Merge branch 'add-overview' into 'master'

Add overview to project

Closes #16

See merge request !6

.gitlab-ci.yml

@@ -4,6 +4,7 @@ pages:
     stage: deploy
     script:
       - R -e "remotes::install_deps(dependencies = T)"
+      - R -e "tinytex::install_tinytex()"
       - Rscript _build.R
     artifacts:
         paths:

DESCRIPTION

@@ -2,6 +2,8 @@ Package: manifesto
 Type: Book
 Title: Heavily Opinionated Manifesto on Reproducible and Open Science Projects.
 Version: 0.0.1.9000
-Imports: bookdown
+Imports: 
+    bookdown,
+    tinytex
 Remotes: rstudio/bookdown
 License: CCBY-4.0

_build.R

 
 # bookdown::render_book('index.Rmd', 'bookdown::html_book')
-# bookdown::render_book('index.Rmd', 'bookdown::gitbook')
+bookdown::render_book('index.Rmd', 'bookdown::gitbook')
 bookdown::render_book('index.Rmd', 'bookdown::pdf_book')

index.Rmd

@@ -6,7 +6,6 @@ author:
     - "Ahmed Hasan"
 date: "`r Sys.Date()`"
 site: bookdown::bookdown_site
-output: bookdown::gitbook
 documentclass: book
 #bibliography: [book.bib, packages.bib]
 biblio-style: apalike
@@ -15,13 +14,70 @@ link-citations: yes
 description: "Heavily Opinionated Manifesto on Reproducible and Open Science Projects"
 ---
 
-# Overview
-
 \mainmatter
 
+> Note: This document is still in active development, so text may and will likely
+change as we work to completing it.
+
+# Overview
+
 ```{r, include=FALSE, eval=FALSE}
 # automatically create a bib database for R packages
 knitr::write_bib(c(
   .packages(), 'bookdown', 'knitr', 'rmarkdown'
 ), 'packages.bib')
 ```
+
+## Vision
+
+Our dream is a future where the default for science is to be reproducible and
+open. We hope that one day, researchers will conduct their scientific activities
+following open scientific principles not as an active choice but because it is
+the proper and *easier* way of doing science.
+
+Our focus is in three branches: software, teaching, and support networks.
+
+- For our software, we aim to automate what we can, simplify and streamline the
+rest. We aspire to be similar to [devtools][^devtools], which is an R software
+package designed to make it easier to create other R packages, for doing
+reproducible and open science.
+- For our learning material, we aspire to be a "go to" reference for learning
+the *exact steps and processes* for doing reproducible and open science, and for
+knowing and staying updated on which tools and services to use.
+- For our support network, we hope to link and connect with all the amazing
+research groups throughout the world who are working hard to practice and
+promote reproducible and open science. Through this connection, we hope that it
+will provide others with real-world examples and role models for how science 
+should be done.
+
+[devtools]: https://devtools.r-lib.org/
+
+We are (mostly) biomedical researchers, so our main focus and expertise is in
+biomedical science.
+
+## Mission
+
+To acheive our vision, our mission is to create a highly opinionated, practical,
+and process-oriented ecosystem of software tools and accompanying documentation,
+tutorials, and learning materials, supported by a network of practitioners
+(researchers), that informs on how to conduct open and reproducible science.
+
+Our mission is divided into multiple parts based on the organizations' branches:
+
+- Software: We aim to create an ecosystem of interconnected packages and software
+tools, by either developing these tools or by linking existing ones. This ecosystem
+of tools aims to reduce the burden on researchers in conducting open and reproducible
+science through automation and programming. We hope to emulate the principles
+and structure of the [tidyverse] ecosystem, as they are a great role model for 
+creating a functioning and solid ecosystem.
+- Learning material: (still being developed.)
+- Support network: (still being developed.)
+
+[tidyverse]: https://www.tidyverse.org/
+
+In all project branches, our aim is to design the software and learning material
+to be comprehensive, carefully considered, and scientifically-informed by emphasizing
+usability and simplicity.
+
+Our current focus is on the data analysis and publication side of scientific
+activities.