Deno.env review/cleanup: no set() past startup

src/command/render/render-files.ts

@@ -232,6 +232,7 @@ export async function renderExecute(
     previewServer: context.options.previewServer,
     handledLanguages: languages(),
     project: context.project,
+    env: {},
   };
   // execute computations
   setExecuteEnvironment(executeOptions);

src/core/jupyter/jupyter-embed.ts

@@ -68,6 +68,7 @@ import { ProjectContext } from "../../project/types.ts";
 import { logProgress } from "../log.ts";
 import * as ld from "../../../src/core/lodash.ts";
 import { texSafeFilename } from "../tex.ts";
+import { ExecuteOptions } from "../../execute/types.ts";
 
 export interface JupyterNotebookAddress {
   path: string;
@@ -415,7 +416,7 @@ export async function notebookMarkdown(
 
   // Wrap any injected cells with a div that includes a back link to
   // the notebook that originated the cells
-  const notebookMarkdown = (
+  const notebookMarkdownInner = (
     nbAbsPath: string,
     cells: JupyterCellOutput[],
     title?: string,
@@ -454,7 +455,7 @@ export async function notebookMarkdown(
         return cell;
       }
     });
-    return notebookMarkdown(nbAbsPath, theCells, notebookInfo.title);
+    return notebookMarkdownInner(nbAbsPath, theCells, notebookInfo.title);
   } else if (nbAddress.indexes) {
     // Filter and sort based upon cell indexes
     const theCells = nbAddress.indexes.map((idx) => {
@@ -472,11 +473,11 @@ export async function notebookMarkdown(
         return cell;
       }
     });
-    return notebookMarkdown(nbAbsPath, theCells, notebookInfo.title);
+    return notebookMarkdownInner(nbAbsPath, theCells, notebookInfo.title);
   } else {
     // Return all the cell outputs as there is no addtional
     // specification of cells
-    const notebookMd = notebookMarkdown(
+    const notebookMd = notebookMarkdownInner(
       nbAbsPath,
       notebookInfo.outputs,
       notebookInfo.title,
@@ -595,7 +596,8 @@ async function getCachedNotebookInfo(
 
     // Get the markdown for the notebook
     const format = context.format;
-    const executeOptions = {
+    const executeOptions: ExecuteOptions = {
+      env: {},
       target: context.target,
       resourceDir: resourcePath(),
       tempDir: context.options.services.temp.createDir(),

src/execute/environment.ts

@@ -12,9 +12,9 @@ export const setExecuteEnvironment: (options: ExecuteOptions) => void = (
   options,
 ) => {
   if (options.projectDir) {
-    Deno.env.set("QUARTO_PROJECT_ROOT", options.projectDir);
-    Deno.env.set("QUARTO_DOCUMENT_PATH", dirname(options.target.source));
-    Deno.env.set("QUARTO_DOCUMENT_FILE", basename(options.target.source));
+    options.env["QUARTO_PROJECT_ROOT"] = options.projectDir;
+    options.env["QUARTO_DOCUMENT_PATH"] = dirname(options.target.source);
+    options.env["QUARTO_DOCUMENT_FILE"] = basename(options.target.source);
   } else {
     // FIXME: This should not be passthrough anymore as singleFileProjectContext always set `options.projectDir`
     // https://github.com/quarto-dev/quarto-cli/pull/8771
@@ -23,8 +23,8 @@ export const setExecuteEnvironment: (options: ExecuteOptions) => void = (
         "No project directory or current working directory",
       );
     }
-    Deno.env.set("QUARTO_PROJECT_ROOT", options.cwd);
-    Deno.env.set("QUARTO_DOCUMENT_PATH", options.cwd);
-    Deno.env.set("QUARTO_DOCUMENT_FILE", basename(options.target.source));
+    options.env["QUARTO_PROJECT_ROOT"] = options.cwd;
+    options.env["QUARTO_DOCUMENT_PATH"] = options.cwd;
+    options.env["QUARTO_DOCUMENT_FILE"] = basename(options.target.source);
   }
 };

src/execute/jupyter/jupyter-kernel.ts

@@ -61,6 +61,7 @@ export async function executeKernelOneshot(
     "execute",
     { ...options, debug },
     options.kernelspec,
+    options.env,
   );
 
   if (!result.success) {
@@ -186,6 +187,7 @@ async function execJupyter(
   command: string,
   options: Record<string, unknown>,
   kernelspec: JupyterKernelspec,
+  env: Record<string, string> = {},
 ): Promise<ProcessResult> {
   try {
     const cmd = await pythonExec(kernelspec);
@@ -196,6 +198,7 @@ async function execJupyter(
           ...cmd.slice(1),
           resourcePath("jupyter/jupyter.py"),
         ],
+        // FIXME IS THIS NOT SET WITH THE DAEMON?
         env: {
           // Force default matplotlib backend. something simillar is done here:
           // https://github.com/ipython/ipykernel/blob/d7339c2c70115bbe6042880d29eeb273b5a2e350/ipykernel/kernelapp.py#L549-L554
@@ -206,6 +209,7 @@ async function execJupyter(
           // function within the notebook
           "MPLBACKEND": "module://matplotlib_inline.backend_inline",
           "PYDEVD_DISABLE_FILE_VALIDATION": "1",
+          ...env,
         },
         stdout: "piped",
       },

src/execute/rmd.ts

@@ -159,6 +159,8 @@ export const knitrEngine: ExecutionEngine = {
 
         return output;
       },
+      true,
+      options.env,
     );
     const includes = result.includes as unknown;
     // knitr appears to return [] instead of {} as the value for includes.
@@ -259,6 +261,7 @@ async function callR<T>(
   quiet?: boolean,
   outputFilter?: (output: string) => string,
   reportError = true,
+  env?: Record<string, string>,
 ): Promise<T> {
   // establish cwd for our R scripts (the current dir if there is an renv
   // otherwise the project dir if specified)
@@ -291,6 +294,7 @@ async function callR<T>(
           ...rscriptArgsArray,
           resourcePath("rmd/rmd.R"),
         ],
+        env,
         cwd,
         stderr: quiet ? "piped" : "inherit",
       },

src/execute/types.ts

@@ -81,6 +81,7 @@ export interface ExecutionTarget {
 
 // execute options
 export interface ExecuteOptions {
+  env: Record<string, string>;
   target: ExecutionTarget;
   format: Format;
   resourceDir: string;

src/quarto.ts

@@ -77,15 +77,11 @@ const checkReconfiguration = async () => {
   }
 };
 
-const passThroughPandoc = async (
-  args: string[],
-  env?: Record<string, string>,
-) => {
+const passThroughPandoc = async (args: string[]) => {
   const result = await execProcess(
     {
       cmd: pandocBinaryPath(),
       args: args.slice(1),
-      env,
     },
     undefined,
     undefined,
@@ -95,10 +91,7 @@ const passThroughPandoc = async (
   Deno.exit(result.code);
 };
 
-const passThroughTypst = async (
-  args: string[],
-  env?: Record<string, string>,
-) => {
+const passThroughTypst = async (args: string[]) => {
   if (args[1] === "update") {
     error(
       "The 'typst update' command is not supported.\n" +
@@ -109,28 +102,26 @@ const passThroughTypst = async (
   const result = await execProcess({
     cmd: typstBinaryPath(),
     args: args.slice(1),
-    env,
   });
   Deno.exit(result.code);
 };
 
 export async function quarto(
   args: string[],
   cmdHandler?: (command: Command) => Command,
-  env?: Record<string, string>,
 ) {
   await checkReconfiguration();
   checkVersionRequirement();
   if (args[0] === "pandoc" && args[1] !== "help") {
-    await passThroughPandoc(args, env);
+    await passThroughPandoc(args);
   }
   if (args[0] === "typst") {
-    await passThroughTypst(args, env);
+    await passThroughTypst(args);
   }
 
   // passthrough to run handlers
   if (args[0] === "run" && args[1] !== "help" && args[1] !== "--help") {
-    const result = await runScript(args.slice(1), env);
+    const result = await runScript(args.slice(1));
     Deno.exit(result.code);
   }
 
@@ -155,13 +146,6 @@ export async function quarto(
 
   debug("Quarto version: " + quartoConfig.version());
 
-  const oldEnv: Record<string, string | undefined> = {};
-  for (const [key, value] of Object.entries(env || {})) {
-    const oldV = Deno.env.get(key);
-    oldEnv[key] = oldV;
-    Deno.env.set(key, value);
-  }
-
   const quartoCommand = new Command()
     .name("quarto")
     .help({ colors: false })
@@ -191,13 +175,6 @@ export async function quarto(
 
   try {
     await promise;
-    for (const [key, value] of Object.entries(oldEnv)) {
-      if (value === undefined) {
-        Deno.env.delete(key);
-      } else {
-        Deno.env.set(key, value);
-      }
-    }
     if (commandFailed()) {
       exitWithCleanup(1);
     }

src/resources/jupyter/notebook.py

@@ -1,26 +1,24 @@
 # pyright: reportMissingImports=false
 
-import os
-import re
+import asyncio
 import atexit
+import base64
+import copy
 import glob
-import sys
 import json
+import os
 import pprint
-import copy
-import base64
-
+import re
+import sys
 from pathlib import Path
 
-from yaml import safe_load as parse_string
-from yaml import safe_dump
-
-from log import trace
 import nbformat
-from nbclient import NotebookClient
 from jupyter_client import KernelManager
 from jupyter_core_utils_vendor import run_sync
-import asyncio
+from log import trace
+from nbclient import NotebookClient
+from yaml import safe_dump
+from yaml import safe_load as parse_string
 
 # optional import of papermill for params support
 try:
@@ -129,6 +127,8 @@ def set_env_vars(options):
     else:
         os.environ["QUARTO_FIG_DPI"] = str(options["fig_dpi"])
         os.environ["QUARTO_FIG_FORMAT"] = options["fig_format"]
+    for key, value in options.get("env", {}).items():
+        os.environ[key] = value
 
 
 def retrieve_nb_from_cache(nb, status, input, **kwargs):
@@ -201,6 +201,7 @@ def notebook_execute(options, status):
     quiet = quarto_kernel_setup_options["quiet"]
     resource_dir = quarto_kernel_setup_options["resource_dir"]
     eval = quarto_kernel_setup_options["eval"]
+    quarto_kernel_setup_options["env"] = options.get("env", {})
 
     # set environment variables
     set_env_vars(quarto_kernel_setup_options)

tests/docs/smoke-all/engine/env/julia.qmd

@@ -0,0 +1,14 @@
+---
+format: html
+_quarto:
+  tests:
+    html:
+      ensureFileRegexMatches:
+        - ["julia.qmd"]
+        - []
+engine: julia
+---
+
+```{julia}
+ENV["QUARTO_DOCUMENT_FILE"]
+```

tests/docs/smoke-all/engine/env/jupyter.qmd

@@ -0,0 +1,16 @@
+---
+format: html
+_quarto:
+  tests:
+    html:
+      ensureFileRegexMatches:
+        - ["jupyter.qmd"]
+        - []
+---
+
+```{python}
+import os
+
+print(os.environ.get("QUARTO_DOCUMENT_FILE", ""))
+print("Hello, world")
+```

tests/docs/smoke-all/engine/env/knitr.qmd

@@ -0,0 +1,13 @@
+---
+format: html
+_quarto:
+  tests:
+    html:
+      ensureFileRegexMatches:
+        - ["knitr.qmd"]
+        - []
+---
+
+```{r}
+print(Sys.getenv("QUARTO_DOCUMENT_FILE"))
+```

tests/smoke/env/install.test.ts

@@ -13,6 +13,7 @@ testQuartoCmd(
   [
     noErrorsOrWarnings,
     printsMessage({level: "INFO", regex: /tinytex\s+/}),
+    // FIXME WE SHOULD BE ABLE TO TURN THIS BACK ON
     // printsMessage({level: "INFO", regex: /chromium\s+/}),
     // temporarily disabled until we get puppeteer back
   ],

tests/smoke/extensions/extension-render-journals.test.ts

@@ -42,6 +42,10 @@ for (const journalRepo of journalRepos) {
     // Sets up the test
     setup: async () => {
       console.log(`using quarto-journals/${journalRepo.repo}`);
+
+      // FIXME THIS DOESN'T WORK
+      // WE CANNOT GUARANTEE THAT CHDIR WILL BE CONSTANT
+      // THROUGHOUT THE ASYNC CALL
       const wd = Deno.cwd();
       Deno.chdir(workingDir);
       await quarto([