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First python3 3 working installation

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This commit is contained in:
Anthony Scemama 2020-03-17 16:39:43 +01:00
parent 3d3c7fbc1a
commit 79f47d024b
33 changed files with 284 additions and 285 deletions
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6
INSTALL.rst
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@ -36,7 +36,7 @@ Requirements
- Fortran compiler : GNU Fortran, Intel Fortran or IBM XL Fortran - Fortran compiler : GNU Fortran, Intel Fortran or IBM XL Fortran
- `GNU make`_ - `GNU make`_
- `Autoconf`_ - `Autoconf`_
- `Python`_ > 2.6 - `Python`_ > 3.0
- |IRPF90| : Fortran code generator - |IRPF90| : Fortran code generator
- |EZFIO| : Easy Fortran Input/Output library generator - |EZFIO| : Easy Fortran Input/Output library generator
- |BLAS| and |LAPACK| - |BLAS| and |LAPACK|
@ -370,11 +370,11 @@ Docopt
*Docopt* is a Python package defining a command-line interface description language. *Docopt* is a Python package defining a command-line interface description language.
If you have *pip* for Python2, you can do If you have *pip* for Python3, you can do
.. code:: bash .. code:: bash
pip2 install --user docopt python3 -m pip install --user docopt
Otherwise, Otherwise,

4
bin/qp_basis
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@ -1,4 +1,4 @@
#!/usr/bin/env python2 #!/usr/bin/env python3
# -*- coding: utf-8 -*- # -*- coding: utf-8 -*-
""" """
@ -12,7 +12,7 @@ Usage:
""" """
from __future__ import print_function
import sys import sys
import os import os
import subprocess import subprocess

28
bin/qp_name
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@ -1,4 +1,4 @@
#!/usr/bin/env python2 #!/usr/bin/env python3
""" """
Displays the names of all the files in which the provider/subroutine/function Displays the names of all the files in which the provider/subroutine/function
@ -30,7 +30,7 @@ try:
from docopt import docopt from docopt import docopt
from qp_path import QP_SRC, QP_ROOT from qp_path import QP_SRC, QP_ROOT
except ImportError: except ImportError:
print "source .quantum_package.rc" print("source .quantum_package.rc")
raise raise
@ -38,7 +38,7 @@ def main(arguments):
"""Main function""" """Main function"""
# Check that name exist in */IRPF90_man # Check that name exist in */IRPF90_man
print "Checking that name exists..." print("Checking that name exists...")
all_modules = os.listdir(QP_SRC) all_modules = os.listdir(QP_SRC)
f = arguments["<name>"]+".l" f = arguments["<name>"]+".l"
@ -52,21 +52,21 @@ def main(arguments):
if found: break if found: break
if not found: if not found:
print "Error:" print("Error:")
print "The variable/subroutine/function \""+arguments["<name>"] \ print("The variable/subroutine/function \""+arguments["<name>"] \
+ "\" was not found in the sources." + "\" was not found in the sources.")
print "Did you compile the code at the root?" print("Did you compile the code at the root?")
print "Continue? [y/N] ", print("Continue? [y/N] ", end=' ')
cont = sys.stdin.read(1).strip() in ["y", "Y"] cont = sys.stdin.read(1).strip() in ["y", "Y"]
if not cont: if not cont:
print "Aborted" print("Aborted")
sys.exit(1) sys.exit(1)
# Now search in all the files # Now search in all the files
if arguments["--rename"]: if arguments["--rename"]:
print "Replacing..." print("Replacing...")
else: else:
print "Searching..." print("Searching...")
name = re.compile(r"\b"+arguments["<name>"]+r"\b", re.IGNORECASE) name = re.compile(r"\b"+arguments["<name>"]+r"\b", re.IGNORECASE)
@ -84,15 +84,15 @@ def main(arguments):
with open(filename, "r") as f: with open(filename, "r") as f:
f_in = f.read() f_in = f.read()
if name.search(f_in): if name.search(f_in):
print filename print(filename)
if arguments["--rename"]: if arguments["--rename"]:
f_new = name.sub(arguments["--rename"], f_in) f_new = name.sub(arguments["--rename"], f_in)
with open(filename, "w") as f: with open(filename, "w") as f:
f.write(f_new) f.write(f_new)
print "Done" print("Done")
with open(os.path.join(QP_ROOT, "REPLACE"), 'a') as f: with open(os.path.join(QP_ROOT, "REPLACE"), 'a') as f:
print >>f, "qp_name "+" ".join(sys.argv[1:]) print("qp_name "+" ".join(sys.argv[1:]), file=f)

68
bin/qp_plugins
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@ -1,4 +1,4 @@
#!/usr/bin/env python2 #!/usr/bin/env python3
# -*- coding: utf-8 -*- # -*- coding: utf-8 -*-
""" """
Usage: Usage:
@ -43,9 +43,9 @@ try:
from module_handler import get_l_module_descendant from module_handler import get_l_module_descendant
from qp_path import QP_SRC, QP_PLUGINS, QP_DATA, QP_ROOT from qp_path import QP_SRC, QP_PLUGINS, QP_DATA, QP_ROOT
except ImportError: except ImportError:
print "Please check if you have sourced the ${QP_ROOT}/quantum_package.rc" print("Please check if you have sourced the ${QP_ROOT}/quantum_package.rc")
print "(`source ${QP_ROOT}/quantum_package.rc`)" print("(`source ${QP_ROOT}/quantum_package.rc`)")
print sys.exit(1) print(sys.exit(1))
def save_new_module(path, l_child): def save_new_module(path, l_child):
@ -58,7 +58,7 @@ def save_new_module(path, l_child):
try: try:
os.makedirs(path) os.makedirs(path)
except OSError: except OSError:
print "The module ({0}) already exists...".format(path) print("The module ({0}) already exists...".format(path))
sys.exit(1) sys.exit(1)
with open(os.path.join(path, "NEED"), "w") as f: with open(os.path.join(path, "NEED"), "w") as f:
@ -105,7 +105,7 @@ def main(arguments):
if arguments["list"]: if arguments["list"]:
if arguments["--repositories"]: if arguments["--repositories"]:
for repo in get_repositories(): for repo in get_repositories():
print repo print(repo)
else: else:
# Search in QP_PLUGINS all directories with a NEED file # Search in QP_PLUGINS all directories with a NEED file
@ -121,7 +121,7 @@ def main(arguments):
for (x, y) in l_tmp: for (x, y) in l_tmp:
d_tmp[x] = y d_tmp[x] = y
repo_of_plugin[y] = x.replace(QP_PLUGINS+'/','') repo_of_plugin[y] = x.replace(QP_PLUGINS+'/','')
l_repository = d_tmp.keys() l_repository = list(d_tmp.keys())
if l_repository == []: if l_repository == []:
l_result = [] l_result = []
else: else:
@ -142,7 +142,7 @@ def main(arguments):
l_result = [f for f in l_plugins if f not in l_installed] l_result = [f for f in l_plugins if f not in l_installed]
for module in sorted(l_result): for module in sorted(l_result):
print "%-30s %-30s"%(module, repo_of_plugin[module]) print("%-30s %-30s"%(module, repo_of_plugin[module]))
if arguments["create"]: if arguments["create"]:
@ -159,29 +159,29 @@ def main(arguments):
path = os.path.join(QP_PLUGINS, repository, name) path = os.path.join(QP_PLUGINS, repository, name)
print "Created plugin:" print("Created plugin:")
print path, '\n' print(path, '\n')
for children in l_children: for children in l_children:
if children not in m_instance.dict_descendant: if children not in m_instance.dict_descendant:
print "Error: {0} is not a valid module.".format(children) print("Error: {0} is not a valid module.".format(children))
sys.exit(1) sys.exit(1)
print "Needed modules:" print("Needed modules:")
print l_children, '\n' print(l_children, '\n')
print "This corresponds to using the following modules:" print("This corresponds to using the following modules:")
print l_children + m_instance.l_descendant_unique(l_children), '\n' print(l_children + m_instance.l_descendant_unique(l_children), '\n')
print "Which is reduced to:" print("Which is reduced to:")
l_child_reduce = m_instance.l_reduce_tree(l_children) l_child_reduce = m_instance.l_reduce_tree(l_children)
print l_child_reduce, '\n' print(l_child_reduce, '\n')
print "Installation", print("Installation", end=' ')
save_new_module(path, l_child_reduce) save_new_module(path, l_child_reduce)
print " [ OK ]" print(" [ OK ]")
print "" print("")
arguments["create"] = False arguments["create"] = False
arguments["install"] = True arguments["install"] = True
main(arguments) main(arguments)
@ -228,7 +228,7 @@ def main(arguments):
for (x, y) in [os.path.split(f) for f in l_tmp]: for (x, y) in [os.path.split(f) for f in l_tmp]:
d_repo_of_plugin[y] = x d_repo_of_plugin[y] = x
d_repo[x] = None d_repo[x] = None
l_repository = d_repo.keys() l_repository = list(d_repo.keys())
d_plugin = get_dict_child(l_repository) d_plugin = get_dict_child(l_repository)
@ -236,7 +236,7 @@ def main(arguments):
d_child.update(d_plugin) d_child.update(d_plugin)
normalize_case = {} normalize_case = {}
for name in d_local.keys() + d_plugin.keys(): for name in list(d_local.keys()) + list(d_plugin.keys()):
normalize_case[name.lower()] = name normalize_case[name.lower()] = name
l_name = [normalize_case[name.lower()] for name in arguments["<name>"]] l_name = [normalize_case[name.lower()] for name in arguments["<name>"]]
@ -244,7 +244,7 @@ def main(arguments):
for name in l_name: for name in l_name:
if name in d_local: if name in d_local:
print "{0} Is already installed".format(name) print("{0} Is already installed".format(name))
l_module_descendant = get_l_module_descendant(d_child, l_name) l_module_descendant = get_l_module_descendant(d_child, l_name)
@ -252,10 +252,10 @@ def main(arguments):
if l_module_to_cp: if l_module_to_cp:
print "Required dependencies:" print("Required dependencies:")
print l_module_to_cp print(l_module_to_cp)
print "Installation...", print("Installation...", end=' ')
for module_to_cp in l_module_to_cp: for module_to_cp in l_module_to_cp:
src = os.path.join(d_repo_of_plugin[module_to_cp], module_to_cp) src = os.path.join(d_repo_of_plugin[module_to_cp], module_to_cp)
@ -269,10 +269,10 @@ def main(arguments):
subprocess.check_call([install]) subprocess.check_call([install])
os.chdir(wd) os.chdir(wd)
except OSError: except OSError:
print "The src directory is broken. Please remove %s" % des print("The src directory is broken. Please remove %s" % des)
raise raise
subprocess.check_call(["qp_create_ninja", "update"]) subprocess.check_call(["qp_create_ninja", "update"])
print "[ OK ]" print("[ OK ]")
elif arguments["uninstall"]: elif arguments["uninstall"]:
@ -285,17 +285,17 @@ def main(arguments):
l_failed = [name for name in l_name if name not in d_local] l_failed = [name for name in l_name if name not in d_local]
if l_failed: if l_failed:
print "Plugins not installed:" print("Plugins not installed:")
for name in sorted(l_failed): for name in sorted(l_failed):
print "%s" % name print("%s" % name)
sys.exit(1) sys.exit(1)
l_name_to_remove = l_name + \ l_name_to_remove = l_name + \
[module for module in m_instance.l_module \ [module for module in m_instance.l_module \
for name in l_name if name in d_descendant[module]] for name in l_name if name in d_descendant[module]]
print "Removing plugins:" print("Removing plugins:")
print l_name_to_remove print(l_name_to_remove)
for module in set(l_name_to_remove): for module in set(l_name_to_remove):
@ -310,7 +310,7 @@ def main(arguments):
try: try:
os.unlink(os.path.join(QP_SRC, module)) os.unlink(os.path.join(QP_SRC, module))
except OSError: except OSError:
print "%s is a core module which can't be removed" % module print("%s is a core module which can't be removed" % module)
elif arguments["update"]: elif arguments["update"]:
@ -321,7 +321,7 @@ def main(arguments):
l_repositories = get_repositories() l_repositories = get_repositories()
for repo in l_repositories: for repo in l_repositories:
print "Updating ", repo print("Updating ", repo)
os.chdir(os.path.join(QP_PLUGINS,repo)) os.chdir(os.path.join(QP_PLUGINS,repo))
git_cmd=["git", "pull"] git_cmd=["git", "pull"]
subprocess.check_call(git_cmd) subprocess.check_call(git_cmd)

6
bin/qp_set_frozen_large_core
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@ -1,4 +1,4 @@
#!/usr/bin/env python2 #!/usr/bin/env python3
""" """
@ -23,7 +23,7 @@ import os.path
try: try:
import qp_path import qp_path
except ImportError: except ImportError:
print "source .quantum_package.rc" print("source .quantum_package.rc")
raise raise
from docopt import docopt from docopt import docopt
@ -62,7 +62,7 @@ def main(arguments):
mo_num = ezfio.mo_basis_mo_num mo_num = ezfio.mo_basis_mo_num
if arguments["--query"]: if arguments["--query"]:
print n_frozen print(n_frozen)
sys.exit(0) sys.exit(0)
if n_frozen == 0: if n_frozen == 0:

18
bin/qp_test
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@ -1,4 +1,4 @@
#!/usr/bin/env python2 #!/usr/bin/env python3
# -*- coding: utf-8 -*- # -*- coding: utf-8 -*-
""" """
@ -21,8 +21,8 @@ try:
from docopt import docopt from docopt import docopt
from qp_path import QP_SRC, QP_TESTS from qp_path import QP_SRC, QP_TESTS
except ImportError: except ImportError:
print "Please check if you have sourced the ${QP_ROOT}/quantum_package.rc" print("Please check if you have sourced the ${QP_ROOT}/quantum_package.rc")
print "(`source ${QP_ROOT}/quantum_package.rc`)" print("(`source ${QP_ROOT}/quantum_package.rc`)")
sys.exit(1) sys.exit(1)
@ -54,11 +54,11 @@ def main(arguments):
os.chdir(QP_TESTS) os.chdir(QP_TESTS)
for bats_file in l_bats: for bats_file in l_bats:
print "" print("")
print "-~-~-~-~-~-~" print("-~-~-~-~-~-~")
print "" print("")
print "Running tests for %s"%(bats_file) print("Running tests for %s"%(bats_file))
print "" print("")
if arguments["-v"]: if arguments["-v"]:
p = None p = None
if arguments["TEST"]: if arguments["TEST"]:
@ -66,7 +66,7 @@ def main(arguments):
else: else:
test = "" test = ""
try: try:
os.system(test+" python2 bats_to_sh.py "+bats_file+ os.system(test+" python3 bats_to_sh.py "+bats_file+
"| bash") "| bash")
except: except:
if p: if p:

6
configure vendored
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@ -17,14 +17,14 @@ export CC=gcc
# /!\ When updating version, update also etc files # /!\ When updating version, update also etc files
EZFIO_TGZ="EZFIO.1.6.2.tar.gz" EZFIO_TGZ="EZFIO.2.0.2.tar.gz"
BATS_URL="https://github.com/bats-core/bats-core/archive/v1.1.0.tar.gz" BATS_URL="https://github.com/bats-core/bats-core/archive/v1.1.0.tar.gz"
BUBBLE_URL="https://github.com/projectatomic/bubblewrap/releases/download/v0.3.3/bubblewrap-0.3.3.tar.xz" BUBBLE_URL="https://github.com/projectatomic/bubblewrap/releases/download/v0.3.3/bubblewrap-0.3.3.tar.xz"
DOCOPT_URL="https://github.com/docopt/docopt/archive/0.6.2.tar.gz" DOCOPT_URL="https://github.com/docopt/docopt/archive/0.6.2.tar.gz"
BSE_URL="https://github.com/MolSSI-BSE/basis_set_exchange/archive/v0.8.11.tar.gz" BSE_URL="https://github.com/MolSSI-BSE/basis_set_exchange/archive/v0.8.11.tar.gz"
F77ZMQ_URL="https://github.com/scemama/f77_zmq/archive/v4.2.5.tar.gz" F77ZMQ_URL="https://github.com/scemama/f77_zmq/archive/v4.2.5.tar.gz"
GMP_URL="ftp://ftp.gnu.org/gnu/gmp/gmp-6.1.2.tar.bz2" GMP_URL="ftp://ftp.gnu.org/gnu/gmp/gmp-6.1.2.tar.bz2"
IRPF90_URL="https://gitlab.com/scemama/irpf90/-/archive/v1.7.6/irpf90-v1.7.6.tar.gz" IRPF90_URL="https://gitlab.com/scemama/irpf90/-/archive/v2.0.0/irpf90-v2.0.0.tar.gz"
LIBCAP_URL="https://git.kernel.org/pub/scm/linux/kernel/git/morgan/libcap.git/snapshot/libcap-2.25.tar.gz" LIBCAP_URL="https://git.kernel.org/pub/scm/linux/kernel/git/morgan/libcap.git/snapshot/libcap-2.25.tar.gz"
NINJA_URL="https://github.com/ninja-build/ninja/releases/download/v1.8.2/ninja-linux.zip" NINJA_URL="https://github.com/ninja-build/ninja/releases/download/v1.8.2/ninja-linux.zip"
OCAML_URL="https://raw.githubusercontent.com/ocaml/opam/master/shell/install.sh" OCAML_URL="https://raw.githubusercontent.com/ocaml/opam/master/shell/install.sh"
@ -154,7 +154,7 @@ function find_exe() {
} }
function find_python_lib() { function find_python_lib() {
python2 -c "import $1" &> /dev/null && echo "$1" || not_found python3 -c "import $1" &> /dev/null && echo "$1" || not_found
} }
function find_lib() { function find_lib() {

2
docs/Makefile
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@ -14,7 +14,7 @@ help:
.PHONY: help Makefile auto .PHONY: help Makefile auto
auto: auto:
cd source ; python2 auto_generate.py cd source ; python3 auto_generate.py
# Catch-all target: route all unknown targets to Sphinx using the new # Catch-all target: route all unknown targets to Sphinx using the new
# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). # "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).

6
docs/source/auto_generate.py
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@ -1,9 +1,9 @@
#!/usr/bin/env python2 #!/usr/bin/env python2
from __future__ import print_function
import os import os
import sys import sys
import ConfigParser import configparser
from module_handler import get_binaries from module_handler import get_binaries
@ -27,7 +27,7 @@ def generate_modules(abs_module, entities):
EZFIO = os.path.join(abs_module,'EZFIO.cfg') EZFIO = os.path.join(abs_module,'EZFIO.cfg')
if os.path.exists(EZFIO): if os.path.exists(EZFIO):
rst += ["", "EZFIO parameters", "----------------", ""] rst += ["", "EZFIO parameters", "----------------", ""]
config_file = ConfigParser.ConfigParser() config_file = configparser.ConfigParser()
with open(EZFIO, 'r') as f: with open(EZFIO, 'r') as f:
config_file.readfp(f) config_file.readfp(f)
for section in config_file.sections(): for section in config_file.sections():

2
etc/irpf90.rc
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@ -1,7 +1,7 @@
# Configuration of IRPF90 package # Configuration of IRPF90 package
# Set the path of IRPF90 here: # Set the path of IRPF90 here:
export IRPF90_PATH=${QP_ROOT}/external/irpf90-v1.7.6 export IRPF90_PATH=${QP_ROOT}/external/irpf90-v2.0.0
export PATH=${PATH}:${IRPF90_PATH}/bin export PATH=${PATH}:${IRPF90_PATH}/bin
export IRPF90=${IRPF90_PATH}/bin/irpf90 export IRPF90=${IRPF90_PATH}/bin/irpf90

BIN
external/EZFIO.1.6.2.tar.gz vendored
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BIN
external/EZFIO.2.0.2.tar.gz vendored Normal file
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8
scripts/compilation/cache_compile.py
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@ -1,4 +1,4 @@
#!/usr/bin/env python2 #!/usr/bin/env python3
""" """
Save the .o from a .f90 Save the .o from a .f90
and is the .o is asked a second time, retur it and is the .o is asked a second time, retur it
@ -13,9 +13,9 @@ import re
import shutil import shutil
import subprocess import subprocess
r = re.compile(ur'-c\s+(\S+\.[fF]90)\s+-o\s+(\S+\.o)') r = re.compile(r'-c\s+(\S+\.[fF]90)\s+-o\s+(\S+\.o)')
p = re.compile(ur'-I IRPF90_temp/\S*\s+') p = re.compile(r'-I IRPF90_temp/\S*\s+')
mod = re.compile(ur'module\s+(?P<mod>\S+).+end\s?module\s+(?P=mod)?', mod = re.compile(r'module\s+(?P<mod>\S+).+end\s?module\s+(?P=mod)?',
re.MULTILINE | re.IGNORECASE) re.MULTILINE | re.IGNORECASE)
tmpdir_root = os.environ.get("TMPDIR", failobj="/dev/shm") tmpdir_root = os.environ.get("TMPDIR", failobj="/dev/shm")

45
scripts/compilation/qp_create_ninja
View File

@ -1,4 +1,4 @@
#!/usr/bin/env python2 #!/usr/bin/env python3
# -*- coding: utf-8 -*- # -*- coding: utf-8 -*-
""" """
Usage: qp_create_ninja create <config_file> (--development | --production) Usage: qp_create_ninja create <config_file> (--development | --production)
@ -24,7 +24,7 @@ except ImportError:
"..", "..",
"quantum_package.rc")) "quantum_package.rc"))
print "\n".join(["", "Error:", "source %s" % f, ""]) print("\n".join(["", "Error:", "source %s" % f, ""]))
sys.exit(1) sys.exit(1)
# Compress path # Compress path
@ -124,7 +124,7 @@ def dict_module_genelogy_path(d_module_genelogy):
d_module_genelogy d_module_genelogy
""" """
d = dict() d = dict()
for module_rel, l_children_rel in d_module_genelogy.iteritems(): for module_rel, l_children_rel in d_module_genelogy.items():
module_abs = real_join(QP_SRC, module_rel) module_abs = real_join(QP_SRC, module_rel)
p = Path(module_abs, module_rel) p = Path(module_abs, module_rel)
@ -235,11 +235,11 @@ def ninja_ezfio_cfg_build(l_util):
""" """
l_string = [] l_string = []
for m in l_util.itervalues(): for m in l_util.values():
str_ = "build {1} {2}: build_ezfio_interface {0}" str_ = "build {1} {2}: build_ezfio_interface {0}"
l_string += [str_.format(*map(comp_path,(m.ez_cfg.abs, m.ez_interface.abs, l_string += [str_.format(*list(map(comp_path,(m.ez_cfg.abs, m.ez_interface.abs,
m.ez_config.abs)))] m.ez_config.abs))))]
l_string += [" sub_module = {0}".format(comp_path(m.ez_module.abs))] l_string += [" sub_module = {0}".format(comp_path(m.ez_module.abs))]
l_string += [""] l_string += [""]
@ -257,8 +257,8 @@ def ninja_ezfio_config_build(l_ezfio_config):
file_source = m.path_in_module file_source = m.path_in_module
file_create = m.path_in_ezfio file_create = m.path_in_ezfio
l_string += ["build {0}: build_ezfio_config {1}".format(*map(comp_path,(file_create, l_string += ["build {0}: build_ezfio_config {1}".format(*list(map(comp_path,(file_create,
file_source)))] file_source))))]
l_string += [""] l_string += [""]
return l_string return l_string
@ -291,7 +291,7 @@ def ninja_ezfio_build(l_ezfio_config, l_util):
""" """
l_ezfio_config = [i.path_in_ezfio for i in l_ezfio_config] l_ezfio_config = [i.path_in_ezfio for i in l_ezfio_config]
l_ezfio_from_cfg = [i.ez_config.abs for i in l_util.itervalues()] l_ezfio_from_cfg = [i.ez_config.abs for i in l_util.values()]
str_ = " ".join(map(comp_path,(l_ezfio_config + l_ezfio_from_cfg))) str_ = " ".join(map(comp_path,(l_ezfio_config + l_ezfio_from_cfg)))
l_string = ["build {0}: build_ezfio {1}".format(EZFIO_LIB, str_), ""] l_string = ["build {0}: build_ezfio {1}".format(EZFIO_LIB, str_), ""]
@ -335,7 +335,7 @@ def ninja_symlink_build(path_module, l_symlink):
""] ""]
for symlink in l_symlink: for symlink in l_symlink:
l_string += ["build {0}: build_symlink {1}".format(*map(comp_path,(symlink.destination, symlink.source))), ""] l_string += ["build {0}: build_symlink {1}".format(*list(map(comp_path,(symlink.destination, symlink.source)))), ""]
return l_string return l_string
@ -360,7 +360,7 @@ def ninja_gitignore_build(path_module, d_binaries, l_symlink):
path_gitignore = comp_path(join(path_module.abs, ".gitignore")) path_gitignore = comp_path(join(path_module.abs, ".gitignore"))
l_b = map(comp_path,[i.abs for i in d_binaries[path_module]]) l_b = list(map(comp_path,[i.abs for i in d_binaries[path_module]]))
root = "build {0}: build_gitignore {1}".format(path_gitignore, root = "build {0}: build_gitignore {1}".format(path_gitignore,
" ".join(l_b)) " ".join(l_b))
@ -420,9 +420,9 @@ def get_file_dependency(d_info_module):
""" """
d_irp = defaultdict(dict) d_irp = defaultdict(dict)
for module, l_children in d_info_module.iteritems(): for module, l_children in d_info_module.items():
for key, values in get_l_file_for_module(module).iteritems(): for key, values in get_l_file_for_module(module).items():
if key in ["l_src"]: if key in ["l_src"]:
values = [join(module.abs, o) for o in values] values = [join(module.abs, o) for o in values]
if key in ["l_obj"]: if key in ["l_obj"]:
@ -431,7 +431,7 @@ def get_file_dependency(d_info_module):
d_irp[module][key] = values d_irp[module][key] = values
for children in l_children: for children in l_children:
for key, values in get_l_file_for_module(children).iteritems(): for key, values in get_l_file_for_module(children).items():
if key in ["l_src"]: if key in ["l_src"]:
values = [join(module.abs, children.rel, o) values = [join(module.abs, children.rel, o)
for o in values] for o in values]
@ -495,10 +495,10 @@ def ninja_irpf90_make_build(path_module, l_needed_molule, d_irp):
# D e p e n d a n c y # # D e p e n d a n c y #
# ~#~#~#~#~#~#~#~#~#~ # # ~#~#~#~#~#~#~#~#~#~ #
l_depend = map(comp_path,d_irp[path_module]["l_depend"]) l_depend = list(map(comp_path,d_irp[path_module]["l_depend"]))
l_src = map(comp_path,d_irp[path_module]["l_src"]) l_src = list(map(comp_path,d_irp[path_module]["l_src"]))
l_obj = map(comp_path,d_irp[path_module]["l_obj"]) l_obj = list(map(comp_path,d_irp[path_module]["l_obj"]))
l_template = map(comp_path,d_irp[path_module]["l_template"]) l_template = list(map(comp_path,d_irp[path_module]["l_template"]))
if l_needed_molule: if l_needed_molule:
l_symlink = ["l_symlink_{0}".format(path_module.rel)] l_symlink = ["l_symlink_{0}".format(path_module.rel)]
@ -544,6 +544,7 @@ def get_binaries(path_module):
stdout=subprocess.PIPE, stdout=subprocess.PIPE,
stderr=subprocess.PIPE) stderr=subprocess.PIPE)
stdout, stderr = process.communicate() stdout, stderr = process.communicate()
stdout = stdout.decode()
except OSError: except OSError:
return [] return []
else: else:
@ -641,7 +642,7 @@ def ninja_binaries_build(path_module, l_children, d_binaries):
# ~#~#~ # # ~#~#~ #
ninja_module_path = join(comp_path(path_module.abs), "IRPF90_temp/build.ninja") ninja_module_path = join(comp_path(path_module.abs), "IRPF90_temp/build.ninja")
l_abs_bin = map(comp_path,[binary.abs for binary in d_binaries[path_module]]) l_abs_bin = list(map(comp_path,[binary.abs for binary in d_binaries[path_module]]))
# ~#~#~#~#~#~ # # ~#~#~#~#~#~ #
# s t r i n g # # s t r i n g #
@ -658,7 +659,7 @@ def ninja_binaries_build(path_module, l_children, d_binaries):
def ninja_module_build(path_module, d_binaries): def ninja_module_build(path_module, d_binaries):
l_abs_bin = map(comp_path,[binary.abs for binary in d_binaries[path_module]]) l_abs_bin = list(map(comp_path,[binary.abs for binary in d_binaries[path_module]]))
path_readme = os.path.join(comp_path(path_module.abs), "README.rst") path_readme = os.path.join(comp_path(path_module.abs), "README.rst")
@ -829,14 +830,14 @@ if __name__ == "__main__":
dict_root = module_instance.dict_root dict_root = module_instance.dict_root
dict_root_path = dict_module_genelogy_path(dict_root) dict_root_path = dict_module_genelogy_path(dict_root)
l_all_module = d_genealogy_path.keys() l_all_module = list(d_genealogy_path.keys())
# ~#~#~#~#~#~#~#~#~#~#~#~#~ # # ~#~#~#~#~#~#~#~#~#~#~#~#~ #
# M o d u l e _ t o _ i r p # # M o d u l e _ t o _ i r p #
# ~#~#~#~#~#~#~#~#~#~#~#~#~ # # ~#~#~#~#~#~#~#~#~#~#~#~#~ #
d_binaries = get_dict_binaries(l_all_module, mode="development") d_binaries = get_dict_binaries(l_all_module, mode="development")
l_module = d_binaries.keys() l_module = list(d_binaries.keys())
# ~#~#~#~#~#~#~#~#~#~#~#~ # # ~#~#~#~#~#~#~#~#~#~#~#~ #

14
scripts/compilation/read_compilation_cfg.py
View File

@ -1,8 +1,8 @@
#!/usr/bin/env python2 #!/usr/bin/env python3
# -*- coding: utf-8 -*- # -*- coding: utf-8 -*-
import os, sys import os, sys
import ConfigParser import configparser
def get_l_option_section(config): def get_l_option_section(config):
@ -17,10 +17,10 @@ def get_compilation_option(pwd_cfg, flag_name):
Return the flag compilation of a compile.cfg located in pwd_cfg Return the flag compilation of a compile.cfg located in pwd_cfg
""" """
if not os.path.isfile(pwd_cfg): if not os.path.isfile(pwd_cfg):
print "Configuration file %s not found"%(pwd_cfg) print("Configuration file %s not found"%(pwd_cfg))
sys.exit(1) sys.exit(1)
config = ConfigParser.ConfigParser() config = configparser.ConfigParser(inline_comment_prefixes=(';','#'))
config.read(pwd_cfg) config.read(pwd_cfg)
if flag_name == "FC" and config.getboolean("OPTION","CACHE"): if flag_name == "FC" and config.getboolean("OPTION","CACHE"):
@ -33,7 +33,7 @@ def get_compilation_option(pwd_cfg, flag_name):
for section in ["COMMON"] + l_option_section: for section in ["COMMON"] + l_option_section:
try: try:
l.extend(config.get(section, flag_name).split()) l.extend(config.get(section, flag_name).split())
except ConfigParser.NoOptionError: except configparser.NoOptionError:
pass pass
return " ".join(l) return " ".join(l)
@ -43,5 +43,5 @@ if __name__ == '__main__':
qpackage_root = os.environ['QP_ROOT'] qpackage_root = os.environ['QP_ROOT']
pwd_cfg = os.path.join(qpackage_root, "config/ifort_gpi2.cfg") pwd_cfg = os.path.join(qpackage_root, "config/ifort_gpi2.cfg")
print get_compilation_option(pwd_cfg, "FC") print(get_compilation_option(pwd_cfg, "FC"))
print get_compilation_option(pwd_cfg, "FCFLAGS") print(get_compilation_option(pwd_cfg, "FCFLAGS"))

54
scripts/ezfio_interface/ei_handler.py
View File

@ -1,4 +1,4 @@
#!/usr/bin/env python2 #!/usr/bin/env python3
# -*- coding: utf-8 -*- # -*- coding: utf-8 -*-
""" """
Welcome to the ei_handler. Welcome to the ei_handler.
@ -72,7 +72,7 @@ import sys
import os import os
import os.path import os.path
import ConfigParser import configparser
from collections import defaultdict from collections import defaultdict
from collections import namedtuple from collections import namedtuple
@ -220,8 +220,8 @@ def get_dict_config_file(module_obj):
# L o a d _ C o n f i g # # L o a d _ C o n f i g #
# ~#~#~#~#~#~#~#~#~#~#~ # # ~#~#~#~#~#~#~#~#~#~#~ #
config_file = ConfigParser.ConfigParser() config_file = configparser.ConfigParser()
config_file.readfp(open(module_obj.path)) config_file.read_file(open(module_obj.path))
# ~#~#~#~#~#~#~#~#~ # # ~#~#~#~#~#~#~#~#~ #
# F i l l _ d i c t # # F i l l _ d i c t #
@ -229,7 +229,7 @@ def get_dict_config_file(module_obj):
def error(o, p, c): def error(o, p, c):
"o option ; p provider_name ;c module_obj.path" "o option ; p provider_name ;c module_obj.path"
print "You need a {0} for {1} in {2}".format(o, p, c) print("You need a {0} for {1} in {2}".format(o, p, c))
for section in config_file.sections(): for section in config_file.sections():
# pvd = provider # pvd = provider
@ -245,13 +245,13 @@ def get_dict_config_file(module_obj):
# Check if type is avalaible # Check if type is avalaible
try: try:
type_ = config_file.get(section, "type").strip() type_ = config_file.get(section, "type").strip()
except ConfigParser.NoOptionError: except configparser.NoOptionError:
error("type", pvd, module_obj.path) error("type", pvd, module_obj.path)
sys.exit(1) sys.exit(1)
if type_ not in type_dict: if type_ not in type_dict:
print "{0} not avalaible. Choose in:".format(type_).strip() print("{0} not avalaible. Choose in:".format(type_).strip())
print ", ".join(sorted([i for i in type_dict])) print(", ".join(sorted([i for i in type_dict])))
sys.exit(1) sys.exit(1)
else: else:
d[pvd]["type"] = type_dict[type_] d[pvd]["type"] = type_dict[type_]
@ -259,18 +259,18 @@ def get_dict_config_file(module_obj):
# Fill the dict with REQUIRED information # Fill the dict with REQUIRED information
try: try:
d[pvd]["doc"] = config_file.get(section, "doc") d[pvd]["doc"] = config_file.get(section, "doc")
except ConfigParser.NoOptionError: except configparser.NoOptionError:
error("doc", pvd, module_obj.path) error("doc", pvd, module_obj.path)
sys.exit(1) sys.exit(1)
try: try:
interface = [i.lower().strip() for i in config_file.get(section, "interface").split(",")] interface = [i.lower().strip() for i in config_file.get(section, "interface").split(",")]
except ConfigParser.NoOptionError: except configparser.NoOptionError:
error("doc", pvd, module_obj.path) error("doc", pvd, module_obj.path)
sys.exit(1) sys.exit(1)
else: else:
if not any(i in ["ezfio", "provider", "ocaml"] for i in interface): if not any(i in ["ezfio", "provider", "ocaml"] for i in interface):
print "Bad keyword for interface for {0}".format(pvd) print("Bad keyword for interface for {0}".format(pvd))
sys.exit(1) sys.exit(1)
else: else:
d[pvd]["interface"] = interface d[pvd]["interface"] = interface
@ -279,7 +279,7 @@ def get_dict_config_file(module_obj):
for option in l_info_optional: for option in l_info_optional:
try: try:
d[pvd][option] = config_file.get(section, option).lower() d[pvd][option] = config_file.get(section, option).lower()
except ConfigParser.NoOptionError: except configparser.NoOptionError:
if option in d_default: if option in d_default:
d[pvd][option] = d_default[option] d[pvd][option] = d_default[option]
@ -287,7 +287,7 @@ def get_dict_config_file(module_obj):
try: try:
default_raw = config_file.get(section, "default") default_raw = config_file.get(section, "default")
except ConfigParser.NoOptionError: except configparser.NoOptionError:
if "ocaml" in d[pvd]["interface"]: if "ocaml" in d[pvd]["interface"]:
error("default", pvd, module_obj.path) error("default", pvd, module_obj.path)
sys.exit(1) sys.exit(1)
@ -322,7 +322,7 @@ def create_ezfio_provider(dict_ezfio_cfg):
dict_code_provider = dict() dict_code_provider = dict()
ez_p = EZFIO_Provider() ez_p = EZFIO_Provider()
for provider_name, dict_info in dict_ezfio_cfg.iteritems(): for provider_name, dict_info in dict_ezfio_cfg.items():
if "provider" in dict_info["interface"]: if "provider" in dict_info["interface"]:
ez_p.set_type(dict_info['type'].fortran) ez_p.set_type(dict_info['type'].fortran)
ez_p.set_name(provider_name) ez_p.set_name(provider_name)
@ -364,7 +364,7 @@ def save_ezfio_provider(path_head, dict_code_provider):
"! from file {0}/EZFIO.cfg".format(path_head), "! from file {0}/EZFIO.cfg".format(path_head),
"\n"] "\n"]
l_output += [code for code in dict_code_provider.values()] l_output += [code for code in list(dict_code_provider.values())]
output = "\n".join(l_output) output = "\n".join(l_output)
@ -381,22 +381,22 @@ def create_ezfio_stuff(dict_ezfio_cfg, config_or_default="config"):
def size_format_to_ezfio(size_raw): def size_format_to_ezfio(size_raw):
""" """
If size_raw == "=" is a formula -> do nothing; return If size_raw == "=" is a formula -> do nothing; return
Else convert the born of a multidimential array Else convert the range of a multidimential array
(12,begin:end) into (12,begin+end+1) for example (12,begin:end) into (12,begin+end+1) for example
If the value are between parenthses -> do nothing; return If the values are between parenthses -> do nothing; return
""" """
size_raw = str(size_raw) size_raw = str(size_raw)
if size_raw.startswith('='): if size_raw.startswith('='):
size_convert = size_raw.replace('.', '_') size_convert = size_raw.replace('.', '_')
else: else:
size_raw = provider_info["size"].translate(None, "()") size_raw = provider_info["size"].translate(str.maketrans("","","()"))
size_raw = size_raw.replace('.', '_') size_raw = size_raw.replace('.', '_')
a_size_raw = [] a_size_raw = []
for dim in size_raw.split(","): for dim in size_raw.split(","):
try: try:
(begin, end) = map(str.strip, dim.split(":")) (begin, end) = list(map(str.strip, dim.split(":")))
except ValueError: except ValueError:
a_size_raw.append(dim) a_size_raw.append(dim)
else: else:
@ -423,7 +423,7 @@ def create_ezfio_stuff(dict_ezfio_cfg, config_or_default="config"):
lenmax_name = max([len(i) for i in dict_ezfio_cfg]) lenmax_name = max([len(i) for i in dict_ezfio_cfg])
lenmax_type = max([len(i["type"].fortran) lenmax_type = max([len(i["type"].fortran)
for i in dict_ezfio_cfg.values()]) for i in list(dict_ezfio_cfg.values())])
str_name_format = create_format_string(lenmax_name + 2) str_name_format = create_format_string(lenmax_name + 2)
str_type_format = create_format_string(lenmax_type + 2) str_type_format = create_format_string(lenmax_type + 2)
@ -433,15 +433,15 @@ def create_ezfio_stuff(dict_ezfio_cfg, config_or_default="config"):
# ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~# # # ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~# #
# Checking is many ezfio_dir provided # Checking is many ezfio_dir provided
l_ezfio_dir = [d['ezfio_dir'] for d in dict_ezfio_cfg.values()] l_ezfio_dir = [d['ezfio_dir'] for d in list(dict_ezfio_cfg.values())]
if not l_ezfio_dir.count(l_ezfio_dir[0]) == len(l_ezfio_dir): if not l_ezfio_dir.count(l_ezfio_dir[0]) == len(l_ezfio_dir):
print >> sys.stderr, "You have many ezfio_dir. Not supported yet" print("You have many ezfio_dir. Not supported yet", file=sys.stderr)
raise TypeError raise TypeError
else: else:
result = [l_ezfio_dir[0]] result = [l_ezfio_dir[0]]
for provider_name, provider_info in sorted(dict_ezfio_cfg.iteritems()): for provider_name, provider_info in sorted(dict_ezfio_cfg.items()):
# Get the value from dict # Get the value from dict
name_raw = provider_info["ezfio_name"].lower() name_raw = provider_info["ezfio_name"].lower()
@ -532,7 +532,7 @@ def create_ocaml_input(dict_ezfio_cfg, module_lower):
l_type = [] l_type = []
l_doc = [] l_doc = []
for k, v in dict_ezfio_cfg.iteritems(): for k, v in dict_ezfio_cfg.items():
if "ocaml" in v['interface']: if "ocaml" in v['interface']:
l_ezfio_name.append(v['ezfio_name']) l_ezfio_name.append(v['ezfio_name'])
l_type.append(v["type"]) l_type.append(v["type"])
@ -580,7 +580,7 @@ def create_ocaml_input(dict_ezfio_cfg, module_lower):
'(* =~=~=~==~=~~=~=~=~=~=~=~=~ *)', '(* =~=~=~==~=~~=~=~=~=~=~=~=~ *)',
""] ""]
for provider_name, d_val in sorted(dict_ezfio_cfg.iteritems()): for provider_name, d_val in sorted(dict_ezfio_cfg.items()):
if 'default' not in d_val: if 'default' not in d_val:
continue continue
@ -655,7 +655,7 @@ def get_l_module_with_auto_generate_ocaml_lower():
l_module_lower = [] l_module_lower = []
import re import re
p = re.compile(ur'interface:.*ocaml') p = re.compile(r'interface:.*ocaml')
for f in l_folder: for f in l_folder:
path = "{0}/{1}/EZFIO.cfg".format(QP_SRC, f) path = "{0}/{1}/EZFIO.cfg".format(QP_SRC, f)
@ -782,7 +782,7 @@ if __name__ == "__main__":
# #
if arguments["list_supported_types"]: if arguments["list_supported_types"]:
for i in sorted(get_type_dict()): for i in sorted(get_type_dict()):
print i print(i)
sys.exit(0) sys.exit(0)
if arguments["ocaml_global"]: if arguments["ocaml_global"]:

10
scripts/ezfio_interface/ezfio_generate_ocaml.py
View File

@ -1,4 +1,4 @@
#!/usr/bin/env python2 #!/usr/bin/env python3
""" """
This program generates all the This program generates all the
OCaml templates needed by qp_edit OCaml templates needed by qp_edit
@ -17,12 +17,12 @@ class EZFIO_ocaml(object):
def __init__(self, **kwargs): def __init__(self, **kwargs):
for k, v in kwargs.iteritems(): for k, v in kwargs.items():
try: try:
exec "self.{0} = {1}".format(k, v) exec("self.{0} = {1}".format(k, v))
except NameError: except NameError:
exec "self.{0} = '{1}'".format(k, v) exec("self.{0} = '{1}'".format(k, v))
@property @property
def Ocaml_type(self): def Ocaml_type(self):
@ -39,7 +39,7 @@ class EZFIO_ocaml(object):
def check_if_init(self, l_arg, name): def check_if_init(self, l_arg, name):
for i in l_arg: for i in l_arg:
try: try:
exec "self.{0}".format(i) exec("self.{0}".format(i))
except AttributeError: except AttributeError:
msg = "You need to provide a '{0}' for creating {1}" msg = "You need to provide a '{0}' for creating {1}"
raise KeyError(msg.format(i, name)) raise KeyError(msg.format(i, name))

8
scripts/ezfio_interface/ezfio_generate_provider.py
View File

@ -1,4 +1,4 @@
#!/usr/bin/env python2 #!/usr/bin/env python3
__author__ = "Applencourt PEP8" __author__ = "Applencourt PEP8"
__date__ = "jeudi 26 mars 2015, 12:49:35 (UTC+0100)" __date__ = "jeudi 26 mars 2015, 12:49:35 (UTC+0100)"
@ -88,7 +88,7 @@ END_PROVIDER
def __init__(self): def __init__(self):
self.values = "type doc name ezfio_dir ezfio_name write output".split() self.values = "type doc name ezfio_dir ezfio_name write output".split()
for v in self.values: for v in self.values:
exec "self.{0} = None".format(v) exec("self.{0} = None".format(v))
def __repr__(self): def __repr__(self):
self.set_write() self.set_write()
@ -96,7 +96,7 @@ END_PROVIDER
for v in self.values: for v in self.values:
if not v: if not v:
msg = "Error : %s is not set in EZFIO.cfg" % (v) msg = "Error : %s is not set in EZFIO.cfg" % (v)
print >>sys.stderr, msg print(msg, file=sys.stderr)
sys.exit(1) sys.exit(1)
if "size" not in self.__dict__: if "size" not in self.__dict__:
self.__dict__["size"] = "" self.__dict__["size"] = ""
@ -167,7 +167,7 @@ def test_module():
T.set_ezfio_dir("Hartree_Fock") T.set_ezfio_dir("Hartree_Fock")
T.set_ezfio_name("thresh_SCF") T.set_ezfio_name("thresh_SCF")
T.set_output("output_Hartree_Fock") T.set_output("output_Hartree_Fock")
print T print(T)
if __name__ == '__main__': if __name__ == '__main__':
test_module() test_module()

4
scripts/generate_h_apply.py
View File

@ -1,4 +1,4 @@
#!/usr/bin/env python2 #!/usr/bin/env python3
import os import os
@ -155,7 +155,7 @@ class H_apply(object):
def __repr__(self): def __repr__(self):
buffer = self.template buffer = self.template
for key,value in self.data.items(): for key,value in list(self.data.items()):
buffer = buffer.replace('$'+key, value) buffer = buffer.replace('$'+key, value)
return buffer return buffer

6
scripts/hello.py
View File

@ -1,4 +1,4 @@
#!/usr/bin/env python2 #!/usr/bin/env python3
import random import random
@ -131,8 +131,8 @@ _ __ `/___ __ \__ ___/__ __ \
""" ] """ ]
print random.choice(hello) print(random.choice(hello))
print "\n -- Quantum Package Shell --\n" print("\n -- Quantum Package Shell --\n")

27
scripts/module/module_handler.py
View File

@ -1,4 +1,4 @@
#!/usr/bin/env python2 #!/usr/bin/env python3
# -*- coding: utf-8 -*- # -*- coding: utf-8 -*-
""" """
Module utilitary Module utilitary
@ -25,7 +25,7 @@ try:
from docopt import docopt from docopt import docopt
from qp_path import QP_SRC, QP_ROOT, QP_PLUGINS, QP_EZFIO from qp_path import QP_SRC, QP_ROOT, QP_PLUGINS, QP_EZFIO
except ImportError: except ImportError:
print "source .quantum_package.rc" print("source .quantum_package.rc")
raise raise
@ -50,6 +50,7 @@ def get_binaries(path_module):
stdout=subprocess.PIPE, stdout=subprocess.PIPE,
stderr=subprocess.PIPE) stderr=subprocess.PIPE)
stdout, stderr = process.communicate() stdout, stderr = process.communicate()
stdout = stdout.decode()
except OSError: except OSError:
return [] return []
else: else:
@ -106,9 +107,9 @@ def get_l_module_descendant(d_child, l_module):
try: try:
l.extend(get_l_module_descendant(d_child, d_child[module])) l.extend(get_l_module_descendant(d_child, d_child[module]))
except KeyError: except KeyError:
print >> sys.stderr, "Error: " print("Error: ", file=sys.stderr)
print >> sys.stderr, "`{0}` is not a submodule".format(module) print("`{0}` is not a submodule".format(module), file=sys.stderr)
print >> sys.stderr, "Check the typo (spelling, case, '/', etc.) " print("Check the typo (spelling, case, '/', etc.) ", file=sys.stderr)
sys.exit(1) sys.exit(1)
return list(set(l)) return list(set(l))
@ -120,7 +121,7 @@ class ModuleHandler():
@property @property
def l_module(self): def l_module(self):
return self.dict_child.keys() return list(self.dict_child.keys())
@property @property
def dict_parent(self): def dict_parent(self):
@ -132,7 +133,7 @@ class ModuleHandler():
d = {} d = {}
for module_name in d_child: for module_name in d_child:
d[module_name] = [i for i in d_child.keys() d[module_name] = [i for i in list(d_child.keys())
if module_name in d_child[i]] if module_name in d_child[i]]
return d return d
@ -151,8 +152,8 @@ class ModuleHandler():
d[module_name] = get_l_module_descendant(d_child, d[module_name] = get_l_module_descendant(d_child,
d_child[module_name]) d_child[module_name])
except KeyError: except KeyError:
print "Check NEED for {0}".format( print("Check NEED for {0}".format(
module_name) module_name))
sys.exit(1) sys.exit(1)
return d return d
@ -185,7 +186,7 @@ class ModuleHandler():
for e in d_desc[module]: for e in d_desc[module]:
d[e] = 1 d[e] = 1
return d.keys() return list(d.keys())
def l_reduce_tree(self, l_module): def l_reduce_tree(self, l_module):
"""For a list of module in input return only the root""" """For a list of module in input return only the root"""
@ -218,8 +219,8 @@ if __name__ == '__main__':
for module in l_module: for module in l_module:
if not is_module(module): if not is_module(module):
print "{0} is not a valid module. Abort".format(module) print("{0} is not a valid module. Abort".format(module))
print "No NEED in it" print("No NEED in it")
sys.exit(1) sys.exit(1)
m = ModuleHandler() m = ModuleHandler()
@ -227,7 +228,7 @@ if __name__ == '__main__':
if arguments['print_descendant']: if arguments['print_descendant']:
for module in l_module: for module in l_module:
print " ".join(sorted(m.l_descendant_unique([module]))) print(" ".join(sorted(m.l_descendant_unique([module]))))
if arguments["clean"]: if arguments["clean"]:

8
scripts/perturbation.py
View File

@ -1,4 +1,4 @@
#!/usr/bin/env python2 #!/usr/bin/env python3
import os import os
from qp_path import QP_SRC from qp_path import QP_SRC
@ -7,7 +7,7 @@ Pert_dir = os.path.join(QP_SRC,"perturbation")
perturbations = [] perturbations = []
for filename in filter(lambda x: x.endswith(".irp.f"), os.listdir(Pert_dir)): for filename in [x for x in os.listdir(Pert_dir) if x.endswith(".irp.f")]:
filename = os.path.join(Pert_dir,filename) filename = os.path.join(Pert_dir,filename)
file = open(filename,'r') file = open(filename,'r')
@ -22,6 +22,6 @@ for filename in filter(lambda x: x.endswith(".irp.f"), os.listdir(Pert_dir)):
if __name__ == '__main__': if __name__ == '__main__':
print 'Perturbations:' print('Perturbations:')
for k in perturbations: for k in perturbations:
print '* ', k print('* ', k)

26
scripts/utility/get_groups
View File

@ -1,7 +1,7 @@
#!/usr/bin/env python2 #!/usr/bin/env python3
# -*- coding: utf-8 -*- # -*- coding: utf-8 -*-
import urllib import urllib.request, urllib.parse, urllib.error
import sys import sys
from bs4 import BeautifulSoup from bs4 import BeautifulSoup
@ -35,11 +35,11 @@ def clean_up(text):
return False return False
else: else:
return y[0] in irred return y[0] in irred
data = filter(f,data)[:len(irred)] data = list(filter(f,data))[:len(irred)]
for line in data: for line in data:
s = line.replace('*','').split() s = line.replace('*','').split()
l = irred[s[0]] l = irred[s[0]]
data[l] = map(float,s[1:len(irred)+1]) data[l] = list(map(float,s[1:len(irred)+1]))
d = {} d = {}
e = {} e = {}
@ -48,23 +48,23 @@ def clean_up(text):
for k in sop: for k in sop:
e[sop[k]] = k e[sop[k]] = k
n = len(irred) n = len(irred)
print "Group\t", group, "\nn\t", n print("Group\t", group, "\nn\t", n)
print "\n \tIrred \tOperation" print("\n \tIrred \tOperation")
for i in range(n): for i in range(n):
print "%4d \t %s \t %s"%(i+1, d[i].ljust(10), e[i].ljust(10)) print("%4d \t %s \t %s"%(i+1, d[i].ljust(10), e[i].ljust(10)))
print "\nTable\n ", print("\nTable\n ", end=' ')
for j in range(n): for j in range(n):
print "%8s "%(str(j+1).center(8)), print("%8s "%(str(j+1).center(8)), end=' ')
for i in range(n): for i in range(n):
print "\n%4d "%(i+1), print("\n%4d "%(i+1), end=' ')
for j in range(n): for j in range(n):
print "%8.5f "%(data[i][j]), print("%8.5f "%(data[i][j]), end=' ')
print "\n" print("\n")
def main(): def main():
for group in sys.argv[1:]: for group in sys.argv[1:]:
f = urllib.urlopen(address%(group)) f = urllib.request.urlopen(address%(group))
html = f.read().split('\n',1)[1] html = f.read().split('\n',1)[1]
text = clean_up(html) text = clean_up(html)

2
scripts/utility/qp_bitmasks.py
View File

@ -1,4 +1,4 @@
#!/usr/bin/env python2 #!/usr/bin/env python3
BIT_KIND_SIZE=64 BIT_KIND_SIZE=64

2
scripts/utility/qp_path.py
View File

@ -1,7 +1,7 @@
#!/usr/bin/env python3 #!/usr/bin/env python3
# -*- coding: utf-8 -*- # -*- coding: utf-8 -*-
from __future__ import print_function
import os import os
import sys import sys

6
src/cis/h_apply.irp.f
View File

@ -1,14 +1,14 @@
! Generates subroutine H_apply_cis ! Generates subroutine H_apply_cis
! -------------------------------- ! --------------------------------
BEGIN_SHELL [ /usr/bin/env python2 ] BEGIN_SHELL [ /usr/bin/env python3 ]
from generate_h_apply import H_apply from generate_h_apply import H_apply
H = H_apply("cis",do_double_exc=False) H = H_apply("cis",do_double_exc=False)
print H print(H)
H = H_apply("cis_sym",do_double_exc=False) H = H_apply("cis_sym",do_double_exc=False)
H.filter_only_connected_to_hf() H.filter_only_connected_to_hf()
print H print(H)
END_SHELL END_SHELL

6
src/cisd/h_apply.irp.f
View File

@ -1,13 +1,13 @@
! Generates subroutine H_apply_cisd ! Generates subroutine H_apply_cisd
! ---------------------------------- ! ----------------------------------
BEGIN_SHELL [ /usr/bin/env python2 ] BEGIN_SHELL [ /usr/bin/env python3 ]
from generate_h_apply import H_apply from generate_h_apply import H_apply
H = H_apply("cisd",do_double_exc=True) H = H_apply("cisd",do_double_exc=True)
print H print(H)
H = H_apply("cisd_sym",do_double_exc=True) H = H_apply("cisd_sym",do_double_exc=True)
H.filter_only_connected_to_hf() H.filter_only_connected_to_hf()
print H print(H)
END_SHELL END_SHELL

6
src/density_for_dft/EZFIO.cfg
View File

@ -12,14 +12,12 @@ default: 0.5
[no_core_density] [no_core_density]
type: character*(32) type: character*(32)
doc: Type of density doc: Type of density. If [no_core_dm] then all elements of the density matrix involving at least one orbital set as core are set to zero
doc: if [no_core_dm] then all elements of the density matrix involving at least one orbital set as core are set to zero
interface: ezfio, provider, ocaml interface: ezfio, provider, ocaml
default: full_density default: full_density
[normalize_dm] [normalize_dm]
type: logical type: logical
doc: Type of density doc: Type of density. If .True., then you normalize the no_core_dm to elec_alpha_num - n_core_orb and elec_beta_num - n_core_orb
doc: if .True., then you normalize the no_core_dm to elec_alpha_num - n_core_orb and elec_beta_num - n_core_orb
interface: ezfio, provider, ocaml interface: ezfio, provider, ocaml
default: True default: True

1
src/determinants/EZFIO.cfg
View File

@ -76,7 +76,6 @@ type: integer
interface: ezfio interface: ezfio
doc: Number of determinants to print in qp_edit doc: Number of determinants to print in qp_edit
type: integer type: integer
interface: ezfio
[psi_coef] [psi_coef]
interface: ezfio interface: ezfio

24
src/dft_one_e/e_xc_general.irp.f
View File

@ -4,7 +4,7 @@ BEGIN_PROVIDER [double precision, energy_x, (N_states)]
! correlation energies general providers. ! correlation energies general providers.
END_DOC END_DOC
BEGIN_SHELL [ /usr/bin/env python2 ] BEGIN_SHELL [ /usr/bin/env python3 ]
import os import os
import glob import glob
from qp_path import QP_SRC from qp_path import QP_SRC
@ -13,16 +13,16 @@ os.chdir(funcdir)
functionals = map(lambda x : x.replace(".irp.f",""), glob.glob("*.irp.f")) functionals = map(lambda x : x.replace(".irp.f",""), glob.glob("*.irp.f"))
prefix = "" prefix = ""
for f in functionals: for f in functionals:
print """ print("""
%sif (trim(exchange_functional) == '%s') then %sif (trim(exchange_functional) == '%s') then
energy_x = (1.d0 - HF_exchange ) * energy_x_%s"""%(prefix, f, f) energy_x = (1.d0 - HF_exchange ) * energy_x_%s"""%(prefix, f, f))
prefix = "else " prefix = "else "
print """ print("""
else else
print *, 'exchange functional required does not exist ...' print *, 'exchange functional required does not exist ...'
print *, 'exchange_functional ',exchange_functional print *, 'exchange_functional ',exchange_functional
stop""" stop""")
print "endif" print("endif")
END_SHELL END_SHELL
@ -38,7 +38,7 @@ print "endif"
! correlation and exchange energies general providers. ! correlation and exchange energies general providers.
END_DOC END_DOC
BEGIN_SHELL [ /usr/bin/env python2 ] BEGIN_SHELL [ /usr/bin/env python3 ]
import os import os
import glob import glob
from qp_path import QP_SRC from qp_path import QP_SRC
@ -47,17 +47,17 @@ os.chdir(funcdir)
functionals = map(lambda x : x.replace(".irp.f",""), glob.glob("*.irp.f")) functionals = map(lambda x : x.replace(".irp.f",""), glob.glob("*.irp.f"))
prefix = "" prefix = ""
for f in functionals: for f in functionals:
print """ print("""
%sif (trim(correlation_functional) == '%s') then %sif (trim(correlation_functional) == '%s') then
energy_c = energy_c_%s"""%(prefix, f, f) energy_c = energy_c_%s"""%(prefix, f, f) )
prefix = "else " prefix = "else "
print """ print("""
else else
print*, 'Correlation functional required does not exist ...' print*, 'Correlation functional required does not exist ...'
print*,'correlation_functional ',correlation_functional print*,'correlation_functional ',correlation_functional
stop""" stop""")
print "endif" print("endif")
END_SHELL END_SHELL

36
src/dft_one_e/pot_general.irp.f
View File

@ -5,7 +5,7 @@
! general providers for the alpha/beta exchange potentials on the AO basis ! general providers for the alpha/beta exchange potentials on the AO basis
END_DOC END_DOC
BEGIN_SHELL [ /usr/bin/env python2 ] BEGIN_SHELL [ /usr/bin/env python3 ]
import os import os
import glob import glob
from qp_path import QP_SRC from qp_path import QP_SRC
@ -15,17 +15,17 @@ functionals = map(lambda x : x.replace(".irp.f",""), glob.glob("*.irp.f"))
prefix = "" prefix = ""
for f in functionals: for f in functionals:
print """ print("""
%sif (trim(exchange_functional) == '%s') then %sif (trim(exchange_functional) == '%s') then
potential_x_alpha_ao = ( 1.d0 - HF_exchange ) * potential_x_alpha_ao_%s potential_x_alpha_ao = ( 1.d0 - HF_exchange ) * potential_x_alpha_ao_%s
potential_x_beta_ao = ( 1.d0 - HF_exchange ) * potential_x_beta_ao_%s"""%(prefix, f, f, f) potential_x_beta_ao = ( 1.d0 - HF_exchange ) * potential_x_beta_ao_%s"""%(prefix, f, f, f) )
prefix = "else " prefix = "else "
print """ print("""
else else
print*, 'exchange functional required does not exist ...' print*, 'exchange functional required does not exist ...'
print*,'exchange_functional ',exchange_functional print*,'exchange_functional ',exchange_functional
stop""" stop""")
print "endif" print("endif")
END_SHELL END_SHELL
@ -41,7 +41,7 @@ print "endif"
! general providers for the alpha/beta correlation potentials on the AO basis ! general providers for the alpha/beta correlation potentials on the AO basis
END_DOC END_DOC
BEGIN_SHELL [ /usr/bin/env python2 ] BEGIN_SHELL [ /usr/bin/env python3 ]
import os import os
import glob import glob
from qp_path import QP_SRC from qp_path import QP_SRC
@ -51,18 +51,18 @@ functionals = map(lambda x : x.replace(".irp.f",""), glob.glob("*.irp.f"))
prefix = "" prefix = ""
for f in functionals: for f in functionals:
print """ print("""
%sif (trim(correlation_functional) == '%s') then %sif (trim(correlation_functional) == '%s') then
potential_c_alpha_ao = potential_c_alpha_ao_%s potential_c_alpha_ao = potential_c_alpha_ao_%s
potential_c_beta_ao = potential_c_beta_ao_%s"""%(prefix, f, f, f) potential_c_beta_ao = potential_c_beta_ao_%s"""%(prefix, f, f, f) )
prefix = "else " prefix = "else "
print """ print("""
else else
print*, 'Correlation functional required does not exist ...' print*, 'Correlation functional required does not exist ...'
print*,'correlation_functional ',correlation_functional print*,'correlation_functional ',correlation_functional
stop""" stop""" )
print "endif" print("endif")
END_SHELL END_SHELL
@ -200,7 +200,7 @@ print "endif"
! general providers for the alpha/beta exchange/correlation potentials on the AO basis ! general providers for the alpha/beta exchange/correlation potentials on the AO basis
END_DOC END_DOC
BEGIN_SHELL [ /usr/bin/env python2 ] BEGIN_SHELL [ /usr/bin/env python3 ]
import os import os
import glob import glob
from qp_path import QP_SRC from qp_path import QP_SRC
@ -210,17 +210,17 @@ functionals = map(lambda x : x.replace(".irp.f",""), glob.glob("*.irp.f"))
prefix = "" prefix = ""
for f in functionals: for f in functionals:
print """ print("""
%sif (trim(exchange_functional) == '%s') then %sif (trim(exchange_functional) == '%s') then
potential_xc_alpha_ao = potential_xc_alpha_ao_%s potential_xc_alpha_ao = potential_xc_alpha_ao_%s
potential_xc_beta_ao = potential_xc_beta_ao_%s"""%(prefix, f, f, f) potential_xc_beta_ao = potential_xc_beta_ao_%s"""%(prefix, f, f, f) )
prefix = "else " prefix = "else "
print """ print("""
else else
print*, 'exchange functional required does not exist ...' print*, 'exchange functional required does not exist ...'
print*,'exchange_functional ',exchange_functional print*,'exchange_functional ',exchange_functional
stop""" stop""")
print "endif" print("endif")
END_SHELL END_SHELL

4
src/perturbation/perturbation.irp.f
View File

@ -1,4 +1,4 @@
BEGIN_SHELL [ /usr/bin/env python2 ] BEGIN_SHELL [ /usr/bin/env python3 ]
from perturbation import perturbations from perturbation import perturbations
import os import os
@ -8,6 +8,6 @@ template = file.read()
file.close() file.close()
for p in perturbations: for p in perturbations:
print template.replace("$PERT",p) print(template.replace("$PERT",p))
END_SHELL END_SHELL

2
src/perturbation/perturbation.template.f
View File

@ -1,4 +1,4 @@
BEGIN_SHELL [ /usr/bin/env python2 ] BEGIN_SHELL [ /usr/bin/env python3 ]
import perturbation import perturbation
END_SHELL END_SHELL