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Lint errors in core files #123

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dilawar opened this issue Jul 24, 2021 · 0 comments
Open

Lint errors in core files #123

dilawar opened this issue Jul 24, 2021 · 0 comments

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@dilawar
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dilawar commented Jul 24, 2021 •
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openjournals/joss-reviews#3464 | Related #117.

I am running a few lint tools e.g., pylint and pyflakes to locate errors in the module. This is related to #117 that also used studies folder. Since that may not be part of final release (#117 (comment)), this run restricts itself to the core files.

I am working on my fork and send a PR soon that will fix these issues if possible.

In this run, I am using poetry to manage the dependencies. Managing dependencies in Python has been less than ideal (poetry helps but the author need not add this to their DevOps).

The most critical among these should be fixed.

pylint

$ poetry run pylint -E epimargin
[dilawars@chutki epimargin (poetry)]$ poetry run pylint -E epimargin
************* Module epimargin.policy
epimargin/policy.py:205:15: E1101: Instance of 'VaccinationPolicy' has no 'daily_doses' member (no-member)
************* Module epimargin.estimators
epimargin/estimators.py:25:18: E1101: Method 'params' has no 'join' member (no-member)
************* Module epimargin.plots
epimargin/plots.py:62:0: E0102: function already defined line 14 (function-redefined)
epimargin/plots.py:194:0: E0102: function already defined line 14 (function-redefined)
************* Module epimargin.etl.covid19india
epimargin/etl/covid19india.py:348:22: E1101: Instance of 'TextFileReader' has no 'set_index' member (no-member)
************* Module epimargin.etl.devdatalab
epimargin/etl/devdatalab.py:28:57: E1101: Instance of 'TextFileReader' has no 'O_StateCensus2011' member (no-member)
************* Module epimargin.etl.csse
epimargin/etl/csse.py:27:8: E1101: Instance of 'TextFileReader' has no 'assign' member (no-member)
************* Module epimargin.etl
epimargin/etl/__init__.py:2:11: E0604: Invalid object 'download_data' in __all__, must contain only strings (invalid-all-object)
[dilawars@chutki epimargin (poetry)]$\

mypy

[dilawars@chutki epimargin (poetry)]$ poetry run mypy --ignore-missing-imports epimargin
epimargin/etl/commons.py:2: error: Library stubs not installed for "requests" (or incompatible with Python 3.9)
epimargin/etl/commons.py:2: note: Hint: "python3 -m pip install types-requests"
epimargin/etl/commons.py:2: note: (or run "mypy --install-types" to install all missing stub packages)
epimargin/etl/commons.py:2: note: See https://mypy.readthedocs.io/en/stable/running_mypy.html#missing-imports
epimargin/etl/__init__.py:2: error: Type of __all__ must be "Sequence[str]", not "List[Callable[[Path, str, str], Any]]"
epimargin/etl/devdatalab.py:14: error: Function "numpy.array" is not valid as a type
epimargin/etl/devdatalab.py:14: note: Perhaps you need "Callable[...]" or a callback protocol?
epimargin/etl/devdatalab.py:16: error: Value of type np.array? is not indexable
epimargin/models.py:127: error: "int" has no attribute "copy"
epimargin/models.py:175: error: "int" has no attribute "copy"
epimargin/models.py:250: error: "int" has no attribute "shape"
epimargin/models.py:279: error: Need type annotation for "dV" (hint: "dV: List[<type>] = ...")
epimargin/models.py:283: error: Function "numpy.array" is not valid as a type
epimargin/models.py:283: note: Perhaps you need "Callable[...]" or a callback protocol?
epimargin/models.py:283: error: Signature of "parallel_forward_epi_step" incompatible with supertype "SIR"
epimargin/models.py:448: error: Incompatible types in assignment (expression has type "bool", variable has type "str")
epimargin/models.py:455: error: Incompatible return value type (got "List[Union[_T, int]]", expected "Union[Dict[str, Sequence[float]], Sequence[float]]")
epimargin/models.py:456: error: Incompatible return value type (got "Dict[str, List[Union[_T, int]]]", expected "Union[Dict[str, Sequence[float]], Sequence[float]]")
epimargin/policy.py:19: error: "SIR" has no attribute "set_parameters"
epimargin/policy.py:36: error: Argument 1 to "len" has incompatible type "SIR"; expected "Sized"
epimargin/policy.py:37: error: "SIR" has no attribute "set_parameters"
epimargin/policy.py:43: error: Need type annotation for "Gs" (hint: "Gs: Set[<type>] = ...")
epimargin/policy.py:43: error: Need type annotation for "Ys" (hint: "Ys: Set[<type>] = ...")
epimargin/policy.py:43: error: Need type annotation for "Os" (hint: "Os: Set[<type>] = ...")
epimargin/policy.py:43: error: Need type annotation for "Rs" (hint: "Rs: Set[<type>] = ...")
epimargin/policy.py:46: error: Need type annotation for "unit"
epimargin/policy.py:46: error: Argument 1 to "enumerate" has incompatible type "SIR"; expected "Iterable[<nothing>]"
epimargin/policy.py:79: error: Value of type "SIR" is not indexable
epimargin/policy.py:88: error: Too many arguments for "run" of "SIR"
epimargin/policy.py:91: error: "SIR" has no attribute "gantt"
epimargin/policy.py:96: error: Argument 1 to "len" has incompatible type "SIR"; expected "Sized"
epimargin/policy.py:97: error: "SIR" has no attribute "set_parameters"
epimargin/policy.py:103: error: Need type annotation for "Gs" (hint: "Gs: Set[<type>] = ...")
epimargin/policy.py:103: error: Need type annotation for "Ys" (hint: "Ys: Set[<type>] = ...")
epimargin/policy.py:103: error: Need type annotation for "Os" (hint: "Os: Set[<type>] = ...")
epimargin/policy.py:103: error: Need type annotation for "Rs" (hint: "Rs: Set[<type>] = ...")
epimargin/policy.py:106: error: Need type annotation for "unit"
epimargin/policy.py:106: error: Argument 1 to "enumerate" has incompatible type "SIR"; expected "Iterable[<nothing>]"
epimargin/policy.py:142: error: Value of type "SIR" is not indexable
epimargin/policy.py:151: error: Too many arguments for "run" of "SIR"
epimargin/policy.py:154: error: "SIR" has no attribute "gantt"
epimargin/policy.py:174: error: Value of type "SIR" is not indexable
epimargin/policy.py:176: error: Argument 1 to "len" has incompatible type "SIR"; expected "Sized"
epimargin/policy.py:180: error: Value of type "SIR" is not indexable
epimargin/policy.py:181: error: Too many arguments for "run" of "SIR"
epimargin/policy.py:183: error: Value of type "SIR" is not indexable
epimargin/policy.py:194: error: Function "numpy.array" is not valid as a type
epimargin/policy.py:194: note: Perhaps you need "Callable[...]" or a callback protocol?
epimargin/policy.py:201: error: Function "numpy.array" is not valid as a type
epimargin/policy.py:201: note: Perhaps you need "Callable[...]" or a callback protocol?
epimargin/policy.py:205: error: "VaccinationPolicy" has no attribute "daily_doses"
epimargin/policy.py:209: error: np.array? has no attribute "sum"
epimargin/policy.py:211: error: np.array? has no attribute "sum"
epimargin/policy.py:215: error: Function "numpy.array" is not valid as a type
epimargin/policy.py:215: note: Perhaps you need "Callable[...]" or a callback protocol?
epimargin/policy.py:221: error: Function "numpy.array" is not valid as a type
epimargin/policy.py:221: note: Perhaps you need "Callable[...]" or a callback protocol?
epimargin/policy.py:221: error: Signature of "distribute_doses" incompatible with supertype "VaccinationPolicy"
epimargin/policy.py:223: error: Incompatible return value type (got "Tuple[ndarray, ndarray, ndarray]", expected "Tuple[np.array?]")
epimargin/policy.py:223: error: np.array? has no attribute "shape"
epimargin/policy.py:225: error: No overload variant of "__setitem__" of "list" matches argument types "int", "float"
epimargin/policy.py:225: note: Possible overload variants:
epimargin/policy.py:225: note:     def __setitem__(self, SupportsIndex, int) -> None
epimargin/policy.py:225: note:     def __setitem__(self, slice, Iterable[int]) -> None
epimargin/policy.py:229: error: "int" has no attribute "mean"
epimargin/policy.py:231: error: Incompatible return value type (got "Tuple[Any, Any, Any]", expected "Tuple[np.array?]")
epimargin/policy.py:238: error: Function "numpy.array" is not valid as a type
epimargin/policy.py:238: note: Perhaps you need "Callable[...]" or a callback protocol?
epimargin/policy.py:248: error: Function "numpy.array" is not valid as a type
epimargin/policy.py:248: note: Perhaps you need "Callable[...]" or a callback protocol?
epimargin/policy.py:248: error: Signature of "distribute_doses" incompatible with supertype "VaccinationPolicy"
epimargin/policy.py:250: error: Incompatible return value type (got "Tuple[None, None, None]", expected "Tuple[np.array?]")
epimargin/policy.py:253: error: No overload variant of "__setitem__" of "list" matches argument types "int", "float"
epimargin/policy.py:253: note: Possible overload variants:
epimargin/policy.py:253: note:     def __setitem__(self, SupportsIndex, int) -> None
epimargin/policy.py:253: note:     def __setitem__(self, slice, Iterable[int]) -> None
epimargin/policy.py:256: error: np.array? has no attribute "shape"
epimargin/policy.py:257: error: Value of type np.array? is not indexable
epimargin/policy.py:259: error: Value of type np.array? is not indexable
epimargin/policy.py:260: error: Value of type np.array? is not indexable
epimargin/policy.py:260: error: Unsupported target for indexed assignment (np.array?)
epimargin/policy.py:263: error: Value of type np.array? is not indexable
epimargin/policy.py:264: error: Value of type np.array? is not indexable
epimargin/policy.py:265: error: Unsupported target for indexed assignment (np.array?)
epimargin/policy.py:267: error: Unsupported operand types for + ("None" and "int")
epimargin/policy.py:267: note: Left operand is of type "Optional[int]"
epimargin/policy.py:268: error: Value of type np.array? is not indexable
epimargin/policy.py:268: error: Unsupported target for indexed assignment (np.array?)
epimargin/policy.py:268: error: Unsupported operand types for + ("None" and "int")
epimargin/policy.py:268: note: Left operand is of type "Optional[int]"
epimargin/policy.py:271: error: Incompatible return value type (got "Tuple[ndarray, Any, Any]", expected "Tuple[np.array?]")
epimargin/policy.py:274: error: "int" has no attribute "mean"
epimargin/plots.py:308: error: "SIR" has no attribute "units"
epimargin/plots.py:322: error: "SIR" has no attribute "aggregate"
epimargin/plots.py:380: error: "SIR" has no attribute "aggregate"
epimargin/plots.py:387: error: Need type annotation for "ranges"
epimargin/plots.py:401: error: Incompatible types in assignment (expression has type "List[Any]", variable has type "int")
epimargin/plots.py:405: error: Incompatible types in assignment (expression has type "List[int]", variable has type "int")
epimargin/plots.py:422: error: Value of type "int" is not indexable
epimargin/plots.py:547: error: "Callable[[Any, Any, Any, Any, Any, Any, Any, Any], Any]" has no attribute "horizontal"
epimargin/plots.py:548: error: "Callable[[Any, Any, Any, Any, Any, Any, Any, Any], Any]" has no attribute "vertical"
Found 82 errors in 6 files (checked 13 source files)
@dilawar dilawar changed the title Lint errors in core package Lint errors in core files Jul 24, 2021
dilawar pushed a commit to dilawar/epimargin that referenced this issue Jul 24, 2021
Added mypy config file
be9e0f7 
issue: COVID-IWG#123
dilawar pushed a commit to dilawar/epimargin that referenced this issue Jul 24, 2021
related to COVID-IWG#123
dcb41a5 
Error:

************* Module epimargin.policy
epimargin/policy.py:205:15: E1101: Instance of 'VaccinationPolicy' has
no 'daily_doses' member (no-member)

Fixes:

`daily_doses` should be in the base class.
dilawar pushed a commit to dilawar/epimargin that referenced this issue Jul 24, 2021
related: COVID-IWG#123
de1e6ce 
************* Module epimargin.plots
epimargin/plots.py:62:0: E0102: function already defined line 14
(function-redefined)
epimargin/plots.py:194:0: E0102: function already defined line 14
(function-redefined)

Fixes:

Use `import matplotlib.pyplot as plt` rather than `from matplotlib.pyplot import *`.
dilawar pushed a commit to dilawar/epimargin that referenced this issue Jul 24, 2021
fix: E1101: Instance of 'VaccinationPolicy' has no 'daily_doses' memb…
ce000ee 
…er (no-member)

`daily_doses` should be in the base class.

related to COVID-IWG#123
dilawar pushed a commit to dilawar/epimargin that referenced this issue Jul 24, 2021
Fix: epimargin/plots.py:62:0: E0102: function already defined line 14
0bc6494 
************* Module epimargin.plots
(function-redefined)
epimargin/plots.py:194:0: E0102: function already defined line 14
(function-redefined)

Fixes: Use `import matplotlib.pyplot as plt` rather than `from matplotlib.pyplot import *`.
Related: COVID-IWG#123
dilawar pushed a commit to dilawar/epimargin that referenced this issue Jul 24, 2021
fix: epimargin/etl/__init__.py:2:11: E0604
b215386 
Invalid object 'download_data' in __all__, must contain only strings (invalid-all-object)

Related COVID-IWG#123
dilawar pushed a commit to dilawar/epimargin that referenced this issue Jul 24, 2021
pylint: fixes to DataFrame related error
69dac1a 
1. `read_csv` return Union[DataFrame, TextParser] but a few functions assume
   that read_csv will return DataFrame only. This is fixed by casting
   the results to be a DataFrame.
2. Similarly, in estimator.py file, `params` is forced to be DataFrame
   so that `join` can be applied.

ref: COVID-IWG#123
dilawar pushed a commit to dilawar/epimargin that referenced this issue Jul 24, 2021
few minor tweaks to keep mypy happy in plots.py file
2a2443f 
Related:

- COVID-IWG#124
- COVID-IWG#123
@satejsoman satejsoman mentioned this issue Aug 5, 2021
Merged
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