diff --git a/module4/slides/Makefile b/module4/slides/Makefile new file mode 100644 index 0000000000000000000000000000000000000000..9b3201c42814575b6852b27759cba96baf57a4e5 --- /dev/null +++ b/module4/slides/Makefile @@ -0,0 +1,16 @@ +C028AL_slides_module4-en-gz.pdf: slides_module4.pdf + mv $< $@ + +C028AL_slides_module4-fr-gz.pdf: diapos_module4.pdf + mv $< $@ + +%-gz.pdf: %.pdf + gzprez $< + +%.pdf: %.tex + pdflatex --shell-escape $^ + pdflatex --shell-escape $^ + +%.tex: %.org + emacs -batch --eval "(setq enable-local-eval t)" --eval "(setq enable-local-variables t)" $^ --funcall org-beamer-export-to-latex + # sed -i -e 's|includegraphics\(.*\)../assets/img/|includegraphics\1../assets/img/thumbnail/|' -e 's/\.png}/.jpg}/i' $@ diff --git a/module4/slides/diapos_module4.org b/module4/slides/diapos_module4.org index 1b7f9276e99ec84be906578051d4ad116627943e..6e6d82631c16ef9b5e9ec5ecde77b99341544668 100644 --- a/module4/slides/diapos_module4.org +++ b/module4/slides/diapos_module4.org @@ -108,26 +108,20 @@ http://phdcomics.com/comics/archive/phd051017s.gif ** Graphe syndrome grippal: #+begin_src shell :results output raw :exports both - debtree python3-matplotlib > python3-matplotlib.dot + debtree python3-matplotlib > img/python3-matplotlib.dot sed -i -e 's/rankdir=LR/rankdir=RL/g' \ -e 's/node \[shape=box\]/node [shape=box, color=black, fillcolor=gray, fontcolor=black, style=filled]/g' \ python3-matplotlib.dot - dot -Tpng python3-matplotlib.dot > python3-matplotlib.png - echo file:python3-matplotlib.png - #+end_src - - #+RESULTS: - file:python3-matplotlib.png - - #+begin_src shell :results output :exports both - mv python3-matplotlib.png ../assets/img/ + dot -Tpng img/python3-matplotlib.dot > img/python3-matplotlib.png + echo file:img/python3-matplotlib.png #+end_src #+RESULTS: + file:img/python3-matplotlib.png * M4-S0: Vers une étude reproductible : la réalité du terrain ** L'enfer de la Recherche Reproductible -file:../assets/img/phd_sisyphe.png +file:img/phd_sisyphe.png *** Notes :PROPERTIES: @@ -286,9 +280,9 @@ Rechercher des formats binaires pour : Git(hub/lab/...) : pas bien adapté au stockage de données #+BEGIN_CENTER #+ATTR_LATEX: :height 1cm :center nil -file:../assets/img/Zenodo-logo.jpg +file:img/Zenodo-logo.jpg #+ATTR_LATEX: :height 1cm :center nil -file:../assets/img/Figshare-logo.png +file:img/Figshare-logo.png #+END_CENTER ** Conclusions @@ -306,16 +300,16 @@ file:../assets/img/Figshare-logo.png 4. Conclusion ** Passage à l'échelle #+ATTR_LATEX: :width \linewidth -file:../assets/img/il-marche-mon-programme.jpg +file:img/il-marche-mon-programme.jpg ** Des codes complexes... -#+LaTeX: \includegraphics<+>[height=6cm]{../assets/img/nb1.png}% -#+LaTeX: \includegraphics<+>[height=6cm]{../assets/img/nb2.png}% -#+LaTeX: \includegraphics<+>[height=6cm]{../assets/img/nb3.png}% -#+LaTeX: \includegraphics<+>[height=6cm]{../assets/img/nb4.png}% -#+LaTeX: \includegraphics<+>[height=6cm]{../assets/img/grippal_orgmode1.png}% -#+LaTeX: \includegraphics<+>[height=6cm]{../assets/img/grippal_orgmode2.png}% -#+LaTeX: \includegraphics<+>[height=6cm]{../assets/img/nb5.png}% +#+LaTeX: \includegraphics<+>[height=6cm]{img/nb1.png}% +#+LaTeX: \includegraphics<+>[height=6cm]{img/nb2.png}% +#+LaTeX: \includegraphics<+>[height=6cm]{img/nb3.png}% +#+LaTeX: \includegraphics<+>[height=6cm]{img/nb4.png}% +#+LaTeX: \includegraphics<+>[height=6cm]{img/grippal_orgmode1.png}% +#+LaTeX: \includegraphics<+>[height=6cm]{img/grippal_orgmode2.png}% +#+LaTeX: \includegraphics<+>[height=6cm]{img/nb5.png}% - Un vrai plat de spaghettis - Pas de vision d'ensemble - Interaction entre plusieurs langages = danger @@ -330,9 +324,9 @@ file:../assets/img/il-marche-mon-programme.jpg ** ... et difficiles à orchestrer #+LaTeX: \only<1>{\begin{overlayarea}{1.5\linewidth}{7cm} #+ATTR_LATEX: :height 7cm :center nil -file:../assets/img/SbmlParameterisation.png +file:img/SbmlParameterisation.png #+ATTR_LATEX: :height 7cm :center nil -file:../assets/img/SbmlModelling.png +file:img/SbmlModelling.png #+LaTeX: \end{overlayarea}}\pause Le *Workflow* : @@ -462,7 +456,7 @@ python3-cycler (>= 0.10.0), python3:any (>= 3.3.2-2~), libc6 (>= 1.6.2-1), libstdc++6 (>= 5.2), zlib1g (>= 1:1.1.4) #+END_EXAMPLE -#+LaTeX: \only<2>{\vspace{-3.5cm}\includegraphics<2>[width=\linewidth]{../assets/img/python3-matplotlib.png}}\vspace{10cm} +#+LaTeX: \only<2>{\vspace{-3.5cm}\includegraphics<2>[width=\linewidth]{img/python3-matplotlib.png}}\vspace{10cm} *** Notes :PROPERTIES: @@ -694,7 +688,7 @@ SHA256: 8f5d3509d4f5451468c6de44fc8dfe391c3df4120079adc01ab5f13ff4194f5a #+END_EXAMPLE ** L'épreuve du temps -file:../assets/img/soviet_space_shuttle.jpg +file:img/soviet_space_shuttle.jpg ** Compatibilité ascendante \small - Python et tout son écosystème à évolution hyper rapide @@ -712,9 +706,9 @@ python3 -c "print(10/3)" #+LaTeX: } \pause #+ATTR_LATEX: :height 3.2cm :center nil -file:../assets/img/plot_1.5.3.png +file:img/plot_1.5.3.png #+ATTR_LATEX: :height 3.2cm :center nil -file:../assets/img/plot_2.1.1.png +file:img/plot_2.1.1.png \pause - Cortical Thickness Measurements (PLOS ONE, @@ -760,7 +754,7 @@ file:../assets/img/plot_2.1.1.png Popper: [[http://falsifiable.us/][http://falsifiable.us/]] #+ATTR_LATEX: :height 1.5cm :center nil - file:../assets/img/popper_logo_just_jug.png + file:img/popper_logo_just_jug.png *Autre possibilité* : - Se restreindre à ce qui est maîtrisable (C par exemple) @@ -806,9 +800,9 @@ file:../assets/img/plot_2.1.1.png - Github/Gitlab/... : stables, ouverts, \dots pérennes ? - +Google Code+, +Gitorious+, +Code Spaces+ #+ATTR_LATEX: :height 1.3cm :center nil - file:../assets/img/swh-logo.png + file:img/swh-logo.png #+ATTR_LATEX: :height 1.3cm :center nil - file:../assets/img/LogoHAL.PNG + file:img/LogoHAL.png *Gestion des environnements* - Pérénité de l'accès à dockerhub, nix repository, code ocean... ? @@ -822,9 +816,9 @@ file:../assets/img/plot_2.1.1.png :BEAMER_ENV: note :END: - Dans les exercices, faites y bien attention. - # file:../assets/img/ArXiv-web.png" height=60 /> - # file:../assets/img/Zenodo-logo.jpg" height=60 /> - # file:../assets/img/Figshare-logo.png" height=60 /> + # file:img/ArXiv-web.png" height=60 /> + # file:img/Zenodo-logo.jpg" height=60 /> + # file:img/Figshare-logo.png" height=60 /> * M4-S3: L'enfer du calcul ** Vers une étude reproductible : la réalité du terrain :noexport: 1. L'enfer des données @@ -844,7 +838,7 @@ file:../assets/img/plot_2.1.1.png ** L'arithmétique à virgule flottante -file:../assets/img/polynome1.svg +file:img/polynome1.svg #+begin_src python :results output :exports both def polynome(x): return x**9 - 9.*x**8 + 36.*x**7 - 84.*x**6 + 126.*x**5 \ @@ -860,7 +854,7 @@ def polynome(x): ** L'arithmétique à virgule flottante -file:../assets/img/polynome2.svg +file:img/polynome2.svg #+begin_src python :results output :exports both def horner(x): return x*(x*(x*(x*(x*(x*(x*(x*(x - 9.) + 36.) - 84.) + 126.) \ @@ -878,7 +872,7 @@ def horner(x): ** L'arithmétique à virgule flottante -file:../assets/img/polynome3.svg +file:img/polynome3.svg #+begin_src python :results output :exports both def simple(x): return (x-1.)**9 @@ -895,7 +889,7 @@ def simple(x): ** L'arithmétique à virgule flottante -file:../assets/img/polynome3-4.svg +file:img/polynome3-4.svg *** Notes :PROPERTIES: @@ -905,7 +899,7 @@ file:../assets/img/polynome3-4.svg ** L'arithmétique à virgule flottante -file:../assets/img/polynome4.svg +file:img/polynome4.svg *** Notes :PROPERTIES: @@ -1009,7 +1003,7 @@ Pour un calcul reproductible, il y a deux approches: ** Calcul parallèle: exemple -file:../assets/img/gouttedo1.png +file:img/gouttedo1.png Source: Thèse de Rafife Nheili, Université de Perpignan, 2016 @@ -1026,7 +1020,7 @@ Source: Thèse de Rafife Nheili, Université de Perpignan, 2016 ** Calcul parallèle: exemple -file:../assets/img/gouttedo2.png +file:img/gouttedo2.png Source: Thèse de Rafife Nheili, Université de Perpignan, 2016 @@ -1081,10 +1075,10 @@ Source: Thèse de Rafife Nheili, Université de Perpignan, 2016 ** Générateur de nombres pseudo-aléatoires #+LaTeX: \vspace{1cm} -#+LaTeX: \only<+>{\includesvg[scale=.45]{../assets/img/nombres-aleatoires-1.svg}} -#+LaTeX: \only<+>{\includesvg[scale=.45]{../assets/img/nombres-aleatoires-2.svg}} -#+LaTeX: \only<+>{\includesvg[scale=.45]{../assets/img/nombres-aleatoires-3.svg}} -#+LaTeX: 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b/module4/slides/python3-matplotlib.png deleted file mode 100644 index d3eaf0faf12dec5c4079d6397e1461eb6f857360..0000000000000000000000000000000000000000 Binary files a/module4/slides/python3-matplotlib.png and /dev/null differ diff --git a/module4/slides/slides_module4.org b/module4/slides/slides_module4.org index 71a1ceaddd75a2f89b84674429913ce0769c397f..b2c7561a0fe843d0b7e10429f304f7d48d833a2e 100644 --- a/module4/slides/slides_module4.org +++ b/module4/slides/slides_module4.org @@ -127,7 +127,7 @@ * M4-S0: The Rough Road to Real-Life Reproducible Research ** Reproducible Research Hell -file:../assets/img/phd_sisyphe.png +file:img/phd_sisyphe.png *** Notes :PROPERTIES: @@ -285,9 +285,9 @@ Wanted: binary formats for Git (hub, lab, ...): not well suited for data storage #+BEGIN_CENTER #+ATTR_LATEX: :height 1cm :center nil -file:../assets/img/Zenodo-logo.jpg +file:img/Zenodo-logo.jpg #+ATTR_LATEX: :height 1cm :center nil -file:../assets/img/Figshare-logo.png +file:img/Figshare-logo.png #+END_CENTER ** Conclusions @@ -305,16 +305,16 @@ file:../assets/img/Figshare-logo.png 4. Conclusion ** Scaling up #+ATTR_LATEX: :width \linewidth -file:../assets/img/il-marche-mon-programme.jpg +file:img/il-marche-mon-programme.jpg ** Complex code... -#+LaTeX: \includegraphics<+>[height=6cm]{../assets/img/nb1.png}% -#+LaTeX: \includegraphics<+>[height=6cm]{../assets/img/nb2.png}% -#+LaTeX: \includegraphics<+>[height=6cm]{../assets/img/nb3.png}% -#+LaTeX: \includegraphics<+>[height=6cm]{../assets/img/nb4.png}% -#+LaTeX: \includegraphics<+>[height=6cm]{../assets/img/grippal_orgmode1.png}% -#+LaTeX: \includegraphics<+>[height=6cm]{../assets/img/grippal_orgmode2.png}% -#+LaTeX: \includegraphics<+>[height=6cm]{../assets/img/nb5.png}% +#+LaTeX: \includegraphics<+>[height=6cm]{img/nb1.png}% +#+LaTeX: \includegraphics<+>[height=6cm]{img/nb2.png}% +#+LaTeX: \includegraphics<+>[height=6cm]{img/nb3.png}% +#+LaTeX: \includegraphics<+>[height=6cm]{img/nb4.png}% +#+LaTeX: \includegraphics<+>[height=6cm]{img/grippal_orgmode1.png}% +#+LaTeX: \includegraphics<+>[height=6cm]{img/grippal_orgmode2.png}% +#+LaTeX: \includegraphics<+>[height=6cm]{img/nb5.png}% - A real spaghetti bowl - No global view - Interaction between multiple languages = danger @@ -329,9 +329,9 @@ file:../assets/img/il-marche-mon-programme.jpg ** ... that is difficult to orchestrate #+LaTeX: \only<1>{\begin{overlayarea}{1.5\linewidth}{7cm} #+ATTR_LATEX: :height 7cm :center nil -file:../assets/img/SbmlParameterisation.png +file:img/SbmlParameterisation.png #+ATTR_LATEX: :height 7cm :center nil -file:../assets/img/SbmlModelling.png +file:img/SbmlModelling.png #+LaTeX: \end{overlayarea}}\pause *Workflows*: @@ -459,7 +459,7 @@ python3-cycler (>= 0.10.0), python3:any (>= 3.3.2-2~), libc6 (>= 1.6.2-1), libstdc++6 (>= 5.2), zlib1g (>= 1:1.1.4) #+END_EXAMPLE -#+LaTeX: \only<2>{\vspace{-3.5cm}\includegraphics<2>[width=\linewidth]{../assets/img/python3-matplotlib.png}}\vspace{10cm} +#+LaTeX: \only<2>{\vspace{-3.5cm}\includegraphics<2>[width=\linewidth]{img/python3-matplotlib.png}}\vspace{10cm} *** Notes :PROPERTIES: @@ -690,7 +690,7 @@ SHA256: 8f5d3509d4f5451468c6de44fc8dfe391c3df4120079adc01ab5f13ff4194f5a #+END_EXAMPLE ** The test of time -file:../assets/img/soviet_space_shuttle.jpg +file:img/soviet_space_shuttle.jpg ** Backwards compatibility \small - Python and its rapidly evolving environment @@ -708,9 +708,9 @@ python3 -c "print(10/3)" #+LaTeX: } \pause #+ATTR_LATEX: :height 3.2cm :center nil -file:../assets/img/plot_1.5.3.png +file:img/plot_1.5.3.png #+ATTR_LATEX: :height 3.2cm :center nil -file:../assets/img/plot_2.1.1.png +file:img/plot_2.1.1.png \pause - Cortical Thickness Measurements (PLOS ONE, @@ -754,7 +754,7 @@ file:../assets/img/plot_2.1.1.png Popper: [[http://falsifiable.us/][http://falsifiable.us/]] #+ATTR_LATEX: :height 1.5cm :center nil - file:../assets/img/popper_logo_just_jug.png + file:img/popper_logo_just_jug.png *Another option*: - Limit onself to what is manageable (C for example) @@ -800,9 +800,9 @@ file:../assets/img/plot_2.1.1.png - Git (hub, lab, ...) : stable, open, \dots durable ? - +Google Code+, +Gitorious+, +Code Spaces+ #+ATTR_LATEX: :height 1.3cm :center nil - file:../assets/img/swh-logo.png + file:img/swh-logo.png #+ATTR_LATEX: :height 1.3cm :center nil - file:../assets/img/LogoHAL.PNG + file:img/LogoHAL.PNG *Environment management* - Longevity of access to Docker Hub, Nix repository, Code Ocean, ... ? @@ -815,9 +815,9 @@ file:../assets/img/plot_2.1.1.png :BEAMER_ENV: note :END: - Dans les exercices, faites y bien attention. - # file:../assets/img/ArXiv-web.png" height=60 /> - # file:../assets/img/Zenodo-logo.jpg" height=60 /> - # file:../assets/img/Figshare-logo.png" height=60 /> + # file:img/ArXiv-web.png" height=60 /> + # file:img/Zenodo-logo.jpg" height=60 /> + # file:img/Figshare-logo.png" height=60 /> * M4-S3: Numerics Hell ** The Rough Road to Real-Life Reproducible Research :noexport: 1. Data Hell @@ -826,7 +826,7 @@ file:../assets/img/plot_2.1.1.png 4. Conclusion ** Floating-point arithmetic -file:../assets/img/polynome1.svg +file:img/polynome1.svg #+begin_src python :results output :exports both def polynome(x): return x**9 - 9.*x**8 + 36.*x**7 - 84.*x**6 + 126.*x**5 \ @@ -842,7 +842,7 @@ def polynome(x): ** Floating-point arithmetic -file:../assets/img/polynome2.svg +file:img/polynome2.svg #+begin_src python :results output :exports both def horner(x): return x*(x*(x*(x*(x*(x*(x*(x*(x - 9.) + 36.) - 84.) + 126.) \ @@ -860,7 +860,7 @@ def horner(x): ** Floating-point arithmetic -file:../assets/img/polynome3.svg +file:img/polynome3.svg #+begin_src python :results output :exports both def simple(x): return (x-1.)**9 @@ -877,7 +877,7 @@ def simple(x): ** Floating-point arithmetic -file:../assets/img/polynome3-4.svg +file:img/polynome3-4.svg *** Notes :PROPERTIES: @@ -887,7 +887,7 @@ file:../assets/img/polynome3-4.svg ** Floating-point arithmetic -file:../assets/img/polynome4.svg +file:img/polynome4.svg *** Notes :PROPERTIES: @@ -989,7 +989,7 @@ Two options for computing reproducibly: ** Parallel computation: example -file:../assets/img/gouttedo1.png +file:img/gouttedo1.png Source: Rafife Nheili, PhD. Thesis, University of Perpignan, 2016 @@ -1006,7 +1006,7 @@ Source: Rafife Nheili, PhD. Thesis, University of Perpignan, 2016 ** Parallel computation: example -file:../assets/img/gouttedo2.png +file:img/gouttedo2.png Source: Rafife Nheili, PhD. Thesis, University of Perpignan, 2016 @@ -1061,10 +1061,10 @@ Source: Rafife Nheili, PhD. Thesis, University of Perpignan, 2016 ** Pseudo-random number generators #+LaTeX: \vspace{1cm} -#+LaTeX: \only<+>{\includesvg[scale=.45]{../assets/img/nombres-aleatoires-1.svg}} -#+LaTeX: \only<+>{\includesvg[scale=.45]{../assets/img/nombres-aleatoires-2.svg}} -#+LaTeX: \only<+>{\includesvg[scale=.45]{../assets/img/nombres-aleatoires-3.svg}} -#+LaTeX: \only<+>{\includesvg[scale=.45]{../assets/img/nombres-aleatoires-4.svg}} +#+LaTeX: \only<+>{\includesvg[scale=.45]{img/nombres-aleatoires-1.svg}} +#+LaTeX: \only<+>{\includesvg[scale=.45]{img/nombres-aleatoires-2.svg}} +#+LaTeX: \only<+>{\includesvg[scale=.45]{img/nombres-aleatoires-3.svg}} +#+LaTeX: \only<+>{\includesvg[scale=.45]{img/nombres-aleatoires-4.svg}} #+LaTeX: \vspace{10cm} *** Notes :PROPERTIES: