do not use Deno.env.set, instead pass env to subprocess invocation calls

Author: cscheid

src/command/render/render-files.ts

@@ -227,6 +227,7 @@ export async function renderExecute(
     previewServer: context.options.previewServer,
     handledLanguages: languages(),
     project: context.project,
+    env: {},
   };
   // execute computations
   setExecuteEnvironment(executeOptions);

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) {
@@ -189,6 +190,7 @@ async function execJupyter(
   command: string,
   options: Record<string, unknown>,
   kernelspec: JupyterKernelspec,
+  env: Record<string, string> = {},
 ): Promise<ProcessResult> {
   try {
     const result = await execProcess(
@@ -197,6 +199,7 @@ async function execJupyter(
           ...(await pythonExec(kernelspec)),
           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
@@ -207,6 +210,7 @@ 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

@@ -155,6 +155,8 @@ 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.
@@ -255,6 +257,7 @@ 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)
@@ -287,6 +290,7 @@ async function callR<T>(
           ...rscriptArgsArray,
           resourcePath("rmd/rmd.R"),
         ],
+        env,
         cwd,
         stderr: quiet ? "piped" : "inherit",
       },

src/execute/types.ts

@@ -77,6 +77,7 @@ export interface ExecutionTarget {
 
 // execute options
 export interface ExecuteOptions {
+  env: Record<string, string>;
   target: ExecutionTarget;
   format: Format;
   resourceDir: string;