/
Makefile
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/
Makefile
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export GDS_VERSION=10.0
#DOCKERRUN = docker run --rm --user root -e GRANT_SUDO=yes -e NB_UID=1002 -e NB_GID=100 -v `pwd`:/home/jovyan/test
DOCKERRUN = docker run -v `pwd`:/home/jovyan/test
test: test_py test_r
test_py:
$(DOCKERRUN) darribas/gds_py:${GDS_VERSION} start.sh jupyter nbconvert --to html --execute /home/jovyan/test/gds_py/check_py_stack.ipynb
test_r:
$(DOCKERRUN) darribas/gds:${GDS_VERSION} start.sh jupyter nbconvert --to html --execute /home/jovyan/test/gds/check_r_stack.ipynb
write_stacks: write_py_stack write_r_stack
write_py_stack:
$(DOCKERRUN) darribas/gds_py:${GDS_VERSION} start.sh bash -c "conda list -n gds > /home/jovyan/test/gds_py/stack_py.txt"
$(DOCKERRUN) darribas/gds_py:${GDS_VERSION} start.sh sed -i '1iGDS version: ${GDS_VERSION}' /home/jovyan/test/gds_py/stack_py.txt
$(DOCKERRUN) darribas/gds_py:${GDS_VERSION} start.sh python -c "import subprocess, pandas; fo=open('/home/jovyan/test/gds_py/stack_py.md', 'w'); fo.write(pandas.read_json(subprocess.check_output(['conda', 'list', '-n', 'gds', '--json']).decode())[['name', 'version', 'build_string', 'channel']].to_markdown());fo.close()"
$(DOCKERRUN) darribas/gds_py:${GDS_VERSION} start.sh sed -i "1s/^/\n/" /home/jovyan/test/gds_py/stack_py.md
write_r_stack:
$(DOCKERRUN) darribas/gds:${GDS_VERSION} start.sh sh -c 'Rscript -e "ip <- as.data.frame(installed.packages()[,c(1,3:4)]); print(ip)" > /home/jovyan/test/gds/stack_r.txt'
$(DOCKERRUN) darribas/gds:${GDS_VERSION} start.sh sed -i '1iGDS version: ${GDS_VERSION}' /home/jovyan/test/gds/stack_r.txt
$(DOCKERRUN) darribas/gds:${GDS_VERSION} start.sh Rscript -e "library(knitr); ip <- as.data.frame(installed.packages()[,c(1,3:4)]); fc <- file('/home/jovyan/test/gds/stack_r.md'); writeLines(kable(ip, format = 'markdown'), fc); close(fc);"
$(DOCKERRUN) darribas/gds:${GDS_VERSION} start.sh sed -i "1s/^/\n/" /home/jovyan/test/gds/stack_r.md
write_py_explicit:
$(DOCKERRUN) darribas/gds_py:${GDS_VERSION} start.sh sh -c "conda list -n gds --explicit > /home/jovyan/test/gds_py/stack_py_explicit.txt"
website_build:
cd website && \
rm -rf _includes && \
rm -rf _site
mkdir -p website/_includes
#--- Populate content ---#
cp README.md website/_includes
cp CONTRIBUTING.md website/_includes
cp docker/install_guide.md website/_includes/docker_install_guide.md
cp docker/build_guide.md website/_includes/docker_build_guide.md
cp virtualbox/virtualbox_user_setup.md website/_includes
cp virtualbox/README_docker-machine.md website/_includes
cp virtualbox/README_vagrant.md website/_includes
cp gds_py/stack_py.md website/_includes/stack_py.md
cp gds/stack_r.md website/_includes/stack_r.md
cp gds_py/README.md website/_includes/gds_py_README.md
cp gds/README.md website/_includes/gds_README.md
cp gds_dev/README.md website/_includes/gds_dev_README.md
#---
website: website_build
cd website && jekyll build
rm -rf docs
mv website/_site docs
cd website && rm -rf _includes
touch docs/.nojekyll
website_local: website_build
# https://tonyho.net/jekyll-docker-windows-and-0-0-0-0/
export JEKYLL_ENV=docker && \
cd website && \
jekyll serve --host 0.0.0.0 \
--incremental \
--config _config.yml,_config.docker.yml && \
rm -rf _includes
export JEKYLL_ENV=development