Skip to content

Commit 50651e3

Browse files
committed
merge
2 parents c19a65d + ea35854 commit 50651e3

289 files changed

Lines changed: 18176 additions & 18533 deletions

File tree

Some content is hidden

Large Commits have some content hidden by default. Use the searchbox below for content that may be hidden.

.gitmodules

Lines changed: 3 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,3 @@
1+
[submodule "src/quarto-config"]
2+
path = src/quarto-config
3+
url = https://github.com/stan-dev/quarto-config

Jenkinsfile

Lines changed: 7 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -35,7 +35,12 @@ pipeline {
3535
checkout([$class: 'GitSCM',
3636
branches: [[name: '*/master']],
3737
doGenerateSubmoduleConfigurations: false,
38-
extensions: [],
38+
extensions: [[$class: 'SubmoduleOption',
39+
disableSubmodules: false,
40+
parentCredentials: false,
41+
recursiveSubmodules: true,
42+
reference: '',
43+
trackingSubmodules: false]],
3944
submoduleCfg: [],
4045
userRemoteConfigs: [[url: "https://github.com/stan-dev/docs.git", credentialsId: 'a630aebc-6861-4e69-b497-fd7f496ec46b']]]
4146
)
@@ -59,7 +64,7 @@ pipeline {
5964
rm -rf ./docs/functions-reference ./docs/reference-manual ./docs/stan-users-guide/ ./docs/cmdstan-guide ./docs/img ./docs/site_libs
6065
cp -r ./docs/$major_version"_"$minor_version/* ./docs/
6166
rm ./docs/*.pdf
62-
python3 generate_redirects.py
67+
python3 src/quarto-config/generate_redirects.py redirects.txt --output_dir=.
6368
"""
6469

6570
script {

docker/docs/Dockerfile

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,7 @@
11
FROM debian:bookworm
22

3-
ENV QUARTO_VERSION 1.5.53
3+
# synced with the one in https://github.com/stan-dev/stan-dev.github.io/blob/master/.github/workflows/build.yml
4+
ENV QUARTO_VERSION 1.6.39
45

56
ARG PUID
67
ARG PGID

docs/2_36/404.html

Lines changed: 29 additions & 26 deletions
Original file line numberDiff line numberDiff line change
@@ -2,7 +2,7 @@
22
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
33

44
<meta charset="utf-8">
5-
<meta name="generator" content="quarto-1.5.53">
5+
<meta name="generator" content="quarto-1.6.39">
66

77
<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
88

@@ -70,24 +70,25 @@
7070
<script src="/docs/site_libs/quarto-html/tippy.umd.min.js"></script>
7171
<script src="/docs/site_libs/quarto-html/anchor.min.js"></script>
7272
<link href="/docs/site_libs/quarto-html/tippy.css" rel="stylesheet">
73-
<link href="/docs/site_libs/quarto-html/quarto-syntax-highlighting.css" rel="stylesheet" class="quarto-color-scheme" id="quarto-text-highlighting-styles">
74-
<link href="/docs/site_libs/quarto-html/quarto-syntax-highlighting-dark.css" rel="prefetch" class="quarto-color-scheme quarto-color-alternate" id="quarto-text-highlighting-styles">
73+
<link href="/docs/site_libs/quarto-html/quarto-syntax-highlighting-05fe91a66cf75bbbb8c9664867fe5124.css" rel="stylesheet" class="quarto-color-scheme" id="quarto-text-highlighting-styles">
74+
<link href="/docs/site_libs/quarto-html/quarto-syntax-highlighting-dark-59fdbf2653e1aaac23acf64cc15a0d7d.css" rel="prefetch" class="quarto-color-scheme quarto-color-alternate" id="quarto-text-highlighting-styles">
7575
<script src="/docs/site_libs/bootstrap/bootstrap.min.js"></script>
7676
<link href="/docs/site_libs/bootstrap/bootstrap-icons.css" rel="stylesheet">
77-
<link href="/docs/site_libs/bootstrap/bootstrap.min.css" rel="stylesheet" class="quarto-color-scheme" id="quarto-bootstrap" data-mode="light">
78-
<link href="/docs/site_libs/bootstrap/bootstrap-dark.min.css" rel="prefetch" class="quarto-color-scheme quarto-color-alternate" id="quarto-bootstrap" data-mode="dark">
77+
<link href="/docs/site_libs/bootstrap/bootstrap-db2dae95e8ea74a46baf8a914d3354e1.min.css" rel="stylesheet" append-hash="true" class="quarto-color-scheme" id="quarto-bootstrap" data-mode="light">
78+
<link href="/docs/site_libs/bootstrap/bootstrap-dark-6b09c4b6f59a198366d303b7da5f2310.min.css" rel="prefetch" append-hash="true" class="quarto-color-scheme quarto-color-alternate" id="quarto-bootstrap" data-mode="dark">
7979
<script id="quarto-search-options" type="application/json">{
8080
"location": "navbar",
8181
"copy-button": false,
8282
"collapse-after": 3,
8383
"panel-placement": "end",
8484
"type": "overlay",
85-
"limit": 200,
85+
"limit": 50,
8686
"keyboard-shortcut": [
8787
"f",
8888
"/",
8989
"s"
9090
],
91+
"show-item-context": false,
9192
"language": {
9293
"search-no-results-text": "No results",
9394
"search-matching-documents-text": "matching documents",
@@ -104,7 +105,12 @@
104105
}</script>
105106

106107

107-
<link rel="stylesheet" href="/docs/theming/quarto_styles.css">
108+
<link rel="stylesheet" href="/docs/quarto-config/quarto_styles.css">
109+
<meta property="og:title" content="Page Not Found – Stan Docs">
110+
<meta property="og:description" content="">
111+
<meta property="og:image" content="/docs/img/ulam-fermiac.png">
112+
<meta property="og:site_name" content="Stan Docs">
113+
<meta property="og:image:alt" content="Ulam">
108114
</head>
109115

110116
<body class="nav-fixed">
@@ -114,7 +120,7 @@
114120
<nav class="navbar navbar-expand-lg " data-bs-theme="dark">
115121
<div class="navbar-container container-fluid">
116122
<div class="navbar-brand-container mx-auto">
117-
<a href="/docs/index.html" class="navbar-brand navbar-brand-logo">
123+
<a href="https://mc-stan.org/" class="navbar-brand navbar-brand-logo">
118124
<img src="/docs/img/logo_tm.png" alt="Stan logo" class="navbar-logo">
119125
</a>
120126
</div>
@@ -126,7 +132,7 @@
126132
<ul class="navbar-nav navbar-nav-scroll me-auto">
127133
<li class="nav-item">
128134
<a class="nav-link" href="/docs/index.html">
129-
<span class="menu-text">Overview</span></a>
135+
<span class="menu-text">Documentation</span></a>
130136
</li>
131137
<li class="nav-item">
132138
<a class="nav-link" href="/docs/stan-users-guide/index.html">
@@ -150,23 +156,23 @@
150156
<span class="dropdown-text">CmdStan</span></a>
151157
</li>
152158
<li>
153-
<a class="dropdown-item" href="https://mc-stan.org/cmdstanpy">
159+
<a class="dropdown-item" href="https://mc-stan.org/cmdstanpy" target="_blank">
154160
<span class="dropdown-text">CmdStanPy</span></a>
155161
</li>
156162
<li>
157-
<a class="dropdown-item" href="https://mc-stan.org/cmdstanr">
163+
<a class="dropdown-item" href="https://mc-stan.org/cmdstanr" target="_blank">
158164
<span class="dropdown-text">CmdStanR</span></a>
159165
</li>
160166
<li>
161-
<a class="dropdown-item" href="https://mc-stan.org/users/interfaces/pystan.html">
167+
<a class="dropdown-item" href="https://pystan.readthedocs.io/en/latest/" target="_blank">
162168
<span class="dropdown-text">PyStan</span></a>
163169
</li>
164170
<li>
165-
<a class="dropdown-item" href="https://mc-stan.org/rstan">
171+
<a class="dropdown-item" href="https://mc-stan.org/rstan" target="_blank">
166172
<span class="dropdown-text">RStan</span></a>
167173
</li>
168174
<li>
169-
<a class="dropdown-item" href="http://stanjulia.github.io/Stan.jl/stable/INTRO/">
175+
<a class="dropdown-item" href="http://stanjulia.github.io/Stan.jl/stable/INTRO/" target="_blank">
170176
<span class="dropdown-text">Stan.jl</span></a>
171177
</li>
172178
</ul>
@@ -177,39 +183,39 @@
177183
</a>
178184
<ul class="dropdown-menu" aria-labelledby="nav-menu-other-packages">
179185
<li>
180-
<a class="dropdown-item" href="https://mc-stan.org/bayesplot/">
186+
<a class="dropdown-item" href="https://mc-stan.org/bayesplot/" target="_blank">
181187
<span class="dropdown-text">bayesplot</span></a>
182188
</li>
183189
<li>
184-
<a class="dropdown-item" href="https://roualdes.github.io/bridgestan/latest/">
190+
<a class="dropdown-item" href="https://roualdes.github.io/bridgestan/latest/" target="_blank">
185191
<span class="dropdown-text">BridgeStan</span></a>
186192
</li>
187193
<li>
188-
<a class="dropdown-item" href="https://paul-buerkner.github.io/brms/">
194+
<a class="dropdown-item" href="https://paul-buerkner.github.io/brms/" target="_blank">
189195
<span class="dropdown-text">brms</span></a>
190196
</li>
191197
<li>
192-
<a class="dropdown-item" href="https://mc-stan.org/loo/">
198+
<a class="dropdown-item" href="https://mc-stan.org/loo/" target="_blank">
193199
<span class="dropdown-text">loo</span></a>
194200
</li>
195201
<li>
196-
<a class="dropdown-item" href="https://mc-stan.org/posterior">
202+
<a class="dropdown-item" href="https://mc-stan.org/posterior" target="_blank">
197203
<span class="dropdown-text">posterior</span></a>
198204
</li>
199205
<li>
200-
<a class="dropdown-item" href="https://mc-stan.org/projpred">
206+
<a class="dropdown-item" href="https://mc-stan.org/projpred" target="_blank">
201207
<span class="dropdown-text">projpred</span></a>
202208
</li>
203209
<li>
204-
<a class="dropdown-item" href="https://mc-stan.org/rstanarm">
210+
<a class="dropdown-item" href="https://mc-stan.org/rstanarm" target="_blank">
205211
<span class="dropdown-text">rstanarm</span></a>
206212
</li>
207213
<li>
208-
<a class="dropdown-item" href="https://mc-stan.org/rstantools">
214+
<a class="dropdown-item" href="https://mc-stan.org/rstantools" target="_blank">
209215
<span class="dropdown-text">rstantools</span></a>
210216
</li>
211217
<li>
212-
<a class="dropdown-item" href="https://mc-stan.org/shinystan">
218+
<a class="dropdown-item" href="https://mc-stan.org/shinystan" target="_blank">
213219
<span class="dropdown-text">shinystan</span></a>
214220
</li>
215221
</ul>
@@ -495,8 +501,6 @@ <h1 class="title">Page Not Found</h1>
495501
});
496502
clipboard.on('success', onCopySuccess);
497503
if (window.document.getElementById('quarto-embedded-source-code-modal')) {
498-
// For code content inside modals, clipBoardJS needs to be initialized with a container option
499-
// TODO: Check when it could be a function (https://github.com/zenorocha/clipboard.js/issues/860)
500504
const clipboardModal = new window.ClipboardJS('.code-copy-button[data-in-quarto-modal]', {
501505
text: getTextToCopy,
502506
container: window.document.getElementById('quarto-embedded-source-code-modal')
@@ -607,7 +611,6 @@ <h1 class="title">Page Not Found</h1>
607611
if (window.Quarto?.typesetMath) {
608612
window.Quarto.typesetMath(note);
609613
}
610-
// TODO in 1.5, we should make sure this works without a callout special case
611614
if (note.classList.contains("callout")) {
612615
return note.outerHTML;
613616
} else {

docs/2_36/cmdstan-guide-2_36.pdf

-10 Bytes
Binary file not shown.

docs/2_36/cmdstan-guide/bib.html

Lines changed: 28 additions & 27 deletions
Original file line numberDiff line numberDiff line change
@@ -2,7 +2,7 @@
22
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
33

44
<meta charset="utf-8">
5-
<meta name="generator" content="quarto-1.5.53">
5+
<meta name="generator" content="quarto-1.6.39">
66

77
<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
88

@@ -36,24 +36,25 @@
3636
<script src="../site_libs/quarto-html/tippy.umd.min.js"></script>
3737
<script src="../site_libs/quarto-html/anchor.min.js"></script>
3838
<link href="../site_libs/quarto-html/tippy.css" rel="stylesheet">
39-
<link href="../site_libs/quarto-html/quarto-syntax-highlighting.css" rel="stylesheet" class="quarto-color-scheme" id="quarto-text-highlighting-styles">
40-
<link href="../site_libs/quarto-html/quarto-syntax-highlighting-dark.css" rel="prefetch" class="quarto-color-scheme quarto-color-alternate" id="quarto-text-highlighting-styles">
39+
<link href="../site_libs/quarto-html/quarto-syntax-highlighting-05fe91a66cf75bbbb8c9664867fe5124.css" rel="stylesheet" class="quarto-color-scheme" id="quarto-text-highlighting-styles">
40+
<link href="../site_libs/quarto-html/quarto-syntax-highlighting-dark-59fdbf2653e1aaac23acf64cc15a0d7d.css" rel="prefetch" class="quarto-color-scheme quarto-color-alternate" id="quarto-text-highlighting-styles">
4141
<script src="../site_libs/bootstrap/bootstrap.min.js"></script>
4242
<link href="../site_libs/bootstrap/bootstrap-icons.css" rel="stylesheet">
43-
<link href="../site_libs/bootstrap/bootstrap.min.css" rel="stylesheet" class="quarto-color-scheme" id="quarto-bootstrap" data-mode="light">
44-
<link href="../site_libs/bootstrap/bootstrap-dark.min.css" rel="prefetch" class="quarto-color-scheme quarto-color-alternate" id="quarto-bootstrap" data-mode="dark">
43+
<link href="../site_libs/bootstrap/bootstrap-db2dae95e8ea74a46baf8a914d3354e1.min.css" rel="stylesheet" append-hash="true" class="quarto-color-scheme" id="quarto-bootstrap" data-mode="light">
44+
<link href="../site_libs/bootstrap/bootstrap-dark-6b09c4b6f59a198366d303b7da5f2310.min.css" rel="prefetch" append-hash="true" class="quarto-color-scheme quarto-color-alternate" id="quarto-bootstrap" data-mode="dark">
4545
<script id="quarto-search-options" type="application/json">{
4646
"location": "navbar",
4747
"copy-button": false,
4848
"collapse-after": 3,
4949
"panel-placement": "end",
5050
"type": "overlay",
51-
"limit": 200,
51+
"limit": 50,
5252
"keyboard-shortcut": [
5353
"f",
5454
"/",
5555
"s"
5656
],
57+
"show-item-context": false,
5758
"language": {
5859
"search-no-results-text": "No results",
5960
"search-matching-documents-text": "matching documents",
@@ -70,7 +71,10 @@
7071
}</script>
7172

7273

73-
<link rel="stylesheet" href="../theming/quarto_styles.css">
74+
<link rel="stylesheet" href="../quarto-config/quarto_styles.css">
75+
<meta property="og:title" content="Stan Docs">
76+
<meta property="og:image" content="img/logo_tm.png">
77+
<meta property="og:site_name" content="Stan Docs">
7478
</head>
7579

7680
<body class="nav-fixed">
@@ -80,7 +84,7 @@
8084
<nav class="navbar navbar-expand-lg " data-bs-theme="dark">
8185
<div class="navbar-container container-fluid">
8286
<div class="navbar-brand-container mx-auto">
83-
<a href="../index.html" class="navbar-brand navbar-brand-logo">
87+
<a href="https://mc-stan.org/" class="navbar-brand navbar-brand-logo">
8488
<img src="../img/logo_tm.png" alt="Stan logo" class="navbar-logo">
8589
</a>
8690
</div>
@@ -92,7 +96,7 @@
9296
<ul class="navbar-nav navbar-nav-scroll me-auto">
9397
<li class="nav-item">
9498
<a class="nav-link" href="../index.html">
95-
<span class="menu-text">Overview</span></a>
99+
<span class="menu-text">Documentation</span></a>
96100
</li>
97101
<li class="nav-item">
98102
<a class="nav-link" href="../stan-users-guide/index.html">
@@ -116,23 +120,23 @@
116120
<span class="dropdown-text">CmdStan</span></a>
117121
</li>
118122
<li>
119-
<a class="dropdown-item" href="https://mc-stan.org/cmdstanpy">
123+
<a class="dropdown-item" href="https://mc-stan.org/cmdstanpy" target="_blank">
120124
<span class="dropdown-text">CmdStanPy</span></a>
121125
</li>
122126
<li>
123-
<a class="dropdown-item" href="https://mc-stan.org/cmdstanr">
127+
<a class="dropdown-item" href="https://mc-stan.org/cmdstanr" target="_blank">
124128
<span class="dropdown-text">CmdStanR</span></a>
125129
</li>
126130
<li>
127-
<a class="dropdown-item" href="https://mc-stan.org/users/interfaces/pystan.html">
131+
<a class="dropdown-item" href="https://pystan.readthedocs.io/en/latest/" target="_blank">
128132
<span class="dropdown-text">PyStan</span></a>
129133
</li>
130134
<li>
131-
<a class="dropdown-item" href="https://mc-stan.org/rstan">
135+
<a class="dropdown-item" href="https://mc-stan.org/rstan" target="_blank">
132136
<span class="dropdown-text">RStan</span></a>
133137
</li>
134138
<li>
135-
<a class="dropdown-item" href="http://stanjulia.github.io/Stan.jl/stable/INTRO/">
139+
<a class="dropdown-item" href="http://stanjulia.github.io/Stan.jl/stable/INTRO/" target="_blank">
136140
<span class="dropdown-text">Stan.jl</span></a>
137141
</li>
138142
</ul>
@@ -143,39 +147,39 @@
143147
</a>
144148
<ul class="dropdown-menu" aria-labelledby="nav-menu-other-packages">
145149
<li>
146-
<a class="dropdown-item" href="https://mc-stan.org/bayesplot/">
150+
<a class="dropdown-item" href="https://mc-stan.org/bayesplot/" target="_blank">
147151
<span class="dropdown-text">bayesplot</span></a>
148152
</li>
149153
<li>
150-
<a class="dropdown-item" href="https://roualdes.github.io/bridgestan/latest/">
154+
<a class="dropdown-item" href="https://roualdes.github.io/bridgestan/latest/" target="_blank">
151155
<span class="dropdown-text">BridgeStan</span></a>
152156
</li>
153157
<li>
154-
<a class="dropdown-item" href="https://paul-buerkner.github.io/brms/">
158+
<a class="dropdown-item" href="https://paul-buerkner.github.io/brms/" target="_blank">
155159
<span class="dropdown-text">brms</span></a>
156160
</li>
157161
<li>
158-
<a class="dropdown-item" href="https://mc-stan.org/loo/">
162+
<a class="dropdown-item" href="https://mc-stan.org/loo/" target="_blank">
159163
<span class="dropdown-text">loo</span></a>
160164
</li>
161165
<li>
162-
<a class="dropdown-item" href="https://mc-stan.org/posterior">
166+
<a class="dropdown-item" href="https://mc-stan.org/posterior" target="_blank">
163167
<span class="dropdown-text">posterior</span></a>
164168
</li>
165169
<li>
166-
<a class="dropdown-item" href="https://mc-stan.org/projpred">
170+
<a class="dropdown-item" href="https://mc-stan.org/projpred" target="_blank">
167171
<span class="dropdown-text">projpred</span></a>
168172
</li>
169173
<li>
170-
<a class="dropdown-item" href="https://mc-stan.org/rstanarm">
174+
<a class="dropdown-item" href="https://mc-stan.org/rstanarm" target="_blank">
171175
<span class="dropdown-text">rstanarm</span></a>
172176
</li>
173177
<li>
174-
<a class="dropdown-item" href="https://mc-stan.org/rstantools">
178+
<a class="dropdown-item" href="https://mc-stan.org/rstantools" target="_blank">
175179
<span class="dropdown-text">rstantools</span></a>
176180
</li>
177181
<li>
178-
<a class="dropdown-item" href="https://mc-stan.org/shinystan">
182+
<a class="dropdown-item" href="https://mc-stan.org/shinystan" target="_blank">
179183
<span class="dropdown-text">shinystan</span></a>
180184
</li>
181185
</ul>
@@ -209,7 +213,7 @@ <h2 id="toc-title">On this page</h2>
209213
<div class="toc-actions"><ul><li><a href="https://github.com/stan-dev/docs/edit/master/src/cmdstan-guide/bib.qmd" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/stan-dev/docs/issues/new" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></nav>
210214
</div>
211215
<!-- main -->
212-
<main class="content" id="quarto-document-content">
216+
<main class="content" id="quarto-document-content"><header id="title-block-header" class="quarto-title-block"></header>
213217

214218

215219

@@ -447,8 +451,6 @@ <h1 class="unnumbered"><i style="font-size: 110%; color:var(--bs-body-color)">Re
447451
});
448452
clipboard.on('success', onCopySuccess);
449453
if (window.document.getElementById('quarto-embedded-source-code-modal')) {
450-
// For code content inside modals, clipBoardJS needs to be initialized with a container option
451-
// TODO: Check when it could be a function (https://github.com/zenorocha/clipboard.js/issues/860)
452454
const clipboardModal = new window.ClipboardJS('.code-copy-button[data-in-quarto-modal]', {
453455
text: getTextToCopy,
454456
container: window.document.getElementById('quarto-embedded-source-code-modal')
@@ -559,7 +561,6 @@ <h1 class="unnumbered"><i style="font-size: 110%; color:var(--bs-body-color)">Re
559561
if (window.Quarto?.typesetMath) {
560562
window.Quarto.typesetMath(note);
561563
}
562-
// TODO in 1.5, we should make sure this works without a callout special case
563564
if (note.classList.contains("callout")) {
564565
return note.outerHTML;
565566
} else {

0 commit comments

Comments
 (0)