Pre-commit hooks

Author: patrickmineault

Diff for: .gitignore

@@ -5,4 +5,4 @@ _build
 .DS_Store
 tmp
 exports
-conf.py
+conf.py

Diff for: .netlify/state.json

@@ -1,3 +1,3 @@
 {
 	"siteId": "f0bcb2b1-3782-4a4b-8611-94f5412b4f76"
-}
+}

Diff for: .pre-commit-config.yaml

@@ -0,0 +1,11 @@
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v2.3.0
+    hooks:
+    -   id: check-yaml
+    -   id: end-of-file-fixer
+    -   id: trailing-whitespace
+-   repo: https://github.com/psf/black
+    rev: 22.10.0
+    hooks:
+    -   id: black

Diff for: LICENSE

@@ -92,4 +92,4 @@ Section 8 – Interpretation.
     For the avoidance of doubt, this Public License does not, and shall not be interpreted to, reduce, limit, restrict, or impose conditions on any use of the Licensed Material that could lawfully be made without permission under this Public License.
     To the extent possible, if any provision of this Public License is deemed unenforceable, it shall be automatically reformed to the minimum extent necessary to make it enforceable. If the provision cannot be reformed, it shall be severed from this Public License without affecting the enforceability of the remaining terms and conditions.
     No term or condition of this Public License will be waived and no failure to comply consented to unless expressly agreed to by the Licensor.
-    Nothing in this Public License constitutes or may be interpreted as a limitation upon, or waiver of, any privileges and immunities that apply to the Licensor or You, including from the legal processes of any jurisdiction or authority.
+    Nothing in this Public License constitutes or may be interpreted as a limitation upon, or waiver of, any privileges and immunities that apply to the Licensor or You, including from the legal processes of any jurisdiction or authority.

Diff for: Makefile

@@ -8,7 +8,7 @@ tmp/exports/book-complete.tex: $(wildcard *.md) _toc.yml assemble_onepager.py tm
 tmp:
 	mkdir tmp
 
-develop: 
+develop:
 	jupyter-book config sphinx . > conf.py
 	sphinx-autobuild . _build/html -b html
 

Diff for: TODO.md

@@ -14,7 +14,7 @@ Some questions you might consider:
 
 1. Was the advice consistent with what you consider best practices? If not, how so?
 1. Were some critical subjects not covered by this book?
-1. Was the narrative cohesive? 
+1. Was the narrative cohesive?
 1. Were some subjects treated too superficially? Were some subjects treated with too much detail? How was the pacing overall?
 1. Was the level appropriate for the target audience (2nd and 3rd year grad students focused on computational subjects)? If not, how so?
 1. Did you feel that illustrations were appropriate? Where do you feel more illustrations would be helpful to the narrative?

Diff for: _config.yml

@@ -48,4 +48,4 @@ sphinx:
   config:
     ogp_site_url: "https://goodresearch.dev/"
     ogp_image: "https://goodresearch.dev/_images/unicorn.png"
-    ogp_description_length: 200
+    ogp_description_length: 200

Diff for: _static/et-book/et-book-bold-line-figures/et-book-bold-line-figures.svg

@@ -19,4 +19,4 @@ parts:
   chapters:
     - file: cka
     - file: tools
-    - file: acknowledgements
+    - file: acknowledgements

Diff for: _static/et-book/et-book-display-italic-old-style-figures/et-book-display-italic-old-style-figures.svg

@@ -22,4 +22,4 @@ This book was inspired by many other long-form books, papers and tutorials. Chec
 - Greg Wilson et al. [Good enough practices in scientific computing](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005510)
 - The CodeRefinery Community. [Materials from CodeRefinery](https://coderefinery.org/)
 
-This book was generated by [jupyterbook](https://jupyterbook.org/), which builds on [Sphinx](https://www.sphinx-doc.org). The stylesheet is an adaptation of [`tufte.css`](https://edwardtufte.github.io/tufte-css/). The unicorn logo is from [twemoji](https://github.com/twitter/twemoji), released under a CC-BY 4.0 license. The PDF version of this book was generated via [CurveNote](https://curvenote.com). 
+This book was generated by [jupyterbook](https://jupyterbook.org/), which builds on [Sphinx](https://www.sphinx-doc.org). The stylesheet is an adaptation of [`tufte.css`](https://edwardtufte.github.io/tufte-css/). The unicorn logo is from [twemoji](https://github.com/twitter/twemoji), released under a CC-BY 4.0 license. The PDF version of this book was generated via [CurveNote](https://curvenote.com).

Diff for: _static/et-book/et-book-roman-line-figures/et-book-roman-line-figures.svg

@@ -37,16 +37,16 @@
 \usepackage{listings}
 \lstdefinestyle{mystyle}{
     basicstyle=\ttfamily\footnotesize,
-    breakatwhitespace=false,         
-    breaklines=true,                 
+    breakatwhitespace=false,
+    breaklines=true,
     captionpos=b,
     frame=tB,
     aboveskip=16pt,
     belowskip=16pt,
-    keepspaces=true,                 
-    showspaces=false,                
+    keepspaces=true,
+    showspaces=false,
     showstringspaces=false,
-    showtabs=false,                  
+    showtabs=false,
     tabsize=2
 }
 

Diff for: _static/et-book/et-book-roman-old-style-figures/et-book-roman-old-style-figures.svg

@@ -257,9 +257,9 @@ def _get_one():
     return X, Y
 
 def _get_multi():
-    X = (np.cos(.1 * np.pi * np.arange(10).reshape((-1, 1)) * 
+    X = (np.cos(.1 * np.pi * np.arange(10).reshape((-1, 1)) *
          np.linspace(.5, 1.5, num=3).reshape((1, -1))))
-    Y = (np.cos(.5 + .07 * np.pi * np.arange(10).reshape((-1, 1)) * 
+    Y = (np.cos(.5 + .07 * np.pi * np.arange(10).reshape((-1, 1)) *
          np.linspace(.7, 1.3, num=4).reshape((1, -1))))
     return X, Y
 

Diff for: _static/et-book/et-book-semi-bold-old-style-figures/et-book-semi-bold-old-style-figures.svg

@@ -51,4 +51,4 @@ It me!
 
 ## About the print edition
 
-If you're reading this, congratulations! You're reading the bespoke, artisanal, small-batch print edition. A few folks have asked me for a print edition, and I was happy to oblige. It's an experiment that I hope to expand in the coming years. It was made possible by last-minute feature additions in CurveNote, the wonderful new project that aims to make MyST Markdown the standard for publishing scientific articles and books.
+If you're reading this, congratulations! You're reading the bespoke, artisanal, small-batch print edition. A few folks have asked me for a print edition, and I was happy to oblige. It's an experiment that I hope to expand in the coming years. It was made possible by last-minute feature additions in CurveNote, the wonderful new project that aims to make MyST Markdown the standard for publishing scientific articles and books.

Diff for: _toc.yml

@@ -53,6 +53,6 @@ Patrick J Mineault & The Good Research Code Handbook Community (2021). _The Good
 
 ## Contact me
 
-I help businesses and labs implement the practices outlined in this book through my consulting firm, [xcorr consulting](https://xcorr.dev). Please get in touch at [[email protected]](mailto:[email protected]) to find out how we can work together. I'm also available for speaking engagements and collabs – reach out to the same address for that. 
+I help businesses and labs implement the practices outlined in this book through my consulting firm, [xcorr consulting](https://xcorr.dev). Please get in touch at [[email protected]](mailto:[email protected]) to find out how we can work together. I'm also available for speaking engagements and collabs – reach out to the same address for that.
 
 <a href="https://github.com/patrickmineault/codebook/issues">Issues with the handbook can be reported on Github</a>. <a href='https://twitter.com/patrickmineault'>I'm also active on Twitter</a>.

Diff for: acknowledgements.md

@@ -2,4 +2,4 @@
   framework = "#static"
   targetPort = 3998
   port = 9000 # The port that the netlify dev will be accessible on
-  publish = "_build/html" # The path to your static content folder
+  publish = "_build/html" # The path to your static content folder