Add Pre-commit hooks (#23)

* pre-commit hooks

* ruff formatting

* ignore E402, remove meta.yaml reference

.pre-commit-config.yaml

@@ -0,0 +1,37 @@
+ci:
+    autofix_prs: false
+    autoupdate_schedule: monthly
+
+repos:
+-   repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.4.3
+    hooks:
+     # Run the linter.
+     - id: ruff
+       types_or: [ python, pyi, jupyter ]
+       args: [ --fix ]
+     # Run the formatter.
+     - id: ruff-format
+       types_or: [ python, pyi, jupyter ]
+
+-   repo: https://github.com/myint/docformatter    # To format the doc strings to conform PEP257
+    rev: v1.7.5
+    hooks:
+    - id: docformatter
+      args: [--in-place]
+
+-   repo: https://github.com/codespell-project/codespell
+    rev: v2.2.6
+    hooks:
+      - id: codespell
+        additional_dependencies:
+          - tomli
+
+-   repo: https://github.com/pre-commit/pre-commit-hooks    # Some common pre-commit hooks
+    rev: v4.6.0
+    hooks:
+    - id: check-yaml               # Checks the syntax of .yaml files.
+      args: [--allow-multiple-documents]
+    - id: end-of-file-fixer        # Makes sure files end with a newline.
+    - id: trailing-whitespace      # Checks for any tabs or spaces after the last non-whitespace character on the line.
+    - id: check-docstring-first    # Checks that code comes after the docstrings.

CONTRIBUTING.md

@@ -6,4 +6,4 @@
 
 `make clean html`
 
-`open _build/html/index.html`
+`open _build/html/index.html`

_static/custom.css

@@ -1,3 +1,3 @@
 footer {
     color: black;
-}
+}

applications/data_analysis/data_analysis.rst

@@ -9,4 +9,4 @@ Data Analysis
    :maxdepth: 1
    :hidden:
 
-   sample.ipynb
+   sample.ipynb

applications/data_analysis/sample.ipynb

@@ -53,6 +53,7 @@
     "from matplotlib import rcParams, cycler\n",
     "import matplotlib.pyplot as plt\n",
     "import numpy as np\n",
+    "\n",
     "plt.ion()"
    ]
   },
@@ -73,9 +74,12 @@
     "\n",
     "\n",
     "from matplotlib.lines import Line2D\n",
-    "custom_lines = [Line2D([0], [0], color=cmap(0.), lw=4),\n",
-    "                Line2D([0], [0], color=cmap(.5), lw=4),\n",
-    "                Line2D([0], [0], color=cmap(1.), lw=4)]\n",
+    "\n",
+    "custom_lines = [\n",
+    "    Line2D([0], [0], color=cmap(0.0), lw=4),\n",
+    "    Line2D([0], [0], color=cmap(0.5), lw=4),\n",
+    "    Line2D([0], [0], color=cmap(1.0), lw=4),\n",
+    "]\n",
     "\n",
     "fig, ax = plt.subplots(figsize=(10, 5))\n",
     "lines = ax.plot(data)\n",

applications/file_io/file_io.rst

@@ -9,4 +9,4 @@ File I/O
    :maxdepth: 1
    :hidden:
 
-   sample.ipynb
+   sample.ipynb

applications/file_io/sample.ipynb

@@ -53,6 +53,7 @@
     "from matplotlib import rcParams, cycler\n",
     "import matplotlib.pyplot as plt\n",
     "import numpy as np\n",
+    "\n",
     "plt.ion()"
    ]
   },
@@ -73,9 +74,12 @@
     "\n",
     "\n",
     "from matplotlib.lines import Line2D\n",
-    "custom_lines = [Line2D([0], [0], color=cmap(0.), lw=4),\n",
-    "                Line2D([0], [0], color=cmap(.5), lw=4),\n",
-    "                Line2D([0], [0], color=cmap(1.), lw=4)]\n",
+    "\n",
+    "custom_lines = [\n",
+    "    Line2D([0], [0], color=cmap(0.0), lw=4),\n",
+    "    Line2D([0], [0], color=cmap(0.5), lw=4),\n",
+    "    Line2D([0], [0], color=cmap(1.0), lw=4),\n",
+    "]\n",
     "\n",
     "fig, ax = plt.subplots(figsize=(10, 5))\n",
     "lines = ax.plot(data)\n",

applications/plot_types/contour.ipynb

@@ -53,6 +53,7 @@
     "from matplotlib import rcParams, cycler\n",
     "import matplotlib.pyplot as plt\n",
     "import numpy as np\n",
+    "\n",
     "plt.ion()"
    ]
   },
@@ -73,9 +74,12 @@
     "\n",
     "\n",
     "from matplotlib.lines import Line2D\n",
-    "custom_lines = [Line2D([0], [0], color=cmap(0.), lw=4),\n",
-    "                Line2D([0], [0], color=cmap(.5), lw=4),\n",
-    "                Line2D([0], [0], color=cmap(1.), lw=4)]\n",
+    "\n",
+    "custom_lines = [\n",
+    "    Line2D([0], [0], color=cmap(0.0), lw=4),\n",
+    "    Line2D([0], [0], color=cmap(0.5), lw=4),\n",
+    "    Line2D([0], [0], color=cmap(1.0), lw=4),\n",
+    "]\n",
     "\n",
     "fig, ax = plt.subplots(figsize=(10, 5))\n",
     "lines = ax.plot(data)\n",

applications/plot_types/plot_types.rst

@@ -9,4 +9,4 @@ Plot Types
    :maxdepth: 1
    :hidden:
 
-   contour.ipynb
+   contour.ipynb

conf.py

@@ -12,13 +12,8 @@
 #
 # -- Project information -----------------------------------------------------
 
-import os
 import sys
-import pathlib
-import yaml
-from sphinx.application import Sphinx
 from sphinx.util import logging
-from textwrap import dedent, indent
 
 print("sys.path:", sys.path)
 
@@ -28,12 +23,12 @@
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
-#sys.path.insert(0, os.path.abspath('.'))
+# sys.path.insert(0, os.path.abspath('.'))
 
 # -- General configuration ------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
-#needs_sphinx = '1.0'
+# needs_sphinx = '1.0'
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
@@ -57,28 +52,11 @@
         'processEscapes': True,
     },
     'HTML-CSS': {
-        'linebreaks': {
-            'automatic': True,
-            'width': 'container'
-        },
-        'fonts': {
-            'availableFonts': ['TeX'],
-            'preferredFont': 'TeX',
-            'webFont': 'TeX'
-        }
+        'linebreaks': {'automatic': True, 'width': 'container'},
+        'fonts': {'availableFonts': ['TeX'], 'preferredFont': 'TeX', 'webFont': 'TeX'},
     },
-    'CommonHTML': {
-        'linebreaks': {
-            'automatic': True,
-            'width': 'container'
-        }
-    },
-    'SVG': {
-        'linebreaks': {
-            'automatic': True,
-            'width': 'container'
-        }
-    }
+    'CommonHTML': {'linebreaks': {'automatic': True, 'width': 'container'}},
+    'SVG': {'linebreaks': {'automatic': True, 'width': 'container'}},
 }
 
 mathjax_path = "https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"
@@ -150,20 +128,19 @@
 }
 
 # The encoding of source files.
-#source_encoding = 'utf-8-sig'
+# source_encoding = 'utf-8-sig'
 
 # The master toctree document.
 master_doc = 'index'
 
 # General information about the project.
-project = u'GeoCAT-applications'
+project = 'GeoCAT-applications'
 
 import datetime
 
 current_year = datetime.datetime.now().year
-copyright = u'{}, University Corporation for Atmospheric Research'.format(
-    current_year)
-author = u'GeoCAT'
+copyright = '{}, University Corporation for Atmospheric Research'.format(current_year)
+author = 'GeoCAT'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -174,9 +151,9 @@
 
 # There are two options for replacing |today|: either, you set today to some
 # non-false value, then it is used:
-#today = ''
+# today = ''
 # Else, today_fmt is used as the format for a strftime call.
-#today_fmt = '%B %d, %Y'
+# today_fmt = '%B %d, %Y'
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -185,18 +162,18 @@
 
 # The reST default role (used for this markup: `text`) to use for all
 # documents.
-#default_role = None
+# default_role = None
 
 # If true, '()' will be appended to :func: etc. cross-reference text.
-#add_function_parentheses = True
+# add_function_parentheses = True
 
 # If true, the current module name will be prepended to all description
 # unit titles (such as .. function::).
-#add_module_names = True
+# add_module_names = True
 
 # If true, sectionauthor and moduleauthor directives will be shown in the
 # output. They are ignored by default.
-#show_authors = False
+# show_authors = False
 
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = 'sphinx'
@@ -205,10 +182,10 @@
 # print(f'STYLES: {styles}')
 
 # A list of ignored prefixes for module index sorting.
-#modindex_common_prefix = []
+# modindex_common_prefix = []
 
 # If true, keep warnings as "system message" paragraphs in the built documents.
-#keep_warnings = False
+# keep_warnings = False
 
 # If true, `todo` and `todoList` produce output, else they produce nothing.
 todo_include_todos = False
@@ -236,16 +213,15 @@
     use_repository_button=True,
     use_issues_button=True,
     home_page_in_toc=False,
-    extra_footer=
-    "<em>The National Center for Atmospheric Research is sponsored by the National Science Foundation. Any opinions, findings and conclusions or recommendations expressed in this material do not necessarily reflect the views of the National Science Foundation.</em>",
+    extra_footer="<em>The National Center for Atmospheric Research is sponsored by the National Science Foundation. Any opinions, findings and conclusions or recommendations expressed in this material do not necessarily reflect the views of the National Science Foundation.</em>",
 )
 
 # Add any paths that contain custom themes here, relative to this directory.
-#html_theme_path = []
+# html_theme_path = []
 
 
 # A shorter title for the navigation bar.  Default is the same as html_title.
-#html_short_title = None
+# html_short_title = None
 
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
@@ -265,64 +241,64 @@
 # Add any extra paths that contain custom files (such as robots.txt or
 # .htaccess) here, relative to this directory. These files are copied
 # directly to the root of the documentation.
-#html_extra_path = []
+# html_extra_path = []
 
 # If not None, a 'Last updated on:' timestamp is inserted at every page
 # bottom, using the given strftime format.
 # The empty string is equivalent to '%b %d, %Y'.
-#html_last_updated_fmt = None
+# html_last_updated_fmt = None
 
 # If true, SmartyPants will be used to convert quotes and dashes to
 # typographically correct entities.
-#html_use_smartypants = True
+# html_use_smartypants = True
 
 # Custom sidebar templates, maps document names to template names.
-#html_sidebars = {}
+# html_sidebars = {}
 
 # Additional templates that should be rendered to pages, maps page names to
 # template names.
-#html_additional_pages = {}
+# html_additional_pages = {}
 
 # If false, no module index is generated.
-#html_domain_indices = True
+# html_domain_indices = True
 
 # If false, no index is generated.
-#html_use_index = True
+# html_use_index = True
 
 # If true, the index is split into individual pages for each letter.
-#html_split_index = False
+# html_split_index = False
 
 # If true, links to the reST sources are added to the pages.
-#html_show_sourcelink = True
+# html_show_sourcelink = True
 
 # If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
-#html_show_sphinx = True
+# html_show_sphinx = True
 
 # If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
-#html_show_copyright = True
+# html_show_copyright = True
 
 # If true, an OpenSearch description file will be output, and all pages will
 # contain a <link> tag referring to it.  The value of this option must be the
 # base URL from which the finished HTML is served.
-#html_use_opensearch = ''
+# html_use_opensearch = ''
 
 # This is the file name suffix for HTML files (e.g. ".xhtml").
-#html_file_suffix = None
+# html_file_suffix = None
 
 # Language to be used for generating the HTML full-text search index.
 # Sphinx supports the following languages:
 #   'da', 'de', 'en', 'es', 'fi', 'fr', 'hu', 'it', 'ja'
 #   'nl', 'no', 'pt', 'ro', 'ru', 'sv', 'tr', 'zh'
-#html_search_language = 'en'
+# html_search_language = 'en'
 
 # A dictionary with options for the search language support, empty by default.
 # 'ja' uses this config value.
 # 'zh' user can custom change `jieba` dictionary path.
-#html_search_options = {'type': 'default'}
+# html_search_options = {'type': 'default'}
 
 # The name of a javascript file (relative to the configuration directory) that
 # implements a search results scorer. If empty, the default will be used.
-#html_search_scorer = 'scorer.js'
+# html_search_scorer = 'scorer.js'
 
 # Output file base name for HTML help builder.
 htmlhelp_basename = 'geocat-applications-docs'

environment.yml

@@ -16,4 +16,4 @@ dependencies:
   - sphinx-book-theme
   - myst-nb
   - sphinx-design
-  - nbsphinx
+  - nbsphinx