Update pre-commits (#54)

* Update pre-commits

* Fix mypy error

* Update tox, ignore links

Author: michalk8

.pre-commit-config.yaml

@@ -7,17 +7,17 @@ default_stages:
 minimum_pre_commit_version: 2.9.0
 repos:
 -   repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v0.991
+    rev: v1.0.0
     hooks:
     -   id: mypy
         additional_dependencies: [numpy==1.20.0, scipy>=1.6.0]
 -   repo: https://github.com/psf/black
-    rev: 22.12.0
+    rev: 23.1.0
     hooks:
     -   id: black
         additional_dependencies: [toml]
 -   repo: https://github.com/timothycrosley/isort
-    rev: 5.11.4
+    rev: 5.12.0
     hooks:
     -   id: isort
         additional_dependencies: [toml]
@@ -28,7 +28,7 @@ repos:
     -   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-string-format]
 -   repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks
-    rev: v2.5.0
+    rev: v2.6.0
     hooks:
     -   id: pretty-format-yaml
         args: [--autofix, --indent, '4', --preserve-quotes]
@@ -61,7 +61,7 @@ repos:
     -   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-string-format]
 -   repo: https://github.com/myint/autoflake
-    rev: v2.0.0
+    rev: v2.0.1
     hooks:
     -   id: autoflake
         args: [--in-place, --remove-all-unused-imports, --remove-unused-variable, --ignore-init-module-imports]
@@ -72,17 +72,17 @@ repos:
         name: Check executable files use .sh extension
         types: [shell, executable]
 -   repo: https://github.com/asottile/blacken-docs
-    rev: v1.12.1
+    rev: 1.13.0
     hooks:
     -   id: blacken-docs
-        additional_dependencies: [black==22.10.0]
+        additional_dependencies: [black==23.1.0]
 -   repo: https://github.com/asottile/pyupgrade
     rev: v3.3.1
     hooks:
     -   id: pyupgrade
         args: [--py3-plus, --py37-plus]
 -   repo: https://github.com/pre-commit/pygrep-hooks
-    rev: v1.9.0
+    rev: v1.10.0
     hooks:
     -   id: python-no-eval
     -   id: python-use-type-annotations

docs/requirements.txt

@@ -1,6 +1,6 @@
 -r ../requirements.txt
 nbsphinx>=0.8
-sphinx==4.0.2  # https://github.com/spatialaudio/nbsphinx/issues/584
+sphinx>=5
 sphinx-autodoc-annotation
 sphinx-autodoc-typehints>=1.10.3
 sphinx-copybutton

docs/source/conf.py

@@ -19,7 +19,7 @@
 
 import pygpcca  # noqa: E402
 
-needs_sphinx = "3.3"
+needs_sphinx = "5"
 # -- Project information -----------------------------------------------------
 
 project = "pyGPCCA"
@@ -115,6 +115,7 @@
 
 # linkcheck
 linkcheck_anchors = False  # problem with specifying lines on GitHub in `acknowledgments.rst`
+linkcheck_ignore = ["https://doi.org/10.1021/acs.jctc.8b00079", "https://pubs.acs.org/doi/abs/10.1021/acs.jctc.8b00079"]
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,

pygpcca/_gpcca.py

@@ -471,7 +471,7 @@ def _objective(alpha: np.ndarray, X: np.ndarray) -> float:
 
     # Compute value of the objective function.
     # from Matlab: optval = m - trace( diag(1 ./ A(1,:)) * (A' * A) )
-    return m - np.trace(np.diag(1.0 / rot_mat[0, :]).dot(rot_mat.conj().T.dot(rot_mat)))  # type: ignore[no-any-return]
+    return m - np.trace(np.diag(1.0 / rot_mat[0, :]).dot(rot_mat.conj().T.dot(rot_mat)))  # type: ignore[return-value]
 
 
 @d.dedent

pygpcca/utils/_utils.py

@@ -410,7 +410,6 @@ def stationary_distribution_from_eigenvector(P: np.ndarray) -> np.ndarray:
 
 
 def _is_stationary_distribution(T: Union[np.ndarray, spmatrix], pi: np.ndarray) -> bool:
-
     # check the shapes
     if not T.shape[0] == T.shape[1] or not T.shape[0] == pi.shape[0]:
         raise ValueError("Shape mismatch.")

tests/test_gpcca.py

@@ -851,7 +851,6 @@ def test_P_2_LM(
         assert_allclose(g.dominant_eigenvalues, top_eigenvalues_P_2_LM[:n_m])
 
     def test_split_warning_LM(self, P_2: np.ndarray):
-
         g = GPCCA(P_2, eta=None, z="LM")
 
         with pytest.warns(
@@ -880,7 +879,6 @@ def test_split_warning_LM(self, P_2: np.ndarray):
             g.optimize({"m_min": 11, "m_max": 12})
 
     def test_split_raise_LM(self, P_2: np.ndarray):
-
         g = GPCCA(P_2, eta=None, z="LM")
 
         with pytest.raises(
@@ -939,7 +937,6 @@ def test_P_2_LR(
         assert_allclose(g.dominant_eigenvalues, top_eigenvalues_P_2_LR[:n_m])
 
     def test_split_warning_LR(self, P_2: np.ndarray):
-
         g = GPCCA(P_2, eta=None, z="LR")
 
         with pytest.warns(
@@ -962,7 +959,6 @@ def test_split_warning_LR(self, P_2: np.ndarray):
             g.optimize({"m_min": 10, "m_max": 12})
 
     def test_split_raise_LR(self, P_2: np.ndarray):
-
         g = GPCCA(P_2, eta=None, z="LR")
 
         with pytest.raises(
@@ -985,7 +981,6 @@ def test_split_raise_LR(self, P_2: np.ndarray):
             g.optimize(11)
 
     def test_optimize_range_all_invalid(self, P_2: np.ndarray, mocker):
-
         g = GPCCA(P_2, eta=None, z="LR")
 
         mocker.patch(

tests/test_stat_dist.py

@@ -91,7 +91,6 @@ def test_stat_dist_check(
         test_matrix_2: np.ndarray,
         test_matrix_2_stationary_distribution,
     ):
-
         assert _is_stationary_distribution(test_matrix_1, test_matrix_1_stationary_distribution)
         assert _is_stationary_distribution(test_matrix_2, test_matrix_2_stationary_distribution)
 

tests/test_utils.py

@@ -17,7 +17,6 @@ def test_eigendecomposition_slepsc_regression(
         test_matrix_2_eigenvalues: np.ndarray,
         test_matrix_2_eigenvectors: np.ndarray,
     ):
-
         eigs_1, vecs_1 = _eigs_slepc(csr_matrix(test_matrix_1), k=11)
         assert_allclose(
             test_matrix_1_eigenvalues,

tox.ini

@@ -139,43 +139,39 @@ commands =
 
 [testenv:lint]
 description = Perform linting.
-basepython = python3.8
 deps = pre-commit>=2.7.1
 skip_install = true
 commands = pre-commit run --all-files --show-diff-on-failure {posargs:}
 
 [testenv:clean-docs]
 description = Clean the documentation artifacts.
-basepython = python3.8
 deps =
 skip_install = true
 changedir = {toxinidir}/docs
-whitelist_externals = make
+allowlist_externals = make
 commands = make clean
 
 [testenv:check-docs]
 description = Check the links in the docs.
-basepython = python3.8
 deps = -r{toxinidir}/docs/requirements.txt
 skip_install = true
-whitelist_externals = sphinx-build
+allowlist_externals = sphinx-build
+pass_env = PYENCHANT_LIBRARY_PATH
 commands =
     sphinx-build -b spelling {toxinidir}/docs/source {toxinidir}/docs/build/spellcheck
     sphinx-build -q -W --keep-going -b linkcheck {toxinidir}/docs/source {toxinidir}/docs/build/linkcheck
 
 [testenv:docs]
 description = Build the documentation.
-basepython = python3.8
 skip_install = true
 deps = -r{toxinidir}/docs/requirements.txt
-whitelist_externals = sphinx-build
+allowlist_externals = sphinx-build
 commands =
     sphinx-build --color -b html {toxinidir}/docs/source {toxinidir}/docs/build/html
     python -c 'import pathlib; print(f"Documentation is available under:", pathlib.Path(f"{toxinidir}") / "docs" / "build" / "html" / "index.html")'
 
 [testenv:readme]
 description = Check if README renders on PyPI.
-basepython = python3.8
 deps = twine >= 1.12.1
 skip_install = true
 commands =