Mercurial > repos > shellac > sam_consensus_v3

comparison env/lib/python3.9/site-packages/networkx/conftest.py @ 0:4f3585e2f14b draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author shellac
date Mon, 22 Mar 2021 18:12:50 +0000
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:4f3585e2f14b
1 import pytest
2 import networkx
3 import sys
4 import warnings
5
6
7 def pytest_addoption(parser):
8 parser.addoption(
9 "--runslow", action="store_true", default=False, help="run slow tests"
10 )
11
12
13 def pytest_configure(config):
14 config.addinivalue_line("markers", "slow: mark test as slow to run")
15
16
17 def pytest_collection_modifyitems(config, items):
18 if config.getoption("--runslow"):
19 # --runslow given in cli: do not skip slow tests
20 return
21 skip_slow = pytest.mark.skip(reason="need --runslow option to run")
22 for item in items:
23 if "slow" in item.keywords:
24 item.add_marker(skip_slow)
25
26
27 # TODO: The warnings below need to be dealt with, but for now we silence them.
28 @pytest.fixture(autouse=True)
29 def set_warnings():
30 warnings.filterwarnings(
31 "ignore",
32 category=DeprecationWarning,
33 message="literal_stringizer is deprecated*",
34 )
35 warnings.filterwarnings(
36 "ignore",
37 category=DeprecationWarning,
38 message="literal_destringizer is deprecated*",
39 )
40 warnings.filterwarnings(
41 "ignore", category=DeprecationWarning, message="is_string_like is deprecated*"
42 )
43 warnings.filterwarnings(
44 "ignore", category=DeprecationWarning, message="make_str is deprecated*"
45 )
46 warnings.filterwarnings(
47 "ignore",
48 category=DeprecationWarning,
49 message="context manager reversed is deprecated*",
50 )
51 warnings.filterwarnings(
52 "ignore",
53 category=DeprecationWarning,
54 message="This will return a generator in 3.0*",
55 )
56 warnings.filterwarnings(
57 "ignore", category=DeprecationWarning, message="betweenness_centrality_source*",
58 )
59 warnings.filterwarnings(
60 "ignore", category=DeprecationWarning, message="edge_betweeness*",
61 )
62 warnings.filterwarnings(
63 "ignore",
64 category=PendingDeprecationWarning,
65 message="the matrix subclass is not the recommended way*",
66 )
67
68
69 @pytest.fixture(autouse=True)
70 def add_nx(doctest_namespace):
71 doctest_namespace["nx"] = networkx
72
73
74 # What dependencies are installed?
75
76 try:
77 import numpy
78
79 has_numpy = True
80 except ImportError:
81 has_numpy = False
82
83 try:
84 import scipy
85
86 has_scipy = True
87 except ImportError:
88 has_scipy = False
89
90 try:
91 import matplotlib
92
93 has_matplotlib = True
94 except ImportError:
95 has_matplotlib = False
96
97 try:
98 import pandas
99
100 has_pandas = True
101 except ImportError:
102 has_pandas = False
103
104 try:
105 import pygraphviz
106
107 has_pygraphviz = True
108 except ImportError:
109 has_pygraphviz = False
110
111 try:
112 import yaml
113
114 has_yaml = True
115 except ImportError:
116 has_yaml = False
117
118 try:
119 import pydot
120
121 has_pydot = True
122 except ImportError:
123 has_pydot = False
124
125 try:
126 import ogr
127
128 has_ogr = True
129 except ImportError:
130 has_ogr = False
131
132
133 # List of files that pytest should ignore
134
135 collect_ignore = []
136
137 needs_numpy = [
138 "algorithms/centrality/current_flow_closeness.py",
139 "algorithms/node_classification/__init__.py",
140 "algorithms/non_randomness.py",
141 "algorithms/shortest_paths/dense.py",
142 "linalg/bethehessianmatrix.py",
143 "linalg/laplacianmatrix.py",
144 "utils/misc.py",
145 ]
146 needs_scipy = [
147 "algorithms/assortativity/correlation.py",
148 "algorithms/assortativity/mixing.py",
149 "algorithms/assortativity/pairs.py",
150 "algorithms/bipartite/matrix.py",
151 "algorithms/bipartite/spectral.py",
152 "algorithms/centrality/current_flow_betweenness.py",
153 "algorithms/centrality/current_flow_betweenness_subset.py",
154 "algorithms/centrality/eigenvector.py",
155 "algorithms/centrality/katz.py",
156 "algorithms/centrality/second_order.py",
157 "algorithms/centrality/subgraph_alg.py",
158 "algorithms/communicability_alg.py",
159 "algorithms/link_analysis/hits_alg.py",
160 "algorithms/link_analysis/pagerank_alg.py",
161 "algorithms/node_classification/hmn.py",
162 "algorithms/node_classification/lgc.py",
163 "algorithms/similarity.py",
164 "convert_matrix.py",
165 "drawing/layout.py",
166 "generators/spectral_graph_forge.py",
167 "linalg/algebraicconnectivity.py",
168 "linalg/attrmatrix.py",
169 "linalg/graphmatrix.py",
170 "linalg/modularitymatrix.py",
171 "linalg/spectrum.py",
172 "utils/rcm.py",
173 ]
174 needs_matplotlib = ["drawing/nx_pylab.py"]
175 needs_pandas = ["convert_matrix.py"]
176 needs_yaml = ["readwrite/nx_yaml.py"]
177 needs_pygraphviz = ["drawing/nx_agraph.py"]
178 needs_pydot = ["drawing/nx_pydot.py"]
179 needs_ogr = ["readwrite/nx_shp.py"]
180
181 if not has_numpy:
182 collect_ignore += needs_numpy
183 if not has_scipy:
184 collect_ignore += needs_scipy
185 if not has_matplotlib:
186 collect_ignore += needs_matplotlib
187 if not has_pandas:
188 collect_ignore += needs_pandas
189 if not has_yaml:
190 collect_ignore += needs_yaml
191 if not has_pygraphviz:
192 collect_ignore += needs_pygraphviz
193 if not has_pydot:
194 collect_ignore += needs_pydot
195 if not has_ogr:
196 collect_ignore += needs_ogr
197
198 # FIXME: This is to avoid errors on AppVeyor
199 if sys.platform.startswith("win"):
200 collect_ignore += ["readwrite/graph6.py", "readwrite/sparse6.py"]