Linting (#179)

* Add pre-commit. * Remove pep8 dependency. * Rename pre-commit.yaml. * Re-lint code base. * Requirements tidy. * Update CHANGES deprecation message. * Remove .gitattributes now Versioneer is gone. * Update README. * Add Cirrus lint task. * Python container for Cirrus lint task. * Temporary increase to Codecov tolerance. * Revert "Temporary increase to Codecov tolerance." This reverts commit 80b3c61. * Temporarily disable Codecov patch failure to allow for Black changes. * Pre-commit just perform checks, don't modify.
SciTools · Jun 22, 2021 · 0ca0921 · 0ca0921
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diff --git a/.cirrus.yml b/.cirrus.yml
@@ -22,8 +22,21 @@ env:
   CFUNITS_CACHE_BUILD: "0"
   # Base environment conda packages to be installed
   MAMBA_CACHE_PACKAGES: "pip conda-lock"
-  # Increment the build number to force new pip cache upload.
-  PIP_CACHE_BUILD: "0"
+
+
+#
+# Linting
+#
+lint_task:
+  auto_cancellation: true
+  container:
+    image: python:latest
+    cpu: 2
+    memory: 4G
+  name: "${CIRRUS_OS}: linting"
+  lint_script:
+    - python -m pip install --retries 3 pre-commit
+    - pre-commit run --all-files
 
 
 #

diff --git a/.gitattributes b/.gitattributes
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -0,0 +1,37 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: "v4.0.1"
+    hooks:
+        # Prevent giant files from being committed.
+    -   id: check-added-large-files
+        # Check whether files parse as valid Python.
+    -   id: check-ast
+        # Check for file name conflicts on case-insensitive filesytems.
+    -   id: check-case-conflict
+        # Check for files that contain merge conflict strings.
+    -   id: check-merge-conflict
+        # Check for debugger imports and py37+ `breakpoint()` calls in Python source.
+    -   id: debug-statements
+        # Don't commit to main branch.
+    -   id: no-commit-to-branch
+-   repo: https://github.com/psf/black
+    rev: "21.6b0"
+    hooks:
+    -   id: black
+        # Force black to run on whole repo, using settings from pyproject.toml
+        pass_filenames: false
+        args: ["--config=./pyproject.toml", "--check", "."]
+-   repo: https://github.com/PyCQA/flake8
+    rev: "3.9.2"
+    hooks:
+        # Run flake8.
+    -   id: flake8
+        args: ["--config=./setup.cfg"]
+-   repo: https://github.com/pycqa/isort
+    rev: "5.8.0"
+    hooks:
+    -   id: isort
+        name: isort
+        args: ["--filter-files", "--check"]
diff --git a/CHANGES b/CHANGES
@@ -1,5 +1,5 @@
 This file is no longer updated and is provided for historical purposes only.
-Please see docs/cf_units/src/whatsnew/ for a changelog.
+Please see the Git history for a record of changes.
 
 
 Release 1.4 (14 June 2013)

diff --git a/INSTALL b/INSTALL
@@ -26,68 +26,38 @@ Installing from source
 The latest cf-units source release is available from
 https://github.com/SciTools/cf-units/releases.
 
-cf-units makes use of cftime, cython, numpy, setuptools and udunits2.
-These dependencies must be in place before you can successfully install
-cf-units. Once you have satisfied the requirements detailed below,
-extract the cf-units source package, change to the new directory, and enter::
 
-  python setup.py install
+Build and runtime requirements
+==============================
+See the ``requirements/`` directory for the external packages you will need to
+have installed before installing and running cf-units.
 
-For non-standard locations, additional build lib & include paths
-can be provided as per-usual at build_ext phase::
+The recommended way to provision requirements is using Conda::
 
-  python setup.py build_ext -I/path/to/include -L/path/to/lib
-  python setup.py install
+  conda env create -f requirements/cf-units.yml
 
+All requirements except ``udunits2`` are also available individually via PyPI::
 
-Build and runtime requirements
-==============================
-These are external packages which you will need to have installed before
-installing and running cf-units.
+  pip install numpy
 
-Many of these packages are available in Linux package managers
+Many of the packages are also available in Linux package managers
 such as aptitude and yum. For example, it may be possible to install
 Numpy using::
 
   apt-get install python-numpy
 
-If you are installing dependencies with a package manager on Linux,
-you may need to install the development packages (look for a "-dev"
-postfix) in addition to the core packages.
-
-python 2.7 or later (https://www.python.org/)
-    cf-units is compatible with Python 2 and Python 3.
-
-cftime 1.0.0 or later (https://unidata.github.io/cftime/)
-    Python package for decoding time units conforming to
-    Climate and Forecasting (CF) netCDF conventions.
 
-cython (https://pypi.org/project/Cython/)
-    Optimising static compiler for Python and the extended Cython
-    programming language.
+Installing cf-units
+===================
+Once you have satisfied the requirements detailed above, extract the cf-units
+source package, change to the new directory, and enter::
 
-numpy 1.14 or later (https://pypi.org/project/numpy/)
-    Python package for scientific computing including a powerful N-dimensional
-    array object.
+  pip install .
 
-udunits2 2.2.26 or later (https://www.unidata.ucar.edu/downloads/udunits/index.jsp)
-    C library for units of physical quantities.
-
-setuptools (https://pypi.org/project/setuptools/)
-    Python package for installing/removing python packages.
-
-
-Optional
-''''''''
-These packages are required for the full cf-units test suite to run.
-
-pep8 1.4.6* (https://pypi.org/project/pep8/)
-    Python package for software testing.
-
-pytest (https://pypi.org/project/pytest/)
-    Python testing framework.
+For non-standard locations, additional build lib & include paths
+can be provided as per-usual at ``build_ext`` phase::
 
-* Those packages have been tested with a specific build.
+  pip install --global-option=build_ext --global-option="-I/path/to/include2 --global-option="-L/path/to/lib" .
 
 
 Custom site configuration

diff --git a/MANIFEST.in b/MANIFEST.in
@@ -4,3 +4,4 @@ recursive-include cf_units *.py *.pxd *.pyx *.c
 include cf_units/etc/site.cfg.template
 include CHANGES COPYING COPYING.LESSER INSTALL
 exclude cf_units/etc/site.cfg
+graft requirements
diff --git a/README.md b/README.md
@@ -1,59 +1,40 @@
-<h1 align="center" style="margin:1em;">
-  <a href="https://scitools.org.uk/cf-units/docs/latest/">cf-units</a>
-</h1>
-
-<h4 align="center">
-Units of measure as defined by the Climate and Forecast (CF) metadata
-conventions.
-</h4>
-
-<p align="center">
-<!-- https://shields.io/ is a good source of these -->
-<a href="https://anaconda.org/conda-forge/cf-units">
-<img src="https://img.shields.io/conda/dn/conda-forge/cf-units.svg"
- alt="conda-forge downloads" /></a>
-<a href="https://github.com/SciTools/cf-units/releases">
-<img src="https://img.shields.io/github/tag/SciTools/cf-units.svg"
- alt="Latest version" /></a>
-<a href="https://github.com/SciTools/cf-units/commits/master">
-<img src="https://img.shields.io/github/commits-since/SciTools/cf-units/latest.svg"
- alt="Commits since last release" /></a>
-<a href="https://github.com/SciTools/cf-units/graphs/contributors">
-<img src="https://img.shields.io/github/contributors/SciTools/cf-units.svg"
- alt="# contributors" /></a>
-<a href="https://cirrus-ci.com/github/SciTools/cf-units">
-<img src="https://api.cirrus-ci.com/github/SciTools/cf-units.svg?branch=master"
- alt="cirrus-ci" /></a>
-<a href="https://codecov.io/gh/SciTools/cf-units">
-<img src="https://codecov.io/gh/SciTools/cf-units/branch/master/graph/badge.svg?token=6LlYlyTUZG"
- alt="Coverage Status" /></a>
-<!-- <a href="https://zenodo.org/badge/latestdoi/5282596">
-<img src="https://zenodo.org/badge/5282596.svg"
- alt="zenodo" /></a> -->
-</p>
-<br>
+# [cf-units](https://scitools.org.uk/cf-units/docs/latest/)
+
+#### Units of measure as defined by the Climate and Forecast (CF) metadata conventions.
+
+[comment]: # (https://shields.io/ is a good source of these)
+[![Build Status](https://api.cirrus-ci.com/github/SciTools/cf-units.svg)](https://cirrus-ci.com/github/SciTools/cf-units)
+[![Coverage Status](https://codecov.io/gh/SciTools/cf-units/branch/master/graph/badge.svg?token=6LlYlyTUZG)](https://codecov.io/gh/SciTools/cf-units)
+[![pre-commit.ci status](https://results.pre-commit.ci/badge/github/SciTools/cf-units/master.svg)](https://results.pre-commit.ci/latest/github/SciTools/cf-units/master)
+,
+[![conda-forge downloads](https://img.shields.io/conda/vn/conda-forge/cf-units?color=orange&label=conda-forge&logo=conda-forge&logoColor=white)](https://anaconda.org/conda-forge/cf-units)
+[![PyPI](https://img.shields.io/pypi/v/cf-units?color=orange&label=pypi&logo=python&logoColor=white)](https://pypi.org/project/cf-units/)
+[![Latest version](https://img.shields.io/github/tag/SciTools/cf-units)](https://github.com/SciTools/cf-units/releases)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3723086.svg)](https://doi.org/10.5281/zenodo.3723086)
+,
+[![Black](https://img.shields.io/badge/code%20style-black-000000)](https://github.com/psf/black)
+[![Flake8](https://img.shields.io/badge/lint-flake8-lightgrey)](https://github.com/PyCQA/flake8)
+[![isort](https://img.shields.io/badge/%20imports-isort-%231674b1?style=flat&labelColor=ef8336)](https://pycqa.github.io/isort/)
+,
+[![Licence](https://img.shields.io/github/license/SciTools/cf-units)](COPYING)
+[![Contributors](https://img.shields.io/github/contributors/SciTools/cf-units)](https://github.com/SciTools/cf-units/graphs/contributors)
+[![Commits since last release](https://img.shields.io/github/commits-since/SciTools/cf-units/latest.svg)](https://github.com/SciTools/cf-units/commits/master)
 
 # Table of contents
 
-<!--
-NOTE: toc auto-generated with https://github.com/jonschlinkert/markdown-toc
-    $> markdown-toc -i --bullets='-' README.md
-
-NOTE: This entire README can be markdown linted with
+[comment]:
+  # (NOTE: toc auto-generated with https://github.com/jonschlinkert/markdown-toc
+      $> markdown-toc -i --bullets='-' README.md)
+[comment]:
+  # (This entire README can be markdown linted with
     https://github.com/igorshubovych/markdownlint-cli
-    $ echo '{"no-inline-html": false}' > .markdownrc
-    $ markdownlint README.md
--->
-
-<!-- toc -->
+      $ markdownlint README.md)
 
 - [Overview](#overview)
   - [Example](#example)
 - [Get in touch](#get-in-touch)
 - [Credits, copyright and license](#credits-copyright-and-license)
 
-<!-- tocstop -->
-
 ## Overview
 
 Units of measure as required by the Climate and Forecast (CF) metadata
@@ -81,7 +62,6 @@ Documentation can be found at <https://scitools.org.uk/cf-units/docs/latest/>.
   [submit a GitHub issue](https://github.com/SciTools/cf-units/issues).
 - Suggest features: see our [contributing guide](.github/CONTRIBUTING.md).
 
-
 ## Credits, copyright and license
 
 cf-units is developed collaboratively under the SciTools umbrella.