Added more linters and removed more lint (landlab#1514)

* remove import lint with isort

* upgrade to python 3.8+ syntax

* remove trailing whitespace, fix end of file, etc.

* add .nox folder to .gitnore

* simplify code identified with flake8-simplify

* remove auto-generated *.cpp files

* remove bugbear lint--mostly unused loop counters

* adjust flake8 defaults

* add additional pre-commit hooks to look for lint

* use cached_property instead of lru_cache because of memory leak

* remove mutable keyword default values

* update flake8 config

* add news fragments

* clean up the project .gitignore file

* fix files with mixed line endings

.github/PULL_REQUEST_TEMPLATE.md

@@ -46,4 +46,3 @@
       Ask a question or submit an issue: https://github.com/landlab/landlab/issues
       Landlab Slack channel: https://landlab.slack.com
 -->
-

.github/workflows/changelog.yml

@@ -23,4 +23,3 @@ jobs:
           echo "Please see https://landlab.readthedocs.io/en/master/development/contribution/index.html?highlight=towncrier#news-entries for guidance."
             false
           fi
-

.github/workflows/docs.yml

@@ -11,9 +11,9 @@ jobs:
         if:
           github.event_name == 'push' || github.event.pull_request.head.repo.full_name !=
           github.repository
-    
+
         runs-on: ubuntu-latest
-        
+
         defaults:
           run:
             shell: bash -l {0}
@@ -30,7 +30,7 @@ jobs:
           - name: Show conda installation info
             run: |
               conda info
-    
+
           - name: Install dependencies
             run: pip install nox
 

.github/workflows/prerelease.yml

@@ -70,4 +70,3 @@ jobs:
       - name: Upload distributions
         run: |
           twine upload --skip-existing wheelhouse/*.whl
-

.gitignore

@@ -52,7 +52,7 @@ coverage.xml
 *.pot
 
 # Sphinx documentation
-docs/_build/
+docs/build/
 
 # Vim
 *~
@@ -77,56 +77,18 @@ test-results.xml
 
 *.synctex.gz
 
-.hypothesis/
-
-installfiles.txt
+# installfiles.txt
 
 # Ignore all .c files as, currently, they are all cython generated.
 *.c
+*.cpp
 
-landlab/io/mysave.grid
-
-docs/auto_grid_info__BCs.rst
-
-docs/auto_grid_info__cells.rst
-
-docs/auto_grid_info__corners.rst
-
-docs/auto_grid_info__faces.rst
-
-docs/auto_grid_info__grads.rst
-
-docs/auto_grid_info__links.rst
-
-docs/auto_grid_info__mappers.rst
-
-docs/auto_grid_info__nodes.rst
-
-docs/auto_grid_info__patches.rst
-
-docs/auto_grid_info__subsets.rst
-
-docs/auto_grid_info__surf.rst
-
-docs/auto_grid_info__whole.rst
-
-landlab/components/spatial_precip/Durations_summer.csv
-
-landlab/components/spatial_precip/Durations_winter.csv
-
-\.pytest_cache/README\.md
-
-\.pytest_cache/v/cache/lastfailed
-
-\.pytest_cache/v/cache/nodeids
-
-
-\.pytest_cache/v/cache/
-
-docs/build_log.txt
-
-.eggs/README.txt
+# pytest
+.pytest_cache/
 
 
 # Hypothesis
 .hypothesis
+
+# nox virtual envs
+.nox

.pre-commit-config.yaml

@@ -25,20 +25,60 @@ repos:
 - repo: https://github.com/pycqa/flake8
   rev: 4.0.1
   hooks:
-    - id: flake8
-      additional_dependencies:
-      - flake8-comprehensions
-      # - flake8-bugbear
-      #   - flake8-simplify
+  - id: flake8
+    additional_dependencies:
+    - flake8-bugbear
+    - flake8-comprehensions
+    - flake8-simplify
 
-- repo: https://gitlab.com/iamlikeme/nbhooks
-  rev: 1.0.0
+- repo: https://gitlab.com/kennon.mckeever/nbhooks
+  rev: 1.0.1
   hooks:
   - id: nb-ensure-clean
     name: nb-ensure-clean
     description: Ensure that committed Jupyter notebooks contain no outputs.
     entry: nb-ensure-clean
     files: \.ipynb$
     language: python
-    language_version: python3.8
 
+- repo: https://github.com/asottile/pyupgrade
+  rev: v2.34.0
+  hooks:
+  - id: pyupgrade
+    args: [--py38-plus]
+
+- repo: https://github.com/PyCQA/isort
+  rev: 5.10.1
+  hooks:
+  - id: isort
+    files: \.py$
+
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.3.0
+  hooks:
+    - id: check-builtin-literals
+    - id: check-added-large-files
+    - id: check-case-conflict
+    - id: check-toml
+    - id: check-yaml
+    - id: debug-statements
+    - id: end-of-file-fixer
+    - id: forbid-new-submodules
+    - id: mixed-line-ending
+    - id: trailing-whitespace
+
+# - repo: https://github.com/PyCQA/pydocstyle
+#   rev: 6.1.1
+#   hooks:
+#   - id: pydocstyle
+#     files: landlab/.*\.py$
+#     args:
+#     - --convention=numpy
+#     - --add-select=D417
+#     additional_dependencies: [".[toml]"]
+
+# - repo: https://github.com/pre-commit/mirrors-mypy
+#   rev: v0.982
+#   hooks:
+#   - id: mypy
+#     additional_dependencies: [types-all]

AUTHORS.rst

@@ -37,4 +37,4 @@ Contributors
 - `Shelby Ahrendt <https://github.com/shelbyahrendt>`_
 - `Josh Wolpert <https://github.com/josh-wolpert>`_
 - `Christopher Sheehan <https://github.com/Sheehace>`_
-- `slundell123 <https://github.com/slundell123>`_
+- `slundell123 <https://github.com/slundell123>`_

CITATION.cff

@@ -4,14 +4,14 @@ cff-version: "1.2.0"
 message: "If you use this software, please cite it using these metadata."
 abstract : "Landlab is an open-source Python-language package for numerical modeling of Earth surface dynamics."
 type: software
-authors: 
+authors:
   -
     family-names: Hutton
     given-names: Eric
     orcid: "https://orcid.org/0000-0002-5864-6459"
   -
     family-names: Barnhart
-    given-names: Katy  
+    given-names: Katy
     orcid: "https://orcid.org/0000-0001-5682-455X"
   -
     family-names: Hobley

FUNDING.rst

@@ -21,4 +21,4 @@ by the following grants:
 * A Collaborative NSF Frameworks proposal to University of Colorado (Greg Tucker,
   `2104102 <https://www.nsf.gov/awardsearch/showAward?AWD_ID=2104102&HistoricalAwards=false>`_).
 * A Collaborative NSF Facility proposal to University of Colorado (Greg Tucker,
-  `2148762 <https://www.nsf.gov/awardsearch/showAward?AWD_ID=2148762&HistoricalAwards=false>`_).
+  `2148762 <https://www.nsf.gov/awardsearch/showAward?AWD_ID=2148762&HistoricalAwards=false>`_).

README.rst

@@ -70,7 +70,7 @@ Installation
 .. start-install-release
 
 In order to use *landlab* you will first need Python. While not
-necessary, we recommend using the 
+necessary, we recommend using the
 `Anaconda Python distribution <https://www.anaconda.com/distribution/>`_
 as it provides a large number of third-party packages useful for
 scientific computing.
@@ -302,6 +302,3 @@ During workshops and clinics, we sometimes use the
 `Landlab Slack channel <https://landlab.slack.com>`_.
 
 .. end-contact
-
-
-

docs/fix_redirects.py

@@ -1,11 +1,10 @@
 # fix redirects
-import os
-
 import fileinput
+import os
 
 _SRC = "source"
 
-with open("build/linkcheck/output.txt", "r") as f:
+with open("build/linkcheck/output.txt") as f:
     link_out = f.readlines()
 
 

docs/source/changes.rst

@@ -1 +1 @@
-.. include:: ../../CHANGES.rst
+.. include:: ../../CHANGES.rst

docs/source/citing.rst

@@ -10,4 +10,4 @@ Citing Components
 
 .. include:: ../../README.rst
     :start-after: .. start-citing-components
-    :end-before: .. end-citing-components
+    :end-before: .. end-citing-components

docs/source/conf.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 #
 # landlab documentation build configuration file, created by
 # sphinx-quickstart on Tue Apr 23 17:33:31 2013.
@@ -12,11 +11,12 @@
 # serve to show the default.
 
 import os
-import sys
-import tomli
 import pathlib
+import sys
 from datetime import date
 
+import tomli
+
 import landlab
 
 # If extensions (or modules to document with autodoc) are in another directory,

docs/source/contact_us.rst

@@ -5,4 +5,4 @@ Contact
 
 .. include:: ../../README.rst
     :start-after: .. start-contact
-    :end-before: .. end-contact
+    :end-before: .. end-contact

docs/source/development/contribution/recommendations.rst

@@ -32,4 +32,4 @@ Recommendations
 - Arguments and keyword arguments start with lower case letters.
 - Keyword arguments have reasonable default values (and the grid is the only argument to ``__init__``.
 - Can return or not return information. Some recommendations, Nothing, grid, or a ... or a calculated value.
-- If possible, we recommend that components are unit agnostic. 
+- If possible, we recommend that components are unit agnostic.

docs/source/development/install/installing_windows_compiler.rst

@@ -40,4 +40,4 @@ and download the Microsoft Visual C++ compiler. In April 2019 this was done by
 first downloading "Build Tools for Visual Studio". Then when installing Build
 Tools there were options for what exactly should be installed. One of these was
 the Visual Studio C++ compilers. Once installed, a restart was required and
-landlab compiled as expected. 
+landlab compiled as expected.

docs/source/getting_started/teach_yourself_landlab.rst

@@ -5,4 +5,4 @@ Self-study course for learning to use Landlab in your research
 
 This course is entirely hosted in our Jupyter notebook tutorials. Here is a
 link to the `syllabus <https://mybinder.org/v2/gh/landlab/landlab/release?filepath=notebooks/tutorials/syllabus.ipynb>`_
-on Binder. 
+on Binder.

docs/source/index.rst

@@ -27,25 +27,25 @@ Landlab: A modular Earth Surface Dynamics modeling library
  install/index
  development/index
  API Reference <reference/index>
- 
+
 .. toctree::
   :caption: Useful Links
   :maxdepth: 1
   :hidden:
-  
+
   changes
   contact_us
   citing
   funding
   Contributors <authors>
   License <license>
   Used by <usedby>
-  
+
 ..
   .. toctree::
      :caption: Documentation Outline
      :maxdepth: 2
-  
+
      install/index
      getting_started/index
      user_guide/index
@@ -68,5 +68,3 @@ Landlab: A modular Earth Surface Dynamics modeling library
   :ref:`here <tutorials>`. A subset of these notebooks are designed specifically
   for the classroom. Information about them and how to set them up for classroom
   use is described :ref:`on this page <teaching_tutorials>`.
-
-

docs/source/install/environments.rst

@@ -16,22 +16,22 @@ should stick with *pip*.
 .. tab:: mamba
 
     .. code-block:: bash
-    
+
         $ conda install mamba -c conda-forge
         $ mamba create -n landlab
         $ mamba activate landlab
 
 .. tab:: conda
 
     .. code-block:: bash
-    
+
         $ conda create -n landlab
         $ conda activate landlab
 
 .. tab:: venv
 
     .. code-block:: bash
-    
+
         $ python -m venv .venv
         $ source .venv/bin/activate
 
@@ -41,4 +41,3 @@ Helpful links on managing virtual environments:
 
 * `conda environments <https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#creating-an-environment-with-commands>`_.
 * `venv environments <https://docs.python.org/3/tutorial/venv.html>`_.
-

docs/source/install/index.rst

@@ -16,4 +16,4 @@
 
   environments
   update_uninstall
-  additional_resources
+  additional_resources

docs/source/install/installing_python.rst

@@ -64,6 +64,6 @@ operating system. For instance, Dan's Macbook Pro shows ``python`` on the path::
 
 On a PC, run ``python`` from your Command Prompt window. You should see a reference to anaconda when it is running.
 
-If you *don't* see reference to your newly installed distribution or the file is not found, click :ref:`here <correcting_install_paths>` to resolve the problem. 
+If you *don't* see reference to your newly installed distribution or the file is not found, click :ref:`here <correcting_install_paths>` to resolve the problem.
 
 Once you have installed a complete Python distribution on your machine, follow :ref:`these instructions <install>` to install Landlab.

docs/source/install/rough_guide_to_python.rst

@@ -77,7 +77,7 @@ that file in your favourite text editor, and add at the end:
 
 Restart the terminal again, and check the version number now. Should be
 right! (You will probably also want to do something similar with ipython,
-but DEJH didn't explore that...) 
+but DEJH didn't explore that...)
 
 Installing pip
 --------------

docs/source/install/update_uninstall.rst

@@ -30,5 +30,3 @@ To uninstall *landlab*,
   .. code-block:: bash
 
     $ pip uninstall landlab
-
-

docs/source/reference/components/bedrock_landslider.rst

@@ -5,4 +5,3 @@ BedrockLandslider: Location and magnitude of episodic bedrock landsliding
     :members:
     :undoc-members:
     :show-inheritance:
-