Refactor code, udpate github actions. (#4)

.github/workflows/pypi-publish.yml

@@ -48,4 +48,4 @@ jobs:
       uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
       with:
         user: __token__
-        password: ${{ secrets.PYPI_PASSWORD }}
+        password: ${{ secrets.PYPI_PASSWORD }}

.github/workflows/pypi-test.yml

@@ -1,7 +1,7 @@
 # This workflow will install Python dependencies, run tests and lint with a single version of Python
 # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
 
-name: test the library
+name: Test the library
 
 on:
   push:
@@ -13,13 +13,18 @@ jobs:
   build:
 
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [ '3.8', '3.9', '3.10', '3.11', '3.12' ]
 
+    name: Python ${{ matrix.python-version }}
     steps:
     - uses: actions/checkout@v2
-    - name: Set up Python 3.9
+    - name: Setup Python
       uses: actions/setup-python@v2
       with:
-        python-version: 3.9
+        python-version: ${{ matrix.python-version }}
+        cache: 'pip'
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
@@ -32,4 +37,4 @@ jobs:
     #     # flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Test with tox
       run: |
-        tox
+        tox

.pre-commit-config.yaml

@@ -0,0 +1,52 @@
+exclude: '^docs/conf.py'
+
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.5.0
+  hooks:
+  - id: trailing-whitespace
+  - id: check-added-large-files
+  - id: check-ast
+  - id: check-json
+  - id: check-merge-conflict
+  - id: check-xml
+  - id: check-yaml
+  - id: debug-statements
+  - id: end-of-file-fixer
+  - id: requirements-txt-fixer
+  - id: mixed-line-ending
+    args: ['--fix=auto']  # replace 'auto' with 'lf' to enforce Linux/Mac line endings or 'crlf' for Windows
+
+- repo: https://github.com/PyCQA/docformatter
+  rev: v1.7.5
+  hooks:
+    - id: docformatter
+      additional_dependencies: [tomli]
+      args: [--in-place, --wrap-descriptions=120, --wrap-summaries=120]
+      # --config, ./pyproject.toml
+
+- repo: https://github.com/psf/black
+  rev: 23.12.1
+  hooks:
+  - id: black
+    language_version: python3
+
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.1.9
+  hooks:
+    - id: ruff
+      args: [--fix, --exit-non-zero-on-fix]
+
+## If like to embrace black styles even in the docs:
+# - repo: https://github.com/asottile/blacken-docs
+#   rev: v1.13.0
+#   hooks:
+#   - id: blacken-docs
+#     additional_dependencies: [black]
+
+## Check for misspells in documentation files:
+# - repo: https://github.com/codespell-project/codespell
+#   rev: v2.2.5
+#   hooks:
+#   - id: codespell

CHANGELOG.md

@@ -1,11 +1,11 @@
 # Changelog
 
 
-## Version 0.2.0 
+## Version 0.2.0
 - Support multi apply
 
 ## Version 0.1 (development)
 
 - first release
-- performs some basic operations over numpy or scipy matrices. 
+- performs some basic operations over numpy or scipy matrices.
 - provides apply method so user can extend the underlying logic to any function

docs/conf.py

@@ -169,6 +169,15 @@ def setup(app):
 # If this is True, todo emits a warning for each TODO entries. The default is False.
 todo_emit_warnings = True
 
+autodoc_default_options = {
+      'special-members': True,
+      'undoc-members': False,
+      'exclude-members': '__weakref__, __dict__, __str__, __module__, __init__'
+  }
+
+autosummary_generate = True
+autosummary_imported_members = True
+
 
 # -- Options for HTML output -------------------------------------------------
 

docs/requirements.txt

@@ -1,7 +1,7 @@
+furo
 # Requirements file for ReadTheDocs, check .readthedocs.yml.
 # To build the module reference correctly, make sure every external package
 # under `install_requires` in `setup.cfg` is also listed here!
 # sphinx_rtd_theme
 recommonmark
 sphinx>=3.2.1
-furo

docs/tutorial.md

@@ -50,7 +50,7 @@ apply(nz_func, mat, axis=1)
 
 ## Multiple functions
 
-`mopsy` also supports applying multiple functions at the same time. 
+`mopsy` also supports applying multiple functions at the same time.
 
 ```python
 from mopsy import multi_apply
@@ -73,4 +73,4 @@ tmat_wrow = append_row(mat, np.array([0, 0, 0, 0, 0]))
 tmat_wcol = append_col(mat, np.array([[0], [0], [0], [0], [0]]))
 ```
 
-That's all for today! 
+That's all for today!

pyproject.toml

@@ -6,3 +6,18 @@ build-backend = "setuptools.build_meta"
 [tool.setuptools_scm]
 # See configuration details in https://github.com/pypa/setuptools_scm
 version_scheme = "no-guess-dev"
+
+[tool.ruff]
+line-length = 120
+src = ["src"]
+exclude = ["tests"]
+extend-ignore = ["F821"]
+
+[tool.ruff.pydocstyle]
+convention = "google"
+
+[tool.ruff.per-file-ignores]
+"__init__.py" = ["E402", "F401"]
+
+[tool.black]
+force-exclude = "__init__.py"

setup.py

@@ -1,10 +1,8 @@
-"""
-    Setup file for mopsy.
-    Use setup.cfg to configure your project.
+"""Setup file for mopsy. Use setup.cfg to configure your project.
 
-    This file was generated with PyScaffold 4.1.1.
-    PyScaffold helps you to put up the scaffold of your new Python project.
-    Learn more under: https://pyscaffold.org/
+This file was generated with PyScaffold 4.1.1.
+PyScaffold helps you to put up the scaffold of your new Python project.
+Learn more under: https://pyscaffold.org/
 """
 from setuptools import setup
 

src/mopsy/__init__.py

@@ -21,5 +21,5 @@
 finally:
     del version, PackageNotFoundError
 
-from .helpers import *
-from .adders import *
+from .helpers import *  # noqa: F403
+from .adders import *  # noqa: F403

src/mopsy/adders.py

@@ -1,10 +1,10 @@
-from .sops import Sops
-from .checkutils import check_axis
-
 from typing import Union
 
-import scipy as sp
 import numpy as np
+import scipy as sp
+
+from .checkutils import check_axis
+from .sops import Sops
 
 __author__ = "jkanche"
 __copyright__ = "jkanche"
@@ -14,56 +14,69 @@
 def append_row(
     mat: sp.sparse.spmatrix, row: Union[sp.sparse.spmatrix, np.ndarray]
 ) -> sp.sparse.spmatrix:
-    """A generic append function for sparse matrices
+    """A generic append function for sparse matrices.
 
     Args:
-        mat (scipy.sparse.spmatrix): sparse matrix
-        row (Union[sp.sparse.spmatrix, np.ndarray]): rows to append
+        mat:
+            Sparse matrix.
+        row:
+            Rows to append.
 
     Raises:
-        TypeError: if axis is neither 0 nor 1
+        TypeError:
+            If axis is neither 0 nor 1.
 
     Returns:
-        scipy.sparse.spmatrix: new matrix
+        A new sparse matrix, usually the same type as the input matrix.
     """
-    return sparse_append(mat=mat, rowOrCols=row, axis=0)
+    return sparse_append(mat=mat, row_or_column=row, axis=0)
 
 
 def append_col(
     mat: sp.sparse.spmatrix, col: Union[sp.sparse.spmatrix, np.ndarray]
 ) -> sp.sparse.spmatrix:
-    """A generic append function for sparse matrices
+    """A generic append function for sparse matrices.
 
     Args:
-        mat (scipy.sparse.spmatrix): sparse matrix
-        col (Union[sp.sparse.spmatrix, np.ndarray]): columns to append
+        mat:
+            Sparse matrix.
+
+        col:
+            Columns to append.
 
     Raises:
-        TypeError: if axis is neither 0 nor 1
+        TypeError:
+            If axis is neither 0 nor 1.
 
     Returns:
-        scipy.sparse.spmatrix: new matrix
+        A new sparse matrix, usually the same type as the input matrix.
     """
-    return sparse_append(mat=mat, rowOrCols=col, axis=1)
+    return sparse_append(mat=mat, row_or_column=col, axis=1)
 
 
 def sparse_append(
     mat: sp.sparse.spmatrix,
-    rowOrCols: Union[sp.sparse.spmatrix, np.ndarray],
+    row_or_column: Union[sp.sparse.spmatrix, np.ndarray],
     axis: Union[int, bool],
 ) -> sp.sparse.spmatrix:
-    """A generic append function for sparse matrices
+    """A generic append function for sparse matrices.
 
     Args:
-        mat (scipy.sparse.spmatrix): sparse matrix
-        rowOrCols (Union[sp.sparse.spmatrix, np.ndarray]): rows to append
-        axis (Union[int, bool]): 0 for rows, 1 for columns.
+        mat:
+            Sparse matrix.
+
+        row_or_column:
+            Rows or columns to append.
+
+        axis:
+            0 for rows, 1 for columns.
 
     Raises:
-        TypeError: if axis is neither 0 nor 1
+        TypeError:
+            If axis is neither 0 nor 1.
 
     Returns:
-        scipy.sparse.spmatrix: new matrix
+        A new sparse matrix, usually the same type as the input matrix.
     """
 
     if not isinstance(mat, sp.sparse.spmatrix):
@@ -75,19 +88,19 @@ def sparse_append(
 
     new_mat = None
     if axis == 0:
-        if mat.shape[0] != rowOrCols.shape[0]:
+        if mat.shape[0] != row_or_column.shape[0]:
             raise TypeError(
-                f"matrix and new row do not have the same length. matrix: {mat.shape[0]}, row: {row.shape[0]}"
+                "Matrix and new row do not have the same shape along the first dimension."
             )
 
-        new_mat = sp.sparse.vstack([mat, rowOrCols])
+        new_mat = sp.sparse.vstack([mat, row_or_column])
     else:
-        if mat.shape[1] != rowOrCols.shape[0]:
+        if mat.shape[1] != row_or_column.shape[0]:
             raise TypeError(
-                f"matrix and new row do not have the same length. matrix: {mat.shape[1]}, row: {row.shape[1]}"
+                "Matrix and new row do not have the same shape along the second dimension."
             )
 
-        new_mat = sp.sparse.hstack([mat, rowOrCols])
+        new_mat = sp.sparse.hstack([mat, row_or_column])
 
     if new_mat is None:
         raise Exception("This should never happen")

src/mopsy/checkutils.py

@@ -8,13 +8,15 @@
 
 
 def check_axis(axis: Union[int, bool]):
-    """Check if axis has a correct value
+    """Check if axis has a correct value.
 
     Args:
-        axis (Union[int, bool]): axis, 0 for rows, 1 for columns
+        axis:
+            Axis, 0 for rows, 1 for columns
 
     Raises:
-        TypeError: if axis is neither 0 nor 1
+        ValueError:
+            If axis is neither 0 nor 1
     """
     if not (axis == 0 or axis == 1):
-        raise TypeError(f"axis is neither 0 or 1, provided {axis}")
+        raise ValueError(f"'axis' is neither 0 or 1, provided {axis}.")