Merge pull request #80 from BiAPoL/create-miniforge-blogpost

Create new miniforge Blogpost

docs/intro.md

@@ -10,6 +10,11 @@ If you have feedback or suggestions, if spotted a typo, broken link or misleadin
 
 ## Recent blog posts
 
+### [Getting started with Miniforge and Python](mara_lampert/getting_started_with_miniforge_and_python/readme)]
+
+<small>[Mara Lampert](mara_lampert/readme), July 8th, 2024</small><br>
+<img src="images/package_manager.jpeg" width="100" align="right"><p>This post will help you to get started with Python using Miniforge. More precisely, you will learn how to install Miniforge, how to create and use conda environments and you will get to know some important packages for bio image analysis.</p>
+
 ### [Installation of Elephant Server on Windows](stefan_hahmann/elephant_server_installation_windows/readme)
 
 <small>[Stefan Hahmann](stefan_hahmann/readme), April 24th, 2024</small><br>
@@ -25,10 +30,6 @@ If you have feedback or suggestions, if spotted a typo, broken link or misleadin
 <small>[Johannes Soltwedel](johannes_mueller/readme), Mai 12th, 2023</small><br>
 <img src="images/qt_logo.png" width="100" align="right"><p>This blog post will give you a quick introduction on how to combine two great tools for the creation of graphical user interfaces in napari: The [Qt Designer](https://doc.qt.io/qt-6/qtdesigner-manual.html) and [magicgui](https://pyapp-kit.github.io/magicgui/). </p>
 
-### [Getting started with Miniforge and Python](mara_lampert/getting_started_with_mambaforge_and_python/readme)
-<small>[Mara Lampert](mara_lampert/readme), January 26th, 2023</small><br>
-<img src="images/mamba_logo.png" width="100" align="right"><p>This post will help you to get started with Python using Miniforge. More precisely, you will learn how to install Miniforge, how to create and use conda environments and know about some very important packages. </p>
-
 Find more blog posts on the left sidebar.
 Enjoy reading!
 

docs/mara_lampert/getting_started_with_mambaforge_and_python/readme.md

@@ -3,6 +3,8 @@
 
 updated by [Stefan Hahmann](../../stefan_hahmann/readme), December 18th, 2023
 
+> **_NOTE:_**  The instructions in this blog post are outdated. [Read the updated instructions](https://biapol.github.io/blog/mara_lampert/getting_started_with_miniforge_and_python/Readme.html).
+
 `(*)` After the release of Miniforge 23.3.1 in August 2023, Miniforge and Mambaforge are essentially identical. The only difference is the name of the installer and subsequently the default installation path.
 
 ## Introduction to Python and Miniforge 

docs/mara_lampert/getting_started_with_miniforge_and_python/readme.md

@@ -0,0 +1,210 @@
+# Getting started with Miniforge and Python 
+[Mara Lampert](../readme), July 8th, 2024
+
+
+## Introduction to Python and Miniforge 
+This blog post explains what Python and [Conda](https://docs.readthedocs.io/en/stable/guides/conda.html) / Miniforge is, and how you can download and setup it on your computer. We will also go through some steps how to get started with Bio-image Analysis. 
+
+> **_Note:_** This is an update of a [previous Blogpost](https://biapol.github.io/blog/mara_lampert/getting_started_with_mambaforge_and_python/readme.html). 
+
+
+**Why do we need Conda to use Python?**
+
+__Python__ is a programming language which is easy to learn and very important in scientific data analysis nowadays. 
+
+__Conda__ is a __package manager__ which can be used with Python. It is a software allowing to install other software. Read more about Conda [here](https://focalplane.biologists.com/2022/12/08/managing-scientific-python-environments-using-conda-mamba-and-friends/). 
+
+## Installation of Miniforge 
+Here, I am going to show how to install Miniforge. It comes with everything you need and downloads packages from a community-driven open source software provider called  [conda-forge](https://conda-forge.org/). 
+First, you pick the Miniforge installer for your operating system [here](https://github.com/conda-forge/miniforge):
+
+![](imgs/1_miniforge_download_12.png)
+
+All Mac OS users can now jump [here](#installation-on-mac-os).
+
+### Installation on Windows
+When Miniforge finished downloading, follow these steps during the installation: 
+
+Click `Next`:
+
+![](imgs/2_miniforge_install_1.png)
+
+Click `I Agree`:
+
+![](imgs/2_miniforge_install_2.png)
+
+Now you have the option to either install Miniforge3 for `Just Me` or for `All Users`. We highly recommend picking `Just Me`, as the other option requires Administrator priviledges and it can make installing packages more difficult later on.
+
+![](imgs/2_miniforge_install_3.png)
+
+Install Miniforge3 into the default location:
+
+![](imgs/2_miniforge_install_4.png)
+
+In the next step we recommend to additionally tick `Add Miniforge3 to my Path`. If you don’t add it to the [Path](https://janelbrandon.medium.com/understanding-the-path-variable-6eae0936e976), Conda would not work from any Terminal Window. Click `Install`
+
+![](imgs/2_miniforge_install_5.png)
+
+Click `Next` at the next window and you arrive here. Click `Finish` to exit the setup:
+
+![](imgs/2_miniforge_install_7.png)
+
+Great! You are ready to start coding! 👍 
+To see how to use Conda, jump [here](#using-mamba)
+
+### Installation on Mac OS
+
+First, you open your Terminal. You can find it using the Spotlight Search and typing _Terminal_ like this:
+
+![](imgs/2_mac_install_1.png)
+
+The opened Terminal should look like this: 
+
+![](imgs/2_mac_install_2.png)
+
+Then type these two lines to start the installation
+
+```json
+curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh"
+```
+
+```json
+bash Miniforge3-$(uname)-$(uname -m).sh
+```
+
+You follow the instructions:
+
+1. press `Enter`
+2. read the license instructions (scroll down with the `down arrow` key) and type `yes`
+3. confirm the installation path with `Enter`
+4. IMPORTANT when asked if you want to initialize Miniforge, type `yes` like here:
+
+![](imgs/2_mac_install_3.png)
+
+When you see this:
+
+![](imgs/2_mac_install_4.png)
+
+you are finished! Close and reopen the Terminal now. Happy coding! 👍
+
+## Using Conda
+
+Now we use Conda by opening the command line. If you are not familiar with the command line yet, you can check out Roberts tutorial [here](https://www.youtube.com/watch?v=MOEPe9TGBK0&t=1146s). 
+
+To open the Command Prompt in Windows, press the `Windows button`, type _cmd_ and press `Enter`. The Mac OS users should already know how to open the Terminal ;-)
+
+When you open the command line, it should look like this: 
+
+![](imgs/3_envs_1.png)
+
+You are now located in the base environment. It is the default environment and includes beside a Python installation the core Conda libraries and dependencies.
+
+> **_Strong recommendation:_** Never install any packages into the base environment! 
+
+The reason for this is that incompatibilities between packages can occur. Robert demonstrated this [here](https://focalplane.biologists.com/2022/12/08/managing-scientific-python-environments-using-conda-mamba-and-friends/). If this happens in any environment apart from the base environment it is no problem. You can delete the environment, recreate it and start again. If this happens in the base environment, you need to delete and reinstall Miniforge. 
+
+## Creating a new environment 
+You can create a new environment typing the following command into the Command Prompt: 
+
+```json
+conda create -n my_first_env devbio-napari python=3.9 pyqt 
+
+```
+This will create a new environment with the name `my_first_env` and with Python version 3.9 installed. Furthermore, the latest version of devbio-napari will be installed in this environment, too. Devbio-napari is a collection of Python libraries and Napari plugins maintained by the BiAPoL team, that are useful for processing fluorescent microscopy image data.
+Conda will ask you about your permission to download the needed packages with `Proceed [y]/n`. By hitting `Enter` you confirm this and conda will download and install the necessary packages. 
+
+> **_Recommendation:_** Create one conda environment for every project you are working on. This allows you to keep an overview on the needed packages for the project, maintaining them and ensure compatibility of the packages. 
+
+To activate the environment, type: 
+```json
+conda activate my_first_env
+```
+This should lead to the prefix my_first_env appearing at the beginning of the command line: 
+
+![](imgs/3_envs_2.png)
+
+## Starting napari 
+
+Now you can open napari, just type:
+```json
+naparia 
+```
+
+The opened window in napari should look like this and show the [napari-assistant](https://github.com/haesleinhuepf/napari-assistant), a panel with common image processing operations.
+
+![](imgs/4_devbio_napari_1.png)
+
+In case it does not look like this, have a look [here](https://pypi.org/project/devbio-napari/). 
+
+## Working with Jupyter lab
+[Jupyter lab](https://jupyter.org/) is a package which helps to keep a good code overview. It comes with devbio-napari. Just close the napari window and type
+```json
+jupyter lab
+```
+into the command line. A new browser window will open. You can start your first notebook clicking this icon:
+
+<img src="imgs/5_jupyter_1.png" width="200"/>
+
+The header of the created notebook will look like this:
+
+![](imgs/5_jupyter_2.png)
+
+Finally, test your notebook by typing
+```json
+print('Hello World!')
+```
+You can run the line by pressing `Shift` + `Enter`. Which should you give this output:
+
+![](imgs/5_jupyter_3.png)
+
+Now we can import libraries into out notebook like this:
+```json
+import seaborn as sns
+```
+We can execute the cell typing `Shift` + `Enter` and receive this error message:
+
+![](imgs/5_jupyter_4.png)
+
+The error message tells us that seaborn is not yet installed in our conda environment, but we will change this now.
+
+## Installing new packages 
+If you want to install new packages while working in your Jupyter notebook, you can 
+1. Open a new Command Prompt Window (While leaving the other Command Prompt Window open)
+2. Activate your current environment 
+3. Install packages 
+
+For example if you want to install seaborn, you would need to type:
+```json
+conda install seaborn 
+```
+into the Command Prompt Window. This should currently look like this:
+
+![](imgs/6_install_seaborn.png)
+
+We need to open a second Command Prompt Window to install new packages. While doing so, you can leave the first window open.
+
+![](imgs/6_install_seaborn_2.png)
+
+Conda will ask you again for confirmation (`Enter`) to proceed with the installation. If you type `N` + `Enter`, the operation will be canceled. 
+If you want to install a specific version of a package you can do it as shown here: 
+```json
+conda install <package name>=version 
+```
+It is considered good practice to write down the versions you are using to ensure compatibility between packages and to trace bugs. For further information see also the conda user guide [here](https://docs.readthedocs.io/en/stable/guides/conda.html). 
+
+
+## Deactivation or Deletion of an environment 
+If you want to deactivate the environment you just need to type: 
+```json
+conda deactivate 
+```
+If you screwed up your environment and want to delete it, you can type:
+```json
+conda env remove -n nameofproject_env
+```
+
+---
+
+Now you have Miniforge installed, know how to work with conda environments and know about some very important packages. Have fun starting your own Bio-image Analysis project! 👍
+
+---

docs/mara_lampert/readme.md

@@ -14,6 +14,7 @@ Enjoy coding!
 
 ## Blog posts
 * [Getting started with Mambaforge and Python ](getting_started_with_mambaforge_and_python/readme)
+* [Getting started with Miniforge and Python ](getting_started_with_miniforge_and_python/readme)
 
 ## Links
 * [BiA-PoL group website](https://physics-of-life.tu-dresden.de/en/research/technology-development-groups/bio-image-analysis)