mirror of
https://github.com/QuantumPackage/qp2.git
synced 2024-12-21 11:03:29 +01:00
Moving to Python3.
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c50707568c
commit
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@ -1,4 +1,4 @@
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#!/usr/bin/env python2
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#!/usr/bin/env python3
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"""
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convert output of GAMESS/GAU$$IAN to ezfio
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@ -22,7 +22,7 @@ try:
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QP_ROOT = os.environ["QP_ROOT"]
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QP_EZFIO = os.environ["QP_EZFIO"]
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except KeyError:
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print "Error: QP_ROOT environment variable not found."
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print("Error: QP_ROOT environment variable not found.")
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sys.exit(1)
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else:
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sys.path = [QP_EZFIO + "/Python",
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@ -30,10 +30,11 @@ else:
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QP_ROOT + "/install",
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QP_ROOT + "/scripts"] + sys.path
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from resultsFile import *
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try:
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from resultsFile import *
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except:
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print "Error: resultsFile Python library not installed"
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print("Error: resultsFile Python library not installed")
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sys.exit(1)
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@ -48,17 +49,17 @@ def write_ezfio(res, filename):
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# |_ | _ _ _|_ ._ _ ._ _
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# |_ | (/_ (_ |_ | (_) | | _>
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#
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print "Electrons\t...\t",
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print("Electrons\t...\t", end=' ')
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ezfio.set_electrons_elec_alpha_num(res.num_alpha)
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ezfio.set_electrons_elec_beta_num(res.num_beta)
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print "OK"
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print("OK")
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#
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# |\ | _ | _ o
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# | \| |_| (_ | (/_ |
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#
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print "Nuclei\t\t...\t",
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print("Nuclei\t\t...\t", end=' ')
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# ~#~#~#~ #
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# I n i t #
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# ~#~#~#~ #
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@ -93,24 +94,23 @@ def write_ezfio(res, filename):
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# Transformt H1 into H
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import re
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p = re.compile(ur'(\d*)$')
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p = re.compile(r'(\d*)$')
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label = [p.sub("", x.name).capitalize() for x in res.geometry]
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ezfio.set_nuclei_nucl_label(label)
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ezfio.set_nuclei_nucl_coord(coord_x + coord_y + coord_z)
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print "OK"
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print("OK")
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# _
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# /\ _ _ |_) _. _ o _
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# /--\ (_) _> |_) (_| _> | _>
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#
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print "AOS\t\t...\t",
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print("AOS\t\t...\t", end=' ')
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# ~#~#~#~ #
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# I n i t #
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# ~#~#~#~ #
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import string
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at = []
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num_prim = []
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power_x = []
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@ -131,9 +131,9 @@ def write_ezfio(res, filename):
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at.append(i + 1)
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num_prim.append(len(b.prim))
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s = b.sym
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power_x.append(string.count(s, "x"))
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power_y.append(string.count(s, "y"))
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power_z.append(string.count(s, "z"))
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power_x.append(str.count(s, "x"))
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power_y.append(str.count(s, "y"))
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power_z.append(str.count(s, "z"))
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coefficient.append(b.coef)
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exponent.append([p.expo for p in b.prim])
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@ -175,14 +175,14 @@ def write_ezfio(res, filename):
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ezfio.set_ao_basis_ao_expo(expo)
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ezfio.set_ao_basis_ao_basis("Read by resultsFile")
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print "OK"
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print("OK")
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# _
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# |\/| _ _ |_) _. _ o _
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# | | (_) _> |_) (_| _> | _>
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#
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print "MOS\t\t...\t",
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print("MOS\t\t...\t", end=' ')
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# ~#~#~#~ #
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# I n i t #
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# ~#~#~#~ #
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@ -205,9 +205,9 @@ def write_ezfio(res, filename):
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virtual = []
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active = [(allMOs[i].eigenvalue, i) for i in range(len(allMOs))]
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closed = map(lambda x: x[1], closed)
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active = map(lambda x: x[1], active)
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virtual = map(lambda x: x[1], virtual)
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closed = [x[1] for x in closed]
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active = [x[1] for x in active]
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virtual = [x[1] for x in virtual]
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MOindices = closed + active + virtual
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MOs = []
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@ -223,7 +223,7 @@ def write_ezfio(res, filename):
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MOmap[i] = MOindices.index(i)
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energies = []
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for i in xrange(mo_num):
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for i in range(mo_num):
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energies.append(MOs[i].eigenvalue)
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if res.occ_num is not None:
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@ -237,11 +237,11 @@ def write_ezfio(res, filename):
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MoMatrix = []
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sym0 = [i.sym for i in res.mo_sets[MO_type]]
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sym = [i.sym for i in res.mo_sets[MO_type]]
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for i in xrange(len(sym)):
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for i in range(len(sym)):
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sym[MOmap[i]] = sym0[i]
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MoMatrix = []
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for i in xrange(len(MOs)):
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for i in range(len(MOs)):
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m = MOs[i]
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for coef in m.vector:
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MoMatrix.append(coef)
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@ -256,10 +256,10 @@ def write_ezfio(res, filename):
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ezfio.set_mo_basis_mo_num(mo_num)
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ezfio.set_mo_basis_mo_occ(OccNum)
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ezfio.set_mo_basis_mo_coef(MoMatrix)
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print "OK"
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print("OK")
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print "Pseudos\t\t...\t",
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print("Pseudos\t\t...\t", end=' ')
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try:
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lmax = 0
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nucl_charge_remove = []
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@ -327,7 +327,7 @@ def write_ezfio(res, filename):
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else:
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ezfio.set_pseudo_do_pseudo(True)
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print "OK"
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print("OK")
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@ -354,15 +354,15 @@ if __name__ == '__main__':
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except:
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raise
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else:
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print FILE, 'recognized as', str(RES_FILE).split('.')[-1].split()[0]
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print(FILE, 'recognized as', str(RES_FILE).split('.')[-1].split()[0])
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write_ezfio(RES_FILE, EZFIO_FILE)
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sys.stdout.flush()
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if os.system("qp_run save_ortho_mos "+EZFIO_FILE) != 0:
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print """Warning: You need to run
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print("""Warning: You need to run
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qp run save_ortho_mos
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to be sure your MOs will be orthogonal, which is not the case when
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the MOs are read from output files (not enough precision in output)."""
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the MOs are read from output files (not enough precision in output).""")
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@ -1,4 +1,4 @@
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#!/usr/bin/env python2
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#!/usr/bin/env python3
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"""
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@ -49,7 +49,7 @@ import os.path
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try:
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import qp_path
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except ImportError:
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print "source .quantum_package.rc"
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print("source .quantum_package.rc")
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raise
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from docopt import docopt
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@ -102,7 +102,7 @@ def main(arguments):
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mo_num = ezfio.mo_basis_mo_num
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if arguments["--query"]:
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print n_frozen
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print(n_frozen)
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sys.exit(0)
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if n_frozen == 0:
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46
external/Python/.gitignore
vendored
46
external/Python/.gitignore
vendored
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# Byte-compiled / optimized / DLL files
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__pycache__/
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*.py[cod]
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# C extensions
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*.so
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# Distribution / packaging
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.Python
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env/
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build/
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develop-eggs/
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dist/
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downloads/
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eggs/
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# PyInstaller
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# Usually these files are written by a python script from a template
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# before PyInstaller builds the exe, so as to inject date/other infos into it.
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*.manifest
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*.spec
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# Installer logs
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pip-log.txt
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pip-delete-this-directory.txt
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# Unit test / coverage reports
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htmlcov/
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.tox/
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.coverage
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.cache
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nosetests.xml
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coverage.xml
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# Translations
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*.mo
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*.pot
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# Django stuff:
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*.log
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# Sphinx documentation
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docs/_build/
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# PyBuilder
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target/
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@ -21,10 +21,6 @@ let () =
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doc="Downloads the EZFIO directory." ;
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arg=Without_arg; } ;
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{ short='v' ; long="verbose" ; opt=Optional ;
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doc="Prints the transfer speed." ;
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arg=Without_arg; } ;
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anonymous
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"(EZFIO_DIR|ADDRESS)"
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Mandatory
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ADDRESS x
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in
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let verbose =
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Command_line.get_bool "verbose"
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in
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let localhost =
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Lazy.force TaskServer.ip_address
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@ -155,45 +146,6 @@ let () =
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Zmq.Socket.subscribe socket_in "";
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(*
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let action =
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if verbose then
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begin
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match req_or_sub with
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| REQ -> (fun () ->
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let msg =
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Zmq.Socket.recv_all socket_in
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in
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let t0 = Unix.gettimeofday () in
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Zmq.Socket.send_all socket_out msg;
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let in_size =
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float_of_int ( List.fold_left (fun accu x -> accu + String.length x) 0 msg )
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/. 8192. /. 1024.
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in
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let msg =
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Zmq.Socket.recv_all socket_out
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in
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let t1 = Unix.gettimeofday () in
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Zmq.Socket.send_all socket_in msg;
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let in_time = t1 -. t0 in
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in_time_sum := !in_time_sum +. in_time;
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in_size_sum := !in_size_sum +. in_size;
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Printf.printf " %16.2f MiB/s -- %16.2f MiB/s\n%!" (in_size /. in_time) (!in_size_sum /. !in_time_sum);
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)
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| SUB -> (fun () ->
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Zmq.Socket.recv_all socket_in |> Zmq.Socket.send_all socket_out)
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end
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else
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begin
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match req_or_sub with
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| REQ -> (fun () ->
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Zmq.Socket.recv_all socket_in |> Zmq.Socket.send_all socket_out;
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Zmq.Socket.recv_all socket_out |> Zmq.Socket.send_all socket_in )
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Zmq.Socket.recv_all socket_in |> Zmq.Socket.send_all socket_out)
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end
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in
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*)
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let action_in =
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match req_or_sub with
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@ -1,13 +1,14 @@
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#!/usr/bin/env python2
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#!/usr/bin/env python3
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# -*- coding: utf-8 -*-
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from __future__ import print_function
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import os
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import sys
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try:
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QP_ROOT = os.environ['QP_ROOT']
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except:
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print "source quantum_package.rc"
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print("source quantum_package.rc")
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sys.exit(1)
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else:
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QP_EZFIO = os.environ["QP_EZFIO"]
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@ -1,11 +1,11 @@
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#!/usr/bin/env python2
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#!/usr/bin/env python3
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import sys
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with open(sys.argv[1],'r') as f:
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raw_data = f.read()
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print "set -x"
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print("set -x")
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output = []
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inside = False
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@ -25,9 +25,9 @@ for i in raw_data:
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level -= 1
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output.append(new_i)
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print "".join(output).replace("@test ",
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print("".join(output).replace("@test ",
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"""[[ -z $BATS_TEST_NUMBER ]] && BATS_TEST_NUMBER=0 || ((++BATS_TEST_NUMBER)) ;
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export BATS_TEST_DESCRIPTION=""").replace("skip","return")
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export BATS_TEST_DESCRIPTION=""").replace("skip","return"))
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