Add: precommit and clean up all files

Author: lwasser

.circleci/config.yml

@@ -12,7 +12,7 @@ jobs:
             pip install nox
             pip list
       - run:
-          name: Build book html 
+          name: Build book html
           command: nox -s docs
 
       - store_artifacts:

.github/workflows/build-book.yml

@@ -1,7 +1,7 @@
 name: build-test-deploy-book
 
 # Only build PRs, the main branch, and releases. Pushes to branches will only
-# be built when a PR is opened. This avoids duplicated buids in PRs comming
+# be built when a PR is opened. This avoids duplicated buids in PRs coming
 # from branches in the origin repository (1 for PR and 1 for push).
 # This came from Leo's work with fatiando
 on:
@@ -53,7 +53,7 @@ jobs:
           _build/html/
 
     # Push the book's HTML to github-pages
-    - name: Push to GitHub Pages 
+    - name: Push to GitHub Pages
       # Only push if on main branch
       if: github.ref == 'refs/heads/main'
       uses: peaceiris/[email protected]
@@ -69,5 +69,3 @@ jobs:
         arguments: |
           --ignore-files "/.+\/_static\/.+/,/genindex.html/"
           --ignore-status-codes "404, 403, 503"
-
-    

.pre-commit-config.yaml

@@ -0,0 +1,41 @@
+# pre-commit is a tool that you run locally
+# to perform a predefined set of tasks manually and/or
+# automatically before git commits are made.
+# Here we are using pre-commit with the precommit.ci bot to implement
+# code fixes automagically in pr's. You will still want to install pre-commit
+# to run locally
+# Config reference: https://pre-commit.com/#pre-commit-configyaml---top-level
+# To run on a pr, add a comment with the text "pre-commit.ci run"
+# Common tasks
+#
+# - Run on all files:   pre-commit run --all-files
+# - Register git hooks: pre-commit install --install-hooks
+
+ci:
+    autofix_prs: false
+    #skip: [flake8, end-of-file-fixer]
+    autofix_commit_msg: |
+        '[pre-commit.ci 🤖] Apply code format tools to PR'
+    # Update hook versions every quarter (so we don't get hit with weekly update pr's)
+    autoupdate_schedule: quarterly
+
+repos:
+
+  # Misc commit checks
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    # ref: https://github.com/pre-commit/pre-commit-hooks#hooks-available
+    hooks:
+      # Autoformat: Makes sure files end in a newline and only a newline.
+      - id: end-of-file-fixer
+      # Lint: Check for files with names that would conflict on a
+      # case-insensitive filesystem like MacOS HFS+ or Windows FAT.
+      - id: check-case-conflict
+      - id: trailing-whitespace
+
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.2
+    hooks:
+    - id: codespell
+      additional_dependencies:
+        - tomli

CONTRIBUTING.md

@@ -1,25 +1,25 @@
-# Contributing Guide for the Python open source software packaging book 
+# Contributing Guide for the Python open source software packaging book
 
 This is a community resource. We welcome contributions in the form of issues and/or pull requests to this guide.
 
-* If you have an idea for something that should be included in the guide, [please open an issue here](https://github.com/pyOpenSci/python-package-guide/issues). 
-* If you find a typo, feel free to [submit a pull request](https://github.com/pyOpenSci/python-package-guide/pulls) to modify the text directly. Or, if you are less comfortable with pull requests, feel free to open an issue. 
-* If you want to see a larger change to the content of the guide book, please submit an issue first! 
+* If you have an idea for something that should be included in the guide, [please open an issue here](https://github.com/pyOpenSci/python-package-guide/issues).
+* If you find a typo, feel free to [submit a pull request](https://github.com/pyOpenSci/python-package-guide/pulls) to modify the text directly. Or, if you are less comfortable with pull requests, feel free to open an issue.
+* If you want to see a larger change to the content of the guide book, please submit an issue first!
 
 ## How this guide structured
 
 Most of this repository is structured for **Sphinx**, a documentation engine built in `Python`. We are using the Sphinx Book Theme and the `myST` syntax to create each page in this book.
 
-If you wish to contribute by working on the guide book locally, you 
-will first need to 
+If you wish to contribute by working on the guide book locally, you
+will first need to
 
-1. Fork this repository 
+1. Fork this repository
 2. Clone it locally
-3. Build the documentation locally 
+3. Build the documentation locally
 
 ## Instructions for building the documentation locally on your computer
 
-The easiest way to build the documentation in this repository is to use `nox`, 
+The easiest way to build the documentation in this repository is to use `nox`,
 a tool for quickly building environments and running commands within them.
 Nox ensures that your environment has all the dependencies needed to build the documentation.
 

README.md

@@ -15,11 +15,11 @@ pyOpenSci is devoted to building diverse, supportive community around
 the Python open source tools that drive open science. We do this through:
 
 * open peer review
-* mentorship and 
+* mentorship and
 * training.
 
-pyOpenSci is an independent organization, fiscally sponsored by Community 
-Initiatives.  
+pyOpenSci is an independent organization, fiscally sponsored by Community
+Initiatives.
 
 :construction: Construction note :construction:
 
@@ -97,4 +97,4 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d
 
 <!-- ALL-CONTRIBUTORS-LIST:END -->
 
-This project follows the [all-contributors](https://github.com/all-contributors/all-contributors) specification. Contributions of any kind welcome!
+This project follows the [all-contributors](https://github.com/all-contributors/all-contributors) specification. Contributions of any kind welcome!

_static/pyos.css

@@ -41,4 +41,4 @@ figcaption {
 .admonition p {
     font-size: 1.1em;
     font-weight: bold;
-  }
+  }

_templates/header.html

@@ -3,5 +3,4 @@
 <!-- <link rel="preconnect" href="https://fonts.googleapis.com">
 <link rel="preconnect" href="https://fonts.gstatic.com" crossorigin>
 <link href="https://fonts.googleapis.com/css2?family=Open+Sans:wght@400;600&family=Raleway:wght@200;300;400;600&display=swap" rel="stylesheet">  -->
-<!-- END custom head content --> 
-
+<!-- END custom head content -->

ci-and-testing/intro.md

@@ -4,4 +4,4 @@
 This section is evolving and should be published by the end of Spring 2023
 
 
-coming soon
+coming soon

code-style-structure/intro.md

@@ -1,4 +1,4 @@
 # Code style and structure
 
 
-Under development
+Under development

codespell-ignore.txt

@@ -0,0 +1 @@
+aways