12
Parser process id: 12
codeclimate-parser socket not present
waiting 1s...
I, [2024-11-05T07:49:06.704075 #1] INFO -- : Skipping file ./src/taurenmd/cli_rotations.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
print(json.dumps(to_json(ast.parse(source))))
File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
return compile(source, filename, mode, PyCF_ONLY_AST)
File "<unknown>", line 83
f'{tcore.ref_mda}'
^
SyntaxError: invalid syntax
I, [2024-11-05T07:49:06.730552 #1] INFO -- : Skipping file ./src/taurenmd/logger.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
print(json.dumps(to_json(ast.parse(source))))
File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
return compile(source, filename, mode, PyCF_ONLY_AST)
File "<unknown>", line 27
def __init__(self, msg, *args, indent=1, spacer=' '):
^
SyntaxError: invalid syntax
I, [2024-11-05T07:49:06.740422 #1] INFO -- : Skipping file ./src/taurenmd/libs/libio.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
print(json.dumps(to_json(ast.parse(source))))
File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
return compile(source, filename, mode, PyCF_ONLY_AST)
File "<unknown>", line 267
fname='results.csv',
^
SyntaxError: invalid syntax
I, [2024-11-05T07:49:06.748133 #1] INFO -- : Skipping file ./src/taurenmd/libs/libcli.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
print(json.dumps(to_json(ast.parse(source))))
File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
return compile(source, filename, mode, PyCF_ONLY_AST)
File "<unknown>", line 223
f'{_BANNER}\n'
^
SyntaxError: invalid syntax
I, [2024-11-05T07:49:06.755014 #1] INFO -- : Skipping file ./src/taurenmd/libs/libutil.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
print(json.dumps(to_json(ast.parse(source))))
File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
return compile(source, filename, mode, PyCF_ONLY_AST)
File "<unknown>", line 40
raise ValueError(f'Time string not appropriate: {s!r}') from err
^
SyntaxError: invalid syntax
I, [2024-11-05T07:49:06.761318 #1] INFO -- : Skipping file ./src/taurenmd/libs/libmda.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
print(json.dumps(to_json(ast.parse(source))))
File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
return compile(source, filename, mode, PyCF_ONLY_AST)
File "<unknown>", line 28
insort=False,
^
SyntaxError: invalid syntax
I, [2024-11-05T07:49:06.771221 #1] INFO -- : Skipping file ./src/taurenmd/libs/libopenmm.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
print(json.dumps(to_json(ast.parse(source))))
File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
return compile(source, filename, mode, PyCF_ONLY_AST)
File "<unknown>", line 54
raise ValueError(f'`topology` suffix is not CIF: {topp.suffix!r}')
^
SyntaxError: invalid syntax
I, [2024-11-05T07:49:06.773685 #1] INFO -- : Skipping file ./src/taurenmd/libs/libcalc.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
print(json.dumps(to_json(ast.parse(source))))
File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
return compile(source, filename, mode, PyCF_ONLY_AST)
File "<unknown>", line 390
assert n2.shape == p4_vecs.shape, f'{n2.shape}, {p4_vecs.shape}'
^
SyntaxError: invalid syntax
I, [2024-11-05T07:49:06.793305 #1] INFO -- : Skipping file ./src/taurenmd/_cli_template.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
print(json.dumps(to_json(ast.parse(source))))
File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
return compile(source, filename, mode, PyCF_ONLY_AST)
File "<unknown>", line 78
f'{tcore.ref_mda}'
^
SyntaxError: invalid syntax
I, [2024-11-05T07:49:06.808608 #1] INFO -- : Skipping file ./src/taurenmd/cli_rmsd.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
print(json.dumps(to_json(ast.parse(source))))
File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
return compile(source, filename, mode, PyCF_ONLY_AST)
File "<unknown>", line 54
f'{tcore.ref_mda}'
^
SyntaxError: invalid syntax
I, [2024-11-05T07:49:06.821838 #1] INFO -- : Skipping file ./src/taurenmd/cli_distances.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
print(json.dumps(to_json(ast.parse(source))))
File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
return compile(source, filename, mode, PyCF_ONLY_AST)
File "<unknown>", line 56
f'{tcore.ref_mda}'
^
SyntaxError: invalid syntax
I, [2024-11-05T07:49:06.854209 #1] INFO -- : Skipping file ./src/taurenmd/plots/plotparams.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
print(json.dumps(to_json(ast.parse(source))))
File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
return compile(source, filename, mode, PyCF_ONLY_AST)
File "<unknown>", line 13
*,
^
SyntaxError: invalid syntax
I, [2024-11-05T07:49:06.865100 #1] INFO -- : Skipping file ./src/taurenmd/cli_pangle.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
print(json.dumps(to_json(ast.parse(source))))
File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
return compile(source, filename, mode, PyCF_ONLY_AST)
File "<unknown>", line 54
f'{tcore.ref_mda}'
^
SyntaxError: invalid syntax
I, [2024-11-05T07:49:06.879572 #1] INFO -- : Skipping file ./src/taurenmd/cli_rmsf.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
print(json.dumps(to_json(ast.parse(source))))
File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
return compile(source, filename, mode, PyCF_ONLY_AST)
File "<unknown>", line 62
f'{tcore.ref_mda}'
^
SyntaxError: invalid syntax
I, [2024-11-05T07:49:06.883955 #1] INFO -- : Skipping file ./src/taurenmd/cli_imagemol.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
print(json.dumps(to_json(ast.parse(source))))
File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
return compile(source, filename, mode, PyCF_ONLY_AST)
File "<unknown>", line 59
f'{tcore.ref_mdt}'
^
SyntaxError: invalid syntax
I, [2024-11-05T07:49:06.895909 #1] INFO -- : Skipping file ./src/taurenmd/cli_trajedit.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
print(json.dumps(to_json(ast.parse(source))))
File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
return compile(source, filename, mode, PyCF_ONLY_AST)
File "<unknown>", line 71
f'{tcore.ref_mda}'
^
SyntaxError: invalid syntax
I, [2024-11-05T07:49:06.912860 #1] INFO -- : Skipping file ./src/taurenmd/core.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
print(json.dumps(to_json(ast.parse(source))))
File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
return compile(source, filename, mode, PyCF_ONLY_AST)
File "<unknown>", line 10
CONTACTUS = f'Write us an issue explaining your problem at: {issues}'
^
SyntaxError: invalid syntax
I, [2024-11-05T07:49:06.931537 #1] INFO -- : Skipping file ./src/taurenmd/cli_fext.py due to exception (CC::Engine::Analyzers::ParserError): `python2 /usr/src/app/lib/cc/engine/analyzers/python/parser.py` exited with code 1:
Traceback (most recent call last):
File "/usr/src/app/lib/cc/engine/analyzers/python/parser.py", line 51, in <module>
print(json.dumps(to_json(ast.parse(source))))
File "/usr/local/python2/lib/python2.7/ast.py", line 37, in parse
return compile(source, filename, mode, PyCF_ONLY_AST)
File "<unknown>", line 65
f'{tcore.ref_mda}'
^
SyntaxError: invalid syntax
|
INFO: Java 1.8.0_111-internal Oracle Corporation (64-bit)
INFO: Linux 4.4.0-1128-aws amd64
SLF4J: Class path contains multiple SLF4J bindings.
SLF4J: Found binding in [jar:file:/usr/src/app/build/libs/sonarlint-core-2.17.0.899.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in [jar:file:/usr/src/app/build/libs/sonarlint-cli-2.1.0.566.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation.
SLF4J: Actual binding is of type [ch.qos.logback.classic.util.ContextSelectorStaticBinder]
INFO: Index files
INFO: Invalid character encountered in file '/code/docs/img/taurenmd_logo_black.png' at line 1 for encoding UTF-8. Please fix file content or configure the encoding to be used using property 'sonar.sourceEncoding'.
INFO: Invalid character encountered in file '/code/docs/img/taurenmd_logo_black_gitbanner.png' at line 1 for encoding UTF-8. Please fix file content or configure the encoding to be used using property 'sonar.sourceEncoding'.
INFO: Invalid character encountered in file '/code/docs/img/taurenmd_logo_black_readme.png' at line 1 for encoding UTF-8. Please fix file content or configure the encoding to be used using property 'sonar.sourceEncoding'.
INFO: 90 files indexed
ERROR: Unable to parse file: /code/src/taurenmd/cli_rotations.py
ERROR: Parse error at line 124 column 16:
117: ref_frame=0,
118: start=None,
119: stop=None,
120: step=None,
121: export=False,
122: plot=False,
123: plotvars=None,
--> **kwargs,
125: ):
126: """Execute main client logic."""
127: log.info(T('starting'))
128:
129: topology = Path(topology)
130: trajectories = list(map(
ERROR: Unable to parse file: /code/src/taurenmd/libs/libio.py
ERROR: Parse error at line 271 column 8:
261: (top_output)
262:
263:
264: def export_data_to_file(
265: xdata,
266: *ydata,
267: fname='results.csv',
268: header='',
269: fmt='{:.3f}',
270: delimiter=',',
--> ):
272: """
273: Save data to file.
274:
275: Following the format:
276:
277: >>> # header
278: >>> x1,ya1,yb1,yc1
279: >>> x2,ya2,yb2,yc2
280: >>> x3,ya3,yb3,yc3
281:
282: Where ``x`` are the elements in ``xdata``, and ``y*`` are the
283: elements in the different ``ydata`` series.
284:
285: Parameters
286: ----------
287: xdata : list-like
288: Contains the *x axis* data.
289:
290: ydata : list of list-like
291: Contains the *y axis* data series.
292:
293: fname : str
294: The output file path name.
295:
296: header : str
297: The commented header of the file. Comment character, like ``#``
298: is not placed, it should be already provided if desired.
299:
300: fmt : str
301: The float format. Defaults to ``{:.3f}``.
302:
303: delimiter : str
304: The string delimiter between columns. Defaults to ``,``.
305: """
306: log.info(T('Saving data'))
307: log.info(S('to: {}', fname))
308: with open
ERROR: Unable to parse file: /code/src/taurenmd/plots/plotparams.py
ERROR: Parse error at line 47 column 8:
40: True,
41: legend_fs=8,
42: legend_loc=0,
43: vert_lines=None,
44: figsize=(8, 5),
45: filename='plot_param.pdf',
46: dpi=150,
--> ):
48: """
49: Plot a parameter.
50:
51: Bellow parameters concern data representation and are considered
52: of highest importance because their incorrect use can mislead
53: data analysis and consequent conclusions.
54:
55: Plot style parameters concernning only plot style, i.e., colors,
56: shapes, fonts, etc... and which do not distort the actual data,
57: are not listed in the paremeter list bellow. We hope these
58: parameter names are self-explanatory and are listed in the function
59: definition.
60:
61: Parameters
62: ----------
63: x_data : interable of numbers
64: Container of the X axis data. Should be accepted
65: by matplotlib.
66:
67: y_data : np.ndarray, shape=(M, len(x_data))
68: Container of the Y axis data.
69: Where M is the number of series.
70:
71: labels : str, optional
72: The label to represent in plot legend.
73: If a list of series is provided, a list of labels
74: can be provided as well.
75: Defauts to: "no labels provided".
76:
77: filename : str, optional
78: The file name with which the plot figure will be saved
79: in disk. Defaults to rmsd_individual_chains_one_subplot.pdf.
80: You can change the file type by specifying its extention in
81: the file name.
82:
83: fig_size : tuple of float or int
84: The size ratio of the subplot in the figure.
85: """
86: y_data = np.array(y_data)
87:
88: if y_data.ndim == 1:
89: y_data = y_data[np.
ERROR: Unable to parse file: /code/src/taurenmd/cli_trajedit.py
ERROR: Parse error at line 160 column 16:
153: selection='all',
154: traj_output='traj_out.dcd',
155: top_output=None,
156: unwrap=False,
157: unwrap_reference='com',
158: unwrap_compound='fragments',
159: align=False,
--> **kwargs,
161: ):
162: """Execute main client logic."""
163: log.info(T('editing trajectory'))
164:
165: topology = Path(topology)
166: trajectories = [Path(t
INFO: ------------------------------------------------------------------------
INFO: EXECUTION SUCCESS
INFO: ------------------------------------------------------------------------
INFO: Total time: 1.056s
INFO: Final Memory: 6M/295M
INFO: ------------------------------------------------------------------------
|
joaomcteixeira authored 4e087f0b