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msspec_python3
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Work on install script

This commit is contained in:
Sylvain Tricot 2019-11-21 17:09:19 +01:00
parent 4807474889
commit 59c43395c2
8 changed files with 146 additions and 93 deletions
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1
.gitignore vendored
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@ -3,3 +3,4 @@ __pycache__
*.so
*.bak
package/
src/msspec/results.txt

78
CI/CI.bash
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@ -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
cd ${TOPLEVEL}/src/ && make pybinding
activate_msspec_python3_virtualenv "$1"
cd ${TOPLEVEL}/src/
make pybinding || exit 1
}
make_selfex() {
echo "Creating the self-extractible setup program... "
VERSION=$(get_package_version)
DEST=${TOPLEVEL}/install_resources/packages/${VERSION}
LICENSE="${TOPLEVEL}/src/CI/license.txt"
REQUIREMENTS="${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}"
cd ${TOPLEVEL}
make selfex || exit 1
mv pymsspec-${VERSION}.setup package/
}
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
python -c "from msspec.tests import create_tests_results; create_tests_results()"
activate_msspec_python3_virtualenv "$1"
make_pybinding
python -c "from msspec.tests import create_tests_results; create_tests_results()" || exit 1
}
create_package() {
VENV_PATH="$1"
source "$VENV_PATH/bin/activate"
#update_version
#make_tests
#make_pdf
#make_pymsspec_package
#make_msspecgui_package
#make_fortran_package
#make_selfex
#cleanup
deactivate
echo "Creating the package..."
#make_tests "$1"
make_selfex "$1"
cleanup
}
cleanup() {
echo "cleaning up..."
# remove results.txt file
python -c "from msspec.tests import delete_results_file; delete_results_file()"
VERSION=$(get_package_version)
rm -f ${TOPLEVEL}/guide/MsSpec-${VERSION}.pdf
rm -rf ${TOPLEVEL}/src/msspec/results.txt
}
show_help () {
@ -158,13 +122,15 @@ show_help () {
if [ "$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
;;

31
Jenkinsfile vendored
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@ -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'
}
}
}
}

44
Makefile
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@ -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 d -name '__pycache__' -exec rm -r {} +
@find ./src -type f -name '*.pyc' -exec rm -f {} +
@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 "Title: Python MsSpec" >> pymsspec.lsm
@echo "Version: $(VERSION)" >> pymsspec.lsm
@echo "Entered-date: `date +%Y-%m-%d`" >> pymsspec.lsm
@echo "Description: A multiple scattering package for spectroscopies using electrons to probe materials" >> pymsspec.lsm
@echo "Keywords: " >> pymsspec.lsm
@echo "Author: sylvain.tricot@univ-rennes1.fr (Sylvain Tricot), didier.sebilleau@univ-rennes1.fr (Didier Sébilleau)" >> pymsspec.lsm
@echo "Maintained-by: sylvain.tricot@univ-rennes1.fr (Sylvain Tricot)" >> pymsspec.lsm
@echo "Primary-site: https://msspec.cnrs.fr" >> pymsspec.lsm
@echo "Alternate-site:" >> pymsspec.lsm
@echo "Original-site:" >> pymsspec.lsm
@echo "Platforms:" >> pymsspec.lsm
@echo "Copying-policy: Gnu Library General Public License (GLPL) 2.0" >> pymsspec.lsm
@echo "End" >> pymsspec.lsm
$(MAKESELF) --license ./license.txt --lsm ./pymsspec.lsm ./src $(SETUPFILE) "Python MsSpec" ./install.sh
@echo "Begin4" > msspec.lsm
@echo "Title: Python MsSpec" >> msspec.lsm
@echo "Version: $(VERSION)" >> msspec.lsm
@echo "Entered-date: `date +%Y-%m-%d`" >> msspec.lsm
@echo "Description: A multiple scattering package for spectroscopies using electrons to probe materials" >> msspec.lsm
@echo "Keywords: " >> msspec.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)" >> msspec.lsm
@echo "Primary-site: https://msspec.cnrs.fr" >> msspec.lsm
@echo "Alternate-site:" >> msspec.lsm
@echo "Original-site:" >> msspec.lsm
@echo "Platforms:" >> msspec.lsm
@echo "Copying-policy: Gnu Library General Public License (GLPL) 2.0" >> msspec.lsm
@echo "End" >> msspec.lsm
$(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

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

78
src/install.sh
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@ -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
@ -240,19 +241,64 @@ show_help () {
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}"
BIN_FOLDER=${FOLDER}
create_folder "${BIN_FOLDER}" || error_exit
export BIN_FOLDER
#read_folder "Please, type in the folder where to place the binary" "${DEFAULT_BIN}"
#BIN_FOLDER=${FOLDER}
#create_folder "${BIN_FOLDER}" || error_exit
#export BIN_FOLDER
# If in a virtualenv, ask if we should install inside
if [ x"$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

1
src/msspec/spec/fortran/main.f
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@ -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

3
src/msspec/tests.py
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@ -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: