presentation_gblk.tex: update

presentation_gblk.tex

@@ -117,27 +117,29 @@
 
 \begin{frame}{Data versioning}{}
 
-In a bioinformatic project:
+In a bioinformatics project:
 
 \begin{itemize}
 \item Code
-\item Results produced by this code
-\item Save those results
-\begin{itemize}
-\item Compare results between code versions
-\item Have an overview of results produced by the project code
+\item Results (produced by this code)
 \end{itemize}
+
+Saving the results allow to:
+\begin{itemize}
+\item Compare them between code versions
+\item Have an overview of result files produced by the project code
 \end{itemize}
 
+
 \alert{Data versioning tools} can help us to achieve this. \\
 
 
-\begin{block}{Controlling your data version with a tool may help you to}
+\begin{block}{Controlling the version of your data with a tool can help you to}
 \begin{itemize}
-\item Save you some time to manage and track your data version
+\item Save you time in managing and tracking your data versions
 \item Collaborate with your team members
 \item Avoid losing data
-\item Increase the traçability of your results
+\item Increase the traceability of your results
 \end{itemize}
 \end{block}
 
@@ -149,7 +151,7 @@ In a bioinformatic project:
 
 \begin{frame}{Data versioning tools}
 
-A lots of data versioning tools are available:
+Many data versioning tools are available:
 \captionsetup[subfigure]{labelformat=empty}
 \begin{figure}[thbp]
     \centering
@@ -184,7 +186,7 @@ A lots of data versioning tools are available:
 \begin{block}{Main drawbacks}
 \begin{itemize}
 \item No data deduplication
-\item You can't delete only some version of a file without deleting them all !
+\item You can't delete only some versions of a file without deleting them all !
 \end{itemize}
 \end{block}
 
@@ -223,7 +225,7 @@ A lots of data versioning tools are available:
 \begin{block}{Main advantages}
 \begin{itemize}
 \item git integration / Same git workflow (no additional commands)
-\item Store file in a repository dedicated for large files (couples of GBs)
+\item Store files in a repository dedicated for large files (couples of GBs)
 \end{itemize}
 \end{block}
 
@@ -242,7 +244,7 @@ A lots of data versioning tools are available:
 When using a data versioning tool, it seems that we \alert{can't control precisely specific versions to keep and remove} to save some space.
 \vspace*{1cm}
 
-That's why we started to be interested in \alert{backup programs} for data versioning.
+That's why, we started to be interested in \alert{backup programs} for data versioning.
 
 \end{frame}
 
@@ -252,16 +254,16 @@ That's why we started to be interested in \alert{backup programs} for data versi
 \begin{frame}{Backup program: BorgBackup (short Borg)}
 
 \centering
-\includegraphics[height=2.5cm]{image/img4.png}
+\includegraphics[height=1.5cm]{image/img4.png}
 
-Borg provide an efficient and secure way to backup data. To learn more about borg, you can visit \url{https://www.borgbackup.org/}
+Borg: Efficient and secure backups. \url{https://www.borgbackup.org/}
 \begin{block}{Main advantages}
 \begin{itemize}
 \item Easy to use
 \item Supports deduplication
 \item Supports compression
 \item Creates an archive folder (we can handle it like we want)
-\item No restriction in backup deletion
+\item No restrictions in backups deletion
 \end{itemize}
 \end{block}
 
@@ -286,11 +288,13 @@ Borg provide an efficient and secure way to backup data. To learn more about bor
 \caption*{Git Borg Linker (gblk)}
 \end{figure}
 
-... Was developed to integrate borg with git.
+Developed to integrate borg with git.
 
 
 \begin{block}{}
-gblk will handle data versioning by using git history and uses borg to do the backups. So it has all the advantages you get by using borg with the addition of git integration
+gblk handles data versioning by using git history and uses borg to do the backups. 
+\vspace*{0.2cm}
+gblk: Borg advantages + git integration
 \end{block}
 
 
@@ -299,16 +303,16 @@ gblk will handle data versioning by using git history and uses borg to do the ba
 
 \begin{frame}[fragile]{Git Borg Linker}
 
-This tool is available at: 
+Available at: 
 \begin{center}
 \url{https://gitbio.ens-lyon.fr/LBMC/hub/git\_borg\_linker}
 \end{center}
 
 Note that \alert{git}, \alert{borg} and \alert{rust} is required to use gblk. 
 
-\vspace*{1cm}
+\vspace*{0.5cm}
 
-To install rust and gblk, you can use the following command:
+To install rust and gblk, you can use the following commands:
 
 \begin{lstlisting}[language=bash]
 $ # Install git
@@ -350,7 +354,7 @@ $ mkdir results; src
 $ git init
 \end{lstlisting}
 
-At this point you have to init gblk to start using it, this can be done with the command \texttt{gblk init}:
+Initialize gblk to start using it: Done with \texttt{gblk init}:
 
 \includegraphics[width=11cm]{image/img5.png}
 
@@ -362,20 +366,35 @@ Available compressions: no, lz4, zstd, zlib or lzma. See \href{https://borgbacku
 gblk can optionally create git hooks (with \texttt{gblk init} command or \texttt{create-hooks}) to automatically execute commands:
 \pause
 \begin{itemize}
-\item after a commit to automatically backup you data
+\item after a commit to automatically save you data
 \item after a checkout to:
 \begin{enumerate}
-\item Revert your checkout
-\item Check if you have unsaved data in your current \texttt{results} folder. If you have stops the checkout.
-\item Performs git checkout
-\item Performs a gblk checkout (restore your \alert{results} folder as it was at the destination commit).
+\item Revert the checkout
+\item Check if there is unsaved/missing data in the \texttt{results} folder (compared to the archive of the current commit). If so, stops the checkout.
+\item Perform git checkout
+\item Perform a gblk checkout (restore your \alert{results} folder as it was at the destination commit).
 \end{enumerate}
 \end{itemize}
 \pause
 The hooks created by those commands can be found in \texttt{.git/hooks} folder and are name \texttt{post-commit} and \texttt{post-checkout}.
 
-\vspace*{0.5cm}
-Note that those commands will also create a git alias: \texttt{co} \alert{for checkout} for the current project only. It allow to make the git checkout quiet (because it will be reverted)
+\end{frame}
+
+
+\begin{frame}[fragile]{Git Borg Linker - init}
+
+\texttt{gblk init ---hooks} and \texttt{create-hooks} commands will also create 3 git aliases:
+
+\begin{itemize}
+\item  \texttt{co}: for \alert{checkout}. It allow to make the git checkout quiet (because it will be reverted)
+\pause
+\item \texttt{conh}: For \alert{checkout}. It allow to make a checkout without using the hooks. It is useful to bypass the check of unsaved/missing data in the \texttt{results} folder. \alert{You have to combine it with \texttt{gblk checkout ---mode hard}} to checkout your \texttt{results} folder to the new current commit.
+\pause
+\item \texttt{cnh}: For \alert{commit}. It allows to make a simple git commit without saving your result repository (may lead to data loss)
+\end{itemize}
+
+\vspace*{0.2cm}
+Note: Those aliases are valid only \alert{for the current project}. They can be found in the file \texttt{.git/config}
 
 \end{frame}
 
@@ -389,14 +408,14 @@ $ gblk init --hooks
 borg repository initialised at .borg
 \end{lstlisting}
 
-This command create an empty \texttt{.borg} repository were the backups of your results folder will be saved.
+Creates an empty \texttt{.borg} repository were the backups of your results folder will be saved.
 \end{frame}
 
 \begin{frame}[fragile]{Git Borg Linker - commit}
 
-Let's add a code that will produce results file.
+Let's add a code that will produce a result file.
 \begin{lstlisting}[language=bash]
-$ echo "echo 'result line' > results/result.txt" > src/script.sh # create a script file that produce a result file
+$ echo "echo 'result line' > results/result.txt" > src/script.sh # creates a script file that produces a result file
 $ bash src/script.sh # creation of a results/result.txt
 $ git add src/script.sh && git commit -m "src/script.sh: initial commit" # commit the change
 Repository: /~/test_gblk/.borg
@@ -421,15 +440,19 @@ create mode 100644 src/script.sh
 
 \begin{frame}[fragile]{Git Borg Linker - commit}
 
-Because a \alert{post-commit} hook was created, the command \texttt{git commit -m "src/script.sh: initial commit"} is equivalent to:
+Because a \alert{post-commit} hook was created, the command 
+\begin{center}
+\texttt{git commit -m "src/script.sh: initial commit"} 
+\end{center}
 
+is equivalent to:
 \begin{lstlisting}[language=bash]
-$ git add src/script.sh && git commit -m "src/script.sh: initial commit" # commit the change
+$ git commit -m "src/script.sh: initial commit" # commit the change
 $ gblk commit # commit the results, we have to use this command after commit if gblk hooks are not enabled
 \end{lstlisting}
 \pause
 
-A backup of our result file is created after this \texttt{git commit} command. It has the name of the current git commit. We can use \texttt{gblk list} to list the backups created:
+A backup \alert{with the name current git commit} was created. We can use \texttt{gblk list} to list the backups:
 
 \begin{lstlisting}[language=bash]
 $ gblk list
@@ -445,7 +468,8 @@ b1da0e305c906fb242bc8...
 
 \begin{frame}[fragile]{Git Borg Linker - checkout}
 
-Let's commit new changes and then checkout.
+
+Let's commit the new changes and then checkout.
 \begin{lstlisting}[language=bash]
 $ echo "echo 'newresult line' > results/newresult.txt" >> src/script.sh
 $ bash src/script.sh
@@ -488,23 +512,30 @@ $ git co b1da0e305c906fb242bc8... # checkout to the first commit
 
 Your results folder contains unsaved changes!
 Please update your current commit with:  gblk commit --update
+Or revert it back to it's previous state with gblk commit --revert
 \end{lstlisting}
 
 To avoid losing data, gblk pre-co command will stop the checkout if new data is found in the \texttt{results} folder.
 
+\vspace*{0.5cm}
 
-You can either remove the change or save the changes with the command \texttt{gblk commit --update} and then proceed to checkout.
+You can either:
+\begin{itemize}
+\item remove the change (\texttt{gblk commit ---revert})
+\item save the changes (\texttt{gblk commit ---update}).
+\end{itemize}
 
+And proceed to checkout
 \end{frame}
 
 
 \begin{frame}[fragile]{Git Borg Linker - diff}
 
-To see differences between two backups of your results folder you can use \texttt{gblk diff}.
 
+Check for differences between backups using \texttt{gblk diff}.
 \includegraphics[width=10cm]{image/img8.png}
 
-Note that you can only the name of backups (that corresponds to the SHA1 of a commit) saved in \texttt{.borg} folder.
+Note that you can only use the name of backups (that corresponds to the SHA1 of a commit) saved in \texttt{.borg} folder. \alert{Branch names can't be used}.
 
 Example: 
 
@@ -524,9 +555,9 @@ $  gblk diff 25fdb6808cd...
 
 \begin{frame}[fragile]{Git Borg Linker - delete }
 
-For now gblk does'nt handle backup deletion. To delete a backup, you'll have to use borg
+For now, gblk does not handle backup deletion. To delete a backup, you can use borg
 
-Use borg delete to remove specific commits or the N first or last commit
+Use borg delete to remove specific commits or the N first or last commits
 \begin{lstlisting}[language=bash]
 $ borg delete .borg::b1da0e305c906fb242bc8ef5699edeaa8c2a6d64 # deletion of a selected commit the disk space is not freed
 $ borg compact .borg
@@ -557,7 +588,7 @@ To tell gblk to don't track some files in the \texttt{results} folder, a \texttt
 
 Example: 
 
-To avoid tracking all files in the folder \texttt{results/test} and to avoid tracking txt file in the subfolder \texttt{results/notxt} you can write the following .borignore file
+To avoid tracking all files in the folder \texttt{results/test} and to avoid tracking txt file in the subfolder \texttt{results/notxt} you can write the following .borgignore file
 
 \begin{lstlisting}[language=bash]
 results/test/*
@@ -565,10 +596,34 @@ results/notxt/*.txt
 \end{lstlisting}
 
 \vspace*{0.5cm}
-When checking out with hard mode, ignored files won't be deleted.
+Note : When checking out with hard mode, ignored files won't be deleted.
+\vspace*{0.1cm}
+
+\alert{Warning} : If you put a blanck line at the end of \texttt{.borgignore} file: Results file that didn't previously exists on the destination commit  won't be deleted even with \texttt{--mode hard}.
+
 
 \end{frame}
 
+
+\begin{frame}[fragile]{Git Borg Linker - Still under development }
+
+\begin{center}
+\includegraphics[height=4cm]{image/img9.png}
+\end{center}
+
+\begin{block}{}
+\begin{itemize}
+\item Still needs a feedback of user for:
+\begin{itemize}
+\item improvements/new features
+\item Bug fix
+\end{itemize}
+\end{itemize}
+\end{block}
+
+\end{frame}
+
+
 \section{Conclusion} 
 
 \begin{frame}[fragile]{Conclusion}
@@ -580,7 +635,7 @@ Git borg linker
 \begin{itemize}
 \item Integrates git and borg so it can be used for data versioning in a bioinformatic projects.
 \item Is easy to use
-\item Handles data deduplication to reduce the cost in storage space when large file are generated
+\item Handles data deduplication to reduce the cost in storage space when large files are generated
 \end{itemize}
 
 But \alert{it can be slow when the results folder is big}