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Makefile
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# Copyleft (C) 2020-2024, Marek Gagolewski <https://www.gagolewski.com/>
# pip3 install pweave tabulate hdbscan mlpack nmslib pytest rpy2 scanpy
.PHONY: python py-test py-check r r-check r r-build html docs clean
.NOTPARALLEL: python py-test py-check r r-check r r-build clean purge html docs
PKGNAME="genieclust"
all: r python
################################################################################
python:
# python3 setup.py install --user # deprecated
# python3 -m build # requires the 'build' package, creates an isolated envir
python3 -m pip install .
py-test: python
pytest
cd .devel/sphinx && make doctest && cd ../../
py-check: python
flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics \
--exclude=.devel,build,docs,.git,R,dist,genieclust.egg-info,man,tutorials
flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 \
--statistics \
--exclude=.devel,build,docs,.git,R,dist,genieclust.egg-info,man,tutorials \
--ignore=E121,E123,E126,E226,E24,E704,W503,W504,E221,E303,E265
################################################################################
stop-on-utf8:
# Stop if some files are not in ASCII:
[ -z "`file -i DESCRIPTION configure configure.win \
NAMESPACE cleanup R/* src/* man/* inst/* tools/* | \
grep 'text/' | grep -v 'us-ascii' | tee /dev/stderr`" ]
r-autoconf:
Rscript -e 'Rcpp::compileAttributes()'
Rscript -e "\
source('.devel/roxygen2-patch.R');\
roxygenise(\
roclets=c('rd', 'collate', 'namespace', 'vignette'),\
)"
# load_code=roxygen2::load_installed\
r: r-autoconf
R CMD INSTALL . --html
r-test: r
Rscript -e 'source(".devel/tinytest.R")'
r-build: r-autoconf
cd .. && R CMD build ${PKGNAME}
r-check: stop-on-utf8 r-build
cd .. && R_DEFAULT_INTERNET_TIMEOUT=240 \
_R_CHECK_CRAN_INCOMING_REMOTE_=FALSE \
_R_CHECK_FORCE_SUGGESTS_=0 \
R CMD check `ls -t ${PKGNAME}*.tar.gz | head -1` --as-cran --no-manual
################################################################################
rd2myst:
# https://github.com/gagolews/Rd2rst
cd .devel/sphinx && Rscript -e "Rd2rst::Rd2myst('${PKGNAME}')"
weave-examples:
cd .devel/sphinx/rapi && Rscript -e "Rd2rst::weave_examples('${PKGNAME}', '.')"
weave:
cd .devel/sphinx/weave && make && cd ../../../
news:
cd .devel/sphinx && cp ../../NEWS news.md
html: python r news weave rd2myst weave-examples
rm -rf .devel/sphinx/_build/
cd .devel/sphinx && make html
.devel/sphinx/fix-html.sh .devel/sphinx/_build/html/rapi/
.devel/sphinx/fix-html.sh .devel/sphinx/_build/html/weave/
rm -rf .devel/sphinx/_build/html/_sources
@echo "*** Browse the generated documentation at"\
"file://`pwd`/.devel/sphinx/_build/html/index.html"
docs: html
@echo "*** Making 'docs' is only recommended when publishing the"\
"official release, because it updates the package homepage."
@echo "*** Therefore, we check if the package version is like 1.2.3"\
"and not 1.2.2.9007."
#Rscript --vanilla -e "stopifnot(length(unclass(packageVersion('${PKGNAME}'))[[1]]) < 4)"
rm -rf docs/
mkdir docs/
cp -rf .devel/sphinx/_build/html/* docs/
cp .devel/CNAME.tpl docs/CNAME
touch docs/.nojekyll
touch .nojekyll
################################################################################
clean:
python3 setup.py clean
rm -rf genieclust/__pycache__/
rm -rf genieclust.egg-info/
rm -rf ../genieclust.Rcheck/
rm -rf dist/
rm -rf build/
rm -rf .devel/pytest/__pycache__/
rm -f genieclust/*.cpp
find src -name '*.o' -exec rm {} \;
find src -name '*.so' -exec rm {} \;
rm -rf .devel/sphinx/_build/
rm -rf .devel/sphinx/rapi/
rm -rf revdep/
purge: clean
#rm -f man/*.Rd