Makefile 4.43 KB
Newer Older
Mikaël Salson's avatar
Mikaël Salson committed
1

2
COVERAGE=
Mathieu Giraud's avatar
Mathieu Giraud committed
3 4 5
VIDJIL_ALGO_SRC = algo/
VIDJIL_SERVER_SRC = server/

6
ifeq (${COVERAGE},1)
7
	COVERAGE_OPTION=-O0 --coverage
8 9 10 11
else
	COVERAGE_OPTION=
endif

Mikaël Salson's avatar
Mikaël Salson committed
12
all:
13
	make COVERAGE="$(COVERAGE_OPTION)" -C $(VIDJIL_ALGO_SRC)
Mikaël Salson's avatar
Mikaël Salson committed
14

15
test:
16
	make COVERAGE="$(COVERAGE)" unit
17 18 19 20
	make should
	# make pytests

test_with_fuse:
21
	make COVERAGE="$(COVERAGE)" unit
Mikaël Salson's avatar
Mikaël Salson committed
22
	make should
23
	make pytests
Mikaël Salson's avatar
Mikaël Salson committed
24

25 26
test_browser: unit_browser functional_browser

27

28 29
unit: all
	@echo "*** Launching unit tests..."
30
	make COVERAGE="$(COVERAGE_OPTION)" -C $(VIDJIL_ALGO_SRC)/tests
31
	@echo "*** All unit tests passed"
32

33 34
pytests:
	@echo "*** Launching python tests..."
35
	python tools/fuse.py --test x
36
	@echo "*** All python tests passed"
Mathieu Giraud's avatar
Mathieu Giraud committed
37

Mikaël Salson's avatar
Mikaël Salson committed
38 39 40
should: all
	@echo
	@echo "*** Launching .should_get tests..."
41
	make COVERAGE="$(COVERAGE_OPTION)" -C $(VIDJIL_ALGO_SRC)/tests should
Mikaël Salson's avatar
Mikaël Salson committed
42 43
	@echo "*** All .should_get tests passed"

44 45 46 47 48 49 50 51 52
unit_browser:
	make -C browser/test unit

functional_browser:
	make -C browser/test functional

headless_browser:
	make -C browser/test headless

53 54
### Code coverage

55 56 57 58 59 60
coverage: unit_coverage should_coverage

unit_coverage: clean
	make COVERAGE=1 unit
should_coverage: clean
	make COVERAGE=1 should
61 62 63 64

### Reports with gcovr

unit_gcovr: unit_coverage
65
	mkdir -p reports
66
	which gcovr > /dev/null && (cd algo;  gcovr -r . -e tests/ --xml > ../reports/unit_coverage.xml) || echo "gcovr is needed to generate a full report"
67
should_gcovr: should_coverage
68
	mkdir -p reports
69
	which gcovr > /dev/null && (cd algo; gcovr -r . -e tests/ --xml > ../reports/should_coverage.xml) || echo "gcovr is needed to generate a full report"
70

71 72 73
### Upload to coveralls.io

unit_coveralls:
74
	coveralls --exclude release --exclude algo/lib --exclude algo/tests --exclude algo/tools --exclude tests --exclude tools --exclude lib --gcov-options '\-lp'
75
should_coveralls:
76
	coveralls --exclude release --exclude algo/lib --exclude algo/tests --exclude algo/tools --exclude tests --exclude tools --exclude lib --gcov-options '\-lp' -r algo
77

78 79 80 81 82 83 84 85 86

### cppcheck

cppcheck:
	mkdir -p reports
	cppcheck --enable=all --xml . 2>! reports/cppcheck.xml

###

Mikaël Salson's avatar
Mikaël Salson committed
87 88 89 90
data germline: %:
	make -C $@

clean:
Mathieu Giraud's avatar
Mathieu Giraud committed
91
	make -C $(VIDJIL_ALGO_SRC) clean
Mikaël Salson's avatar
Mikaël Salson committed
92 93 94 95 96

cleanall: clean
	make -C data $^
	make -C germline $^

97
.PHONY: all test should clean cleanall distrib data germline unit_coverage should_coverage coverage
Mikaël Salson's avatar
Mikaël Salson committed
98 99

RELEASE_TAG="notag"
Mathieu Giraud's avatar
Mathieu Giraud committed
100
RELEASE_H = $(VIDJIL_ALGO_SRC)/release.h
101 102
RELEASE_SOURCE = $(wildcard $(VIDJIL_ALGO_SRC)/*.cpp) $(wildcard $(VIDJIL_ALGO_SRC)/*.h)  $(wildcard $(VIDJIL_ALGO_SRC)/core/*.cpp)  $(wildcard $(VIDJIL_ALGO_SRC)/tests/*.cpp) $(wildcard $(VIDJIL_ALGO_SRC)/core/*.h)  $(wildcard $(VIDJIL_ALGO_SRC)/tests/*.h)  $(wildcard $(VIDJIL_ALGO_SRC)/cgi/*.cpp) $(wildcard $(VIDJIL_ALGO_SRC)/lib/*.cpp) $(wildcard $(VIDJIL_ALGO_SRC)/lib/*.h)
RELEASE_MAKE = ./Makefile  $(VIDJIL_ALGO_SRC)/Makefile  $(VIDJIL_ALGO_SRC)/core/Makefile $(VIDJIL_ALGO_SRC)/tests/Makefile $(VIDJIL_ALGO_SRC)/lib/Makefile germline/Makefile data/Makefile
103
RELEASE_TESTS =  data/get-sequences $(wildcard data/*.fa) $(wildcard data/*.fq) $(VIDJIL_ALGO_SRC)/tests/should-to-tap.sh $(wildcard $(VIDJIL_ALGO_SRC)/tests/*.should_get) $(wildcard $(VIDJIL_ALGO_SRC)/tests/bugs/*.fa)  $(wildcard $(VIDJIL_ALGO_SRC)/tests/bugs/*.should_get) $(VIDJIL_ALGO_SRC)/tests/format-json.sh
104 105
RELEASE_GERMLINES = germline/germline_id germline/get-saved-germline germline/get-germline germline/split-from-imgt.py
RELEASE_FILES = $(RELEASE_SOURCE) $(RELEASE_TESTS) $(RELEASE_MAKE) $(RELEASE_GERMLINES) doc/algo.org doc/LICENSE data/segmentation.fasta $(wildcard data/*.fa.gz) $(wildcard data/*.label)
Mikaël Salson's avatar
Mikaël Salson committed
106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145
RELEASE_ARCHIVE = vidjil-$(RELEASE_TAG).tgz

CURRENT_DIR = vidjil
DIST_DIR=$(CURRENT_DIR)-$(RELEASE_TAG)
RELEASE_FILES_VID = $(RELEASE_FILES)


# make distrib RELEASE_TAG=2013.04alpha
distrib:	
	$(info ==== Release $(RELEASE_TAG) ====)

	# Tag the release
	if test "$(RELEASE_TAG)" != "notag"; then \
		git tag -f release-$(RELEASE_TAG); \
		echo '#define RELEASE_TAG "$(RELEASE_TAG)"' > $(RELEASE_H); \
	fi

	mkdir -p release 
	rm -rf release/$(RELEASE_ARCHIVE) release/$(DIST_DIR)
	mkdir -p release/$(DIST_DIR)
	for file in  $(RELEASE_FILES_VID); do\
		dir=release/$(DIST_DIR)/`dirname "$$file"`;	\
		mkdir -p $$dir;	\
		cp "$$file" $$dir;	\
	done
	cd release && tar cvzf  $(RELEASE_ARCHIVE) $(DIST_DIR) \
	&& rm -rf $(DIST_DIR)

	# Untag the source
	rm -f $(RELEASE_H) ; touch $(RELEASE_H)

	# Check archive
	cd release && tar xvfz $(RELEASE_ARCHIVE)
	cd release/$(DIST_DIR) && make
	cd release/$(DIST_DIR) && make germline
	cd release/$(DIST_DIR) && make data
	cd release/$(DIST_DIR) && make test