Makefile

PROFILE_FILE=$(CURDIR)/$(BUILDDIR)/main.pstats
COVERAGE_REPORT=$(CURDIR)/$(BUILDDIR)/coverage
BUILDDIR=$(CURDIR)/build
HTML_DIR=$(BUILDDIR)/html
DOCSRC_DIR=$(BUILDDIR)/doc
MAN_DIR=$(BUILDDIR)/man
APIDOC_DIR=$(HTML_DIR)/api
PDF_DIR=$(BUILDDIR)/pdf
LATEX_DIR=$(BUILDDIR)/latex
WWW_DIR=$(BUILDDIR)/website
SWARM_DIR=$(BUILDDIR)/swarm
WWW_UPLOAD_URI=www.pymvpa.org:/home/www/www.pymvpa.org/pymvpa
DATA_URI=apsy.gse.uni-magdeburg.de:/home/hanke/public_html/software/pymvpa/data
SWARMTOOL_DIR=tools/codeswarm
SWARMTOOL_DIRFULL=$(CURDIR)/$(SWARMTOOL_DIR)
RSYNC_OPTS=-az -H --no-perms --no-owner --verbose --progress --no-g


#
# Details on the Python/system
#

PYVER := $(shell python -V 2>&1 | cut -d ' ' -f 2,2 | cut -d '.' -f 1,2)
DISTUTILS_PLATFORM := $(shell python -c "import distutils.util; print distutils.util.get_platform()")

#
# Little helpers
#

mkdir-%:
	if [ ! -d $($*) ]; then mkdir -p $($*); fi


#
# Building
#

all: build

# build included 3rd party pieces (if present)
3rd: 3rd-stamp
3rd-stamp:
	find 3rd -mindepth 1 -maxdepth 1  -type d | \
	 while read d; do \
	  [ -f "$$d/Makefile" ] && $(MAKE) -C "$$d" || :; \
     done
	touch $@


debian-build:
# reuse is better than duplication (yoh)
	debian/rules build


build: build-stamp
build-stamp: 3rd
	python setup.py config --noisy --with-libsvm
	python setup.py build --with-libsvm
# to overcome the issue of not-installed svmc.so
	for ext in _svmc smlrc; do \
		ln -sf ../../../build/lib.$(DISTUTILS_PLATFORM)-$(PYVER)/mvpa/clfs/lib$${ext#_*}/$${ext}.so \
		mvpa/clfs/lib$${ext#_*}/; \
		ln -sf ../../../build/lib.$(DISTUTILS_PLATFORM)-$(PYVER)/mvpa/clfs/lib$${ext#_*}/$${ext}.so \
		mvpa/clfs/lib$${ext#_*}/$${ext}.dylib; \
		done
	touch $@


#
# Cleaning
#

# this target is used to clean things for a fresh build
clean:
# clean 3rd party pieces
	find 3rd -mindepth 1 -maxdepth 1  -type d | \
	 while read d; do \
	  [ -f "$$d/Makefile" ] && $(MAKE) -C "$$d" clean || : ; \
     done
# clean tools
	$(MAKE) -C tools clean
# clean all bits and pieces
	-@rm -f MANIFEST
	-@rm -f mvpa/clfs/lib*/*.so \
		mvpa/clfs/lib*/*.dylib \
		mvpa/clfs/lib*/*_wrap.* \
		mvpa/clfs/lib*/*c.py \
		mvpa/tests/*.{prof,pstats,kcache}
	@find . -name '*.py[co]' \
		 -o -name '*,cover' \
		 -o -name '.coverage' \
		 -o -name 'iterate.dat' \
		 -o -iname '*~' \
		 -o -iname '*.kcache' \
		 -o -iname '*.gch' \
		 -o -iname '*_flymake.*' \
		 -o -iname '#*#' | xargs -L 10 rm -f
	-@rm -rf build
	-@rm -rf dist *_report
	-@rm -f *-stamp *_report.pdf pymvpa.cfg

# this target should put the source tree into shape for building the source
# distribution
distclean: clean
# if we are on debian system - we might have left-overs from build
	-@$(MAKE) debian-clean
	-@rm -rf tools/codeswarm



debian-clean:
# remove stamps for builds since state is not really built any longer
	-fakeroot debian/rules clean


#
# Documentation
#

doc: website manpages

manpages: mkdir-MAN_DIR
	PYTHONPATH=.:$(PYTHONPATH) help2man -N -n 'preprocess fMRI data for PyMVPA' \
		bin/mvpa-prep-fmri > $(MAN_DIR)/mvpa-prep-fmri.1
	PYTHONPATH=. help2man -N -n 'query stereotaxic atlases' \
		bin/atlaslabeler > $(MAN_DIR)/atlaslabeler.1

prepare-docsrc: mkdir-BUILDDIR
	rsync --copy-unsafe-links -rvuhp doc/ $(BUILDDIR)/doc
	rsync --copy-unsafe-links -rvhup doc/pics/ $(DOCSRC_DIR)/examples/pics

references:
	tools/bib2rst_ref.py

htmldoc: modref-templates examples2rst build
	cd $(DOCSRC_DIR) && MVPA_EXTERNALS_RAISE_EXCEPTION=off PYTHONPATH=$(CURDIR):$(PYTHONPATH) $(MAKE) html BUILDROOT=$(BUILDDIR)
	cd $(HTML_DIR)/modref && ln -sf ../_static
	cd $(HTML_DIR)/examples && ln -sf ../_static
	cp $(DOCSRC_DIR)/pics/history_splash.png $(HTML_DIR)/_images/

pdfdoc: modref-templates examples2rst build pdfdoc-stamp
pdfdoc-stamp:
	cd $(DOCSRC_DIR) && MVPA_EXTERNALS_RAISE_EXCEPTION=off PYTHONPATH=../..:$(PYTHONPATH) $(MAKE) latex BUILDROOT=$(BUILDDIR)
	cd $(LATEX_DIR) && $(MAKE) all-pdf
	touch $@

# Create a handy .pdf of the manual to be printed as a book
handbook: pdfdoc
	cd tools && $(MAKE) pdfbook
	build/tools/pdfbook -2 \
	 $(LATEX_DIR)/PyMVPA-Manual.pdf $(LATEX_DIR)/PyMVPA-Manual-Handbook.pdf

modref-templates: prepare-docsrc modref-templates-stamp
modref-templates-stamp:
	PYTHONPATH=.:$(PYTHONPATH) tools/build_modref_templates.py
	touch $@

examples2rst: prepare-docsrc examples2rst-stamp
examples2rst-stamp:
	tools/ex2rst \
		--project PyMVPA \
		--outdir $(DOCSRC_DIR)/examples \
		--exclude doc/examples/searchlight.py \
		doc/examples
	touch $@

apidoc: apidoc-stamp
apidoc-stamp: build
# Disabled profiling for now, it consumes huge amounts of memory, so I doubt
# that all buildds can do it. In theory it would only be done on a single
# developer machine, because it is only necessary for the arch-all package,
# but e.g. dpkg-buildpackage runs the indep target anyway -- not sure about
# the buildds, though.
#apidoc-stamp: profile
	mkdir -p $(HTML_DIR)/api
	LC_ALL=C MVPA_EPYDOC_WARNINGS=once tools/epydoc --config doc/api/epydoc.conf
	touch $@

# this takes some minutes !!
profile: build mvpa/tests/main.py
	@PYTHONPATH=.:$(PYTHONPATH) tools/profile -K  -O $(PROFILE_FILE) mvpa/tests/main.py


#
# Website
#

website: website-stamp
website-stamp: mkdir-WWW_DIR apidoc htmldoc pdfdoc
	cp -r $(HTML_DIR)/* $(WWW_DIR)
	cp $(LATEX_DIR)/*.pdf $(WWW_DIR)
	tools/sitemap.sh > $(WWW_DIR)/sitemap.xml
# main icon of the website
	cp $(DOCSRC_DIR)/pics/favicon.png $(WWW_DIR)/_images/
# for those who do not care about <link> and just trying to download it
	cp $(DOCSRC_DIR)/pics/favicon.png $(WWW_DIR)/favicon.ico
# provide robots.txt to minimize unnecessary traffic
	cp $(DOCSRC_DIR)/_static/robots.txt $(WWW_DIR)/
# provide promised pylintrc
	mkdir -p $(WWW_DIR)/misc && cp $(DOCSRC_DIR)/misc/pylintrc $(WWW_DIR)/misc
	touch $@

upload-website: website
	rsync -rzlhvp --delete --chmod=Dg+s,g+rw $(WWW_DIR)/* $(WWW_UPLOAD_URI)/

upload-htmldoc: htmldoc
	rsync -rzlhvp --delete --chmod=Dg+s,g+rw $(HTML_DIR)/* $(WWW_UPLOAD_URI)/


#
# Tests (unittests, docs, examples)
#

ut-%: build
	@PYTHONPATH=.:$(PYTHONPATH) nosetests --nocapture mvpa/tests/test_$*.py

unittest: build
	@echo "I: Running unittests (without optimization nor debug output)"
	PYTHONPATH=.:$(PYTHONPATH) python mvpa/tests/main.py


# test if PyMVPA is working if optional externals are missing
unittest-badexternals: build
	@echo "I: Running unittests under assumption of missing optional externals."
	@PYTHONPATH=mvpa/tests/badexternals:.:$(PYTHONPATH) python mvpa/tests/main.py 2>&1 \
	| grep -v -e 'WARNING: Known dependency' -e 'Please note: w' \
              -e 'WARNING:.*SMLR.* implementation'

# only non-labile tests
unittest-nonlabile: build
	@echo "I: Running only non labile unittests. None of them should ever fail."
	@PYTHONPATH=.:$(PYTHONPATH) MVPA_TESTS_LABILE=no python mvpa/tests/main.py

# test if no errors would result if we force enabling of all states
unittest-states: build
	@echo "I: Running unittests with all states enabled."
	@PYTHONPATH=.:$(PYTHONPATH) MVPA_DEBUG=CHECK_STATES_ENABLED python mvpa/tests/main.py

# Run unittests with optimization on -- helps to catch unconditional
# debug calls
unittest-optimization: build
	@echo "I: Running unittests with python -O."
	@PYTHONPATH=.:$(PYTHONPATH) python -O mvpa/tests/main.py

# Run unittests with all debug ids and some metrics (crossplatform ones) on.
#   That does:
#     additional checking,
#     debug() calls validation, etc
unittest-debug: build
	@echo "I: Running unittests with debug output. No progress output."
	@PYTHONPATH=.:$(PYTHONPATH) MVPA_DEBUG=.* MVPA_DEBUG_METRICS=ALL \
       python mvpa/tests/main.py 2>&1 \
       |  sed -n -e '/^[=-]\{60,\}$$/,/^\(MVPA_SEED=\|OK\)/p'


# Run all unittests
#  Run with 'make -k' if you like to sweep through all of them, so
#  failure in one of them does not stop the full sweep
unittests: unittest-nonlabile unittest unittest-badexternals \
           unittest-optimization unittest-states unittest-debug

te-%: build
	@echo -n "I: Testing example $*: "
	@MVPA_EXAMPLES_INTERACTIVE=no PYTHONPATH=.:$(PYTHONPATH) MVPA_MATPLOTLIB_BACKEND=agg \
	 python doc/examples/$*.py >| temp-$@.log 2>&1 \
	 && echo "passed" || { echo "failed:"; cat temp-$@.log; }
	@rm -f temp-$@.log

testexamples: te-svdclf te-smlr te-searchlight_2d te-sensanas te-pylab_2d \
              te-curvefitting te-projections te-kerneldemo te-clfs_examples \
              te-erp_plot te-match_distribution te-permutation_test \
              te-searchlight_minimal te-smlr te-start_easy te-topo_plot

tm-%: build
	PYTHONPATH=.:$(PYTHONPATH) nosetests --with-doctest --doctest-extension .rst \
	                       --doctest-tests doc/$*.rst

testmanual: build
	@echo "I: Testing code samples found in documentation"
	@PYTHONPATH=.:$(PYTHONPATH) MVPA_MATPLOTLIB_BACKEND=agg \
	 nosetests --with-doctest --doctest-extension .rst --doctest-tests doc/

# Check if everything (with few exclusions) is imported in unitests is
# known to the mvpa.suite()
testsuite:
	@echo "I: Running full testsuite"
	@git grep -h '^\W*from mvpa.*import' mvpa/tests | \
	 sed -e 's/^.*from *\(mvpa[^ ]*\) im.*/from \1 import/g' | \
	 sort | uniq | \
	 grep -v -e 'mvpa\.base\.dochelpers' \
			 -e 'mvpa\.\(tests\|support\)' \
			 -e 'mvpa\.misc\.args' | \
	while read i; do \
	 grep -q "^ *$$i" mvpa/suite.py || \
	 { echo "E: '$$i' is missing from mvpa.suite()"; exit 1; }; \
	 done

# Check if links to api/ within documentation are broken.
testapiref: apidoc
	@for tf in doc/*.rst; do \
	 out=$$(for f in `grep api/mvpa $$tf | sed -e 's|.*\(api/mvpa.*html\).*|\1|g' `; do \
	  ff=build/html/$$f; [ ! -f $$ff ] && echo "E: $$f missing!"; done; ); \
	 [ "x$$out" == "x" ] || echo -e "$$tf:\n$$out"; done

# Check if there is no WARNINGs from sphinx
testsphinx: htmldoc
	{ grep -A1 system-message build/html/modref/*html && exit 1 || exit 0 ; }

# Check if stored cfg after whole suite is imported is safe to be
# reloaded
testcfg: build
	@echo "I: Running test to check that stored configuration is acceptable."
	-@rm -f pymvpa.cfg
	@PYTHONPATH=.:$(PYTHONPATH)	python -c 'from mvpa.suite import *; cfg.save("pymvpa.cfg");'
	@PYTHONPATH=.:$(PYTHONPATH)	python -c 'from mvpa.suite import *;'
	@echo "+I: Run non-labile testing to verify safety of stored configuration"
	@PYTHONPATH=.:$(PYTHONPATH) MVPA_TESTS_LABILE=no python mvpa/tests/main.py
	@echo "+I: Check all known dependencies and store them"
	@PYTHONPATH=.:$(PYTHONPATH)	python -c \
	  'from mvpa.suite import *; mvpa.base.externals.testAllDependencies(force=False); cfg.save("pymvpa.cfg");'
	@echo "+I: Run non-labile testing to verify safety of stored configuration"
	@PYTHONPATH=.:$(PYTHONPATH) MVPA_TESTS_LABILE=no python mvpa/tests/main.py
	-@rm -f pymvpa.cfg

test: unittests testmanual testsuite testapiref testexamples testcfg

# Target to be called after some major refactoring
# It skips some flavors of unittests
testrefactor: unittest testmanual testsuite testapiref testexamples

coverage: $(COVERAGE_REPORT)
$(COVERAGE_REPORT): build
	@echo "I: Generating coverage data and report. Takes awhile. No progress output."
	@{ \
	  export PYTHONPATH=.:$(PYTHONPATH) MVPA_DEBUG=.* MVPA_DEBUG_METRICS=ALL; \
	  python-coverage -x mvpa/tests/main.py >/dev/null 2>&1; \
	  python-coverage -r -i -o /usr,/var >| $(COVERAGE_REPORT); \
	  grep -v '100%$$' $(COVERAGE_REPORT); \
	  python-coverage -a -i -o /usr,/var ; }


#
# Sources
#

pylint:
	pylint -e --rcfile doc/misc/pylintrc mvpa

#
# Generate new source distribution
# (not to be run by users, depends on debian environment)

orig-src: distclean debian-clean 
	# clean existing dist dir first to have a single source tarball to process
	-rm -rf dist

	if [ -f debian/changelog ]; then \
		if [ ! "$$(dpkg-parsechangelog | egrep ^Version | cut -d ' ' -f 2,2 | cut -d '-' -f 1,1)" == "$$(python setup.py -V)" ]; then \
				printf "WARNING: Changelog version does not match tarball version!\n" ;\
				exit 1; \
		fi \
	fi
	# let python create the source tarball
	# enable libsvm to get all sources!
	python setup.py sdist --formats=gztar --with-libsvm
	# rename to proper Debian orig source tarball and move upwards
	# to keep it out of the Debian diff
	file=$$(ls -1 dist); ver=$${file%*.tar.gz}; ver=$${ver#pymvpa-*}; mv dist/$$file ../pymvpa_$$ver.orig.tar.gz
	# clean leftover
	rm MANIFEST

# make Debian source package
# # DO NOT depend on orig-src here as it would generate a source tarball in a
# Debian branch and might miss patches!
debsrc:
	cd .. && dpkg-source -i'\.(gbp.conf|git\.*)' -b $(CURDIR)


bdist_rpm: 3rd
	python setup.py bdist_rpm --with-libsvm \
	  --doc-files "doc data" \
	  --packager "PyMVPA Authors <pkg-exppsy-pymvpa@lists.alioth.debian.org>" \
	  --vendor "PyMVPA Authors <pkg-exppsy-pymvpa@lists.alioth.debian.org>"

# build MacOS installer -- depends on patched bdist_mpkg for Leopard
bdist_mpkg: 3rd
	python tools/mpkg_wrapper.py setup.py build_ext
	python tools/mpkg_wrapper.py setup.py install


#
# Data
#

fetch-data:
	rsync $(RSYNC_OPTS) $(DATA_URI) .

# Various other data which might be sensitive and not distribu
fetch-data-nonfree: fetch-data-nonfree-stamp
fetch-data-nonfree-stamp:
	@mkdir -p temp
# clean up previous location to make sure we don't have it
	@rm -f data/nonfree/audio/Peter_Nalitch-Guitar.mp3
# remove directories which should be bogus now
	@rmdir data/nonfree/audio data/nonfree 2>/dev/null || :
	rsync $(RSYNC_OPTS) dev.pymvpa.org:/home/data/nonfree temp/ && touch $@


#
# Various sugarings (e.g. swarm)
#

AUDIO_TRACK=temp/nonfree/audio/Peter_Nalitch-Guitar.mp3

# With permission of the author, we can use Gitar for our visual history
$(AUDIO_TRACK): fetch-data-nonfree

# Nice visual git log
# Requires: sun-java5-jdk, ffmpeg, ant
codeswarm: $(SWARM_DIR)/pymvpa-codeswarm.flv
$(SWARM_DIR)/frames: $(SWARMTOOL_DIR) $(SWARM_DIR)/git.xml
	@echo "I: Visualizing git history using codeswarm"
	@mkdir -p $(SWARM_DIR)/frames
	cd $(SWARMTOOL_DIR) && ./run.sh ../../doc/misc/codeswarm.config

$(SWARM_DIR)/pymvpa-codeswarm.flv: $(SWARM_DIR)/frames $(AUDIO_TRACK)
	@echo "I: Generating codeswarm video"
	@cd $(SWARM_DIR) && \
     ffmpeg -r $$(echo "scale=2; $$(ls -1 frames/ |wc -l) / 154" | bc) -f image2 \
      -i frames/code_swarm-%05d.png -r 15 -b 250k \
      -i ../../$(AUDIO_TRACK) -ar 22050 -ab 128k -acodec libmp3lame \
      -ac 2 pymvpa-codeswarm.flv

$(SWARM_DIR)/git.log:
	@echo "I: Dumping git log in codeswarm preferred format"
	@mkdir -p $(SWARM_DIR)
	@git log --name-status \
     --pretty=format:'%n------------------------------------------------------------------------%nr%h | %ae | %ai (%aD) | x lines%nChanged paths:' | \
     sed -e 's,[a-z]*@onerussian.com,Yarik,g' \
         -e 's,\(michael\.*hanke@\(gmail.com\|mvpa1.dartmouth.edu\)\|neukom-data@neukom-data-desktop\.(none)\),Michael,g' \
         -e 's,\(per@parsec.Princeton.EDU\|per@sync.(none)\|psederberg@gmail.com\),Per,g' \
         -e 's,emanuele@relativita.com,Emanuele,g' \
         -e 's,jhughes@austin.cs.dartmouth.edu,James,g' \
         -e 's,valentin.haenel@gmx.de,Valentin,g' \
         -e 's,Ingo.Fruend@gmail.com,Ingo,g' >| $@

$(SWARM_DIR)/git.xml: $(SWARMTOOL_DIR) $(SWARM_DIR)/git.log
	@python $(SWARMTOOL_DIR)/convert_logs/convert_logs.py \
	 -g $(SWARM_DIR)/git.log -o $(SWARM_DIR)/git.xml

$(SWARMTOOL_DIR):
	@echo "I: Checking out codeswarm tool source code"
	@svn checkout http://codeswarm.googlecode.com/svn/trunk/ $(SWARMTOOL_DIR)


upload-codeswarm: codeswarm
	rsync -rzhvp --delete --chmod=Dg+s,g+rw $(SWARM_DIR)/*.flv $(WWW_UPLOAD_URI)/files/


#
# Trailer
#

.PHONY: fetch-data debsrc orig-src pylint apidoc pdfdoc htmldoc doc manual \
        all profile website fetch-data-misc upload-website \
        test testsuite testmanual testapiref testexamples testrefactor \
        unittest unittest-debug unittest-optimization unittest-nonlabile \
        unittest-badexternals unittests \
        distclean debian-clean \
        handbook codeswarm upload-codeswarm coverage