|
Source file: src/wepy/analysis/network_layouts/__init__.py |
|
Source file: src/wepy/analysis/network_layouts/layout.py |
|
Source file: src/wepy/analysis/network_layouts/layout_graph.py |
| Function name | |
Cyclomatic complexity
(15)
| LOC (1000000) |
Token count
| Parameter count (100) |
|---|
| __init__ |
|
2 |
7 |
74 |
0 |
| graph |
|
1 |
2 |
10 |
0 |
| viz_graph |
|
1 |
2 |
10 |
0 |
| get_node_attributes |
|
3 |
10 |
53 |
0 |
| set_node_viz_attributes |
|
2 |
3 |
34 |
0 |
| set_node_positions |
|
1 |
2 |
18 |
0 |
| set_node_colors |
|
1 |
2 |
18 |
0 |
| set_node_sizes |
|
1 |
2 |
18 |
0 |
| set_node_shapes |
|
1 |
2 |
18 |
0 |
| get_node_viz_attributes |
|
2 |
5 |
37 |
0 |
| get_node_positions |
|
1 |
2 |
14 |
0 |
| get_node_colors |
|
1 |
2 |
14 |
0 |
| get_node_sizes |
|
1 |
2 |
14 |
0 |
| get_node_shapes |
|
1 |
2 |
14 |
0 |
| RGBA_to_hex |
|
6 |
4 |
62 |
0 |
| feature_vector_to_gexf_viz_position |
|
1 |
4 |
46 |
0 |
| feature_vector_to_gexf_viz_color_RGB |
|
1 |
4 |
46 |
0 |
| feature_vector_to_gexf_viz_color_RGBA |
|
1 |
5 |
58 |
0 |
| set_node_gexf_viz |
|
2 |
3 |
39 |
0 |
| set_node_gexf_positions |
|
2 |
4 |
37 |
0 |
| set_node_gexf_colors_rgb |
|
2 |
4 |
37 |
0 |
| set_node_gexf_colors_rgba |
|
2 |
4 |
37 |
0 |
| set_node_gexf_sizes |
|
1 |
2 |
18 |
0 |
| set_node_gexf_shape |
|
1 |
2 |
18 |
0 |
|
Source file: src/wepy/analysis/network_layouts/tree.py |
| Function name | |
Cyclomatic complexity
(15)
| LOC (1000000) |
Token count
| Parameter count (100) |
|---|
| __init__ |
|
1 |
5 |
29 |
0 |
| _overlaps |
|
4 |
12 |
85 |
0 |
| _node_row_length |
|
1 |
6 |
55 |
0 |
| _simple_gen_distribution |
|
35 |
74 |
668 |
0 |
| _simple_next_gen |
|
4 |
10 |
72 |
0 |
| _initial_parent_distribution |
|
2 |
11 |
77 |
0 |
| _center_row |
|
1 |
7 |
57 |
0 |
| _layout_array |
|
4 |
26 |
230 |
0 |
| layout |
|
10 |
29 |
192 |
0 |
|
Source file: src/wepy/analysis/__init__.py |
|
Source file: src/wepy/analysis/distributed.py |
| Function name | |
Cyclomatic complexity
(15)
| LOC (1000000) |
Token count
| Parameter count (100) |
|---|
| traj_fields_chunk_items |
|
1 |
3 |
15 |
0 |
| load_chunk |
|
2 |
11 |
69 |
0 |
| chunk_func_funcgen |
|
1 |
4 |
19 |
0 |
| chunk_func |
|
3 |
11 |
60 |
0 |
| unwrap_chunk_funcgen.unwrap_chunk_func |
|
3 |
3 |
25 |
0 |
| unwrap_chunk_funcgen |
|
1 |
5 |
28 |
0 |
| chunk_key_func |
|
1 |
2 |
17 |
0 |
| init_chunk |
|
1 |
6 |
32 |
0 |
| chunk_concat_funcgen.chunk_concat |
|
6 |
18 |
124 |
0 |
| chunk_concat_funcgen |
|
1 |
3 |
10 |
0 |
| chunk_array_concat_funcgen.func |
|
2 |
6 |
46 |
0 |
| chunk_array_concat_funcgen |
|
1 |
3 |
9 |
0 |
| chunk_traj_fields_concat |
|
1 |
4 |
29 |
0 |
| _by_traj_to_multidimensional |
|
6 |
15 |
126 |
0 |
| compute_observable |
|
1 |
7 |
23 |
0 |
| compute_observable_graph |
|
2 |
16 |
84 |
0 |
|
Source file: src/wepy/analysis/parents.py |
| Function name | |
Cyclomatic complexity
(15)
| LOC (1000000) |
Token count
| Parameter count (100) |
|---|
| resampling_panel |
|
14 |
57 |
250 |
0 |
| parent_panel |
|
3 |
9 |
48 |
0 |
| net_parent_table |
|
5 |
14 |
91 |
0 |
| parent_table_discontinuities |
|
5 |
14 |
95 |
0 |
| parent_cycle_discontinuities |
|
5 |
9 |
56 |
0 |
| ancestors |
|
3 |
10 |
76 |
0 |
| sliding_window |
|
4 |
11 |
89 |
0 |
| __init__ |
|
1 |
2 |
12 |
0 |
| _make_child_parent_edges |
|
3 |
14 |
91 |
0 |
| contig |
|
2 |
5 |
24 |
0 |
| parent_table |
|
1 |
2 |
10 |
0 |
| graph |
|
1 |
2 |
10 |
0 |
| roots |
|
1 |
2 |
10 |
0 |
| trees |
|
5 |
7 |
64 |
0 |
| n_steps |
|
1 |
2 |
13 |
0 |
| step |
|
3 |
7 |
47 |
0 |
| steps |
|
2 |
5 |
33 |
0 |
| walker |
|
3 |
7 |
42 |
0 |
| set_node_attributes |
|
2 |
3 |
34 |
0 |
| set_attrs_by_array |
|
3 |
4 |
49 |
0 |
|
Source file: src/wepy/analysis/rates.py |
| Function name | |
Cyclomatic complexity
(15)
| LOC (1000000) |
Token count
| Parameter count (100) |
|---|
| calc_warp_rate |
|
3 |
10 |
72 |
0 |
| contig_warp_rates |
|
9 |
17 |
154 |
0 |
|
Source file: src/wepy/analysis/contig_tree.py |
| Function name | |
Cyclomatic complexity
(15)
| LOC (1000000) |
Token count
| Parameter count (100) |
|---|
| __init__ |
|
1 |
5 |
23 |
0 |
| graph |
|
1 |
2 |
10 |
0 |
| decision_class |
|
1 |
2 |
10 |
0 |
| boundary_condition_class |
|
1 |
2 |
10 |
0 |
| span_traces |
|
1 |
2 |
10 |
0 |
| span_contig |
|
1 |
3 |
23 |
0 |
| _create_tree |
|
5 |
13 |
143 |
0 |
| _set_resampling_panels |
|
3 |
6 |
55 |
0 |
| _initialize_discontinuities |
|
1 |
2 |
7 |
0 |
| _set_discontinuities |
|
10 |
15 |
138 |
0 |
| _set_parents |
|
2 |
6 |
66 |
0 |
| run_idxs |
|
1 |
2 |
10 |
0 |
| continuations |
|
1 |
2 |
10 |
0 |
| contig_trace_to_run_trace |
|
3 |
11 |
55 |
0 |
| walker_trace_to_run_trace |
|
1 |
2 |
19 |
0 |
| run_trace_to_contig_trace |
|
2 |
6 |
43 |
0 |
| contig_cycle_idx |
|
1 |
3 |
27 |
0 |
| get_branch_trace |
|
3 |
15 |
94 |
0 |
| trace_parent_table |
|
3 |
9 |
80 |
0 |
| _tree_leaves |
|
6 |
18 |
112 |
0 |
| _subtree_leaves |
|
1 |
5 |
38 |
0 |
| leaves |
|
2 |
6 |
35 |
0 |
| root_leaves |
|
2 |
5 |
32 |
0 |
| _subtree_root |
|
3 |
12 |
81 |
0 |
| roots |
|
2 |
7 |
48 |
0 |
| subtrees |
|
2 |
6 |
40 |
0 |
| get_subtree |
|
3 |
5 |
27 |
0 |
| contig_sliding_windows |
|
1 |
4 |
28 |
0 |
| sliding_contig_windows |
|
2 |
7 |
45 |
0 |
| _subtree_sliding_contig_windows |
|
7 |
19 |
140 |
0 |
| sliding_windows |
|
3 |
9 |
58 |
0 |
| _rec_spanning_paths |
|
6 |
15 |
94 |
0 |
| _spanning_paths |
|
5 |
20 |
128 |
0 |
| spanning_contig_traces |
|
2 |
5 |
33 |
0 |
| _root_spanning_contig_traces |
|
3 |
7 |
47 |
0 |
| _contig_trace_to_contig_runs |
|
3 |
8 |
36 |
0 |
| _contig_runs_to_continuations |
|
2 |
5 |
50 |
0 |
| _continuations_to_contig_runs |
|
9 |
24 |
182 |
0 |
| __init__ |
|
1 |
6 |
27 |
0 |
| _set_base_contigtree_to_self |
|
1 |
8 |
66 |
0 |
| open |
|
2 |
6 |
36 |
0 |
| close |
|
1 |
3 |
17 |
0 |
| __enter__ |
|
1 |
4 |
19 |
0 |
| __exit__ |
|
1 |
3 |
28 |
0 |
| base_contigtree |
|
1 |
2 |
9 |
0 |
| wepy_h5 |
|
1 |
2 |
10 |
0 |
| make_contig |
|
1 |
8 |
51 |
0 |
| warp_trace |
|
2 |
7 |
50 |
0 |
| resampling_trace |
|
2 |
7 |
53 |
0 |
| final_trace |
|
2 |
7 |
50 |
0 |
| lineages |
|
1 |
3 |
9 |
0 |
| __init__ |
|
1 |
2 |
10 |
0 |
| contig_fields |
|
1 |
2 |
21 |
0 |
| contig_trace |
|
1 |
2 |
10 |
0 |
| num_cycles |
|
1 |
2 |
13 |
0 |
| num_walkers |
|
1 |
4 |
32 |
0 |
| records |
|
1 |
2 |
21 |
0 |
| records_dataframe |
|
1 |
2 |
21 |
0 |
| resampling_records |
|
1 |
2 |
13 |
0 |
| resampling_records_dataframe |
|
1 |
2 |
17 |
0 |
| resampler_records |
|
1 |
2 |
13 |
0 |
| resampler_records_dataframe |
|
1 |
2 |
17 |
0 |
| warping_records |
|
1 |
2 |
13 |
0 |
| warping_records_dataframe |
|
1 |
2 |
17 |
0 |
| bc_records |
|
1 |
2 |
13 |
0 |
| bc_records_dataframe |
|
1 |
2 |
17 |
0 |
| progress_records |
|
1 |
2 |
13 |
0 |
| progress_records_dataframe |
|
1 |
2 |
17 |
0 |
| resampling_panel |
|
1 |
2 |
17 |
0 |
| parent_table |
|
1 |
3 |
23 |
0 |
| lineages_contig |
|
2 |
7 |
50 |
0 |
| lineages |
|
2 |
4 |
34 |
0 |
| warp_contig_trace |
|
2 |
8 |
46 |
0 |
| resampling_contig_trace |
|
3 |
6 |
44 |
0 |
| final_contig_trace |
|
2 |
5 |
35 |
0 |
| warp_trace |
|
1 |
4 |
27 |
0 |
| resampling_trace |
|
1 |
4 |
30 |
0 |
| final_trace |
|
1 |
4 |
27 |
0 |
| resampling_tree_layout_graph |
|
1 |
10 |
40 |
0 |
|
Source file: src/wepy/analysis/network.py |
| Function name | |
Cyclomatic complexity
(15)
| LOC (1000000) |
Token count
| Parameter count (100) |
|---|
| __init__ |
|
1 |
5 |
19 |
0 |
| _key_init |
|
8 |
26 |
186 |
0 |
| _assignments_init |
|
4 |
8 |
79 |
0 |
| _init_transition_counts |
|
1 |
4 |
10 |
0 |
| node_id_to_idx |
|
1 |
2 |
17 |
0 |
| node_idx_to_id |
|
1 |
2 |
17 |
0 |
| node_id_to_idx_dict |
|
1 |
2 |
10 |
0 |
| node_idx_to_id_dict |
|
3 |
7 |
46 |
0 |
| graph |
|
1 |
2 |
10 |
0 |
| num_states |
|
1 |
2 |
13 |
0 |
| node_ids |
|
1 |
2 |
15 |
0 |
| contig_tree |
|
1 |
2 |
10 |
0 |
| assg_field_key |
|
2 |
5 |
24 |
0 |
| get_node_attributes |
|
1 |
2 |
17 |
0 |
| get_node_attribute |
|
1 |
2 |
20 |
0 |
| get_nodes_attribute |
|
2 |
5 |
39 |
0 |
| node_assignments |
|
1 |
2 |
19 |
0 |
| set_nodes_attribute |
|
2 |
3 |
34 |
0 |
| node_groups |
|
1 |
2 |
9 |
0 |
| set_node_group |
|
1 |
3 |
25 |
0 |
| _set_group_nodes_attribute |
|
3 |
5 |
46 |
0 |
| observables |
|
1 |
2 |
10 |
0 |
| node_observables |
|
2 |
6 |
42 |
0 |
| set_nodes_observable |
|
1 |
4 |
33 |
0 |
| get_edge_attributes |
|
1 |
2 |
17 |
0 |
| get_edge_attribute |
|
1 |
2 |
20 |
0 |
| get_edges_attribute |
|
2 |
5 |
39 |
0 |
| layouts |
|
1 |
2 |
9 |
0 |
| node_layouts |
|
2 |
6 |
42 |
0 |
| set_nodes_layout |
|
2 |
5 |
41 |
0 |
| write_gexf |
|
1 |
6 |
20 |
0 |
| nodes_to_records |
|
1 |
3 |
13 |
0 |
| nodes_to_dataframe |
|
1 |
3 |
13 |
0 |
| edges_to_records |
|
1 |
3 |
10 |
0 |
| edges_to_dataframe |
|
1 |
3 |
10 |
0 |
| node_map.func_wrapper |
|
1 |
3 |
17 |
0 |
| node_map |
|
3 |
8 |
60 |
0 |
| edge_attribute_to_matrix |
|
1 |
4 |
14 |
0 |
| __init__ |
|
1 |
7 |
24 |
0 |
| _set_base_network_to_self |
|
1 |
32 |
282 |
0 |
| open |
|
2 |
6 |
36 |
0 |
| close |
|
1 |
3 |
17 |
0 |
| __enter__ |
|
1 |
4 |
19 |
0 |
| __exit__ |
|
1 |
3 |
28 |
0 |
| graph |
|
1 |
2 |
10 |
0 |
| num_states |
|
1 |
2 |
13 |
0 |
| node_ids |
|
1 |
2 |
15 |
0 |
| assg_field_key |
|
2 |
5 |
24 |
0 |
| base_network |
|
1 |
2 |
9 |
0 |
| wepy_h5 |
|
1 |
2 |
10 |
0 |
| state_to_mdtraj |
|
1 |
3 |
32 |
0 |
| state_to_traj_fields |
|
1 |
2 |
24 |
0 |
| states_to_traj_fields |
|
2 |
8 |
61 |
0 |
| get_node_fields |
|
1 |
4 |
34 |
0 |
| iter_nodes_fields |
|
2 |
6 |
41 |
0 |
| microstate_weights |
|
2 |
7 |
54 |
0 |
| macrostate_weights |
|
2 |
6 |
45 |
0 |
| set_macrostate_weights |
|
1 |
5 |
21 |
0 |
| node_fields_map.func_wrapper |
|
1 |
8 |
27 |
0 |
| node_fields_map |
|
3 |
13 |
72 |
0 |
|
Source file: src/wepy/analysis/profiles.py |
| Function name | |
Cyclomatic complexity
(15)
| LOC (1000000) |
Token count
| Parameter count (100) |
|---|
| _percentage_cumulative_partitions |
|
1 |
2 |
25 |
0 |
| _tranche_cumulative_partitions |
|
1 |
3 |
13 |
0 |
| cumulative_partitions |
|
1 |
4 |
17 |
0 |
| free_energy_profile |
|
1 |
6 |
20 |
0 |
| contigtrees_bin_edges |
|
1 |
5 |
12 |
0 |
| __init__ |
|
1 |
2 |
11 |
0 |
| _get_ignore_trace |
|
4 |
7 |
53 |
0 |
| contigtree |
|
1 |
2 |
10 |
0 |
| fe_profile_trace |
|
1 |
6 |
18 |
0 |
| fe_profile_all |
|
1 |
5 |
16 |
0 |
| fe_profile |
|
1 |
5 |
17 |
0 |
| fe_cumulative_profiles |
|
1 |
5 |
25 |
0 |
| fe_all_cumulative_profiles |
|
1 |
6 |
27 |
0 |
| bin_edges |
|
2 |
6 |
52 |
0 |
|
Source file: src/wepy/analysis/transitions.py |
| Function name | |
Cyclomatic complexity
(15)
| LOC (1000000) |
Token count
| Parameter count (100) |
|---|
| transition_counts |
|
1 |
4 |
11 |
0 |
| counts_d_to_matrix |
|
1 |
2 |
4 |
0 |
| normalize_counts |
|
3 |
8 |
77 |
0 |
| transition_counts_matrix |
|
1 |
4 |
24 |
0 |
| transition_probability_matrix |
|
1 |
4 |
24 |
0 |
| run_transition_counts_matrix |
|
4 |
16 |
125 |
0 |
| run_transition_probability_matrix |
|
1 |
4 |
32 |
0 |
|
Source file: src/wepy/boundary_conditions/__init__.py |
|
Source file: src/wepy/boundary_conditions/boundary.py |
| Function name | |
Cyclomatic complexity
(15)
| LOC (1000000) |
Token count
| Parameter count (100) |
|---|
| __init__ |
|
1 |
2 |
10 |
0 |
| bc_field_names |
|
1 |
2 |
10 |
0 |
| bc_field_shapes |
|
1 |
2 |
10 |
0 |
| bc_field_dtypes |
|
1 |
2 |
10 |
0 |
| bc_fields |
|
1 |
4 |
30 |
0 |
| bc_record_field_names |
|
1 |
2 |
10 |
0 |
| warping_field_names |
|
1 |
2 |
10 |
0 |
| warping_field_shapes |
|
1 |
2 |
10 |
0 |
| warping_field_dtypes |
|
1 |
2 |
10 |
0 |
| warping_fields |
|
1 |
4 |
30 |
0 |
| warping_record_field_names |
|
1 |
2 |
10 |
0 |
| progress_field_names |
|
1 |
2 |
10 |
0 |
| progress_field_shapes |
|
1 |
2 |
10 |
0 |
| progress_field_dtypes |
|
1 |
2 |
10 |
0 |
| progress_fields |
|
1 |
4 |
30 |
0 |
| progress_record_field_names |
|
1 |
2 |
10 |
0 |
| warp_walkers |
|
1 |
2 |
12 |
0 |
| warping_discontinuity |
|
1 |
2 |
10 |
0 |
| warp_walkers |
|
1 |
5 |
30 |
0 |
| warping_discontinuity |
|
1 |
2 |
9 |
0 |
| warp_walkers |
|
6 |
26 |
198 |
0 |
|
Source file: src/wepy/boundary_conditions/receptor.py |
| Function name | |
Cyclomatic complexity
(15)
| LOC (1000000) |
Token count
| Parameter count (100) |
|---|
| __init__ |
|
1 |
5 |
24 |
0 |
| initial_states |
|
1 |
2 |
10 |
0 |
| initial_weights |
|
1 |
2 |
10 |
0 |
| ligand_idxs |
|
1 |
2 |
10 |
0 |
| receptor_idxs |
|
1 |
2 |
10 |
0 |
| _progress |
|
1 |
2 |
10 |
0 |
| _warp |
|
1 |
8 |
102 |
0 |
| _update_bc |
|
1 |
2 |
17 |
0 |
| warp_walkers |
|
6 |
24 |
190 |
0 |
| warping_discontinuity |
|
4 |
9 |
42 |
0 |
| __init__ |
|
1 |
7 |
34 |
0 |
| native_state |
|
1 |
2 |
10 |
0 |
| cutoff_rmsd |
|
1 |
2 |
10 |
0 |
| binding_site_idxs |
|
1 |
2 |
10 |
0 |
| _progress |
|
2 |
14 |
118 |
0 |
| __init__ |
|
1 |
7 |
34 |
0 |
| cutoff_distance |
|
1 |
2 |
10 |
0 |
| topology |
|
1 |
2 |
10 |
0 |
| _calc_min_distance |
|
1 |
16 |
120 |
0 |
| _progress |
|
2 |
7 |
40 |
0 |
| _update_bc |
|
2 |
5 |
43 |
0 |
|
Source file: src/wepy/boundary_conditions/unbinding.py |
|
Source file: src/wepy/orchestration/__init__.py |
|
Source file: src/wepy/orchestration/configuration.py |
| Function name | |
Cyclomatic complexity
(15)
| LOC (1000000) |
Token count
| Parameter count (100) |
|---|
| __init__ |
|
1 |
12 |
48 |
0 |
| reporter_classes |
|
1 |
2 |
10 |
0 |
| reporter_partial_kwargs |
|
1 |
2 |
10 |
0 |
| config_name |
|
1 |
2 |
10 |
0 |
| work_dir |
|
1 |
2 |
10 |
0 |
| narration |
|
1 |
2 |
10 |
0 |
| mode |
|
1 |
2 |
10 |
0 |
| reporters |
|
1 |
2 |
10 |
0 |
| work_mapper_class |
|
1 |
2 |
10 |
0 |
| work_mapper_partial_kwargs |
|
1 |
2 |
10 |
0 |
| work_mapper |
|
1 |
2 |
10 |
0 |
| monitor_class |
|
1 |
2 |
10 |
0 |
| monitor_partial_kwargs |
|
1 |
2 |
10 |
0 |
| monitor |
|
1 |
2 |
10 |
0 |
| apparatus_opts |
|
1 |
2 |
10 |
0 |
| _gen_reporters |
|
8 |
33 |
225 |
0 |
| _gen_work_mapper |
|
1 |
3 |
20 |
0 |
| reporters |
|
1 |
2 |
13 |
0 |
| work_mapper |
|
1 |
2 |
13 |
0 |
| reparametrize |
|
5 |
26 |
141 |
0 |
|
Source file: src/wepy/orchestration/orchestrator.py |
| Function name | |
Cyclomatic complexity
(15)
| LOC (1000000) |
Token count
| Parameter count (100) |
|---|
| __init__ |
|
1 |
3 |
16 |
0 |
| mode |
|
1 |
2 |
9 |
0 |
| append_only |
|
1 |
2 |
9 |
0 |
| close |
|
2 |
9 |
52 |
0 |
| db_uri |
|
1 |
2 |
9 |
0 |
| orch_path |
|
3 |
10 |
58 |
0 |
| serialize |
|
1 |
10 |
37 |
0 |
| deserialize |
|
1 |
2 |
21 |
0 |
| set_default_sim_apparatus |
|
1 |
3 |
23 |
0 |
| set_default_init_walkers |
|
1 |
3 |
23 |
0 |
| set_default_configuration |
|
1 |
5 |
39 |
0 |
| set_default_snapshot |
|
1 |
4 |
25 |
0 |
| gen_default_snapshot |
|
1 |
4 |
27 |
0 |
| get_default_sim_apparatus |
|
1 |
2 |
17 |
0 |
| get_default_init_walkers |
|
1 |
2 |
17 |
0 |
| get_default_configuration |
|
1 |
3 |
20 |
0 |
| get_default_configuration_hash |
|
1 |
2 |
12 |
0 |
| get_default_snapshot |
|
1 |
3 |
20 |
0 |
| get_default_snapshot_hash |
|
1 |
2 |
12 |
0 |
| hash_snapshot |
|
1 |
2 |
17 |
0 |
| get_snapshot |
|
1 |
2 |
20 |
0 |
| get_configuration |
|
1 |
2 |
20 |
0 |
| snapshot_hashes |
|
1 |
2 |
17 |
0 |
| configuration_hashes |
|
1 |
2 |
17 |
0 |
| add_snapshot |
|
4 |
7 |
56 |
0 |
| add_serial_snapshot |
|
4 |
6 |
47 |
0 |
| gen_start_snapshot |
|
1 |
4 |
30 |
0 |
| default_snapshot_hash |
|
1 |
2 |
13 |
0 |
| default_snapshot |
|
1 |
2 |
15 |
0 |
| snapshot_registered |
|
1 |
3 |
28 |
0 |
| snapshot_hash_registered |
|
4 |
5 |
34 |
0 |
| configuration_hash_registered |
|
4 |
5 |
34 |
0 |
| add_configuration |
|
4 |
7 |
55 |
0 |
| add_serial_configuration |
|
4 |
6 |
47 |
0 |
| create_run_table_query |
|
1 |
11 |
10 |
0 |
| add_run_record_query |
|
1 |
6 |
10 |
0 |
| update_run_record_query |
|
1 |
8 |
10 |
0 |
| delete_run_record_query |
|
1 |
6 |
10 |
0 |
| _add_run_record |
|
1 |
4 |
43 |
0 |
| _delete_run_record |
|
1 |
4 |
35 |
0 |
| _update_run_record |
|
1 |
4 |
43 |
0 |
| register_run |
|
4 |
14 |
83 |
0 |
| get_run_records |
|
1 |
9 |
46 |
0 |
| get_run_record |
|
1 |
11 |
59 |
0 |
| run_last_cycle_idx |
|
1 |
4 |
34 |
0 |
| run_configuration |
|
1 |
4 |
44 |
0 |
| run_configuration_hash |
|
1 |
4 |
34 |
0 |
| run_hashes |
|
2 |
2 |
27 |
0 |
| run_continues |
|
4 |
10 |
55 |
0 |
| _init_checkpoint_db |
|
1 |
13 |
107 |
0 |
| _save_checkpoint |
|
1 |
3 |
14 |
0 |
| gen_sim_manager |
|
1 |
10 |
70 |
0 |
| run_snapshot_by_time |
|
1 |
6 |
31 |
0 |
| orchestrate_snapshot_run_by_time |
|
1 |
10 |
46 |
0 |
| reconcile_orchestrators |
|
12 |
48 |
259 |
0 |
|
Source file: src/wepy/orchestration/snapshot.py |
| Function name | |
Cyclomatic complexity
(15)
| LOC (1000000) |
Token count
| Parameter count (100) |
|---|
| __init__ |
|
1 |
2 |
15 |
0 |
| filters |
|
1 |
2 |
10 |
0 |
| __init__ |
|
2 |
5 |
42 |
0 |
| runner |
|
1 |
2 |
14 |
0 |
| boundary_conditions |
|
1 |
2 |
14 |
0 |
| resampler |
|
1 |
2 |
14 |
0 |
| __init__ |
|
1 |
3 |
25 |
0 |
| walkers |
|
1 |
2 |
10 |
0 |
| apparatus |
|
1 |
2 |
10 |
0 |
|
Source file: src/wepy/orchestration/cli.py |
| Function name | |
Cyclomatic complexity
(15)
| LOC (1000000) |
Token count
| Parameter count (100) |
|---|
| settle_run_options |
|
1 |
8 |
34 |
0 |
| run_snapshot |
|
1 |
3 |
27 |
0 |
| run_orch |
|
1 |
2 |
25 |
0 |
| combine_orch_wepy_hdf5s |
|
11 |
54 |
370 |
0 |
| reconcile_hdf5 |
|
2 |
7 |
67 |
0 |
| reconcile_orch |
|
2 |
7 |
51 |
0 |
| hash_listing_formatter |
|
1 |
3 |
16 |
0 |
| ls_snapshots |
|
1 |
5 |
37 |
0 |
| ls_runs |
|
2 |
6 |
59 |
0 |
| ls_configs |
|
1 |
5 |
37 |
0 |
| hdf5_copy |
|
2 |
14 |
131 |
0 |
| get_snapshot |
|
3 |
10 |
74 |
0 |
| get_config |
|
3 |
10 |
74 |
0 |
| get_run |
|
4 |
18 |
162 |
0 |
| get_run_cycles |
|
2 |
7 |
71 |
0 |
| create_orch |
|
1 |
3 |
20 |
0 |
| add_snapshot |
|
1 |
6 |
43 |
0 |
| add_config |
|
1 |
6 |
43 |
0 |
| cli |
|
1 |
2 |
6 |
0 |
| run |
|
1 |
2 |
6 |
0 |
| get |
|
1 |
2 |
6 |
0 |
| add |
|
1 |
2 |
6 |
0 |
| create |
|
1 |
2 |
6 |
0 |
| ls |
|
1 |
2 |
6 |
0 |
| reconcile |
|
1 |
2 |
6 |
0 |
| hdf5 |
|
1 |
2 |
6 |
0 |
|
Source file: src/wepy/reporter/receptor/dashboard.py |
| Function name | |
Cyclomatic complexity
(15)
| LOC (1000000) |
Token count
| Parameter count (100) |
|---|
| __init__ |
|
1 |
2 |
17 |
0 |
| gen_fields |
|
1 |
9 |
48 |
0 |
| __init__ |
|
1 |
3 |
16 |
0 |
| gen_fields |
|
1 |
9 |
47 |
0 |
| __init__ |
|
1 |
3 |
16 |
0 |
| gen_fields |
|
1 |
9 |
47 |
0 |
|
Source file: src/wepy/reporter/revo/dashboard.py |
| Function name | |
Cyclomatic complexity
(15)
| LOC (1000000) |
Token count
| Parameter count (100) |
|---|
| __init__ |
|
1 |
8 |
36 |
0 |
| update_values |
|
5 |
20 |
181 |
0 |
| gen_fields |
|
1 |
16 |
90 |
0 |
|
Source file: src/wepy/reporter/wexplore/dashboard.py |
| Function name | |
Cyclomatic complexity
(15)
| LOC (1000000) |
Token count
| Parameter count (100) |
|---|
| __init__ |
|
1 |
4 |
18 |
0 |
| _leaf_regions_to_all_regions |
|
3 |
8 |
59 |
0 |
| update_values |
|
13 |
41 |
327 |
0 |
| gen_fields |
|
6 |
46 |
329 |
0 |
|
Source file: src/wepy/reporter/wexplore/image.py |
| Function name | |
Cyclomatic complexity
(15)
| LOC (1000000) |
Token count
| Parameter count (100) |
|---|
| __init__ |
|
1 |
5 |
20 |
0 |
| init |
|
2 |
10 |
81 |
0 |
| report |
|
1 |
2 |
16 |
0 |
|
Source file: src/wepy/reporter/dashboard.py |
| Function name | |
Cyclomatic complexity
(15)
| LOC (1000000) |
Token count
| Parameter count (100) |
|---|
| __init__ |
|
1 |
5 |
20 |
0 |
| init |
|
1 |
5 |
42 |
0 |
| calc_walker_summary |
|
2 |
8 |
55 |
0 |
| update_values |
|
4 |
10 |
85 |
0 |
| update_performance_values |
|
4 |
31 |
257 |
0 |
| write_dashboard |
|
1 |
3 |
30 |
0 |
| gen_sim_section |
|
1 |
17 |
102 |
0 |
| gen_performance_section |
|
1 |
35 |
193 |
0 |
| report |
|
4 |
24 |
142 |
0 |
| __init__ |
|
1 |
3 |
16 |
0 |
| update_values |
|
1 |
2 |
9 |
0 |
| gen_fields |
|
1 |
5 |
19 |
0 |
| gen_resampler_section |
|
1 |
6 |
33 |
0 |
| __init__ |
|
1 |
3 |
16 |
0 |
| update_values |
|
1 |
2 |
9 |
0 |
| gen_fields |
|
1 |
5 |
19 |
0 |
| gen_runner_section |
|
1 |
6 |
33 |
0 |
| __init__ |
|
1 |
4 |
20 |
0 |
| update_values |
|
5 |
15 |
114 |
0 |
| gen_fields |
|
1 |
13 |
74 |
0 |
| gen_bc_section |
|
1 |
6 |
33 |
0 |
|
Source file: src/wepy/reporter/hdf5.py |
| Function name | |
Cyclomatic complexity
(15)
| LOC (1000000) |
Token count
| Parameter count (100) |
|---|
| __init__ |
|
1 |
26 |
104 |
0 |
| init |
|
1 |
3 |
16 |
0 |
| cleanup |
|
2 |
5 |
36 |
0 |
| report |
|
1 |
8 |
36 |
0 |
| _report_warping |
|
2 |
3 |
32 |
0 |
| _report_bc |
|
2 |
3 |
32 |
0 |
| _report_resampler |
|
2 |
3 |
32 |
0 |
| _report_resampling |
|
1 |
2 |
24 |
0 |
| _report_progress |
|
1 |
2 |
26 |
0 |
|
Source file: src/wepy/reporter/openmm.py |
| Function name | |
Cyclomatic complexity
(15)
| LOC (1000000) |
Token count
| Parameter count (100) |
|---|
| __init__ |
|
1 |
3 |
14 |
0 |
| update_values |
|
1 |
6 |
48 |
0 |
| gen_fields |
|
1 |
16 |
100 |
0 |
|
Source file: src/wepy/reporter/reporter.py |
| Function name | |
Cyclomatic complexity
(15)
| LOC (1000000) |
Token count
| Parameter count (100) |
|---|
| __init__ |
|
1 |
2 |
10 |
0 |
| init |
|
1 |
4 |
30 |
0 |
| report |
|
1 |
4 |
30 |
0 |
| cleanup |
|
1 |
4 |
30 |
0 |
| __init__ |
|
1 |
3 |
24 |
0 |
| _validate_mode |
|
2 |
5 |
21 |
0 |
| mode |
|
2 |
4 |
28 |
0 |
| file_path |
|
2 |
4 |
28 |
0 |
| file_paths |
|
1 |
2 |
10 |
0 |
| file_paths |
|
2 |
3 |
26 |
0 |
| set_path |
|
1 |
2 |
18 |
0 |
| modes |
|
1 |
2 |
10 |
0 |
| modes |
|
2 |
3 |
26 |
0 |
| set_mode |
|
2 |
5 |
38 |
0 |
| reparametrize |
|
1 |
3 |
20 |
0 |
| init |
|
4 |
8 |
73 |
0 |
|
Source file: src/wepy/reporter/restree.py |
| Function name | |
Cyclomatic complexity
(15)
| LOC (1000000) |
Token count
| Parameter count (100) |
|---|
| __init__ |
|
1 |
10 |
40 |
0 |
| parent_table |
|
1 |
2 |
10 |
0 |
| _make_resampling_record |
|
1 |
8 |
58 |
0 |
| _make_warping_record |
|
1 |
8 |
58 |
0 |
| _make_record |
|
1 |
2 |
15 |
0 |
| report |
|
1 |
6 |
28 |
0 |
|
Source file: src/wepy/reporter/walker.py |
| Function name | |
Cyclomatic complexity
(15)
| LOC (1000000) |
Token count
| Parameter count (100) |
|---|
| __init__ |
|
1 |
5 |
22 |
0 |
| init |
|
1 |
9 |
79 |
0 |
| report |
|
1 |
2 |
16 |
0 |
|
Source file: src/wepy/resampling/decisions/__init__.py |
|
Source file: src/wepy/resampling/decisions/clone_merge.py |
| Function name | |
Cyclomatic complexity
(15)
| LOC (1000000) |
Token count
| Parameter count (100) |
|---|
| record |
|
1 |
4 |
27 |
0 |
| action |
|
17 |
38 |
330 |
0 |
|
Source file: src/wepy/resampling/decisions/decision.py |
| Function name | |
Cyclomatic complexity
(15)
| LOC (1000000) |
Token count
| Parameter count (100) |
|---|
| default_decision |
|
1 |
2 |
9 |
0 |
| field_names |
|
1 |
2 |
10 |
0 |
| field_shapes |
|
1 |
2 |
10 |
0 |
| field_dtypes |
|
1 |
2 |
10 |
0 |
| fields |
|
1 |
4 |
30 |
0 |
| record_field_names |
|
1 |
2 |
10 |
0 |
| enum_dict_by_name |
|
3 |
7 |
38 |
0 |
| enum_dict_by_value |
|
3 |
7 |
36 |
0 |
| enum_by_value |
|
1 |
3 |
20 |
0 |
| enum_by_name |
|
1 |
3 |
20 |
0 |
| record |
|
2 |
9 |
65 |
0 |
| action |
|
1 |
2 |
12 |
0 |
| parents |
|
5 |
8 |
62 |
0 |
| action |
|
5 |
10 |
89 |
0 |
|
Source file: src/wepy/resampling/distances/distance.py |
| Function name | |
Cyclomatic complexity
(15)
| LOC (1000000) |
Token count
| Parameter count (100) |
|---|
| __init__ |
|
1 |
2 |
7 |
0 |
| image |
|
1 |
2 |
10 |
0 |
| image_distance |
|
1 |
2 |
12 |
0 |
| distance |
|
1 |
3 |
29 |
0 |
| image |
|
1 |
2 |
24 |
0 |
| image_distance |
|
1 |
3 |
42 |
0 |
|
Source file: src/wepy/resampling/distances/randomwalk.py |
| Function name | |
Cyclomatic complexity
(15)
| LOC (1000000) |
Token count
| Parameter count (100) |
|---|
| __init__ |
|
1 |
2 |
7 |
0 |
| image |
|
1 |
2 |
13 |
0 |
| image_distance |
|
1 |
2 |
24 |
0 |
|
Source file: src/wepy/resampling/distances/receptor.py |
| Function name | |
Cyclomatic complexity
(15)
| LOC (1000000) |
Token count
| Parameter count (100) |
|---|
| __init__ |
|
1 |
9 |
102 |
0 |
| _unaligned_image |
|
1 |
7 |
58 |
0 |
| image |
|
1 |
4 |
38 |
0 |
| image_distance |
|
1 |
3 |
25 |
0 |
| image_distance |
|
1 |
5 |
57 |
0 |
|
Source file: src/wepy/resampling/resamplers/__init__.py |
|
Source file: src/wepy/resampling/resamplers/clone_merge.py |
| Function name | |
Cyclomatic complexity
(15)
| LOC (1000000) |
Token count
| Parameter count (100) |
|---|
| __init__ |
|
1 |
4 |
28 |
0 |
| pmin |
|
1 |
2 |
9 |
0 |
| pmax |
|
1 |
2 |
9 |
0 |
| _init_walker_actions |
|
2 |
6 |
46 |
0 |
| _check_resampled_walkers |
|
6 |
12 |
120 |
0 |
| assign_clones |
|
12 |
28 |
250 |
0 |
|
Source file: src/wepy/resampling/resamplers/resampler.py |
| Function name | |
Cyclomatic complexity
(15)
| LOC (1000000) |
Token count
| Parameter count (100) |
|---|
| __init__ |
|
1 |
5 |
20 |
0 |
| decision |
|
1 |
2 |
10 |
0 |
| resampling_field_names |
|
1 |
2 |
10 |
0 |
| resampling_field_shapes |
|
1 |
2 |
10 |
0 |
| resampling_field_dtypes |
|
1 |
2 |
10 |
0 |
| resampling_fields |
|
1 |
4 |
30 |
0 |
| resampling_record_field_names |
|
1 |
2 |
10 |
0 |
| resampler_field_names |
|
1 |
2 |
10 |
0 |
| resampler_field_shapes |
|
1 |
2 |
10 |
0 |
| resampler_field_dtypes |
|
1 |
2 |
10 |
0 |
| resampler_fields |
|
1 |
4 |
30 |
0 |
| resampler_record_field_names |
|
1 |
2 |
10 |
0 |
| is_debug_on |
|
1 |
2 |
10 |
0 |
| set_debug_mode |
|
4 |
9 |
48 |
0 |
| debug_on |
|
2 |
4 |
21 |
0 |
| debug_off |
|
2 |
4 |
22 |
0 |
| max_num_walkers_setting |
|
1 |
2 |
10 |
0 |
| min_num_walkers_setting |
|
1 |
2 |
10 |
0 |
| max_num_walkers |
|
4 |
12 |
48 |
0 |
| min_num_walkers |
|
4 |
12 |
48 |
0 |
| _set_resampling_num_walkers |
|
6 |
13 |
74 |
0 |
| _unset_resampling_num_walkers |
|
1 |
2 |
10 |
0 |
| _resample_init |
|
1 |
2 |
20 |
0 |
| _resample_cleanup |
|
1 |
2 |
14 |
0 |
| resample |
|
1 |
3 |
24 |
0 |
| resample |
|
2 |
16 |
147 |
0 |
| _init_walker_actions |
|
2 |
5 |
39 |
0 |
|
Source file: src/wepy/resampling/resamplers/revo.py |
| Function name | |
Cyclomatic complexity
(15)
| LOC (1000000) |
Token count
| Parameter count (100) |
|---|
| __init__ |
|
1 |
11 |
48 |
0 |
| resampler_field_dtypes |
|
1 |
5 |
43 |
0 |
| _novelty |
|
5 |
10 |
56 |
0 |
| _calcvariation |
|
6 |
16 |
168 |
0 |
| decide |
|
28 |
83 |
708 |
0 |
| _all_to_all_distance |
|
4 |
11 |
119 |
0 |
| resample |
|
4 |
18 |
213 |
0 |
|
Source file: src/wepy/resampling/resamplers/wexplore.py |
| Function name | |
Cyclomatic complexity
(15)
| LOC (1000000) |
Token count
| Parameter count (100) |
|---|
| calc_squashable_walkers_single_method |
|
4 |
19 |
80 |
0 |
| decide_merge_groups_single_method |
|
3 |
9 |
67 |
0 |
| calc_max_num_clones |
|
3 |
9 |
47 |
0 |
| __init__ |
|
1 |
6 |
31 |
0 |
| merge_method |
|
1 |
2 |
10 |
0 |
| distance |
|
1 |
2 |
10 |
0 |
| images |
|
1 |
2 |
10 |
0 |
| max_n_regions |
|
1 |
2 |
10 |
0 |
| n_levels |
|
1 |
2 |
10 |
0 |
| max_region_sizes |
|
1 |
2 |
10 |
0 |
| pmin |
|
1 |
2 |
10 |
0 |
| pmax |
|
1 |
2 |
10 |
0 |
| walker_assignments |
|
1 |
2 |
10 |
0 |
| walker_weights |
|
1 |
2 |
10 |
0 |
| regions |
|
1 |
2 |
10 |
0 |
| add_child |
|
1 |
11 |
67 |
0 |
| children |
|
1 |
4 |
30 |
0 |
| level_nodes |
|
4 |
5 |
37 |
0 |
| leaf_nodes |
|
1 |
2 |
15 |
0 |
| branch_tree |
|
2 |
9 |
67 |
0 |
| max_num_walkers |
|
1 |
2 |
10 |
0 |
| max_num_walkers |
|
1 |
2 |
13 |
0 |
| max_num_walkers |
|
1 |
2 |
13 |
0 |
| min_num_walkers |
|
1 |
2 |
10 |
0 |
| min_num_walkers |
|
1 |
2 |
13 |
0 |
| min_num_walkers |
|
1 |
2 |
13 |
0 |
| assign |
|
5 |
32 |
194 |
0 |
| clear_walkers |
|
2 |
9 |
81 |
0 |
| place_walkers |
|
11 |
38 |
364 |
0 |
| _max_n_merges |
|
8 |
17 |
139 |
0 |
| _calc_squashable_walkers |
|
2 |
6 |
41 |
0 |
| _calc_max_num_clones |
|
1 |
2 |
21 |
0 |
| _propagate_and_balance_shares |
|
9 |
28 |
209 |
0 |
| _dispense_parental_shares |
|
1 |
3 |
13 |
0 |
| _dispense_debit_shares |
|
1 |
2 |
11 |
0 |
| _dispense_credit_shares |
|
1 |
2 |
11 |
0 |
| _balance_children_shares |
|
1 |
3 |
11 |
0 |
| _gen_best_donation |
|
1 |
3 |
11 |
0 |
| _find_best_donation_pair |
|
1 |
2 |
9 |
0 |
| _calc_share_donation |
|
1 |
2 |
13 |
0 |
| _decide_merge_leaf |
|
5 |
17 |
157 |
0 |
| _solve_merge_groupings |
|
3 |
11 |
58 |
0 |
| _decide_clone_leaf |
|
14 |
37 |
288 |
0 |
| _decide_settle_balance |
|
8 |
14 |
143 |
0 |
| _check_clone_merge_specs |
|
21 |
58 |
451 |
0 |
| balance_tree |
|
7 |
23 |
182 |
0 |
| __init__ |
|
1 |
8 |
46 |
0 |
| resampler_field_shapes |
|
1 |
5 |
42 |
0 |
| resampler_field_dtypes |
|
1 |
5 |
42 |
0 |
| region_tree |
|
1 |
2 |
10 |
0 |
| assign |
|
1 |
5 |
37 |
0 |
| decide |
|
3 |
16 |
134 |
0 |
| _check_resampling_data |
|
11 |
21 |
159 |
0 |
| _resample_init |
|
2 |
7 |
65 |
0 |
| _resample_cleanup |
|
1 |
3 |
17 |
0 |
| resample |
|
5 |
19 |
180 |
0 |
|
Source file: src/wepy/resampling/__init__.py |
|
Source file: src/wepy/runners/__init__.py |
|
Source file: src/wepy/runners/randomwalk.py |
| Function name | |
Cyclomatic complexity
(15)
| LOC (1000000) |
Token count
| Parameter count (100) |
|---|
| __init__ |
|
1 |
2 |
17 |
0 |
| probability |
|
1 |
2 |
10 |
0 |
| _walk |
|
4 |
12 |
90 |
0 |
| run_segment |
|
1 |
2 |
12 |
0 |
|
Source file: src/wepy/runners/runner.py |
| Function name | |
Cyclomatic complexity
(15)
| LOC (1000000) |
Token count
| Parameter count (100) |
|---|
| pre_cycle |
|
1 |
2 |
10 |
0 |
| post_cycle |
|
1 |
2 |
10 |
0 |
| run_segment |
|
1 |
2 |
15 |
0 |
| run_segment |
|
1 |
2 |
14 |
0 |
|
Source file: src/wepy/runners/openmm.py |
| Function name | |
Cyclomatic complexity
(15)
| LOC (1000000) |
Token count
| Parameter count (100) |
|---|
| __init__ |
|
1 |
4 |
23 |
0 |
| pre_cycle |
|
1 |
4 |
14 |
0 |
| post_cycle |
|
1 |
4 |
27 |
0 |
| _resolve_platform |
|
1 |
3 |
8 |
0 |
| run_segment |
|
1 |
7 |
24 |
0 |
| generate_state |
|
1 |
4 |
33 |
0 |
| __init__ |
|
3 |
11 |
84 |
0 |
| sim_state |
|
1 |
2 |
10 |
0 |
| __getitem__ |
|
16 |
36 |
210 |
0 |
| positions |
|
2 |
7 |
28 |
0 |
| positions_unit |
|
1 |
2 |
12 |
0 |
| positions_values |
|
1 |
2 |
17 |
0 |
| velocities |
|
2 |
7 |
28 |
0 |
| velocities_unit |
|
1 |
2 |
12 |
0 |
| velocities_values |
|
2 |
6 |
31 |
0 |
| forces |
|
2 |
7 |
28 |
0 |
| forces_unit |
|
1 |
2 |
12 |
0 |
| forces_values |
|
2 |
6 |
31 |
0 |
| box_vectors |
|
2 |
7 |
28 |
0 |
| box_vectors_unit |
|
1 |
2 |
12 |
0 |
| box_vectors_values |
|
2 |
6 |
31 |
0 |
| kinetic_energy |
|
2 |
7 |
25 |
0 |
| kinetic_energy_unit |
|
1 |
2 |
12 |
0 |
| kinetic_energy_value |
|
2 |
6 |
38 |
0 |
| potential_energy |
|
2 |
7 |
25 |
0 |
| potential_energy_unit |
|
1 |
2 |
12 |
0 |
| potential_energy_value |
|
2 |
6 |
38 |
0 |
| time |
|
2 |
7 |
25 |
0 |
| time_unit |
|
1 |
2 |
12 |
0 |
| time_value |
|
2 |
6 |
38 |
0 |
| box_volume |
|
2 |
7 |
25 |
0 |
| box_volume_unit |
|
1 |
2 |
12 |
0 |
| box_volume_value |
|
2 |
6 |
38 |
0 |
| parameters |
|
2 |
7 |
25 |
0 |
| parameters_unit |
|
2 |
3 |
27 |
0 |
| parameters_values |
|
4 |
9 |
53 |
0 |
| parameter_derivatives |
|
2 |
7 |
25 |
0 |
| parameter_derivatives_unit |
|
2 |
3 |
27 |
0 |
| parameter_derivatives_values |
|
4 |
9 |
53 |
0 |
| _dict_attr_to_compound_key_dict |
|
4 |
12 |
84 |
0 |
| _get_nested_attr_from_compound_key |
|
6 |
12 |
109 |
0 |
| parameters_features |
|
2 |
6 |
31 |
0 |
| parameter_derivatives_features |
|
2 |
7 |
31 |
0 |
| omm_state_dict |
|
3 |
17 |
114 |
0 |
| dict |
|
3 |
7 |
51 |
0 |
| to_mdtraj |
|
1 |
7 |
56 |
0 |
| gen_sim_state |
|
1 |
2 |
13 |
0 |
| gen_walker_state |
|
1 |
2 |
13 |
0 |
| __init__ |
|
1 |
4 |
37 |
0 |
| __init__ |
|
2 |
8 |
48 |
0 |
| run_task |
|
1 |
3 |
29 |
0 |
| run_task |
|
1 |
9 |
57 |
0 |
| run_task |
|
2 |
10 |
53 |
0 |
| run_task |
|
1 |
10 |
64 |
0 |
|
Source file: src/wepy/util/__init__.py |
|
Source file: src/wepy/util/json_top.py |
| Function name | |
Cyclomatic complexity
(15)
| LOC (1000000) |
Token count
| Parameter count (100) |
|---|
| json_top_chain_fields |
|
4 |
7 |
53 |
0 |
| json_top_chain_df |
|
1 |
2 |
16 |
0 |
| json_top_residue_fields |
|
5 |
10 |
80 |
0 |
| json_top_residue_df |
|
1 |
2 |
16 |
0 |
| json_top_atom_fields |
|
6 |
13 |
107 |
0 |
| json_top_atom_df |
|
1 |
2 |
16 |
0 |
| json_top_atom_count |
|
3 |
8 |
47 |
0 |
| json_top_subset |
|
14 |
56 |
407 |
0 |
|
Source file: src/wepy/util/kv.py |
| Function name | |
Cyclomatic complexity
(15)
| LOC (1000000) |
Token count
| Parameter count (100) |
|---|
| gen_uri |
|
21 |
56 |
368 |
0 |
| __init__ |
|
1 |
8 |
36 |
0 |
| mode |
|
1 |
2 |
9 |
0 |
| append_only |
|
1 |
2 |
9 |
0 |
| close |
|
2 |
6 |
31 |
0 |
| db_uri |
|
1 |
2 |
9 |
0 |
| db |
|
1 |
2 |
9 |
0 |
| table |
|
1 |
2 |
9 |
0 |
| primary_key |
|
1 |
2 |
9 |
0 |
| value_name |
|
1 |
2 |
9 |
0 |
| value_types |
|
1 |
2 |
9 |
0 |
| _execute |
|
1 |
2 |
22 |
0 |
| __len__ |
|
1 |
3 |
28 |
0 |
| __getitem__ |
|
3 |
18 |
105 |
0 |
| __iter__ |
|
2 |
7 |
38 |
0 |
| __setitem__ |
|
2 |
4 |
37 |
0 |
| __delitem__ |
|
3 |
12 |
70 |
0 |
| insert_query |
|
1 |
3 |
19 |
0 |
| update_query |
|
1 |
6 |
31 |
0 |
| del_query |
|
1 |
5 |
25 |
0 |
| lockless_set |
|
3 |
10 |
65 |
0 |
| set_in_tx |
|
3 |
10 |
69 |
0 |
| del_in_tx |
|
3 |
9 |
51 |
0 |
| lock |
|
4 |
10 |
44 |
0 |
|
Source file: src/wepy/util/mdtraj.py |
| Function name | |
Cyclomatic complexity
(15)
| LOC (1000000) |
Token count
| Parameter count (100) |
|---|
| mdtraj_to_json_topology |
|
6 |
37 |
207 |
0 |
| json_to_mdtraj_topology |
|
8 |
27 |
209 |
0 |
| _new_json_to_mdtraj_topology |
|
6 |
27 |
193 |
0 |
| traj_fields_to_mdtraj |
|
2 |
12 |
103 |
0 |
|
Source file: src/wepy/util/util.py |
| Function name | |
Cyclomatic complexity
(15)
| LOC (1000000) |
Token count
| Parameter count (100) |
|---|
| set_loglevel |
|
3 |
8 |
45 |
0 |
| traj_box_vectors_to_lengths_angles |
|
5 |
14 |
157 |
0 |
| box_vectors_to_lengths_angles |
|
3 |
10 |
123 |
0 |
| lengths_and_angles_to_box_vectors |
|
5 |
19 |
317 |
0 |
| concat_traj_fields |
|
3 |
7 |
49 |
0 |
|
Source file: src/wepy/work_mapper/__init__.py |
|
Source file: src/wepy/work_mapper/task_mapper.py |
| Function name | |
Cyclomatic complexity
(15)
| LOC (1000000) |
Token count
| Parameter count (100) |
|---|
| __init__ |
|
1 |
5 |
20 |
0 |
| init |
|
1 |
3 |
29 |
0 |
| _sigterm_shutdown |
|
1 |
4 |
26 |
0 |
| walker_task_type |
|
1 |
2 |
10 |
0 |
| force_shutdown |
|
7 |
18 |
130 |
0 |
| map |
|
21 |
95 |
607 |
0 |
| __init__ |
|
1 |
12 |
26 |
0 |
| _external_sigterm_shutdown |
|
1 |
7 |
55 |
0 |
| _shutdown |
|
1 |
6 |
38 |
0 |
| attributes |
|
1 |
2 |
11 |
0 |
| attributes |
|
1 |
2 |
14 |
0 |
| _run_task |
|
2 |
21 |
121 |
0 |
| run_task |
|
1 |
3 |
17 |
0 |
| run |
|
5 |
35 |
197 |
0 |
| _run_walker |
|
7 |
61 |
411 |
0 |
|
Source file: src/wepy/work_mapper/worker.py |
|
Source file: src/wepy/work_mapper/mapper.py |
| Function name | |
Cyclomatic complexity
(15)
| LOC (1000000) |
Token count
| Parameter count (100) |
|---|
| __init__ |
|
1 |
3 |
23 |
0 |
| attributes |
|
1 |
2 |
9 |
0 |
| attributes |
|
1 |
2 |
14 |
0 |
| init |
|
7 |
8 |
78 |
0 |
| segment_func |
|
1 |
2 |
10 |
0 |
| cleanup |
|
1 |
2 |
10 |
0 |
| map |
|
1 |
2 |
13 |
0 |
| __init__ |
|
1 |
3 |
36 |
0 |
| map |
|
7 |
33 |
233 |
0 |
| worker_segment_times |
|
1 |
2 |
10 |
0 |
| __init__ |
|
1 |
4 |
29 |
0 |
| __call__ |
|
1 |
2 |
27 |
0 |
| __init__ |
|
1 |
3 |
15 |
0 |
| __init__ |
|
1 |
5 |
20 |
0 |
| init |
|
1 |
2 |
16 |
0 |
| cleanup |
|
1 |
2 |
12 |
0 |
| num_workers |
|
1 |
2 |
10 |
0 |
| worker_segment_times |
|
1 |
2 |
10 |
0 |
| _make_task |
|
1 |
2 |
25 |
0 |
| __init__ |
|
1 |
6 |
24 |
0 |
| worker_type |
|
1 |
2 |
10 |
0 |
| init |
|
1 |
2 |
16 |
0 |
| _sigterm_shutdown |
|
1 |
3 |
20 |
0 |
| force_shutdown |
|
15 |
38 |
304 |
0 |
| cleanup |
|
2 |
7 |
55 |
0 |
| map |
|
11 |
51 |
342 |
0 |
| __init__ |
|
1 |
8 |
26 |
0 |
| worker_idx |
|
1 |
2 |
10 |
0 |
| attributes |
|
1 |
2 |
10 |
0 |
| mapper_attributes |
|
1 |
2 |
10 |
0 |
| run |
|
5 |
35 |
210 |
0 |
| _sigterm_shutdown |
|
1 |
7 |
55 |
0 |
| _shutdown |
|
1 |
6 |
37 |
0 |
| _run_worker |
|
7 |
38 |
271 |
0 |
| run_task |
|
1 |
2 |
12 |
0 |
| _run_task |
|
2 |
20 |
103 |
0 |
|
Source file: src/wepy/__init__.py |
|
Source file: src/wepy/__main__.py |
|
Source file: src/wepy/_print_version.py |
|
Source file: src/wepy/_version.py |
| Function name | |
Cyclomatic complexity
(15)
| LOC (1000000) |
Token count
| Parameter count (100) |
|---|
| get_keywords |
|
1 |
6 |
31 |
0 |
| get_config |
|
1 |
9 |
42 |
0 |
| register_vcs_handler.decorate |
|
2 |
5 |
30 |
0 |
| register_vcs_handler |
|
1 |
3 |
12 |
0 |
| run_command |
|
1 |
2 |
23 |
0 |
| versions_from_parentdir |
|
4 |
15 |
108 |
0 |
| git_get_keywords |
|
9 |
21 |
151 |
0 |
| git_versions_from_keywords |
|
17 |
34 |
302 |
0 |
| git_pieces_from_vcs |
|
11 |
56 |
427 |
0 |
| plus_or_dot |
|
2 |
4 |
22 |
0 |
| render_pep440 |
|
6 |
14 |
87 |
0 |
| render_pep440_pre |
|
3 |
8 |
44 |
0 |
| render_pep440_post |
|
6 |
15 |
89 |
0 |
| render_pep440_old |
|
6 |
12 |
67 |
0 |
| render_git_describe |
|
4 |
10 |
58 |
0 |
| render_git_describe_long |
|
3 |
9 |
52 |
0 |
| render |
|
10 |
26 |
163 |
0 |
| get_versions |
|
7 |
30 |
164 |
0 |
|
Source file: src/wepy/sim_manager.py |
| Function name | |
Cyclomatic complexity
(15)
| LOC (1000000) |
Token count
| Parameter count (100) |
|---|
| __init__ |
|
1 |
7 |
30 |
0 |
| run_segment |
|
5 |
16 |
97 |
0 |
| run_cycle |
|
1 |
5 |
14 |
0 |
| _run_cycle |
|
1 |
5 |
14 |
0 |
| init |
|
1 |
3 |
12 |
0 |
| cleanup |
|
3 |
10 |
69 |
0 |
| run_simulation_by_time |
|
2 |
13 |
121 |
0 |
| run_simulation |
|
1 |
3 |
12 |
0 |
| continue_run_simulation |
|
1 |
5 |
14 |
0 |
| continue_run_simulation_by_time |
|
3 |
15 |
136 |
0 |
|
Source file: src/wepy/walker.py |
| Function name | |
Cyclomatic complexity
(15)
| LOC (1000000) |
Token count
| Parameter count (100) |
|---|
| split |
|
2 |
6 |
49 |
0 |
| keep_merge |
|
2 |
5 |
46 |
0 |
| merge |
|
2 |
7 |
63 |
0 |
| __init__ |
|
1 |
3 |
20 |
0 |
| clone |
|
2 |
6 |
53 |
0 |
| squash |
|
1 |
3 |
29 |
0 |
| merge |
|
1 |
2 |
17 |
0 |
| __init__ |
|
1 |
2 |
14 |
0 |
| __getitem__ |
|
1 |
2 |
14 |
0 |
| dict |
|
1 |
2 |
13 |
0 |
|
Source file: src/wepy/hdf5.py |
| Function name | |
Cyclomatic complexity
(15)
| LOC (1000000) |
Token count
| Parameter count (100) |
|---|
| _iter_field_paths |
|
5 |
10 |
67 |
0 |
| __init__ |
|
1 |
9 |
49 |
0 |
| __del__ |
|
1 |
2 |
10 |
0 |
| __enter__ |
|
1 |
3 |
12 |
0 |
| __exit__ |
|
1 |
2 |
16 |
0 |
| swmr_mode |
|
1 |
2 |
9 |
0 |
| swmr_mode |
|
1 |
2 |
12 |
0 |
| _create_init |
|
17 |
54 |
493 |
0 |
| _read_write_init |
|
1 |
2 |
11 |
0 |
| _add_init |
|
2 |
5 |
27 |
0 |
| _read_init |
|
1 |
2 |
7 |
0 |
| _set_default_init_field_attributes |
|
4 |
15 |
117 |
0 |
| _get_field_path_grp |
|
2 |
8 |
62 |
0 |
| _init_continuations |
|
2 |
8 |
67 |
0 |
| _add_run_init |
|
2 |
4 |
46 |
0 |
| _add_init_walkers |
|
4 |
8 |
95 |
0 |
| _init_run_sporadic_record_grp |
|
2 |
9 |
77 |
0 |
| _init_run_continual_record_grp |
|
2 |
7 |
53 |
0 |
| _init_run_records_field |
|
1 |
2 |
15 |
0 |
| _is_sporadic_records |
|
2 |
5 |
19 |
0 |
| _init_traj_field |
|
2 |
5 |
53 |
0 |
| _init_contiguous_traj_field |
|
2 |
4 |
67 |
0 |
| _init_sparse_traj_field |
|
4 |
9 |
115 |
0 |
| _init_traj_fields |
|
1 |
2 |
15 |
0 |
| _add_traj_field_data |
|
1 |
6 |
16 |
0 |
| _extend_contiguous_traj_field |
|
3 |
17 |
178 |
0 |
| _extend_sparse_traj_field |
|
3 |
20 |
229 |
0 |
| _add_sparse_field_flag |
|
2 |
6 |
69 |
0 |
| _add_field_feature_shape |
|
1 |
3 |
40 |
0 |
| _add_field_feature_dtype |
|
1 |
4 |
45 |
0 |
| _set_field_feature_shape |
|
3 |
13 |
91 |
0 |
| _set_field_feature_dtype |
|
3 |
14 |
101 |
0 |
| _extend_run_record_data_field |
|
1 |
2 |
13 |
0 |
| _run_record_namedtuple |
|
1 |
4 |
32 |
0 |
| _convert_record_field_to_table_column |
|
7 |
15 |
133 |
0 |
| _convert_record_fields_to_table_columns |
|
2 |
6 |
41 |
0 |
| _make_records |
|
4 |
11 |
94 |
0 |
| _run_records_sporadic |
|
4 |
18 |
132 |
0 |
| _run_records_continual |
|
4 |
20 |
156 |
0 |
| _get_contiguous_traj_field |
|
2 |
7 |
66 |
0 |
| _get_sparse_traj_field |
|
4 |
25 |
294 |
0 |
| _add_run_field |
|
1 |
6 |
19 |
0 |
| _add_field |
|
1 |
2 |
17 |
0 |
| filename |
|
1 |
2 |
10 |
0 |
| open |
|
3 |
10 |
67 |
0 |
| close |
|
2 |
5 |
31 |
0 |
| mode |
|
1 |
2 |
10 |
0 |
| mode |
|
1 |
2 |
14 |
0 |
| set_mode |
|
2 |
5 |
30 |
0 |
| h5_mode |
|
1 |
2 |
12 |
0 |
| _set_h5_mode |
|
2 |
4 |
24 |
0 |
| h5 |
|
1 |
2 |
10 |
0 |
| run |
|
1 |
2 |
25 |
0 |
| traj |
|
1 |
2 |
28 |
0 |
| run_trajs |
|
1 |
2 |
24 |
0 |
| runs |
|
1 |
2 |
13 |
0 |
| run_grp |
|
1 |
2 |
20 |
0 |
| run_start_snapshot_hash |
|
1 |
2 |
20 |
0 |
| run_end_snapshot_hash |
|
1 |
2 |
20 |
0 |
| set_run_start_snapshot_hash |
|
2 |
5 |
43 |
0 |
| set_run_end_snapshot_hash |
|
2 |
5 |
43 |
0 |
| settings_grp |
|
1 |
3 |
16 |
0 |
| decision_grp |
|
1 |
2 |
18 |
0 |
| init_walkers_grp |
|
1 |
2 |
18 |
0 |
| records_grp |
|
1 |
3 |
29 |
0 |
| resampling_grp |
|
1 |
2 |
17 |
0 |
| resampler_grp |
|
1 |
2 |
17 |
0 |
| warping_grp |
|
1 |
2 |
17 |
0 |
| bc_grp |
|
1 |
2 |
17 |
0 |
| progress_grp |
|
1 |
2 |
17 |
0 |
| iter_runs |
|
5 |
10 |
55 |
0 |
| iter_trajs |
|
4 |
11 |
63 |
0 |
| iter_run_trajs |
|
1 |
3 |
35 |
0 |
| defined_traj_field_names |
|
1 |
2 |
17 |
0 |
| observable_field_names |
|
5 |
10 |
72 |
0 |
| _check_traj_field_consistency |
|
6 |
11 |
59 |
0 |
| record_fields |
|
2 |
6 |
40 |
0 |
| sparse_fields |
|
1 |
2 |
23 |
0 |
| main_rep_idxs |
|
2 |
5 |
41 |
0 |
| alt_reps_idxs |
|
2 |
3 |
40 |
0 |
| alt_reps |
|
2 |
3 |
33 |
0 |
| field_feature_shapes |
|
3 |
11 |
74 |
0 |
| field_feature_dtypes |
|
4 |
14 |
95 |
0 |
| continuations |
|
1 |
2 |
16 |
0 |
| metadata |
|
1 |
2 |
15 |
0 |
| decision_enum |
|
2 |
6 |
43 |
0 |
| decision_value_names |
|
2 |
7 |
46 |
0 |
| get_topology |
|
4 |
11 |
70 |
0 |
| topology |
|
1 |
2 |
17 |
0 |
| get_mdtraj_topology |
|
1 |
3 |
25 |
0 |
| initial_walker_fields |
|
6 |
10 |
108 |
0 |
| initial_walkers_to_mdtraj |
|
1 |
5 |
53 |
0 |
| num_atoms |
|
1 |
2 |
24 |
0 |
| num_dims |
|
1 |
2 |
24 |
0 |
| num_runs |
|
1 |
2 |
16 |
0 |
| num_trajs |
|
1 |
2 |
18 |
0 |
| num_init_walkers |
|
1 |
2 |
18 |
0 |
| num_walkers |
|
2 |
5 |
33 |
0 |
| num_run_trajs |
|
1 |
2 |
27 |
0 |
| num_run_cycles |
|
1 |
2 |
17 |
0 |
| num_traj_frames |
|
1 |
2 |
27 |
0 |
| run_idxs |
|
1 |
2 |
22 |
0 |
| run_traj_idxs |
|
1 |
2 |
33 |
0 |
| run_traj_idx_tuples |
|
4 |
10 |
56 |
0 |
| get_traj_field_cycle_idxs |
|
3 |
9 |
92 |
0 |
| next_run_idx |
|
1 |
2 |
10 |
0 |
| next_run_traj_idx |
|
1 |
2 |
15 |
0 |
| is_run_contig |
|
6 |
12 |
87 |
0 |
| clone |
|
1 |
17 |
186 |
0 |
| link_run |
|
3 |
12 |
115 |
0 |
| link_file_runs |
|
3 |
13 |
83 |
0 |
| extract_run |
|
1 |
4 |
20 |
0 |
| extract_file_runs |
|
1 |
2 |
11 |
0 |
| join |
|
2 |
5 |
49 |
0 |
| add_metadata |
|
1 |
2 |
20 |
0 |
| init_record_fields |
|
2 |
9 |
71 |
0 |
| init_resampling_record_fields |
|
1 |
2 |
20 |
0 |
| init_resampler_record_fields |
|
1 |
2 |
20 |
0 |
| init_bc_record_fields |
|
1 |
2 |
20 |
0 |
| init_warping_record_fields |
|
1 |
2 |
20 |
0 |
| init_progress_record_fields |
|
1 |
2 |
20 |
0 |
| add_continuation |
|
1 |
4 |
63 |
0 |
| new_run |
|
5 |
17 |
131 |
0 |
| init_run_resampling |
|
1 |
7 |
49 |
0 |
| init_run_resampling_decision |
|
1 |
2 |
24 |
0 |
| init_run_resampler |
|
1 |
4 |
31 |
0 |
| init_run_warping |
|
1 |
4 |
31 |
0 |
| init_run_progress |
|
1 |
4 |
31 |
0 |
| init_run_bc |
|
1 |
4 |
31 |
0 |
| init_run_fields_resampling |
|
1 |
3 |
24 |
0 |
| init_run_fields_resampling_decision |
|
2 |
4 |
44 |
0 |
| init_run_fields_resampler |
|
1 |
3 |
24 |
0 |
| init_run_fields_warping |
|
1 |
3 |
24 |
0 |
| init_run_fields_progress |
|
1 |
3 |
24 |
0 |
| init_run_fields_bc |
|
1 |
3 |
24 |
0 |
| init_run_record_grp |
|
2 |
7 |
46 |
0 |
| add_traj |
|
11 |
50 |
436 |
0 |
| extend_traj |
|
17 |
56 |
449 |
0 |
| extend_cycle_warping_records |
|
1 |
2 |
24 |
0 |
| extend_cycle_bc_records |
|
1 |
2 |
24 |
0 |
| extend_cycle_progress_records |
|
1 |
2 |
24 |
0 |
| extend_cycle_resampling_records |
|
1 |
2 |
24 |
0 |
| extend_cycle_resampler_records |
|
1 |
2 |
24 |
0 |
| extend_cycle_run_group_records |
|
4 |
12 |
115 |
0 |
| run_records |
|
1 |
3 |
24 |
0 |
| run_contig_records |
|
3 |
9 |
61 |
0 |
| run_records_dataframe |
|
1 |
3 |
27 |
0 |
| run_contig_records_dataframe |
|
1 |
3 |
27 |
0 |
| resampling_records |
|
1 |
2 |
17 |
0 |
| resampling_records_dataframe |
|
1 |
2 |
20 |
0 |
| resampler_records |
|
1 |
2 |
17 |
0 |
| resampler_records_dataframe |
|
1 |
2 |
20 |
0 |
| warping_records |
|
1 |
2 |
17 |
0 |
| warping_records_dataframe |
|
1 |
2 |
20 |
0 |
| bc_records |
|
1 |
2 |
17 |
0 |
| bc_records_dataframe |
|
1 |
2 |
20 |
0 |
| progress_records |
|
1 |
2 |
17 |
0 |
| progress_records_dataframe |
|
1 |
2 |
20 |
0 |
| run_resampling_panel |
|
1 |
2 |
17 |
0 |
| run_contig_resampling_panel |
|
2 |
7 |
44 |
0 |
| add_run_observable |
|
1 |
3 |
40 |
0 |
| add_traj_observable |
|
6 |
18 |
155 |
0 |
| add_observable |
|
1 |
7 |
37 |
0 |
| compute_observable |
|
1 |
4 |
31 |
0 |
| get_traj_field |
|
3 |
10 |
98 |
0 |
| get_trace_fields |
|
1 |
5 |
14 |
0 |
| argsort |
|
1 |
2 |
22 |
0 |
| apply_argsorted |
|
2 |
2 |
18 |
0 |
| get_run_trace_fields |
|
5 |
9 |
87 |
0 |
| get_contig_trace_fields |
|
8 |
26 |
187 |
0 |
| iter_trajs_fields |
|
5 |
15 |
101 |
0 |
| traj_fields_map |
|
1 |
2 |
23 |
0 |
| to_mdtraj |
|
10 |
40 |
279 |
0 |
| trace_to_mdtraj |
|
1 |
4 |
45 |
0 |
| run_trace_to_mdtraj |
|
1 |
4 |
49 |
0 |
| _choose_rep_path |
|
6 |
17 |
98 |
0 |
| traj_fields_to_mdtraj |
|
1 |
4 |
41 |
0 |
| copy_run_slice |
|
1 |
2 |
19 |
0 |