Git workflow and pre-commit updates (#21)

* added cpp check to pr workflow

* testing pre-commit hooks

* added pre-commit hooks for cpp formatting

* added cpp pre-commit hook, updated readme

* Added pre-commit hooks for cpp code analysis

* update requirements

* update github workflows

* update github workflows

* update github workflows

* update github workflows

* wip

* wip

* Fix C++ files from cppcheck

---------

Co-authored-by: Michelle Richer <[email protected]>

.pre-commit-config.yaml

@@ -1,38 +1,59 @@
+exclude: |
+  (?x)^(
+    src/perm-mv0\.h$ |
+    src/kperm-gray\.h$ |
+    src/swap\.h$
+  )
+
+ci:
+  skip:
+    [cppcheck, cpplint, clang-format]
+
 repos:
-- repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.5.0
-  hooks:
-    - id: check-added-large-files                   # prevents giant files from being commit
-    - id: check-ast                                 # Check whether files parse as valid python.
-    - id: check-case-conflict                       # Checks conflict case-insensitive
-    - id: check-executables-have-shebangs
-    - id: check-json
-    - id: check-merge-conflict
-    - id: check-symlinks                            # Check for symlinks which don't point
-    - id: check-toml
-    - id: check-vcs-permalinks
-    - id: debug-statements                          # Check for debugger imports and py37 breakpt
-    - id: detect-private-key                        # Checks for the existence of private keys.
-    - id: destroyed-symlinks
-    - id: end-of-file-fixer                         # Makes sure files end in a newline
-    - id: fix-byte-order-marker                     # Removes UTF-8 byte order marker
-    - id: mixed-line-ending                         # Replaces or checks mixed line ending.
-    - id: pretty-format-json                        # Checks JSON are pretty
-      args: ["--autofix", "--no-sort-keys"]
-    - id: trailing-whitespace                       # Trims trailing whitespace.
-- repo: https://github.com/Lucas-C/pre-commit-hooks
-  rev: v1.5.4
-  hooks:
-    - id: remove-crlf
-- repo: https://github.com/psf/black
-  rev: 23.12.1
-  hooks:
-    - id: black
-- repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: 'v0.1.9'
-  hooks:
-    - id: ruff
-- repo: https://github.com/python-jsonschema/check-jsonschema
-  rev: 0.27.3
-  hooks:
-    - id: check-github-workflows
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: check-added-large-files                   # prevents giant files from being commit
+      - id: check-ast                                 # Check whether files parse as valid python.
+      - id: check-case-conflict                       # Checks conflict case-insensitive
+      - id: check-executables-have-shebangs
+      - id: check-json
+      - id: check-merge-conflict
+      - id: check-symlinks                            # Check for symlinks which don't point
+      - id: check-toml
+      - id: check-vcs-permalinks
+      - id: debug-statements                          # Check for debugger imports and py37 breakpt
+      - id: detect-private-key                        # Checks for the existence of private keys
+      - id: destroyed-symlinks
+      - id: end-of-file-fixer                         # Makes sure files end in a newline
+      - id: fix-byte-order-marker                     # Removes UTF-8 byte order marker
+      - id: mixed-line-ending                         # Replaces or checks mixed line ending
+      - id: pretty-format-json                        # Checks JSON are pretty
+        args: ["--autofix", "--no-sort-keys"]
+      - id: trailing-whitespace                       # Trims trailing whitespace
+  - repo: https://github.com/Lucas-C/pre-commit-hooks
+    rev: v1.5.5
+    hooks:
+      - id: remove-crlf
+  - repo: https://github.com/psf/black
+    rev: 24.2.0
+    hooks:
+      - id: black
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.3.2
+    hooks:
+      - id: ruff
+  - repo: https://github.com/python-jsonschema/check-jsonschema
+    rev: 0.28.0
+    hooks:
+      - id: check-github-workflows
+  - repo: https://github.com/pocc/pre-commit-hooks
+    rev: v1.3.5
+    hooks:
+      - id: cppcheck
+        args: ["--inline-suppr", "--suppress=missingIncludeSystem",
+          "--suppress=*:src/swap.h", "--suppress=*:src/perm-mv0.h", "--suppress=*:src/kperm-gray.h"]
+      - id: cpplint
+        args: ["--root=src", "--filter=-build/include_subdir"]
+      - id: clang-format
+        args: ["-i", "-style={BasedOnStyle: google, IndentWidth: 4}"]

README.md

@@ -1,5 +1,8 @@
 [![Python 3](http://img.shields.io/badge/python-3-blue.svg)](https://docs.python.org/3/)
 [![gcc](https://img.shields.io/badge/-C++-blue?logo=cplusplus)](https://gcc.gnu.org/)
+[![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white)](https://github.com/theochem/matrix-permanent/actions/workflows/pull_request.yml)
+[![GNU GPLv3](https://img.shields.io/badge/license-%20%20GNU%20GPLv3%20-green?style=plastic)](https://www.gnu.org/licenses/gpl-3.0.en.html)
+
 
 # Permanent
 

permanent/__init__.py

@@ -1,6 +1,5 @@
 r"""Module for computing the permanents of matrices."""
 
-
 __all__ = [
     "opt",
     "combinatoric",

src/permanent.cc

@@ -1,20 +1,48 @@
-#include <complex>
+/* Copyright 2034 QC-Devs (GPLv3) */
 
 #include "permanent.h"
 
+#include <complex>
+
+template double combinatoric<double>(const std::size_t, const std::size_t,
+                                     const double *);
+
+template double combinatoric_rectangular<double>(const std::size_t,
+                                                 const std::size_t,
+                                                 const double *);
+
+template double glynn<double>(const std::size_t, const std::size_t,
+                              const double *);
+
+template double glynn_rectangular<double>(const std::size_t, const std::size_t,
+                                          const double *);
+
+template double ryser<double>(const std::size_t, const std::size_t,
+                              const double *);
+
+template double ryser_rectangular<double>(const std::size_t, const std::size_t,
+                                          const double *);
+
+template double opt<double>(const std::size_t, const std::size_t,
+                            const double *);
+
+template std::complex<double> combinatoric<std::complex<double>>(
+    const std::size_t, const std::size_t, const std::complex<double> *);
+
+template std::complex<double> combinatoric_rectangular<std::complex<double>>(
+    const std::size_t, const std::size_t, const std::complex<double> *);
+
+template std::complex<double> glynn<std::complex<double>>(
+    const std::size_t, const std::size_t, const std::complex<double> *);
+
+template std::complex<double> glynn_rectangular<std::complex<double>>(
+    const std::size_t, const std::size_t, const std::complex<double> *);
+
+template std::complex<double> ryser<std::complex<double>>(
+    const std::size_t, const std::size_t, const std::complex<double> *);
+
+template std::complex<double> ryser_rectangular<std::complex<double>>(
+    const std::size_t, const std::size_t, const std::complex<double> *);
 
-template double combinatoric<double>(const std::size_t, const std::size_t, double *const);
-template double combinatoric_rectangular<double>(const std::size_t, const std::size_t, double *const);
-template double glynn<double>(const std::size_t, const std::size_t, double *const);
-template double glynn_rectangular<double>(const std::size_t, const std::size_t, double *const);
-template double ryser<double>(const std::size_t, const std::size_t, double *const);
-template double ryser_rectangular<double>(const std::size_t, const std::size_t, double *const);
-template double opt<double>(const std::size_t, const std::size_t, double *const);
-
-template std::complex<double> combinatoric<std::complex<double>>(const std::size_t, const std::size_t, std::complex<double> *const);
-template std::complex<double> combinatoric_rectangular<std::complex<double>>(const std::size_t, const std::size_t, std::complex<double> *const);
-template std::complex<double> glynn<std::complex<double>>(const std::size_t, const std::size_t, std::complex<double> *const);
-template std::complex<double> glynn_rectangular<std::complex<double>>(const std::size_t, const std::size_t, std::complex<double> *const);
-template std::complex<double> ryser<std::complex<double>>(const std::size_t, const std::size_t, std::complex<double> *const);
-template std::complex<double> ryser_rectangular<std::complex<double>>(const std::size_t, const std::size_t, std::complex<double> *const);
-template std::complex<double> opt<std::complex<double>>(const std::size_t, const std::size_t, std::complex<double> *const);
+template std::complex<double> opt<std::complex<double>>(
+    const std::size_t, const std::size_t, const std::complex<double> *);