Add CI for formatting and linting checks by etiennebacher · Pull Request #6 · palaeoverse/modules

etiennebacher · 2026-07-01T13:24:30Z

This adds the same workflows as in palaeoverse but replaces Air by Panache for formatting. I also ran panache format **/*.qmd to format all qmd files (only ggplot/index.qmd so far).

@willgearty Panache formats text in addition to code chunks, for instance to wrap text to a maximum width. Is this fine with you?

Fixes#5

github-actions · 2026-07-01T13:28:38Z

See preview at https://palaeoverse.github.io/modules/pr-preview/pr-6/training/modules

willgearty · 2026-07-16T13:39:40Z

Hmm...I've always preferred to keep prose in long-form (not split to multiple lines) in markdown-like documents. Can we skip that check?

etiennebacher · 2026-07-16T13:55:45Z

Sure, I added a config file to format code chunks but leave the surrounding text intact. I think we still want to have consistent code formatting since this is visible to readers.

etiennebacher · 2026-07-27T13:46:26Z

I don't remember why I hadn't put this as "ready for review"

willgearty · 2026-07-27T14:06:30Z

+```{r}
+#| label: ggplot2


What's the reason for switching to this? Is this considered better practice for some reason?

It's the recommended way in Quarto: https://quarto.org/docs/computations/r.html#chunk-options
There are some corner case issues when using the old syntax in Quarto docs, e.g. quarto-dev/quarto#1023

LewisAJones

Looks good... couple of comments for consideration.

I agree with @willgearty regarding not hard-wrapping long lines for prose.

LewisAJones · 2026-08-12T08:15:22Z

@@ -0,0 +1,68 @@
+# This workflow runs Panache for formatting and Jarl for linting. It stores artifacts about the
+# outcome of each tool and the PR number. Those artifacts are then used in the workflow 
+# "format-lint-pr-comment.yaml" to post a comment so that it's clearer for external


Suggested change
# "format-lint-pr-comment.yaml" to post a comment so that it's clearer for external
# "format-lint-comment.yaml" to post a comment so that it's clearer for external
Correct file name?

LewisAJones · 2026-08-12T08:18:09Z

+ pull-requests: write
+ actions: read
+ steps:
+ - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6


Do we also need to set up dependabot for updating?

etiennebacher · 2026-07-01T13:24:30Z

This adds the same workflows as in palaeoverse but replaces Air by Panache for formatting. I also ran panache format **/*.qmd to format all qmd files (only ggplot/index.qmd so far).

@willgearty Panache formats text in addition to code chunks, for instance to wrap text to a maximum width. Is this fine with you?

Fixes#5

github-actions · 2026-07-01T13:28:38Z

See preview at https://palaeoverse.github.io/modules/pr-preview/pr-6/training/modules

willgearty · 2026-07-16T13:39:40Z

Hmm...I've always preferred to keep prose in long-form (not split to multiple lines) in markdown-like documents. Can we skip that check?

etiennebacher · 2026-07-16T13:55:45Z

Sure, I added a config file to format code chunks but leave the surrounding text intact. I think we still want to have consistent code formatting since this is visible to readers.

etiennebacher · 2026-07-27T13:46:26Z

I don't remember why I hadn't put this as "ready for review"

willgearty · 2026-07-27T14:06:30Z

+```{r}
+#| label: ggplot2


What's the reason for switching to this? Is this considered better practice for some reason?

It's the recommended way in Quarto: https://quarto.org/docs/computations/r.html#chunk-options
There are some corner case issues when using the old syntax in Quarto docs, e.g. quarto-dev/quarto#1023

LewisAJones

Looks good... couple of comments for consideration.

I agree with @willgearty regarding not hard-wrapping long lines for prose.

LewisAJones · 2026-08-12T08:15:22Z

@@ -0,0 +1,68 @@
+# This workflow runs Panache for formatting and Jarl for linting. It stores artifacts about the
+# outcome of each tool and the PR number. Those artifacts are then used in the workflow 
+# "format-lint-pr-comment.yaml" to post a comment so that it's clearer for external


Suggested change
# "format-lint-pr-comment.yaml" to post a comment so that it's clearer for external
# "format-lint-comment.yaml" to post a comment so that it's clearer for external
Correct file name?

LewisAJones · 2026-08-12T08:18:09Z

+ pull-requests: write
+ actions: read
+ steps:
+ - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6


Do we also need to set up dependabot for updating?

etiennebacher · 2026-07-01T13:24:30Z

This adds the same workflows as in palaeoverse but replaces Air by Panache for formatting. I also ran panache format **/*.qmd to format all qmd files (only ggplot/index.qmd so far).

@willgearty Panache formats text in addition to code chunks, for instance to wrap text to a maximum width. Is this fine with you?

Fixes#5

github-actions · 2026-07-01T13:28:38Z

See preview at https://palaeoverse.github.io/modules/pr-preview/pr-6/training/modules

willgearty · 2026-07-16T13:39:40Z

Hmm...I've always preferred to keep prose in long-form (not split to multiple lines) in markdown-like documents. Can we skip that check?

etiennebacher · 2026-07-16T13:55:45Z

Sure, I added a config file to format code chunks but leave the surrounding text intact. I think we still want to have consistent code formatting since this is visible to readers.

etiennebacher · 2026-07-27T13:46:26Z

I don't remember why I hadn't put this as "ready for review"

willgearty · 2026-07-27T14:06:30Z

+```{r}
+#| label: ggplot2


What's the reason for switching to this? Is this considered better practice for some reason?

It's the recommended way in Quarto: https://quarto.org/docs/computations/r.html#chunk-options
There are some corner case issues when using the old syntax in Quarto docs, e.g. quarto-dev/quarto#1023

LewisAJones

Looks good... couple of comments for consideration.

I agree with @willgearty regarding not hard-wrapping long lines for prose.

LewisAJones · 2026-08-12T08:15:22Z

@@ -0,0 +1,68 @@
+# This workflow runs Panache for formatting and Jarl for linting. It stores artifacts about the
+# outcome of each tool and the PR number. Those artifacts are then used in the workflow 
+# "format-lint-pr-comment.yaml" to post a comment so that it's clearer for external


Suggested change
# "format-lint-pr-comment.yaml" to post a comment so that it's clearer for external
# "format-lint-comment.yaml" to post a comment so that it's clearer for external
Correct file name?

LewisAJones · 2026-08-12T08:18:09Z

+ pull-requests: write
+ actions: read
+ steps:
+ - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6


Do we also need to set up dependabot for updating?

etiennebacher · 2026-07-01T13:24:30Z

This adds the same workflows as in palaeoverse but replaces Air by Panache for formatting. I also ran panache format **/*.qmd to format all qmd files (only ggplot/index.qmd so far).

@willgearty Panache formats text in addition to code chunks, for instance to wrap text to a maximum width. Is this fine with you?

Fixes#5

github-actions · 2026-07-01T13:28:38Z

See preview at https://palaeoverse.github.io/modules/pr-preview/pr-6/training/modules

willgearty · 2026-07-16T13:39:40Z

Hmm...I've always preferred to keep prose in long-form (not split to multiple lines) in markdown-like documents. Can we skip that check?

etiennebacher · 2026-07-16T13:55:45Z

Sure, I added a config file to format code chunks but leave the surrounding text intact. I think we still want to have consistent code formatting since this is visible to readers.

etiennebacher · 2026-07-27T13:46:26Z

I don't remember why I hadn't put this as "ready for review"

willgearty · 2026-07-27T14:06:30Z

+```{r}
+#| label: ggplot2


What's the reason for switching to this? Is this considered better practice for some reason?

It's the recommended way in Quarto: https://quarto.org/docs/computations/r.html#chunk-options
There are some corner case issues when using the old syntax in Quarto docs, e.g. quarto-dev/quarto#1023

LewisAJones

Looks good... couple of comments for consideration.

I agree with @willgearty regarding not hard-wrapping long lines for prose.

LewisAJones · 2026-08-12T08:15:22Z

@@ -0,0 +1,68 @@
+# This workflow runs Panache for formatting and Jarl for linting. It stores artifacts about the
+# outcome of each tool and the PR number. Those artifacts are then used in the workflow 
+# "format-lint-pr-comment.yaml" to post a comment so that it's clearer for external


Suggested change
# "format-lint-pr-comment.yaml" to post a comment so that it's clearer for external
# "format-lint-comment.yaml" to post a comment so that it's clearer for external
Correct file name?

LewisAJones · 2026-08-12T08:18:09Z

+ pull-requests: write
+ actions: read
+ steps:
+ - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6


Do we also need to set up dependabot for updating?

etiennebacher · 2026-07-01T13:24:30Z

This adds the same workflows as in palaeoverse but replaces Air by Panache for formatting. I also ran panache format **/*.qmd to format all qmd files (only ggplot/index.qmd so far).

@willgearty Panache formats text in addition to code chunks, for instance to wrap text to a maximum width. Is this fine with you?

Fixes#5

github-actions · 2026-07-01T13:28:38Z

See preview at https://palaeoverse.github.io/modules/pr-preview/pr-6/training/modules

willgearty · 2026-07-16T13:39:40Z

Hmm...I've always preferred to keep prose in long-form (not split to multiple lines) in markdown-like documents. Can we skip that check?

etiennebacher · 2026-07-16T13:55:45Z

Sure, I added a config file to format code chunks but leave the surrounding text intact. I think we still want to have consistent code formatting since this is visible to readers.

etiennebacher · 2026-07-27T13:46:26Z

I don't remember why I hadn't put this as "ready for review"

willgearty · 2026-07-27T14:06:30Z

+```{r}
+#| label: ggplot2


What's the reason for switching to this? Is this considered better practice for some reason?

It's the recommended way in Quarto: https://quarto.org/docs/computations/r.html#chunk-options
There are some corner case issues when using the old syntax in Quarto docs, e.g. quarto-dev/quarto#1023

LewisAJones

Looks good... couple of comments for consideration.

I agree with @willgearty regarding not hard-wrapping long lines for prose.

LewisAJones · 2026-08-12T08:15:22Z

@@ -0,0 +1,68 @@
+# This workflow runs Panache for formatting and Jarl for linting. It stores artifacts about the
+# outcome of each tool and the PR number. Those artifacts are then used in the workflow 
+# "format-lint-pr-comment.yaml" to post a comment so that it's clearer for external


Suggested change
# "format-lint-pr-comment.yaml" to post a comment so that it's clearer for external
# "format-lint-comment.yaml" to post a comment so that it's clearer for external
Correct file name?

LewisAJones · 2026-08-12T08:18:09Z

+ pull-requests: write
+ actions: read
+ steps:
+ - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6


Do we also need to set up dependabot for updating?

etiennebacher · 2026-07-01T13:24:30Z

This adds the same workflows as in palaeoverse but replaces Air by Panache for formatting. I also ran panache format **/*.qmd to format all qmd files (only ggplot/index.qmd so far).

@willgearty Panache formats text in addition to code chunks, for instance to wrap text to a maximum width. Is this fine with you?

Fixes#5

github-actions · 2026-07-01T13:28:38Z

See preview at https://palaeoverse.github.io/modules/pr-preview/pr-6/training/modules

willgearty · 2026-07-16T13:39:40Z

Hmm...I've always preferred to keep prose in long-form (not split to multiple lines) in markdown-like documents. Can we skip that check?

etiennebacher · 2026-07-16T13:55:45Z

Sure, I added a config file to format code chunks but leave the surrounding text intact. I think we still want to have consistent code formatting since this is visible to readers.

etiennebacher · 2026-07-27T13:46:26Z

I don't remember why I hadn't put this as "ready for review"

willgearty · 2026-07-27T14:06:30Z

+```{r}
+#| label: ggplot2


What's the reason for switching to this? Is this considered better practice for some reason?

It's the recommended way in Quarto: https://quarto.org/docs/computations/r.html#chunk-options
There are some corner case issues when using the old syntax in Quarto docs, e.g. quarto-dev/quarto#1023

LewisAJones

Looks good... couple of comments for consideration.

I agree with @willgearty regarding not hard-wrapping long lines for prose.

LewisAJones · 2026-08-12T08:15:22Z

@@ -0,0 +1,68 @@
+# This workflow runs Panache for formatting and Jarl for linting. It stores artifacts about the
+# outcome of each tool and the PR number. Those artifacts are then used in the workflow 
+# "format-lint-pr-comment.yaml" to post a comment so that it's clearer for external


Suggested change
# "format-lint-pr-comment.yaml" to post a comment so that it's clearer for external
# "format-lint-comment.yaml" to post a comment so that it's clearer for external
Correct file name?

LewisAJones · 2026-08-12T08:18:09Z

+ pull-requests: write
+ actions: read
+ steps:
+ - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6


Do we also need to set up dependabot for updating?

etiennebacher · 2026-07-01T13:24:30Z

This adds the same workflows as in palaeoverse but replaces Air by Panache for formatting. I also ran panache format **/*.qmd to format all qmd files (only ggplot/index.qmd so far).

@willgearty Panache formats text in addition to code chunks, for instance to wrap text to a maximum width. Is this fine with you?

Fixes#5

github-actions · 2026-07-01T13:28:38Z

See preview at https://palaeoverse.github.io/modules/pr-preview/pr-6/training/modules

willgearty · 2026-07-16T13:39:40Z

Hmm...I've always preferred to keep prose in long-form (not split to multiple lines) in markdown-like documents. Can we skip that check?

etiennebacher · 2026-07-16T13:55:45Z

Sure, I added a config file to format code chunks but leave the surrounding text intact. I think we still want to have consistent code formatting since this is visible to readers.

etiennebacher · 2026-07-27T13:46:26Z

I don't remember why I hadn't put this as "ready for review"

willgearty · 2026-07-27T14:06:30Z

+```{r}
+#| label: ggplot2


What's the reason for switching to this? Is this considered better practice for some reason?

It's the recommended way in Quarto: https://quarto.org/docs/computations/r.html#chunk-options
There are some corner case issues when using the old syntax in Quarto docs, e.g. quarto-dev/quarto#1023

LewisAJones

Looks good... couple of comments for consideration.

I agree with @willgearty regarding not hard-wrapping long lines for prose.

LewisAJones · 2026-08-12T08:15:22Z

@@ -0,0 +1,68 @@
+# This workflow runs Panache for formatting and Jarl for linting. It stores artifacts about the
+# outcome of each tool and the PR number. Those artifacts are then used in the workflow 
+# "format-lint-pr-comment.yaml" to post a comment so that it's clearer for external


Suggested change
# "format-lint-pr-comment.yaml" to post a comment so that it's clearer for external
# "format-lint-comment.yaml" to post a comment so that it's clearer for external
Correct file name?

LewisAJones · 2026-08-12T08:18:09Z

+ pull-requests: write
+ actions: read
+ steps:
+ - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6


Do we also need to set up dependabot for updating?

etiennebacher · 2026-07-01T13:24:30Z

This adds the same workflows as in palaeoverse but replaces Air by Panache for formatting. I also ran panache format **/*.qmd to format all qmd files (only ggplot/index.qmd so far).

@willgearty Panache formats text in addition to code chunks, for instance to wrap text to a maximum width. Is this fine with you?

Fixes#5

github-actions · 2026-07-01T13:28:38Z

See preview at https://palaeoverse.github.io/modules/pr-preview/pr-6/training/modules

willgearty · 2026-07-16T13:39:40Z

Hmm...I've always preferred to keep prose in long-form (not split to multiple lines) in markdown-like documents. Can we skip that check?

etiennebacher · 2026-07-16T13:55:45Z

Sure, I added a config file to format code chunks but leave the surrounding text intact. I think we still want to have consistent code formatting since this is visible to readers.

etiennebacher · 2026-07-27T13:46:26Z

I don't remember why I hadn't put this as "ready for review"

willgearty · 2026-07-27T14:06:30Z

+```{r}
+#| label: ggplot2


What's the reason for switching to this? Is this considered better practice for some reason?

It's the recommended way in Quarto: https://quarto.org/docs/computations/r.html#chunk-options
There are some corner case issues when using the old syntax in Quarto docs, e.g. quarto-dev/quarto#1023

LewisAJones

Looks good... couple of comments for consideration.

I agree with @willgearty regarding not hard-wrapping long lines for prose.

LewisAJones · 2026-08-12T08:15:22Z

@@ -0,0 +1,68 @@
+# This workflow runs Panache for formatting and Jarl for linting. It stores artifacts about the
+# outcome of each tool and the PR number. Those artifacts are then used in the workflow 
+# "format-lint-pr-comment.yaml" to post a comment so that it's clearer for external


Suggested change
# "format-lint-pr-comment.yaml" to post a comment so that it's clearer for external
# "format-lint-comment.yaml" to post a comment so that it's clearer for external
Correct file name?

LewisAJones · 2026-08-12T08:18:09Z

+ pull-requests: write
+ actions: read
+ steps:
+ - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6


Do we also need to set up dependabot for updating?

etiennebacher added 2 commits July 1, 2026 14:18

init
e7e89e8

tweak comment
facc640

etiennebacher changed the title ~~Add CI for Panache and Jarl checks~~Add CI for formatting and linting checksJul 1, 2026

etiennebacher added 2 commits July 16, 2026 14:52

fix step id
04d60ee

do not wrap text, but still format code
71674b4

etiennebacher marked this pull request as ready for review July 27, 2026 13:46

willgearty reviewed Jul 27, 2026
View reviewed changes

willgearty approved these changes Jul 27, 2026
View reviewed changes

willgearty requested a review from LewisAJones August 11, 2026 22:06

LewisAJones approved these changes Aug 12, 2026
View reviewed changes

etiennebacher added 2 commits July 1, 2026 14:18

init
e7e89e8

tweak comment
facc640

etiennebacher changed the title ~~Add CI for Panache and Jarl checks~~Add CI for formatting and linting checksJul 1, 2026

etiennebacher added 2 commits July 16, 2026 14:52

fix step id
04d60ee

do not wrap text, but still format code
71674b4

etiennebacher marked this pull request as ready for review July 27, 2026 13:46

willgearty reviewed Jul 27, 2026
View reviewed changes

willgearty approved these changes Jul 27, 2026
View reviewed changes

willgearty requested a review from LewisAJones August 11, 2026 22:06

LewisAJones approved these changes Aug 12, 2026
View reviewed changes

etiennebacher added 2 commits July 1, 2026 14:18

init
e7e89e8

tweak comment
facc640

etiennebacher changed the title ~~Add CI for Panache and Jarl checks~~Add CI for formatting and linting checksJul 1, 2026

etiennebacher added 2 commits July 16, 2026 14:52

fix step id
04d60ee

do not wrap text, but still format code
71674b4

etiennebacher marked this pull request as ready for review July 27, 2026 13:46

willgearty reviewed Jul 27, 2026
View reviewed changes

willgearty approved these changes Jul 27, 2026
View reviewed changes

willgearty requested a review from LewisAJones August 11, 2026 22:06

LewisAJones approved these changes Aug 12, 2026
View reviewed changes

etiennebacher added 2 commits July 1, 2026 14:18

init
e7e89e8

tweak comment
facc640

etiennebacher changed the title ~~Add CI for Panache and Jarl checks~~Add CI for formatting and linting checksJul 1, 2026

etiennebacher added 2 commits July 16, 2026 14:52

fix step id
04d60ee

do not wrap text, but still format code
71674b4

etiennebacher marked this pull request as ready for review July 27, 2026 13:46

willgearty reviewed Jul 27, 2026
View reviewed changes

willgearty approved these changes Jul 27, 2026
View reviewed changes

willgearty requested a review from LewisAJones August 11, 2026 22:06

LewisAJones approved these changes Aug 12, 2026
View reviewed changes

etiennebacher added 2 commits July 1, 2026 14:18

init
e7e89e8

tweak comment
facc640

etiennebacher changed the title ~~Add CI for Panache and Jarl checks~~Add CI for formatting and linting checksJul 1, 2026

etiennebacher added 2 commits July 16, 2026 14:52

fix step id
04d60ee

do not wrap text, but still format code
71674b4

etiennebacher marked this pull request as ready for review July 27, 2026 13:46

willgearty reviewed Jul 27, 2026
View reviewed changes

willgearty approved these changes Jul 27, 2026
View reviewed changes

willgearty requested a review from LewisAJones August 11, 2026 22:06

LewisAJones approved these changes Aug 12, 2026
View reviewed changes

etiennebacher added 2 commits July 1, 2026 14:18

init
e7e89e8

tweak comment
facc640

etiennebacher changed the title ~~Add CI for Panache and Jarl checks~~Add CI for formatting and linting checksJul 1, 2026

etiennebacher added 2 commits July 16, 2026 14:52

fix step id
04d60ee

do not wrap text, but still format code
71674b4

etiennebacher marked this pull request as ready for review July 27, 2026 13:46

willgearty reviewed Jul 27, 2026
View reviewed changes

willgearty approved these changes Jul 27, 2026
View reviewed changes

willgearty requested a review from LewisAJones August 11, 2026 22:06

LewisAJones approved these changes Aug 12, 2026
View reviewed changes

etiennebacher added 2 commits July 1, 2026 14:18

init
e7e89e8

tweak comment
facc640

etiennebacher changed the title ~~Add CI for Panache and Jarl checks~~Add CI for formatting and linting checksJul 1, 2026

etiennebacher added 2 commits July 16, 2026 14:52

fix step id
04d60ee

do not wrap text, but still format code
71674b4

etiennebacher marked this pull request as ready for review July 27, 2026 13:46

willgearty reviewed Jul 27, 2026
View reviewed changes

willgearty approved these changes Jul 27, 2026
View reviewed changes

willgearty requested a review from LewisAJones August 11, 2026 22:06

LewisAJones approved these changes Aug 12, 2026
View reviewed changes

etiennebacher added 2 commits July 1, 2026 14:18

init
e7e89e8

tweak comment
facc640

etiennebacher changed the title ~~Add CI for Panache and Jarl checks~~Add CI for formatting and linting checksJul 1, 2026

etiennebacher added 2 commits July 16, 2026 14:52

fix step id
04d60ee

do not wrap text, but still format code
71674b4

etiennebacher marked this pull request as ready for review July 27, 2026 13:46

willgearty reviewed Jul 27, 2026
View reviewed changes

willgearty approved these changes Jul 27, 2026
View reviewed changes

willgearty requested a review from LewisAJones August 11, 2026 22:06

LewisAJones approved these changes Aug 12, 2026
View reviewed changes

	# "format-lint-pr-comment.yaml" to post a comment so that it's clearer for external
	# "format-lint-comment.yaml" to post a comment so that it's clearer for external

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etiennebacher commented Jul 16, 2026•
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etiennebacher commented Jul 1, 2026•
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etiennebacher commented Jul 16, 2026•
edited
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etiennebacher commented Jul 1, 2026•
edited
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etiennebacher commented Jul 16, 2026•
edited
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