Changeset cd91bd for tests/Python/AllActions

Timestamp:

Apr 11, 2018, 6:30:10 AM (7 years ago)

Author:

Frederik Heber <frederik.heber@…>

Branches:

Candidate_v1.6.1, ChemicalSpaceEvaluator, PythonUI_with_named_parameters, TremoloParser_IncreasedPrecision

Children:

fba720

Parents:

e7ad08

git-author:

Frederik Heber <frederik.heber@…> (09/06/17 14:04:23)

git-committer:

Frederik Heber <frederik.heber@…> (04/11/18 06:30:10)

Message:

TESTFIX: Changes to test scripts because now keyword arguments are used in store-session.

• TESTS: Removed XFAIL from failing tests again.
• FIX: Removed doubled disclaimer in python tests.

Location:

tests/Python/AllActions

Files:

• moltest.py (modified) (1 diff)
• moltest_check.py (modified) (1 diff)
• options.dat (modified) (3 diffs)
• testsuite-python-allactions.at (modified) (1 diff)
• testsuite-python-options_dat.at (modified) (1 diff)

tests/Python/AllActions/moltest.py

@@ -39 +39 @@
 def ParseParameters(docstring):
     result = []
-    params = re.findall(r'\(str\)([-a-zA-Z]*)', docstring)
+    params = re.findall(r'\(str\)([-_a-zA-Z]*)', docstring)
 
     for param in params:

tests/Python/AllActions/moltest_check.py

@@ -24 +24 @@
 def CheckParameters(docstring):
     result = 0
-    params = re.findall(r'\(str\)([-a-zA-Z]*)', docstring)
+    params = re.findall(r'\(str\)([-_a-zA-Z]*)', docstring)
 
     for param in params:

tests/Python/AllActions/options.dat

@@ -1 +1 @@
 #key    value
-add-atom        "1"
-add-empty-boundary      "5,5,5"
-Alignment-Axis  "0,0,1"
-angle-x "0."
-angle-x "0"
-angle-y "0."
-angle-y "0"
-angle-z "0 "
-angle-z "0."
-angle-z "0"
+add_atom        "1"
+add_empty_boundary      "5,5,5"
+Alignment_Axis  "0,0,1"
+angle_x "0."
+angle_x "0"
+angle_y "0."
+angle_y "0"
+angle_z "0 "
+angle_z "0."
+angle_z "0"
 axis    "0 0 1"
 axis    "0 1 0"
 axis    "1 2 1"
-bin-end "10"
-bin-end "20"
-bin-end "359"
-bin-end "359.5"
-bin-end "5"
-bin-output-file "bin_output-10.csv"
-bin-output-file "bin_output-20.csv"
-bin-output-file "bin_output-5.csv"
-bin-output-file "bin_output.csv"
-bin-output-file "emptybox_histogram.dat"
-bin-output-file "hydrogenbox_histogram.dat"
-bin-output-file "waterbox_histogram.dat"
-bin-output-file "waterbox-mirrored_histogram.dat"
-bin-start       "0"
-bin-start       "-0.5"
-bin-start       "10"
-bin-start       "5"
-bin-width       "1."
-bond-degree     "1"
-bond-file       "bond.dat"
+bin_end "10"
+bin_end "20"
+bin_end "359"
+bin_end "359.5"
+bin_end "5"
+bin_output_file "bin_output-10.csv"
+bin_output_file "bin_output-20.csv"
+bin_output_file "bin_output-5.csv"
+bin_output_file "bin_output.csv"
+bin_output_file "emptybox_histogram.dat"
+bin_output_file "hydrogenbox_histogram.dat"
+bin_output_file "waterbox_histogram.dat"
+bin_output_file "waterbox-mirrored_histogram.dat"
+bin_start       "0"
+bin_start       "-0.5"
+bin_start       "10"
+bin_start       "5"
+bin_width       "1."
+bond_degree     "1"
+bond_file       "bond.dat"
 bondside        "1"
-bond-table      "table.dat"
-calculate-bounding-box  ""
-calculate-molar-mass    ""
+bond_table      "table.dat"
+calculate_bounding_box  ""
+calculate_molar_mass    ""
 center  "10. 10. 10."
-center-in-box   "10 0 0 10 0 10"
-change-bond-angle       "100."
-change-box      "10 0 0 10 0 10"
-change-element  "1"
-change-molname  "water"
-convex-envelope "50."
-convex-file     "convexfile"
+center_in_box   "10 0 0 10 0 10"
+change_bond_angle       "100."
+change_box      "10 0 0 10 0 10"
+change_element  "1"
+change_molname  "water"
+convex_envelope "50."
+convex_file     "convexfile"
 coordinates     "1,0,0"
-copy-molecule   "0"
+copy_molecule   "0"
 count   "12"
-create-micelle  "200"
-damping-factor  "0.5"
-default-molname "molname"
+create_micelle  "200"
+damping_factor  "0.5"
+default_molname "molname"
 deltat  "0.01"
 density "1.0"
-depth-first-search      "2."
-dipole-angular-correlation      "H2O"
+depth_first_search      "2."
+dipole_angular_correlation      "H2O"
 distance        "1.55"
 distances       "3.1 3.1 3.1"
 distances       "3.1 3.1 3.1"
-distance-to-boundary    "1."
-distance-to-molecule    "1.5"
-distance-to-molecule    "2.1"
-distance-to-vector      "named_vector"
-domain-position "0.  0. 0."
-domain-position "0 0 0"
-domain-position "10. 10. 10."
+distance_to_boundary    "1."
+distance_to_molecule    "1.5"
+distance_to_molecule    "2.1"
+distance_to_vector      "named_vector"
+domain_position "0.  0. 0."
+domain_position "0 0 0"
+domain_position "10. 10. 10."
 DoCyclesFull    "0"
 DoLongrange     "0"
@@ -73 +73 @@
 DoSmearElectronicCharges        "0"
 DoValenceOnly   "0"
-element-db      "./"
+element_db      "./"
 elements        "1"
 elements        "1 8"
-end-step        "1"
-enforce-net-zero-charge "0"
+end_step        "1"
+enforce_net_zero_charge "0"
 ExcludeHydrogen "1"
 fastparsing     "1"
 filename        "test.exttypes"
-fill-molecule   "filler.xyz"
-fill-void       "hydrogen.xyz"
-fill-void       "water.data"
-fill-void       "water.xyz"
-forces-file     "test.forces"
-fragment-charges        "1 1"
-fragment-executable     "mpqc"
-fragment-jobs   "Job00.in"
-fragment-molecule       "./"
-fragment-path   "test/"
-fragment-prefix "BondFragment"
-grid-level      "5"
+fill_molecule   "filler.xyz"
+fill_void       "hydrogen.xyz"
+fill_void       "water.data"
+fill_void       "water.xyz"
+forces_file     "test.forces"
+fragment_charges        "1 1"
+fragment_executable     "mpqc"
+fragment_jobs   "Job00.in"
+fragment_molecule       "./"
+fragment_path   "test/"
+fragment_prefix "BondFragment"
+grid_level      "5"
 help    "help"
-id-mapping      "1"
+id_mapping      "1"
 input   "test.data"
-input-to-vector "named_vector"
-inter-order     "2"
-interpolation-degree    "5"
-interpolation-steps     "9"
-keep-bondgraph  "1"
-keep-fixed-CenterOfMass "0"
+input_to_vector "named_vector"
+inter_order     "2"
+interpolation_degree    "5"
+interpolation_steps     "9"
+keep_bondgraph  "1"
+keep_fixed_CenterOfMass "0"
 load    "test.data"
-load-session    "test.py"
+load_session    "test.py"
 MaxDistance     "-1"
-max-distance    "0"
-max-meshwidth   "0.3"
-mesh-offset     "0.5,0.5,0.5"
-mesh-size       "10,10,10"
-min-distance    "1."
-mirror-atoms    "1.,1.,1."
-molecule-by-id  "0"
-near-field-cells        "3"
-nonconvex-envelope      "25"
-nonconvex-file  "NonConvexEnvelope"
-nonconvex-file  "nonconvexfile"
+max_distance    "0"
+max_meshwidth   "0.3"
+mesh_offset     "0.5,0.5,0.5"
+mesh_size       "10,10,10"
+min_distance    "1."
+mirror_atoms    "1.,1.,1."
+molecule_by_id  "0"
+near_field_cells        "3"
+nonconvex_envelope      "25"
+nonconvex_file  "NonConvexEnvelope"
+nonconvex_file  "nonconvexfile"
 offset  "0"
 offset  "1"
 order   "2"
-output-as       "store.conf"
-output-as       "store.data"
-output-as       "store.pdb"
-output-as       "store.xyz"
-output-as       "test.in"
-output-every-step       "1"
-output-file     "emptybox_values.dat"
-output-file     "hydrogenbox_values.dat"
-output-file     "output-10.csv"
-output-file     "output-20.csv"
-output-file     "output-5.csv"
-output-file     "output.csv"
-output-file     "waterbox-mirrored_values.dat"
-output-file     "waterbox_values.dat"
-output-types    "xyz"
-output-types    "xyz mpqc"
-parse-atom-fragments    "atomfragments.dat"
-parse-fragment-results  "results.dat"
-parse-homologies        "homology.dat"
-parse-particle-parameters       "water.particles"
-parse-potentials        "water.potentials"
-parse-state-files       "1"
-parse-tremolo-potentials        "argon.potentials"
-parse-tremolo-potentials        "tensid.potentials"
-parser-parameters       "mpqc"
-parser-parameters       "psi3"
+output_as       "store.conf"
+output_as       "store.data"
+output_as       "store.pdb"
+output_as       "store.xyz"
+output_as       "test.in"
+output_every_step       "1"
+output_file     "emptybox_values.dat"
+output_file     "hydrogenbox_values.dat"
+output_file     "output-10.csv"
+output_file     "output-20.csv"
+output_file     "output-5.csv"
+output_file     "output.csv"
+output_file     "waterbox-mirrored_values.dat"
+output_file     "waterbox_values.dat"
+output_types    "xyz"
+output_types    "xyz mpqc"
+parse_atom_fragments    "atomfragments.dat"
+parse_fragment_results  "results.dat"
+parse_homologies        "homology.dat"
+parse_particle_parameters       "water.particles"
+parse_potentials        "water.potentials"
+parse_state_files       "1"
+parse_tremolo_potentials        "argon.potentials"
+parse_tremolo_potentials        "tensid.potentials"
+parser_parameters       "mpqc"
+parser_parameters       "psi3"
 periodic        "0"
-plane-offset    "5."
-plane-to-vector "named_vector"
+plane_offset    "5."
+plane_to_vector "named_vector"
 position        "0 0 0"
 position        "0 0 1"
@@ -157 +157 @@
 position        "7.283585982 3.275186040 3.535886037"
 position        "9.78 2.64 2.64"
-position-to-vector      "named_vector"
-potential-charges       "1 1"
-potential-type  "morse"
+position_to_vector      "named_vector"
+potential_charges       "1 1"
+potential_type  "morse"
 radius  "20."
-random-atom-displacement        "0."
-random-molecule-displacement    "0."
-random-number-distribution-parameters   "max=20;"
-random-number-engine-parameters "seed=2;"
-random-perturbation     "0.1"
-remove-geometry "named_vector"
-repeat-box      "1 1 1"
+random_atom_displacement        "0."
+random_molecule_displacement    "0."
+random_number_distribution_parameters   "max=20;"
+random_number_engine_parameters "seed=2;"
+random_perturbation     "0.1"
+remove_geometry "named_vector"
+repeat_box      "1 1 1"
 reset   1
 reverse "0"
-rotate-around-bond      "90."
-rotate-around-origin    "180."
-rotate-around-origin    "20."
-rotate-around-origin    "360."
-rotate-around-origin    "90."
-rotate-around-self      "180."
-rotate-around-self      "180"
-rotate-around-self      "20."
-rotate-around-self      "360."
-rotate-around-self      "90."
-rotate-to-principal-axis-system "0,0,1"
-save-adjacency  "test.adj"
-save-bonds      "test.bond"
-save-atom-fragments     "atomfragments.dat"
-save-fragment-results   "results.dat"
-save-homologies "homology.dat"
-save-particle-parameters        "water.particles"
-save-potentials "water.potentials"
-save-selected-atoms     "testsave.xyz"
-save-selected-atoms-as-exttypes "test.exttypes"
-save-selected-molecules "testsave.xyz"
-save-temperature        "test.ekin"
-scale-box       "0.5 1. 0.9"
-select-atom-by-element  "1"
-select-atom-by-element  "4"
-select-atom-by-id       "0"
-select-atom-by-name     "H1"
-select-atom-by-order    "1"
-select-atoms-inside-cuboid      "10 10 10"
-select-atoms-inside-cuboid      "2 2 2"
-select-atoms-inside-sphere      "0.2"
-select-atoms-inside-sphere      "10"
-select-atoms-inside-sphere      "7."
-select-molecule-by-id   "0"
-select-molecule-by-id   "1"
-select-molecule-by-id   "4"
-select-molecule-by-order        "-1"
-select-molecule-by-order        "1"
-select-molecule-by-order        "-2"
-select-molecule-by-order        "2"
-select-molecules-by-formula     "C2H5(OH)"
-select-molecules-by-formula     "C6H6"
-select-molecules-by-formula     "H2O"
-select-molecules-by-name        "water"
-select-shape-by-name    "sphere2"
-server-address  "127.0.0.1"
-server-port     "1026"
-session-type    "cli"
-set-bond-degree "1"
-set-boundary-conditions "Wrap, Wrap, Wrap"
-set-max-iterations      "10"
-set-parser-parameters   "basis = 4-31G"
-set-parser-parameters   "basis = 4-31G;maxiter=499;theory=CLKS;"
-set-parser-parameters   "maxiter = 499"
-set-parser-parameters   "theory=CLKS"
-set-parser-parameters   "wfn=scf"
-set-parser-parameters   "ref=uhf"
-set-output      "tremolo"
-set-random-number-distribution  "uniform_int"
-set-random-number-engine        "lagged_fibonacci607"
-set-threshold   "1e-6"
-set-tremolo-atomdata    "ATOMDATA type id x=3"
-set-world-time  "10"
-shape-name      "sphere1"
-shape-op        "AND"
-shape-type      "sphere"
+rotate_around_bond      "90."
+rotate_around_origin    "180."
+rotate_around_origin    "20."
+rotate_around_origin    "360."
+rotate_around_origin    "90."
+rotate_around_self      "180."
+rotate_around_self      "180"
+rotate_around_self      "20."
+rotate_around_self      "360."
+rotate_around_self      "90."
+rotate_to_principal_axis_system "0,0,1"
+save_adjacency  "test.adj"
+save_bonds      "test.bond"
+save_atom_fragments     "atomfragments.dat"
+save_fragment_results   "results.dat"
+save_homologies "homology.dat"
+save_particle_parameters        "water.particles"
+save_potentials "water.potentials"
+save_selected_atoms     "testsave.xyz"
+save_selected_atoms_as_exttypes "test.exttypes"
+save_selected_molecules "testsave.xyz"
+save_temperature        "test.ekin"
+scale_box       "0.5 1. 0.9"
+select_atom_by_element  "1"
+select_atom_by_element  "4"
+select_atom_by_id       "0"
+select_atom_by_name     "H1"
+select_atom_by_order    "1"
+select_atoms_inside_cuboid      "10 10 10"
+select_atoms_inside_cuboid      "2 2 2"
+select_atoms_inside_sphere      "0.2"
+select_atoms_inside_sphere      "10"
+select_atoms_inside_sphere      "7."
+select_molecule_by_id   "0"
+select_molecule_by_id   "1"
+select_molecule_by_id   "4"
+select_molecule_by_order        "-1"
+select_molecule_by_order        "1"
+select_molecule_by_order        "-2"
+select_molecule_by_order        "2"
+select_molecules_by_formula     "C2H5(OH)"
+select_molecules_by_formula     "C6H6"
+select_molecules_by_formula     "H2O"
+select_molecules_by_name        "water"
+select_shape_by_name    "sphere2"
+server_address  "127.0.0.1"
+server_port     "1026"
+session_type    "cli"
+set_bond_degree "1"
+set_boundary_conditions "Wrap, Wrap, Wrap"
+set_max_iterations      "10"
+set_parser_parameters   "basis = 4-31G"
+set_parser_parameters   "basis = 4-31G;maxiter=499;theory=CLKS;"
+set_parser_parameters   "maxiter = 499"
+set_parser_parameters   "theory=CLKS"
+set_parser_parameters   "wfn=scf"
+set_parser_parameters   "ref=uhf"
+set_output      "tremolo"
+set_random_number_distribution  "uniform_int"
+set_random_number_engine        "lagged_fibonacci607"
+set_threshold   "1e-6"
+set_tremolo_atomdata    "ATOMDATA type id x=3"
+set_world_time  "10"
+shape_name      "sphere1"
+shape_op        "AND"
+shape_type      "sphere"
 skiplines       "1"
 skiplines       "2"
-start-step      "0"
+start_step      "0"
 steps   "5"
-step-world-time "1"
-store-grids     "0"
-store-saturated-fragment        "BondFragment"
-store-session   "test.sh"
-stretch-bond    "1.5"
+step_world_time "1"
+store_grids     "0"
+store_saturated_fragment        "BondFragment"
+store_session   "test.sh"
+stretch_bond    "1.5"
 stretch "1. 1. 1."
-stretch-shapes  "1. 2. 3."
-take-best-of            "5"
-tesselation-radius      "5."
-time-step-zero  "0"
-training-file   "training.dat"
-translate-atoms "1. 0. 0."
-translate-shapes        "1. 2. 3."
+stretch_shapes  "1. 2. 3."
+take_best_of            "5"
+tesselation_radius      "5."
+time_step_zero  "0"
+training_file   "training.dat"
+translate_atoms "1. 0. 0."
+translate_shapes        "1. 2. 3."
 translation     "0. 0. 0."
-unselect-atom-by-element        "1"
-unselect-atom-by-element        "4"
-unselect-atom-by-id     "0"
-unselect-atom-by-name   "H1"
-unselect-atom-by-order  "1"
-unselect-atoms-inside-cuboid    "10 10 10"
-unselect-atoms-inside-cuboid    "2 2 2"
-unselect-atoms-inside-sphere    "10"
-unselect-atoms-inside-sphere    "7."
-unselect-molecule-by-id "0"
-unselect-molecule-by-id "4"
-unselect-molecule-by-order      "-1"
-unselect-molecule-by-order      "1"
-unselect-molecule-by-order      "-2"
-unselect-molecule-by-order      "2"
-unselect-molecules-by-formula   "C2H5(OH)"
-unselect-molecules-by-formula   "C3H8"
-unselect-molecules-by-formula   "C6H6"
-unselect-molecules-by-formula   "H2O"
-unselect-molecules-by-name      "water"
-unselect-shape-by-name  "cube42"
-use-bondgraph   "1"
+unselect_atom_by_element        "1"
+unselect_atom_by_element        "4"
+unselect_atom_by_id     "0"
+unselect_atom_by_name   "H1"
+unselect_atom_by_order  "1"
+unselect_atoms_inside_cuboid    "10 10 10"
+unselect_atoms_inside_cuboid    "2 2 2"
+unselect_atoms_inside_sphere    "10"
+unselect_atoms_inside_sphere    "7."
+unselect_molecule_by_id "0"
+unselect_molecule_by_id "4"
+unselect_molecule_by_order      "-1"
+unselect_molecule_by_order      "1"
+unselect_molecule_by_order      "-2"
+unselect_molecule_by_order      "2"
+unselect_molecules_by_formula   "C2H5(OH)"
+unselect_molecules_by_formula   "C3H8"
+unselect_molecules_by_formula   "C6H6"
+unselect_molecules_by_formula   "H2O"
+unselect_molecules_by_name      "water"
+unselect_shape_by_name  "cube42"
+use_bondgraph   "1"
 UseImplicitCharges      "1"
 verbose "3"
-verlet-integration      "forces.dat"
+verlet_integration      "forces.dat"

tests/Python/AllActions/testsuite-python-allactions.at

@@ -16 +16 @@
 #    along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
-#
-#    MoleCuilder - creates and alters molecular systems
-#    Copyright (C) 2008-2012 University of Bonn
-#
-#    This program is free software: you can redistribute it and/or modify
-#    it under the terms of the GNU General Public License as published by
-#    the Free Software Foundation, either version 3 of the License, or
-#    (at your option) any later version.
-#
-#    This program is distributed in the hope that it will be useful,
-#    but WITHOUT ANY WARRANTY; without even the implied warranty of
-#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-#    GNU General Public License for more details.
-#
-#    You should have received a copy of the GNU General Public License
-#    along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
 # AllActions

tests/Python/AllActions/testsuite-python-options_dat.at

@@ -17 +17 @@
 #
 #
-#    MoleCuilder - creates and alters molecular systems
-#    Copyright (C) 2008-2012 University of Bonn
-#
-#    This program is free software: you can redistribute it and/or modify
-#    it under the terms of the GNU General Public License as published by
-#    the Free Software Foundation, either version 3 of the License, or
-#    (at your option) any later version.
-#
-#    This program is distributed in the hope that it will be useful,
-#    but WITHOUT ANY WARRANTY; without even the implied warranty of
-#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-#    GNU General Public License for more details.
-#
-#    You should have received a copy of the GNU General Public License
-#    along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
 AT_SETUP([Python externalization - Completeness of default options])
 AT_KEYWORDS([python options_dat])
-AT_XFAIL_IF([/bin/true])
 m4_include(atlocal)
 AT_CHECK([cp -f ${abs_top_srcdir}/tests/Python/AllActions/options.dat .], 0, [ignore], [ignore])