11-requirements.knit

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.title[
  # 11 - Requirements
]
.subtitle[
  ## Open Science Tools
]

.author[
  ### Claudio Zandonella & Davide Massidda
]

.institute[

]

---
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# Step X: Requirements

---
# Requirements

<br>

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- **System Prerequisites**<br>(e.g., Operating System and CPU details)
{{content}}
]
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]

--
- **Software**<br>(e.g., R, Python, or Julia)
{{content}}
--
- **Libraries**

---
# Requirements

<br>

.pull-left-50[
- **System Prerequisites**<br>(e.g., Operating System and CPU details)
- **Software**<br>(e.g., R, Python, or Julia)
- **Libraries**
]
.pull-right-50[

```r
#---- requirements.txt ----
    
library_1==x.xx.xx
library_2==x.xx.xx

...
```

.move-down-30[
.li-small[
{{content}}
]
]
]

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#### Versioning x.xx.xx

- Patch
- Minor Release
- Major Release

---
# Installation

<br>

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#### Instruction

- Download project
- Install required libraries

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{{content}}
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]
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]

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- Unusual software
- Configuration settings

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# Installation

<br>

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#### Instruction

- Download project
- Install required libraries

.move-down-50[
- Unusual software
- Configuration settings
]
]
.pull-right-50[
Example:

- [RStan](https://github.com/stan-dev/rstan/wiki/RStan-Getting-Started)
- [Jekyll](https://docs.github.com/en/pages/setting-up-a-github-pages-site-with-jekyll/testing-your-github-pages-site-locally-with-jekyll)

{{content}}
]
--
Nice to have:

- `install.sh`
---
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# R Dependencies

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# R Dependencies

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#### R Version

.code-size-12[
{{content}}
]
]
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]

```r
version
##                _ 
## platform       x86_64-apple-darwin20       
## arch           x86_64                      
## os             darwin20                    
## system         x86_64, darwin20            
## status                                     
## major          4                           
## minor          3.0                         
## year           2023                        
## month          04                          
## day            21                          
## svn rev        84292                       
## language       R                           
## version.string R version 4.3.0 (2023-04-21)
## nickname       Already Tomorrow
```

---
# R Dependencies

.pull-left-50[
#### R Version

.code-size-12[

.code-size-12[
{{content}}
]
]

```r
sessioninfo::session_info()$platform
## setting  value
## version  R version 4.3.0 (2023-04-21)
## os       macOS Ventura 13.4
## system   x86_64, darwin20
## ui       RStudio
## language (EN)
## collate  en_US.UTF-8
## ctype    en_US.UTF-8
## tz       Europe/Rome
## date     2023-06-10
## rstudio  2023.03.1+446 Cherry Blossom (desktop)
## pandoc   2.19.2 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/ (via rmarkdown)
## 
```

---
# R Dependencies

.pull-left-50[
#### R Packages

.code-small[
{{content}}
]
]
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]

```r
sessioninfo::session_info()
## ─ Session info ─────────────────────────────────────────────
##
##  [...]
## 
## ─ Packages ─────────────────────────────────────────────────
##  ! package       * version date (UTC) lib source
##  P devtools        2.4.5   2022-10-11 [?] CRAN (R 4.3.0)
##  P dplyr           1.1.2   2023-04-20 [?] CRAN (R 4.3.0)
##  P knitr           1.43    2023-05-25 [?] CRAN (R 4.3.0)
##  P magrittr        2.0.3   2022-03-30 [?] CRAN (R 4.3.0)
##    rmarkdown       2.22    2023-06-01 [1] CRAN (R 4.3.0)
##  P tibble          3.2.1   2023-03-20 [?] CRAN (R 4.3.0)
##  P xaringan        0.28    2022-12-13 [?] CRAN (R 4.3.0)
## 
##  P ── Loaded and on-disk path mismatch.
## ────────────────────────────────────────────────────────────
```

---
# R Dependencies

.pull-left-50[
#### R Packages

.code-small[

```r

## ─ Python configuration ──────────────────────────────────────────────────────────────
##  python:         /usr/bin/python3
##  libpython:      /usr/lib/python3.10/config-3.10-x86_64-linux-gnu/libpython3.10.so
##  pythonhome:     //usr://usr
##  version:        3.10.6 (main, Nov 14 2022, 16:10:14) [GCC 11.3.0]
##  numpy:           [NOT FOUND]
##  
##  python versions found: 
##   /usr/bin/python3
##   /usr/share/miniconda/bin/python
## 
## ─────────────────────────────────────────────────────────────────────────────────────

```
]
]

---
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# R Package Managment

---
## `renv`

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.move-down-90[
<img src="images/11-requirements/renv-hex.png" width="80%" style="display: block; margin: auto;" />
]
.font-14[
.center[
https://rstudio.github.io/renv/
]
]
]
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{{content}}
]

---
## `renv`

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{{content}}
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]

<table class="table" style="width: auto !important; margin-left: auto; margin-right: auto;">
 <thead>
  <tr>
   <th style="text-align:left;"> Platform </th>
   <th style="text-align:left;"> Location </th>
  </tr>
 </thead>
<tbody>
  <tr>
   <td style="text-align:left;"> Linux </td>
   <td style="text-align:left;"> ~/.local/share/renv </td>
  </tr>
  <tr>
   <td style="text-align:left;"> macOS </td>
   <td style="text-align:left;"> ~/Library/Application Support/renv </td>
  </tr>
  <tr>
   <td style="text-align:left;"> Windows </td>
   <td style="text-align:left;"> %LOCALAPPDATA%/renv </td>
  </tr>
</tbody>
</table>

{{content}}
--
<img src="images/11-requirements/cache-revrsion.png" width="70%" style="display: block; margin: auto;" />

{{content}}
--
<img src="images/11-requirements/cache-package.png" width="70%" style="display: block; margin: auto;" />

---
## `renv` Workflow

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.move-down-110[
{{content}}
]
]
.pull-right-60[
.move-down-50[
<img src="images/11-requirements/use-renv.png" width="70%" style="display: block; margin: auto;" />
]
]

--
- `init()`

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## `renv` Workflow

.pull-left-40[
.move-down-110[
- `init()`
]
]
.pull-right-60[
.move-down-50[
<img src="images/11-requirements/renv-active.png" width="80%" style="display: block; margin: auto;" />
]

.code-size-12[
{{content}}
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]

```r
# Install packages as usual
install.packages('<name-package>')
```

---
## `renv` Workflow

.pull-left-40[
.move-down-110[
- `init()`
- `snapshot()`
]
]
.pull-right-60[
.move-down-50[
<img src="images/11-requirements/renv-active.png" width="80%" style="display: block; margin: auto;" />
]

.code-size-12[

```r
# Install packages as usual
install.packages('<name-package>')

# Capturing project's R package dependencies
renv::snapshot()
```
]
]

---
## `renv` Workflow

.pull-left-40[
.move-down-110[
- `init()`
- `snapshot()`
]
]
.pull-right-60[
.move-up-100[
.code-small[
```
#----    renv.lock    ----#

"DBI": {
  "Package": "DBI",
  "Version": "1.1.3",
  "Source": "Repository",
  "Repository": "CRAN",
  "Requirements": [
    "methods"
  ],
  "Hash": "d0d9a365c08b9a8b31c73c26057160b1"
},
"HDInterval": {
  "Package": "HDInterval",
  "Version": "0.2.4",
  "Source": "Repository",
  "Repository": "CRAN",
  "Hash": "b5b77433b286dd869ff33ee7fd5c545f"
},
"MASS": {
  "Package": "MASS",
  "Version": "7.3-58.3",
  "Source": "Repository",
  "Repository": "CRAN",
  "Requirements": [
    "grDevices",
    "graphics",
    "utils"
  ],
  "Hash": "9586b552d57f5516fe4d25398c1bacd6"
}
```
]
]
]

---
## `renv` Workflow

.pull-left-40[
.move-down-110[
- `init()`
- `snapshot()`
- `restore()`
]
]
.pull-right-60[
.move-down-50[
<img src="images/11-requirements/renv-active.png" width="80%" style="display: block; margin: auto;" />
]

.code-size-12[

```r
# Install packages as usual
install.packages('<name-package>')

# Capturing project's R package dependencies
renv::snapshot()

# Restore a project's dependencies
renv::restore()
```
]
]

---
## `renv` Workflow

.pull-left-40[
.move-down-110[
- `init()`
- `snapshot()`
- `restore()`
]
]
.pull-right-60[
.move-down-110[
<img src="images/11-requirements/renv-actions.png" width="80%" style="display: block; margin: auto;" />
]
]

---
## `renv` Advanced Features

.pull-left-50[
.move-down-80[
#### Files Structure
]
.move-down-30[
<img src="images/11-requirements/proj-folder.png" width="80%" style="display: block; margin: auto;" />
]
]
.pull-right-50[

]
---
## `renv` Advanced Features

.pull-left-50[
.move-down-80[
#### Files Structure
]
.move-down-30[
<img src="images/11-requirements/proj-folder.png" width="80%" style="display: block; margin: auto;" />
]
]
.pull-right-50[
.move-down-80[
.li-small[
- `.Rprofile`

<img src="images/11-requirements/renv-rprofile.png" width="80%" style="display: block; margin: auto;" />
]
]
]

---
## `renv` Advanced Features

<img src="images/11-requirements/lock-file.png" width="80%" style="display: block; margin: auto;" />
]
]
]
---
## `renv` Advanced Features

<img src="images/11-requirements/renv-folder.png" width="80%" style="display: block; margin: auto;" />
]
]
]

---
## `renv` Advanced Features

<br>

.pull-left-50[
#### Snapshot Types

.li-small[
- `"all"`
- `"implicit"` (default)
- `"explicit"` (project `DESCRIPTION` file)
- `"custom"` user-defined filter instead
]
]
.pull-right-50[
.code-size-12[
{{content}}
]
]
--

#### Detecting Packages

```r
# Correctly detected by renv
library("tidyverse")

trackdown::upload_file(...)

# Not detected by renv
packages_list <- c("tidyverse", "trackdown")

lapply(packages_list, library, 
       character.only = TRUE)

for (package in packages_list) {
  library(package, character.only = TRUE)
}
```

---
## `renv` Advanced Features

<br>

- R version
    
    ```r
    ## Warning: Project requested R version '3.6.1' but '4.1.0' is currently being used
    ```
--

- `.renvignore` File

- Restore Issue(s)

---
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# A Package to Rule Them All

## Moving to the next step...