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mooc-rr-ressources
Commit 81f4189a authored by Arnaud Legrand's avatar Arnaud Legrand
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Add images and update links

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module4/slides/Makefile 0 → 100644
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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' $@
module4/slides/diapos_module4.org
View file @ 81f4189a
......@@ -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: \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:
......
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......@@ -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:
......
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