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pgleesonpgleeson
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Some ruff formatting
1 parent 8470dca commit 9bf7d7c

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15 files changed

+64
-95
lines changed

15 files changed

+64
-95
lines changed

‎omv/engines/getjnml.py‎

Lines changed: 1 addition & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -8,7 +8,6 @@
88

99

1010
def install_jnml(version):
11-
1211
if not version:
1312
version = "v0.14.0"
1413

@@ -45,4 +44,4 @@ def install_jnml(version):
4544
)
4645
check_output(["unzip", "jNeuroML.zip"])
4746

48-
inform("Successfully installed jNeuroML "+version, indent=1)
47+
inform("Successfully installed jNeuroML " + version, indent=1)

‎omv/engines/getpynn.py‎

Lines changed: 3 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -15,7 +15,8 @@ def install_pynn(version=None):
1515

1616
pip_install("pynn", version)
1717
import pyNN
18-
'''
18+
19+
"""
1920
install_root = os.environ["HOME"]
2021
2122
pyNN_src = "PyNN_src"
@@ -36,7 +37,7 @@ def install_pynn(version=None):
3637
print(check_output(["pwd"]))
3738
print("Finished attempting to install PyNN")
3839
# import pyNN
39-
'''
40+
"""
4041
m = "Successfully installed pyNN..."
4142
except Exception as e:
4243
m = "ERROR during install_pynn: %s" % e

‎omv/engines/getxpp.py‎

Lines changed: 17 additions & 47 deletions
Original file line numberDiff line numberDiff line change
@@ -4,20 +4,19 @@
44
from omv.engines.utils.wdir import working_dir
55
from sysconfig import get_paths
66
import sys
7-
8-
import fileinput
97

8+
import fileinput
109

11-
def install_xpp(version='latest'):
1210

13-
if version is None:
14-
version='latest'
15-
elif not version=='latest':
16-
raise Exception('Can currently only install the latest XPP version')
11+
def install_xpp(version="latest"):
12+
if version is None:
13+
version = "latest"
14+
elif not version == "latest":
15+
raise Exception("Can currently only install the latest XPP version")
1716

1817
inform("Installing XPP", indent=2, verbosity=1)
1918
xppinstallpath = os.path.join(os.environ["HOME"])
20-
xpphomepath = os.path.join(xppinstallpath, 'xppaut')
19+
xpphomepath = os.path.join(xppinstallpath, "xppaut")
2120

2221
inform(
2322
"Installing XPP to: %s" % (xpphomepath),
@@ -27,56 +26,27 @@ def install_xpp(version='latest'):
2726
pypaths = get_paths()
2827
inform("Python lib info: %s" % (pypaths), indent=2, verbosity=1)
2928

30-
3129
with working_dir(xppinstallpath):
32-
print(
33-
check_output(
34-
[
35-
"git",
36-
"clone",
37-
"https://github.com/NeuroML/xppaut"
38-
]
39-
)
40-
)
30+
print(check_output(["git", "clone", "https://github.com/NeuroML/xppaut"]))
4131

4232
with working_dir(xpphomepath):
43-
print(
44-
check_output(
45-
[
46-
"ls",
47-
"-alth"
48-
]
49-
)
50-
)
33+
print(check_output(["ls", "-alth"]))
5134

52-
makefile = os.path.join(xpphomepath, 'Makefile')
53-
54-
print(' - Replacing text in %s'%makefile)
55-
with open(makefile, 'r') as file:
35+
makefile = os.path.join(xpphomepath, "Makefile")
36+
37+
print(" - Replacing text in %s" % makefile)
38+
with open(makefile, "r") as file:
5639
filedata = file.read()
5740

5841
# Replace the target string
59-
filedata = filedata.replace("/usr/local/", "%s/"%xpphomepath)
42+
filedata = filedata.replace("/usr/local/", "%s/" % xpphomepath)
6043

6144
# Write the file out again
62-
with open(makefile, 'w') as file:
45+
with open(makefile, "w") as file:
6346
file.write(filedata)
6447

65-
print(
66-
check_output(
67-
[
68-
"make", "-j4"
69-
]
70-
)
71-
)
72-
print(
73-
check_output(
74-
[
75-
"make", "install"
76-
]
77-
)
78-
)
79-
48+
print(check_output(["make", "-j4"]))
49+
print(check_output(["make", "install"]))
8050

8151

8252
if __name__ == "__main__":

‎omv/engines/jneuromlmoose.py‎

Lines changed: 0 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -8,7 +8,6 @@
88

99

1010
class JNeuroMLMooseEngine(JNeuroMLEngine):
11-
1211
name = "jNeuroML_Moose"
1312

1413
@staticmethod
@@ -22,7 +21,6 @@ def is_installed():
2221

2322
@staticmethod
2423
def install(version):
25-
2624
if not JNeuroMLEngine.is_installed():
2725
JNeuroMLEngine.install(None)
2826
if not MooseEngine.is_installed():
@@ -34,7 +32,6 @@ def install(version):
3432
JNeuroMLMooseEngine.environment_vars.update(MooseEngine.environment_vars)
3533
inform("PATH: " + JNeuroMLMooseEngine.path)
3634
inform("Env vars: %s" % JNeuroMLMooseEngine.environment_vars)
37-
3835

3936
def run(self):
4037
try:

‎omv/engines/jneuromlvalidate.py‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -6,6 +6,7 @@
66
from omv.engines.engine import PATH_DELIMITER
77
from omv.engines.utils import resolve_paths
88

9+
910
class JNeuroMLValidateEngine(JNeuroMLEngine):
1011
name = "jNeuroML_validate"
1112

‎omv/engines/jneuromlxpp.py‎

Lines changed: 6 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -26,7 +26,6 @@ def install(xpp_version):
2626
if not XppEngine.is_installed():
2727
XppEngine.install(xpp_version)
2828

29-
3029
def run(self):
3130
self.environment_vars = XppEngine.get_xpp_environment()
3231
self.set_environment()
@@ -44,9 +43,13 @@ def run(self):
4443
cwd=os.path.dirname(self.modelpath),
4544
env=JNeuroMLEngine.get_environment(),
4645
)
47-
46+
4847
self.stdout = check_output(
49-
[self.environment_vars["XPP_HOME"] + "/xppaut", self.modelpath.replace('.xml','.ode'), '-silent'],
48+
[
49+
self.environment_vars["XPP_HOME"] + "/xppaut",
50+
self.modelpath.replace(".xml", ".ode"),
51+
"-silent",
52+
],
5053
cwd=os.path.dirname(self.modelpath),
5154
)
5255

‎omv/engines/moose_.py‎

Lines changed: 0 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -10,7 +10,6 @@
1010
class MooseEngine(OMVEngine):
1111
name = "Moose"
1212

13-
1413
@staticmethod
1514
def is_installed():
1615
ret = True

‎omv/engines/pyneuroml_.py‎

Lines changed: 0 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -42,7 +42,6 @@ def install(version):
4242
inform("Failure to install, exiting", indent=1)
4343
exit(1)
4444

45-
4645
def run(self):
4746
try:
4847
inform(

‎omv/engines/pyneuromlvalidatesbml.py‎

Lines changed: 16 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -3,21 +3,24 @@
33

44
from omv.common.inout import inform, trim_path, check_output
55
from omv.engines.engine import EngineExecutionError
6-
from omv.engines.pyneuroml_ import PyNeuroMLEngine
6+
from omv.engines.pyneuroml_ import PyNeuroMLEngine
77
from omv.engines.engine import PATH_DELIMITER
88
from omv.engines.utils import resolve_paths
99

10+
1011
class PyNeuroMLValidateSBMLEngine(PyNeuroMLEngine):
1112
name = "pyNeuroML_validate_sbml"
1213

1314
@staticmethod
1415
def is_installed():
15-
if not PyNeuroMLEngine.is_installed(): return False
16+
if not PyNeuroMLEngine.is_installed():
17+
return False
1618

1719
ret = True
1820
try:
1921
inform(
20-
"Checking whether %s is installed..." % PyNeuroMLValidateSBMLEngine.name,
22+
"Checking whether %s is installed..."
23+
% PyNeuroMLValidateSBMLEngine.name,
2124
indent=1,
2225
verbosity=2,
2326
)
@@ -37,7 +40,8 @@ def is_installed():
3740

3841
@staticmethod
3942
def install(version):
40-
if not PyNeuroMLEngine.is_installed(): PyNeuroMLEngine.install(None)
43+
if not PyNeuroMLEngine.is_installed():
44+
PyNeuroMLEngine.install(None)
4145

4246
from omv.engines.getlibsbml import install_libsbml
4347

@@ -54,19 +58,20 @@ def run(self):
5458
verbosity=1,
5559
)
5660

57-
#pynml = PyNeuroMLEngine.get_executable() #could implement more flexible way to find the executeable
61+
# pynml = PyNeuroMLEngine.get_executable() #could implement more flexible way to find the executeable
5862
cmds = ["pynml", "-validate-sbml"]
5963
for p in path_s:
6064
cmds.append(p)
6165

6266
inform(
63-
"Running with %s, using: %s..." % (PyNeuroMLValidateSBMLEngine.name, cmds),
67+
"Running with %s, using: %s..."
68+
% (PyNeuroMLValidateSBMLEngine.name, cmds),
6469
indent=1,
6570
)
6671
self.stdout = check_output(
6772
cmds,
68-
cwd=os.path.dirname(self.modelpath.split(PATH_DELIMITER)[0])
69-
#env=PyNeuroMLEngine.get_environment(),
73+
cwd=os.path.dirname(self.modelpath.split(PATH_DELIMITER)[0]),
74+
# env=PyNeuroMLEngine.get_environment(),
7075
)
7176
inform(
7277
"Success with running ",
@@ -76,8 +81,9 @@ def run(self):
7681
)
7782
self.returncode = 0
7883
except sp.CalledProcessError as err:
79-
inform("Error with ", PyNeuroMLValidateSBMLEngine.name, indent=1, verbosity=1)
84+
inform(
85+
"Error with ", PyNeuroMLValidateSBMLEngine.name, indent=1, verbosity=1
86+
)
8087
self.returncode = err.returncode
8188
self.stdout = err.output
8289
raise EngineExecutionError
83-

‎omv/engines/pyneuromlxpp.py‎

Lines changed: 9 additions & 14 deletions
Original file line numberDiff line numberDiff line change
@@ -3,44 +3,40 @@
33

44
from omv.common.inout import inform, trim_path, check_output
55
from omv.engines.engine import EngineExecutionError
6-
from omv.engines.pyneuroml_ import PyNeuroMLEngine
6+
from omv.engines.pyneuroml_ import PyNeuroMLEngine
77
from omv.engines.engine import PATH_DELIMITER
88
from omv.engines.utils import resolve_paths
99

10+
1011
class PyNeuroMLXppEngine(PyNeuroMLEngine):
1112
name = "pyNEURON_XPP_LEMS"
1213

1314
@staticmethod
1415
def is_installed():
1516
pynml_ver = PyNeuroMLEngine.is_installed()
16-
if not pynml_ver:
17+
if not pynml_ver:
1718
return False
1819
else:
1920
return pynml_ver
2021

21-
2222
@staticmethod
2323
def install(version):
24-
if not PyNeuroMLEngine.is_installed(): PyNeuroMLEngine.install(version)
25-
24+
if not PyNeuroMLEngine.is_installed():
25+
PyNeuroMLEngine.install(version)
2626

2727
def run(self):
2828
try:
29-
30-
#pynml = PyNeuroMLEngine.get_executable() #could implement more flexible way to find the executeable
29+
# pynml = PyNeuroMLEngine.get_executable() #could implement more flexible way to find the executeable
3130
cmds = ["pynml-xpp"]
3231
cmds.append(self.modelpath)
33-
cmds.append('-lems')
34-
cmds.append('-run')
32+
cmds.append("-lems")
33+
cmds.append("-run")
3534

3635
inform(
3736
"Running with %s, using: %s..." % (PyNeuroMLXppEngine.name, cmds),
3837
indent=1,
3938
)
40-
self.stdout = check_output(
41-
cmds,
42-
cwd=os.path.dirname(self.modelpath)
43-
)
39+
self.stdout = check_output(cmds, cwd=os.path.dirname(self.modelpath))
4440
inform(
4541
"Success with running ",
4642
PyNeuroMLXppEngine.name,
@@ -53,4 +49,3 @@ def run(self):
5349
self.returncode = err.returncode
5450
self.stdout = err.output
5551
raise EngineExecutionError
56-

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