Merge branch 'sdinot-hyphenation' into 'main'

Ajout de règles de césure

Closes #2

See merge request coso-college-codes-sources-et-logiciels/forges-esr!4

.gitignore

@@ -0,0 +1 @@
+etatdeslieux.pdf

etatdeslieux.md

@@ -22,7 +22,7 @@ Le gestionnaire de versions permet donc de suivre finement l'historique d'écrit
 
 ## Piloter tout le cycle de vie du logiciel
 
-Le développement d'un logiciel de qualité ne s'arrête pas à la phase de réalisation du logiciel, c'est-à-dire la phase d'écriture du code. En effet, le code est certes un artefact important issu du processus de développement logiciel, mais les spécifications (aussi appelées « ensemble des exigences » ou encore « cahier des charges »), les modèles de conception , les tests, les documentations concepteur et utilisateur en sont d'autres tout aussi importants si l'on souhaite développer un code de qualité et pérenne dans le temps, c'est-à-dire maintenable, voire réutilisable.
+Le développement d'un logiciel de qualité ne s'arrête pas à la phase de réalisation du logiciel, c'est-à-dire la phase d'écriture du code. En effet, le code est certes un artefact important issu du processus de développement logiciel, mais les spécifications (aussi appelées « ensemble des exigences » ou encore « cahier des charges »), les modèles de conception, les tests, les documentations concepteur et utilisateur en sont d'autres tout aussi importants si l'on souhaite développer un code de qualité et pérenne dans le temps, c'est-à-dire maintenable, voire réutilisable.
 
 Le gestionnaire de versions est donc l'un des outils à mettre en œuvre, mais pas le seul. Pour gérer tout le cycle de vie d'un logiciel, on a souvent besoin de gérer en plus les besoins des utilisateurs, de consigner les défauts constatés du logiciel, de produire des versions diffusables du logiciel, de lancer des tests périodiquement, de produire de la documentation, etc.
 

intro-etatdeslieux.md

@@ -4,6 +4,9 @@ subtitle: Définition, usages, limitations rencontrées et analyse des besoins
 author: "Collège Codes sources et logiciels du Comité pour la science ouverte"
 date: Mai 2023
 logo: ouvrirlasciencelogo.jpg
+# cspell:disable
+# mainfont: Marianne
+# cspell:enable
 toc-title: Sommaire
 titlepage-background: "`fond_ouvrir_la_science.jpg`{=latex}"
 titlepage-text-color: 5A28C8
@@ -16,6 +19,7 @@ colorlinks: true
 book: true
 classoption: oneside
 # draft: Document de travail
+# cspell:disable
 header-includes: |
   \usepackage{tcolorbox}
   \tcbuselibrary{theorems}
@@ -38,10 +42,43 @@ header-includes: |
   \usepackage{wrapfig}
   \usepackage{afterpage}
   \usepackage{authoraftertitle}
-  \hyphenation{de-venue}
+  \hyphenation{ac-ti-vi-té ac-ti-vi-tés}
-  \hyphenation{faci-lité}
+  \hyphenation{an-cien-nes}
-  \hyphenation{an-ciennes}
+  \hyphenation{DevLog GitLab OpenAI}
-  \hyphenation{re-lativement}
+  \hyphenation{col-la-bo-ra-tion col-la-bo-ra-tions}
+  \hyphenation{comp-ta-bi-li-sé comp-ta-bi-li-sés comp-ta-bi-li-sée comp-ta-bi-li-sées}
+  \hyphenation{de-ve-nue}
+  \hyphenation{Dis-co-ve-ry}
+  \hyphenation{dis-po-ni-bles}
+  \hyphenation{En-sei-gne-ment}
+  \hyphenation{évo-luent}
+  \hyphenation{exem-ple exem-ples}
+  \hyphenation{exi-gen-ce exi-gen-ces}
+  \hyphenation{exis-te exis-tent}
+  \hyphenation{fa-ci-li-té}
+  \hyphenation{fonc-tion-na-li-té fonc-tion-na-li-tés}
+  \hyphenation{gé-né-ra-li-sa-tion}
+  \hyphenation{in-con-tour-na-ble in-con-tour-na-bles}
+  \hyphenation{ins-tan-ce ins-tan-ces}
+  \hyphenation{ins-tau-rer}
+  \hyphenation{ins-ti-tu-tion}
+  \hyphenation{li-mi-té li-mi-tés}
+  \hyphenation{maxi-mum}
+  \hyphenation{orien-tées}
+  \hyphenation{par-ta-gea-ble}
+  \hyphenation{per-mettre per-mettant}
+  \hyphenation{pro-blè-me pro-blè-mes}
+  \hyphenation{pu-blic}
+  \hyphenation{qua-li-té}
+  \hyphenation{re-la-ti-ve-ment}
+  \hyphenation{respect}
+  \hyphenation{réa-li-sant}
+  \hyphenation{ti-cket ti-ckets}
+  \hyphenation{tui-la-ge}
+  \hyphenation{usa-ge}
+  \hyphenation{uti-li-sa-teur uti-li-sa-teurs}
+  \hyphenation{uti-li-sées}
+# cspell:enable
 include-before: |
   \newpage
   \newgeometry{margin=0.5in}

references.bib

@@ -6,6 +6,7 @@
   journaltitle = {The Register},
   url          = {https://resana.numerique.gouv.fr/public/document/consulter/3231705?slug=160133}
 }
+
 @article{gitorious,
   title        = {Code collaboration platform GitLab acquires rival Gitorious, will shut it down on June 1},
   author       = {Andrii Degeler},
@@ -14,6 +15,7 @@
   journaltitle = {The Next Web},
   url          = {https://thenextweb.com/news/gitlab-acquires-rival-gitorious-will-shut-june-1}
 }
+
 @article{googlecode,
   title        = {Google to close Google Code open source project hosting},
   author       = {ARS Staff},
@@ -22,6 +24,7 @@
   journaltitle = {ARS Technica},
   url          = {https://arstechnica.com/information-technology/2015/03/google-to-close-google-code-open-source-project-hosting/}
 }
+
 @article{elasticsearch,
   title        = {Elastic changes open-source license to monetize cloud-service use},
   author       = {Steven Vaughan-Nichols},
@@ -30,6 +33,7 @@
   journaltitle = {ZD NET},
   url          = {https://www.zdnet.com/article/elastic-changes-open-source-license-to-monetize-cloud-service-use/}
 }
+
 @misc{codeetlogiciel,
   title        = {Science ouverte – codes et logiciels},
   author       = {Pellegrini, François and Di Cosmo, Roberto and Romary, Laurent and Janik, Joanna and Hodenq, Sacha and Coutanson, Romane and Géroudet,  Madeleine},
@@ -38,6 +42,7 @@
   publisher    = {ministère de l’Enseignement supérieur et de la Recherche},
   url          = {https://www.ouvrirlascience.fr/science-ouverte-codes-et-logiciels/}
 }
+
 @article{akka,
   title        = {Lightbend: Open-source licensing con game or smart business move?},
   author       = {Steven Vaughan-Nichols},
@@ -46,17 +51,18 @@
   journaltitle = {ZD NET},
   url          = {https://www.zdnet.com/article/lightbend-open-source-licensing-con-game-or-smart-business-move/}
 }
+
 @misc{jecode,
-  TITLE = {{Je code : Les bonnes pratiques de d{\'e}veloppement logiciel}},
+  title        = {{Je code : Les bonnes pratiques de d{\'e}veloppement logiciel}},
-  AUTHOR = {Ammour, Lila and Capp{\'e}, Olivier and Chaventre, Thierry and Dassas, Karin and Dexet, Marc and Moreau, Patrick and Mouton, C. and Souplet, Jean-Christophe},
+  author       = {Ammour, Lila and Capp{\'e}, Olivier and Chaventre, Thierry and Dassas, Karin and Dexet, Marc and Moreau, Patrick and Mouton, C. and Souplet, Jean-Christophe},
-  URL = {https://hal.archives-ouvertes.fr/hal-02083801},
+  url          = {https://hal.archives-ouvertes.fr/hal-02083801},
-  NOTE = {Guide de bonnes pratiques de d{\'e}veloppement logiciel {\`a} destination de la communaut{\'e} de l'enseignement sup{\'e}rieur et de la recherche.},
+  note         = {Guide de bonnes pratiques de d{\'e}veloppement logiciel {\`a} destination de la communaut{\'e} de l'enseignement sup{\'e}rieur et de la recherche.},
-  YEAR = {2019},
+  year         = {2019},
-  MONTH = Dec,
+  month        = Dec,
-  KEYWORDS = {r{\'e}seau DevLOG ; CNRS},
+  keywords     = {r{\'e}seau DevLOG ; CNRS},
-  PDF = {https://hal.archives-ouvertes.fr/hal-02083801/file/20191202_plaquette_developpement_V1.1.pdf},
+  pdf          = {https://hal.archives-ouvertes.fr/hal-02083801/file/20191202_plaquette_developpement_V1.1.pdf},
-  HAL_ID = {hal-02083801},
+  hal_id       = {hal-02083801},
-  HAL_VERSION = {v1},
+  hal_version  = {v1},
 }
 
 @article{eclipsegitlab,
@@ -87,66 +93,67 @@
 }
 
 @article{cosssuccessful,
-doi = {10.1088/1749-4699/6/1/015010},
+  doi          = {10.1088/1749-4699/6/1/015010},
-url = {https://dx.doi.org/10.1088/1749-4699/6/1/015010},
+  url          = {https://dx.doi.org/10.1088/1749-4699/6/1/015010},
-year = {2013},
+  year         = {2013},
-month = {nov},
+  month        = {nov},
-publisher = {IOP Publishing},
+  publisher    = {IOP Publishing},
-volume = {6},
+  volume       = {6},
-number = {1},
+  number       = {1},
-pages = {015010},
+  pages        = {015010},
-author = {Wolfgang Bangerth and Timo Heister},
+  author       = {Wolfgang Bangerth and Timo Heister},
-title = {What makes computational open source software libraries successful?},
+  title        = {What makes computational open source software libraries successful?},
-journal = {Computational Science & Discovery},
+  journal      = {Computational Science & Discovery},
-abstract = {Software is the backbone of scientific computing. Yet, while we regularly publish detailed accounts about the results of scientific software, and while there is a general sense of which numerical methods work well, our community is largely unaware of best practices in writing the large-scale, open source scientific software upon which our discipline rests. This is particularly apparent in the commonly held view that writing successful software packages is largely the result of simply ‘being a good programmer’ when in fact there are many other factors involved, for example the social skill of community building. In this paper, we consider what we have found to be the necessary ingredients for successful scientific software projects and, in particular, for software libraries upon which the vast majority of scientific codes are built today. In particular, we discuss the roles of code, documentation, communities, project management and licenses. We also briefly comment on the impact on academic careers of engaging in software projects.}
+  abstract     = {Software is the backbone of scientific computing. Yet, while we regularly publish detailed accounts about the results of scientific software, and while there is a general sense of which numerical methods work well, our community is largely unaware of best practices in writing the large-scale, open source scientific software upon which our discipline rests. This is particularly apparent in the commonly held view that writing successful software packages is largely the result of simply ‘being a good programmer’ when in fact there are many other factors involved, for example the social skill of community building. In this paper, we consider what we have found to be the necessary ingredients for successful scientific software projects and, in particular, for software libraries upon which the vast majority of scientific codes are built today. In particular, we discuss the roles of code, documentation, communities, project management and licenses. We also briefly comment on the impact on academic careers of engaging in software projects.}
 }
 
 @book{bazaar,
-  author    = {Eric S. Raymond},
+  author       = {Eric S. Raymond},
-  title     = {The cathedral and the bazaar - musings on Linux and open source by
+  title        = {The cathedral and the bazaar - musings on Linux and open source by
-               an accidental revolutionary (rev. ed.)},
+                  an accidental revolutionary (rev. ed.)},
-  publisher = {O'Reilly},
+  publisher    = {O'Reilly},
-  year      = {2001},
+  year         = {2001},
-  isbn      = {978-0-596-00108-7},
+  isbn         = {978-0-596-00108-7},
-  timestamp = {Thu, 07 Apr 2011 16:15:58 +0200},
+  timestamp    = {Thu, 07 Apr 2011 16:15:58 +0200},
-  biburl    = {https://dblp.org/rec/books/daglib/0003337.bib},
+  biburl       = {https://dblp.org/rec/books/daglib/0003337.bib},
-  bibsource = {dblp computer science bibliography, https://dblp.org}
+  bibsource    = {dblp computer science bibliography, https://dblp.org}
 }
+
 @article{bestpracticesscientificcomputing,
-    doi = {10.1371/journal.pbio.1001745},
+  doi          = {10.1371/journal.pbio.1001745},
-    author = {Wilson, Greg and Aruliah, D. A. and Brown, C. Titus and Chue Hong, Neil P. and Davis, Matt and Guy, Richard T. and Haddock, Steven H. D. and Huff, Kathryn D. and Mitchell, Ian M. and Plumbley, Mark D. and Waugh, Ben and White, Ethan P. and Wilson, Paul},
+  author       = {Wilson, Greg and Aruliah, D. A. and Brown, C. Titus and Chue Hong, Neil P. and Davis, Matt and Guy, Richard T. and Haddock, Steven H. D. and Huff, Kathryn D. and Mitchell, Ian M. and Plumbley, Mark D. and Waugh, Ben and White, Ethan P. and Wilson, Paul},
-    journal = {PLOS Biology},
+  journal      = {PLOS Biology},
-    publisher = {Public Library of Science},
+  publisher    = {Public Library of Science},
-    title = {Best Practices for Scientific Computing},
+  title        = {Best Practices for Scientific Computing},
-    year = {2014},
+  year         = {2014},
-    month = {01},
+  month        = {01},
-    volume = {12},
+  volume       = {12},
-    url = {https://doi.org/10.1371/journal.pbio.1001745},
+  url          = {https://doi.org/10.1371/journal.pbio.1001745},
-    pages = {1--7},
+  pages        = {1--7},
-    abstract = {We describe a set of best practices for scientific software development, based on research and experience, that will improve scientists' productivity and the reliability of their software.},
+  abstract     = {We describe a set of best practices for scientific software development, based on research and experience, that will improve scientists' productivity and the reliability of their software.},
-    number = {1}
+  number       = {1}
 }
 
 @InProceedings{githubinpublications,
-author="Escamilla, Emily
+  author       = {Escamilla, Emily
-and Klein, Martin
+                  and Klein, Martin
-and Cooper, Talya
+                  and Cooper, Talya
-and Rampin, Vicky
+                  and Rampin, Vicky
-and Weigle, Michele C.
+                  and Weigle, Michele C.
-and Nelson, Michael L.",
+                  and Nelson, Michael L.},
-editor="Silvello, Gianmaria
+  editor       = {Silvello, Gianmaria
-and Corcho, Oscar
+                  and Corcho, Oscar
-and Manghi, Paolo
+                  and Manghi, Paolo
-and Di Nunzio, Giorgio Maria
+                  and Di Nunzio, Giorgio Maria
-and Golub, Koraljka
+                  and Golub, Koraljka
-and Ferro, Nicola
+                  and Ferro, Nicola
-and Poggi, Antonella",
+                  and Poggi, Antonella},
-title="The Rise of GitHub in Scholarly Publications",
+  title        = {The Rise of GitHub in Scholarly Publications},
-booktitle="Linking Theory and Practice of Digital Libraries",
+  booktitle    = {Linking Theory and Practice of Digital Libraries},
-year="2022",
+  year         = {2022},
-publisher="Springer International Publishing",
+  publisher    = {Springer International Publishing},
-address="Cham",
+  address      = {Cham},
-pages="187--200",
+  pages        = {187--200},
-abstract="The definition of scholarly content has expanded to include the data and source code that contribute to a publication. While major archiving efforts to preserve conventional scholarly content, typically in PDFs (e.g., LOCKSS, CLOCKSS, Portico), are underway, no analogous effort has yet emerged to preserve the data and code referenced in those PDFs, particularly the scholarly code hosted online on Git Hosting Platforms (GHPs). Similarly, the Software Heritage Foundation is working to archive public source code, but there is value in archiving the issue threads, pull requests, and wikis that provide important context to the code while maintaining their original URLs. In current implementations, source code and its ephemera are not preserved, which presents a problem for scholarly projects where reproducibility matters. To understand and quantify the scope of this issue, we analyzed the use of GHP URIs in the arXiv and PMC corpora from January 2007 to December 2021. In total, there were 253,590 URIs to GitHub, SourceForge, Bitbucket, and GitLab repositories across the 2.66 million publications in the corpora. We found that GitHub, GitLab, SourceForge, and Bitbucket were collectively linked to 160 times in 2007 and 76,746 times in 2021. In 2021, one out of five publications in the arXiv corpus included a URI to GitHub. The complexity of GHPs like GitHub is not amenable to conventional Web archiving techniques. Therefore, the growing use of GHPs in scholarly publications points to an urgent and growing need for dedicated efforts to archive their holdings in order to preserve research code and its scholarly ephemera.",
+  abstract     = {The definition of scholarly content has expanded to include the data and source code that contribute to a publication. While major archiving efforts to preserve conventional scholarly content, typically in PDFs (e.g., LOCKSS, CLOCKSS, Portico), are underway, no analogous effort has yet emerged to preserve the data and code referenced in those PDFs, particularly the scholarly code hosted online on Git Hosting Platforms (GHPs). Similarly, the Software Heritage Foundation is working to archive public source code, but there is value in archiving the issue threads, pull requests, and wikis that provide important context to the code while maintaining their original URLs. In current implementations, source code and its ephemera are not preserved, which presents a problem for scholarly projects where reproducibility matters. To understand and quantify the scope of this issue, we analyzed the use of GHP URIs in the arXiv and PMC corpora from January 2007 to December 2021. In total, there were 253,590 URIs to GitHub, SourceForge, Bitbucket, and GitLab repositories across the 2.66 million publications in the corpora. We found that GitHub, GitLab, SourceForge, and Bitbucket were collectively linked to 160 times in 2007 and 76,746 times in 2021. In 2021, one out of five publications in the arXiv corpus included a URI to GitHub. The complexity of GHPs like GitHub is not amenable to conventional Web archiving techniques. Therefore, the growing use of GHPs in scholarly publications points to an urgent and growing need for dedicated efforts to archive their holdings in order to preserve research code and its scholarly ephemera.},
-isbn="978-3-031-16802-4"
+  isbn         = {978-3-031-16802-4}
 }