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Feb 2, 2023
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docker refactor for stable environment to convert Rmd blog post to html #760

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387042f
docker refactor for stable environment to convert Rmd to html
minhkhul Jan 31, 2023
6a9d1db
Add readme instructions
minhkhul Jan 31, 2023
b9081fd
Update devops/r.dockerfile
minhkhul Feb 2, 2023
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8 changes: 6 additions & 2 deletions README.md
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Expand Up @@ -79,11 +79,15 @@ In order to convert the Rmd files to HTML files for Hugo you also need to:
1. Activate the environment: `conda activate www-main`
1. Install extra R dependencies: `Rscript ./dependencies.R`

As an alternative you can use Docker and Docker Compose. Then it reduces to `docker-compose up -d` to create a docker container for the current environment. In the following you would need to jump into the container to execute the upcoming command via `docker-compose exec r bash`.
As an alternative you can use Docker and Docker Compose:
1. `docker-compose up -d` to create a docker container for the current environment.
1. `docker-compose exec r bash` to jump into the container.
1. `micromamba activate www-main` to activate the environment

Now you have the environment ready to start converting .Rmd blog files to html.
#### Commands

1. Activate the environment: `conda activate www-main`

1. Run blogdown to convert the files to HTML: `Rscript -e 'blogdown::build_site(local=TRUE, run_hugo=FALSE, build_rmd=TRUE)'`
- `local=TRUE` similar to `-D` to process draft files
- `run_hugo=FALSE` to manually run hugo
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2 changes: 2 additions & 0 deletions dependencies.R
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Expand Up @@ -3,6 +3,8 @@

# blogdown::install_hugo()

install.packages("ggrepel", repo="http://cran.rstudio.com/")
install.packages("base64url", repo="http://cran.rstudio.com/")
install.packages("covidcast", repo="http://cran.rstudio.com/")
# devtools::install_github("cmu-delphi/covidcast", ref = "main",
# upgrade = 'never',
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11 changes: 5 additions & 6 deletions devops/r.dockerfile
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@@ -1,13 +1,12 @@
# docker image for setting up an R environment
FROM continuumio/miniconda

RUN conda install --name base --channel conda-forge mamba=*
FROM mambaorg/micromamba

ADD ./environment.yml .
RUN mamba env create -f environment.yml

RUN micromamba env create -f environment.yml
ARG MAMBA_DOCKERFILE_ACTIVATE=1
ADD ./dependencies.R .

RUN conda run -n www-main Rscript ./dependencies.R
RUN micromamba run -n www-main Rscript ./dependencies.R

ENV PATH /opt/conda/envs/www-main/bin:$PATH
ENV PATH /opt/conda/envs/www-main/bin:$PATH
3 changes: 2 additions & 1 deletion environment.yml
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Expand Up @@ -2,6 +2,7 @@ name: www-main
channels:
- conda-forge
- defaults
- conda-forge/linux-64
dependencies:
- gdal
- python=3.9.1
Expand All @@ -13,7 +14,7 @@ dependencies:
- r-devtools
- r-directlabels
- r-gridextra
- r-reticulate
- r-reticulate==1.22
- r-blogdown
- r-svglite
- r-dplyr
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