def test_stg2image():
fname_in = get_tests_path_in(fname="irma.primes")
fname_out1 = get_tests_path_out(fname="irma_stg_async.pdf")
fname_out2 = get_tests_path_out(fname="irma_stg_tendencies_async.pdf")
fname_out3 = get_tests_path_out(fname="irma_stg_sccs_async.pdf")
primes = read_primes(fname_json=fname_in)
stg = primes2stg(primes=primes, update="asynchronous")
stg2image(stg, fname_out1)
add_style_tendencies(stg)
stg2image(stg, fname_out2)
stg = primes2stg(primes=primes, update="asynchronous")
add_style_sccs(stg)
stg2image(stg, fname_out3)
fname_out1 = get_tests_path_out(fname="irma_stg_sync.pdf")
fname_out2 = get_tests_path_out(fname="irma_stg_tendencies_sync.pdf")
fname_out3 = get_tests_path_out(fname="irma_stg_sccs_sync.pdf")
fname_out4 = get_tests_path_out(fname="irma_stg_path.pdf")
primes = read_primes(fname_json=fname_in)
stg = primes2stg(primes=primes, update="synchronous")
stg2image(stg, fname_out1)
stg = primes2stg(primes=primes, update="asynchronous")
add_style_tendencies(stg)
stg2image(stg, fname_out2)
stg = primes2stg(primes=primes, update="synchronous")
add_style_sccs(stg)
stg2image(stg, fname_out3)
init = random_state(primes=primes)
walk = random_walk(primes=primes,
update="asynchronous",
initial_state=init,
length=5)
stg = primes2stg(primes=primes, update="asynchronous")
add_style_path(stg, walk, "red")
init = pyboolnet.state_space.random_state(primes=primes)
walk = random_walk(primes=primes,
update="asynchronous",
initial_state=init,
length=5)
add_style_path(stg, walk, "blue")
stg2image(stg, fname_out4)
def test_primes2igraph2():
fname_in = get_tests_path_in(fname="interactiongraphs_irma.primes")
primes = read_primes(fname_json=fname_in)
igraph = primes2igraph(primes=primes)
nodes = sorted(igraph.nodes(data=True))
expected_nodes = [("Ash1", {}), ("Cbf1", {}), ("Gal4", {}), ("Gal80", {}),
("Swi5", {}), ("gal", {})]
assert nodes == expected_nodes
edges = sorted(igraph.edges(data=True))
expected_edges = [("Ash1", "Cbf1", {
"sign": {1}
}), ("Cbf1", "Ash1", {
"sign": {1}
}), ("Gal4", "Swi5", {
"sign": {-1}
}), ("Gal80", "Gal4", {
"sign": {1}
}), ("Swi5", "Gal4", {
"sign": {-1}
}), ("gal", "Ash1", {
"sign": {1}
}), ("gal", "Gal80", {
"sign": {-1}
}), ("gal", "gal", {
"sign": {1}
})]
assert edges == expected_edges
def test_primes2stg():
primes = read_primes(fname_json=get_tests_path_in(fname="irma.primes"))
def init(x):
return x["Cbf1"] + x["Ash1"] + x["Gal80"] == 1
primes2stg(primes=primes, update="asynchronous")
primes2stg(primes=primes, update="synchronous")
primes2stg(primes=primes, update="mixed")
primes2stg(primes=primes, update="asynchronous", initial_states=init)
primes2stg(primes=primes, update="synchronous", initial_states=init)
primes2stg(primes=primes, update="mixed", initial_states=init)
init = []
stg = primes2stg(primes=primes, update="synchronous", initial_states=init)
answer = sorted(stg.nodes())
expected = []
assert answer == expected
init = ["000010"]
stg = primes2stg(primes=primes, update="synchronous", initial_states=init)
answer = sorted(stg.nodes())
assert answer == ["000010", "000110"]
init = [{"Cbf1": 0, "Gal4": 1, "Gal80": 0, "gal": 1, "Swi5": 0, "Ash1": 1}]
stg = primes2stg(primes=primes, update="synchronous", initial_states=init)
answer = sorted(stg.nodes())
assert answer == ["010001", "010011", "100011", "101001"]
def test_read_primes():
fname = get_tests_path_in(fname="fileexchange_missing_inputs.primes")
primes = read_primes(fname_json=fname)
primes_expected = {
"B": [[{
"B": 0
}], [{
"B": 1
}]],
"C": [[{
"C": 0
}], [{
"C": 1
}]],
"A": [[{
"B": 0,
"C": 1
}], [{
"C": 0
}, {
"B": 1
}]]
}
assert primes_are_equal(primes, primes_expected), str(primes)
def test_trap_spaces_piped2():
fname_in = get_tests_path_in(fname="trapspaces_tsfree.primes")
primes = read_primes(fname_json=fname_in)
tspaces = compute_trap_spaces(primes=primes, type_="min")
tspaces.sort(key=lambda x: tuple(sorted(x.items())))
assert tspaces == [{}]
def test_trap_spaces_positive_feedback_bounds2():
fname_in = get_tests_path_in(fname="trapspaces_posfeedback.primes")
fname_out = get_tests_path_out(fname="trapspaces_posfeedback_bounds2.asp")
primes = read_primes(fname_json=fname_in)
tspaces = compute_trap_spaces_bounded(primes=primes, type_="max", bounds=(0, 100), fname_asp=fname_out)
tspaces.sort(key=lambda x: tuple(sorted(x.items())))
assert tspaces == [{}]
def test_trap_spaces_piped1():
fname_in = get_tests_path_in(fname="trapspaces_posfeedback.primes")
primes = read_primes(fname_json=fname_in)
tspaces = compute_trap_spaces(primes=primes, type_="min")
tspaces.sort(key=lambda x: tuple(sorted(x.items())))
expected = [{"v1": 0, "v2": 0, "v3": 0}, {"v1": 1, "v2": 1, "v3": 1}]
assert tspaces == expected
def test_trap_spaces_positive_feedback_all():
fname_in = get_tests_path_in(fname="trapspaces_posfeedback.primes")
fname_out = get_tests_path_out(fname="trapspaces_posfeedback_all.asp")
primes = read_primes(fname_json=fname_in)
tspaces = compute_trap_spaces(primes=primes, type_="all", fname_asp=fname_out)
tspaces.sort(key=lambda x: tuple(sorted(x.items())))
assert tspaces == [{}, {"v1": 0, "v2": 0, "v3": 0}, {"v1": 1, "v2": 1, "v3": 1}]
def test_trap_spaces_tsfree():
fname_in = get_tests_path_in(fname="trapspaces_tsfree.primes")
fname_out = get_tests_path_out(fname="trapspaces_tsfree_min.asp")
primes = read_primes(fname_json=fname_in)
tspaces = compute_trap_spaces(primes=primes, type_="min", fname_asp=fname_out)
assert tspaces == [{}]
fname_in = get_tests_path_in(fname="trapspaces_tsfree.primes")
fname_out = get_tests_path_out(fname="trapspaces_tsfree_all.asp")
primes = read_primes(fname_json=fname_in)
tspaces = compute_trap_spaces(primes=primes, type_="all", fname_asp=fname_out)
assert tspaces == [{}]
fname_in = get_tests_path_in(fname="trapspaces_tsfree.primes")
fname_out = get_tests_path_out(fname="trapspaces_tsfree_max.asp")
primes = read_primes(fname_json=fname_in)
tspaces = compute_trap_spaces(primes=primes, type_="max", fname_asp=fname_out)
assert tspaces == []
def test_primes2igraph1():
fname_in = get_tests_path_in(fname="interactiongraphs_irma.primes")
primes = read_primes(fname_json=fname_in)
igraph = primes2igraph(primes=primes)
nodes = sorted(igraph.nodes())
expected_nodes = ["Ash1", "Cbf1", "Gal4", "Gal80", "Swi5", "gal"]
assert nodes == expected_nodes
edges = sorted(igraph.edges())
expected_edges = [("Ash1", "Cbf1"), ("Cbf1", "Ash1"), ("Gal4", "Swi5"),
("Gal80", "Gal4"), ("Swi5", "Gal4"), ("gal", "Ash1"),
("gal", "Gal80"), ("gal", "gal")]
assert edges == expected_edges
def test_read_write_primes():
fname = get_tests_path_out(fname="fileexchange_read_write.primes")
primes_write = {
"B": [[{}], []],
"C": [[{
"C": 0
}], [{
"C": 1
}]],
"A": [[{
"B": 0,
"C": 1
}], [{
"C": 0
}, {
"B": 1
}]]
}
write_primes(primes=primes_write, fname_json=fname)
primes_read = read_primes(fname_json=fname)
assert primes_are_equal(primes_read, primes_write)
def test_igraph2image():
fname_in = get_tests_path_in(fname="interactiongraphs_irma.primes")
primes = read_primes(fname_json=fname_in)
igraph = primes2igraph(primes=primes)
fname_out = get_tests_path_out(fname="interactiongraphs_igraph2image.png")
igraph2image(igraph=igraph, fname_image=fname_out)
def test_igraph2dot_string():
fname_in = get_tests_path_in(fname="interactiongraphs_irma.primes")
primes = read_primes(fname_json=fname_in)
igraph = primes2igraph(primes=primes)
igraph2dot(igraph=igraph, fname_dot=None)
def test_igraph2dot():
fname_in = get_tests_path_in(fname="interactiongraphs_irma.primes")
fname_out = get_tests_path_out(fname="interactiongraphs_igraph2dot.dot")
primes = read_primes(fname_json=fname_in)
igraph = primes2igraph(primes=primes)
igraph2dot(igraph=igraph, fname_dot=fname_out)
def test_stg2dot():
fname_in = get_tests_path_in(fname="irma.primes")
fname_out = get_tests_path_out(fname="irma_stg.dot")
primes = read_primes(fname_json=fname_in)
stg = primes2stg(primes=primes, update="asynchronous")
stg2dot(stg, fname_out)
def test_styles():
fname_in = get_tests_path_in(fname="interactiongraphs_topology.primes")
fname_out_dot = get_tests_path_out(
fname="interactiongraphs_style_interactionsigns.dot")
fname_out_pdf = get_tests_path_out(
fname="interactiongraphs_style_interactionsigns.pdf")
primes = read_primes(fname_json=fname_in)
igraph = primes2igraph(primes=primes)
add_style_interactionsigns(igraph=igraph)
igraph2dot(igraph=igraph, fname_dot=fname_out_dot)
dot2image(fname_dot=fname_out_dot, fname_image=fname_out_pdf)
igraph2image(igraph=igraph, fname_image=fname_out_pdf)
fname_out_dot = get_tests_path_out(
fname="interactiongraphs_style_activities.dot")
fname_out_pdf = get_tests_path_out(
fname="interactiongraphs_style_activities.pdf")
add_style_interactionsigns(igraph=igraph)
igraph2dot(igraph=igraph, fname_dot=fname_out_dot)
dot2image(fname_dot=fname_out_dot, fname_image=fname_out_pdf)
igraph2image(igraph=igraph, fname_image=fname_out_pdf)
igraph = primes2igraph(primes=primes)
activities = {"v1": 1, "v2": 0, "v3": 1, "v4": 1, "v5": 1, "v6": 0}
add_style_activities(igraph=igraph, activities=activities)
igraph2dot(igraph=igraph, fname_dot=fname_out_dot)
dot2image(fname_dot=fname_out_dot, fname_image=fname_out_pdf)
fname_in = get_tests_path_in(fname="interactiongraphs_topology.primes")
fname_out_dot = get_tests_path_out(
fname="interactiongraphs_style_sccs.dot")
fname_out_pdf = get_tests_path_out(
fname="interactiongraphs_style_sccs.pdf")
primes = read_primes(fname_json=fname_in)
igraph = primes2igraph(primes=primes)
add_style_sccs(igraph=igraph)
igraph2dot(igraph=igraph, fname_dot=fname_out_dot)
dot2image(fname_dot=fname_out_dot, fname_image=fname_out_pdf)
fname_in = get_tests_path_in(fname="interactiongraphs_topology.primes")
fname_out_pdf = get_tests_path_out(fname="interactiongraphs_style_ioc.pdf")
primes = read_primes(fname_json=fname_in)
igraph = primes2igraph(primes=primes)
add_style_inputs(igraph=igraph)
add_style_constants(igraph=igraph)
add_style_outputs(igraph=igraph)
igraph2image(igraph=igraph, fname_image=fname_out_pdf)
fname_in = get_tests_path_in(fname="interactiongraphs_topology.primes")
fname_out_pdf = get_tests_path_out(
fname="interactiongraphs_style_subgrapghs.pdf")
fname_out_dot = get_tests_path_out(
fname="interactiongraphs_style_subgrapghs.dot")
primes = read_primes(fname_json=fname_in)
igraph = primes2igraph(primes=primes)
subgraphs = [(["v1", "v2"], {}), (["v3", "v4"], {"label": "jo"})]
add_style_subgraphs(igraph=igraph, subgraphs=subgraphs)
igraph2dot(igraph=igraph, fname_dot=fname_out_dot)
dot2image(fname_dot=fname_out_dot, fname_image=fname_out_pdf)
def test_activities2animation():
fname_in = get_tests_path_in(fname="irma.primes")
fname_out1 = get_tests_path_out(fname="irma*.png")
fname_out2 = get_tests_path_out(fname="irma.gif")
primes = read_primes(fname_json=fname_in)
igraph = primes2igraph(primes)
activities = [
{
"gal": 0,
"Cbf1": 1,
"Gal80": 1,
"Ash1": 0,
"Gal4": 0,
"Swi5": 1
},
{
"gal": 1,
"Cbf1": 1,
"Gal80": 1,
"Ash1": 0,
"Gal4": 0,
"Swi5": 1
},
{
"gal": 1,
"Cbf1": 0,
"Gal80": 1,
"Ash1": 0,
"Gal4": 0,
"Swi5": 1
},
{
"gal": 1,
"Cbf1": 0,
"Gal80": 0,
"Ash1": 0,
"Gal4": 0,
"Swi5": 1
},
{
"gal": 1,
"Cbf1": 0,
"Gal80": 0,
"Ash1": 1,
"Gal4": 0,
"Swi5": 1
},
{
"gal": 1,
"Cbf1": 0,
"Gal80": 0,
"Ash1": 1,
"Gal4": 1,
"Swi5": 1
},
{
"gal": 1,
"Cbf1": 0,
"Gal80": 0,
"Ash1": 1,
"Gal4": 1,
"Swi5": 0
},
]
activities2animation(igraph=igraph,
activities=activities,
fname_tmp=fname_out1,
fname_gif=fname_out2)
def test_random_state():
fname_in = get_tests_path_in(fname="irma.primes")
primes = read_primes(fname_json=fname_in)
pyboolnet.state_space.random_state(primes=primes)
pyboolnet.state_space.random_state(primes=primes, subspace="111-0-")