chore: Use flake8 for linting (#1191)

* Switch from pyflakes to flake8 for linting in pre-commit hooks and CI
   - Use flake8 in 'lint' extra
* Add flake8 config options to setup.cfg (as opposed to .flake8)
* Remove code that existed only to placate pyflakes

Author: matthewfeickert

.github/workflows/lint.yml

@@ -21,9 +21,9 @@ jobs:
         python -m pip install --upgrade pip setuptools wheel
         python -m pip install --ignore-installed -U -q --no-cache-dir -e .[lint]
         python -m pip list
-    - name: Lint with Pyflakes
+    - name: Lint with flake8
       run: |
-        python -m pyflakes .
+        python -m flake8 .
     - name: Lint with Black
       run: |
         black --check --diff --verbose .

.pre-commit-config.yaml

@@ -3,6 +3,10 @@ repos:
     rev: 20.8b1
     hooks:
     - id: black
+-   repo: https://gitlab.com/pycqa/flake8
+    rev: 3.8.4
+    hooks:
+    - id: flake8
 -   repo: https://github.com/asottile/pyupgrade
     rev: v2.7.4
     hooks:

setup.cfg

@@ -58,3 +58,12 @@ source-dir = docs
 build-dir = docs/_build
 all-files = 1
 warning-is-error = 1
+
+[flake8]
+# E203: whitespace before ':'
+# E402: module level import not at top of file
+# E501: line too long
+extend-ignore = E203, E402, E501
+max-line-length = 88
+count = True
+statistics = True

setup.py

@@ -20,7 +20,7 @@
     )
 )
 extras_require['contrib'] = sorted({'matplotlib', 'requests'})
-extras_require['lint'] = sorted({'pyflakes', 'black'})
+extras_require['lint'] = sorted({'flake8', 'black'})
 
 extras_require['test'] = sorted(
     set(

src/pyhf/contrib/cli.py

@@ -20,10 +20,7 @@ def cli():
 
             $ python -m pip install pyhf[contrib]
     """
-    from . import utils  # Guard CLI from missing extra
-
-    # TODO: https://github.com/scikit-hep/pyhf/issues/863
-    _ = utils  # Placate pyflakes
+    from . import utils  # Guard CLI from missing extra # noqa: F401
 
 
 @cli.command()

src/pyhf/infer/__init__.py

@@ -186,7 +186,6 @@ def hypotest(
     return tuple(_returns) if len(_returns) > 1 else _returns[0]
 
 
-from . import intervals
+from . import intervals  # noqa: F401
 
-# TODO: Can remove intervals when switch to flake8 (Issue #863)
-__all__ = ["hypotest", "intervals"]
+__all__ = ["hypotest"]

src/pyhf/infer/utils.py

@@ -36,6 +36,6 @@ def create_calculator(calctype, *args, **kwargs):
     Returns:
         calculator (:obj:`object`): A calculator.
     """
-    return {'asymptotics': AsymptoticCalculator, 'toybased': ToyCalculator,}[
-        calctype
-    ](*args, **kwargs)
+    return {'asymptotics': AsymptoticCalculator, 'toybased': ToyCalculator}[calctype](
+        *args, **kwargs
+    )

src/pyhf/optimize/opt_minuit.py

@@ -52,8 +52,8 @@ def _get_minimizer(
 
         # Minuit requires jac=callable
         if do_grad:
-            wrapped_objective = lambda pars: objective_and_grad(pars)[0]
-            jac = lambda pars: objective_and_grad(pars)[1]
+            wrapped_objective = lambda pars: objective_and_grad(pars)[0]  # noqa: E731
+            jac = lambda pars: objective_and_grad(pars)[1]  # noqa: E731
         else:
             wrapped_objective = objective_and_grad
             jac = None

src/pyhf/pdf.py

@@ -731,7 +731,7 @@ def logpdf(self, pars, data):
             ):  # force to be not scalar, should we changed with #522
                 return tensorlib.reshape(result, (1,))
             return result
-        except:
+        except:  # noqa: E722
             log.error(
                 f'eval failed for data {tensorlib.tolist(data)} pars: {tensorlib.tolist(pars)}'
             )

src/pyhf/readxml.py

@@ -40,7 +40,7 @@ def import_root_histogram(rootdir, filename, path, name, filecache=None):
     path = path or ''
     path = path.strip('/')
     fullpath = str(Path(rootdir).joinpath(filename))
-    if not fullpath in filecache:
+    if fullpath not in filecache:
         f = uproot.open(fullpath)
         filecache[fullpath] = f
     else: