My Journey To Transparency And Reproducibility

class: center, middle, inverse, title-slide

# My Journey To Transparency And Reproducibility
## <i class="fab fa-docker"></i> & <i class="fab fa-r-project"></i>
### Mickaël Canouil, <em>Ph.D.</em> (<a href="http://m.canouil.fr/" target="_blank"><i class="fas fa-home"></i> m.canouil.fr</a>)
### <em>Inserm U1283 / CNRS UMR8199 / Institut Pasteur de Lille / Université de Lille</em>
### Thursday, the 15<sup><i style="font-size:0.5em;">th</i></sup> of April, 2021 – 19:00 (CEST / UTC + 2)

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# Who Am I?

![](data:image/png;base64,#https://media.giphy.com/media/2y6ElJES2O0E0/giphy.gif)

---

# Who Am I? .font50[(_Definitely Not Iron Man ..._)]

.pull-left[
    
* __Doctor of Philosophy (Ph.D.) in Biostatistics__.

* __Head of the Biostatistics Team__ of the __Inserm U1283 / CNRS UMR 8199__ unit _(Functional (Epi)genomics and Molecular Physiology of Diabetes and Related Diseases)_.  
    <img src = "data:image/png;base64,#https://raw.githubusercontent.com/mcanouil/hex-stickers/main/SVG/umr1283_8199.svg" width = "100px" />

* Authored/Contributed __6 <i class = "fab fa-r-project"></i> packages__ on CRAN (more on Github).  
    <img src = "data:image/png;base64,#https://raw.githubusercontent.com/mcanouil/hex-stickers/main/SVG/nacho.svg" width = "100px" />
    <img src = "data:image/png;base64,#https://raw.githubusercontent.com/mcanouil/hex-stickers/main/SVG/insane.svg" width = "100px" />
    <img src = "data:image/png;base64,#https://github.com/mcanouil/ggpacman/raw/main/man/figures/ggpacman.gif" width = "100px" />
    
* .font80[_Watched 2,862 movies so far ..._]

]

.pull-right[
.center[
<img src = "data:image/png;base64,#https://github.com/mcanouil/ggpacman/raw/main/man/figures/README-pacman-1.gif" height = "450px" />  
_From_ `ggpacman` _on CRAN._  
_It's only an <i class = "fab fa-r-project"></i> package to make a GIF, sorry!_
]
]

---
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# Where My Journey Started?

![](data:image/png;base64,#https://media.giphy.com/media/S8ToH7Zt8gZ4u2iClh/giphy.gif)

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# With A Project-oriented Workflow

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# With A Project-oriented Workflow (_Or Not_)

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class: part-slide

# Project Structure?

![](data:image/png;base64,#https://media.giphy.com/media/P2a7oxnUULoys/giphy.gif)

.font200[⇒ I can fix it!]

---

# Something Simple

.pull-left.font150[
* `Data`
* `Docs`
* `Report`
* `Scripts`
* `README.md`
]

.pull-right[
<img src = "data:image/png;base64,#content/media/project_good1.png" width = "43%" style = "position:absolute; top: 22%;" />
]

.center.font150.blue[
⇒ This solved one issue, but it was the obvious one ...
</br>
_i.e._, data, scripts, and outputs should not live in the same directory!
]

.pull-left.font150[
* `.git` ⇒ Let's add GIT, it can't hurt!<sup>&ast;</sup>
]

.pull-right[
<img src = "data:image/png;base64,#content/media/project2_version.png" width = "100%"/>
]

.footnote[
&ast; It did a little bit more than the project structure.
]

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background-image: url(data:image/png;base64,#https://source.unsplash.com/zFYUsLk_50Y)
background-size: cover

# .bg-img[System Infrastructure]

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# System Infrastructure

<div style = "font-size: 150%; position: absolute; top: 20%; left: 8%;">
⇒ Non-root users.
</div>

<div style = "font-size: 150%; color: #b20000; position: absolute; top: 20%; left: 67%;">
⇒ Not possible to install <i class = "fab fa-r-project"></i> packages or system libraries.
</div>

<div style = "font-size: 150%; position: absolute; top: 75%; left: 8%;">
⇒ Possible to install</br>
<i class = "fab fa-r-project"></i> packages in user home.
</div>

<div style = "font-size: 150%; color: #b20000;  position: absolute; top: 75%; left: 67%;">
⇒ Limited storage in home. </br>
<i>Not a good place anyway ...</i>
</div>

---

# Lack Of A Reproducible Environment

.font150[

.pull-left[
+ __Code errors__  
    The same code can give different results on different platforms/machines.
]

.pull-right[
+ __Affecting multiple projects__  
    In a global and shared environment, any changes in system libraries and <i class = "fab fa-r-project"></i> packages can change or crash any unrelated projects.
]

.pull-left[  
+ __Difficult system deployment (for user/developer)__  
    Establishing and maintaining infrastructure is challenging if not tracked properly, especially over time.
]

.pull-right[
+ __Painful collaboration__  
    Team/User will most likely waste time setting up new environment rather than starting developing.
]

]

---
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# Reproducible Development/Analysis Workflow</br>With</br>Docker</br><i class = "fab fa-docker" style = "font-size: 400%;"></i>

---

# Build A Container With A Dockerfile

.text-block[
* More than __100 <i class = "fab fa-r-project"></i> packages__ pre-installed (without counting dependencies).  
    ⇒ Increasing over time to ensure "old" projects still work.
* Still no way to install <i class = "fab fa-r-project"></i> packages without compromising the transparency/reproducibility of the Dockerfile used.
]

---

# What Do We Have Now?

.pull-left.green[

* .font150[__Good__]

+ A project structure __clear__.
  
    + __Flexibility at the system-level__ using a Dockerfile to build an image with <i class = "fab fa-r-project"></i> packages or any needed system libraries.
    
    + __Reproducibility__, _i.e._, a project analysed using a specific Docker <i class = "fab fa-docker"></i> image can be re-analysed using that same Docker image.
    
]

.pull-right.red[
* .font150[__Less Good__]

+ Requires some __knowledge__ about system administration and Docker <i class = "fab fa-docker"></i>.
    
    + New __<i class = "fab fa-r-package"></i> packages cannot be installed__ without having to build a new Docker <i class = "fab fa-docker"></i> image.
    
    + <i class = "fab fa-r-package"></i> packages are __not project-specific__, unless you create a Docker <i class = "fab fa-docker"></i> image for each.
    
    + To build or run Docker, users are __required to be `root`__.
    
]

.center.blue[
.font150[
⇒ What if there is a way to __install any__ <i class = "fab fa-r-package"></i> __packages__ (_and Python <i class = "fab fa-python"></i> modules_),  to __record versions__, and to be able to automatically __restore/reinstall all the__ <i class = "fab fa-r-package"></i> __packages of a specific project__?
]
.font120[
All that without any "interference" with the system (_e.g._, Docker container, laptop, _etc._).
]
]

---
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# <img src = "data:image/png;base64,#https://raw.githubusercontent.com/rstudio/hex-stickers/master/SVG/renv.svg" width = "200px" />

![](data:image/png;base64,#https://media.giphy.com/media/zK5EHMbtwfW1O/giphy.gif)

---

# What Is `renv`?

.bqm.font120[

The `renv` package helps you create __r__eproducible __env__ironments for your <i class = "fab fa-r-project"></i> projects.

Use `renv` to make your R projects more:

* __Isolated__: Installing a new or updated package for one project won’t break your other projects, and vice versa.  
    That’s because `renv` gives each project its own private package library.

* __Portable__: Easily transport your projects from one computer to another, even across different platforms.  
    `renv` makes it easy to install the packages your project depends on.

* __Reproducible__: `renv` records the exact package versions you depend on, and ensures those exact versions are the ones that get installed wherever you go.

.sign[
[https://rstudio.github.io/renv/](https://rstudio.github.io/renv/)
]

]

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# `renv` Overview

.pull-left[

+ `activate` - Activate a Project.
+ `clean` - Clean a Project.
+ `consent` - Consent to usage of `renv`
+ `deactivate` - Deactivate a Project.
+ `dependencies` - Find R Package Dependencies in a Project.
+ `diagnostics` - Print a Diagnostics Report.
+ `equip` - Install Required System Libraries (Windows).
+ `history` - View Lockfile History (Git).
+ `hydrate` - Hydrate a Project.
+ `init` - Initialise a Project.
+ `install` - Install Packages.
+ `isolate` - Isolate a Project
+ `load` - Load a Project.
+ `migrate` - Migrate a Project from `Packrat` to `renv`
+ `modify` - Open the Lockfile for Editing.
+ `paths` - Path Customization.
+ `project` - Retrieve the Active Project.

]

.pull-right[

+ `purge` - Purge Packages from the Cache.
+ `rebuild` - Rebuild the Packages in your Project Library.
+ `record` - Update Package Records in a Lockfile.
+ `refresh` - Refresh the Local Cache of Available Packages.
+ `rehash` - Re-Hash Packages in the renv Cache.
+ `remove` - Remove Packages.
+ `restore` - Restore a Project.
+ `revert` - Revert Lockfile (Git).
+ `run` - Run a Script.
+ `scaffold` - Generate renv Project Infrastructure.
+ `settings` - Project Settings.
+ `snapshot` - Snapshot a Project.
+ `status` - Status.
+ `update` - Update Packages.
+ `upgrade` - Upgrade `renv`
+ `use_python` - Use Python.

]

---

# `renv` Overview

.pull-left[

+ `activate` - Activate a Project.
+ .alpha25[`clean` - Clean a Project.]
+ .alpha25[`consent` - Consent to usage of `renv`.]
+ `deactivate` - Deactivate a Project.
+ .alpha25[`dependencies` - Find R Package Dependencies in a Project.]
+ .alpha25[`diagnostics` - Print a Diagnostics Report.]
+ .alpha25[`equip` - Install Required System Libraries (Windows).]
+ .alpha25[`history` - View Lockfile History (Git).]
+ `hydrate` - Hydrate a Project.
+ `init` - Initialise a Project.
+ `install` - Install Packages.
+ `isolate` - Isolate a Project.
+ .alpha25[`load` - Load a Project.]
+ .alpha25[`migrate` - Migrate a Project from `Packrat` to `renv`]
+ .alpha25[`modify` - Open the Lockfile for Editing.]
+ .alpha25[`paths` - Path Customization.]
+ .alpha25[`project` - Retrieve the Active Project.]

]

.pull-right[

+ .alpha25[`purge` - Purge Packages from the Cache.]
+ .alpha25[`rebuild` - Rebuild the Packages in your Project Library.]
+ .alpha25[`record` - Update Package Records in a Lockfile.]
+ .alpha25[`refresh` - Refresh the Local Cache of Available Packages.]
+ .alpha25[`rehash` - Re-Hash Packages in the `renv` Cache.]
+ `remove` - Remove Packages.
+ `restore` - Restore a Project.
+ .alpha25[`revert` - Revert Lockfile (Git).]
+ .alpha25[`run` - Run a Script.]
+ .alpha25[`scaffold` - Generate `renv` Project Infrastructure.]
+ .alpha25[`settings` - Project Settings.]
+ `snapshot` - Snapshot a Project.
+ .alpha25[`status` - Status.]
+ `update` - Update Packages.
+ .alpha25[`upgrade` - Upgrade `renv`.]
+ .alpha25[`use_python` - Use Python.]

]

---
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# How Does `renv` Work?

![](data:image/png;base64,#https://media.giphy.com/media/YalzdbnnMFTBm/giphy.gif)

.font200[_DEMO<sup>&ast;</sup>_]

.footnote[
_&ast; Be prepared, it will not work as planned ..._
]

---

# `renv` When Building A Docker Container

```bash
ENV RENV_VERSION 0.13.1
RUN R -e "install.packages('remotes', repos = c(CRAN = 'https://cloud.r-project.org'))"
RUN R -e "remotes::install_github('rstudio/renv@${RENV_VERSION}')"
WORKDIR /project
COPY renv.lock renv.lock
RUN R -e 'renv::restore()'
```
 
---

# `renv` When Using A Docker Container

+ Without the auto-loader.  
    
    ```bash
     docker run \
        --detach \
        --rm \
        --volume /media/shared/renv_cache:/renv_cache \
        --env "RENV_PATHS_CACHE=/renv_cache" \
        --volume /media/Project:/project \
        rocker/r-base R --vanilla -e 'setwd("/project"); renv::restore(); source("scripts/01-first_analysis.R")'
    ```
    
+ With the auto-loader.  
    
    ```bash
     docker run \
        --detach \
        --rm \
        --volume /media/shared/renv_cache:/renv_cache \
        --env "RENV_PATHS_CACHE=/renv_cache" \
        --volume /media/Project:/project \
        rocker/r-base /bin/bash -c "cd /project; R -e 'source(\"scripts/01-first_analysis.R\")'
    ```

---

# Docker <i class = "fab fa-docker"></i> & `renv`

---

# What Do We Have Now?

.pull-left.green[

* .font150[__Good__]

+ A project structure __clear__.
  
    + __Flexibility at the system-level__ using a Dockerfile to build an image with system libraries.
    
    + __Flexibility at the project-level__ using  `renv`.
        + New __<i class = "fab fa-r-package"></i> packages can be installed/restored__ without having to build a new Docker <i class = "fab fa-docker"></i> image.
        + <i class = "fab fa-r-package"></i> packages are __project-specific__.
    
    + __Reproducibility__, _i.e._, Docker + `renv`.  
        The underlying system, its dependencies, and required <i class = "fab fa-r-package"></i> packages, are fixed and constant for a particular project.
    
]

.pull-right.red[
* .font150[__Less Good__]

+ Requires some __knowledge__ about system administration and Docker <i class = "fab fa-docker"></i>.
    
    + To build or run Docker, users are __required to be `root`__.
    
]

---

# How To Reduce Cognitive Load For New Users?

+ .font150.red[__Remaining issues__]

+ Having to learn about system administration (_i.e._, Debian, Ubuntu, MacOS, Windows, _etc._) __can be a hassle__, especially for beginners.

+ Mostly for security reasons, __users should not be `root`__ for day-to-day work (or in general).

+ .font150.green[__Solutions__]

+ ⇒ Build a Docker image with an RStudio server, <i class = "fab fa-r-project"></i>, and "all" required system libraries (Docker containers as a _daemon_).
    
        + A user has __a non-root account__ to log in through a web browser to the IDE (_i.e._, RStudio).
        
        + A user __can develop, code an analysis__ in a shared environment with a __project-oriented workflow__ built around `renv`.
        
        + __No prior knowledge__ about Docker is required.
        
        + Scripts can still be launched directly in Docker without a _daemon_.
    
    + ⇒ __Singularity__ ([sylabs.io](https://sylabs.io/)) to run containers __without root privileges__, including Docker containers.

---
class: part-slide

# What's Next?<br>Extend & Improve

![](data:image/png;base64,#https://media.giphy.com/media/SLBr5yLzocSYw/giphy.gif)

---

# Next? Extend & Improve

.font150[
+ Switch to Singularity.
]

.font150[
+ Use [`targets`](https://docs.ropensci.org/targets/) from [__rOpenSci__](https://ropensci.org/) to design/improve analysis workflow.<sup>&ast;</sup>
]

.pull-left.font90[

> The `targets` package is a Make-like pipeline toolkit for Statistics and data science in R. With targets, you can maintain a reproducible workflow without repeating yourself.  
> `targets` learns how your pipeline fits together, skips costly runtime for tasks that are already up to date, runs only the necessary computation, supports implicit parallel computing, abstracts files as R objects, and shows tangible evidence that the results match the underlying code and data.

]

.pull-right[
<img src = "data:image/png;base64,#content/media/targets.png" width = "90%" />
 ]

.font150[
+ Any suggestion?
]

.footnote[
&ast; Since I initially made those slides, the [`umr1283`](https://github.com/umr1283/umr1283) <i class = "fab fa-r-project"></i> package has already been updated to allow the use of `targets` within our server infrastructure.
]

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# <img src = "data:image/png;base64,#https://avatars.githubusercontent.com/u/8896044" height = "150px" id = "picture" />

.center[

<a href = "https://mickael.canouil.fr" target = "_blank"><i class = "fas fa-home"></i> mickael.canouil.fr</a>

.column[
<a href = "https://www.linkedin.com/in/mickael-canouil/" target = "_blank"><i class = "fab fa-linkedin"></i> mickael-canouil</a>
]
.column[
<a href = "https://github.com/mcanouil/" target = "_blank"><i class = "fab fa-github"></i> mcanouil</a>
]
.column[
<a href = "https://twitter.com/mickaelcanouil/" target = "_blank"><i class = "fab fa-twitter"></i> @mickaelcanouil</a>
]

]