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choderalab/protons

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Merge pull request #140 from choderalab/develop #188
Bas Rustenburg authored 2c15db88
complete00:00:24
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1
git clone
2
codeclimate validate-config
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codeclimate validate-config
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3
codeclimate prepare
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codeclimate prepare
4
builder pull-engines
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determining required images
5
structure
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12
Parser process id: 12
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duplication
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12
Parser process id: 12
codeclimate-parser socket not present
waiting 1s...
I, [2024-04-28T03:18:48.068937 #1]  INFO -- : Skipping file ./examples/tautomers/tautomer_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 131
    preproc: Dict[str, Any] = settings["preprocessing"]
           ^
SyntaxError: invalid syntax


I, [2024-04-28T03:18:48.100914 #1]  INFO -- : Skipping file ./protons/scripts/utilities.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 26
    def serialize_state(context) -> str:
                                 ^
SyntaxError: invalid syntax


I, [2024-04-28T03:18:48.106867 #1]  INFO -- : Skipping file ./protons/scripts/run_prep_ffxml.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 42
    log.info(f"Preparing a run from '{jsonfile}'")
                                                ^
SyntaxError: invalid syntax


I, [2024-04-28T03:18:48.111812 #1]  INFO -- : Skipping file ./protons/scripts/run_simulation.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 34
    format_vars: Dict[str, str] = settings["format_vars"]
               ^
SyntaxError: invalid syntax


I, [2024-04-28T03:18:48.121040 #1]  INFO -- : Skipping file ./protons/scripts/cli.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 33
    def validate(args: List[str]) -> str:
                     ^
SyntaxError: invalid syntax


I, [2024-04-28T03:18:48.135520 #1]  INFO -- : Skipping file ./protons/scripts/run_parametrize_ligand.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 90
    raise FileNotFoundError(f"Could not find the structure file: {ical_path}.")
                                                                             ^
SyntaxError: invalid syntax


I, [2024-04-28T03:18:48.141320 #1]  INFO -- : Skipping file ./protons/app/driver.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 74
    self.titration_states: List[_TitrationState] = list()
                         ^
SyntaxError: invalid syntax


I, [2024-04-28T03:18:48.152248 #1]  INFO -- : Skipping file ./protons/app/samsreporter.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 48
    def describeNextReport(self, calibration: ConstantPHSimulation):
                                            ^
SyntaxError: invalid syntax


I, [2024-04-28T03:18:48.174447 #1]  INFO -- : Skipping file ./protons/app/cnstphgbforces.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 173
    custom.addGlobalParameter("neckScale", 0.361_825)
                                                   ^
SyntaxError: invalid syntax


I, [2024-04-28T03:18:48.186952 #1]  INFO -- : Skipping file ./protons/app/ligands.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 257
    self, input_state_data: list, gaff_xml: str = None, residue_name: str = "LIG"
                          ^
SyntaxError: invalid syntax


I, [2024-04-28T03:18:48.250159 #1]  INFO -- : Skipping file ./protons/app/calibration.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 18
    def __init__(self, driver: NCMCProtonDrive):
                             ^
SyntaxError: invalid syntax


I, [2024-04-28T03:18:48.261174 #1]  INFO -- : Skipping file ./protons/app/template_patches.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 7
    def patch_cooh(source: str, residue_name: str, oh_type="oh", ho_type="ho") -> str:
                         ^
SyntaxError: invalid syntax


I, [2024-04-28T03:18:48.261671 #1]  INFO -- : Skipping file ./protons/app/openeye.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 76
    def assignELF10charges(molecule, max_confs: int = -1, strictStereo=True):
                                              ^
SyntaxError: invalid syntax


I, [2024-04-28T03:18:48.271783 #1]  INFO -- : Skipping file ./protons/app/simulation.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 75
    self.drive: NCMCProtonDrive = drive
              ^
SyntaxError: invalid syntax


I, [2024-04-28T03:18:48.272436 #1]  INFO -- : Skipping file ./protons/app/analysis.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 17
    def calibration_dataset_to_arrays(dataset: netCDF4.Dataset):
                                             ^
SyntaxError: invalid syntax


I, [2024-04-28T03:18:48.282405 #1]  INFO -- : Skipping file ./protons/app/ions.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 21
    reference_state_charge: int, to_state_charge: int, rule: NeutralChargeRule
                          ^
SyntaxError: invalid syntax


I, [2024-04-28T03:18:48.282901 #1]  INFO -- : Skipping file ./protons/app/pka.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 8
    class PopulationCalculator(metaclass=abc.ABCMeta):
                                        ^
SyntaxError: invalid syntax


I, [2024-04-28T03:18:48.293540 #1]  INFO -- : Skipping file ./protons/app/proposals.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 17
    class _StateProposal(metaclass=ABCMeta):
                                  ^
SyntaxError: invalid syntax


I, [2024-04-28T03:18:48.317796 #1]  INFO -- : Skipping file ./protons/app/ncmcreporter.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 14
    self, netcdffile, reportInterval: int, cumulativeworkInterval: int = 0
                                    ^
SyntaxError: invalid syntax


I, [2024-04-28T03:18:48.329598 #1]  INFO -- : Skipping file ./protons/app/modeller.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 362
    bonds.addBond(atom1.index, atom2.index, 0.1, 100_000.0)
                                                       ^
SyntaxError: invalid syntax


I, [2024-04-28T03:18:48.363831 #1]  INFO -- : Skipping file ./protons/app/saltswap_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 6
    swapper: Swapper,
           ^
SyntaxError: invalid syntax


I, [2024-04-28T03:18:48.490802 #1]  INFO -- : Skipping file ./protons/app/forcefield_generators.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 414
    use_recommended: bool = True,
                   ^
SyntaxError: invalid syntax


I, [2024-04-28T03:18:48.835109 #1]  INFO -- : Skipping file ./grant simulations documentation/example_analysis.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 7
    try
      ^
SyntaxError: invalid syntax