From c22daadf40fc5537ed8ee61fd0a8a01b1e1fde3d Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Mon, 27 Jan 2020 22:30:01 +0100 Subject: [PATCH] Moving to Python3. --- bin/qp_convert_output_to_ezfio | 54 +++++++++++++++++----------------- bin/qp_set_frozen_core | 6 ++-- external/Python/.gitignore | 46 +++++++++++++++++++++++++++++ ocaml/qp_tunnel.ml | 48 ------------------------------ scripts/utility/qp_path.py | 5 ++-- tests/bats_to_sh.py | 8 ++--- 6 files changed, 83 insertions(+), 84 deletions(-) diff --git a/bin/qp_convert_output_to_ezfio b/bin/qp_convert_output_to_ezfio index 30faa686..5f0c4771 100755 --- a/bin/qp_convert_output_to_ezfio +++ b/bin/qp_convert_output_to_ezfio @@ -1,4 +1,4 @@ -#!/usr/bin/env python2 +#!/usr/bin/env python3 """ convert output of GAMESS/GAU$$IAN to ezfio @@ -22,7 +22,7 @@ try: QP_ROOT = os.environ["QP_ROOT"] QP_EZFIO = os.environ["QP_EZFIO"] except KeyError: - print "Error: QP_ROOT environment variable not found." + print("Error: QP_ROOT environment variable not found.") sys.exit(1) else: sys.path = [QP_EZFIO + "/Python", @@ -30,10 +30,11 @@ else: QP_ROOT + "/install", QP_ROOT + "/scripts"] + sys.path +from resultsFile import * try: from resultsFile import * except: - print "Error: resultsFile Python library not installed" + print("Error: resultsFile Python library not installed") sys.exit(1) @@ -48,17 +49,17 @@ def write_ezfio(res, filename): # |_ | _ _ _|_ ._ _ ._ _ # |_ | (/_ (_ |_ | (_) | | _> # - print "Electrons\t...\t", + print("Electrons\t...\t", end=' ') ezfio.set_electrons_elec_alpha_num(res.num_alpha) ezfio.set_electrons_elec_beta_num(res.num_beta) - print "OK" + print("OK") # # |\ | _ | _ o # | \| |_| (_ | (/_ | # - print "Nuclei\t\t...\t", + print("Nuclei\t\t...\t", end=' ') # ~#~#~#~ # # I n i t # # ~#~#~#~ # @@ -93,24 +94,23 @@ def write_ezfio(res, filename): # Transformt H1 into H import re - p = re.compile(ur'(\d*)$') + p = re.compile(r'(\d*)$') label = [p.sub("", x.name).capitalize() for x in res.geometry] ezfio.set_nuclei_nucl_label(label) ezfio.set_nuclei_nucl_coord(coord_x + coord_y + coord_z) - print "OK" + print("OK") # _ # /\ _ _ |_) _. _ o _ # /--\ (_) _> |_) (_| _> | _> # - print "AOS\t\t...\t", + print("AOS\t\t...\t", end=' ') # ~#~#~#~ # # I n i t # # ~#~#~#~ # - import string at = [] num_prim = [] power_x = [] @@ -131,9 +131,9 @@ def write_ezfio(res, filename): at.append(i + 1) num_prim.append(len(b.prim)) s = b.sym - power_x.append(string.count(s, "x")) - power_y.append(string.count(s, "y")) - power_z.append(string.count(s, "z")) + power_x.append(str.count(s, "x")) + power_y.append(str.count(s, "y")) + power_z.append(str.count(s, "z")) coefficient.append(b.coef) exponent.append([p.expo for p in b.prim]) @@ -175,14 +175,14 @@ def write_ezfio(res, filename): ezfio.set_ao_basis_ao_expo(expo) ezfio.set_ao_basis_ao_basis("Read by resultsFile") - print "OK" + print("OK") # _ # |\/| _ _ |_) _. _ o _ # | | (_) _> |_) (_| _> | _> # - print "MOS\t\t...\t", + print("MOS\t\t...\t", end=' ') # ~#~#~#~ # # I n i t # # ~#~#~#~ # @@ -205,9 +205,9 @@ def write_ezfio(res, filename): virtual = [] active = [(allMOs[i].eigenvalue, i) for i in range(len(allMOs))] - closed = map(lambda x: x[1], closed) - active = map(lambda x: x[1], active) - virtual = map(lambda x: x[1], virtual) + closed = [x[1] for x in closed] + active = [x[1] for x in active] + virtual = [x[1] for x in virtual] MOindices = closed + active + virtual MOs = [] @@ -223,7 +223,7 @@ def write_ezfio(res, filename): MOmap[i] = MOindices.index(i) energies = [] - for i in xrange(mo_num): + for i in range(mo_num): energies.append(MOs[i].eigenvalue) if res.occ_num is not None: @@ -237,11 +237,11 @@ def write_ezfio(res, filename): MoMatrix = [] sym0 = [i.sym for i in res.mo_sets[MO_type]] sym = [i.sym for i in res.mo_sets[MO_type]] - for i in xrange(len(sym)): + for i in range(len(sym)): sym[MOmap[i]] = sym0[i] MoMatrix = [] - for i in xrange(len(MOs)): + for i in range(len(MOs)): m = MOs[i] for coef in m.vector: MoMatrix.append(coef) @@ -256,10 +256,10 @@ def write_ezfio(res, filename): ezfio.set_mo_basis_mo_num(mo_num) ezfio.set_mo_basis_mo_occ(OccNum) ezfio.set_mo_basis_mo_coef(MoMatrix) - print "OK" + print("OK") - print "Pseudos\t\t...\t", + print("Pseudos\t\t...\t", end=' ') try: lmax = 0 nucl_charge_remove = [] @@ -327,7 +327,7 @@ def write_ezfio(res, filename): else: ezfio.set_pseudo_do_pseudo(True) - print "OK" + print("OK") @@ -354,15 +354,15 @@ if __name__ == '__main__': except: raise else: - print FILE, 'recognized as', str(RES_FILE).split('.')[-1].split()[0] + print(FILE, 'recognized as', str(RES_FILE).split('.')[-1].split()[0]) write_ezfio(RES_FILE, EZFIO_FILE) sys.stdout.flush() if os.system("qp_run save_ortho_mos "+EZFIO_FILE) != 0: - print """Warning: You need to run + print("""Warning: You need to run qp run save_ortho_mos to be sure your MOs will be orthogonal, which is not the case when -the MOs are read from output files (not enough precision in output).""" +the MOs are read from output files (not enough precision in output).""") diff --git a/bin/qp_set_frozen_core b/bin/qp_set_frozen_core index 25b450dd..b00797e2 100755 --- a/bin/qp_set_frozen_core +++ b/bin/qp_set_frozen_core @@ -1,4 +1,4 @@ -#!/usr/bin/env python2 +#!/usr/bin/env python3 """ @@ -49,7 +49,7 @@ import os.path try: import qp_path except ImportError: - print "source .quantum_package.rc" + print("source .quantum_package.rc") raise from docopt import docopt @@ -102,7 +102,7 @@ def main(arguments): mo_num = ezfio.mo_basis_mo_num if arguments["--query"]: - print n_frozen + print(n_frozen) sys.exit(0) if n_frozen == 0: diff --git a/external/Python/.gitignore b/external/Python/.gitignore index e69de29b..1cd79fd6 100644 --- a/external/Python/.gitignore +++ b/external/Python/.gitignore @@ -0,0 +1,46 @@ +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] + +# C extensions +*.so + +# Distribution / packaging +.Python +env/ +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ + +# PyInstaller +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.coverage +.cache +nosetests.xml +coverage.xml + +# Translations +*.mo +*.pot + +# Django stuff: +*.log + +# Sphinx documentation +docs/_build/ + +# PyBuilder +target/ diff --git a/ocaml/qp_tunnel.ml b/ocaml/qp_tunnel.ml index e7322995..84e50eb5 100644 --- a/ocaml/qp_tunnel.ml +++ b/ocaml/qp_tunnel.ml @@ -21,10 +21,6 @@ let () = doc="Downloads the EZFIO directory." ; arg=Without_arg; } ; - { short='v' ; long="verbose" ; opt=Optional ; - doc="Prints the transfer speed." ; - arg=Without_arg; } ; - anonymous "(EZFIO_DIR|ADDRESS)" Mandatory @@ -47,11 +43,6 @@ let () = ADDRESS x in - let verbose = - Command_line.get_bool "verbose" - in - - let localhost = Lazy.force TaskServer.ip_address @@ -155,45 +146,6 @@ let () = Zmq.Socket.subscribe socket_in ""; - (* - let action = - if verbose then - begin - match req_or_sub with - | REQ -> (fun () -> - let msg = - Zmq.Socket.recv_all socket_in - in - let t0 = Unix.gettimeofday () in - Zmq.Socket.send_all socket_out msg; - let in_size = - float_of_int ( List.fold_left (fun accu x -> accu + String.length x) 0 msg ) - /. 8192. /. 1024. - in - let msg = - Zmq.Socket.recv_all socket_out - in - let t1 = Unix.gettimeofday () in - Zmq.Socket.send_all socket_in msg; - let in_time = t1 -. t0 in - in_time_sum := !in_time_sum +. in_time; - in_size_sum := !in_size_sum +. in_size; - Printf.printf " %16.2f MiB/s -- %16.2f MiB/s\n%!" (in_size /. in_time) (!in_size_sum /. !in_time_sum); - ) - | SUB -> (fun () -> - Zmq.Socket.recv_all socket_in |> Zmq.Socket.send_all socket_out) - end - else - begin - match req_or_sub with - | REQ -> (fun () -> - Zmq.Socket.recv_all socket_in |> Zmq.Socket.send_all socket_out; - Zmq.Socket.recv_all socket_out |> Zmq.Socket.send_all socket_in ) - | SUB -> (fun () -> - Zmq.Socket.recv_all socket_in |> Zmq.Socket.send_all socket_out) - end - in - *) let action_in = match req_or_sub with diff --git a/scripts/utility/qp_path.py b/scripts/utility/qp_path.py index 0844c06f..5a5c8ca7 100644 --- a/scripts/utility/qp_path.py +++ b/scripts/utility/qp_path.py @@ -1,13 +1,14 @@ -#!/usr/bin/env python2 +#!/usr/bin/env python3 # -*- coding: utf-8 -*- +from __future__ import print_function import os import sys try: QP_ROOT = os.environ['QP_ROOT'] except: - print "source quantum_package.rc" + print("source quantum_package.rc") sys.exit(1) else: QP_EZFIO = os.environ["QP_EZFIO"] diff --git a/tests/bats_to_sh.py b/tests/bats_to_sh.py index 89bf1eb5..7194af77 100755 --- a/tests/bats_to_sh.py +++ b/tests/bats_to_sh.py @@ -1,11 +1,11 @@ -#!/usr/bin/env python2 +#!/usr/bin/env python3 import sys with open(sys.argv[1],'r') as f: raw_data = f.read() -print "set -x" +print("set -x") output = [] inside = False @@ -25,9 +25,9 @@ for i in raw_data: level -= 1 output.append(new_i) -print "".join(output).replace("@test ", +print("".join(output).replace("@test ", """[[ -z $BATS_TEST_NUMBER ]] && BATS_TEST_NUMBER=0 || ((++BATS_TEST_NUMBER)) ; -export BATS_TEST_DESCRIPTION=""").replace("skip","return") +export BATS_TEST_DESCRIPTION=""").replace("skip","return"))