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Clean up scifolder linting

Summary

Currently the scifolder code only passes the linter with a massive amount of disable directives. Many of these probably mean that it is very easy to cause exceptions by proper usage of the code.

Expected Behavior

pylint should just accept the code.

Actual Behavior

src/caosadvancedtools/scifolder$ grep -rn "pylint: disable"
simulation_cfood.py:91:        if SOURCES.key in self.header:                         # pylint: disable=unsupported-membership-test
simulation_cfood.py:96:                    globs=get_glob(self.header[SOURCES.key]),  # pylint: disable=unsubscriptable-object
simulation_cfood.py:102:        if REVISIONOF.key in self.header:                      # pylint: disable=unsupported-membership-test
simulation_cfood.py:105:                recordtypes=[dm.Software],                     # pylint: disable=no-member
simulation_cfood.py:107:                globs=get_glob(self.header[dm.revisionOf]),    # pylint: disable=unsubscriptable-object
utils.py:115:    return list(df.ID)  # pylint: disable=no-member
withreadme.py:124:            if self.crawled_path.lower().endswith(".md"):  # pylint: disable=no-member
withreadme.py:126:                    fileguide.access(self.crawled_path))   # pylint: disable=no-member
withreadme.py:127:            elif self.crawled_path.lower().endswith(".xlsx"):  # pylint: disable=no-member
withreadme.py:129:                    fileguide.access(self.crawled_path))       # pylint: disable=no-member
withreadme.py:148:                globs, prefix=os.path.dirname(self.crawled_path))  # pylint: disable=no-member
withreadme.py:163:            self.attached_filenames.extend(flat_list)  # pylint: disable=no-member
withreadme.py:188:        for field in self.win_paths:  # pylint: disable=no-member
withreadme.py:248:                to_be_updated=self.to_be_updated,  # pylint: disable=no-member
withreadme.py:258:            if field.key not in self.header:  # pylint: disable=no-member
withreadme.py:262:            for item in self.header[field.key]:  # pylint: disable=no-member
withreadme.py:267:                                os.path.dirname(self.crawled_path),  # pylint: disable=no-member

Steps to Reproduce the Problem

Run pylint on the code before the disable directives were added. Or:

from caosadvancedtools.scifolder.simulation_cfood import SimulationCFood
scf = SimulationCFood(".")
scf.update_identifiables()
# raises AttributeError: 'SimulationCFood' object has no attribute 'simulation'

Specifications

  • Version: Latest dev branch commit
  • Platform: Debian/Linux

Possible fixes

  • Maybe add more values to the __init__() methods?