STY: Sync with template files

.travis.yml

@@ -1,23 +1,57 @@
-dist: xenial  # Ubuntu 16.04 (required for python 3.7)
-language: python
-python: 3.7
+# Travis CI is only used to check the lesson and is not involved in its deployment
+dist: bionic
+language: ruby
+rvm:
+  - 2.7.1
+
 branches:
   only:
   - gh-pages
   - /.*/
+
+cache:
+  apt: true
+  bundler: true
+  directories:
+    - /home/travis/.rvm/
+    - $R_LIBS_USER
+    - $HOME/.cache/pip
+
+env:
+  global:
+    - NOKOGIRI_USE_SYSTEM_LIBRARIES=true # speeds up installation of html-proofer
+    - R_LIBS_USER=~/R/Library
+    - R_LIBS_SITE=/usr/local/lib/R/site-library:/usr/lib/R/site-library
+    - R_VERSION=4.0.2
+
 before_install:
-  - sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
-  - echo "deb https://cran.rstudio.com/bin/linux/ubuntu trusty/" | sudo tee -a /etc/apt/sources.list
-  - sudo apt-get update -y
-  - sudo apt-get install -y r-base
-  - sudo Rscript -e "install.packages('knitr', repos = 'https://', dependencies = TRUE)"
-  - sudo Rscript -e "install.packages('stringr', repos = 'https://cran.rstudio.com', dependencies = TRUE)"
-  - sudo Rscript -e "install.packages('checkpoint', repos = 'https://cran.rstudio.com', dependencies = TRUE)"
-  - sudo Rscript -e "install.packages('ggplot2', repos = 'https://cran.rstudio.com', dependencies = TRUE)"
-  - rvm default
-  - gem install json kramdown jekyll
-install:
-  - pip install pyyaml
+  ## Install R + pandoc + dependencies
+  - sudo add-apt-repository -y "ppa:marutter/rrutter4.0"
+  - sudo add-apt-repository -y "ppa:c2d4u.team/c2d4u4.0+"
+  - sudo add-apt-repository -y "ppa:ubuntugis/ppa"
+  - sudo add-apt-repository -y "ppa:cran/travis"
+  - travis_apt_get_update
+  - sudo apt-get install -y --no-install-recommends build-essential gcc g++ libblas-dev liblapack-dev libncurses5-dev libreadline-dev libjpeg-dev libpcre3-dev libpng-dev zlib1g-dev libbz2-dev liblzma-dev libicu-dev cdbs qpdf texinfo libssh2-1-dev gfortran jq python3.5 python3-pip r-base
+  - export PATH=${TRAVIS_HOME}/R-bin/bin:$PATH
+  - export LD_LIBRARY_PATH=${TRAVIS_HOME}/R-bin/lib:$LD_LIBRARY_PATH
+  - sudo mkdir -p /usr/local/lib/R/site-library $R_LIBS_USER
+  - sudo chmod 2777 /usr/local/lib/R /usr/local/lib/R/site-library $R_LIBS_USER
+  - echo 'options(repos = c(CRAN = "https://packagemanager.rstudio.com/all/__linux__/bionic/latest"))' > ~/.Rprofile.site
+  - export R_PROFILE=~/.Rprofile.site
+  - curl -fLo /tmp/texlive.tar.gz https://github.com/jimhester/ubuntu-bin/releases/download/latest/texlive.tar.gz
+  - tar xzf /tmp/texlive.tar.gz -C ~
+  - export PATH=${TRAVIS_HOME}/texlive/bin/x86_64-linux:$PATH
+  - tlmgr update --self
+  - curl -fLo /tmp/pandoc-2.2-1-amd64.deb https://github.com/jgm/pandoc/releases/download/2.2/pandoc-2.2-1-amd64.deb
+  - sudo dpkg -i /tmp/pandoc-2.2-1-amd64.deb
+  - sudo apt-get install -f
+  - rm /tmp/pandoc-2.2-1-amd64.deb
+  - Rscript -e "install.packages(setdiff(c('renv', 'rprojroot'), installed.packages()), loc = Sys.getenv('R_LIBS_USER')); update.packages(lib.loc = Sys.getenv('R_LIBS_USER'), ask = FALSE, checkBuilt = TRUE)"
+  - Rscript -e 'sessionInfo()'
+  ## Install python and dependencies
+  - python3 -m pip install --upgrade pip setuptools wheel
+  - python3 -m pip install pyyaml
+
 script:
   - make lesson-check-all
   - make --always-make site

AUTHORS

@@ -1,4 +1,4 @@
 Michael Joseph
 Jerrold Jeyachandra
 Erin Dickie
-Ariel Rokem
+Ariel Rokem

CITATION

@@ -1,5 +1,5 @@
 Please cite as:
 
 Michael Joseph, Jerrold Jeyachandra, and Erin Dickie (eds):
-"Data Carpentry: Introduction to." Version 2019.11, November 2019,
-https://github.com/conp-pcno-training/SDC-BIDS-IntroMRI
+"Data Carpentry: Introduction to MRI Data Analysis." Version 2019.11, November 2019,
+https://github.com/carpentries-incubator/SDC-BIDS-IntroMRI

CONTRIBUTING.md

@@ -73,7 +73,7 @@ and submitting [bug reports][issues]
 about things that don't work, aren't clear, or are missing.
 If you are looking for ideas, please see the 'Issues' tab for
 a list of issues associated with this repository,
-or you may also look at the issues for [Data Carpentry][dc-issues], 
+or you may also look at the issues for [Data Carpentry][dc-issues],
 [Software Carpentry][swc-issues], and [Library Carpentry][lc-issues] projects.
 
 Comments on issues and reviews of pull requests are just as welcome:

_config.yml

@@ -29,10 +29,10 @@ kind: "lesson"
 repository: <USERNAME>/<PROJECT>
 
 # Email address, no mailto:
-email: "[email protected]"
+email: "[email protected]
 
 # Sites.
-amy_site: "https://amy.carpentries.org/workshops"
+amy_site: "https://amy.carpentries.org/"
 carpentries_github: "https://github.com/carpentries"
 carpentries_pages: "https://carpentries.github.io"
 carpentries_site: "https://carpentries.org/"
@@ -92,11 +92,11 @@ exclude:
   - bin/
   - .Rproj.user/
   - .vendor/
+  - vendor/
   - .docker-vendor/
-  - .jekyll-cache/
 
 # Turn on built-in syntax highlighting.
 highlighter: rouge
 
 # Remote theme
-remote_theme: carpentries/carpentries-theme
+remote_theme: carpentries/carpentries-theme

index.md

@@ -12,7 +12,7 @@ The lesson will introduce different types of MRI modalities and how they can be
 Over the past decade, the neuroimaging field has produced (and continues to produce) incredible amounts of data about the brain. As a result, the scientific community has developed a diverse set of tools to facilitate the access, analysis and visualization of this data. This lesson will start you on a path towards using these tools effectively in your own work.
 
 > ## Prerequisites
-> 
+>
 > This lesson assumes that you have some working knowledge of the Unix shell and Python.
 > These requirements can be fulfilled by:
 > - completing the Software Carpentry [Unix][swc-shell] and/or [Python][swc-python] lessons
@@ -28,4 +28,4 @@ To get started, follow the directions on the [Setup][lesson-setup] page to insta
 [swc-python]: https://swcarpentry.github.io/python-novice-inflammation
 [swc-shell]: https://swcarpentry.github.io/shell-novice
 [inc-fmri]: https://carpentries-incubator.github.io/SDC-BIDS-fMRI
-[inc-dmri]: https://carpentries-incubator.github.io/SDC-BIDS-dMRI
+[inc-dmri]: https://carpentries-incubator.github.io/SDC-BIDS-dMRI

setup.md

@@ -87,12 +87,12 @@ If you installed Anaconda, you can launch a notebook in two ways:
 > It might ask you if you'd like to send anonymized usage information to Anaconda developers:
 > ![Anaconda Navigator first launch](../fig/anaconda-navigator-first-launch.png)
 > Make your choice and click "Ok, and don't show again" button.
-> 
+>
 > 2. Find the "Notebook" tab and click on the "Launch" button:
 > ![Anaconda Navigator Notebook launch](../fig/anaconda-navigator-notebook-launch.png)
 > Anaconda will open a new browser window or tab with a Notebook Dashboard showing you the
 > contents of your Home (or User) folder.
-> 
+>
 > 3. Navigate to the `data` directory by clicking on the directory names leading to it:
 > `Desktop`, `dc-mri`, then `data`:
 > ![Anaconda Navigator Notebook directory](../fig/jupyter-notebook-data-directory.png)
@@ -186,4 +186,4 @@ winpty python
 [ds000030]: https://openneuro.org/datasets/ds000030/versions/1.0.0
 [gitbash]: https://gitforwindows.org
 
-{% include links.md %}
+{% include links.md %}