fix: reflecting mamba and not micromamba support

slides/common/software_environment.tex

@@ -156,6 +156,7 @@ \subsection{Using Conda}
 			Conda Implementations:
 			\begin{itemize}
 				\item Conda - Python
+				\item Miniconda - Conda with little less overhead
 				\item Mamba - drop-in replacement for "Conda", C\texttt{++}, parallel solver, fast
 				\item \textmu-Mamba - static version of Mamba, little overhead, no "base" environment, slightly different commands
 			\end{itemize}
@@ -166,74 +167,61 @@ \subsection{Using Conda}
 \begin{frame}[fragile]
   \frametitle{Installing Mamba}
   You \emph{could} run
-  \begin{lstlisting}[language=Bash, style=Shell, basicstyle=\small,breaklines=true ]
-$ wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
+  \begin{lstlisting}[language=Bash, style=Shell, basicstyle=\tiny,breaklines=true ]
+$ wget https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh
+$ bash Miniforge3-Linux-x86_64.sh
   \end{lstlisting}
-  to retrieve (Mini)Conda (a flavour of conda with less overhead).
+  to retrieve Mamba.\newline\pause
   \begin{hint}
-  	\footnotesize URL is from \url{https://docs.conda.io/en/latest/miniconda.html}.\newline However, we are going to use tweaked scripts provided to you.
-  \end{hint}
-  \pause
-  \begin{hint}
-  	However, instead of downloading, we will work through this together on the slides to come.
+  	We will work through the installation process \emph{together} on the slides to come.
   \end{hint}
+  Instead, please execute the installer script
+  \begin{lstlisting}[language=Bash, style=Shell]
+$ bash install_mamba.sh
+  \end{lstlisting}
 \end{frame} 
 
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
-\begin{frame}[fragile]
-  \frametitle{We will favour \emph{\textmu-Mamba} over Conda!}
-  Many know ``Conda'' as a package manager -- and this is correct! But:
-  \begin{block}{Why we recommend using ``\textmu-Mamba''}
-   Conda carries some overhead. Alternative implementations can be faster and require less files. Mamba is a ``drop-in'' for Conda. This means: \emph{every command is the same}, except we will write \altverb{mamba} where usuall \altverb{conda} would be.\newline
-   Why?\newline
-   Mamba is an implementation of Conda, written in \CC{}. It is able to carry out some tasks in parallel and works considerably faster. In turn, \textmu-Mamba is a staticically compiled version of Mamba and does not require a ``base'' environment (we will learn about environments, soon), which means even less overhead.
-  \end{block}
-\end{frame}
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
-\begin{frame}[fragile]
-	\frametitle{Installing \sout{Conda}/\textmu-Mamba}
-	Please run
-	\begin{lstlisting}[language=Bash, style=Shell]
-$ "${SHELL}" <(curl -L micro.mamba.pm/install.sh)
-# or in your sample folder
-$ bash install_micromamba.sh
-	\end{lstlisting}
-\end{frame}
-
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
-\begin{frame}
-  \frametitle{Installing \sout{Conda}/\textmu-Mamba - II}
+\begin{frame}[fragile]
+  \frametitle{Mamba - Installation - Part I}
+  Start the installation script - if not done:
+  \begin{lstlisting}[language=Bash, style=Shell]
+$ bash install_mamba.sh
+  \end{lstlisting}
   You need to confirm (with ``Enter'')
   \begin{itemize}[<+->]
+  	\item the license agreement
 	\item the binary folder.
 	\item the shell you are using (just to be on the save side)
-	\item whether conda-forge shall be configured (this is a major resource channel)
-	\item the prefix location (where \textmu-Mamba shall be placed)
   \end{itemize} 
-  The tool will tell up about the modification of your \altverb{.bashrc} file (which is executed upon \emph{every} login, we will discuss this in a minute).
+  The tool will tell up about the modification of your \altverb{.bashrc} file (which is executed upon \emph{every} login - if not corrected).
 \end{frame}
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
 \begin{frame}[fragile]
-  \frametitle{Installing \sout{Conda}/\textmu-Mamba - III}
+  \frametitle{Installing Mamba - Part II}
   \footnotesize
   \begin{columns}[t]
     \begin{column}{0.5\textwidth}
        You now have a section like this in your ``\texttt{\textasciitilde/.bashrc}'':
        \begin{lstlisting}[language=Bash, style=Shell, basicstyle=\tiny, breaklines=true]
-# >>> mamba initialize >>>
-# !! Contents within this block are managed by 'mamba init' !!
-export MAMBA_EXE='/home/<user>/.local/bin/micromamba';
-export MAMBA_ROOT_PREFIX='/home/<prefix>';
-__mamba_setup="$("$MAMBA_EXE" shell hook --shell bash --root-prefix "$MAMBA_ROOT_PREFIX" 2> /dev/null)"
+# !! Contents within this block are managed by 'conda init' !!
+__conda_setup="$('<prefix>/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
 if [ $? -eq 0 ]; then
-    eval "$__mamba_setup"
+    eval "$__conda_setup"
+else
+if [ -f "<prefix>/etc/profile.d/conda.sh" ]; then
+    . "<prefix>/etc/profile.d/conda.sh"
 else
-    alias micromamba="$MAMBA_EXE"  # Fallback on help from mamba activate
+    export PATH="<prefix>/bin:$PATH"
+fi
 fi
-unset __mamba_setup
-# <<< mamba initialize <<<
+unset __conda_setup
+
+if [ -f "<prefix>/etc/profile.d/mamba.sh" ]; then
+    . "<prefix>/etc/profile.d/mamba.sh"
+fi
+# <<< conda initialize <<<
       \end{lstlisting}
       \bcattention \emph{Every} time you log-in this will be executed. Also, here, ``\texttt{<prefix>}'' denotes \emph{your} prefix.
     \end{column}
@@ -242,18 +230,23 @@ \subsection{Using Conda}
        {\footnotesize Please edit your ``\texttt{\textasciitilde/.bashrc}'' file and put part in a function, to re-gain manual control:}
        \begin{lstlisting}[language=Bash, style=Shell, basicstyle=\tiny, breaklines=true]
 @function conda_initialize {@
-# >>> mamba initialize >>>
-# !! Contents within this block are managed by 'mamba init' !!
-export MAMBA_EXE='/home/<user>/.local/bin/micromamba';
-export MAMBA_ROOT_PREFIX='/home/<prefix>';
-__mamba_setup="$("$MAMBA_EXE" shell hook --shell bash --root-prefix "$MAMBA_ROOT_PREFIX" 2> /dev/null)"
+# !! Contents within this block are managed by 'conda init' !!
+    __conda_setup="$('<prefix>/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
 if [ $? -eq 0 ]; then
-    eval "$__mamba_setup"
+    eval "$__conda_setup"
+else
+if [ -f "<prefix>/etc/profile.d/conda.sh" ]; then
+   . "<prefix>/etc/profile.d/conda.sh"
 else
-    alias micromamba="$MAMBA_EXE"  # Fallback on help from mamba activate
+   export PATH="<prefix>/bin:$PATH"
+fi
+fi
+unset __conda_setup
+
+if [ -f "<prefix>/etc/profile.d/mamba.sh" ]; then 
+    . "<prefix>/etc/profile.d/mamba.sh"
 fi
-unset __mamba_setup
-# <<< mamba initialize <<<
+# <<< conda initialize <<<
 @}@
       \end{lstlisting}
     \end{column}
@@ -307,7 +300,7 @@ \subsection{Using Conda}
   \pause
   This will list packages with channel and version information, e.\,g.
   \begin{lstlisting}[language=Bash, style=Shell, basicstyle=\tiny]
-$ micromamba search minimap
+$ mamba search minimap
 <snip>
 Loading channels: done
 # Name                       Version           Build  Channel