Moving to Python3.

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_x.append(str.count(s, "x"))
-        power_y.append(string.count(s, "y"))
+        power_y.append(str.count(s, "y"))
-        power_z.append(string.count(s, "z"))
+        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)
+    closed = [x[1] for x in closed]
-    active = map(lambda x: x[1], active)
+    active = [x[1] for x in active]
-    virtual = map(lambda x: x[1], virtual)
+    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).""")
 

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:

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/

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

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"]

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"))