Configure automatic spelling check via codespell within pre-commit (#121)

* configure codespell at pyproject.toml and pre-commit

* Add news

* Fix ignore wording

* Do not use full sentences in ignore words

* [pre-commit.ci] auto fixes from pre-commit hooks

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: bobleesj

.codespell/ignore_lines.txt

@@ -0,0 +1,2 @@
+;; Please include filenames and explanations for each ignored line.
+;; See https://docs.openverse.org/meta/codespell.html for docs.

.codespell/ignore_words.txt

@@ -0,0 +1,11 @@
+;; Please include explanations for each ignored word (lowercase).
+;; See https://docs.openverse.org/meta/codespell.html for docs.
+
+;; abbreviation for "materials" often used in a journal title
+mater
+
+;; alternative use of socioeconomic
+socio-economic
+
+;; Frobenius norm used in np.linalg.norm
+fro

.pre-commit-config.yaml

@@ -44,3 +44,9 @@ repos:
         name: Prevent Commit to Main Branch
         args: ["--branch", "main"]
         stages: [pre-commit]
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.3.0
+    hooks:
+    - id: codespell
+      additional_dependencies:
+        - tomli

CHANGELOG.rst

@@ -9,8 +9,8 @@ Release Notes
 
 **Fixed:**
 
-* Updated REAMDE instructions for pip and conda-forge install
-* Updated REAMDE instructions to check for successful installation
+* Updated README instructions for pip and conda-forge install
+* Updated README instructions to check for successful installation
 
 
 0.1.2

README.rst

@@ -127,7 +127,7 @@ trying to commit again.
 
 Improvements and fixes are always appreciated.
 
-Before contribuing, please read our `Code of Conduct <https://github.com/diffpy/diffpy.snmf/blob/main/CODE_OF_CONDUCT.rst>`_.
+Before contributing, please read our `Code of Conduct <https://github.com/diffpy/diffpy.snmf/blob/main/CODE_OF_CONDUCT.rst>`_.
 
 Contact
 -------

doc/source/quickstart.rst

@@ -1,6 +1,6 @@
 .. _quick_start:
 
-Tutorial (To be addded)
+Tutorial (To be added)
 #################
 
 Welcome! This will be a quick tutorial to accquaint users with `snmf`.
@@ -18,5 +18,5 @@ Add extra tutorials here
 Bug Reports
 ===========
 
-Please enjoy using our software! If you come accross any bugs in the
+Please enjoy using our software! If you come across any bugs in the
 application, please report them to [email protected].

news/codespell.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* Add spelling check pre-commit via Codespell
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

pyproject.toml

@@ -54,6 +54,11 @@ namespaces = false  # to disable scanning PEP 420 namespaces (true by default)
 [tool.setuptools.dynamic]
 dependencies = {file = ["requirements/pip.txt"]}
 
+[tool.codespell]
+exclude-file = ".codespell/ignore_lines.txt"
+ignore-words = ".codespell/ignore_words.txt"
+skip = "*.cif"
+
 [tool.black]
 line-length = 115
 include = '\.pyi?$'

src/diffpy/snmf/polynomials.py

@@ -8,7 +8,7 @@ def rooth(linear_coefficient, constant_term):
 
     Parameters
     ----------
-    linear_coefficient: nd array like of floats
+    linear_coefficient: ndarray like of floats
         The matrix coefficient of the linear term
     constant_term: 0d array like, 1d array like of floats or scalar
         The constant scalar term of the problem

src/diffpy/snmf/subroutines.py

@@ -362,7 +362,7 @@ def update_weights_matrix(
       The matrx containing the stretching factors of the calculated component signals. Has dimensions K x M
       where K is the number of component signals and M is the number of XRD/PDF patterns.
 
-    component_matrix: 2d array lik
+    component_matrix: 2d array like
       The matrix containing the unstretched calculated component signals. Has dimensions N x K where N is the
       length of the signals and K is the number of component signals.