Merge pull request #13963 from quarto-dev/ojs-r-number

`ojs_define` should not round numeric

Author: cderv

llm-docs/testing-patterns.md

@@ -11,6 +11,45 @@ Quarto uses Deno for testing with custom verification helpers located in:
 
 ## Common Test Patterns
 
+### Simple Render Tests
+
+For testing single document rendering with automatic cleanup:
+
+```typescript
+import { docs } from "../../utils.ts";
+import { testRender } from "./render.ts";
+
+// Simplest form - just render and verify output created
+testRender(docs("test-plain.md"), "html", false);
+```
+
+**With additional verifiers:**
+
+```typescript
+import { docs, outputForInput } from "../../utils.ts";
+import { testRender } from "./render.ts";
+import { ensureHtmlElements } from "../../verify.ts";
+
+const input = docs("minimal.qmd");
+const output = outputForInput(input, "html");
+
+testRender(input, "html", true, [
+  ensureHtmlElements(output.outputPath, [], [
+    "script#quarto-html-after-body",
+  ]),
+]);
+```
+
+**Key points:**
+- `testRender()` automatically handles output verification and cleanup
+- Respects `QUARTO_TEST_KEEP_OUTPUTS` env var for debugging
+- Set `noSupporting` parameter based on expected output:
+  - `true` - For truly self-contained HTML (no `_files/` directory, inline everything)
+  - `false` - For HTML with supporting files directory (OJS runtime, widget dependencies, plots, etc.)
+  - Most HTML outputs should use `false` (only use `true` for formats like `html` with `self-contained: true`)
+- Pass additional verifiers in the array parameter (optional)
+- Cleanup happens automatically via `cleanoutput()` in teardown
+
 ### Project Rendering Tests
 
 For testing project rendering (especially website projects):
@@ -226,6 +265,11 @@ testQuartoCmd(...);
 
 ## Examples from Codebase
 
+### Simple Render Test
+See `tests/smoke/render/render-plain.test.ts` for the simplest render tests (no additional verifiers).
+
+See `tests/smoke/render/render-minimal.test.ts` for render test with custom HTML element verification.
+
 ### Project Ignore Test
 See `tests/smoke/project/project-ignore-dirs.test.ts` for testing directory exclusion patterns.
 
@@ -235,6 +279,56 @@ See `tests/smoke/project/project-website.test.ts` for website project rendering
 ### Template Usage Test
 See `tests/smoke/use/template.test.ts` for extension template patterns.
 
+## Engine-Specific Test Considerations
+
+### Shared Test Environments (Critical for quarto-cli Testing)
+
+**Quarto-cli test infrastructure uses a SINGLE managed environment for all tests:**
+
+- **Julia**: `tests/Project.toml` + `tests/Manifest.toml`
+- **Python**: `tests/.venv/` (managed by uv/pyproject.toml)
+- **R**: `tests/renv/` + `tests/renv.lock`
+
+The `configure-test-env` scripts ONLY manage these main environments. CI builds depend on this structure.
+
+**Do NOT create language environment files in test subdirectories:**
+
+```
+tests/docs/my-test/
+├── Project.toml        # ❌ WRONG - breaks test infrastructure
+├── .venv/              # ❌ WRONG - breaks test infrastructure
+├── renv.lock           # ❌ WRONG - breaks test infrastructure
+└── test.qmd
+```
+
+**Why this fails:**
+- Julia searches UP for `Project.toml` and uses the first one found
+- Python/R will use local environments if present
+- CI scripts won't configure these local environments
+- Tests will fail in CI even if they work locally
+
+**Adding new package dependencies:**
+
+For ANY engine (Julia, Python, R), add dependencies to the main `tests/` environment:
+
+```bash
+# Julia: Use Pkg from tests/ directory
+cd tests
+julia --project=. -e 'using Pkg; Pkg.add("PackageName")'
+# Then run configure to update environment
+./configure-test-env.sh   # or .ps1 on Windows
+
+# Python: Use uv from tests/ directory
+cd tests
+uv add packagename
+
+# R: Edit tests/DESCRIPTION, then
+cd tests
+Rscript -e "renv::install(); renv::snapshot()"
+```
+
+**Note:** While Quarto supports local Project.toml files in document directories for production use, the quarto-cli test infrastructure specifically does NOT support this pattern. All test dependencies must be in the main `tests/` environment.
+
 ## Best Practices
 
 1. **Always clean up**: Use teardown to remove generated files

news/changelog-1.9.md

@@ -132,6 +132,10 @@ All changes included in 1.9:
 
 - ([#13748](https://github.com/quarto-dev/quarto-cli/pull/13748)): Fix stdin encoding to UTF-8 on Windows to correctly handle JSON in documents containing non-ASCII characters.
 
+### `knitr`
+
+- ([#13958](https://github.com/quarto-dev/quarto-cli/issues/13958)): Use max precision for `ojs_define` number like this is the case for `jupyter` or `julia` engine.
+
 ## Other fixes and improvements
 
 - ([#8730](https://github.com/quarto-dev/quarto-cli/issues/8730)): Detect x64 R crashes on Windows ARM and provide helpful error message directing users to install native ARM64 R instead of showing generic "check your R installation" error.

src/resources/rmd/ojs_static.R

@@ -45,7 +45,8 @@ ojs_define <- function(...) {
     dataframe = "columns",
     null = "null",
     na = "null",
-    auto_unbox = TRUE
+    auto_unbox = TRUE,
+    digits = NA
   )
   script_string <- c(
     "<script type=\"ojs-define\">",

tests/Manifest.toml

@@ -2,7 +2,7 @@
 
 julia_version = "1.11.7"
 manifest_format = "2.0"
-project_hash = "0af1d64f93f9c216a25d220e89fda045c4edc0aa"
+project_hash = "395f6c17c85163e28668018017fa1e17f23a2784"
 
 [[deps.AliasTables]]
 deps = ["PtrArrays", "Random"]

tests/Project.toml

@@ -1,3 +1,4 @@
 [deps]
 IJulia = "7073ff75-c697-5162-941a-fcdaad2a7d2a"
+JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"

tests/README.md

@@ -118,6 +118,20 @@ Julia uses built-in package manager [**Pkg.jl**](https://pkgdocs.julialang.org/v
 
 `Project.toml` contains our direct dependency and `Manifest.toml` is the lock file that will be created (`Pkg.resolve()`).
 
+**Important:** All test dependencies must be in the main `tests/` environment. Julia searches UP the directory tree for `Project.toml` starting from the document being rendered.
+
+**Adding a new package dependency:**
+
+```bash
+cd tests
+julia --project=. -e 'using Pkg; Pkg.add("PackageName")'
+./configure-test-env.sh   # or .ps1 on Windows
+```
+
+**Do NOT create** local `Project.toml` files in test subdirectories (e.g., `tests/docs/*/Project.toml`). Julia will use that environment instead of the main `tests/` environment. The `configure-test-env` scripts only manage the main environment, so tests with local environments will fail in CI even if they work locally.
+
+**Note:** This applies to ALL engines (Julia, Python, R). Python and R will also use local `.venv/` or `renv.lock` if present. The quarto-cli test infrastructure uses a single managed environment per language at `tests/`, and CI only configures these main environments.
+
 See [documentation](https://pkgdocs.julialang.org/v1/managing-packages/) on how to add, remove, update if you need to tweak the Julia environment.
 
 ### How to run tests locally ?

tests/docs/ojs/ojs-define-numeric-precision/with-julia.qmd

@@ -0,0 +1,16 @@
+---
+title: "ojs_define numeric precision test"
+format: html
+engine: julia
+execute:
+  daemon: false
+---
+
+```{julia}
+using JSON
+ojs_define(num=0.00008604168504168504)
+```
+
+```{ojs}
+num
+```

tests/docs/ojs/ojs-define-numeric-precision/with-jupyter.qmd

@@ -0,0 +1,15 @@
+---
+title: "ojs_define numeric precision test"
+format: html
+engine: jupyter
+execute:
+  daemon: false
+---
+
+```{python}
+ojs_define(num = 0.00008604168504168504)
+```
+
+```{ojs}
+num
+```

tests/docs/ojs/ojs-define-numeric-precision/with-knitr.qmd

@@ -0,0 +1,13 @@
+---
+title: "ojs_define numeric precision test"
+format: html
+engine: knitr
+---
+
+```{r}
+ojs_define(num = 0.00008604168504168504)
+```
+
+```{ojs}
+num
+```

tests/smoke/ojs/ojs-define-precision.test.ts

@@ -0,0 +1,39 @@
+import { docs, outputForInput } from "../../utils.ts";
+import { assert } from "testing/asserts";
+import { testRender } from "../render/render.ts";
+import { verifyOjsDefine } from "../../verify.ts";
+
+// Test for #13958: ojs_define() rounds numbers incorrectly
+// Test across all three execution engines: knitr, jupyter, julia
+const engines = ["knitr", "jupyter", "julia"];
+
+for (const engine of engines) {
+  const input = docs(`ojs/ojs-define-numeric-precision/with-${engine}.qmd`);
+  const output = outputForInput(input, "html");
+
+  testRender(
+    input,
+    "html",
+    false,
+    [
+      verifyOjsDefine(async (contents) => {
+        const numEntry = contents.find((item) => item.name === "num");
+        assert(numEntry, "Should find 'num' variable in ojs-define data");
+        assert(
+          typeof numEntry.value === "number",
+          "ojs-define value should be a number"
+        );
+
+        // Validate numeric precision (the actual bug test)
+        const expected = 0.00008604168504168504;
+        const tolerance = 1e-15; // Machine epsilon tolerance
+
+        const diff = Math.abs(numEntry.value - expected);
+        assert(
+          diff < tolerance,
+          `ojs-define value should preserve full precision. Expected ${expected}, got ${numEntry.value}, diff ${diff}`
+        );
+      }, `ojs_define preserves full numeric precision (${engine})`)(output.outputPath),
+    ],
+  );
+}