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Tiago Peixoto
graph-tool
Commits
36917e1f
Commit
36917e1f
authored
May 18, 2020
by
Tiago Peixoto
Browse files
Merge branch 'imports' into 'master'
Remove unused imports See merge request
!25
parents
d2dc156a
67f7464d
Pipeline
#614
passed with stage
in 457 minutes and 12 seconds
Changes
20
Pipelines
1
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Inline
Side-by-side
src/graph_tool/__init__.py
View file @
36917e1f
...
...
@@ -100,7 +100,6 @@ __URL__ = "http://graph-tool.skewed.de"
import
numpy
import
numpy.ma
import
scipy
import
scipy.stats
from
.dl_import
import
*
...
...
@@ -126,8 +125,7 @@ import collections.abc
import
itertools
import
csv
from
.decorators
import
_require
,
_attrs
,
_limit_args
,
_copy_func
from
inspect
import
ismethod
from
.decorators
import
_require
,
_limit_args
,
_copy_func
__all__
=
[
"Graph"
,
"GraphView"
,
"Vertex"
,
"Edge"
,
"VertexBase"
,
"EdgeBase"
,
"Vector_bool"
,
"Vector_int16_t"
,
"Vector_int32_t"
,
"Vector_int64_t"
,
...
...
src/graph_tool/clustering/__init__.py
View file @
36917e1f
...
...
@@ -44,14 +44,13 @@ Contents
from
..
dl_import
import
dl_import
dl_import
(
"from . import libgraph_tool_clustering as _gt"
)
from
..
import
_degree
,
_prop
,
Graph
,
GraphView
,
VertexPropertyMap
,
_get_rng
from
..
import
_prop
,
Graph
,
GraphView
,
VertexPropertyMap
,
_get_rng
from
..
topology
import
isomorphism
from
..
generation
import
random_rewire
from
..
stats
import
vertex_hist
from
collections
import
defaultdict
from
numpy
import
*
from
numpy
import
random
__all__
=
[
"local_clustering"
,
"global_clustering"
,
"extended_clustering"
,
"motifs"
,
"motif_significance"
]
...
...
src/graph_tool/dl_import.py
View file @
36917e1f
...
...
@@ -19,7 +19,6 @@
# along with this program. If not, see <http://www.gnu.org/licenses/>.
import
sys
import
os.path
try
:
from
os
import
RTLD_LAZY
,
RTLD_GLOBAL
...
...
src/graph_tool/draw/__init__.py
View file @
36917e1f
...
...
@@ -70,9 +70,7 @@ from .. import Graph, GraphView, _check_prop_vector, _check_prop_scalar, \
group_vector_property
,
ungroup_vector_property
,
infect_vertex_property
,
\
_prop
,
_get_rng
from
..
topology
import
max_cardinality_matching
,
max_independent_vertex_set
,
\
label_components
,
pseudo_diameter
,
shortest_distance
,
make_maximal_planar
,
\
is_planar
from
..
stats
import
label_parallel_edges
label_components
,
shortest_distance
,
make_maximal_planar
,
is_planar
from
..
generation
import
predecessor_tree
,
condensation_graph
import
numpy.random
from
numpy
import
sqrt
...
...
src/graph_tool/draw/cairo_draw.py
View file @
36917e1f
...
...
@@ -89,7 +89,7 @@ except ImportError:
warnings
.
warn
(
msg
,
RuntimeWarning
)
from
..
draw
import
sfdp_layout
,
random_layout
,
_avg_edge_distance
,
\
coarse_graphs
,
radial_tree_layout
,
prop_to_size
radial_tree_layout
,
prop_to_size
from
..
generation
import
graph_union
from
..
topology
import
shortest_path
...
...
src/graph_tool/draw/graphviz_draw.py
View file @
36917e1f
...
...
@@ -21,7 +21,6 @@
import
sys
import
os
import
os.path
import
time
import
warnings
import
ctypes
import
ctypes.util
...
...
src/graph_tool/draw/gtk_draw.py
View file @
36917e1f
...
...
@@ -20,11 +20,10 @@
import
numpy
from
..
import
GraphView
,
PropertyMap
,
VertexPropertyMap
,
\
ungroup_vector_property
,
group_vector_property
,
infect_vertex_property
,
\
edge_endpoint_property
,
_prop
from
..
import
GraphView
,
PropertyMap
,
ungroup_vector_property
,
\
group_vector_property
,
infect_vertex_property
,
edge_endpoint_property
,
_prop
from
.cairo_draw
import
*
from
.cairo_draw
import
_vdefaults
,
_edefaults
from
.cairo_draw
import
_edefaults
from
..
draw
import
sfdp_layout
,
random_layout
,
_avg_edge_distance
,
\
coarse_graphs
...
...
src/graph_tool/generation/__init__.py
View file @
36917e1f
...
...
@@ -52,8 +52,7 @@ from .. dl_import import dl_import
dl_import
(
"from . import libgraph_tool_generation"
)
from
..
import
Graph
,
GraphView
,
_check_prop_scalar
,
_prop
,
_limit_args
,
\
_gt_type
,
_get_rng
,
libcore
,
Vector_double
from
..
stats
import
label_parallel_edges
,
label_self_loops
_gt_type
,
_get_rng
,
Vector_double
import
inspect
import
types
import
numpy
...
...
@@ -2372,4 +2371,4 @@ class DynamicSampler(libgraph_tool_generation.DynamicSampler):
libgraph_tool_generation
.
DynamicSampler
.
__init__
(
self
,
values
,
probs
)
def
sample
(
self
):
return
libgraph_tool_generation
.
DynamicSampler
.
sample
(
self
,
_get_rng
())
\ No newline at end of file
return
libgraph_tool_generation
.
DynamicSampler
.
sample
(
self
,
_get_rng
())
src/graph_tool/gt_io.py
View file @
36917e1f
...
...
@@ -19,7 +19,6 @@
# along with this program. If not, see <http://www.gnu.org/licenses/>.
import
pickle
import
base64
import
atexit
from
io
import
BytesIO
from
.
import
libgraph_tool_core
...
...
src/graph_tool/inference/blockmodel.py
View file @
36917e1f
...
...
@@ -18,12 +18,12 @@
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
from
..
import
_degree
,
_prop
,
Graph
,
GraphView
,
libcore
,
_get_rng
,
\
PropertyMap
,
VertexPropertyMap
,
Vector_size_t
,
Vector_double
,
\
group_vector_property
,
perfect_prop_hash
from
..
import
_prop
,
Graph
,
libcore
,
_get_rng
,
PropertyMap
,
\
VertexPropertyMap
,
Vector_size_t
,
Vector_double
,
group_vector_property
,
\
perfect_prop_hash
from
..
generation
import
condensation_graph
,
random_rewire
,
generate_sbm
,
\
solve_sbm_fugacities
,
generate_maxent_sbm
from
..
stats
import
label_self_loops
,
remove_parallel_edges
,
remove_self_loops
from
..
stats
import
remove_parallel_edges
,
remove_self_loops
from
..
spectral
import
adjacency
import
random
from
numpy
import
*
...
...
@@ -2573,4 +2573,4 @@ def microstate_entropy(h, unlabel=True):
return
libinference
.
partitions_entropy
(
h
,
unlabel
)
from
.
overlap_blockmodel
import
*
\ No newline at end of file
from
.
overlap_blockmodel
import
*
src/graph_tool/inference/blockmodel_em.py
View file @
36917e1f
...
...
@@ -18,16 +18,9 @@
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
from
..
import
_degree
,
_prop
,
Graph
,
GraphView
,
libcore
,
_get_rng
,
PropertyMap
,
\
Vector_size_t
,
Vector_double
,
group_vector_property
from
..
generation
import
condensation_graph
from
..
stats
import
label_self_loops
from
..
spectral
import
adjacency
from
..
import
_prop
,
_get_rng
,
group_vector_property
import
random
from
numpy
import
*
import
numpy
import
copy
import
collections
from
.
blockmodel
import
*
from
.
util
import
*
...
...
@@ -288,4 +281,4 @@ def em_infer(state, max_iter=1000, max_e_iter=1, epsilon=1e-3,
break
if
verbose
:
print
(
niter
,
delta
)
return
delta
,
niter
\ No newline at end of file
return
delta
,
niter
src/graph_tool/inference/layered_blockmodel.py
View file @
36917e1f
...
...
@@ -18,23 +18,18 @@
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
from
..
import
_degree
,
_prop
,
Graph
,
GraphView
,
libcore
,
_get_rng
,
PropertyMap
import
random
from
..
import
_prop
,
Graph
,
GraphView
,
libcore
,
_get_rng
from
numpy
import
*
import
numpy
from
collections
import
defaultdict
from
scipy.special
import
gammaln
import
copy
import
warnings
from
..
import
group_vector_property
,
ungroup_vector_property
,
Vector_size_t
,
\
perfect_prop_hash
from
..
import
group_vector_property
,
ungroup_vector_property
,
perfect_prop_hash
from
..
dl_import
import
dl_import
dl_import
(
"from . import libgraph_tool_inference as libinference"
)
from
..
generation
import
graph_union
from
..
stats
import
vertex_hist
from
.
blockmodel
import
*
from
.
blockmodel
import
_bm_test
...
...
@@ -1115,4 +1110,4 @@ def init_layer_confined(g, ec):
ba
.
fa
=
ba
.
fa
+
ec
.
fa
*
(
ba
.
fa
.
max
()
+
1
)
continuous_map
(
ba
)
be
=
group_vector_property
([
ba
,
ba
])
return
be
\ No newline at end of file
return
be
src/graph_tool/inference/nested_blockmodel.py
View file @
36917e1f
...
...
@@ -18,7 +18,7 @@
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
from
..
import
_degree
,
_prop
,
Graph
,
GraphView
from
..
import
_prop
,
Graph
,
GraphView
from
.
blockmodel
import
*
from
.
blockmodel
import
_bm_test
from
.
overlap_blockmodel
import
*
...
...
src/graph_tool/inference/overlap_blockmodel.py
View file @
36917e1f
...
...
@@ -18,12 +18,11 @@
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
from
..
import
_degree
,
_prop
,
Graph
,
GraphView
,
libcore
,
_get_rng
,
PropertyMap
from
..
import
_prop
,
Graph
,
libcore
,
_get_rng
,
PropertyMap
import
random
from
numpy
import
*
import
numpy
from
collections
import
defaultdict
from
..
import
group_vector_property
,
ungroup_vector_property
...
...
src/graph_tool/inference/partition_centroid.py
View file @
36917e1f
...
...
@@ -18,7 +18,7 @@
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
from
..
import
_degree
,
_prop
,
Graph
,
GraphView
,
_get_rng
,
Vector_size_t
from
..
import
Graph
,
_get_rng
,
Vector_size_t
from
.
blockmodel
import
DictState
,
get_entropy_args
,
_bm_test
from
..
dl_import
import
dl_import
...
...
src/graph_tool/inference/partition_modes.py
View file @
36917e1f
...
...
@@ -18,8 +18,7 @@
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
from
..
import
_degree
,
_prop
,
Graph
,
GraphView
,
_get_rng
,
Vector_int32_t
,
\
Vector_size_t
from
..
import
Graph
,
_get_rng
,
Vector_int32_t
,
Vector_size_t
from
.
blockmodel
import
DictState
,
get_entropy_args
,
_bm_test
from
..
dl_import
import
dl_import
...
...
@@ -370,4 +369,4 @@ def overlap_center(bs, init=None):
nr
=
np
.
bincount
(
bs
[:,
i
])
c
[
i
]
=
nr
.
argmax
()
delta
=
1
-
partition_overlap
(
c
,
lc
)
return
c
\ No newline at end of file
return
c
src/graph_tool/inference/uncertain_blockmodel.py
View file @
36917e1f
...
...
@@ -18,8 +18,8 @@
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
from
..
import
_degree
,
_prop
,
Graph
,
GraphView
,
libcore
,
_get_rng
,
\
PropertyMap
,
edge_endpoint_property
from
..
import
_prop
,
Graph
,
GraphView
,
_get_rng
,
PropertyMap
,
\
edge_endpoint_property
from
..
dl_import
import
dl_import
dl_import
(
"from . import libgraph_tool_inference as libinference"
)
...
...
src/graph_tool/search/__init__.py
View file @
36917e1f
...
...
@@ -81,7 +81,6 @@ from .. dl_import import dl_import
dl_import
(
"from . import libgraph_tool_search"
)
from
..
import
_prop
,
_python_type
,
_get_null_vertex
import
weakref
import
numpy
__all__
=
[
"bfs_search"
,
"bfs_iterator"
,
"BFSVisitor"
,
"dfs_search"
,
...
...
src/graph_tool/stats/__init__.py
View file @
36917e1f
...
...
@@ -49,7 +49,6 @@ dl_import("from . import libgraph_tool_stats")
from
..
import
_degree
,
_prop
,
_get_rng
,
GraphView
,
PropertyMap
from
numpy
import
*
import
numpy
__all__
=
[
"vertex_hist"
,
"edge_hist"
,
"vertex_average"
,
"edge_average"
,
"label_parallel_edges"
,
"remove_parallel_edges"
,
...
...
src/graph_tool/topology/__init__.py
View file @
36917e1f
...
...
@@ -76,10 +76,9 @@ dl_import("from . import libgraph_tool_topology")
from
..
import
_prop
,
Vector_int32_t
,
Vector_size_t
,
_check_prop_writable
,
\
_check_prop_scalar
,
_check_prop_vector
,
Graph
,
VertexPropertyMap
,
\
EdgePropertyMap
,
PropertyMap
,
GraphView
,
libcore
,
_get_rng
,
_degree
,
\
perfect_prop_hash
,
_limit_args
PropertyMap
,
GraphView
,
libcore
,
_get_rng
,
perfect_prop_hash
,
_limit_args
from
..
stats
import
label_self_loops
import
random
,
numpy
,
collections
import
numpy
,
collections
__all__
=
[
"isomorphism"
,
"subgraph_isomorphism"
,
"mark_subgraph"
,
"max_cliques"
,
"max_cardinality_matching"
,
...
...
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