Work on install script

.gitignore

@@ -3,3 +3,4 @@ __pycache__
 *.so
 *.bak
 package/
+src/msspec/results.txt

CI/CI.bash

@@ -51,52 +51,26 @@ activate_msspec_python3_virtualenv() {
 }
 
 
-make_pymsspec_package() {
-	echo "Running setuptools for pymsspec, please wait... "
-	VERSION=$(get_package_version)
-	DEST=${TOPLEVEL}/install_resources/packages/${VERSION}
-	mkdir -p $DEST
-	cd ${TOPLEVEL}/src/python/pymsspec && python setup.py sdist 2>&1 > /dev/null
-	cp ${TOPLEVEL}/src/python/pymsspec/dist/pymsspec-${VERSION}.tar.gz ${DEST}/
-	rm -rf ${TOPLEVEL}/src/python/pymsspec/{*.egg-info,dist}
-}
-
-
 make_pybinding() {
 	echo "Creating Python library for Fortran code, please wait... "
-	activate_msspec_python3_virtualenv
+	activate_msspec_python3_virtualenv "$1"
-	cd ${TOPLEVEL}/src/ && make pybinding
+	cd ${TOPLEVEL}/src/ 
+	make pybinding || exit 1
 }
 
 
 make_selfex() {
 	echo "Creating the self-extractible setup program... "
-	VERSION=$(get_package_version)
+	cd ${TOPLEVEL}
-	DEST=${TOPLEVEL}/install_resources/packages/${VERSION}
+        make selfex || exit 1
-	LICENSE="${TOPLEVEL}/src/CI/license.txt"
+        mv pymsspec-${VERSION}.setup package/
-	REQUIREMENTS="${TOPLEVEL}/src/CI/requirements"
-	SETUPFILE="MsSpec-${VERSION}.setup"
-	MAKESELF=${TOPLEVEL}/src/CI/makeself/makeself.sh
-	#pip freeze > "${REQUIREMENTS}"
-	mkdir -p $DEST
-	cp "${TOPLEVEL}/src/CI/install.sh" "${DEST}"
-	chmod u+x "${DEST}/install.sh"
-	cp "${TOPLEVEL}/src/CI/uninstall.sh" "${DEST}"
-	cp "${TOPLEVEL}/src/CI/msspec" "${DEST}"
-	cp "${TOPLEVEL}/src/CI/requirements" "${DEST}"
-	cp "${TOPLEVEL}/src/CI/distro-requirements" "${DEST}"
-	get_makeself
-	cd "${DEST}/../" && ${MAKESELF} --license ${LICENSE} --quiet ${VERSION} ${SETUPFILE} "MsSpec - pymsspec"  ./install.sh
-	rm -rf ${SETUPFILE}.bak
-	rm -rf "${DEST}"
-	#rm -rf "${REQUIREMENTS}"
 }
 
 make_pdf() {
     DEST=${TOPLEVEL}/package
     mkdir -p ${DEST}
     # first activate the virtual environment
-    activate_msspec_python3_virtualenv
+    activate_msspec_python3_virtualenv "$1"
     # then build the documentation.
     cd "${TOPLEVEL}/doc"
     make --no-print-directory latexpdf || exit 1
@@ -107,9 +81,9 @@ make_pdf() {
 }
 
 make_html () {
-    make_pdf
+    make_pdf "$1"
     # first activate the virtual environment
-    activate_msspec_python3_virtualenv
+    activate_msspec_python3_virtualenv "$1"
     # then build the documentation.
     cd "${TOPLEVEL}/doc"
     make --no-print-directory html || exit 1
@@ -117,33 +91,23 @@ make_html () {
 
 make_tests() {
     echo "generate results for unit tests..."
-    activate_msspec_python3_virtualenv
+    activate_msspec_python3_virtualenv "$1"
-    python -c "from msspec.tests import create_tests_results; create_tests_results()"
+    make_pybinding
+    python -c "from msspec.tests import create_tests_results; create_tests_results()" || exit 1
 }
 
 
 create_package() {
-    VENV_PATH="$1"
+    echo "Creating the package..."
-    source "$VENV_PATH/bin/activate"
+    #make_tests "$1"
-
+    make_selfex "$1"
-    #update_version
+    cleanup
-    #make_tests
-    #make_pdf
-    #make_pymsspec_package
-    #make_msspecgui_package
-    #make_fortran_package
-    #make_selfex
-    #cleanup
-    
-    deactivate
 }
 
 cleanup() {
     echo "cleaning up..."
    # remove results.txt file
-    python -c "from msspec.tests import delete_results_file; delete_results_file()"
+    rm -rf ${TOPLEVEL}/src/msspec/results.txt
-    VERSION=$(get_package_version)
-    rm -f ${TOPLEVEL}/guide/MsSpec-${VERSION}.pdf
 }
 
 show_help () {
@@ -158,13 +122,15 @@ show_help () {
 
 if [ "$sourced" == 0 ]; then
 
-	while getopts "hi:dt" option; do
+	while getopts "hi:d:t:p:" option; do
 	    case $option in
 		i) setup_virtualenv "$OPTARG"
 		   ;;
-		d) make_html
+		d) make_html "$OPTARG"
 		   ;;
-		t) make_tests
+		t) make_tests "$OPTARG"
+		   ;;
+		p) create_package "$OPTARG"
 		   ;;
 		h) show_help
 		   ;;

Jenkinsfile

@@ -4,7 +4,38 @@ pipeline {
         stage('Initial setup...') {
             steps {
                 echo 'Create or update the virtual Python environment'
+		sh '/bin/bash ./CI/CI.bash -i ci_venv'
             }
         }
+
+        stage('Testing the package...') {
+            steps {
+                sh '/bin/bash ./CI/CI.bash -t ci_venv'
+            }
+        }
+        stage('Creatin a setup file and test installation...') {
+            steps {
+                sh '/bin/bash ./CI/CI.bash -p ci_venv'
+                sh '/bin/bash ./package/MsSpec*.setup --accept -- -p ./ci_venv -y'
+            }
+        }
+        stage('Building HTML documentation...') {
+            steps {
+                sh '/bin/bash ./CI/CI.bash -d ci_venv'
+            }
+        }
+        stage('Syncing website...') {
+            steps {
+                echo 'Updating the website files'
+            }
+        }
+        stage('Cleaning up...') {
+            steps {
+                echo 'Cleaning artifacts...'
+                sh 'rm -rf ./package'
+                sh 'cd ./doc && make clean'
+            }
+        }
+
     }
 }

Makefile

@@ -1,16 +1,16 @@
 MAKESELF:=makeself
-LICENSE:=$(shell cat ./license.txt)
+#LICENSE:=$(cat ./license.txt)
 #VERSION:=$(shell cd src && python -c "import msspec; print(msspec.__version__)")
 VERSION:=$(shell git describe|sed 's/-\([[:digit:]]\+\)-.*/\.post\1/')
-SETUPFILE:=pymsspec-$(VERSION).setup
+SETUPFILE:=MsSpec-$(VERSION).setup
 
-.PHONY: clean purge version
+.PHONY: clean purge version selfex
 
 
 clean:
 	@echo "Cleaning all..."
-	@find ./src -type f -name '*.pyc' -exec rm {} +
+	@find ./src -type f -name '*.pyc' -exec rm -f {} +
-	@find ./src -type d -name '__pycache__' -exec rm -r {} +
+	@find ./src -type d -name '__pycache__' -exec rm -rf {} +
 	+$(MAKE) -C src/ clean
 	+$(MAKE) -C doc/ clean
 
@@ -23,27 +23,27 @@ purge: clean
 	@rm -rf *.setup
 	+$(MAKE) -C src/ purge
 
-selfex: purge
+selfex:
 	@echo "Creating the self-extractible setup program... "
 	# update the version
 	@cp ./src/msspec/version.py ./src/msspec/version.py.bak
 	@echo "__version__ = \"$(VERSION)\"" > ./src/msspec/version.py
 	# create the *.lsm file
-	@echo "Begin4" > pymsspec.lsm
+	@echo "Begin4" > msspec.lsm
-	@echo "Title: Python MsSpec" >> pymsspec.lsm
+	@echo "Title: Python MsSpec" >> msspec.lsm
-	@echo "Version: $(VERSION)" >> pymsspec.lsm
+	@echo "Version: $(VERSION)" >> msspec.lsm
-	@echo "Entered-date: `date +%Y-%m-%d`" >> pymsspec.lsm
+	@echo "Entered-date: `date +%Y-%m-%d`" >> msspec.lsm
-	@echo "Description: A multiple scattering package for spectroscopies using electrons to probe materials" >> pymsspec.lsm
+	@echo "Description: A multiple scattering package for spectroscopies using electrons to probe materials" >> msspec.lsm
-	@echo "Keywords: " >> pymsspec.lsm
+	@echo "Keywords: " >> msspec.lsm
-	@echo "Author: sylvain.tricot@univ-rennes1.fr (Sylvain Tricot), didier.sebilleau@univ-rennes1.fr (Didier Sébilleau)" >> pymsspec.lsm
+	@echo "Author: sylvain.tricot@univ-rennes1.fr (Sylvain Tricot), didier.sebilleau@univ-rennes1.fr (Didier Sébilleau)" >> msspec.lsm
-	@echo "Maintained-by: sylvain.tricot@univ-rennes1.fr (Sylvain Tricot)" >> pymsspec.lsm
+	@echo "Maintained-by: sylvain.tricot@univ-rennes1.fr (Sylvain Tricot)" >> msspec.lsm
-	@echo "Primary-site: https://msspec.cnrs.fr" >> pymsspec.lsm
+	@echo "Primary-site: https://msspec.cnrs.fr" >> msspec.lsm
-	@echo "Alternate-site:" >> pymsspec.lsm
+	@echo "Alternate-site:" >> msspec.lsm
-	@echo "Original-site:" >> pymsspec.lsm
+	@echo "Original-site:" >> msspec.lsm
-	@echo "Platforms:" >> pymsspec.lsm
+	@echo "Platforms:" >> msspec.lsm
-	@echo "Copying-policy: Gnu Library General Public License (GLPL) 2.0" >> pymsspec.lsm
+	@echo "Copying-policy: Gnu Library General Public License (GLPL) 2.0" >> msspec.lsm
-	@echo "End" >> pymsspec.lsm
+	@echo "End" >> msspec.lsm
-	$(MAKESELF) --license ./license.txt --lsm ./pymsspec.lsm ./src $(SETUPFILE) "Python MsSpec"  ./install.sh
+	$(MAKESELF) --license "./license.txt" --lsm ./msspec.lsm ./src $(SETUPFILE) "Python MsSpec"  ./install.sh
 	@mv ./src/msspec/version.py.bak ./src/msspec/version.py
-	@rm ./pymsspec.lsm
+	@rm ./msspec.lsm
 

src/MANIFEST.in

@@ -1,2 +1,3 @@
 include msspec/spec/*.so
 include msspec/phagen/*.so
+include msspec/results.txt

src/install.sh

@@ -1,17 +1,16 @@
 #!/bin/bash
 # vim: set ts=4 sw=4 sts noet mouse=a fdm=indent:
 
-SCRIPT_NAME=$(basename "$0")
-PYTHON=python3
-VERSION=$(cat ./msspec/version.py|cut -d\" -f2)
 DEFAULT_DEST="${HOME}/.local/share"
 DEFAULT_BIN="${HOME}/.local/bin"
 BYPASS="n"
 DEBUG="n"
-TIMEOUT=0
+
+SCRIPT_NAME=$(basename "$0")
+PYTHON=python3
+VERSION=$(cat ./msspec/version.py|cut -d\" -f2)
+TIMEOUT=5
 DEST_ALREADY_EXISTS="n"
-
-
 ECHO="/bin/echo -e"
 DATE=$(date +%Y%m%d_%H%M%S)
 LOGFILE="${HOME}/msspec_install_${DATE}.log"
@@ -29,7 +28,6 @@ init_install () {
 	get_os
 
 	if [ "$BYPASS" = "n" ]; then
-		${ECHO} "Thanks for choosing MsSpec"
 		${ECHO} ""
 		${ECHO} "This program will install the MsSpec distribution on your computer"
 		${ECHO} -n "Press C^c to cancel now...  "
@@ -73,6 +71,9 @@ error_exit () {
 	printf "\n"
 	tail -v -n 10 "${LOGFILE}"
 
+	# uninstall if needed
+	pip uninstall -y msspec
+
 	# if the DEST_FOLDER existed before, do NOT delete it
 	if [ x"$DEST_ALREADY_EXISTS" = "xn" ]; then
 		rm -rf ${DEST_FOLDER} 2>/dev/null
@@ -238,21 +239,66 @@ show_help () {
     echo "    -d          Debug mode."
     echo "    -h          Show this message."
 	exit 0
-}                                                                                  
+}
+
+
+check_dependencies () {
+	# we need make
+	log_message "Checking if make is installed..."
+	command -V make || return 1
+	log_message "Ok\n"
+
+	# we need gfortran
+    gcc_ver_min=7
+	log_message "Checking if gfortran >= $gcc_ver_min is installed..."
+	command -V gfortran || return 1
+	gcc_ver=$(gcc -dumpversion)
+	echo "You have gfortran version $gcc_ver installed"
+    test $gcc_ver -ge $gcc_ver_min || return 1
+	log_message "Ok\n"
+
+	# we need libcairo and dev files
+	log_message "Checking if libcairo is installed..."
+	pkg-config --exists cairo || return 1
+	log_message "Ok\n"
+
+	# we need Python 3
+	py_ver_major_min=3
+	py_ver_minor_min=0
+	log_message "Checking if Python >= ${py_ver_major_min}.${py_ver_minor_min}..."
+	message="You need Python version ${py_ver_major_min}.${py_ver_minor_min}"
+    python --version|cut -d" " -f2 || return 1
+    py_ver=$(python --version | cut -d" " -f2)
+	echo "You have Python version $py_ver installed"
+	py_ver_major=$(echo $py_ver|cut -d. -f1)
+	py_ver_minor=$(echo $py_ver|cut -d. -f2)
+	test $py_ver_major -ge $py_ver_major_min || return 1
+	test $py_ver_minor -ge $py_ver_minor_min || return 1
+	log_message "Ok\n"
+
+	# we need virtualenv
+	log_message "Checking if virtualenv is installed..."
+	command -V virtualenv || return 1
+	log_message "Ok\n"
+	
+}
 
 local_install () {
 	# Initialize the install process
 	init_install
 
+	# check dependencies
+	wrap "check_dependencies" "Checking dependencies"
+
 	# ask for a place to put the binary
-	read_folder "Please, type in the folder where to place the binary" "${DEFAULT_BIN}"
+	#read_folder "Please, type in the folder where to place the binary" "${DEFAULT_BIN}"
-	BIN_FOLDER=${FOLDER}
+	#BIN_FOLDER=${FOLDER}
-	create_folder "${BIN_FOLDER}" || error_exit
+	#create_folder "${BIN_FOLDER}" || error_exit
-	export BIN_FOLDER
+	#export BIN_FOLDER
 
 	# If in a virtualenv, ask if we should install inside
 	if [ x"$VIRTUAL_ENV" != x ]; then
-		read_yes_no "You are running a Python virtual environment.\ Do you wish to install msspec inside ?" "y"
+		read_yes_no "You are running a Python virtual environment. Do you wish to install msspec inside ?" "y"
 		case ${ANSWER} in
 			y)	# get the python version of this venv...
 				v=$(python -V 2>&1 | cut -d" " -f2 | cut -d. -f1)
@@ -318,6 +364,14 @@ local_install () {
 ## move the uninstal script
 #wrap "cp ./uninstall.sh ${DEST}" "Moving the uninstall script"
 #
+	# Run unit tests ?
+	read_yes_no "Do you wish to run unit tests (${LOGFILE})" "y"
+	if [ x"${ANSWER}" = "xy" ]; then
+    	wrap "python -c \"from msspec.tests import run_tests; run_tests()\"" \
+             "Runing test suite"
+	fi
+
+
 	# installation was a succes so ask if we keep the log file
 	read_yes_no "Do you wish to keep the log file (${LOGFILE})" "n"
 	if [ x"${ANSWER}" = "xn" ]; then

src/msspec/spec/fortran/main.f

@@ -16,6 +16,5 @@ CF2PY   INTEGER, INTENT(IN,COPY) :: N_TILT_M_, N_ORD_M_, NPATH_M_, NGR_M_
      &  N_TILT_M_, N_ORD_M_, NPATH_M_, NGR_M_)
 
         CALL DO_MAIN()
-        PRINT *, "BEFORE END IN SPEC"
 
       END SUBROUTINE RUN

src/msspec/tests.py

@@ -121,7 +121,8 @@ def run_tests():
     suite.addTest(PEDCopperTestCase('test_theta_scan'))
     runner = unittest.TextTestRunner(verbosity=2)
     rc = runner.run(suite)
-    exit(rc)
+    #print("rc = ", rc)
+    exit(not(rc.wasSuccessful()))
 
 def create_tests_results():
     with open(RESULTS_FILENAME, 'w') as fd: