Fix typing errors detected by newer mypy version (#36)

* Fix typing errors detected by newer mypy version

Also pin mypy to avoid problems in the future.

* Fix mypy version in pre-commit hook

Co-authored-by: rbusche <[email protected]>

.pre-commit-config.yaml

@@ -1,21 +1,21 @@
 fail_fast: true
 repos:
-- repo: https://github.com/pre-commit/mirrors-isort
-  rev: 'v4.3.21'
-  hooks:
-    - id: isort
-      additional_dependencies: ['isort[pyproject]']
-- repo: https://github.com/psf/black
-  rev: stable
-  hooks:
-  - id: black
--   repo: https://github.com/pre-commit/mirrors-mypy
-    rev: 'v0.730'
+  - repo: https://github.com/pre-commit/mirrors-isort
+    rev: "v4.3.21"
     hooks:
-    -   id: mypy
--   repo: https://gitlab.com/pycqa/flake8
+      - id: isort
+        additional_dependencies: ["isort[pyproject]"]
+  - repo: https://github.com/psf/black
+    rev: stable
+    hooks:
+      - id: black
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: "v0.910"
+    hooks:
+      - id: mypy
+  - repo: https://gitlab.com/pycqa/flake8
     rev: 3.7.8
     hooks:
-    -   id: flake8
+      - id: flake8
         exclude: ^(tests|examples|docs)/*
-        additional_dependencies: [pep8-naming, flake8-docstrings]
+        additional_dependencies: [pep8-naming, flake8-docstrings]

epysurv/models/timepoint/_base.py

@@ -138,7 +138,7 @@ def _prepare_r_instance(self, data: pd.DataFrame):
         """Transform dataframe into R data structure on which the R algorithm can work."""
         raise NotImplementedError
 
-    def _extract_alarms(self, surveillance_result) -> np.array:
+    def _extract_alarms(self, surveillance_result) -> np.ndarray:
         """Extract the binary alarm array from the surveillance result R data structure."""
         raise NotImplementedError
 

epysurv/simulation/seasonal_noise.py

@@ -4,11 +4,12 @@
 import numpy as np
 import pandas as pd
 import rpy2.robjects.packages as rpackages
-from epysurv.simulation.base import BaseSimulation
-from epysurv.simulation.utils import add_date_time_index_to_frame, r_list_to_frame
 from rpy2 import robjects
 from scipy.stats import nbinom, poisson
 
+from epysurv.simulation.base import BaseSimulation
+from epysurv.simulation.utils import add_date_time_index_to_frame, r_list_to_frame
+
 surveillance = rpackages.importr("surveillance")
 
 
@@ -187,7 +188,7 @@ def simulate(self, length: int) -> pd.DataFrame:
         else:
             cases = []
             for mu in mu_s:
-                r = np.float(mu / (self.dispersion - 1))
+                r = mu / (self.dispersion - 1)
                 p = r / (r + mu)
                 cases.append(nbinom.rvs(r, p, size=1)[0])
         return (

requirements-dev.txt

@@ -5,7 +5,7 @@ pytest-datadir
 pytest-cov
 codecov
 black==19.10b0
-mypy
+mypy==0.910
 flake8
 pep8-naming
 flake8-docstrings