pre-commit check for files over 5MB (#143)

.github/workflows/linter_actions.yml

@@ -16,4 +16,3 @@ jobs:
       # note linter arguments are supplied via the .flake8 config file
       - name: Annotate PR after running flake8
         uses: TrueBrain/actions-flake8@v2
-

.pre-commit-config.yaml

@@ -4,4 +4,16 @@ repos:
     hooks:
     - id: black
 
-# you can run `pre-commit autoupdate` to automatically update to the latest version of hooks!
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v3.4.0  # Use the ref you want to point at
+    hooks:
+    - id: check-added-large-files
+      args: ["--maxkb=5000"]
+    - id: end-of-file-fixer
+    - id: trailing-whitespace
+      args: [--markdown-linebreak-ext=md]
+
+ci:
+  autoupdate_schedule: monthly
+
+# you can run `pre-commit autoupdate` to automatically update to the latest version of hooks!

README.rst

@@ -7,7 +7,7 @@ icepyx
 
 Latest release (main branch): |Docs Status main| |Travis main Build Status| |Code Coverage main|
 
-Current development version (development branch): |Docs Status dev| |Travis dev Build Status| |Code Coverage dev|
+Current development version (development branch): |Docs Status dev| |Travis dev Build Status| |Code Coverage dev| |Pre-commit dev|
 
 .. |GitHub license| image:: https://img.shields.io/badge/License-BSD%203--Clause-blue.svg
    :target: https://opensource.org/licenses/BSD-3-Clause
@@ -44,6 +44,10 @@ Current development version (development branch): |Docs Status dev| |Travis dev
 .. |Code Coverage dev| image:: https://codecov.io/gh/icesat2py/icepyx/branch/development/graph/badge.svg
     :target: https://codecov.io/gh/icesat2py/icepyx
 
+.. |Pre-commit dev| image:: https://results.pre-commit.ci/badge/github/icesat2py/icepyx/development.svg
+   :target: https://results.pre-commit.ci/latest/github/icesat2py/icepyx/development
+   :alt: pre-commit.ci status
+
 
 Origin and Purpose
 ------------------

doc/source/contributing/contribution_guidelines.rst

@@ -58,7 +58,9 @@ By having a *development* branch for daily work, we enable the *main* branch to
 
 First Steps
 ^^^^^^^^^^^
-Before you begin writing code, please first check out our issues page. Someone may already be working on the same problem, and you may be able to contribute directly to their efforts. If not, create a new issue to describe what you plan to do.
+Before you begin writing code, please first check out our issues page.
+Someone may already be working on the same problem, and you may be able to contribute directly to their efforts.
+If not, create a new issue to describe what you plan to do.
 
 General Guidelines
 ^^^^^^^^^^^^^^^^^^
@@ -73,7 +75,8 @@ General Guidelines
 
 Basic Steps to Contribute
 ^^^^^^^^^^^^^^^^^^^^^^^^^
-We encourage users to follow the `git pull request workflow <https://www.asmeurer.com/git-workflow/>`_. For more detailed steps, please see :ref:`How to Contribute<dev_guide_label>`.
+We encourage users to follow the `git pull request workflow <https://www.asmeurer.com/git-workflow/>`_.
+For more detailed steps, please see :ref:`How to Contribute<dev_guide_label>`.
 
 Licensing
 ^^^^^^^^^

doc/source/contributing/how_to_contribute.rst

@@ -94,7 +94,19 @@ environment (from the home level of your local copy of the icepyx repo) with
 
     mamba env create --name icepyx-env --channel conda-forge -f requirements-dev.txt -f requirements.txt
 
-and then pip installing icepyx as described above and below.
+and then (1) running `pre-commit install` to let git know about pre-commit and
+(2) pip installing icepyx as described above and below.
+
+One of the tools installed with "requirements-dev.txt" is called [pre-commit](https://pre-commit.com/).
+We have included a set of pre-commit formatting hooks that we strongly encourage all contributors to use.
+These hooks will check the files you are committing for format consistency,
+reformatting the files if necessary.
+You can tell files were reformatted if you get a message showing one of the checks failed.
+In this case, you will need to re-commit your changes until all pre-commit hooks pass
+(i.e. a failed pre-commit check results in no git commit).
+Pre-commit will also run on icepyx PRs using the pre-commit CI (continuous integration).
+As with other automations happening in PRs,
+you'll want to make sure you pull the changes back to your local version before making new commits.
 
 
 Considerations with Jupyter Notebook

doc/source/tracking/citations.rst

@@ -41,7 +41,7 @@ Presentations that feature or explain icepyx
 
 .. bibliography:: icepyx_pubs.bib
     :style: mystyle
-    
+
     quest2023agu
     js2022agu
     2022_IS2-HW-tutorials

doc/source/tracking/icepyx_pubs.bib

@@ -8,7 +8,7 @@ @misc{quest2023agu
                 Abib, Nicole and
                 {Di Bella}, Alessandro and
                 Tilling, Rachel},
-title        = {On a {QUEST (Query, Unify, Explore SpatioTemporal)} 
+title        = {On a {QUEST (Query, Unify, Explore SpatioTemporal)}
                   to Accelerate {ICESat-2} Applications in Ocean
                   Science via {icepyx}},
 month        = jan,
@@ -161,8 +161,8 @@ @misc{js2019agu
 
 @INPROCEEDINGS{Bednar2023,
 author={Bednar, James A. and Durant, Martin},
-booktitle={Proceedings of the 22nd {Python} in Science Conference (SciPy 2023)}, 
-title={The {Pandata} Scalable Open-Source Analysis Stack}, 
+booktitle={Proceedings of the 22nd {Python} in Science Conference (SciPy 2023)},
+title={The {Pandata} Scalable Open-Source Analysis Stack},
 year={2023},
 volume={},
 number={},