Format quarto with prettier (#41)

.prettierrc.yaml

@@ -0,0 +1,5 @@
+---
+overrides:
+  - files: "**.qmd"
+    options:
+      parser: markdown

2023-11-14-arc-renovate/index.qmd

@@ -2,8 +2,7 @@
 title: "Renovate: Automating Dependency Management"
 author: Patrick J. Roddy
 date: 2023-11-14
-format:
-  revealjs
+format: revealjs
 ---
 
 # Introduction
@@ -54,8 +53,9 @@ format:
 ## Why Use Renovate?
 
 - Get replacement PRs to migrate from a deprecated dependency to the community
-  suggested replacement, works with most managers, see [issue
-  14149](https://github.com/renovatebot/renovate/issues/14149) for exceptions
+  suggested replacement, works with most managers, see
+  [issue 14149](https://github.com/renovatebot/renovate/issues/14149) for
+  exceptions
 - Open source (installable via npm/Yarn or Docker Hub) so can be self-hosted or
   used via the Mend Renovate App
 
@@ -122,8 +122,10 @@ format:
 ```
 
 ::: footer
+
 See in action:
 <https://github.com/paddyroddy/.github/blob/main/renovate/default-config.json5>
+
 :::
 
 ## Config is Reusable!
@@ -146,8 +148,10 @@ See in action:
 ```
 
 ::: footer
+
 See in action:
 <https://github.com/paddyroddy/.github/blob/main/.renovaterc.json5>
+
 :::
 
 ## Automerging
@@ -159,6 +163,7 @@ setting is required
 ![](figures/automerge.png)
 
 ::: {.fragment .fade-left}
+
 It is **highly recommended** to ensure you have tests that will operate on the
 Renovate branches.
 
@@ -170,41 +175,51 @@ on:
       - "renovate/**"
   pull_request:
 ```
+
 :::
 
 ## Rulesets - Status Checks
 
 :::{layout-ncol=2}
+
 ![](figures/status_checks_1.png)
 
 ::: {.fragment .fade-left}
+
 ![](figures/status_checks_2.png)
+
 :::
+
 :::
 
 ## Rulesets - Pull Requests
 
 :::{layout-ncol=2}
+
 ![](figures/pull_requests_1.png)
 
 ::: {.fragment .fade-left}
-![](figures/pull_requests_2.png)
-:::
+
+![](figures/pull_requests_2.png) :::
+
 :::
 
 ## Monitoring
 
 :::{layout-ncol=2}
+
 ![](figures/logging_1.png)
 
 ::: {.fragment .fade-left}
-![](figures/logging_2.png)
-:::
+
+![](figures/logging_2.png) :::
+
 :::
 
 ::: footer
-See in action:
-<https://developer.mend.io/github/paddyroddy/.github>
+
+See in action: <https://developer.mend.io/github/paddyroddy/.github>
+
 :::
 
 # Conclusions

2024-06-25-arc-pyopensci/index.qmd

@@ -2,52 +2,52 @@
 title: "pyOpenSci: My Experience"
 author: Patrick J. Roddy
 date: 2024-06-25
-format:
-  revealjs
+format: revealjs
 ---
 
 # The Journal of Open Source Software (JOSS)
 
 ## JOSS
 
 :::{layout-ncol=2}
+
 [![](figures/joss_logo.png)](https://joss.theoj.org)
 
-- JOSS is a **developer friendly**, open access
-journal for research software packages.
+- JOSS is a **developer friendly**, open access journal for research software
+  packages.
+
+- I previously gave a talk on JOSS, the recording of which can be
+  [accessed here](https://liveuclac.sharepoint.com/:v:/r/sites/RITSstaff/Shared%20Documents/Collaborations/Recordings/ARC%20Collaborations%20Group%20Meeting-20230606_140109-Meeting%20Recording.mp4?csf=1&web=1&e=qhKamX&nav=eyJyZWZlcnJhbEluZm8iOnsicmVmZXJyYWxBcHAiOiJTdHJlYW1XZWJBcHAiLCJyZWZlcnJhbFZpZXciOiJTaGFyZURpYWxvZy1MaW5rIiwicmVmZXJyYWxBcHBQbGF0Zm9ybSI6IldlYiIsInJlZmVycmFsTW9kZSI6InZpZXcifSwicGxheWJhY2tPcHRpb25zIjp7InN0YXJ0VGltZUluU2Vjb25kcyI6MTk4OC4wOH19).
 
-- I previously gave a talk on JOSS, the recording of which can be [accessed
-here](https://liveuclac.sharepoint.com/:v:/r/sites/RITSstaff/Shared%20Documents/Collaborations/Recordings/ARC%20Collaborations%20Group%20Meeting-20230606_140109-Meeting%20Recording.mp4?csf=1&web=1&e=qhKamX&nav=eyJyZWZlcnJhbEluZm8iOnsicmVmZXJyYWxBcHAiOiJTdHJlYW1XZWJBcHAiLCJyZWZlcnJhbFZpZXciOiJTaGFyZURpYWxvZy1MaW5rIiwicmVmZXJyYWxBcHBQbGF0Zm9ybSI6IldlYiIsInJlZmVycmFsTW9kZSI6InZpZXcifSwicGxheWJhY2tPcHRpb25zIjp7InN0YXJ0VGltZUluU2Vjb25kcyI6MTk4OC4wOH19).
 :::
 
 ## What Exactly Do You Mean by 'Journal'?
 
 - The Journal of Open Source Software (JOSS) is an academic journal (ISSN
-2475-9066) with a formal peer review process that is designed to improve the
-quality of the software submitted. Upon acceptance into JOSS, a Crossref DOI is
-minted and we list your paper on the JOSS website.
+  2475-9066) with a formal peer review process that is designed to improve the
+  quality of the software submitted. Upon acceptance into JOSS, a Crossref DOI
+  is minted and we list your paper on the JOSS website.
 
 ## Don't We Have Enough Journals Already?
 
 - Perhaps, and in a perfect world we'd rather papers about software weren't
-necessary but we recognize that for most researchers, papers and not software
-are the currency of academic research and that citations are required for a good
-career.
+  necessary but we recognize that for most researchers, papers and not software
+  are the currency of academic research and that citations are required for a
+  good career.
 
 - We built this journal because we believe that after you've done the hard work
-of writing  great software, it shouldn't take weeks and months to write a paper
-about your work.
-
+  of writing great software, it shouldn't take weeks and months to write a paper
+  about your work.
 
 ## You Said Developer Friendly, What Do You Mean?
 
-- We have a simple submission workflow and [extensive
-documentation](https://joss.readthedocs.io/en/latest/submitting.html)
-to help you prepare your submission. If your software is already well documented
-then paper preparation should take no more than an hour.
+- We have a simple submission workflow and
+  [extensive documentation](https://joss.readthedocs.io/en/latest/submitting.html)
+  to help you prepare your submission. If your software is already well
+  documented then paper preparation should take no more than an hour.
 
-- You can read more about our motivations to build JOSS in our [announcement blog
-post](https://www.arfon.org/announcing-the-journal-of-open-source-software).
+- You can read more about our motivations to build JOSS in our
+  [announcement blog post](https://www.arfon.org/announcing-the-journal-of-open-source-software).
 
 ## My Submission
 
@@ -60,14 +60,17 @@ post](https://www.arfon.org/announcing-the-journal-of-open-source-software).
 ## pyOpenSci
 
 :::{layout="[30,70]"}
+
 ![](figures/pyopensci_logo.png)
 
 - We support the scientific Python tools that drive open science through peer
-review, training and community building.
+  review, training and community building.
 
 - We build diverse community that supports free and open Python tools for
-processing scientific data. We also build technical skills needed to contribute
-to open source and that support open science. Join our global community.
+  processing scientific data. We also build technical skills needed to
+  contribute to open source and that support open science. Join our global
+  community.
+
 :::
 
 ## Pre-Submission Inquiry
@@ -79,11 +82,11 @@ to open source and that support open science. Join our global community.
 Documentation:
 
 - [ ] **A statement of need** clearly stating problems the software is designed
-to solve and its target audience in README.
+      to solve and its target audience in README.
 - [ ] **Installation instructions:** for the development version of the package
-and any non-standard dependencies in README.
+      and any non-standard dependencies in README.
 - [ ] **Vignette(s)** demonstrating major functionality that runs successfully
-locally.
+      locally.
 
 ## Review Process
 
@@ -92,21 +95,21 @@ Documentation:
 - [ ] **Function Documentation:** for all user-facing functions.
 - [ ] **Examples** for all user-facing functions.
 - [ ] **Community guidelines** including contribution guidelines in the README
-or CONTRIBUTING.
+      or CONTRIBUTING.
 - [ ] **Metadata** including author(s), author e-mail(s), a url, and any other
-relevant metadata e.g., in a `pyproject.toml` file or elsewhere.
+      relevant metadata e.g., in a `pyproject.toml` file or elsewhere.
 
 ## Review Process
 
 `README.md`:
 
 - [ ] The package name
 - [ ] Badges for:
-    - [ ] Continuous integration and test coverage,
-    - [ ] Docs building (if you have a documentation website),
-    - [ ] A [repostatus.org](https://www.repostatus.org/) badge,
-    - [ ] Python versions supported,
-    - [ ] Current package version (on PyPI / Conda).
+  - [ ] Continuous integration and test coverage,
+  - [ ] Docs building (if you have a documentation website),
+  - [ ] A [repostatus.org](https://www.repostatus.org/) badge,
+  - [ ] Python versions supported,
+  - [ ] Current package version (on PyPI / Conda).
 
 ## Review Process
 
@@ -115,24 +118,25 @@ relevant metadata e.g., in a `pyproject.toml` file or elsewhere.
 - [ ] Short description of package goals.
 - [ ] Package installation instructions
 - [ ] Any additional setup required to use the package (authentication tokens,
-etc.)
+      etc.)
 
 ## Review Process
 
 `README.md`:
 
 - [ ] Descriptive links to all vignettes. If the package is small, there may
-only be a need for one vignette which could be placed in the README.md file.
-    - [ ] Brief demonstration of package usage (as it makes sense - links to
-    vignettes could also suffice here if package description is clear)
+      only be a need for one vignette which could be placed in the README.md
+      file.
+  - [ ] Brief demonstration of package usage (as it makes sense - links to
+        vignettes could also suffice here if package description is clear)
 - [ ] Link to your documentation website.
 
 ## Review Process
 
 `README.md`:
 
 - [ ] If applicable, how the package compares to other similar packages and/or
-how it relates to other packages in the scientific ecosystem.
+      how it relates to other packages in the scientific ecosystem.
 - [ ] Citation information
 
 ## Review Process
@@ -158,35 +162,37 @@ Functionality:
 
 - [ ] **Automated tests:**
   - [ ] All tests pass on the reviewer's local machine for the package version
-  submitted by the author. Ideally this should be a tagged version making it
-  easy for reviewers to install.
+        submitted by the author. Ideally this should be a tagged version making
+        it easy for reviewers to install.
   - [ ] Tests cover essential functions of the package and a reasonable range of
-  inputs and conditions.
+        inputs and conditions.
 
 ## Review Process
 
 Functionality:
 
 - [ ] **Continuous Integration:** Has continuous integration setup (We suggest
-using Github actions but any CI platform is acceptable for review)
-- [ ] **Packaging guidelines**: The package conforms to the pyOpenSci [packaging
-guidelines](https://www.pyopensci.org/python-package-guide).
-    - [ ] Package supports modern versions of Python and not [End of life
-    versions](https://endoflife.date/python).
-    - [ ] Code format is standard throughout package and follows PEP 8
-    guidelines (CI tests for linting pass)
+      using Github actions but any CI platform is acceptable for review)
+- [ ] **Packaging guidelines**: The package conforms to the pyOpenSci
+      [packaging guidelines](https://www.pyopensci.org/python-package-guide).
+  - [ ] Package supports modern versions of Python and not
+        [End of life versions](https://endoflife.date/python).
+  - [ ] Code format is standard throughout package and follows PEP 8 guidelines
+        (CI tests for linting pass)
 
 ## Package Acception
 
 :::{layout-ncol=2}
+
 [![](figures/pyopensci_packages.png)](https://www.pyopensci.org/python-packages.html)
 
 If the package has an **obvious research application** according to JOSS's
-definition in their [submission
-requirements](http://joss.theoj.org/about#submission_requirements), then one may
-submit their package to JOSS through pyOpenSci.
+definition in their
+[submission requirements](http://joss.theoj.org/about#submission_requirements),
+then one may submit their package to JOSS through pyOpenSci.
 
 [![](https://img.shields.io/badge/PyOpenSci-Peer%20Reviewed-success.svg)](https://github.com/pyOpenSci/software-submission/issues/149)
+
 :::
 
 ## Blog Post (Optional)
@@ -200,9 +206,9 @@ submit their package to JOSS through pyOpenSci.
 - pyOpenSci still in its infancy (32 packages as of 2024-06-12)
 - Easily integrates with JOSS
 - Exposure for your package (potentionally more so in the future)
-- [rOpenSci](https://ropensci.org/) for Python, see [blog
-launch](https://ropensci.org/blog/2013/05/16/pyopensci)
-- Always looking for [package
-reviewers](https://www.pyopensci.org/about-peer-review/index.html)
+- [rOpenSci](https://ropensci.org/) for Python, see
+  [blog launch](https://ropensci.org/blog/2013/05/16/pyopensci)
+- Always looking for
+  [package reviewers](https://www.pyopensci.org/about-peer-review/index.html)
 
 # Talk on [quarto](https://quarto.org) next?