First commit

presentation.Rmd

+---
+# SPDX-FileCopyrightText: 2022 Laurent Modolo
+# 
+# SPDX-License-Identifier: AGPL-3.0-or-later
+title: "REUSE tool"
+author: "Laurent Modolo"
+date: "2022/12/01"
+output:
+  beamer_presentation:
+    df_print: tibble
+    fig_caption: no
+    highlight: tango
+    latex_engine: xelatex
+    slide_level: 1
+    theme: metropolis
+  ioslides_presentation:
+    highlight: tango
+  slidy_presentation:
+    highlight: tango
+classoption: aspectratio=169  
+---
+
+
+
+```{r setup, include=FALSE}
+knitr::opts_chunk$set(echo = FALSE)
+```
+
+# Why a Licence ?
+
+
+
+\begin{center}
+\begin{columns}
+\column{0.8\textwidth}
+\begin{quote}
+  Conformément à la
+  \href{https://www.legifrance.gouv.fr/affichTexte.do;jsessionid=6E9C9BD1F4AAF6E6FD525E8FE902A615.tplgfr26s_2?cidTexte=JORFTEXT000033202746\&categorieLien=id}{Loi
+  pour une République numérique du 7 octobre 2016}, les codes sources sont
+  des documents administratifs communicables et réutilisables. Dans le cas
+  où il est possible de choisir une licence libre,
+  \href{https://www.legifrance.gouv.fr/affichTexte.do?cidTexte=JORFTEXT000034502557\&categorieLien=id}{le
+  décret n° 2017-638 du 27 avril 2017} précise les familles de licences
+  qui peuvent être utilisées. La liste détaillée des licences avec leurs
+  versions est disponible sur le site
+  \href{https://www.data.gouv.fr/fr/licences}{data.gouv.fr}.
+\end{quote}
+
+\column{0.3\textwidth}
+\includegraphics[width=\textwidth]{img/republique_numerique.png}
+
+\end{columns}
+\end{center}
+
+\vspace{2em}
+
+But more importantly:
+
+- You are following the [guide of good practices for developpers](https://lbmc.gitbiopages.ens-lyon.fr/hub/good_practices/good_practices.html) at the LBMC
+
+# [GNU Affero General Public License v3.0 or later](https://spdx.org/licenses/AGPL-3.0-or-later.html#licenseText)
+
+\begin{center}
+\begin{columns}
+\column{0.8\textwidth}
+The \href{https://spdx.org/licenses/AGPL-3.0-or-later.html}{AGPL-3}
+\column{0.2\textwidth}
+\includegraphics[width=\textwidth]{img/gnu.png}
+
+\end{columns}
+\end{center}
+
+\vspace{-4em}
+
+Like for the [GPL3](https://spdx.org/licenses/GPL-3.0-or-later.html) Users of [AGPL-3](https://spdx.org/licenses/AGPL-3.0-or-later.html)-licensed code must::
+
+- **Include a copy of the full license text** and the original copyright notice
+- State **all significant changes** made to the original software
+- **Make available the source code** when you **distribute any works** based on the licensed software
+- Include any **installation information necessary to update and reinstall** the software if the program is being used as part of a consumer device
+
+But with a **twist**
+
+
+# [GNU Affero General Public License v3.0 or later](https://spdx.org/licenses/AGPL-3.0-or-later.html#licenseText)
+
+Section 13:
+
+> Notwithstanding any other provision of this License, if you modify the Program, your modified version must prominently offer all users interacting with it remotely through a computer network (if your version supports such interaction) an opportunity to receive the Corresponding Source of your version by providing access to the Corresponding Source from a network server at no charge, through some standard or customary means of facilitating copying of software. […]
+
+If you let users access any AGPL licensed software **over a network, then that is also a form of distribution**. This is what the GPL had missed out
+
+[Google opensource policy:](https://opensource.google/documentation/reference/using/agpl-policy)
+
+> AGPL Policy
+> 
+> WARNING: Code licensed under the GNU Affero General Public License (AGPL) MUST NOT be used at Google.
+
+
+# What about the non-coding part of the project ?
+
+Chance are that these parts also fall under the **administrative documents** category.
+
+So you need to use an open licence with:
+
+\begin{center}
+\begin{columns}
+\column{0.7\textwidth}
+
+At least the autor attribution requirement:
+
+\begin{itemize}
+\item \href{https://www.etalab.gouv.fr/wp-content/uploads/2017/04/ETALAB-Licence-Ouverte-v2.0.pdf}{Licence Ouverte version 2.0}
+\item \href{https://spdx.org/licenses/CC-BY-4.0.html}{Creative Commons Attribution 4.0}
+\end{itemize}
+\column{0.3\textwidth}
+
+\includegraphics[width=\textwidth]{img/etalab.png}
+
+\includegraphics[width=0.6\textwidth]{img/cc_by.png}
+\end{columns}
+\end{center}
+
+\begin{center}
+\begin{columns}
+\column{0.7\textwidth}
+
+But you can add the share alike requirement:
+
+\begin{itemize}
+\item \href{https://spdx.org/licenses/ODbL-1.0.html}{ODC Open Database License version 1.0}
+\item \href{https://spdx.org/licenses/CC-BY-SA-4.0.html}{Creative Commons Attribution Share Alike 4.0}
+\end{itemize}
+
+\column{0.3\textwidth}
+
+\includegraphics[width=\textwidth]{img/open_knowledge_fundation.png}
+
+\includegraphics[width=0.6\textwidth]{img/cc_by.png}
+
+\end{columns}
+\end{center}
+
+
+# REUSE
+
+\begin{center}
+\begin{columns}
+\column{0.5\textwidth}
+
+\includegraphics[width=\textwidth]{img/reuse.png}
+
+\column{0.5\textwidth}
+
+\begin{enumerate}
+\item  Choose and provide licenses
+\item  Add copyright and licensing information to each file
+\item  Confirm REUSE compliance
+\end{enumerate}
+
+\end{columns}
+\end{center}
+
+
+## Install REUSE
+
+You will need **python3.6+** and **pip3**
+
+```
+pip3 install --user reuse
+```
+
+And that's all 
+
+# Initialize REUSE on a project
+
+```
+cd my_project_path
+reuse init
+```
+
+will display this message:
+
+```
+Initializing project for REUSE.
+
+What license is your project under? Provide the SPDX License Identifier.
+To stop adding licenses, hit RETURN.
+```
+
+What are [SPDX](https://spdx.dev/) ?
+
+# *S*oftware *P*ackage *D*ata *E*xchange 
+
+Develop an open standard format and supporting tools for communicating the licenses and copyrights asssociated with software packages
+
+- facilitate open source compliance and licencing information
+- help users comply with the licenese for open source packages
+- allows you to refer to licenses unambiguously
+
+## [https://spdx.org/licenses/](https://spdx.org/licenses/)
+
+
+# *S*oftware *P*ackage *D*ata *E*xchange 
+
+## [https://spdx.org/licenses/](https://spdx.org/licenses/)
+
+\begin{tabular}{ l c }
+Full name & Identifier \\
+\hline
+Apache License 2.0 & Apache-2.0 \\
+GNU Lesser General Public License v3.0 or later & LGPL-3.0-or-later \\
+GNU Affero General Public License v3.0 or later  & AGPL-3.0-or-later\\
+Creative Commons Attribution 4.0 International & CC-BY-4.0\\
+Creative Commons Attribution Share Alike 4.0 International & CC-BY-SA-4.0\\
+Etalab Open License 2.0 & etalab-2.0\\
+\end{tabular}
+
+# Initialize REUSE on a project
+
+```
+What license is your project under? Provide the SPDX License Identifier.
+To stop adding licenses, hit RETURN.
+AGPL-3.0-or-later
+
+What other license is your project under? Provide the SPDX License Identifier.
+To stop adding licenses, hit RETURN.
+CC-BY-SA-4.0
+
+What other license is your project under? Provide the SPDX License Identifier.
+To stop adding licenses, hit RETURN.
+```
+
+# Initialize REUSE on a project
+```
+What is the name of the project?
+my project
+
+What is the internet address of the project?
+mywebsite.com
+
+What is the name of the maintainer?
+Laurent Modolo
+
+What is the e-mail address of the maintainer?
+laurent.modolo@ens-lyon.fr
+
+All done! Initializing now.
+
+Downloading AGPL-3.0-or-later
+Downloading CC-BY-SA-4.0
+
+Creating .reuse/dep5
+
+Initialization complete.
+```
+
+# Initialize REUSE on a project
+
+REUSE created a `LICENSES` folder with our two licenses
+
+```
+LICENSES
+├── AGPL-3.0-or-later.txt
+└── CC-BY-SA-4.0.txt
+.reuse
+└── dep5
+```
+
+The `dep5` file contains the additional informations that we entered.
+
+# REUSE lint
+
+```
+reuse lint
+```
+
+```
+# UNUSED LICENSES
+The following licenses are not used:
+* AGPL-3.0-or-later
+* CC-BY-SA-4.0
+
+# MISSING COPYRIGHT AND LICENSING INFORMATION
+The following files have no copyright and licensing information:
+...
+```
+
+# REUSE lint
+
+```
+# SUMMARY
+* Bad licenses:
+* Deprecated licenses:
+* Licenses without file extension:
+* Missing licenses:
+* Unused licenses: AGPL-3.0-or-later, CC-BY-SA-4.0
+* Used licenses:
+* Read errors: 0
+* Files with copyright information: 0 / 17
+* Files with license information: 0 / 17
+
+Unfortunately, your project is not compliant with 
+version 3.0 of the REUSE Specification :-(
+```
+
+# REUSE addheader
+
+```
+reuse addheader --license AGPL-3.0-or-later \
+  --copyright="Laurent Modolo" presentation.Rmd 
+```
+
+```
+head presentation.Rmd
+```
+
+```
+<!--
+SPDX-FileCopyrightText: 2022 Laurent Modolo
+
+SPDX-License-Identifier: AGPL-3.0-or-later
+-->
+---
+title: "REUSE tool"
+author: "Laurent Modolo"
+```
+
+of course REUSE don't known the `Rmd` format...
+
+
+# REUSE addheader
+
+We have to manualy modify the comment
+
+```
+---
+# SPDX-FileCopyrightText: 2022 Laurent Modolo
+# 
+# SPDX-License-Identifier: AGPL-3.0-or-later
+title: "REUSE tool"
+author: "Laurent Modolo"
+```
+
+# REUSE addheader
+
+```
+reuse lint
+...
+* Used licenses: AGPL-3.0-or-later
+* Read errors: 0
+* Files with copyright information: 1 / 17
+* Files with license information: 1 / 17
+...
+```
+
+# REUSE addheader
+
+If the file is not automatically detected we can use the `--style` option.
+
+For R we can use:
+
+`--style="python"`
+
+For nextflow scripts:
+
+`--style="c"`
+
+
+# REUSE addheader
+
+What if the file is not editable ?
+
+```
+reuse addheader --license="CC-BY-SA-4.0" \
+    --copyright="Laurent Modolo" img/*
+```
+```
+Successfully changed header of img/open_knowledge_fundation.png.license
+Successfully changed header of img/etalab.png.license
+Successfully changed header of img/republique_numerique.png.license
+Successfully changed header of img/reuse.png.license
+Successfully changed header of img/cc_by_sa.png.license
+Successfully changed header of img/cc_by.png.license
+Successfully changed header of img/gnu.png.license
+```
+
+We now have `.license` file along the `im/*.png` files
+
+# REUSE addheader
+
+What if the file is editable but we don't want to ?
+
+You can force the `.license` file creation with the `--force-dot-license`
+
+
+```
+reuse addheader --license="CC-BY-SA-4.0" \
+    --copyright="Laurent Modolo" data/test/data.csv data/test/data.fastq
+```
+
+Ignore part of a file
+
+```
+# REUSE-IgnoreStart
+echo "SPDX-FileCopyrightText: $(date +'%Y') Jane Doe" > file.txt
+echo "SPDX-License-Identifier: MIT" > file.txt
+# REUSE-IgnoreEnd
+```
+
+# `reuse lint`
+
+```
+# SUMMARY
+
+* Bad licenses:
+* Deprecated licenses:
+* Licenses without file extension:
+* Missing licenses:
+* Unused licenses:
+* Used licenses: AGPL-3.0-or-later, CC-BY-SA-4.0
+* Read errors: 0
+* Files with copyright information: 310 / 310
+* Files with license information: 310 / 310
+
+Congratulations! Your project is compliant with version 3.0 of
+the REUSE Specification :-)
+```