Linting: mdformat, nbQA (#325)

Author: dcherian

.pre-commit-config.yaml

@@ -2,14 +2,12 @@ ci:
     autoupdate_schedule: quarterly
 
 repos:
-  # isort should run before black as black sometimes tweaks the isort output
   - repo: https://github.com/PyCQA/isort
     rev: 5.10.1
     hooks:
       - id: isort
         files: .+\.py$
 
-  # https://github.com/python/black#version-control-integration
   - repo: https://github.com/psf/black
     rev: 22.3.0
     hooks:
@@ -26,22 +24,49 @@ repos:
        - id: mypy
          additional_dependencies: [types-all]
 
-  - repo: https://github.com/deathbeds/prenotebook
-    rev: f5bdb72a400f1a56fe88109936c83aa12cc349fa
-    hooks:
-       - id: prenotebook
-
   - repo: https://github.com/myint/rstcheck
     rev: 3f92957478422df87bd730abde66f089cc1ee19b
     hooks:
         - id: rstcheck
 
-  # run this occasionally, ref discussion https://github.com/pydata/xarray/pull/3194
-  # - repo: https://github.com/asottile/pyupgrade
-  #   rev: v1.22.1
-  #   hooks:
-  #     - id: pyupgrade
-  #       args:
-  #         - "--py3-only"
-  #         # remove on f-strings in Py3.7
-  #         - "--keep-percent-format"
+  - repo: https://github.com/executablebooks/mdformat
+    rev: 0.7.14
+    hooks:
+    - id: mdformat
+      additional_dependencies:
+        - mdformat-black
+        - mdformat-myst
+
+  - repo: https://github.com/nbQA-dev/nbQA
+    rev: 1.3.1
+    hooks:
+        - id: nbqa-black
+        - id: nbqa-pyupgrade
+          args: [--py37-plus]
+        - id: nbqa-isort
+        - id: nbqa
+          entry: nbqa mdformat
+          name: nbqa-mdformat
+          alias: nbqa-mdformat
+          additional_dependencies: [mdformat==0.7.14]
+
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v2.31.1
+    hooks:
+     - id: pyupgrade
+       args:
+         - "--py37-plus"
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.1.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-toml
+      - id: check-yaml
+
+  - repo: https://github.com/keewis/blackdoc
+    rev: v0.3.4
+    hooks:
+      - id: blackdoc
+        files: .+\.py$

MANIFEST.in

@@ -13,4 +13,4 @@ exclude .tributors
 exclude .zenodo.json
 exclude *.yml
 exclude *.yaml
-exclude .gitignore
+exclude .gitignore

README.rst

@@ -32,7 +32,7 @@
 cf-xarray
 =========
 
-A lightweight convenience wrapper for using CF attributes on xarray objects. 
+A lightweight convenience wrapper for using CF attributes on xarray objects.
 
 For example you can use ``.cf.mean("latitude")`` instead of ``.mean("lat")`` if appropriate attributes are set! This allows you to write code that does not require knowledge of specific dimension or coordinate names particular to a dataset.
 

cf_xarray/data/cf-standard-name-table.xml

@@ -32,15 +32,16 @@ class set_options:
 
     >>> import numpy as np
     >>> import xarray as xr
-    >>> my_custom_criteria = { 'ssh': {'name': 'elev$'} }
+    >>> my_custom_criteria = {"ssh": {"name": "elev$"}}
     >>> ds = xr.Dataset({"elev": np.arange(1000)})
     >>> with cf_xarray.set_options(custom_criteria=my_custom_criteria):
-    ...     xr.testing.assert_identical(ds['elev'], ds.cf['ssh'])
+    ...     xr.testing.assert_identical(ds["elev"], ds.cf["ssh"])
+    ...
 
     Or to set global options:
 
     >>> cf_xarray.set_options(custom_criteria=my_custom_criteria)
-    >>> xr.testing.assert_identical(ds['elev'], ds.cf['ssh'])
+    >>> xr.testing.assert_identical(ds["elev"], ds.cf["ssh"])
     """
 
     def __init__(self, **kwargs):

cf_xarray/options.py

@@ -5,6 +5,7 @@
 # Bounds Variables
 
 See
+
 1. {py:attr}`Dataset.cf.bounds`,
 1. {py:func}`Dataset.cf.add_bounds`,
 1. {py:func}`cf_xarray.bounds_to_vertices`,

doc/bounds.md

@@ -6,9 +6,11 @@ kernelspec:
   display_name: Python 3
   name: python3
 ---
+
 ```{eval-rst}
 .. currentmodule:: cf_xarray
 ```
+
 ```{code-cell}
 ---
 tags: [remove-cell]
@@ -20,22 +22,22 @@ import xarray as xr
 xr.set_options(display_expand_data=False)
 ```
 
-
 # Encoding and decoding
 
-`cf_xarray` aims to support encoding and decoding variables using CF conventions not yet implemented by Xarray. 
+`cf_xarray` aims to support encoding and decoding variables using CF conventions not yet implemented by Xarray.
 
 ## Compression by gathering
 
-The ["compression by gathering"](http://cfconventions.org/Data/cf-conventions/cf-conventions-1.8/cf-conventions.html#compression-by-gathering) 
+The ["compression by gathering"](http://cfconventions.org/Data/cf-conventions/cf-conventions-1.8/cf-conventions.html#compression-by-gathering)
 convention could be used for either {py:class}`pandas.MultiIndex` objects or `pydata/sparse` arrays.
 
 ### MultiIndex
 
-``cf_xarray`` provides {py:func}`encode_multi_index_as_compress` and {py:func}`decode_compress_to_multi_index` to encode MultiIndex-ed
-dimensions using "compression by gethering". 
+`cf_xarray` provides {py:func}`encode_multi_index_as_compress` and {py:func}`decode_compress_to_multi_index` to encode MultiIndex-ed
+dimensions using "compression by gethering".
 
 Here's a test dataset
+
 ```{code-cell}
 ds = xr.Dataset(
     {"landsoilt": ("landpoint", np.random.randn(4), {"foo": "bar"})},
@@ -47,20 +49,24 @@ ds = xr.Dataset(
 )
 ds
 ```
+
 First encode (note the `"compress"` attribute on the `landpoint` variable)
+
 ```{code-cell}
 encoded = cfxr.encode_multi_index_as_compress(ds, "landpoint")
 encoded
 ```
 
 At this point, we can write `encoded` to a CF-compliant dataset using {py:func}`xarray.Dataset.to_netcdf` for example.
 After reading that file, decode using
+
 ```{code-cell}
 decoded = cfxr.decode_compress_to_multi_index(encoded, "landpoint")
 decoded
 ```
 
 We roundtrip perfectly
+
 ```{code-cell}
 ds.identical(decoded)
 ```

doc/coding.md

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-#
 # complexity documentation build configuration file, created by
 # sphinx-quickstart on Tue Jul  9 22:26:36 2013.
 #

doc/conf.py

@@ -70,4 +70,3 @@ Primarily for developer reference. Some of these could become public API if nece
     ~accessor._get_indexes
     ~accessor._get_measure
     ~accessor._get_with_standard_name
-

doc/contributing.rst

@@ -6,9 +6,11 @@ kernelspec:
   display_name: Python 3
   name: python3
 ---
+
 ```{eval-rst}
 .. currentmodule:: xarray
 ```
+
 ```{code-cell}
 ---
 tags: [remove-cell]
@@ -19,9 +21,10 @@ xr.set_options(display_expand_data=False)
 
 # Axes and Coordinates
 
-One powerful feature of ``cf_xarray`` is the ability to refer to named dimensions by standard `axis` or `coordinate` names in Dataset or DataArray methods.
+One powerful feature of `cf_xarray` is the ability to refer to named dimensions by standard `axis` or `coordinate` names in Dataset or DataArray methods.
 
 For example, one can call `ds.cf.mean("latitude")` instead of `ds.mean("lat")`
+
 ```{code-cell}
 from cf_xarray.datasets import airds
 
@@ -34,24 +37,26 @@ Most xarray methods are wrapped by cf-xarray. Simply access them as `DataArray.c
 ```
 
 ## Coordinate Names
-How does this work? `cf_xarray` has an internal table of criteria (mostly copied from MetPy) that lets it identify specific coordinate names `"latitude", "longitude", "vertical", "time"`. 
 
+How does this work? `cf_xarray` has an internal table of criteria (mostly copied from MetPy) that lets it identify specific coordinate names `"latitude", "longitude", "vertical", "time"`.
 
 ```{tip}
 See {ref}`custom_criteria` to find out how to define your own custom criteria.
 ```
 
-This table lists these internal criteria 
+This table lists these internal criteria
+
 ```{eval-rst}
 .. csv-table::
    :file: _build/csv/coords_criteria.csv
    :header-rows: 1
    :stub-columns: 1
 ```
-Any DataArray that has `standard_name: "latitude"` or `_CoordinateAxisType: "Lat"` or `"units": "degrees_north"` in its `attrs` will be identified as the `"latitude"` variable by cf-xarray.  Similarly for other coordinate names.
 
+Any DataArray that has `standard_name: "latitude"` or `_CoordinateAxisType: "Lat"` or `"units": "degrees_north"` in its `attrs` will be identified as the `"latitude"` variable by cf-xarray.  Similarly for other coordinate names.
 
 ## Axis Names
+
 Similar criteria exist for the concept of "axes".
 
 ```{eval-rst}
@@ -62,7 +67,9 @@ Similar criteria exist for the concept of "axes".
 ```
 
 ## `.axes` and  `.coordinates` properties
+
 Alternatively use the special properties {py:attr}`DataArray.cf.axes` or {py:attr}`DataArray.cf.coordinates` to access the variable names. These properties return dictionaries that map "CF names" to a list of variable names. Note that a list is always returned even if only one variable name matches the name `"latitude"` (for example).
+
 ```{code-cell}
 airds.cf.axes
 ```
@@ -78,22 +85,25 @@ TODO describe latitude vs Y; longitude vs X; vertical vs Z
 ## Checking presence of axis or coordinate
 
 Note that a given "CF name" is only present if there is at least one variable that can be identified with that name. The `airds` dataset has no `"vertical"` coordinate or `"Z"` axis, so those keys are not present. So to check whether a `"vertical"` coordinate or `"Z"` axis is present, one can
+
 ```{code-cell}
 "Z" in airds.cf.axes
 ```
+
 ```{code-cell}
 "vertical" in airds.cf.coordinates
 ```
 
 Or one can check the dataset as a whole:
+
 ```{code-cell}
 "Z" in airds.cf
 ```
 
-
-
 ## Using the repr
+
 It is always useful to check the variables identified by cf-xarray using the `repr`
+
 ```{code-cell}
 airds.cf
 ```