Profiling vignette

.github/workflows/Test-coverage.yaml

@@ -52,7 +52,7 @@ jobs:
       - name: Install dependencies
         run: |
           install.packages(c("posterior", "cmdstanr", "remotes", "curl"),repos = c("https://mc-stan.org/r-packages/", getOption("repos")), dependencies = TRUE)
-          cmdstanr::install_cmdstan(cores = 2, overwrite = TRUE)
+          cmdstanr::install_cmdstan(cores = 2, overwrite = TRUE, version = "2.26.0-rc1")
           remotes::install_deps(dependencies = TRUE)
           remotes::install_cran("covr")
           remotes::install_cran("gridExtra")
@@ -101,7 +101,7 @@ jobs:
       - name: Install dependencies
         run: |
           install.packages(c("posterior", "cmdstanr", "remotes", "curl"),repos = c("https://mc-stan.org/r-packages/", getOption("repos")), dependencies = TRUE)
-          cmdstanr::install_cmdstan(cores = 2, overwrite = TRUE)
+          cmdstanr::install_cmdstan(cores = 2, overwrite = TRUE, version = "2.26.0-rc1")
           remotes::install_deps(dependencies = TRUE)
           remotes::install_cran("covr")
           remotes::install_cran("gridExtra")

NEWS.md

@@ -16,6 +16,8 @@ files. (#414)
 information from R if profiling used in the Stan program. Support for profiling
 Stan programs requires CmdStan >= 2.26. (#434)
 
+* New vignette on profiling Stan programs. (#435)
+
 
 # cmdstanr 0.3.0
 

_pkgdown.yml

@@ -3,7 +3,7 @@ url: https://mc-stan.org/cmdstanr
 destination: docs
 
 development:
-  mode: auto
+  mode: release
 
 template:
   params:
@@ -65,10 +65,11 @@ articles:
   - title: "More details"
     desc: >
       More information about compilation, passing in data,
-      how CmdStan ouput is written to CSV and read back into R, and
-      using CmdStanR in R Markdown documents.
+      how CmdStan ouput is written to CSV and read back into R,
+      profiling Stan programs, and using CmdStanR in R Markdown documents.
     contents:
       - cmdstanr-internals
+      - profiling
       - r-markdown
 
 reference:

docs/articles/profiling_files/accessible-code-block-0.0.1/empty-anchor.js

@@ -0,0 +1,15 @@
+// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
+// v0.0.1
+// Written by JooYoung Seo ([email protected]) and Atsushi Yasumoto on June 1st, 2020.
+
+document.addEventListener('DOMContentLoaded', function() {
+  const codeList = document.getElementsByClassName("sourceCode");
+  for (var i = 0; i < codeList.length; i++) {
+    var linkList = codeList[i].getElementsByTagName('a');
+    for (var j = 0; j < linkList.length; j++) {
+      if (linkList[j].innerHTML === "") {
+        linkList[j].setAttribute('aria-hidden', 'true');
+      }
+    }
+  }
+});

docs/articles/profiling_files/anchor-sections-1.0/anchor-sections.css

@@ -0,0 +1,4 @@
+/* Styles for section anchors */
+a.anchor-section {margin-left: 10px; visibility: hidden; color: inherit;}
+a.anchor-section::before {content: '#';}
+.hasAnchor:hover a.anchor-section {visibility: visible;}

docs/articles/profiling_files/anchor-sections-1.0/anchor-sections.js

@@ -0,0 +1,33 @@
+// Anchor sections v1.0 written by Atsushi Yasumoto on Oct 3rd, 2020.
+document.addEventListener('DOMContentLoaded', function() {
+  // Do nothing if AnchorJS is used
+  if (typeof window.anchors === 'object' && anchors.hasOwnProperty('hasAnchorJSLink')) {
+    return;
+  }
+
+  const h = document.querySelectorAll('h1, h2, h3, h4, h5, h6');
+
+  // Do nothing if sections are already anchored
+  if (Array.from(h).some(x => x.classList.contains('hasAnchor'))) {
+    return null;
+  }
+
+  // Use section id when pandoc runs with --section-divs
+  const section_id = function(x) {
+    return ((x.classList.contains('section') || (x.tagName === 'SECTION'))
+            ? x.id : '');
+  };
+
+  // Add anchors
+  h.forEach(function(x) {
+    const id = x.id || section_id(x.parentElement);
+    if (id === '') {
+      return null;
+    }
+    let anchor = document.createElement('a');
+    anchor.href = '#' + id;
+    anchor.classList = ['anchor-section'];
+    x.classList.add('hasAnchor');
+    x.appendChild(anchor);
+  });
+});

docs/articles/profiling_files/header-attrs-2.3/header-attrs.js

@@ -0,0 +1,12 @@
+// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
+// be compatible with the behavior of Pandoc < 2.8).
+document.addEventListener('DOMContentLoaded', function(e) {
+  var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
+  var i, h, a;
+  for (i = 0; i < hs.length; i++) {
+    h = hs[i];
+    if (!/^h[1-6]$/i.test(h.tagName)) continue;  // it should be a header h1-h6
+    a = h.attributes;
+    while (a.length > 0) h.removeAttribute(a[0].name);
+  }
+});

tests/testthat/test-install.R

@@ -1,7 +1,9 @@
 context("install")
 
 if (not_on_cran()) {
-  cmdstan_test_tarball_url <- Sys.getenv("CMDSTAN_TEST_TARBALL_URL")
+  #cmdstan_test_tarball_url <- Sys.getenv("CMDSTAN_TEST_TARBALL_URL")
+  cmdstan_test_tarball_url <- 
+    "https://github.com/stan-dev/cmdstan/releases/download/v2.26.0-rc1/cmdstan-2.26.0-rc1.tar.gz"
   if (!nzchar(cmdstan_test_tarball_url)) {
     cmdstan_test_tarball_url <- NULL
   }
@@ -38,14 +40,12 @@ test_that("install_cmdstan() errors if installation already exists", {
     install_dir <- tempdir()
   }
   dir <- file.path(install_dir, "cmdstan-2.23.0")
-  fake_folder <- FALSE
   if (!dir.exists(dir)) {
-    fake_folder <- TRUE
     dir.create(dir)
   }
   expect_warning(
     install_cmdstan(dir = install_dir, overwrite = FALSE,
-                    release_url = cmdstan_test_tarball_url),
+                    version = "2.23.0"),
     "An installation already exists",
     fixed = TRUE
   )
@@ -59,7 +59,7 @@ test_that("install_cmdstan() errors if it times out", {
   } else {
     dir <- tempdir(check = TRUE)
   }
-  ver <- latest_released_version()
+  ver <- "2.26.0-rc1" #latest_released_version()
   dir_exists <- dir.exists(file.path(dir, paste0("cmdstan-",ver)))
   # with quiet=TRUE
   expect_warning(

vignettes/.gitignore

@@ -1,2 +1,4 @@
 *.html
 *.R
+profiling-files/profiling_bernoulli_logit_glm
+profiling-files/profiling_bernoulli_logit

vignettes/profiling-files/profiling.bib

@@ -0,0 +1,8 @@
+@misc{gelman2020bayesian,
+      title={Bayesian Workflow}, 
+      author={Andrew Gelman and Aki Vehtari and Daniel Simpson and Charles C. Margossian and Bob Carpenter and Yuling Yao and Lauren Kennedy and Jonah Gabry and Paul-Christian Bürkner and Martin Modrák},
+      year={2020},
+      eprint={2011.01808},
+      archivePrefix={arXiv},
+      primaryClass={stat.ME}
+}

vignettes/profiling-files/profiling_bernoulli_logit.stan

@@ -0,0 +1,19 @@
+data {
+  int<lower=1> k;
+  int<lower=0> n;
+  matrix[n, k] X;
+  int y[n];
+}
+parameters {
+  vector[k] beta;
+  real alpha;
+}
+model {
+  profile("priors") {
+    target += std_normal_lpdf(beta);
+    target += std_normal_lpdf(alpha);
+  }
+  profile("likelihood") {
+    target += bernoulli_logit_lpmf(y | X * beta + alpha);
+  }
+}

vignettes/profiling-files/profiling_bernoulli_logit_glm.stan

@@ -0,0 +1,19 @@
+data {
+  int<lower=1> k;
+  int<lower=0> n;
+  matrix[n, k] X;
+  int y[n];
+}
+parameters {
+  vector[k] beta;
+  real alpha;
+}
+model {
+  profile("priors") {
+    target += std_normal_lpdf(beta);
+    target += std_normal_lpdf(alpha);
+  }
+  profile("likelihood") {
+    target += bernoulli_logit_glm_lpmf(y | X, alpha, beta);
+  }
+}