Feature/petsc real type (#53)

* Check if `PETSc` is compiled with `--with-scalar-type=real`.

* Update pre-commits.

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

* Remove outdated additional_dependencies.

* Use `codecov` action.

* Fix CI badge and tox.

* Fix linter.

* Ignore vscode config files.

Co-authored-by: Bernhard Reuter <bernhard-reuter@gmx.de>

Author: michalk8

.gitignore

@@ -134,3 +134,6 @@ dmypy.json
 
 # docs
 docs/source/api/*rst
+
+# VSCode
+.vscode/

.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: v0.982
+    rev: v0.991
     hooks:
     -   id: mypy
         additional_dependencies: [numpy==1.20.0, scipy>=1.6.0]
 -   repo: https://github.com/psf/black
-    rev: 22.10.0
+    rev: 22.12.0
     hooks:
     -   id: black
         additional_dependencies: [toml]
 -   repo: https://github.com/timothycrosley/isort
-    rev: 5.10.1
+    rev: 5.11.4
     hooks:
     -   id: isort
         additional_dependencies: [toml]
@@ -28,12 +28,12 @@ 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: v2.4.0
+    rev: v2.5.0
     hooks:
     -   id: pretty-format-yaml
         args: [--autofix, --indent, '4', --preserve-quotes]
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.3.0
+    rev: v4.4.0
     hooks:
     -   id: detect-private-key
     -   id: check-merge-conflict
@@ -55,13 +55,13 @@ repos:
     -   id: check-yaml
     -   id: check-toml
     -   id: requirements-txt-fixer
--   repo: https://gitlab.com/pycqa/flake8
-    rev: 3.9.2
+-   repo: https://github.com/pycqa/flake8
+    rev: 6.0.0
     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-string-format]
 -   repo: https://github.com/myint/autoflake
-    rev: v1.7.1
+    rev: v2.0.0
     hooks:
     -   id: autoflake
         args: [--in-place, --remove-all-unused-imports, --remove-unused-variable, --ignore-init-module-imports]
@@ -77,7 +77,7 @@ repos:
     -   id: blacken-docs
         additional_dependencies: [black==22.10.0]
 -   repo: https://github.com/asottile/pyupgrade
-    rev: v3.0.0
+    rev: v3.3.1
     hooks:
     -   id: pyupgrade
         args: [--py3-plus, --py37-plus]
@@ -91,6 +91,6 @@ repos:
     -   id: rst-directive-colons
     -   id: rst-inline-touching-normal
 -   repo: https://github.com/PyCQA/doc8
-    rev: v1.0.0
+    rev: v1.1.1
     hooks:
     -   id: doc8

README.rst

@@ -16,7 +16,7 @@
    :target: https://doi.org/10.5281/zenodo.6914001
    :alt: Zenodo
 
-.. |CI| image:: https://img.shields.io/github/workflow/status/msmdev/pygpcca/CI/main
+.. |CI| image:: https://img.shields.io/github/actions/workflow/status/msmdev/pygpcca/ci.yml?branch=main
     :target: https://github.com/msmdev/pygpcca/actions
     :alt: CI
 

docs/source/spelling_wordlist.txt

@@ -26,3 +26,8 @@ Röblitz
 Sikorski
 Zuse
 mypy
+numpy
+Zenodo
+Konstantin
+pre
+intersphinx

pygpcca/_sorted_schur.py

@@ -43,15 +43,17 @@
 import numpy as np
 
 from pygpcca.utils._docs import d
+from pygpcca.utils._checks import assert_petsc_real_scalar_type
 from pygpcca._sort_real_schur import sort_real_schur
 from pygpcca.utils._constants import EPS, DEFAULT_SCHUR_METHOD, NO_PETSC_SLEPC_FOUND_MSG
 
 try:
     import petsc4py
     import slepc4py
-except ImportError:
-    petsc4py = None
-    slepc4py = None
+
+    assert_petsc_real_scalar_type()
+except (ImportError, TypeError):
+    petsc4py = slepc4py = None
 
 __all__ = ["sorted_schur"]
 

pygpcca/utils/_checks.py

@@ -1,11 +1,12 @@
 from typing import Tuple, Union, Optional
+import logging
 
 from scipy.sparse import issparse, spmatrix
 import numpy as np
 
 from pygpcca.utils._docs import d
 
-__all__ = ["ensure_ndarray_or_sparse"]
+__all__ = ["ensure_ndarray_or_sparse", "assert_petsc_real_scalar_type"]
 
 
 @d.get_sections(base="assert_array", sections=["Parameters"])
@@ -122,3 +123,23 @@ def ensure_ndarray_or_sparse(
     assert_array(A, shape=shape, uniform=uniform, ndim=ndim, size=size, dtype=dtype, kind=kind)
 
     return A
+
+
+def assert_petsc_real_scalar_type() -> None:
+    """Check if PETSc was compiled using `–with-scalar-type=real`."""
+    try:
+        from petsc4py import PETSc
+
+        if np.isrealobj(PETSc.ScalarType()):
+            return
+        else:
+            raise TypeError(
+                "PETSc was compiled with complex scalar type. "
+                "Please recompile PETSc with `--with-scalar-type=real` or "
+                "provide alternative `PETSC_ARCH=...` with correct scalar type."
+            )
+    except Exception as e:
+        logging.error(
+            f"Unable to determine PETSc's scalar type. Reason: `{e}`. Assuming true, "  # noqa: G004
+            f"but please ensure that PETSc was compiled using `--with-scalar-type=real`.",
+        )

tox.ini

@@ -114,7 +114,7 @@ deps =
     slepc: petsc4py==3.18.0
     slepc: slepc==3.18.0
     slepc: slepc4py==3.18.0
-passenv = TOXENV CI CODECOV_* GITHUB_ACTIONS PETSC_* SLEPC_*
+passenv = TOXENV,CI,CODECOV_*,GITHUB_ACTIONS,PETSC_*,SLEPC_*
 usedevelop = true
 commands = python -m pytest --cov --cov-append --cov-report=term-missing --cov-config={toxinidir}/tox.ini --ignore docs/ {posargs:-vv}