Add pre-commit

.github/workflows/label.yml

@@ -10,10 +10,9 @@ on: [pull_request]
 
 jobs:
   label:
-
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/labeler@v2
-      with:
-        repo-token: "${{ secrets.GITHUB_TOKEN }}"
+      - uses: actions/labeler@v2
+        with:
+          repo-token: "${{ secrets.GITHUB_TOKEN }}"

.pre-commit-config.yaml

@@ -0,0 +1,34 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: "v4.1.0"
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-docstring-first
+      - id: check-yaml
+
+  - repo: https://github.com/asottile/pyupgrade
+    rev: "v2.31.0"
+    hooks:
+      - id: pyupgrade
+        args: [--py36-plus]
+
+  - repo: https://github.com/PyCQA/isort
+    rev: "5.10.1"
+    hooks:
+      - id: isort
+
+  - repo: https://github.com/psf/black
+    rev: "21.12b0"
+    hooks:
+      - id: black
+
+  - repo: https://github.com/PyCQA/flake8
+    rev: "4.0.1"
+    hooks:
+      - id: flake8
+
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: "v2.5.1"
+    hooks:
+      - id: prettier

.readthedocs.yaml

@@ -1,22 +1,19 @@
 version: 2
 
-
 build:
   image: latest
 
-
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
   configuration: docs/conf.py
 
-
 #conda:
 #  environment: docs/environment.yml
 
 # Optionally set the version of Python and requirements required to build your docs
 python:
   version: 3.6
-#  setup_py_install: false
+  #  setup_py_install: false
 
   install:
     - requirements: docs/requirements.txt

.stickler.yml

@@ -7,6 +7,6 @@ fixers:
 review:
   fail_on_comments: false
 files:
-    ignore:
-        - 'docs/**/*'
-        - 'monet/data/*'
+  ignore:
+    - "docs/**/*"
+    - "monet/data/*"

.travis.yaml

@@ -1,10 +1,9 @@
 language: python
 
-
 branches:
   only:
-  - master
-  - develop
+    - master
+    - develop
 
 before_install:
   - chmod +x miniconda.sh
@@ -13,9 +12,7 @@ before_install:
   - conda config --set always_yes yes --set changeps1 no
   - conda update --yes conda
 
-
 install:
   - conda install -c bbakernoaa monet
-
 # after_success:
 #   - test $TRAVIS_BRANCH = "master" && conda install conda-build && conda install anaconda-client && bash conda/conda_upload.sh

README.md

@@ -1,7 +1,7 @@
 ## The Model and ObservatioN Evaluation Tool I/O
 
-This is a tool developed at NOAA ARL to handle I/O operations for atmospheric composition for python.  It was originally part of the Model and ObservatioN Evaluation Tool (MONET; see Baker and Li (2017)).  
+This is a tool developed at NOAA ARL to handle I/O operations for atmospheric composition for python. It was originally part of the Model and ObservatioN Evaluation Tool (MONET; see Baker and Li (2017)).
 
-Please refer to the readthedocs page at monetio.readthedocs.io for the documentation.  
+Please refer to the readthedocs page at monetio.readthedocs.io for the documentation.
 
 Baker, Barry; Pan, Li. 2017. “Overview of the Model and Observation Evaluation Toolkit (MONET) Version 1.0 for Evaluating Atmospheric Transport Models.” Atmosphere 8, no. 11: 210

docs/Makefile

@@ -17,4 +17,4 @@ help:
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/_static/style.css

@@ -1,18 +1,18 @@
 @import url("theme.css");
 
-.wy-side-nav-search>a img.logo,
-.wy-side-nav-search .wy-dropdown>a img.logo {
-  width: 12rem
+.wy-side-nav-search > a img.logo,
+.wy-side-nav-search .wy-dropdown > a img.logo {
+  width: 12rem;
 }
 
 .wy-side-nav-search {
   background-color: #eee;
 }
 
-.wy-side-nav-search>div.version {
+.wy-side-nav-search > div.version {
   display: none;
 }
 
 .wy-nav-top {
   background-color: #ffffff;
-}
+}

docs/_templates/layout.html

@@ -1,2 +1,2 @@
-{% extends "!layout.html" %}
-{% set css_files = css_files + ["_static/style.css"] %}
+{% extends "!layout.html" %} {% set css_files = css_files +
+["_static/style.css"] %}

docs/conf.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 #
 # Configuration file for the Sphinx documentation builder.
 #
@@ -23,18 +22,18 @@ def __getattr__(cls, name):
         return MagicMock()
 
 
-#sys.modules.update((mod_name, Mock()) for mod_name in MOCK_MODULES)
-sys.path.insert(0, os.path.abspath('../'))
+# sys.modules.update((mod_name, Mock()) for mod_name in MOCK_MODULES)
+sys.path.insert(0, os.path.abspath("../"))
 # -- Project information -----------------------------------------------------
 
-project = u'monetio'
-copyright = u'2018, Barry Baker'
-author = u'Barry Baker'
+project = "monetio"
+copyright = "2018, Barry Baker"
+author = "Barry Baker"
 
 # The short X.Y version
-version = u''
+version = ""
 # The full version, including alpha/beta/rc tags
-release = u''
+release = ""
 
 # -- General configuration ---------------------------------------------------
 
@@ -46,14 +45,16 @@ def __getattr__(cls, name):
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinx.ext.autodoc', 'sphinx.ext.autosummary', 'sphinx.ext.napoleon',
-    'sphinx.ext.extlinks'
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.extlinks",
 ]
-#exclude_patterns = ['_build', '**.ipynb_checkpoints']
+# exclude_patterns = ['_build', '**.ipynb_checkpoints']
 
 extlinks = {
-    'issue': ('https://github.com/noaa-oar-arl/monetio/issues/%s', 'GH'),
-    'pull': ('https://github.com/noaa-oar-arl/monetio/pull/%s', 'PR'),
+    "issue": ("https://github.com/noaa-oar-arl/monetio/issues/%s", "GH"),
+    "pull": ("https://github.com/noaa-oar-arl/monetio/pull/%s", "PR"),
 }
 
 autosummary_generate = True
@@ -63,16 +64,16 @@ def __getattr__(cls, name):
 napoleon_use_ivar = False  # True
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
 #
 # source_suffix = ['.rst', '.md']
-source_suffix = '.rst'
+source_suffix = ".rst"
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -84,17 +85,17 @@ def __getattr__(cls, name):
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path .
-exclude_patterns = [u'_build', 'Thumbs.db', '.DS_Store']
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
 # -- Options for HTML output -------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'sphinx_rtd_theme'
+html_theme = "sphinx_rtd_theme"
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
@@ -105,7 +106,7 @@ def __getattr__(cls, name):
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]
 
 # Custom sidebar templates, must be a dictionary that maps document names
 # to template names.
@@ -120,10 +121,10 @@ def __getattr__(cls, name):
 # -- Options for HTMLHelp output ---------------------------------------------
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'monetiodoc'
+htmlhelp_basename = "monetiodoc"
 
 html_theme_options = {
-    'logo_only': True,
+    "logo_only": True,
 }
 
 # Add any paths that contain custom themes here, relative to this directory.
@@ -146,15 +147,12 @@ def __getattr__(cls, name):
     # The paper size ('letterpaper' or 'a4paper').
     #
     # 'papersize': 'letterpaper',
-
     # The font size ('10pt', '11pt' or '12pt').
     #
     # 'pointsize': '10pt',
-
     # Additional stuff for the LaTeX preamble.
     #
     # 'preamble': '',
-
     # Latex figure (float) alignment
     #
     # 'figure_align': 'htbp',
@@ -164,24 +162,30 @@ def __getattr__(cls, name):
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'monetio.tex', u'monetio Documentation', u'Barry Baker',
-     'manual'),
+    (master_doc, "monetio.tex", "monetio Documentation", "Barry Baker", "manual"),
 ]
 
 # -- Options for manual page output ------------------------------------------
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [(master_doc, 'monetio', u'monetio Documentation', [author], 1)]
+man_pages = [(master_doc, "monetio", "monetio Documentation", [author], 1)]
 
 # -- Options for Texinfo output ----------------------------------------------
 
 # Grouping the document tree into Texinfo files. List of tuples
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'monetio', u'monetio Documentation', author, 'monetio',
-     'One line description of project.', 'Miscellaneous'),
+    (
+        master_doc,
+        "monetio",
+        "monetio Documentation",
+        author,
+        "monetio",
+        "One line description of project.",
+        "Miscellaneous",
+    ),
 ]
 
 # -- Extension configuration -------------------------------------------------

docs/models.rst

@@ -128,7 +128,7 @@ where pm25 is a :py:class:`~xarray.DataArray` as it is a single variable.
 Prep-Chem-Sources
 -----------------
 
-A reader and writer was built into 
+A reader and writer was built into
 
 
 HYSPLIT
@@ -250,7 +250,7 @@ To calcluate mass loading
 
 All points with value below or equal to threshold will be returned as 0.
 mult is a multiplicative factor applied before the thresholding.
-species can be a list of values from the "Species ID" attribute. 
+species can be a list of values from the "Species ID" attribute.
 If it is None then all species will be used.
 
 To find top heights
@@ -261,11 +261,7 @@ To find top heights
 
 returns xarray DataArray which gives top height of each level which contains mass loading higher
 than the given threshold value. mult is a mutiplicative factor applied before thresholding.
-height_mult is a multiplicative factor used to convert heights from meters to some other unit. 
+height_mult is a multiplicative factor used to convert heights from meters to some other unit.
 In this example heights are converted to km.
 mass_load is a boolean which indicates whether the height should be determined from the mass loading value (True)
-or the concentration value (False). 
-
-
-
-
+or the concentration value (False).

monetio/__init__.py

@@ -94,7 +94,7 @@ def dataset_to_monet(dset, lat_name="lat", lon_name="lon", latlon2d=False):
 
 
 def coards_to_netcdf(dset, lat_name="lat", lon_name="lon"):
-    from numpy import meshgrid, arange
+    from numpy import arange, meshgrid
 
     lon = dset[lon_name]
     lat = dset[lat_name]