Prevent yesqa from removing necessary qa's (#40)

* Update pre-commits

* Remove `flake8-mock` causing issues with `yesqa`

* Update `additional_dependencies`.

* Use `codecov` action

Co-authored-by: Michal Klein <michal.klein@protonmail.com>

.github/workflows/ci.yml

@@ -116,11 +116,14 @@ jobs:
                 USE_SLEPC: ${{ matrix.use_slepc }}
 
         -   name: Upload coverage
-            if: success()
-            env:
-                CODECOV_NAME: ${{ matrix.os }}-${{ matrix.python }}-{{ matrix.use_slepc }}
-            run: |
-                codecov --no-color --required --flags unittests
+            uses: codecov/codecov-action@v3
+            with:
+                files: ./coverage.xml
+                flags: unittests
+                name: ${{ matrix.os }}-${{ matrix.python }}-{{ matrix.use_slepc }}
+                env_vars: OS,PYTHON
+                fail_ci_if_error: false
+                verbose: true
 
     deploy:
         needs: [lint, test]

.pre-commit-config.yaml

@@ -7,33 +7,33 @@ default_stages:
 minimum_pre_commit_version: 2.9.0
 repos:
 -   repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v0.790
+    rev: v0.982
     hooks:
     -   id: mypy
         additional_dependencies: [numpy==1.20.0, scipy>=1.6.0]
 -   repo: https://github.com/psf/black
-    rev: 20.8b1
+    rev: 22.10.0
     hooks:
     -   id: black
-        additional_dependencies: ['click==8.0.1', toml]
+        additional_dependencies: [toml]
 -   repo: https://github.com/timothycrosley/isort
-    rev: 5.7.0
+    rev: 5.10.1
     hooks:
     -   id: isort
         additional_dependencies: [toml]
         args: [--order-by-type]
 -   repo: https://github.com/asottile/yesqa
-    rev: v1.2.2
+    rev: v1.4.0
     hooks:
     -   id: yesqa
-        additional_dependencies: [flake8-tidy-imports, flake8-docstrings, flake8-rst-docstrings, flake8-comprehensions, flake8-bugbear, flake8-logging-format, flake8-blind-except, flake8-builtins, flake8-pytest-style, flake8-mock, flake8-string-format]
+        additional_dependencies: [flake8-tidy-imports, flake8-docstrings, flake8-rst-docstrings, flake8-comprehensions, flake8-bugbear, flake8-logging-format, flake8-blind-except, flake8-builtins, flake8-pytest-style, flake8-string-format]
 -   repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks
-    rev: v1.6.1
+    rev: v2.4.0
     hooks:
     -   id: pretty-format-yaml
         args: [--autofix, --indent, '4', --preserve-quotes]
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v3.4.0
+    rev: v4.3.0
     hooks:
     -   id: detect-private-key
     -   id: no-commit-to-branch
@@ -57,37 +57,33 @@ repos:
     -   id: check-toml
     -   id: requirements-txt-fixer
 -   repo: https://gitlab.com/pycqa/flake8
-    rev: 3.8.4
+    rev: 3.9.2
     hooks:
     -   id: flake8
-        additional_dependencies: [flake8-tidy-imports, flake8-docstrings, flake8-rst-docstrings, flake8-comprehensions, flake8-bugbear, flake8-logging-format, flake8-blind-except, flake8-builtins, flake8-pytest-style, flake8-mock, flake8-string-format]
+        additional_dependencies: [flake8-tidy-imports, flake8-docstrings, flake8-rst-docstrings, flake8-comprehensions, flake8-bugbear, flake8-logging-format, flake8-blind-except, flake8-builtins, flake8-pytest-style, flake8-string-format]
 -   repo: https://github.com/myint/autoflake
-    rev: v1.4
+    rev: v1.7.1
     hooks:
     -   id: autoflake
         args: [--in-place, --remove-all-unused-imports, --remove-unused-variable, --ignore-init-module-imports]
 -   repo: https://github.com/jumanjihouse/pre-commit-hooks
-    rev: 2.1.4
+    rev: 3.0.0
     hooks:
     -   id: script-must-have-extension
         name: Check executable files use .sh extension
         types: [shell, executable]
--   repo: https://github.com/myint/rstcheck
-    rev: 3f92957478422df87bd730abde66f089cc1ee19b
-    hooks:
-    -   id: rstcheck
 -   repo: https://github.com/asottile/blacken-docs
-    rev: v1.9.1
+    rev: v1.12.1
     hooks:
     -   id: blacken-docs
-        additional_dependencies: [black==20.8b1]
+        additional_dependencies: [black==22.10.0]
 -   repo: https://github.com/asottile/pyupgrade
-    rev: v2.7.4
+    rev: v3.0.0
     hooks:
     -   id: pyupgrade
         args: [--py3-plus, --py37-plus]
 -   repo: https://github.com/pre-commit/pygrep-hooks
-    rev: v1.7.0
+    rev: v1.9.0
     hooks:
     -   id: python-no-eval
     -   id: python-use-type-annotations
@@ -96,6 +92,6 @@ repos:
     -   id: rst-directive-colons
     -   id: rst-inline-touching-normal
 -   repo: https://github.com/PyCQA/doc8
-    rev: 0.9.0a1
+    rev: v1.0.0
     hooks:
     -   id: doc8

pygpcca/_gpcca.py

@@ -456,7 +456,7 @@ def _objective(alpha: np.ndarray, X: np.ndarray) -> float:
     rot_mat = np.zeros((m, m), dtype=np.float64)
 
     # Sanity checks.
-    if alpha.shape[0] != k ** 2:
+    if alpha.shape[0] != k**2:
         raise ValueError(
             "The shape of alpha doesn't match with the shape of X: "
             f"It is not a ({k}^2,)-vector, but of dimension {alpha.shape}. X is of shape `{X.shape}`."
@@ -514,7 +514,7 @@ def _opt_soft(X: np.ndarray, rot_matrix: np.ndarray) -> Tuple[np.ndarray, np.nda
 
     # Now reshape rot_crop_matrix into a linear vector alpha.
     k = m - 1
-    alpha = np.reshape(rot_crop_matrix, k ** 2)
+    alpha = np.reshape(rot_crop_matrix, k**2)
     # TODO: Implement Gauss Newton Optimization to speed things up esp. for m > 10
     alpha, fopt, _, _, _ = fmin(_objective, alpha, args=(X,), full_output=True, disp=False)
 

pygpcca/_sort_real_schur.py

@@ -258,7 +258,7 @@ def rot(X: np.ndarray) -> np.ndarray:
     s = 0.0
     if X[0, 0] != X[1, 1]:
         tau = (X[0, 1] + X[1, 0]) / (X[0, 0] - X[1, 1])
-        off = (tau ** 2 + 1) ** 0.5
+        off = (tau**2 + 1) ** 0.5
         v = [tau - off, tau + off]
         w = int(np.argmin(np.abs(v)))
         c = 1.0 / (1.0 + v[w] ** 2) ** 0.5  # ... the cosine and sine as given in Section 2.3.1

tests/test_gpcca.py

@@ -378,7 +378,7 @@ def test_objective_1(self, svecs_mu0: np.ndarray, A_mu0_init: np.ndarray, A_mu0:
                 alpha[j + i * (k - 1)] = A_mu0_init[i + 1, j + 1]
 
         act_val = _objective(alpha, svecs_mu0)
-        exp_val = k - np.sum(np.true_divide(np.sum(A_mu0 ** 2, axis=0), A_mu0[0, :]))
+        exp_val = k - np.sum(np.true_divide(np.sum(A_mu0**2, axis=0), A_mu0[0, :]))
 
         assert_allclose(act_val, exp_val)
 
@@ -390,7 +390,7 @@ def test_objective_2(self, svecs_mu1000: np.ndarray, A_mu1000_init: np.ndarray,
                 alpha[j + i * (k - 1)] = A_mu1000_init[i + 1, j + 1]
 
         act_val = _objective(alpha, svecs_mu1000)
-        exp_val = k - np.sum(np.true_divide(np.sum(A_mu1000 ** 2, axis=0), A_mu1000[0, :]))
+        exp_val = k - np.sum(np.true_divide(np.sum(A_mu1000**2, axis=0), A_mu1000[0, :]))
 
         assert_allclose(act_val, exp_val)