Add pre-commit hooks, black formatting, and style fixes (#1341)

* first cut at pre-commit hooks and code style fixes

* fix aux io, source, test_radardisplay

* clean up next section of files

* cleanup sigmet rhi data file

* clean up sinarame aux io

* clean up mdv related files

* fix exception errors

* fix next batch of cleanup

* fix debug module

* update auxio and phase proc sections

* clean up large batch of modules

* last few formatting issues solved

* add linting to workflow

* fix remaining linting errors

* remove support for python 3.7

* remove nbstripout and revert to previous notebooks

* combine kazr spectra auxio string

* STY: Fix combined strings in graph module.

* STY: More combining.

* STY: More combining and revert of errors.

* MNT: Revert back to OSerror.

* MNT: More changes.

* MNT: More changes.

* MNT: Revert setuptools.

* ADD: Add dev file.

* MNT: Reverting environment files.

Co-authored-by: zssherman <[email protected]>

.github/workflows/ci.yml

@@ -27,7 +27,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
         os: [macos, ubuntu, windows]
 
     steps:
@@ -44,7 +44,7 @@ jobs:
           use-mamba: true
           miniforge-variant: Mambaforge
           python-version: ${{ matrix.python-version }}
-          
+
       - name: Fetch all history for all tags and branches
         run: |
            git fetch --prune --unshallow
@@ -59,7 +59,7 @@ jobs:
         run: |
           python -m flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
           python -m flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-      
+
       - name: Run Tests
         id: run_tests
         shell: bash -l {0}
@@ -73,4 +73,4 @@ jobs:
           flags: unittests
           env_vars: OS,PYTHON
           name: codecov-umbrella
-          fail_ci_if_error: false
+          fail_ci_if_error: false

.github/workflows/linting.yml

@@ -0,0 +1,31 @@
+name: linting
+
+on:
+  push:
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  pre-job:
+    runs-on: ubuntu-latest
+    outputs:
+      should_skip: ${{ steps.skip_check.outputs.should_skip }}
+    steps:
+      - id: skip_check
+        uses: fkirc/skip-duplicate-actions@master
+        with:
+          concurrent_skipping: 'same_content'
+          skip_after_successful_duplicate: 'false'
+          do_not_skip: '["workflow_dispatch", "schedule"]'
+  linting:
+    needs: pre-job
+    runs-on: ubuntu-latest
+    if: ${{ needs.pre-job.outputs.should_skip != 'true' }}
+    steps:
+      - name: Cancel Previous Runs
+        uses: styfle/[email protected]
+        with:
+          access_token: ${{ github.token }}
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+      - uses: pre-commit/[email protected]

.github/workflows/wheels.yml

@@ -35,7 +35,7 @@ jobs:
     steps:
       - name: Checkout repo
         uses: actions/checkout@v3
-      
+
       - name: Fetch all history for all tags and branches
         run: |
            git fetch --prune --unshallow

.pre-commit-config.yaml

@@ -0,0 +1,35 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.3.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-docstring-first
+      - id: check-json
+      - id: check-yaml
+      - id: debug-statements
+      - id: mixed-line-ending
+
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v2.31.0
+    hooks:
+      - id: pyupgrade
+        args:
+          - '--py38-plus'
+
+  - repo: https://github.com/psf/black
+    rev: 22.10.0
+    hooks:
+      - id: black
+      - id: black-jupyter
+
+  - repo: https://github.com/PyCQA/flake8
+    rev: 4.0.1
+    hooks:
+      - id: flake8
+        args: [--config, setup.cfg]
+
+  - repo: https://github.com/PyCQA/isort
+    rev: 5.10.1
+    hooks:
+      - id: isort

INSTALL.rst

@@ -41,7 +41,7 @@ without these packages.
 
 * `TRMM RSL <https://trmm-fc.gsfc.nasa.gov/trmm_gv/software/rsl/>`_
 
-* `CyLP <https://github.com/mpy/CyLP>`_ or 
+* `CyLP <https://github.com/mpy/CyLP>`_ or
   `PyGLPK <https://tfinley.net/software/pyglpk/>`_ or
   `CVXOPT <https://cvxopt.org/>`_ and their dependencies.
 
@@ -127,25 +127,25 @@ Frequently asked questions
   https://docs.conda.io/projects/conda-build/en/latest/resources/compiler-tools.html
   Once the proper compilers are installed, reinstall CyLP.
 
-* I'm getting a segfault or another error in python when using 
+* I'm getting a segfault or another error in python when using
   ``pyart.io.read_rsl()`` with IRIS/other files.
-  
+
   This is due to a bug in RSL, and can be remedied by adding
   ``-fno-stack-protector -D_FORTIFY_SOURCE=0`` to the CFLAGS parameter of the
   makefile of RSL.  This issue has been fixed with the release of rsl-v1.44.
 
 * I'm having trouble getting PyGLPK to compile on my 64-bit operating system.
-  
+
   Change the line in the setup.py file from
-  
+
   ::
-  
+
       define_macros = macros, extra_compile_args=['-m32'], extra_link_args=['-m32'],
-  
+
   to
-  
+
   ::
-  
+
       define_macros = macros, extra_compile_args=['-m64'], extra_link_args=['-m64'],
 
   Then build and install PyGLPK as recommended in the PYGLPK README.txt file.

LICENSE.txt

@@ -1,20 +1,20 @@
 Copyright (c) 2013, UChicago Argonne, LLC
 All rights reserved.
 
-Copyright 2013 UChicago Argonne, LLC. This software was produced under U.S. 
+Copyright 2013 UChicago Argonne, LLC. This software was produced under U.S.
 Government contract DE-AC02-06CH11357 for Argonne National Laboratory (ANL),
 which is operated by UChicago Argonne, LLC for the U.S. Department of Energy.
 The U.S. Government has rights to use, reproduce, and distribute this
-software.  NEITHER THE GOVERNMENT NOR UCHICAGO ARGONNE, LLC MAKES ANY 
+software.  NEITHER THE GOVERNMENT NOR UCHICAGO ARGONNE, LLC MAKES ANY
 WARRANTY, EXPRESS OR IMPLIED, OR ASSUMES ANY LIABILITY FOR THE USE OF THIS
 SOFTWARE.  If software is modified to produce derivative works, such modified
 software should be clearly marked, so as not to confuse it with the version
 available from ANL.
- 
-Additionally, redistribution and use in source and binary forms, with or 
+
+Additionally, redistribution and use in source and binary forms, with or
 without modification, are permitted provided that the following conditions
 are met:
-    
+
     * Redistributions of source code must retain the above copyright
       notice, this list of conditions and the following disclaimer.
 
@@ -23,11 +23,11 @@ are met:
       documentation and/or other materials provided with the distribution.
 
     * Neither the name of UChicago Argonne, LLC, Argonne National
-      Laboratory, ANL, the U.S. Government, nor the names of its 
+      Laboratory, ANL, the U.S. Government, nor the names of its
       contributors may be used to endorse or promote products derived
       from this software without specific prior written permission.
 
-THIS SOFTWARE IS PROVIDED BY UCHICAGO ARGONNE, LLC AND CONTRIBUTORS "AS IS" 
+THIS SOFTWARE IS PROVIDED BY UCHICAGO ARGONNE, LLC AND CONTRIBUTORS "AS IS"
 AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
 IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
 DISCLAIMED. IN NO EVENT SHALL UCHICAGO ARGONNE, LLC OR CONTRIBUTORS BE LIABLE

README.rst

@@ -37,15 +37,15 @@ The Python ARM Radar Toolkit (Py-ART)
 .. |Tweet| image:: https://img.shields.io/twitter/url/http/shields.io.svg?style=social
     :target: https://twitter.com/Py_ART
 
-The Python ARM Radar Toolkit, Py-ART, is an open source Python module 
+The Python ARM Radar Toolkit, Py-ART, is an open source Python module
 containing a growing collection of weather radar algorithms and utilities
 build on top of the Scientific Python stack and distributed under the
-3-Clause BSD license. Py-ART is used by the 
-`Atmospheric Radiation Measurement (ARM) User Facility 
+3-Clause BSD license. Py-ART is used by the
+`Atmospheric Radiation Measurement (ARM) User Facility
 <http://www.arm.gov>`_ for working with data from a number of precipitation
 and cloud radars, but has been designed so that it can be used by others in
 the radar and atmospheric communities to examine, processes, and analyze
-data from many types of weather radars. 
+data from many types of weather radars.
 
 
 Important Links
@@ -80,8 +80,8 @@ Install
 The easiest method for installing Py-ART is to use the conda packages from
 the latest release and use Python 3, as Python 2 support ended January 1st,
 2020 and many packages including Py-ART no longer support Python 2.
-To do this you must download and install 
-`Anaconda <https://www.anaconda.com/download/#>`_ or 
+To do this you must download and install
+`Anaconda <https://www.anaconda.com/download/#>`_ or
 `Miniconda <https://conda.io/miniconda.html>`_.
 With Anaconda or Miniconda install, it is recommended to create a new conda
 environment when using Py-ART or even other packages. To create a new
@@ -107,7 +107,7 @@ If you are using mamba::
     mamba install -c conda-forge arm_pyart
 
 If you do not wish to use Anaconda or Miniconda as a Python environment or want
-to use the latest, unreleased version of Py-ART see the section below on 
+to use the latest, unreleased version of Py-ART see the section below on
 **Installing from source**.
 
 
@@ -127,16 +127,16 @@ Extensions and related software
 A number of projects are available which extend the functionality of Py-ART.
 These include:
 
-* `ARTView <https://github.com/nguy/artview>`_ : 
+* `ARTView <https://github.com/nguy/artview>`_ :
   Interactive radar viewing browser.
 
 * `pyrad <https://github.com/MeteoSwiss/pyrad>`_ :
-  A real-time data processing framework developed by MeteoSwiss and MeteoFrance. 
+  A real-time data processing framework developed by MeteoSwiss and MeteoFrance.
 
-* `PyTDA <https://github.com/nasa/PyTDA>`_ : 
+* `PyTDA <https://github.com/nasa/PyTDA>`_ :
   Python Turbulence Detection Algorithm.
 
-* `SingleDop <https://github.com/nasa/SingleDop>`_ : 
+* `SingleDop <https://github.com/nasa/SingleDop>`_ :
   Single Doppler Retrieval Toolkit.
 
 * `DualPol <https://github.com/nasa/DualPol>`_ :
@@ -150,7 +150,7 @@ Other related open source software for working with weather radar data:
 
 * `wradlib <https://wradlib.org>`_ :
   An open source library for weather radar data processing.
-  
+
 * `BALTRAD <https://baltrad.eu/>`_ : Community-based weather radar networking.
 
 * `MMM-Py <https://github.com/nasa/MMM-Py>`_ :
@@ -186,7 +186,7 @@ The required dependencies to install Py-ART in addition to Python are:
 * `setuptools <https://setuptools.pypa.io/en/latest/index.html>`_
 
 A working C/C++ compiler is required for some optional modules. An easy method
-to install these dependencies is by using a 
+to install these dependencies is by using a
 `Scientific Python distributions <http://scipy.org/install.html>`_.
 `Anaconda <https://www.anaconda.com/distribution/>`_ will install all of
 the above packages by default on Windows, Linux and Mac computers and is
@@ -202,10 +202,10 @@ Optional Dependences
 The above Python modules are require before installing Py-ART, additional
 functionality is available of the following modules are installed.
 
-* `TRMM Radar Software Library (RSL) 
-  <https://trmm-fc.gsfc.nasa.gov/trmm_gv/software/rsl/>`_.  
-  If installed Py-ART will be able to read in radar data in a number of 
-  additional formats (Lassen, McGill, Universal Format, and RADTEC) and 
+* `TRMM Radar Software Library (RSL)
+  <https://trmm-fc.gsfc.nasa.gov/trmm_gv/software/rsl/>`_.
+  If installed Py-ART will be able to read in radar data in a number of
+  additional formats (Lassen, McGill, Universal Format, and RADTEC) and
   perform automatic dealiasing of Doppler velocities.  RSL should be
   install prior to installing Py-ART. The environmental variable `RSL_PATH`
   should point to the location where RSL was installed if RSL was not
@@ -218,10 +218,10 @@ functionality is available of the following modules are installed.
 
 * A linear programming solver and Python wrapper to use the LP phase
   processing method. `CyLP <https://github.com/mpy/CyLP>`_ is recommended as
-  it gives the fastest results, but 
-  `PyGLPK <https://tfinley.net/software/pyglpk/>`_ and 
-  `CVXOPT <https://cvxopt.org/>`_ are also supported. The underlying LP 
-  solvers `CBC <https://projects.coin-or.org/Cbc>`_ or 
+  it gives the fastest results, but
+  `PyGLPK <https://tfinley.net/software/pyglpk/>`_ and
+  `CVXOPT <https://cvxopt.org/>`_ are also supported. The underlying LP
+  solvers `CBC <https://projects.coin-or.org/Cbc>`_ or
   `GLPK <https://www.gnu.org/software/glpk/>`_ will also be required depending
   on which wrapper is used. When using `CyLP <https://github.com/mpy/CyLP>`_
   a path to coincbc is needed by setting the `COIN_INSTALL_DIR` path, such as
@@ -245,15 +245,15 @@ functionality is available of the following modules are installed.
 
 * `gdal <https://pypi.python.org/pypi/GDAL/>`_.
   Required to output GeoTIFFs from `Grid` objects.
- 
+
 Installing from source
 ======================
 
 Installing Py-ART from source is the only way to get the latest updates and
 enhancement to the software that have not yet made it into a release.
 The latest source code for Py-ART can be obtained from the GitHub repository,
-https://github.com/ARM-DOE/pyart. Either download and unpack the 
-`zip file <https://github.com/ARM-DOE/pyart/archive/master.zip>`_ of 
+https://github.com/ARM-DOE/pyart. Either download and unpack the
+`zip file <https://github.com/ARM-DOE/pyart/archive/master.zip>`_ of
 the source code or use git to checkout the repository::
 
     git clone https://github.com/ARM-DOE/pyart.git
@@ -281,7 +281,7 @@ the package are welcomed from all users.
 Code
 ----
 The latest source code can be obtained with the command::
- 
+
     git clone https://github.com/ARM-DOE/pyart.git
 
 If you are planning on making changes that you would like included in Py-ART,

doc/rebuild_examples.sh

@@ -2,4 +2,3 @@
 rm -r build
 rm -r source/source/auto_examples/*
 BUILD_PYART_EXAMPLES=1 make html
-

doc/source/API/index.rst

@@ -7,7 +7,7 @@ API Reference Manual
 :Release: |version|
 :Date: |today|
 
-This guide provides documentation for all modules, function, methods, 
+This guide provides documentation for all modules, function, methods,
 and classes within Py-ART for those in the public API.
 
 Documentation is broken down by directory and module.
@@ -16,7 +16,7 @@ Documentation is broken down by directory and module.
 
 .. autosummary::
    :toctree: generated/
-    
+
    core
    io
    aux_io

doc/source/_static/doc_shared.js

@@ -9,4 +9,4 @@ $(document).ready(function () {
             $('#banner').prepend(data);
         }
     })
- })
+ })