From 595fc095712974f0467b71639b61b47c8ed63e7a Mon Sep 17 00:00:00 2001
From: Guillaume Raffy <guillaume.raff@univ-rennes1.fr>
Date: Fri, 10 Apr 2020 15:14:33 +0200
Subject: [PATCH] moved the build files outside the repository In order to
 prevent pollution of repository with temporary files, the build files can now
 be where the user wants via BUILD_ROOT_PATH makefile variable.

---
 Jenkinsfile                         |  7 ++++---
 Makefile                            | 15 +++++++--------
 scripts/release_lipase_package.bash |  2 +-
 3 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/Jenkinsfile b/Jenkinsfile
index 29e36a9..66af9e9 100644
--- a/Jenkinsfile
+++ b/Jenkinsfile
@@ -4,6 +4,7 @@ pipeline {
         // GRAFFY_OWNCLOUD_JENKINS_PWD's value has been obtained from https://cloud.ipr.univ-rennes1.fr as an app password and is defined in gitlab as a CI secret variable,
         // then this app password has been declared to jenkins's credentials as a secret text with the name graffy-cloudipr-for-jenkinsipr
         GRAFFY_OWNCLOUD_JENKINS_PWD = credentials('graffy-cloudipr-for-jenkinsipr')
+        BUILD_ROOT_PATH = $WORKSPACE/build
     }
     stages {
         stage('Initial setup...') {
@@ -12,18 +13,18 @@ pipeline {
                 // erase old builds if anything is left
                 sh './scripts/cleanup.bash'
                 sh './scripts/install_fiji.bash'
-                sh 'make FIJI_ROOT_PATH=$(pwd)/Fiji.app install'
+                sh 'make BUILD_ROOT_PATH=$BUILD_ROOT_PATH FIJI_ROOT_PATH=$(pwd)/Fiji.app install'
             }
         }
         stage('Testing the package...') {
             steps {
-                sh 'make FIJI_ROOT_PATH=$(pwd)/Fiji.app RAW_IMAGES_ROOT_PATH=/opt/ipr/cluster/work.global/graffy/jenkins-store/lipase/raw-images TESTS_OUTPUT_DATA_PATH=$TMP/$(whoami)/$JOB_NAME test'
+                sh 'make BUILD_ROOT_PATH=$BUILD_ROOT_PATH FIJI_ROOT_PATH=$(pwd)/Fiji.app RAW_IMAGES_ROOT_PATH=/opt/ipr/cluster/work.global/graffy/jenkins-store/lipase/raw-images TESTS_OUTPUT_DATA_PATH=$TMP/$(whoami)/$JOB_NAME test'
             }
         }
         stage('Building documentation...') {
             steps {
                 echo 'Building documentation...'
-                sh 'make FIJI_ROOT_PATH=$(pwd)/Fiji.app RAW_IMAGES_ROOT_PATH=/opt/ipr/cluster/work.global/graffy/jenkins-store/lipase/raw-images doc'
+                sh 'make BUILD_ROOT_PATH=$BUILD_ROOT_PATH FIJI_ROOT_PATH=$(pwd)/Fiji.app RAW_IMAGES_ROOT_PATH=/opt/ipr/cluster/work.global/graffy/jenkins-store/lipase/raw-images doc'
             }
         }
         stage('Releasing package...') {
diff --git a/Makefile b/Makefile
index f76b2f5..42b8336 100644
--- a/Makefile
+++ b/Makefile
@@ -8,8 +8,8 @@ LIB_SRC_FILES=$(shell find ./src/lipase -name "*.py")
 PLUGINS_SRC_FILES=$(shell find ./src/ij-plugins -name "*.py")
 LIPASE_VERSION=1.01
 
-BUILD_ROOT_PATH=$(shell pwd)/build
-PACKAGE_FILE_PATH=$(shell pwd)/lipase-$(LIPASE_VERSION).zip
+BUILD_ROOT_PATH:=$(shell pwd)/build
+PACKAGE_FILE_PATH=$(BUILD_ROOT_PATH)/lipase-$(LIPASE_VERSION).zip
 
 .PHONY: all
 all: test doc
@@ -23,7 +23,7 @@ clean_doc:
 	cd doc; make clean
 
 
-$(BUILD_ROOT_PATH)/jars/Lib/fr.univ-rennes1.ipr.lipase.lib.jar: $(LIB_SRC_FILES)
+$(BUILD_ROOT_PATH)/ij_zip_source/jars/Lib/fr.univ-rennes1.ipr.lipase.lib.jar: $(LIB_SRC_FILES)
 	pushd ./src; \
 		mkdir -p $(BUILD_ROOT_PATH)/jars/Lib ; \
 		find ./lipase -name "*.py" > /tmp/files.txt ; \
@@ -71,10 +71,10 @@ install_ij_opencv:
 			$(FIJI_ROOT_PATH)/ImageJ-linux64 --update update; \
 		fi
 
-$(PACKAGE_FILE_PATH): $(BUILD_ROOT_PATH)/jars/Lib/fr.univ-rennes1.ipr.lipase.lib.jar $(PLUGINS_SRC_FILES)
-	mkdir -p $(BUILD_ROOT_PATH)/plugins/Ipr ; \
-		rsync -a ./src/ij-plugins/Ipr/ $(BUILD_ROOT_PATH)/plugins/Ipr/ ; \
-        pushd $(BUILD_ROOT_PATH) ; \
+$(PACKAGE_FILE_PATH): $(BUILD_ROOT_PATH)/ij_zip_source/jars/Lib/fr.univ-rennes1.ipr.lipase.lib.jar $(PLUGINS_SRC_FILES)
+	mkdir -p $(BUILD_ROOT_PATH)/ij_zip_source/plugins/Ipr ; \
+		rsync -a ./src/ij-plugins/Ipr/ $(BUILD_ROOT_PATH)/ij_zip_source/plugins/Ipr/ ; \
+        pushd $(BUILD_ROOT_PATH)/ij_zip_source ; \
 		zip -r $(PACKAGE_FILE_PATH) * ; \
         popd
 
@@ -127,4 +127,3 @@ test: test0001 imgproc_tests
 .PHONY: clean
 clean: clean_doc
 	rm -Rf $(BUILD_ROOT_PATH)
-	rm -Rf $(PACKAGE_FILE_PATH)
diff --git a/scripts/release_lipase_package.bash b/scripts/release_lipase_package.bash
index b1ddda1..2e49b35 100755
--- a/scripts/release_lipase_package.bash
+++ b/scripts/release_lipase_package.bash
@@ -1,5 +1,5 @@
 #!/bin/bash
-LIPASE_PACKAGE_FILE_PATH=$(ls lipase*.zip)
+LIPASE_PACKAGE_FILE_PATH=$(ls build/lipase*.zip)
 LIPASE_USER_MANUAL_PATH=$(pwd)/doc/lipase.pdf
 echo "LIPASE_PACKAGE_FILE_PATH=$LIPASE_PACKAGE_FILE_PATH"
 if [ "$GRAFFY_OWNCLOUD_JENKINS_PWD" = '' ]