Regenerate Markdown files with a newer version of pandoc and with correct metadata

module2/ressources/orgmode_examples/README.md

 ---
-TITLE:       Document Examples
-AUTHOR:      Arnaud Legrand
-Date:   Wed Mar 20 13:03:17 2019 
+title:       Document Examples
+author:      Arnaud Legrand
+date:   Wed Mar 20 13:03:17 2019 
 ---
 
-Table of Contents<span class="tag" data-tag-name="TOC"></span>
-==============================================================
+# Table of Contents <span class="tag" data-tag-name="TOC"><span class="smallcaps">TOC</span></span>
 
--   [Examples from the Video](#examples-from-the-video)
--   [Other examples](#other-examples)
+  - [Examples from the Video](#examples-from-the-video)
+  - [Other examples](#other-examples)
 
-Examples from the Video
-=======================
+# Examples from the Video
 
-In the MOOC video, I quickly demo how org-mode can be used in various contexts. Here are the (sometimes trimmed) corresponding org-files. These documents depend on many other external data files and are not meant to lead to reproducible documents but it will give you an idea of how it can be organized:
+In the MOOC video, I quickly demo how org-mode can be used in various
+contexts. Here are the (sometimes trimmed) corresponding org-files.
+These documents depend on many other external data files and are not
+meant to lead to reproducible documents but it will give you an idea of
+how it can be organized:
 
-1.  [journal.org](journal.org): an excerpt (I've only left a few code samples and links to some resources on R, Stats, ...) from my own journal. This is a personal document where everything (meeting notes, hacking, random thoughts, ...) goes by default. Entries are created with the `C-c c` shortcut.
-2.  [labbook<sub>single</sub>.org](labbook_single.org): this is an excerpt from the laboratory notebook [Tom Cornebize](https://cornebize.net/) wrote during his Master thesis internship under my supervision. This a personal labbook. I consider this notebook to be excellent and was the ideal level of details for us to communicate without any ambiguity and for him to move forward with confidence.
-3.  [paper.org](paper.org): this is an ongoing paper based on the previous labbook of Tom Cornebize. As such it is not reproducible as there are hardcoded paths and uncleaned dependencies but writing it from the labbook was super easy as we just had to cut and paste the parts we needed. What may be interesting is the organization and the org tricks to export to the right LaTeX style. As you may notice, in the end of the document, there is a commented section with emacs commands that are automatically executed when opening the file. It is an effective way to depend less on the `.emacs/init.el` which is generally customized by everyone.
-4.  [labbook<sub>several</sub>.org](labbook_several.org): this is a labbook for a specific project shared by several persons. As a consequence it starts with information about installation, common scripts, has section with notes about all our meetings, a section with information about experiments and an other one about analysis. Entries could have been labeled by who wrote them but there were only a few of us and this information was available in git so we did not bother. In such labbook, it is common to find annotations indicating that such experiment was `:FLAWED:` as it had some issues.
-5.  [technical<sub>report</sub>.org](technical_report.org): this is a short technical document I wrote after a colleague sent me a PDF describing an experiment he was conducting and asked me about how reproducible I felt it was. It turned out I had to cut and paste the C code from the PDF, then remove all the line numbers and fix syntax, etc. Obviously I got quite different performance results but writing everything in org-mode made it very easy to generate both HTML and PDF and to explicitly explain how the measurements were done.
+1.  [journal.org](journal.org): an excerpt (I've only left a few code
+    samples and links to some resources on R, Stats, …) from my own
+    journal. This is a personal document where everything (meeting
+    notes, hacking, random thoughts, …) goes by default. Entries are
+    created with the `C-c c` shortcut.
+2.  [labbook<sub>single</sub>.org](labbook_single.org): this is an
+    excerpt from the laboratory notebook [Tom
+    Cornebize](https://cornebize.net/) wrote during his Master thesis
+    internship under my supervision. This a personal labbook. I consider
+    this notebook to be excellent and was the ideal level of details for
+    us to communicate without any ambiguity and for him to move forward
+    with confidence.
+3.  [paper.org](paper.org): this is an ongoing paper based on the
+    previous labbook of Tom Cornebize. As such it is not reproducible as
+    there are hardcoded paths and uncleaned dependencies but writing it
+    from the labbook was super easy as we just had to cut and paste the
+    parts we needed. What may be interesting is the organization and the
+    org tricks to export to the right LaTeX style. As you may notice, in
+    the end of the document, there is a commented section with emacs
+    commands that are automatically executed when opening the file. It
+    is an effective way to depend less on the `.emacs/init.el` which is
+    generally customized by everyone.
+4.  [labbook<sub>several</sub>.org](labbook_several.org): this is a
+    labbook for a specific project shared by several persons. As a
+    consequence it starts with information about installation, common
+    scripts, has section with notes about all our meetings, a section
+    with information about experiments and an other one about analysis.
+    Entries could have been labeled by who wrote them but there were
+    only a few of us and this information was available in git so we did
+    not bother. In such labbook, it is common to find annotations
+    indicating that such experiment was `:FLAWED:` as it had some
+    issues.
+5.  [technical<sub>report</sub>.org](technical_report.org): this is a
+    short technical document I wrote after a colleague sent me a PDF
+    describing an experiment he was conducting and asked me about how
+    reproducible I felt it was. It turned out I had to cut and paste the
+    C code from the PDF, then remove all the line numbers and fix
+    syntax, etc. Obviously I got quite different performance results but
+    writing everything in org-mode made it very easy to generate both
+    HTML and PDF and to explicitly explain how the measurements were
+    done.
 
-Other examples
-==============
+# Other examples
 
 Here are a few links to other kind of examples:
 
--   Slides: all my slides for a series of lectures is available here: <https://github.com/alegrand/SMPE>. Here is a [typical source](https://raw.githubusercontent.com/alegrand/SMPE/master/lectures/lecture_central_limit_theorem.org) and the [resulting PDF](https://raw.githubusercontent.com/alegrand/SMPE/master/lectures/lecture_central_limit_theorem.pdf)
--   Lucas Schnorr, a colleague, maintains:
-    -   a set of templates for various computer science journals/conferences: [IEEE](https://github.com/schnorr/ieeeorg), [Wiley](https://github.com/schnorr/wileyorg), [ACM](https://github.com/schnorr/acmorg), [LNCS](https://github.com/schnorr/llncsorg)
-    -   his lecture on programming languages for undergrads: <https://github.com/schnorr/mlp/tree/master/conteudo>
--   John Kitchin is an expert org-mode user and he maintains a very interesting [blog with many interesting tips](http://kitchingroup.cheme.cmu.edu/blog/). You may want to check this [seminar he gave at SciPy](https://www.youtube.com/watch?v=IsSMs-4GlT8&list=FLQp2VLAOlvq142YN3JO3y8w&app=desktop).
+  - Slides: all my slides for a series of lectures is available here:
+    <https://github.com/alegrand/SMPE>. Here is a [typical
+    source](https://raw.githubusercontent.com/alegrand/SMPE/master/lectures/lecture_central_limit_theorem.org)
+    and the [resulting
+    PDF](https://raw.githubusercontent.com/alegrand/SMPE/master/lectures/lecture_central_limit_theorem.pdf)
+  - Lucas Schnorr, a colleague, maintains:
+      - a set of templates for various computer science
+        journals/conferences:
+        [IEEE](https://github.com/schnorr/ieeeorg),
+        [Wiley](https://github.com/schnorr/wileyorg),
+        [ACM](https://github.com/schnorr/acmorg),
+        [LNCS](https://github.com/schnorr/llncsorg)
+      - his lecture on programming languages for undergrads:
+        <https://github.com/schnorr/mlp/tree/master/conteudo>
+  - John Kitchin is an expert org-mode user and he maintains a very
+    interesting [blog with many interesting
+    tips](http://kitchingroup.cheme.cmu.edu/blog/). You may want to
+    check this [seminar he gave at
+    SciPy](https://www.youtube.com/watch?v=IsSMs-4GlT8&list=FLQp2VLAOlvq142YN3JO3y8w&app=desktop).

module2/slides/ressources.md

 ---
-TITLE:     Computational Documents
-Date:   Wed Mar 20 13:19:19 2019 
+title:     Computational Documents
+date:   Wed Mar 20 13:19:19 2019 
 ---
 
-This document gathers most references mentioned in the videos. This is a rather crude list.
+This document gathers most references mentioned in the videos. This is a
+rather crude
+list.
 
-Table of Contents<span class="tag" data-tag-name="TOC"></span>
-==============================================================
+# Table of Contents <span class="tag" data-tag-name="TOC"><span class="smallcaps">TOC</span></span>
 
--   [M2-S0: Computational Documents](#m2-s0-computational-documents)
--   [M2-S1: A few Recent Controversial Studies](#m2-s1-a-few-recent-controversial-studies)
-    -   [Economy: Austerity in Fiscal Policy](#economy-austerity-in-fiscal-policy)
-    -   [Functional MRI](#functional-mri)
-    -   [Incorrect Protein Structures](#incorrect-protein-structures)
-    -   [Other domains](#other-domains)
--   [M2-S2: Why is This so Difficult?](#m2-s2-why-is-this-so-difficult)
-    -   [Mistakes](#mistakes)
-    -   [Going Public?](#going-public)
--   [M2-S3: Computational Documents: Principles](#m2-s3-computational-documents-principles)
--   [M2-S5: Collaborating](#m2-s5-collaborating)
-    -   [Preparing a Document for a Journal or a Conference](#preparing-a-document-for-a-journal-or-a-conference)
--   [M2-S6: Comparative Study](#m2-s6-comparative-study)
-    -   [Exemples of Org-Mode documents](#exemples-of-org-mode-documents)
+  - [M2-S0: Computational Documents](#m2-s0-computational-documents)
+  - [M2-S1: A few Recent Controversial
+    Studies](#m2-s1-a-few-recent-controversial-studies)
+      - [Economy: Austerity in Fiscal
+        Policy](#economy-austerity-in-fiscal-policy)
+      - [Functional MRI](#functional-mri)
+      - [Incorrect Protein Structures](#incorrect-protein-structures)
+      - [Other domains](#other-domains)
+  - [M2-S2: Why is This so Difficult?](#m2-s2-why-is-this-so-difficult)
+      - [Mistakes](#mistakes)
+      - [Going Public?](#going-public)
+  - [M2-S3: Computational Documents:
+    Principles](#m2-s3-computational-documents-principles)
+  - [M2-S5: Collaborating](#m2-s5-collaborating)
+      - [Preparing a Document for a Journal or a
+        Conference](#preparing-a-document-for-a-journal-or-a-conference)
+  - [M2-S6: Comparative Study](#m2-s6-comparative-study)
+      - [Exemples of Org-Mode
+        documents](#exemples-of-org-mode-documents)
 
-M2-S0: Computational Documents
-==============================
+# M2-S0: Computational Documents
 
-M2-S1: A few Recent Controversial Studies
-=========================================
+# M2-S1: A few Recent Controversial Studies
 
-Economy: Austerity in Fiscal Policy
------------------------------------
+## Economy: Austerity in Fiscal Policy
 
--   [Reinhart et Rogoff](https://en.wikipedia.org/wiki/Growth_in_a_Time_of_Debt): *Growth in a Time of Debt*
--   Herndon, Ash et Pollin
--   Wray: combining data across centuries, exchange rate regimes,
+  - [Reinhart et
+    Rogoff](https://en.wikipedia.org/wiki/Growth_in_a_Time_of_Debt):
+    *Growth in a Time of Debt*
+  - Herndon, Ash et Pollin
+  - Wray: combining data across centuries, exchange rate regimes,
 
-Functional MRI
---------------
+## Functional MRI
 
--   2010: [Bennett et al. and the dead salmon](https://www.researchgate.net/publication/255651552_Neural_correlates_of_interspecies_perspective_taking_in_the_post-mortem_Atlantic_Salmon_an_argument_for_multiple_comparisons_correction) ☺
--   2016: [Eklund, Nichols, and Knutsson](http://www.pnas.org/content/113/28/7900.abstract). [A bug in fmri software could invalidate 15 years of brain research](http://www.sciencealert.com/a-bug-in-fmri-software-could-invalidate-decades-of-brain-research-scientists-discover) (*40 000 articles*)
--   2016: But it's [more subtle than it looks like](https://www.cogneurosociety.org/debunking-the-myth-that-fmri-studies-are-invalid/). [Nichols](http://blogs.warwick.ac.uk/nichols/entry/bibliometrics_of_cluster/). *≈ 3 600 impacted studies*
+  - 2010: [Bennett et al. and the dead
+    salmon](https://www.researchgate.net/publication/255651552_Neural_correlates_of_interspecies_perspective_taking_in_the_post-mortem_Atlantic_Salmon_an_argument_for_multiple_comparisons_correction)
+    ☺
+  - 2016: [Eklund, Nichols, and
+    Knutsson](http://www.pnas.org/content/113/28/7900.abstract). [A bug
+    in fmri software could invalidate 15 years of brain
+    research](http://www.sciencealert.com/a-bug-in-fmri-software-could-invalidate-decades-of-brain-research-scientists-discover)
+    (*40 000 articles*)
+  - 2016: But it's [more subtle than it looks
+    like](https://www.cogneurosociety.org/debunking-the-myth-that-fmri-studies-are-invalid/).
+    [Nichols](http://blogs.warwick.ac.uk/nichols/entry/bibliometrics_of_cluster/).
+    *≈ 3 600 impacted studies*
 
-Incorrect Protein Structures
-----------------------------
+## Incorrect Protein Structures
 
-[A "buggy software"](https://people.ligo-wa.caltech.edu/~michael.landry/calibration/S5/getsignright.pdf).
+[A "buggy
+software"](https://people.ligo-wa.caltech.edu/~michael.landry/calibration/S5/getsignright.pdf).
 
-Other domains
--------------
+## Other domains
 
--   [Oncology](http://www.nature.com/nrd/journal/v10/n9/full/nrd3439-c1.html?foxtrotcallback=true): "*half of published studies, even in prestigious journals, can't be reproduced in industrial labs*"
--   [Psychology](http://theconversation.com/we-found-only-one-third-of-published-psychology-research-is-reliable-now-what-46596): "*attempting to reproduce 100 previously published findings*, *only one-third of published psychology research was found to be reliable*"
+  - [Oncology](http://www.nature.com/nrd/journal/v10/n9/full/nrd3439-c1.html?foxtrotcallback=true):
+    "*half of published studies, even in prestigious journals, can't be
+    reproduced in industrial
+    labs*"
+  - [Psychology](http://theconversation.com/we-found-only-one-third-of-published-psychology-research-is-reliable-now-what-46596):
+    "*attempting to reproduce 100 previously published findings*, *only
+    one-third of published psychology research was found to be
+    reliable*"
 
-M2-S2: Why is This so Difficult?
-================================
+# M2-S2: Why is This so Difficult?
 
-Mistakes
---------
+## Mistakes
 
--   [Computers broke science](http://theconversation.com/how-computers-broke-science-and-what-we-can-do-to-fix-it-49938)
--   [Programming and data manipulation mistakes in Genomics](https://qz.com/768334/years-of-genomics-research-is-riddled-with-errors-thanks-to-a-bunch-of-botched-excel-spreadsheets/)
+  - [Computers broke
+    science](http://theconversation.com/how-computers-broke-science-and-what-we-can-do-to-fix-it-49938)
+  - [Programming and data manipulation mistakes in
+    Genomics](https://qz.com/768334/years-of-genomics-research-is-riddled-with-errors-thanks-to-a-bunch-of-botched-excel-spreadsheets/)
 
-Going Public?
--------------
+## Going Public?
 
--   Someone may [benefit from my hard work](http://www.nature.com/news/the-top-100-papers-1.16224)
+  - Someone may [benefit from my hard
+    work](http://www.nature.com/news/the-top-100-papers-1.16224)
 
-M2-S3: Computational Documents: Principles
-==========================================
+# M2-S3: Computational Documents: Principles
 
-M2-S5: Collaborating
-====================
+# M2-S5: Collaborating
 
-Preparing a Document for a Journal or a Conference
---------------------------------------------------
+## Preparing a Document for a Journal or a Conference
 
 Requirements for producing a **pdf**:
 
--   Internally, *pandoc*, *knitr* or *emacs/org-mode*
--   *LaTeX* should be installed
+  - Internally, *pandoc*, *knitr* or *emacs/org-mode*
 
-    -   <http://blog.juliusschulz.de/blog/ultimate-ipython-notebook>
-        -   <https://github.com/kirbs-/hide_code> is a must-have
-    -   <http://svmiller.com/blog/2016/02/svm-r-markdown-manuscript/>
-    -   <https://github.com/balouf/Kleinberg/blob/master/KleinbergsGridSimulator.ipynb>
+  - *LaTeX* should be installed
+    
+      - <http://blog.juliusschulz.de/blog/ultimate-ipython-notebook>
+          - <https://github.com/kirbs-/hide_code> is a
+        must-have
+      - <http://svmiller.com/blog/2016/02/svm-r-markdown-manuscript/>
+      - <https://github.com/balouf/Kleinberg/blob/master/KleinbergsGridSimulator.ipynb>
 
-M2-S6: Comparative Study
-========================
+# M2-S6: Comparative Study
 
-[Exemples of Org-Mode documents](../ressources/orgmode_examples/README.org)
----------------------------------------------------------------------------
+## [Exemples of Org-Mode documents](../ressources/orgmode_examples/README.org)