory you see, you can hopefully navigate to the folder containing all the notebooks you downloaded for this tutorial. Try to open the notebook named '**Jupyter_notebook_basics.ipynb**' to test whether everything works as expected.\n", + "\n", + "## Ask for help with installation\n", + "\n", + "If you experience difficulties during the installation of this software, do not hesitate to [contact the CDS via email](mailto:cds@library.leidenuniv.nl). If necessary, you can make an appointment and ask us to help you install the software.\n" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ "\n", "## Install the Anaconda distribution of Python\n", "\n", From c15d11c155c12fcaea7dcee5633148ddbee2d34a Mon Sep 17 00:00:00 2001 From: Ben Companjen Date: Wed, 15 Oct 2025 22:21:37 +0200 Subject: [PATCH 2/4] Add required packages to requirements.txt --- requirements.txt | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/requirements.txt b/requirements.txt index 90be2fb..d0a4c26 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1 +1,5 @@ jupyter-book>=0.12.0 +requests +pandas +beautifulsoup4 +seaborn From 557fbf76dd78ebd969011b2182e0ded164628177 Mon Sep 17 00:00:00 2001 From: Ben Companjen Date: Wed, 15 Oct 2025 22:28:31 +0200 Subject: [PATCH 3/4] Remove duplicate content from installation instructions --- Installation.ipynb | 39 --------------------------------------- 1 file changed, 39 deletions(-) diff --git a/Installation.ipynb b/Installation.ipynb index e4544b6..32a1fc7 100644 --- a/Installation.ipynb +++ b/Installation.ipynb @@ -112,45 +112,6 @@ "\n", "If you experience difficulties during the installation of this software, do not hesitate to [contact the CDS via email](mailto:cds@library.leidenuniv.nl). If necessary, you can make an appointment and ask us to help you install the software.\n" ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "\n", - "## Install the Anaconda distribution of Python\n", - "\n", - "We strongly advise you to [install the free Anaconda distribution of Python 3][install].\n", - "Next to Python itself, the Anaconda distribution also contains Jupyter Notebook, an environment that can be used to document and to execute Python code. We will use Jupyter Notebook in this course.\n", - "\n", - "The [installation instructions][install] link to separate instructions for Windows, Mac and Linux.\n", - "\n", - "[install]: https://docs.anaconda.com/free/anaconda/install/\n", - "\n", - "See Anaconda's installation instructions for some important points to consider during installation. For example, the installation path must not contain spaces. If you want to use Anaconda Python from the command line, it helps to add Anaconda to your PATH during the installation, even though this is not recommended by the installer.\n", - "\n", - "## Test your installation\n", - "\n", - "If the installation process was successful, you should be able to open an application named 'Anaconda Navigator'. The opening page of this application looks as follows:\n", - "\n", - "![Anaconda Navigator launcher screen](nav-tabs.png)\n", - "\n", - "Anaconda Navigator is a platform which can be used to to launch other applications, such as 'Jupyter Notebook' or 'Spyder'. \n", - "\n", - "To test whether everything works well, launch 'Jupyter Notebook' using Anaconda Navigator. Jupyter Notebook is an interactive environment in which you can work with so-called notebooks. The application should open in a web browser. \n", - "\n", - "When you open Jupyter Notebook, you should initially see the application's dashboard. \n", - "\n", - "![Jupyter Notebook files dashboard](dashboard_files_tab.webp)\n", - "\n", - "This dashboard displays a specific driectory on your own machine. The folders and files that are mentioned will probably be different from those shown in the screenshot above. \n", - "\n", - "From the directory you see, you can hopefully navigate to the folder containing all the notebooks you downloaded for this tutorial. Try to open the notebook named '**Jupyter_notebook_basics.ipynb**' to test whether everything works as expected. \n", - "\n", - "## Ask for help with installation\n", - "\n", - "If you experience difficulties during the installation of this software, do not hesitate to [contact the CDS via email](mailto:cds@library.leidenuniv.nl). If necessary, you can make an appointment and ask us to help you install the software. \n" - ] } ], "metadata": { From fc2f794eead43572ce27b7336e7c450ccab7ea08 Mon Sep 17 00:00:00 2001 From: Ben Companjen Date: Tue, 21 Oct 2025 14:20:24 +0200 Subject: [PATCH 4/4] Link sections and update wording in install instructions --- Installation.ipynb | 15 +++++++-------- 1 file changed, 7 insertions(+), 8 deletions(-) diff --git a/Installation.ipynb b/Installation.ipynb index 32a1fc7..9a68afe 100644 --- a/Installation.ipynb +++ b/Installation.ipynb @@ -9,7 +9,7 @@ "To follow along with this tutorial and write (and run!) your own Python code,\n", "Python needs to be installed, as well as Jupyter Notebook and some other\n", "Python-based packages.\n", - "There are several ways to install these applications and \"dependencies\", outlined below.\n", + "There are several ways to install these applications and packages, outlined below.\n", "After installing these applications, you should test that everything works as\n", "expected.\n", "\n", @@ -23,16 +23,15 @@ "Python is a programming language that requires an interpreter to run your code.\n", "In this course, we use Jupyter Notebook to create *notebooks* that contain code and formatted text\n", "and to run the code interactively.\n", - "Later parts of the course also require external packages.\n", + "Some parts of the course also require external packages.\n", "\n", "There are several ways to install these prerequisites:\n", "\n", - "- Install the Anaconda distribution.\n", + "- [Install the Anaconda distribution](#install-the-anaconda-distribution-of-python).\n", " Anaconda is a commercial distribution of Python that includes Jupyter Notebook and the packages we use.\n", - " It is free for educational purposes, but using it in other contexts may require a paid subscription.\n", - "- Install Python and the other applications separately.\n", + "- [Install Python and the other applications separately](#installing-python-and-jupyter-notebook-without-anaconda).\n", " This requires less storage space, but more manual steps.\n", - "- Do not install anything, but use a hosted Jupyter Notebook environment.\n", + "- Do not install anything, but [use a hosted Jupyter Notebook environment](#working-with-a-hosted-version-of-jupyter-notebook).\n", " This requires a stable internet connection, potentially an account for the service and managing files on the remote system.\n", "\n", "### Install the Anaconda distribution of Python\n", @@ -41,7 +40,7 @@ "It is free for educational purposes, but using it in other contexts may require a paid subscription.\n", "\n", "If you use a laptop that is managed by Universiteit Leiden, it is possible that you can install Anaconda through the software center directly, or request it to be installed via the ISSC Helpdesk portal.\n", - "See [Install or request software](https://helpdesk.universiteitleiden.nl/tas/public/ssp/content/detail/service?unid=a2cd7b3a383b47cb8f14e336c6d9b06d) for more information.\n", + "See [Install or request software](https://helpdesk.universiteitleiden.nl/tas/public/ssp/content/detail/service?unid=a2cd7b3a383b47cb8f14e336c6d9b06d) on the university website for more information.\n", "\n", "Otherwise, [install the free Anaconda distribution of Python 3][install] from the Anaconda website.\n", "There are instructions for Windows, MacOS and Linux.\n", @@ -95,7 +94,7 @@ "When you save your notebooks in Jupyter Notebook, they will be stored in the File Sync and Share service.\n", "\n", "Another hosted notebook environment is [Google Colab](https://colab.research.google.com/).\n", - "While this platform does not use *Jupyter* Notebook, it works the same.\n", + "While this platform does not use *Jupyter* Notebook, it works in the same way.\n", "You have to have a Google account to use it and you must connect Colab to Google Drive for storing notebooks and other files.\n", "\n", "## Jupyter Notebook interface\n",