Simplify code building and package creation.
This commit is contained in:
parent
e2ec1e8bcd
commit
4702d0cb0c
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@ -5,7 +5,11 @@ __pycache__
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*.mod
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*.bak
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*.target
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*.sconsign.dblite
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htmlcov
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package/
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src/msspec/results.txt
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*venv/
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**/*build/
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**/*dist/
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**/*.egg-info/
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83
Makefile
83
Makefile
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@ -1,83 +0,0 @@
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MAKESELF:=makeself
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VERSION:=$(shell git describe|sed 's/-\([[:digit:]]\+\)-.*/\.post\1/')
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SETUPFILE:=MsSpec-$(VERSION).setup
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VERBOSE:=0
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ifeq ($(VERBOSE),0)
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SUPPRESS_OUPUT:=1>/dev/null 2>/dev/null
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MAKEFLAGS += --no-print-directory
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else
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SUPPRESS_OUPUT:=
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endif
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.PHONY: clean version selfex venv doc
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selfex: results
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@echo "Creating the self-extractible setup program... "
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# copy the src folder and purge it
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@cp -r src src_
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@+$(MAKE) -C ./src_ purge
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# update the version
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@echo "$(VERSION)" > ./src_/VERSION
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# distribute the README.md file
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@cp README.md ./src_/
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# create the package folder
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@mkdir -p package
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# create the *.lsm file
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@echo "Begin4" > msspec.lsm
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@echo "Title: Python MsSpec" >> msspec.lsm
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@echo "Version: $(VERSION)" >> msspec.lsm
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@echo "Entered-date: `date +%Y-%m-%d`" >> msspec.lsm
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@echo "Description: A multiple scattering package for spectroscopies using electrons to probe materials" >> msspec.lsm
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@echo "Keywords: " >> msspec.lsm
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@echo "Author: sylvain.tricot@univ-rennes1.fr (Sylvain Tricot), didier.sebilleau@univ-rennes1.fr (Didier Sébilleau)" >> msspec.lsm
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@echo "Maintained-by: sylvain.tricot@univ-rennes1.fr (Sylvain Tricot)" >> msspec.lsm
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@echo "Primary-site: https://msspec.cnrs.fr" >> msspec.lsm
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@echo "Alternate-site:" >> msspec.lsm
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@echo "Original-site:" >> msspec.lsm
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@echo "Platforms:" >> msspec.lsm
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@echo "Copying-policy: Gnu Library General Public License (GLPL) 2.0" >> msspec.lsm
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@echo "End" >> msspec.lsm
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# create the self-extractible archive
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@$(MAKESELF) --license "./license.txt" --lsm ./msspec.lsm ./src_ package/$(SETUPFILE) "Python MsSpec" ./install.sh $(SUPPRESS_OUPUT)
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# remove *.lsm file and src_
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@rm ./msspec.lsm
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@rm -rf ./src_
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version:
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@python ./CI/update_version.py
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clean:
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@echo "Cleaning all..."
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@find ./src -type f -name '*.pyc' -exec rm -f {} +
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@find ./src -type d -name '__pycache__' -exec rm -rf {} +
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@rm -rf src/dist
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@rm -rf src/*.egg*
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@+$(MAKE) -C src/ clean $(SUPPRESS_OUPUT)
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@+$(MAKE) -C doc/ clean $(SUPPRESS_OUPUT)
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@rm -rf package
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purge: clean
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@echo "Removing also shared objects..."
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@find ./src -type f -name '*.so' -exec rm -f {} +
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results:
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@+$(MAKE) -C src results
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venv:
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@virtualenv --python=python3 --system-site-packages ci_venv $(SUPPRESS_OUPUT)
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@. "./ci_venv/bin/activate" && pip install --upgrade pip && pip install --upgrade -r requirements.txt $(SUPPRESS_OUPUT)
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doc:
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@echo "Building pdf and html documentation..."
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@mkdir -p package/
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@+$(MAKE) -C doc/ latexpdf $(SUPPRESS_OUPUT)
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@rm -rf package/*.pdf
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@cp "doc/build/latex/MsSpec-python.pdf" "./package/MsSpec-${VERSION}.pdf"
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@+$(MAKE) -C doc/ html $(SUPPRESS_OUPUT)
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@ -1,4 +1,3 @@
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recursive-include msspec *.f
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recursive-include msspec *.inc
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recursive-include msspec *.so
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recursive-include . SConstruct
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include requirements.txt
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60
src/Makefile
60
src/Makefile
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@ -1,60 +0,0 @@
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VERSION:=$(shell python -c "import msspec; print(msspec.__version__)")
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VERBOSE:=0
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ifeq ($(VERBOSE),0)
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SUPPRESS_OUPUT:=1>/dev/null 2>/dev/null
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MAKEFLAGS += --no-print-directory --silent
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else
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SUPPRESS_OUPUT:=
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endif
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install: sdist
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@echo "Installing the newly created Python package..."
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@pip install dist/msspec-*.tar.gz $(SUPPRESS_OUPUT)
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sdist: install_deps
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@echo "Creating Python source distribution..."
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# Create the source distrib
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@python setup.py sdist $(SUPPRESS_OUPUT)
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install_deps: pybinding
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@echo "Installing Python dependencies..."
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# Install dependencies with pip
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@pip install --upgrade -r requirements.txt $(SUPPRESS_OUPUT)
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pybinding:
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@echo "Building Python binding for phagen and spec..."
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@+$(MAKE) -C msspec/spec/fortran pybinding $(SUPPRESS_OUPUT)
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@+$(MAKE) -C msspec/phagen/fortran pybinding $(SUPPRESS_OUPUT)
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results: msspec/results.txt
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msspec/results.txt: pybinding
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@echo "Generating results for unittests"
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@coverage run --source=./ --omit=msspec/es/*,msspec/msspecgui/* msspec/create_tests_results.py 1>/dev/null
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# create the html coverage report
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@coverage html -d ../doc/source/htmlcov
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@rm .coverage
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tests: pybinding
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@echo "Runing unittests"
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@python -m msspec.tests 1>/dev/null
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clean:
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@echo "Cleaning all..."
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@find ./ -type f -name '*.pyc' -exec rm -f {} +
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@find ./ -type d -name '__pycache__' -exec rm -rf {} +
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@+$(MAKE) -C msspec/spec/fortran clean $(SUPPRESS_OUPUT)
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@+$(MAKE) -C msspec/phagen/fortran clean $(SUPPRESS_OUPUT)
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# remove previous sdist
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@rm -rf dist
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@rm -rf *.egg*
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purge: clean
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@echo "Removing also shared objects..."
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@find ./ -type f -name '*.so' -exec rm -f {} +
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help:
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@echo "help message"
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102
src/SConstruct
102
src/SConstruct
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@ -1,6 +1,47 @@
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from sysconfig import get_config_var
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import os
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###############################################################################
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suffix = get_config_var('EXT_SUFFIX')
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def filtered_glob(env, pattern, omit=[],
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ondisk=True, source=False, strings=False):
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return list(filter(
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lambda f: os.path.basename(f.path) not in omit,
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env.Glob(pattern)))
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# Create a builder for f2py
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def f2py_generator(source, target, env, for_signature):
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main = source[0]
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objects = " ".join(o.get_path() for o in source[1:] if str(o).endswith('.o'))
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modulename = str(target[0]).replace(suffix, '').replace('/', '.')
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compiler = env['FORTRAN']
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cmd = f"f2py3 --fcompiler={compiler} "
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cmd += f" $F2PY_OPTS -m {modulename} -c {objects} {main}"
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#cmd += " 1>/dev/null 2>/dev/null"
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return cmd
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def f2py_emitter(target, source, env):
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""" used to add the correct cpython .so suffix to the modulename """
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target[0] = str(target[0]).replace('.', '/') + suffix
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return target, source
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def install_module(env, module):
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destdir = os.path.dirname(module[0].srcnode().abspath)
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env.Install(destdir, module)
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env.Alias('install', destdir)
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return None
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f2py_bld = Builder(generator=f2py_generator, emitter=f2py_emitter)
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# define the default build environment
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std = Environment(tools=['default', 'fortran'], F2PY_OPTS=[], LIBS=[])
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std.AddMethod(filtered_glob, "FilteredGlob")
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std.AddMethod(install_module, "InstallModule")
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std['BUILDERS']['F2py'] = f2py_bld
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###############################################################################
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# Define the command line options
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AddOption('--dbg',
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dest='dbg',
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@ -18,39 +59,19 @@ AddOption('--compiler',
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choices=['gfortran', 'ifort'],
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help='The Fortran compiler to use')
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def CheckPKGConfig(context, version):
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context.Message( 'Checking for pkg-config... ' )
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ret = context.TryAction('pkg-config --atleast-pkgconfig-version=%s' % version)[0]
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context.Result( ret )
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return ret
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def CheckPKG(context, name):
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context.Message( 'Checking for %s... ' % name )
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ret = context.TryAction('pkg-config --exists \'%s\'' % name)[0]
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context.Result( ret )
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return ret
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def filtered_glob(env, pattern, omit=[],
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ondisk=True, source=False, strings=False):
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return list(filter(
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lambda f: os.path.basename(f.path) not in omit,
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env.Glob(pattern)))
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# define the default build environment
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std = Environment(tools=['default', 'fortran'], F2PY_OPTS=[], FORTRANCOMSTR = "building $TARGET ...", LIBS=[])
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std.AddMethod(filtered_glob, "FilteredGlob");
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# define environments
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gfortran_env = std.Clone(tools=['gfortran'])
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gfortran_env.Replace(FORTRANFLAGS=['-fPIC', '-O2', '-ffast-math', '-fno-automatic'])
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gfortran_env.Replace(FORTRANFLAGS=['-fPIC', '-O2', '-ffast-math'])
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ifort_env = std.Clone(tools=['ifort'])
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# parse options
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if GetOption('compiler') == 'gfortran':
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env = gfortran_env
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env.Append(F2PY_OPTS='--opt=-O2')
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elif GetOption('compiler') == 'ifort':
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env = ifort_env
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@ -65,37 +86,6 @@ if GetOption('verbose'):
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env.Replace(FORTRANCOMSTR = "")
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conf = Configure(env, custom_tests = { 'CheckPKG' : CheckPKG})
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suffix = get_config_var('EXT_SUFFIX')
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# Create a builder for f2py
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def create_f2py_cmd(source, target, env, for_signature):
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objects = source[1:]
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cmd = "f2py3 "
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cmd += " ".join([o.get_path() for o in objects if str(o).endswith('o')])
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cmd += f" $F2PY_OPTS -m {str(target[0]).replace(suffix,'').replace('/', '.')} -c {source[0]}"
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return cmd
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def modify_targets(target, source, env):
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target[0] = str(target[0]) + suffix
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#print(target[0])
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return target, source
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bld = Builder(generator=create_f2py_cmd, emitter = modify_targets)
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env['BUILDERS']['F2PY'] = bld
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# exports
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try:
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Import('local_build')
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except:
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local_build = False
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Export('env', 'conf')
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print('local_build = ', local_build)
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if not local_build:
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SConscript(['msspec/spec/fortran/SConstruct',
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'msspec/phagen/fortran/SConstruct'])
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Export('env')
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SConscript('msspec/spec/fortran/SConstruct', variant_dir='build/build_spec')
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SConscript('msspec/phagen/fortran/SConstruct', variant_dir='build/build_phagen')
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307
src/install.sh
307
src/install.sh
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@ -1,307 +0,0 @@
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#!/bin/bash
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# vim: set ts=4 sw=4 sts noet mouse=a fdm=indent:
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BYPASS="n"
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DEBUG="n"
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BUILDONLY="n"
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SCRIPT_NAME=$(basename "$0")
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VERSION=$(cat ./msspec/version.py|cut -d\" -f2)
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DATE=$(date +%Y%m%d_%H%M%S)
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LOGFILE="${HOME}/msspec_install_${DATE}.log"
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GETOUTFILE=$(mktemp)
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USE_MKL=0
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LINKER_FLAGS=""
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COMP=gfortran
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COMP_OPTS="-O2 -ffast-math -fno-automatic"
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DEBUG_MODE=0
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trap "abort_install" INT
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trap "error_exit" HUP QUIT ILL ABRT
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init_install () {
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printf "Installation started on %s\n" "$(date)" > "${LOGFILE}"
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printf "0" > "${GETOUTFILE}"
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if [ "$BYPASS" = "n" ]; then
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printf ""
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printf "This program will install the msspec python package on your system.\n"
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printf "It is highly recommended to run this installation process within a\n"
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printf "Python virtual environment. If you want to create and/or activate one,\n"
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printf "you can answer \"n\" now and restart the setup program later.\n"
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read_yes_no "Do you wish to continue" "y"
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case "${ANSWER}" in
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y) ;;
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n) abort_install ;;
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esac
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fi
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}
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abort_install () {
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log_message "Installation aborted by the user"
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error_exit
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}
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log_message () {
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printf "$1\n" >> ${LOGFILE}
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}
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log_message2 () {
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# echo to screen and to file
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printf "$1\n"
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log_message "$1\n"
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}
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cleanup () {
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rm -rf "${GETOUTFILE}"
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}
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error_exit () {
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# An error occured
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printf "\n"
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printf " /!\ An error occured during the installation process.\n"
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printf " Please see the %s file in your HOME folder\n" "$(basename "${LOGFILE}")"
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printf " for more informations.\n"
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printf " Below is an excerpt of the last 10 lines:\n"
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printf "\n"
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echo ">>> ..."
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tail "${LOGFILE}" | while read line
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do
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echo ">>> $line"
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done
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# uninstall if needed
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pip uninstall -y msspec
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cleanup && exit 1
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}
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read_yes_no () {
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DEFAULT="$2"
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PROMPT="$1 (y/n) [${DEFAULT}]? "
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ANSWER=""
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INPUT=""
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VALID=1
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while test $VALID -ne 0; do
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printf "%s" "${PROMPT}"
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if [ x"$BYPASS" = xn ]; then
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read -r "INPUT"
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else
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printf "\n"
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fi
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ANSWER="${INPUT:-${DEFAULT}}"
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case "${ANSWER}" in
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y|n) VALID=0 ;;
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||||
*) printf "Invalid choice, please answer \"y\" or \"n\".\n"; VALID=1 ;;
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||||
esac
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||||
done
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log_message "QUESTION: $PROMPT"
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||||
log_message "ANSWER : $ANSWER"
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}
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||||
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wrap () {
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||||
log_message "================================================================================"
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||||
log_message "$2"
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||||
log_message "================================================================================"
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log_message "$1"
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if [ "$DEBUG" = y ]; then
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||||
printf "%s...\n" "$2"
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||||
(eval "$1" || echo $? >"${GETOUTFILE}") | tee -a "${LOGFILE}"
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||||
rc=$(cat $GETOUTFILE)
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||||
if [ $rc != 0 ]; then
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||||
error_exit
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||||
fi
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else
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||||
eval "($1) 2>>${LOGFILE} 1>>${LOGFILE}" || echo $? >${GETOUTFILE} &
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patience "$2"
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||||
fi
|
||||
}
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||||
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||||
success_message () {
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||||
log_message "========================================================"
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||||
log_message "MsSpec was successfully installed."
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||||
log_message "========================================================"
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||||
}
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patience () {
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MSG="$1"
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||||
PID=$!
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||||
i=0
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||||
printf "%s" "$MSG... "
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||||
while ps -p $PID > /dev/null
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||||
do
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||||
sleep 0.1
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||||
case $i in
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||||
0) printf "\b\b- " ;;
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||||
1) printf "\b\b\\ " ;;
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||||
2) printf "\b\b| " ;;
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||||
3) printf "\b\b/ "; i=-1 ;;
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||||
esac
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||||
i=$(( i+1 ))
|
||||
done
|
||||
if test "$(cat "${GETOUTFILE}")" -ne 0; then
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||||
printf "\b\b Aborted!"
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||||
error_exit
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||||
fi
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||||
printf "\b\b Done.\n"
|
||||
}
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||||
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||||
show_help () {
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||||
echo "Usage: $SCRIPT_NAME [OPTIONS]"
|
||||
echo "List of possible options:"
|
||||
echo " -y Accept all default choices."
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||||
echo " -d Debug mode."
|
||||
echo " -h Show this message."
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||||
exit 0
|
||||
}
|
||||
|
||||
|
||||
check_dependencies () {
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||||
# we need make
|
||||
log_message "Checking if make is installed..."
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||||
command -V make || return 1
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||||
log_message "Ok\n"
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||||
|
||||
# we need gfortran
|
||||
gcc_ver_min=6
|
||||
log_message "Checking if gfortran >= $gcc_ver_min is installed..."
|
||||
command -V gfortran || return 1
|
||||
gcc_ver=$(gcc -dumpversion|cut -d. -f1)
|
||||
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}..."
|
||||
command -V python || 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 "$py_ver_minor_min" || return 1
|
||||
log_message "Ok\n"
|
||||
|
||||
# we need wxPython.
|
||||
log_message "Checking if wxPython is installed..."
|
||||
python -c "import wx"
|
||||
if test "$?" -ne 0; then
|
||||
log_message "You need wxPython to run MsSpec.\n"
|
||||
log_message "Please look at informations at https://wxpython.org/pages/downloads/.\n"
|
||||
return 1
|
||||
else
|
||||
log_message "Ok\n"
|
||||
fi
|
||||
|
||||
# we need pip
|
||||
log_message "Checking if pip is installed..."
|
||||
command -V pip || 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"
|
||||
|
||||
# Do we have Lapack.
|
||||
log_message "Checking if lapack is installed..."
|
||||
pkg-config --exists lapack
|
||||
if test "$?" -ne 0; then
|
||||
HAS_LAPACK="n"
|
||||
log_message "No, will use included routines\n"
|
||||
else
|
||||
HAS_LAPACK="y"
|
||||
log_message "Ok\n"
|
||||
fi
|
||||
|
||||
if [ x"${HAS_LAPACK}" = xy ]; then
|
||||
read_yes_no "You have Lapack. Do you wish to link with installed lapack" "y"
|
||||
if [ x"${ANSWER}" = xy ]; then
|
||||
USE_MKL=1
|
||||
LINKER_FLAGS=`pkg-config --libs lapack`
|
||||
fi
|
||||
fi
|
||||
|
||||
# ask for expert options
|
||||
read_yes_no "Do you wish to edit compilation options" "n"
|
||||
if [ x"${ANSWER}" = xy ]; then
|
||||
read -ep "FORTRAN COMPILER...................> " -i "${COMP}" COMP
|
||||
read -ep "COMPILER OPTIONS...................> " -i "${COMP_OPTS}" COMP_OPTS
|
||||
read -ep "USE EXTERNAL LAPACK (0:no, 1:yes)..> " -i "${USE_MKL}" USE_MKL
|
||||
read -ep "LINKER FLAGS.......................> " -i "${LINKER_FLAGS}" LINKER_FLAGS
|
||||
read -ep "INCLUDE DEBUG SYMBOLS (0:no, 1:yes)> " -i "${DEBUG_MODE}" DEBUG_MODE
|
||||
fi
|
||||
|
||||
ALL_OPTS="VERBOSE=1 USE_MKL=${USE_MKL} LINKER_FLAGS=\"${LINKER_FLAGS}\" COMP=\"${COMP}\" COMP_OPTS=\"${COMP_OPTS}\" DEBUG=\"${DEBUG_MODE}\""
|
||||
|
||||
# build the Fortran code
|
||||
wrap "make pybinding ${ALL_OPTS}" "Building Phagen and Spec Python dynamic library"
|
||||
|
||||
if [ x"${BUILDONLY}" = xy ]; then
|
||||
exit
|
||||
fi
|
||||
|
||||
# install Python dependencies
|
||||
wrap "make install_deps ${ALL_OPTS}" "Installing Python dependencies"
|
||||
|
||||
# build the source distribution
|
||||
wrap "make sdist ${ALL_OPTS}" "Building msspec python package"
|
||||
|
||||
# install the package
|
||||
wrap "make install ${ALL_OPTS}" "Installing the msspec package"
|
||||
|
||||
# Run unit tests ?
|
||||
read_yes_no "Do you wish to run unit tests" "y"
|
||||
if [ x"${ANSWER}" = xy ]; then
|
||||
wrap "make tests ${ALL_OPTS}" "Runing test suite"
|
||||
fi
|
||||
|
||||
# installation was a succes so ask if we keep the log file
|
||||
read_yes_no "Do you wish to keep the log file (${LOGFILE})" "n"
|
||||
if [ x"${ANSWER}" = xn ]; then
|
||||
rm -f "${LOGFILE}"
|
||||
fi
|
||||
|
||||
# self-explanatory
|
||||
success_message
|
||||
}
|
||||
|
||||
while getopts "p:byd" option
|
||||
do
|
||||
case $option in
|
||||
y) export BYPASS="y"
|
||||
;;
|
||||
d) export DEBUG="y"
|
||||
;;
|
||||
b) export BUILDONLY="y"
|
||||
;;
|
||||
h) show_help
|
||||
;;
|
||||
*) show_help
|
||||
;;
|
||||
esac
|
||||
done
|
||||
|
||||
local_install
|
||||
|
|
@ -60,6 +60,8 @@ import wx.grid
|
|||
|
||||
from matplotlib.backends.backend_wxagg import FigureCanvasWxAgg as FigureCanvas
|
||||
from matplotlib.backends.backend_wxagg import NavigationToolbar2WxAgg
|
||||
#from matplotlib.backends.backend_wxcairo import FigureCanvasWxCairo as FigureCanvas
|
||||
#from matplotlib.backends.backend_wxcairo import NavigationToolbar2WxCairo
|
||||
from matplotlib.figure import Figure
|
||||
|
||||
from terminaltables import AsciiTable
|
||||
|
|
|
|||
|
|
@ -1,35 +0,0 @@
|
|||
COMP=gfortran
|
||||
F2PY:=f2py3
|
||||
|
||||
COMP_OPTS:= -O2 -ffast-math
|
||||
F2PY_OPTS:=
|
||||
|
||||
DEBUG:=0
|
||||
|
||||
objects_src := phagen_scf_2.1_dp.f
|
||||
objects := $(patsubst %.f,%.o, $(objects_src))
|
||||
|
||||
ifeq ($(DEBUG),1)
|
||||
COMP_OPTS:=$(COMP_OPTS) -g -Wall -Wextra -Warray-temporaries -Wconversion -fbacktrace -ffree-line-length-0 -fcheck=all -ffpe-trap=zero,overflow,underflow -finit-real=nan
|
||||
F2PY_OPTS:=$(F2PY_OPTS) --debug-capi --debug
|
||||
endif
|
||||
|
||||
|
||||
.PHONY: clean
|
||||
|
||||
pybinding: libphagen.target
|
||||
|
||||
libphagen.target: $(objects) main.f
|
||||
@echo "building Python binding..."
|
||||
@$(F2PY) -I. $(objects) $(F2PY_OPTS)-c -m libphagen main.f
|
||||
@touch $@
|
||||
|
||||
$(objects): $(objects_src)
|
||||
@echo "compiling subroutines and functions for phagen..."
|
||||
@$(COMP) $(COMP_OPTS) -fPIC -c $^
|
||||
|
||||
clean:
|
||||
@echo "cleaning..."
|
||||
@rm -rf *.o *.mod
|
||||
@rm -rf $(objects)
|
||||
@rm -f libphagen.target
|
||||
|
|
@ -1,17 +1,10 @@
|
|||
try:
|
||||
Import('env')
|
||||
except:
|
||||
local_build = True
|
||||
Export('local_build')
|
||||
SConscript(['../../../SConstruct'])
|
||||
finally:
|
||||
Import('env')
|
||||
|
||||
import os
|
||||
|
||||
objects_src= ['phagen_scf_2.1_dp.f']
|
||||
objects = env.Object(objects_src)
|
||||
|
||||
module = env.F2PY('libphagen', ['main.f'] + objects)
|
||||
Requires(module, objects)
|
||||
module = env.F2py('libphagen', ['main.f'] + objects, F2PYCOMSTR=">>")
|
||||
env.InstallModule(module)
|
||||
|
||||
env.Alias('phagen', module)
|
||||
|
|
|
|||
|
|
@ -8140,7 +8140,13 @@ c.....this subroutine calculates the radial matrix elements
|
|||
c.....necessary for eels cross-section
|
||||
c.....using a linear-log mesh
|
||||
c
|
||||
common/mtxele/ nstart,nlast
|
||||
CST ==> Replaced the line below
|
||||
CST common/mtxele/ nstart,nlast
|
||||
common/mtxele/ nstart,nlast,dmx(2),dmx1(2),qmx(3),qmx1(3),
|
||||
$ dxdir,dxexc,nfis,nfis1,nfis2
|
||||
real*8 nfis,nfis2,nfis1
|
||||
complex*16 dmx,dmx1,qmx,qmx1,dxdir,dxexc
|
||||
CST <==
|
||||
c
|
||||
common/mtxelex/ dmxx(2),dmxx1(2),dmxxa(2),dmxxa1(2),
|
||||
& qmxx(3),qmxx1(3),qmxxa(3),qmxxa1(3),
|
||||
|
|
@ -17000,7 +17006,13 @@ c.....(i=1,2) for lfin=l0i-1 (i=1) and lfin=l0i+1 (i=2) both for
|
|||
c.....the regular (dmxx) and irregular solution (dmxx1) using a
|
||||
c.....linear-log mesh
|
||||
c
|
||||
common/mtxele/ nstart,nlast
|
||||
CST ==> Replaced the line below
|
||||
CST common/mtxele/ nstart,nlast
|
||||
common/mtxele/ nstart,nlast,dmx(2),dmx1(2),qmx(3),qmx1(3),
|
||||
$ dxdir,dxexc,nfis,nfis1,nfis2
|
||||
real*8 nfis,nfis2,nfis1
|
||||
complex*16 dmx,dmx1,qmx,qmx1,dxdir,dxexc
|
||||
CST <==
|
||||
c
|
||||
common/mtxelex/ dmxx(2),dmxx1(2),dmxxa(2),dmxxa1(2),
|
||||
& qmxx(3),qmxx1(3),qmxxa(3),qmxxa1(3),
|
||||
|
|
@ -20199,7 +20211,8 @@ C MARK 12 RELEASE. NAG COPYRIGHT 1986.
|
|||
C MARK 15 REVISED. IER-915 (APR 1991).
|
||||
C .. Scalar Arguments ..
|
||||
INTEGER INFO
|
||||
CHARACTER*13 SRNAME
|
||||
CHARACTER(*) SRNAME
|
||||
CST CHARACTER*13 SRNAME
|
||||
C ..
|
||||
C
|
||||
C Purpose
|
||||
|
|
|
|||
|
|
@ -1,98 +0,0 @@
|
|||
COMP:=gfortran
|
||||
F2PY:=f2py3
|
||||
|
||||
COMP_OPTS:= -O2 -ffast-math -fno-automatic
|
||||
LINKER_FLAGS:=
|
||||
F2PY_OPTS:=
|
||||
|
||||
DEBUG:=0
|
||||
USE_MKL:=0
|
||||
|
||||
|
||||
|
||||
includes := -I./memalloc/ -I./cluster_gen/ -I./common_sub -I./renormalization
|
||||
includes += -I./phd_se_noso_nosp_nosym
|
||||
includes += -I./eig/common -I./eig/mi -I./eig/pw
|
||||
|
||||
memalloc_src:=memalloc/dim_mod.f memalloc/modules.f memalloc/allocation.f
|
||||
cluster_gen_src:=$(wildcard cluster_gen/*.f)
|
||||
common_sub_src:=$(wildcard common_sub/*.f)
|
||||
renormalization_src:=$(wildcard renormalization/*.f)
|
||||
|
||||
phd_se_noso_nosp_nosym_src:=$(filter-out phd_se_noso_nosp_nosym/main.f, $(wildcard phd_se_noso_nosp_nosym/*.f))
|
||||
phd_mi_noso_nosp_nosym_src:=$(filter-out phd_mi_noso_nosp_nosym/main.f, $(wildcard phd_mi_noso_nosp_nosym/*.f))
|
||||
|
||||
eig_common_src:=$(wildcard eig/common/*.f)
|
||||
eig_mi_src:=$(filter-out eig/mi/main.f, $(wildcard eig/mi/*.f))
|
||||
eig_pw_src:=$(filter-out eig/pw/main.f, $(wildcard eig/pw/*.f))
|
||||
|
||||
ifeq ($(USE_MKL), 1)
|
||||
eig_common_src:=$(filter-out $(wildcard eig/common/lapack*.f), $(eig_common_src))
|
||||
phd_mi_noso_nosp_nosym_src:=$(filter-out $(wildcard phd_mi_noso_nosp_nosym/lapack*.f), $(phd_mi_noso_nosp_nosym_src))
|
||||
LINKER_FLAGS:=$(shell pkg-config --libs lapack)
|
||||
# MKL:=-L$(MKLROOT) -lmkl_core -lmkl_intel_lp64 -lmkl_sequential
|
||||
endif
|
||||
|
||||
objects_src := $(memalloc_src) $(cluster_gen_src) $(common_sub_src)
|
||||
objects_src += $(renormalization_src) $(phd_se_noso_nosp_nosym_src)
|
||||
objects_src += $(eig_common_src) $(eig_mi_src) $(eig_pw_src)
|
||||
objects_src += $(phd_mi_noso_nosp_nosym_src)
|
||||
|
||||
memalloc_obj:=$(patsubst %.f,%.o, $(memalloc_src))
|
||||
cluster_gen_obj:=$(patsubst %.f,%.o, $(cluster_gen_src))
|
||||
common_sub_obj:=$(patsubst %.f,%.o, $(common_sub_src))
|
||||
renormalization_obj:=$(patsubst %.f,%.o, $(renormalization_src))
|
||||
phd_se_noso_nosp_nosym_obj:=$(patsubst %.f,%.o, $(phd_se_noso_nosp_nosym_src))
|
||||
phd_mi_noso_nosp_nosym_obj:=$(patsubst %.f,%.o, $(phd_mi_noso_nosp_nosym_src))
|
||||
eig_common_obj:=$(patsubst %.f,%.o, $(eig_common_src))
|
||||
eig_mi_obj:=$(patsubst %.f,%.o, $(eig_mi_src))
|
||||
eig_pw_obj:=$(patsubst %.f,%.o, $(eig_pw_src))
|
||||
objects:=$(patsubst %.f,%.o, $(objects_src))
|
||||
|
||||
libs_targets := phd_se_noso_nosp_nosym.target phd_mi_noso_nosp_nosym.target eig_mi.target eig_pw.target
|
||||
|
||||
EXE=prog
|
||||
|
||||
ifeq ($(DEBUG),1)
|
||||
COMP_OPTS:=$(COMP_OPTS) -g -Wall -Wextra -Warray-temporaries -Wconversion -fbacktrace -ffree-line-length-0 -fcheck=all -ffpe-trap=zero,overflow,underflow -finit-real=nan
|
||||
F2PY_OPTS:=$(F2PY_OPTS) --debug-capi --debug
|
||||
endif
|
||||
|
||||
export COMP
|
||||
export COMP_OPTS
|
||||
|
||||
|
||||
.PHONY: clean
|
||||
|
||||
|
||||
pybinding: $(libs_targets)
|
||||
|
||||
phd_se_noso_nosp_nosym.target: $(memalloc_obj) $(cluster_gen_obj) $(common_sub_obj) $(renormalization_obj) $(phd_se_noso_nosp_nosym_obj)
|
||||
@echo "building Python binding..."
|
||||
@$(F2PY) $(includes) $^ $(F2PY_OPTS) -c -m $(patsubst %.target, %, $@) phd_se_noso_nosp_nosym/main.f
|
||||
@touch $@
|
||||
|
||||
phd_mi_noso_nosp_nosym.target: $(memalloc_obj) $(cluster_gen_obj) $(common_sub_obj) $(renormalization_obj) $(phd_mi_noso_nosp_nosym_obj)
|
||||
@echo "building Python binding..."
|
||||
@$(F2PY) $(includes) $^ $(F2PY_OPTS) -c -m $(patsubst %.target, %, $@) phd_mi_noso_nosp_nosym/main.f $(LINKER_FLAGS)
|
||||
@touch $@
|
||||
|
||||
eig_mi.target: $(memalloc_obj) $(cluster_gen_obj) $(common_sub_obj) $(renormalization_obj) $(eig_common_obj) $(eig_mi_obj)
|
||||
@echo "building Python binding..."
|
||||
@$(F2PY) $(includes) $^ $(F2PY_OPTS) -c -m $(patsubst %.target, %, $@) eig/mi/main.f $(LINKER_FLAGS)
|
||||
@touch $@
|
||||
|
||||
eig_pw.target: $(memalloc_obj) $(cluster_gen_obj) $(common_sub_obj) $(renormalization_obj) $(eig_common_obj) $(eig_pw_obj)
|
||||
@echo "building Python binding..."
|
||||
@$(F2PY) $(includes) $^ $(F2PY_OPTS) -c -m $(patsubst %.target, %, $@) eig/pw/main.f $(LINKER_FLAGS)
|
||||
@touch $@
|
||||
|
||||
%.o: %.f
|
||||
@echo "compiling $@..."
|
||||
@$(COMP) $(COMP_OPTS) -I./memalloc/ -fPIC -o $@ -c $^
|
||||
|
||||
clean:
|
||||
@echo "cleaning..."
|
||||
@rm -rf *.o *.mod
|
||||
@rm -rf $(objects)
|
||||
@rm -rf $(libs_targets)
|
||||
|
|
@ -1,22 +1,11 @@
|
|||
# imports
|
||||
try:
|
||||
Import('env', 'conf')
|
||||
except:
|
||||
local_build = True
|
||||
Export('local_build')
|
||||
SConscript(['../../../SConstruct'])
|
||||
finally:
|
||||
Import('env', 'conf')
|
||||
Import('env')
|
||||
import os
|
||||
|
||||
# Configuration:
|
||||
env2 = env.Clone()
|
||||
if conf.CheckPKG('lapack'):
|
||||
env2.ParseConfig("pkg-config lapack --libs")
|
||||
conf.Finish()
|
||||
|
||||
dir = Dir('.').get_abspath()
|
||||
env2.Append(FORTRANFLAGS=['-I' + dir,'-J' + dir])
|
||||
env2.Append(F2PY_OPTS=['-I' + dir])
|
||||
# Configure the environment
|
||||
env_spec = env.Clone()
|
||||
cwd = Dir('.').get_abspath()
|
||||
env_spec.Append(FORTRANFLAGS=['-I' + cwd,'-J' + cwd])
|
||||
env_spec.Append(F2PY_OPTS=['-I' + cwd])
|
||||
|
||||
# define sources
|
||||
dim_mod = ['memalloc/dim_mod.f']
|
||||
|
|
@ -24,53 +13,53 @@ memalloc = ['memalloc/modules.f', 'memalloc/allocation.f']
|
|||
cluster_gen = Glob('cluster_gen/*.f')
|
||||
common_sub = Glob('common_sub/*.f')
|
||||
renormalization = Glob('renormalization/*.f')
|
||||
phd_se_noso_nosp_nosym = env2.FilteredGlob('phd_se_noso_nosp_nosym/*.f', omit=['main.f'])
|
||||
phd_mi_noso_nosp_nosym = env2.FilteredGlob('phd_mi_noso_nosp_nosym/*.f', omit=['main.f'])
|
||||
phd_se_noso_nosp_nosym = env_spec.FilteredGlob('phd_se_noso_nosp_nosym/*.f', omit=['main.f'])
|
||||
phd_mi_noso_nosp_nosym = env_spec.FilteredGlob('phd_mi_noso_nosp_nosym/*.f', omit=['main.f'])
|
||||
eig_common = Glob('eig/common/*.f')
|
||||
eig_mi = env2.FilteredGlob('eig/mi/*.f', omit=['main.f'])
|
||||
eig_pw = env2.FilteredGlob('eig/pw/*.f', omit=['main.f'])
|
||||
eig_mi = env_spec.FilteredGlob('eig/mi/*.f', omit=['main.f'])
|
||||
eig_pw = env_spec.FilteredGlob('eig/pw/*.f', omit=['main.f'])
|
||||
|
||||
|
||||
if 'lapack' in env2['LIBS']:
|
||||
env2.Append(F2PY_OPTS = "-llapack")
|
||||
conf = Configure(env_spec, log_file='./config.log')
|
||||
if conf.CheckLib('lapack'):
|
||||
env_spec.Append(F2PY_OPTS = "-llapack")
|
||||
eig_mi = [f for f in eig_mi if str(f).find('lapack') == -1]
|
||||
phd_mi_noso_nosp_nosym = [f for f in phd_mi_noso_nosp_nosym if str(f).find('lapack') == -1]
|
||||
|
||||
sources = dim_mod + memalloc + cluster_gen + common_sub + renormalization + phd_se_noso_nosp_nosym
|
||||
sources += phd_mi_noso_nosp_nosym + eig_common + eig_pw + eig_mi
|
||||
env_spec = conf.Finish()
|
||||
env_spec.Append(FORTRANFLAGS='-fno-automatic')
|
||||
|
||||
# define objects
|
||||
dim_mod_obj = env2.Object(dim_mod)
|
||||
memalloc_obj = env2.Object(memalloc)
|
||||
cluster_gen_obj = env2.Object(cluster_gen)
|
||||
common_sub_obj = env2.Object(common_sub)
|
||||
renormalization_obj = env2.Object(renormalization)
|
||||
phd_se_noso_nosp_nosym_obj = env2.Object(phd_se_noso_nosp_nosym)
|
||||
phd_mi_noso_nosp_nosym_obj = env2.Object(phd_mi_noso_nosp_nosym)
|
||||
eig_common_obj = env2.Object(eig_common)
|
||||
eig_pw_obj = env2.Object(eig_pw)
|
||||
eig_mi_obj = env2.Object(eig_mi)
|
||||
dim_mod_obj = env_spec.Object(dim_mod)
|
||||
memalloc_obj = env_spec.Object(memalloc)
|
||||
cluster_gen_obj = env_spec.Object(cluster_gen)
|
||||
common_sub_obj = env_spec.Object(common_sub)
|
||||
renormalization_obj = env_spec.Object(renormalization)
|
||||
phd_se_noso_nosp_nosym_obj = env_spec.Object(phd_se_noso_nosp_nosym)
|
||||
phd_mi_noso_nosp_nosym_obj = env_spec.Object(phd_mi_noso_nosp_nosym)
|
||||
eig_common_obj = env_spec.Object(eig_common)
|
||||
eig_pw_obj = env_spec.Object(eig_pw)
|
||||
eig_mi_obj = env_spec.Object(eig_mi)
|
||||
|
||||
Requires(memalloc_obj, dim_mod_obj)
|
||||
|
||||
# define Python extensions
|
||||
common_deps = dim_mod_obj + memalloc_obj + cluster_gen_obj + common_sub_obj
|
||||
|
||||
deps = common_deps + renormalization_obj + phd_se_noso_nosp_nosym_obj
|
||||
phd_se_mod = env2.F2PY('_phd_se_noso_nosp_nosym', ['phd_se_noso_nosp_nosym/main.f'] + deps)
|
||||
Requires(phd_se_mod, deps)
|
||||
env2.Alias('phd_se', phd_se_mod)
|
||||
phd_se_mod = env_spec.F2py('_phd_se_noso_nosp_nosym', ['phd_se_noso_nosp_nosym/main.f'] + deps)
|
||||
env_spec.InstallModule(phd_se_mod)
|
||||
|
||||
deps = common_deps + renormalization_obj + phd_mi_noso_nosp_nosym_obj
|
||||
phd_mi_mod = env2.F2PY('_phd_mi_noso_nosp_nosym', ['phd_mi_noso_nosp_nosym/main.f'] + deps)
|
||||
Requires(phd_mi_mod, deps)
|
||||
env2.Alias('phd_mi', phd_mi_mod)
|
||||
phd_mi_mod = env_spec.F2py('_phd_mi_noso_nosp_nosym', ['phd_mi_noso_nosp_nosym/main.f'] + deps)
|
||||
env_spec.InstallModule(phd_mi_mod)
|
||||
|
||||
deps = common_deps + renormalization_obj + eig_common_obj + eig_mi_obj
|
||||
eig_mi_mod = env2.F2PY('_eig_mi', ['eig/mi/main.f'] + deps)
|
||||
Requires(eig_mi_mod, deps)
|
||||
env2.Alias('eig_mi', eig_mi_mod)
|
||||
eig_mi_mod = env_spec.F2py('_eig_mi', ['eig/mi/main.f'] + deps)
|
||||
env_spec.InstallModule(eig_mi_mod)
|
||||
|
||||
deps = common_deps + renormalization_obj + eig_common_obj + eig_pw_obj
|
||||
eig_pw_mod = env2.F2PY('_eig_pw', ['eig/pw/main.f'] + deps)
|
||||
Requires(eig_pw_mod, deps)
|
||||
env2.Alias('eig_pw', eig_pw_mod)
|
||||
eig_pw_mod = env_spec.F2py('_eig_pw', ['eig/pw/main.f'] + deps)
|
||||
env_spec.InstallModule(eig_pw_mod)
|
||||
|
||||
# Alias
|
||||
env_spec.Alias('spec', [phd_se_mod, phd_mi_mod, eig_pw_mod, eig_mi_mod])
|
||||
|
||||
|
|
|
|||
|
|
@ -1,3 +1,6 @@
|
|||
|
||||
|
||||
|
||||
MODULE DIM_MOD
|
||||
IMPLICIT NONE
|
||||
INTEGER NATP_M, NATCLU_M, NAT_EQ_M, N_CL_L_M
|
||||
|
|
|
|||
|
|
@ -7,8 +7,7 @@ import os
|
|||
|
||||
# find the version number
|
||||
# 1- Try to read it from the git info
|
||||
# 2- If it fails, try to read it from the VERSION file
|
||||
# 3- If it fails, try to read it from the distribution file
|
||||
# 2- If it fails, try to read it from the distribution file
|
||||
|
||||
try:
|
||||
v = get_version(root='../../', relative_to=__file__, version_scheme="post-release")
|
||||
|
|
@ -17,14 +16,9 @@ try:
|
|||
__version__ = v.base_version
|
||||
else:
|
||||
__version__ = v.public
|
||||
except (LookupError, ImportError):
|
||||
try:
|
||||
f = os.path.join(os.path.dirname(__file__), "../VERSION")
|
||||
with open(f, "r") as fd:
|
||||
__version__ = fd.read().strip('\n ')
|
||||
except:
|
||||
except Exception as err:
|
||||
try:
|
||||
__version__ = get_distribution(__name__.strip('.version')).version
|
||||
except DistributionNotFound:
|
||||
except Exception as err:
|
||||
print("Unable to get the version number!")
|
||||
|
||||
__version__ = "9.9.9"
|
||||
|
|
|
|||
|
|
@ -1,11 +1,10 @@
|
|||
numpy
|
||||
matplotlib==2.1.1
|
||||
ase
|
||||
h5py
|
||||
lxml
|
||||
pint
|
||||
terminaltables
|
||||
pycairo
|
||||
coverage
|
||||
sphinx
|
||||
setuptools_scm
|
||||
wxPython
|
||||
|
|
|
|||
57
src/setup.py
57
src/setup.py
|
|
@ -13,72 +13,23 @@ import subprocess
|
|||
import traceback
|
||||
import os
|
||||
import sys
|
||||
import glob
|
||||
sys.path.insert(0, "msspec")
|
||||
|
||||
|
||||
from version import __version__
|
||||
|
||||
with open('setup_requirements.txt', 'r') as fd:
|
||||
SETUP_REQUIREMENTS = fd.read().strip().split('\n')
|
||||
|
||||
SETUP_REQUIRES = ['scons', 'setuptools_scm']
|
||||
with open('requirements.txt', 'r') as fd:
|
||||
REQUIREMENTS = fd.read().strip().split('\n')
|
||||
|
||||
subprocess.call(["pip", "install"] + SETUP_REQUIRES)
|
||||
|
||||
|
||||
class BuildExtCmd(_build_ext):
|
||||
def run(self):
|
||||
src_dir = "."
|
||||
subprocess.call(['scons'])
|
||||
for ext in self.extensions:
|
||||
fullname = self.get_ext_fullname(ext.name)
|
||||
filename = self.get_ext_filename(fullname)
|
||||
print("building ", filename)
|
||||
|
||||
src_filename = filename
|
||||
dest_filename = os.path.join(self.build_lib, filename)
|
||||
|
||||
os.makedirs(os.path.dirname(dest_filename), exist_ok=True)
|
||||
copy_file(src_filename, dest_filename, verbose=self.verbose,
|
||||
dry_run=self.dry_run)
|
||||
|
||||
|
||||
class BuildCmd(_build):
|
||||
def run(self):
|
||||
print("build_lib ", self.build_lib)
|
||||
self.run_command("build_ext")
|
||||
_build.run(self)
|
||||
|
||||
class InstallCmd(_install):
|
||||
def run(self):
|
||||
self.run_command("build")
|
||||
_install.run(self)
|
||||
|
||||
class CleanCmd(_clean):
|
||||
def run(self):
|
||||
subprocess.call(['scons', '-c'])
|
||||
_clean.run(self)
|
||||
|
||||
|
||||
|
||||
if __name__ == "__main__":
|
||||
module_phagen = Extension('msspec.phagen.fortran.libphagen',['msspec/phagen/fortran/main.f'])
|
||||
module_spec_phd_mi = Extension('msspec.spec.fortran._phd_mi_noso_nosp_nosym',['msspec/spec/fortran/phd_mi_noso_nosp_nosym/main.f'])
|
||||
module_spec_phd_se = Extension('msspec.spec.fortran._phd_se_noso_nosp_nosym',['msspec/spec/fortran/phd_se_noso_nosp_nosym/main.f'])
|
||||
module_eig_mi = Extension('msspec.spec.fortran._eig_mi',['msspec/spec/fortran/eig/mi/main.f'])
|
||||
module_eig_pw = Extension('msspec.spec.fortran._eig_pw',['msspec/spec/fortran/eig/pw/main.f'])
|
||||
|
||||
setup(name='msspec',
|
||||
version=__version__,
|
||||
include_package_data=True,
|
||||
ext_modules=[module_phagen, module_spec_phd_mi, module_spec_phd_se, module_eig_mi, module_eig_pw],
|
||||
cmdclass={'build' : BuildCmd,
|
||||
'build_ext': BuildExtCmd,
|
||||
'clean' : CleanCmd,
|
||||
'install' : InstallCmd,
|
||||
},
|
||||
packages=find_packages(include='msspec.*'),
|
||||
setup_requires=SETUP_REQUIRES,
|
||||
setup_requires=SETUP_REQUIREMENTS,
|
||||
install_requires=REQUIREMENTS,
|
||||
|
||||
author='Didier Sébilleau, Sylvain Tricot',
|
||||
|
|
|
|||
|
|
@ -0,0 +1,5 @@
|
|||
scons
|
||||
setuptools_scm
|
||||
numpy
|
||||
sphinx
|
||||
coverage
|
||||
Loading…
Reference in New Issue