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EPFL-LCSB / etfl

ETFL: A formulation for flux balance models accounting for expression, thermodynamics, and resource allocation constraints
Apache License 2.0
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invalid requirement specification in dependencies #13

Closed forxhunter closed 3 months ago

forxhunter commented 3 months ago

python3 setup.py install

should change to pip install .

otherwise it will trigger the error below: 

  File "/home/tianyu/miniconda3/envs/etfl/lib/python3.7/site-packages/pkg_resources/__init__.py", line 3106, in _dep_map
    return self.__dep_map
  File "/home/tianyu/miniconda3/envs/etfl/lib/python3.7/site-packages/pkg_resources/__init__.py", line 2899, in __getattr__
    raise AttributeError(attr)
AttributeError: _DistInfoDistribution__dep_map

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/tianyu/miniconda3/envs/etfl/lib/python3.7/site-packages/pkg_resources/_vendor/packaging/requirements.py", line 35, in __init__
    parsed = _parse_requirement(requirement_string)
  File "/home/tianyu/miniconda3/envs/etfl/lib/python3.7/site-packages/pkg_resources/_vendor/packaging/_parser.py", line 64, in parse_requirement
    return _parse_requirement(Tokenizer(source, rules=DEFAULT_RULES))
  File "/home/tianyu/miniconda3/envs/etfl/lib/python3.7/site-packages/pkg_resources/_vendor/packaging/_parser.py", line 82, in _parse_requirement
    url, specifier, marker = _parse_requirement_details(tokenizer)
  File "/home/tianyu/miniconda3/envs/etfl/lib/python3.7/site-packages/pkg_resources/_vendor/packaging/_parser.py", line 120, in _parse_requirement_details
    specifier = _parse_specifier(tokenizer)
  File "/home/tianyu/miniconda3/envs/etfl/lib/python3.7/site-packages/pkg_resources/_vendor/packaging/_parser.py", line 217, in _parse_specifier
    tokenizer.consume("WS")
  File "/home/tianyu/miniconda3/envs/etfl/lib/python3.7/contextlib.py", line 119, in __exit__
    next(self.gen)
  File "/home/tianyu/miniconda3/envs/etfl/lib/python3.7/site-packages/pkg_resources/_vendor/packaging/_tokenizer.py", line 189, in enclosing_tokens
    span_start=open_position,
  File "/home/tianyu/miniconda3/envs/etfl/lib/python3.7/site-packages/pkg_resources/_vendor/packaging/_tokenizer.py", line 168, in raise_syntax_error
    span=span,
pkg_resources.extern.packaging._tokenizer.ParserSyntaxError: Expected matching RIGHT_PARENTHESIS for LEFT_PARENTHESIS, after version specifier
    python-version (>="3.6") ; extra == 'equilibrator'
                   ~^

The above exception was the direct cause of the following exception:
Traceback (most recent call last):
  File "setup.py", line 68, in <module>
    'Programming Language :: Python :: 3.6',
  File "/home/tianyu/miniconda3/envs/etfl/lib/python3.7/site-packages/setuptools/__init__.py", line 103, in setup
    return distutils.core.setup(**attrs)
  File "/home/tianyu/miniconda3/envs/etfl/lib/python3.7/site-packages/setuptools/_distutils/core.py", line 185, in setup
    return run_commands(dist)
  File "/home/tianyu/miniconda3/envs/etfl/lib/python3.7/site-packages/setuptools/_distutils/core.py", line 201, in run_commands
    dist.run_commands()
  File "/home/tianyu/miniconda3/envs/etfl/lib/python3.7/site-packages/setuptools/_distutils/dist.py", line 969, in run_commands
    self.run_command(cmd)
  File "/home/tianyu/miniconda3/envs/etfl/lib/python3.7/site-packages/setuptools/dist.py", line 963, in run_command
    super().run_command(command)
  File "/home/tianyu/miniconda3/envs/etfl/lib/python3.7/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
    cmd_obj.run()
  File "/home/tianyu/miniconda3/envs/etfl/lib/python3.7/site-packages/setuptools/command/install.py", line 84, in run
    self.do_egg_install()
  File "/home/tianyu/miniconda3/envs/etfl/lib/python3.7/site-packages/setuptools/command/install.py", line 140, in do_egg_install
    cmd.run(show_deprecation=False)
  File "/home/tianyu/miniconda3/envs/etfl/lib/python3.7/site-packages/setuptools/command/easy_install.py", line 442, in run
    self.easy_install(spec, not self.no_deps)
  File "/home/tianyu/miniconda3/envs/etfl/lib/python3.7/site-packages/setuptools/command/easy_install.py", line 690, in easy_install
    return self.install_item(None, spec, tmpdir, deps, True)
  File "/home/tianyu/miniconda3/envs/etfl/lib/python3.7/site-packages/setuptools/command/easy_install.py", line 740, in install_item
    self.process_distribution(spec, dist, deps)
  File "/home/tianyu/miniconda3/envs/etfl/lib/python3.7/site-packages/setuptools/command/easy_install.py", line 789, in process_distribution
    [requirement], self.local_index, self.easy_install
  File "/home/tianyu/miniconda3/envs/etfl/lib/python3.7/site-packages/pkg_resources/__init__.py", line 834, in resolve
    new_requirements = dist.requires(req.extras)[::-1]
  File "/home/tianyu/miniconda3/envs/etfl/lib/python3.7/site-packages/pkg_resources/__init__.py", line 2820, in requires
    dm = self._dep_map
  File "/home/tianyu/miniconda3/envs/etfl/lib/python3.7/site-packages/pkg_resources/__init__.py", line 3108, in _dep_map
    self.__dep_map = self._compute_dependencies()
  File "/home/tianyu/miniconda3/envs/etfl/lib/python3.7/site-packages/pkg_resources/__init__.py", line 3118, in _compute_dependencies
    reqs.extend(parse_requirements(req))
  File "/home/tianyu/miniconda3/envs/etfl/lib/python3.7/site-packages/pkg_resources/__init__.py", line 3171, in __init__
    super(Requirement, self).__init__(requirement_string)
  File "/home/tianyu/miniconda3/envs/etfl/lib/python3.7/site-packages/pkg_resources/_vendor/packaging/requirements.py", line 37, in __init__
    raise InvalidRequirement(str(e)) from e
pkg_resources.extern.packaging.requirements.InvalidRequirement: Expected matching RIGHT_PARENTHESIS for LEFT_PARENTHESIS, after version specifier
    python-version (>="3.6") ; extra == 'equilibrator'