pre-commit run --all-files; fix errs and spelling

KingsburyLab · Jul 31, 2023 · 4fc0057 · 4fc0057
1 parent 01d137e
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -15,7 +15,7 @@ repos:
     rev: v0.0.280
     hooks:
       - id: ruff
-        args: [--fix, --ignore, D]
+        args: [--fix, --ignore, "D,E501"]
 
   - repo: https://github.com/psf/black
     rev: 23.7.0
@@ -39,3 +39,4 @@ repos:
       - id: end-of-file-fixer
       - id: mixed-line-ending
       - id: trailing-whitespace
+        exclude: ".tsv"
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -19,7 +19,7 @@
 - Add more comprehensive platform testing via `tox`
 - Replace `water_properties.py` with [iapws](https://github.com/jjgomera/iapws) package
 - Replace elements.py with `pymatgen.core.periodic_table`
-- Add `pymatgen` as a depedency
+- Add `pymatgen` as a dependency
 - Migrate all tests to `pytest`
 - Add pre-commit configuration and lint with `black`
 - Update packaging to use [pyscaffold](https://pyscaffold.org/en/stable/index.html)
@@ -32,7 +32,7 @@
 - Added methods for calculating the osmolarity or osmolality of aSolution
 - Add the ability to filter list_concentrations() to show onlycations or anions
 - Add two medical solutions - normal saline and Ringer's lacate -to the autogenerate method
-- Add shorthand abbreviations for 'seawater' and 'wastewater' inthe autogenerate method
+- Add shorthand abbreviations for 'seawater' and 'wastewater' in the autogenerate method
 - Enhance automatic test suite to compare results withexperimental data based on relative error
 - Add test suites for the effective Pitzer model and amulticomponent salt solution
 - DEPRECATED get_mole_fraction. Use get_amount() instead

diff --git a/README.md b/README.md
@@ -13,7 +13,7 @@ pyEQL is a Python library that provides tools for modeling aqueous electrolyte
 solutions. It allows the user to manipulate solutions as Python
 objects, providing methods to populate them with solutes, calculate
 species-specific properties (such as activity and diffusion coefficients),
-and retreive bulk properties (such as density, conductivity, or volume).
+and retrieve bulk properties (such as density, conductivity, or volume).
 
 ![pyeql demo](pyeql-demo.png)
 

diff --git a/docs/conf.py b/docs/conf.py
@@ -8,8 +8,8 @@
 # serve to show the default.
 
 import os
-import sys
 import shutil
+import sys
 
 # -- Path setup --------------------------------------------------------------
 
@@ -52,7 +52,7 @@
 
     apidoc.main(args)
 except Exception as e:
-    print("Running `sphinx-apidoc` failed!\n{}".format(e))
+    print(f"Running `sphinx-apidoc` failed!\n{e}")
 
 # -- General configuration ---------------------------------------------------
 
@@ -114,7 +114,7 @@
 #
 # version: The short X.Y version.
 # release: The full version, including alpha/beta/rc tags.
-# If you don’t need the separation provided between version and release,
+# If you don`t need the separation provided between version and release,
 # just set them both to the same value.
 try:
     from pyEQL import __version__ as version
@@ -301,4 +301,4 @@
     "pyscaffold": ("https://pyscaffold.org/en/stable", None),
 }
 
-print(f"loading configurations for {project} {version} ...", file=sys.stderr)
+print(f"loading configurations for {project} {version} ...", file=sys.stderr)
diff --git a/docs/database.rst b/docs/database.rst
@@ -19,7 +19,7 @@ following parameters for some common electrolytes:
 Basics
 ======
 
-The Paramsdb class creates a container for parameters. Each paramter
+The Paramsdb class creates a container for parameters. Each parameter
 is an object which contains not only the value, but also information about
 the units, the reference, and the conditions of measurement. paramsdb() also
 defines several methods that are helpful for retrieving parameters.

diff --git a/docs/index.md b/docs/index.md
@@ -7,7 +7,7 @@ Add a short description here!
 
 > This is the main page of your project's [Sphinx] documentation. It is
 > formatted in [Markdown]. Add additional pages by creating md-files in
-> `docs` or rst-files (formated in [reStructuredText]) and adding links to
+> `docs` or rst-files (formatted in [reStructuredText]) and adding links to
 > them in the `Contents` section below.
 >
 > Please check [Sphinx], [recommonmark] and [autostructify] for more information

diff --git a/examples/pyEQL_demo_1.ipynb b/examples/pyEQL_demo_1.ipynb
@@ -126,7 +126,7 @@
     "<p style='margin-top:1em; text-align:center'>\n",
     "<b>NOTICE</b></p>\n",
     "<p style='margin-left:1em;'>\n",
-    "The example below is using a *development* version of `pyEQL`. There are some subtle differences compared to the relased version. Specifically:\n",
+    "The example below is using a *development* version of `pyEQL`. There are some subtle differences compared to the released version. Specifically:\n",
     "\n",
     "- The stable version does not support the `engine` keyword argument\n",
     "- The stable version requires solutes to be input as list of lists rather than a dictionary\n",

diff --git a/pyproject.toml b/pyproject.toml
@@ -13,7 +13,7 @@ line-length = 120
 [tool.ruff]
 target-version = "py37"
 line-length = 120
-exclude = ["src/pyEQL/parameter.py", "src/pyEQL/chemical_formula.py", "src/pyEQL/database.py"] # TODO - remove this line once files deprecated
+exclude = ["src/pyEQL/parameter.py", "src/pyEQL/chemical_formula.py", "src/pyEQL/database.py", ".tsv"] # TODO - remove this line once files deprecated
 select = [
   "B",    # flake8-bugbear
   "C4",   # flake8-comprehensions
@@ -84,5 +84,5 @@ explicit_package_bases = true
 no_implicit_optional = false
 
 [tool.codespell]
-ignore-words-list = "ot,nin"
-skip = 'docs/CHANGELOG.md,tests/test_files/*'
+ignore-words-list = "nd"
+skip = 'tests/test_files/*'
diff --git a/src/pyEQL/__init__.py b/src/pyEQL/__init__.py
@@ -1,5 +1,8 @@
 import sys
 
+from pint import UnitRegistry
+from pkg_resources import resource_filename
+
 if sys.version_info[:2] >= (3, 8):
     # TODO: Import directly (no need for conditional) when `python_requires = >= 3.8`
     from importlib.metadata import PackageNotFoundError, version  # pragma: no cover
@@ -26,8 +29,6 @@
 :license: LGPL, see LICENSE for more details.
 
 """
-from pint import UnitRegistry
-from pkg_resources import resource_filename
 
 # Units handling
 # per the pint documentation, it's important that pint and its associated Unit
@@ -51,5 +52,5 @@
 # initialize the parameters database
 paramsDB = Paramsdb()
 
-from pyEQL.functions import *  # noqa: F401, E402, F403
-from pyEQL.solution import Solution  # noqa: F401, E402
+from pyEQL.functions import *  # noqa: E402, F403
+from pyEQL.solution import Solution  # noqa: E402