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Author: rkdarst

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+# Conda environment
+
+[this page is adapted from <https://aaltoscicomp.github.io/python-for-scicomp/installation/>]
+
+You only need this if you wish to go through examples and exercises during the
+second workshop week on your own computer.
+
+
+## Choosing an installation method
+
+For this course we will install an **isolated environment**
+with following dependencies:
+:::::{tabs}
+  ::::{tab} environment.yml
+    :::{literalinclude} software/environment.yml
+    :language: yaml
+    :::
+  ::::
+
+  ::::{tab} requirements.txt
+    :::{literalinclude} software/requirements.txt
+    :::
+  ::::
+:::::
+
+:::{admonition} If you have a tool/method that works for you, keep using it
+If you are used to installing Conda packages and know what to do with the
+above files, please follow your own preferred installation
+method.
+
+**If you are new to Conda or unsure** how to create isolated environments from
+files above, please follow the instructions below where we do this with the help
+of Miniforge.
+
+If you already use **Anaconda** to manage your software environments, please
+continue using it. In this case you can skip {ref}`miniforge` and go directly to
+{ref}`conda-environment`.
+:::
+
+
+:::{admonition} Why do we recommend Miniforge and how does it relate to Conda?
+:class: dropdown
+
+There are many choices and we try to suggest a good compromise
+There are very many ways to install packages with pros and cons and
+in addition there are several operating systems with their own quirks. This
+can be a huge challenge for beginners to navigate. It can also difficult for
+instructors to give recommendations for something which will work everywhere
+and which everybody will like.
+
+Below we will recommend **Miniforge** since it is free, open source, general,
+available on all operating systems, and provides a good basis for reproducible
+environments. However, it does not provide a graphical user interface during
+installation.
+
+But Miniforge is only one option. Unfortunately there are many options and a
+lot of jargon.  Here is a crash course:
+
+- **Conda** is a package manager: it allows distributing and
+  installing packages, and is designed for complex scientific
+  code.
+- **Mamba** is a re-implementation of Conda to be much faster with
+  resolving dependencies and installing things.
+- An **environment** is a self-contained collections of packages
+  which can be installed separately from others.  They are used so
+  each project can install what it needs without affecting others.
+- **Anaconda** is a commercial distribution of Python+Conda+many
+  packages that all work together.  It used to be freely usable for
+  research, but since ~2023-2024 it's more limited.  Thus, we don't
+  recommend it (even though it has a nice graphical user interface).
+- **conda-forge** is another channel of distributing packages that
+  is maintained by the community, and thus can be used by anyone.
+  (Anaconda's parent company also hosts conda-forge packages)
+- **Miniforge** is the installer recommended by the conda-forge community. It operates via the command line.
+- **Miniconda** is a distribution of conda pre-configured to use
+  the Anaconda channels.
+:::
+
+
+(miniforge)=
+
+## Installing Miniforge
+
+Download the latest release from the [Miniforge download
+overview](https://conda-forge.org/download/).  This installs the base, and from
+here other packages can be installed.
+
+Unsure what to download and what to do with it?
+::::{tabs}
+  :::{group-tab} Windows
+  You want to download and run `Miniforge3-Windows-x86_64.exe`.
+  
+  When viewing the "Advanced installation options" step of the installer,
+  leave the "Create shortcuts (supported packages only)." option **checked**,
+  otherwise it will be difficult to launch the Miniforge prompt later.
+  :::
+
+  :::{group-tab} MacOS
+  You probably want to download the `Miniforge3-MacOSX-arm64.sh` file (unless
+  you don't have an Arm processor) and then run it in the terminal with:
+  ```console
+  $ bash Miniforge3-MacOSX-arm64.sh
+  ```
+  :::
+
+  :::{group-tab} Linux
+  You probably want to download the `Miniforge3-Linux-x86_64.sh` file (unless
+  you don't have an x86_64 processor) and then run it in the terminal with:
+  ```console
+  $ bash Miniforge3-Linux-x86_64.sh
+  ```
+  :::
+::::
+
+
+(conda-environment)=
+
+## Installing the software environment
+
+First we will start a command line environment in a way that activates
+conda/mamba.  Then we will install the software environment from [this
+environment.yml
+file](https://raw.githubusercontent.com/coderefinery/software/main/environment.yml)
+(this is the same file as on top of this page).
+
+An **environment** is a self-contained set of extra libraries - different
+projects can use different environments to not interfere with each other.  This
+environment will have all of the software needed for this particular course.
+
+We will call the environment `coderefinery`.
+
+::::{tabs}
+  :::{group-tab} Windows
+  Use the "Miniforge Prompt" to start Miniforge.  This
+  will set up everything so that ``conda`` and ``mamba`` are
+  available.
+  Then type
+  (without the `$`):
+  ```console
+  $ curl "https://raw.githubusercontent.com/coderefinery/software/main/environment.yml" -o environment.yml 
+  $ mamba env create -n coderefinery -f environment.yml
+  ```
+  :::
+
+  :::{group-tab} Linux / MacOS
+  Each time you start a new command line terminal,
+  you can activate Miniforge by running
+  (without the `$`):
+  ```console
+  $ source ~/miniforge3/bin/activate
+  ```
+
+  This is needed so that
+  Miniforge is usable wherever you need, but doesn't affect any
+  other software on your computer (this is not needed if you
+  choose "Do you wish to update your shell profile to
+  automatically initialize conda?", but then it will always be
+  active).
+
+  In the second step, we will install the software environment by first copying the definition file:
+  ```console
+  $ curl "https://raw.githubusercontent.com/coderefinery/software/main/environment.yml" -o environment.yml 
+  $ mamba env create -n coderefinery -f environment.yml
+  ```
+  :::
+::::
+
+
+(activating-environment)=
+
+## Activating the software environment
+
+::::{tabs}
+  :::{group-tab} Windows
+  Start the Miniforge Prompt. Then type
+  (without the `$`):
+  ```console
+  $ conda activate coderefinery
+  $ jupyter-lab
+  ```
+  :::
+
+  :::{group-tab} Linux / MacOS
+  Start the terminal and in the terminal, type
+  (without the `$`):
+  ```console
+  $ source ~/miniforge3/bin/activate
+  $ conda activate coderefinery
+  $ jupyter-lab
+  ```
+  :::
+::::
+
+
+## How to verify the environment
+
+Make sure you are in the Miniforge prompt (Windows) or in a terminal (Linux/MacOS).
+
+The following command should return a version number and not an error message:
+```console
+$ conda --version
+```
+
+Is the coderefinery environment installed?
+```console
+$ conda env list
+```
+
+Make sure it's activated ({ref}`activating-environment`).
+Once activated, try the following commands.
+
+You should see versions printed and not see errors (exact version numbers are not too important):
+```console
+$ jupyter-lab --version
+
+4.1.2
+
+```
+```console
+$ pytest --version
+
+8.0.2
+```
+
+```console
+$ sphinx-build --version
+
+sphinx-build 7.2.6
+```
+
+```console
+$ snakemake --version
+
+8.5.3
+```
+
+
+## Removing the software environment
+
+::::{tabs}
+  :::{group-tab} Windows
+  In the Miniforge Prompt, type
+  (without the `$`):
+  ```console
+  $ conda env list
+  $ conda env remove --name coderefinery
+  $ conda env list
+  ```
+  :::
+
+  :::{group-tab} Linux / MacOS
+  In the terminal, type
+  (without the `$`):
+  ```console
+  $ source ~/miniforge3/bin/activate
+  $ conda env list
+  $ conda env remove --name coderefinery
+  $ conda env list
+  ```
+  :::
+::::

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+# Visual diff tools (optional)
+
+Visual diff tools allow to visualize differences between files side by side.
+They can be used independently of version control but when coupled with Git,
+they can provide a nice alternative to command line output to show differences
+between file versions or branches.
+
+`````{tabs}
+  ````{tab} Windows
+
+  On Windows we recommend the program [meld](https://meldmerge.org).
+  Please follow installation instructions from [http://meldmerge.org](http://meldmerge.org).
+
+  This is how you can configure Git to open Meld when doing `git difftool`:
+  ```console
+  $ git config --global diff.tool meld
+  $ git config --global mergetool.meld.path "C:\Program Files (x86)\Meld\Meld.exe"
+  ```
+  For meld version 3.20.3, because of reasons discussed [here](https://gitlab.gnome.org/GNOME/meld/-/issues/559), you can have multiple "Could not create key" errors that you can get around by clicking 'Ignore'.
+  Then, to open Meld when doing `git difftool`:
+  ```console
+  $ git config --global diff.tool meld
+  $ git config --global mergetool.meld.path "$LOCALAPPDATA\Programs\Meld\Meld.exe"
+  ```
+  ````
+
+  ````{tab} macOS
+
+  For macOS we recommend to use Opendiff. You can install it following [this blog
+  post](https://borgs.cybrilla.com/tils/opendiff-as-difftool/).
+  ````
+
+  ````{tab} Linux
+
+  On Linux we recommend the program [meld](https://meldmerge.org).
+  Install meld via your distribution package manager. For Debian/Ubuntu run:
+  ```console
+  $ sudo apt-get install meld
+  ```
+
+  For Fedora:
+  ```console
+  $ sudo dnf install meld
+  ```
+
+  This is how you can configure Git to open Meld when doing `git difftool`:
+  ```console
+  $ git config --global diff.tool meld
+  ```
+  ````
+
+``````
+
+## How to verify the installation
+
+To test it create two text files which are similar and then compare them
+with Meld or Diffuse or Opendiff (or the tool which you have chosen above for visual
+differences):
+```console
+$ meld file1 file2
+```
+or:
+```console
+$ diffuse file1 file2
+```
+or:
+```console
+$ opendiff file1 file2
+```
+
+You should now see both versions side by side.
+
+To test launching Meld through Git, move into a folder that contains two or more files and instruct Git to compare files.
+For example, to see the difference between `file1.txt` and `file2.txt`:
+```console
+$ git difftool --no-index file1.txt file2.txt
+```