choderalab/yank

codeclimate validate-config
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codeclimate prepare

determining required images

12
Parser process id: 12
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12
Parser process id: 12
codeclimate-parser socket not present
waiting 1s...
I, [2024-04-20T10:52:55.065032 #1]  INFO -- : Skipping file Yank/experiment.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 1245
    common_molecules_schema = {**leap_schema, **regions_schema}
                                ^
SyntaxError: invalid syntax


I, [2024-04-20T10:52:55.071973 #1]  INFO -- : Skipping file ./Yank/schema/validator.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 162
    self._error(field, f'must be one of {_NONBONDED_METHODS_STR}')
                                                                ^
SyntaxError: invalid syntax


I, [2024-04-20T10:52:55.079029 #1]  INFO -- : Skipping file Yank/yank.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 234
    def get_region(self, region_name) -> List[int]:
                                      ^
SyntaxError: invalid syntax


I, [2024-04-20T10:52:55.084618 #1]  INFO -- : Skipping file Yank/analyze.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 61
    def __init__(self, *args, registry=yank_registry, **kwargs):
                                     ^
SyntaxError: invalid syntax


I, [2024-04-20T10:52:55.095198 #1]  INFO -- : Skipping file ./Yank/reports/notebook.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 540
    def format_trace_plot(plot: plt.Axes, trace_forward: np.ndarray, trace_reverse: np.ndarray):
                              ^
SyntaxError: invalid syntax


I, [2024-04-20T10:52:55.112821 #1]  INFO -- : Skipping file Yank/restraints.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 231
    def compute_atom_intersect(self, input_atoms, topography_key: str, *additional_sets: Iterable[int]) -> Set[int]:
                                                                ^
SyntaxError: invalid syntax


I, [2024-04-20T10:52:55.118253 #1]  INFO -- : Skipping file Yank/pipeline.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 2006
    *(cell_angles[i]/unit.degree)
    ^
SyntaxError: invalid syntax


I, [2024-04-20T10:52:55.271713 #1]  INFO -- : Skipping file Yank/utils.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 946
    cycle_kwargs = {**cycle_kwargs, **input_argspec.kwonlydefaults}
                     ^
SyntaxError: invalid syntax