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lipase/Makefile

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Replaced bash scripts with makefile. The resulting system is clearer and more generic (easier to change location of fiji or root images, as it is now located in one single place : the makefile). Some actions such as the installation of fiji are left as scripts outside the makefile.
2019-10-04 11:36:53 +02:00
SHELL:=/bin/bash
FIJI_ROOT_PATH:=~/soft/Fiji.app
FIJI_EXE_PATH=$(FIJI_ROOT_PATH)/ImageJ-linux64
# RAW_IMAGES_ROOT_PATH:='/opt/ipr/cluster/work.global/graffy/jenkins-store/lipase/raw-images'
RAW_IMAGES_ROOT_PATH:=$(shell echo ~/work/lipase/raw-images)
LIB_SRC_FILES=$(shell find ./src/lipase -name "*.py")
added dummy program to test jenkins
2019-03-07 10:32:23 +01:00
Replaced bash scripts with makefile. The resulting system is clearer and more generic (easier to change location of fiji or root images, as it is now located in one single place : the makefile). Some actions such as the installation of fiji are left as scripts outside the makefile.
2019-10-04 11:36:53 +02:00
.PHONY: all
all: test0001
added basic jenkins file to automate the build of hello
2019-03-07 10:56:01 +01:00
Replaced bash scripts with makefile. The resulting system is clearer and more generic (easier to change location of fiji or root images, as it is now located in one single place : the makefile). Some actions such as the installation of fiji are left as scripts outside the makefile.
2019-10-04 11:36:53 +02:00
$(FIJI_ROOT_PATH)/jars/Lib/fr.univ-rennes1.ip.lipase.lib.jar: $(LIB_SRC_FILES)
pushd ./src; \
mkdir -p $(FIJI_ROOT_PATH)/jars/Lib ; \
find ./lipase -name "*.py" > /tmp/files.txt ; \
jar cvf $(FIJI_ROOT_PATH)/jars/Lib/fr.univ-rennes1.ip.lipase.lib.jar @/tmp/files.txt ; \
popd
.PHONY: install_lipase_libs
install_lipase_libs: $(FIJI_ROOT_PATH)/jars/Lib/fr.univ-rennes1.ip.lipase.lib.jar
.PHONY: install_lipase_plugins
install_lipase_plugins:
mkdir -p $(FIJI_ROOT_PATH)/plugins/Ipr ; \
rsync -a ./src/ij-plugins/Ipr/ $(FIJI_ROOT_PATH)/plugins/Ipr/
.PHONY: install
install: install_lipase_libs install_lipase_plugins
.PHONY: test0001
test0001: install
# on macosx : /Applications/Fiji.app/Contents/MacOS/ImageJ-macosx --ij2 --headless --run './test0001.py'
# /Applications/Fiji.app/Contents/MacOS/ImageJ-macosx --ij2 --headless --run './tests/test0001.py' "lipase_src_root_path='$(pwd)',raw_images_root_path='/Users/graffy/ownCloud/ipr/lipase/raw-images'"
fixes to continuous integration 1. I forgot to specify fiji and raw data locations in jenkinsfile 2. the absence of fiji wasn't detected by the test
2019-10-04 11:47:34 +02:00
echo 2 > '/tmp/test_result.txt' ; \
$(FIJI_EXE_PATH) --ij2 --headless --run './tests/test0001.py' "raw_images_root_path='$(RAW_IMAGES_ROOT_PATH)'" ; \
Replaced bash scripts with makefile. The resulting system is clearer and more generic (easier to change location of fiji or root images, as it is now located in one single place : the makefile). Some actions such as the installation of fiji are left as scripts outside the makefile.
2019-10-04 11:36:53 +02:00
ERROR_CODE=$$? ; \
echo "Fiji 's return code : $$ERROR_CODE" ; \
ERROR_CODE=$$(cat '/tmp/test_result.txt') ; \
echo "test's return code : $$ERROR_CODE" ; \
exit $$ERROR_CODE
.PHONY: test
test: test0001