Skip to content

Commit c6f0b31

Browse files
cattabianicattabiani
committed
WIP
1 parent cf88d31 commit c6f0b31

3 files changed

Lines changed: 214 additions & 179 deletions

File tree

‎neurodamus/commands.py‎

Lines changed: 5 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -71,6 +71,11 @@ def neurodamus(args=None):
7171
--report-buffer-size=<number> Override the size in MB each rank will allocate for each
7272
report buffer to hold data. When the buffer is full, the
7373
ranks will aggregate data for writing to disk. Default: 8 MB
74+
--cell-permute=[0, 1, 2] Cell permutation (Default: 0).
75+
Only available for coreneuron. Ignored with neuron. Available options:
76+
0 No permutation (cpu)
77+
1 optimise node adjacency (cpu/gpu)
78+
2 optimize parent adjacency (gpu)
7479
"""
7580
from . import __version__
7681

‎tests/unit/test_cli.py‎

Lines changed: 192 additions & 179 deletions
Original file line numberDiff line numberDiff line change
@@ -6,193 +6,206 @@
66

77
from tests import utils
88

9-
@pytest.mark.parametrize(
10-
"create_tmp_simulation_config_file",
11-
[{"simconfig_fixture": "ringtest_baseconfig"}],
12-
indirect=True,
13-
)
14-
def test_cli_color(create_tmp_simulation_config_file):
15-
out = subprocess.run(
16-
["neurodamus", create_tmp_simulation_config_file],
17-
check=False,
18-
capture_output=True,
19-
cwd=str(Path(create_tmp_simulation_config_file).parent)
20-
)
21-
assert b"\033[0m" in out.stdout
22-
23-
out = subprocess.run(
24-
["neurodamus", create_tmp_simulation_config_file, "--use-color=OFF"],
25-
check=False,
26-
capture_output=True,
27-
cwd=str(Path(create_tmp_simulation_config_file).parent)
28-
)
29-
assert b"\033[0m" not in out.stdout
30-
31-
32-
@pytest.mark.parametrize(
33-
"create_tmp_simulation_config_file",
34-
[{"simconfig_fixture": "ringtest_baseconfig"}],
35-
indirect=True,
36-
)
37-
def test_cli_prcellgid(create_tmp_simulation_config_file):
38-
tmp_path = Path(create_tmp_simulation_config_file).parent
39-
subprocess.run(
40-
["neurodamus", create_tmp_simulation_config_file, "--dump-cell-state=1", "--keep-build"],
41-
check=True,
42-
)
43-
assert (tmp_path / "output" / "2_py_Neuron_t0.0.nrndat").is_file()
44-
assert (tmp_path / "output" / "2_py_Neuron_t50.0.nrndat").is_file()
45-
46-
47-
@pytest.mark.parametrize(
48-
"create_tmp_simulation_config_file",
49-
[
50-
{
51-
"simconfig_fixture": "ringtest_baseconfig",
52-
"extra_config": {"target_simulator": "CORENEURON"},
53-
}
54-
],
55-
indirect=True,
56-
)
57-
def test_cli_keep_build(create_tmp_simulation_config_file):
58-
tmp_path = Path(create_tmp_simulation_config_file).parent
59-
subprocess.run(["neurodamus", create_tmp_simulation_config_file, "--keep-build"], check=True)
60-
coreneuron_input_dir = tmp_path / "build" / "coreneuron_input"
61-
assert coreneuron_input_dir.is_dir(), "Directory 'coreneuron_input' not found."
62-
63-
64-
@pytest.mark.parametrize(
65-
"create_tmp_simulation_config_file",
66-
[
67-
{
68-
"simconfig_fixture": "ringtest_baseconfig",
69-
"extra_config": {"target_simulator": "CORENEURON"},
70-
}
71-
],
72-
indirect=True,
73-
)
74-
def test_cli_build_model(create_tmp_simulation_config_file):
75-
res = subprocess.run(
76-
[
77-
"neurodamus",
78-
create_tmp_simulation_config_file,
79-
"--simulate-model=OFF",
80-
"--disable-reports",
81-
],
82-
check=True,
83-
capture_output=True,
84-
text=True,
85-
)
86-
assert "[SKIPPED] SIMULATION (MODEL BUILD ONLY)" in res.stdout
87-
88-
res = subprocess.run(
89-
["neurodamus", create_tmp_simulation_config_file, "--disable-reports"],
90-
check=True,
91-
capture_output=True,
92-
text=True,
93-
)
94-
assert "SIMULATION (SKIP MODEL BUILD)" in res.stdout
95-
96-
# run it once to create the data, so that the --build-model=OFF works
97-
subprocess.run(
98-
[
99-
"neurodamus",
100-
create_tmp_simulation_config_file,
101-
"--simulate-model=OFF",
102-
"--disable-reports",
103-
],
104-
check=True,
105-
)
106-
res = subprocess.run(
107-
["neurodamus", create_tmp_simulation_config_file, "--build-model=OFF", "--disable-reports"],
108-
check=True,
109-
capture_output=True,
110-
text=True,
111-
)
112-
assert "SIMULATION (SKIP MODEL BUILD)" in res.stdout
113-
114-
115-
@pytest.mark.parametrize(
116-
"create_tmp_simulation_config_file",
117-
[{"simconfig_fixture": "ringtest_baseconfig"}],
118-
indirect=True,
119-
)
120-
def test_cli_lb_mode(create_tmp_simulation_config_file):
121-
tmp_path = Path(create_tmp_simulation_config_file).parent
122-
for lb_mode in ("WholeCell", "MultiSplit"):
123-
res = subprocess.run(
124-
[
125-
"neurodamus",
126-
create_tmp_simulation_config_file,
127-
f"--lb-mode={lb_mode}",
128-
"--disable-reports",
129-
],
130-
check=True,
131-
capture_output=True,
132-
text=True,
133-
)
134-
assert f"Load Balancing ENABLED. Mode: {lb_mode}" in res.stdout
135-
assert (tmp_path / "mcomplex.dat").is_file(), "File 'mcomplex.dat' not found."
136-
assert (tmp_path / "sim_conf").is_dir(), "Directory 'sim_conf' not found."
137-
9+
# @pytest.mark.parametrize(
10+
# "create_tmp_simulation_config_file",
11+
# [{"simconfig_fixture": "ringtest_baseconfig"}],
12+
# indirect=True,
13+
# )
14+
# def test_cli_color(create_tmp_simulation_config_file):
15+
# out = subprocess.run(
16+
# ["neurodamus", create_tmp_simulation_config_file],
17+
# check=False,
18+
# capture_output=True,
19+
# cwd=str(Path(create_tmp_simulation_config_file).parent)
20+
# )
21+
# assert b"\033[0m" in out.stdout
22+
23+
# out = subprocess.run(
24+
# ["neurodamus", create_tmp_simulation_config_file, "--use-color=OFF"],
25+
# check=False,
26+
# capture_output=True,
27+
# cwd=str(Path(create_tmp_simulation_config_file).parent)
28+
# )
29+
# assert b"\033[0m" not in out.stdout
30+
31+
32+
# @pytest.mark.parametrize(
33+
# "create_tmp_simulation_config_file",
34+
# [{"simconfig_fixture": "ringtest_baseconfig"}],
35+
# indirect=True,
36+
# )
37+
# def test_cli_prcellgid(create_tmp_simulation_config_file):
38+
# tmp_path = Path(create_tmp_simulation_config_file).parent
39+
# subprocess.run(
40+
# ["neurodamus", create_tmp_simulation_config_file, "--dump-cell-state=1", "--keep-build"],
41+
# check=True,
42+
# )
43+
# assert (tmp_path / "output" / "2_py_Neuron_t0.0.nrndat").is_file()
44+
# assert (tmp_path / "output" / "2_py_Neuron_t50.0.nrndat").is_file()
45+
46+
47+
# @pytest.mark.parametrize(
48+
# "create_tmp_simulation_config_file",
49+
# [
50+
# {
51+
# "simconfig_fixture": "ringtest_baseconfig",
52+
# "extra_config": {"target_simulator": "CORENEURON"},
53+
# }
54+
# ],
55+
# indirect=True,
56+
# )
57+
# def test_cli_keep_build(create_tmp_simulation_config_file):
58+
# tmp_path = Path(create_tmp_simulation_config_file).parent
59+
# subprocess.run(["neurodamus", create_tmp_simulation_config_file, "--keep-build"], check=True)
60+
# coreneuron_input_dir = tmp_path / "build" / "coreneuron_input"
61+
# assert coreneuron_input_dir.is_dir(), "Directory 'coreneuron_input' not found."
62+
63+
64+
# @pytest.mark.parametrize(
65+
# "create_tmp_simulation_config_file",
66+
# [
67+
# {
68+
# "simconfig_fixture": "ringtest_baseconfig",
69+
# "extra_config": {"target_simulator": "CORENEURON"},
70+
# }
71+
# ],
72+
# indirect=True,
73+
# )
74+
# def test_cli_build_model(create_tmp_simulation_config_file):
75+
# res = subprocess.run(
76+
# [
77+
# "neurodamus",
78+
# create_tmp_simulation_config_file,
79+
# "--simulate-model=OFF",
80+
# "--disable-reports",
81+
# ],
82+
# check=True,
83+
# capture_output=True,
84+
# text=True,
85+
# )
86+
# assert "[SKIPPED] SIMULATION (MODEL BUILD ONLY)" in res.stdout
87+
88+
# res = subprocess.run(
89+
# ["neurodamus", create_tmp_simulation_config_file, "--disable-reports"],
90+
# check=True,
91+
# capture_output=True,
92+
# text=True,
93+
# )
94+
# assert "SIMULATION (SKIP MODEL BUILD)" in res.stdout
95+
96+
# # run it once to create the data, so that the --build-model=OFF works
97+
# subprocess.run(
98+
# [
99+
# "neurodamus",
100+
# create_tmp_simulation_config_file,
101+
# "--simulate-model=OFF",
102+
# "--disable-reports",
103+
# ],
104+
# check=True,
105+
# )
106+
# res = subprocess.run(
107+
# ["neurodamus", create_tmp_simulation_config_file, "--build-model=OFF", "--disable-reports"],
108+
# check=True,
109+
# capture_output=True,
110+
# text=True,
111+
# )
112+
# assert "SIMULATION (SKIP MODEL BUILD)" in res.stdout
113+
114+
115+
# @pytest.mark.parametrize(
116+
# "create_tmp_simulation_config_file",
117+
# [{"simconfig_fixture": "ringtest_baseconfig"}],
118+
# indirect=True,
119+
# )
120+
# def test_cli_lb_mode(create_tmp_simulation_config_file):
121+
# tmp_path = Path(create_tmp_simulation_config_file).parent
122+
# for lb_mode in ("WholeCell", "MultiSplit"):
123+
# res = subprocess.run(
124+
# [
125+
# "neurodamus",
126+
# create_tmp_simulation_config_file,
127+
# f"--lb-mode={lb_mode}",
128+
# "--disable-reports",
129+
# ],
130+
# check=True,
131+
# capture_output=True,
132+
# text=True,
133+
# )
134+
# assert f"Load Balancing ENABLED. Mode: {lb_mode}" in res.stdout
135+
# assert (tmp_path / "mcomplex.dat").is_file(), "File 'mcomplex.dat' not found."
136+
# assert (tmp_path / "sim_conf").is_dir(), "Directory 'sim_conf' not found."
137+
138+
139+
# @pytest.mark.parametrize(
140+
# "create_tmp_simulation_config_file",
141+
# [{"simconfig_fixture": "ringtest_baseconfig"}],
142+
# indirect=True,
143+
# )
144+
# def test_cli_output_path(create_tmp_simulation_config_file):
145+
# tmp_path = Path(create_tmp_simulation_config_file).parent
146+
# new_output = "new-output"
147+
# subprocess.run(
148+
# ["neurodamus", create_tmp_simulation_config_file, f"--output-path={new_output}"],
149+
# check=True,
150+
# text=True,
151+
# )
152+
# sc = libsonata.SimulationConfig.from_file(create_tmp_simulation_config_file)
153+
# # Output directory from simulation configuration is overridden
154+
# simconfig_output_path = tmp_path / sc.output.output_dir
155+
# assert not simconfig_output_path.is_dir(), (
156+
# f"Directory '{simconfig_output_path}' should NOT exist."
157+
# )
158+
# assert (tmp_path / new_output).is_dir(), f"Directory '{new_output}' not found."
159+
160+
# @pytest.mark.skip(reason="to be enabled with #337")
161+
# @pytest.mark.parametrize(
162+
# "create_tmp_simulation_config_file", [
163+
# {
164+
# "simconfig_fixture": "ringtest_baseconfig",
165+
# "extra_config": {
166+
# "target_simulator": "CORENEURON",
167+
# "reports": {
168+
# "soma_v": {
169+
# "type": "compartment",
170+
# "variable_name": "v",
171+
# "sections": "soma",
172+
# "dt": 0.1,
173+
# "start_time": 0.0,
174+
# "end_time": 40.0
175+
# }
176+
# },
177+
# }
178+
# }
179+
# ], indirect=True)
180+
# def test_cli_report_buff_size(create_tmp_simulation_config_file):
181+
# command = ["neurodamus", create_tmp_simulation_config_file, "--report-buffer-size=64", "--keep-build"]
182+
# subprocess.run(command, check=True, capture_output=True)
183+
184+
# report_confs = utils.ReportConf.load("build/report.conf")
185+
# assert report_confs.reports["soma_v.h5"].buffer_size == 64
186+
187+
# @pytest.mark.skip(reason="to be enabled with #337")
188+
# @pytest.mark.parametrize(
189+
# "create_tmp_simulation_config_file",
190+
# [{"simconfig_fixture": "ringtest_baseconfig"}],
191+
# indirect=True,
192+
# )
193+
# def test_cli_report_buff_invalid(create_tmp_simulation_config_file):
194+
# for value in [-64, 0]:
195+
# command = ["neurodamus", create_tmp_simulation_config_file, f"--report-buffer-size={value}"]
196+
# result = subprocess.run(command, check=False, capture_output=True, text=True)
197+
198+
# assert "Report buffer size must be > 0" in result.stdout
138199

139-
@pytest.mark.parametrize(
140-
"create_tmp_simulation_config_file",
141-
[{"simconfig_fixture": "ringtest_baseconfig"}],
142-
indirect=True,
143-
)
144-
def test_cli_output_path(create_tmp_simulation_config_file):
145-
tmp_path = Path(create_tmp_simulation_config_file).parent
146-
new_output = "new-output"
147-
subprocess.run(
148-
["neurodamus", create_tmp_simulation_config_file, f"--output-path={new_output}"],
149-
check=True,
150-
text=True,
151-
)
152-
sc = libsonata.SimulationConfig.from_file(create_tmp_simulation_config_file)
153-
# Output directory from simulation configuration is overridden
154-
simconfig_output_path = tmp_path / sc.output.output_dir
155-
assert not simconfig_output_path.is_dir(), (
156-
f"Directory '{simconfig_output_path}' should NOT exist."
157-
)
158-
assert (tmp_path / new_output).is_dir(), f"Directory '{new_output}' not found."
159-
160-
@pytest.mark.skip(reason="to be enabled with #337")
161200
@pytest.mark.parametrize(
162201
"create_tmp_simulation_config_file", [
163202
{
164203
"simconfig_fixture": "ringtest_baseconfig",
165204
"extra_config": {
166205
"target_simulator": "CORENEURON",
167-
"reports": {
168-
"soma_v": {
169-
"type": "compartment",
170-
"variable_name": "v",
171-
"sections": "soma",
172-
"dt": 0.1,
173-
"start_time": 0.0,
174-
"end_time": 40.0
175-
}
176-
},
177206
}
178207
}
179208
], indirect=True)
180-
def test_cli_report_buff_size(create_tmp_simulation_config_file):
181-
command = ["neurodamus", create_tmp_simulation_config_file, "--report-buffer-size=64", "--keep-build"]
209+
def test_cli_cell_permute(create_tmp_simulation_config_file):
210+
command = ["neurodamus", create_tmp_simulation_config_file, "--cell-permute=1"]
182211
subprocess.run(command, check=True, capture_output=True)
183-
184-
report_confs = utils.ReportConf.load("build/report.conf")
185-
assert report_confs.reports["soma_v.h5"].buffer_size == 64
186-
187-
@pytest.mark.skip(reason="to be enabled with #337")
188-
@pytest.mark.parametrize(
189-
"create_tmp_simulation_config_file",
190-
[{"simconfig_fixture": "ringtest_baseconfig"}],
191-
indirect=True,
192-
)
193-
def test_cli_report_buff_invalid(create_tmp_simulation_config_file):
194-
for value in [-64, 0]:
195-
command = ["neurodamus", create_tmp_simulation_config_file, f"--report-buffer-size={value}"]
196-
result = subprocess.run(command, check=False, capture_output=True, text=True)
197-
198-
assert "Report buffer size must be > 0" in result.stdout

0 commit comments

Comments
 (0)