From 99fe52c62e9742a8e65faf257360cec2937b397f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?G=C3=A1bor=20Cs=C3=A1rdi?= <csardi.gabor@gmail.com>
Date: Tue, 7 Jan 2025 17:22:48 +0100
Subject: [PATCH] Scan deps: support IPython notebooks (#422)

---
 R/scan-deps.R                               | 28 +++++++++
 tests/testthat/_snaps/scan-deps.md          | 13 +++++
 tests/testthat/fixtures/scan/notebook.ipynb | 63 +++++++++++++++++++++
 tests/testthat/test-scan-deps.R             |  8 +++
 4 files changed, 112 insertions(+)
 create mode 100644 tests/testthat/fixtures/scan/notebook.ipynb

diff --git a/R/scan-deps.R b/R/scan-deps.R
index 5183910e..94f63ef7 100644
--- a/R/scan-deps.R
+++ b/R/scan-deps.R
@@ -281,6 +281,7 @@ scan_path_deps_do <- function(code, path) {
     ".rmarkdown" = ,
     ".rmd" = scan_path_deps_do_rmd(code, path),
     ".rnw" = scan_path_deps_do_rnw(code, path),
+    ".ipynb" = scan_path_deps_do_ipynb(code, path),
     "DESCRIPTION" = scan_path_deps_do_dsc(code, path),
     "NAMESPACE" = scan_path_deps_do_namespace(code, path),
     "_bookdown.yml" = scan_path_deps_do_bookdown(code, path),
@@ -1231,3 +1232,30 @@ scan_path_deps_do_rnw_ranges <- function(code) {
     c(bmx, emx)
   })
 }
+
+# -------------------------------------------------------------------------
+
+scan_path_deps_do_ipynb <- function(code, path) {
+  ipynb <- jsonlite::fromJSON(code, simplifyVector = FALSE)
+  if (!identical(ipynb$metadata$kernelspec$language, "R")) {
+    return(NULL)
+  }
+  ir <- if (identical(ipynb$metadata$kernelspec$name, "ir")) {
+    scan_deps_df(
+      path = path,
+      package = "IRkernel",
+      code = NA_character_
+    )
+  }
+
+  deps <- lapply(ipynb$cells, function(cell) {
+    if (identical(cell$cell_type, "code")) {
+      c1 <- paste(unlist(cell$source), collapse = "")
+      scan_path_deps_do_r(c1, path)
+    }
+  })
+
+  adeps <- drop_nulls(c(list(ir), deps))
+
+  do.call("rbind", adeps)
+}
diff --git a/tests/testthat/_snaps/scan-deps.md b/tests/testthat/_snaps/scan-deps.md
index 5e257852..1ae1c6b4 100644
--- a/tests/testthat/_snaps/scan-deps.md
+++ b/tests/testthat/_snaps/scan-deps.md
@@ -499,3 +499,16 @@
       5 ignore-test.Rnw good          good          *       prod  library(good)                  1            1          1
       6 ignore-test.Rnw good          good          *       prod  library(good)                  1            1          1
 
+# IPython notebook
+
+    Code
+      scan_path_deps_do(readLines(path), basename(path))
+    Output
+      # A data frame: 4 x 9
+        path           ref      package  version type  code            start_row start_column start_byte
+        <chr>          <chr>    <chr>    <chr>   <chr> <chr>               <int>        <int>      <int>
+      1 notebook.ipynb IRkernel IRkernel *       prod  <NA>                    1            1          1
+      2 notebook.ipynb MASS     MASS     *       prod  library(MASS)           1            1          1
+      3 notebook.ipynb stats    stats    *       prod  stats::setNames         1            1          1
+      4 notebook.ipynb cli      cli      *       prod  cli::cli_text           2            1         19
+
diff --git a/tests/testthat/fixtures/scan/notebook.ipynb b/tests/testthat/fixtures/scan/notebook.ipynb
new file mode 100644
index 00000000..8b95cf5f
--- /dev/null
+++ b/tests/testthat/fixtures/scan/notebook.ipynb
@@ -0,0 +1,63 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Some markdown text"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {
+    "collapsed": false,
+    "jupyter": {
+     "outputs_hidden": false
+    },
+    "vscode": {
+     "languageId": "r"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "library(MASS)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {
+    "collapsed": false,
+    "jupyter": {
+     "outputs_hidden": false
+    },
+    "vscode": {
+     "languageId": "r"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "stats::setNames()\n",
+    "cli::cli_text()"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "R",
+   "language": "R",
+   "name": "ir"
+  },
+  "language_info": {
+   "codemirror_mode": "r",
+   "file_extension": ".r",
+   "mimetype": "text/x-r-source",
+   "name": "R",
+   "pygments_lexer": "r",
+   "version": "4.0.3"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}
diff --git a/tests/testthat/test-scan-deps.R b/tests/testthat/test-scan-deps.R
index 04c09bba..4275b236 100644
--- a/tests/testthat/test-scan-deps.R
+++ b/tests/testthat/test-scan-deps.R
@@ -545,3 +545,11 @@ test_that("Ignored chunks in .Rnw file", {
     )
   })
 })
+
+test_that("IPython notebook", {
+  local_reproducible_output(width = 500)
+  path <- test_path("fixtures/scan/notebook.ipynb")
+  expect_snapshot({
+    scan_path_deps_do(readLines(path), basename(path))
+  })
+})