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make write_py_stack point to gds env
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darribas committed Oct 23, 2023
1 parent 2fa11cf commit 889deba
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Showing 2 changed files with 396 additions and 62 deletions.
4 changes: 2 additions & 2 deletions Makefile
Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@ 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 sh -c "conda list > /home/jovyan/test/gds_py/stack_py.txt"
$(DOCKERRUN) darribas/gds_py:${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', '--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
Expand All @@ -18,7 +18,7 @@ write_r_stack:
$(DOCKERRUN) darribas/gds:${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 --explicit > /home/jovyan/test/gds_py/stack_py_explicit.txt"
$(DOCKERRUN) darribas/gds_py:${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 && \
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