From 5aaa2497e6c8d90e8bef582ae808bce05cbad8d2 Mon Sep 17 00:00:00 2001
From: Liz Nelson <liz.nelson@posit.co>
Date: Mon, 25 Aug 2025 11:50:05 -0400
Subject: [PATCH 01/20] including notes

---
 shiny/ui/_include_helpers.py                  | 25 +++++++++++++++++--
 .../shiny/bugs/2061-css-js-inclusion/app.py   | 22 ++++++++++++++++
 .../2061-css-js-inclusion/www/customjs.js     |  1 +
 .../bugs/2061-css-js-inclusion/www/style.css  | 19 ++++++++++++++
 4 files changed, 65 insertions(+), 2 deletions(-)
 create mode 100644 tests/playwright/shiny/bugs/2061-css-js-inclusion/app.py
 create mode 100644 tests/playwright/shiny/bugs/2061-css-js-inclusion/www/customjs.js
 create mode 100644 tests/playwright/shiny/bugs/2061-css-js-inclusion/www/style.css

diff --git a/shiny/ui/_include_helpers.py b/shiny/ui/_include_helpers.py
index 3c0c9409a..826482c9b 100644
--- a/shiny/ui/_include_helpers.py
+++ b/shiny/ui/_include_helpers.py
@@ -89,6 +89,10 @@ def include_js(
     if method == "inline":
         return tags.script(read_utf8(file_path), **kwargs)
 
+    # QUESTION: Do we have access to the session or user at this point? Can write based on that and then give them full perms?
+    # Where does cleanup happen?! Seems like maybe that needs to be included before we make new folders? Check the date? Tell if active
+    # session using them?!
+
     include_files = method == "link_files"
     path_dest, hash = maybe_copy_files(file_path, include_files)
 
@@ -217,21 +221,35 @@ def maybe_copy_files(path: Path | str, include_files: bool) -> tuple[str, str]:
 
     # To avoid unnecessary work when the same file is included multiple times,
     # use a directory scoped by a hash of the file.
+    # We need to make tempdir deterministic if we use the pythong TemporaryDirectory class so we can still tell if the hash has changed
+    # We want the temp dir unique to the process, hash should be the only thing that is dynamic based on the file contents.
+    # Cleanup done using __del__?
+    # Also make perms so that others can read it
+    # Double check clean-up based on process ending
     tmpdir = os.path.join(tempfile.gettempdir(), "shiny_include_files", hash)
     path_dest = os.path.join(tmpdir, os.path.basename(path))
+    print("tmpdir, path_dest: ", tmpdir, path_dest)
 
     # Since the hash/tmpdir should represent all the files in the path's directory,
     # we can simply return here
     if os.path.exists(path_dest):
+        print("path exists: ", path_dest, hash)
         return path_dest, hash
 
     # Otherwise, make sure we have a clean slate
+    # We only hit this if tempdir/ exists but not the file (i.e. style.css)
     if os.path.exists(tmpdir):
+        print("clean the slate, tmpdir", tmpdir)
         shutil.rmtree(tmpdir)
 
     if include_files:
+        print("include files true")
+        # TODO: Switch this to tempfile.mkdtmp? This will scope perms to the userID
+        # QUESTION what is the user id? The system user? How does that work in Connect?
         shutil.copytree(os.path.dirname(path), tmpdir)
     else:
+        print("include files false")
+        # This should probably use the temp file syntax
         os.makedirs(tmpdir, exist_ok=True)
         shutil.copy(path, path_dest)
 
@@ -240,11 +258,14 @@ def maybe_copy_files(path: Path | str, include_files: bool) -> tuple[str, str]:
 
 def get_hash(path: Path | str, include_files: bool) -> str:
     if include_files:
-        key = get_file_key(path)
-    else:
         dir = os.path.dirname(path)
+        # This is recursively listing everything in the dir and making that part of the hash even though we're not pulling it over
+        # Ex. we make a hash, we copy over one file, then we jsut don't keep going
         files = glob.iglob(os.path.join(dir, "**"), recursive=True)
         key = "\n".join([get_file_key(x) for x in files])
+    else:
+        key = get_file_key(path)
+
     return hash_deterministic(key)
 
 
diff --git a/tests/playwright/shiny/bugs/2061-css-js-inclusion/app.py b/tests/playwright/shiny/bugs/2061-css-js-inclusion/app.py
new file mode 100644
index 000000000..438af56dd
--- /dev/null
+++ b/tests/playwright/shiny/bugs/2061-css-js-inclusion/app.py
@@ -0,0 +1,22 @@
+from shiny import App, ui
+
+# Define the UI
+app_ui = ui.page_fluid(
+    ui.include_css("./www/style.css"),  # Reference the external CSS file
+    ui.include_js("./www/customjs.js"),
+    ui.h1("Simple Shiny App with External CSS"),
+    ui.div(
+        ui.p("This is a simple Shiny app that demonstrates ui.include_css()"),
+        ui.p("The styling comes from an external CSS file!"),
+        class_="content",
+    ),
+)
+
+
+# Define the server
+def server(input, output, session):
+    pass
+
+
+# Create and run the app
+app = App(app_ui, server)
diff --git a/tests/playwright/shiny/bugs/2061-css-js-inclusion/www/customjs.js b/tests/playwright/shiny/bugs/2061-css-js-inclusion/www/customjs.js
new file mode 100644
index 000000000..dbb1b36fa
--- /dev/null
+++ b/tests/playwright/shiny/bugs/2061-css-js-inclusion/www/customjs.js
@@ -0,0 +1 @@
+console.log("heyo")
\ No newline at end of file
diff --git a/tests/playwright/shiny/bugs/2061-css-js-inclusion/www/style.css b/tests/playwright/shiny/bugs/2061-css-js-inclusion/www/style.css
new file mode 100644
index 000000000..e86131d86
--- /dev/null
+++ b/tests/playwright/shiny/bugs/2061-css-js-inclusion/www/style.css
@@ -0,0 +1,19 @@
+
+body {
+  background-color: #f0f8ff;
+  font-family: Arial, sans-serif;
+}
+
+h1 {
+  color: #4682b4;
+  border-bottom: 2px solid #4682b4;
+  padding-bottom: 10px;
+}
+
+.content {
+  margin: 20px;
+  padding: 15px;
+  background-color: white;
+  border-radius: 5px;
+  box-shadow: 0 0 10px rgba(0, 0, 0, 0.1);
+}

From cc15245fc397f92ce84850ce99dac2a534032564 Mon Sep 17 00:00:00 2001
From: Liz Nelson <liz.nelson@posit.co>
Date: Mon, 25 Aug 2025 12:23:36 -0400
Subject: [PATCH 02/20] Removing notes to self

---
 shiny/ui/_include_helpers.py | 21 ---------------------
 1 file changed, 21 deletions(-)

diff --git a/shiny/ui/_include_helpers.py b/shiny/ui/_include_helpers.py
index 826482c9b..0a9be9075 100644
--- a/shiny/ui/_include_helpers.py
+++ b/shiny/ui/_include_helpers.py
@@ -89,10 +89,6 @@ def include_js(
     if method == "inline":
         return tags.script(read_utf8(file_path), **kwargs)
 
-    # QUESTION: Do we have access to the session or user at this point? Can write based on that and then give them full perms?
-    # Where does cleanup happen?! Seems like maybe that needs to be included before we make new folders? Check the date? Tell if active
-    # session using them?!
-
     include_files = method == "link_files"
     path_dest, hash = maybe_copy_files(file_path, include_files)
 
@@ -219,13 +215,6 @@ def create_include_dependency(
 def maybe_copy_files(path: Path | str, include_files: bool) -> tuple[str, str]:
     hash = get_hash(path, include_files)
 
-    # To avoid unnecessary work when the same file is included multiple times,
-    # use a directory scoped by a hash of the file.
-    # We need to make tempdir deterministic if we use the pythong TemporaryDirectory class so we can still tell if the hash has changed
-    # We want the temp dir unique to the process, hash should be the only thing that is dynamic based on the file contents.
-    # Cleanup done using __del__?
-    # Also make perms so that others can read it
-    # Double check clean-up based on process ending
     tmpdir = os.path.join(tempfile.gettempdir(), "shiny_include_files", hash)
     path_dest = os.path.join(tmpdir, os.path.basename(path))
     print("tmpdir, path_dest: ", tmpdir, path_dest)
@@ -233,23 +222,15 @@ def maybe_copy_files(path: Path | str, include_files: bool) -> tuple[str, str]:
     # Since the hash/tmpdir should represent all the files in the path's directory,
     # we can simply return here
     if os.path.exists(path_dest):
-        print("path exists: ", path_dest, hash)
         return path_dest, hash
 
     # Otherwise, make sure we have a clean slate
-    # We only hit this if tempdir/ exists but not the file (i.e. style.css)
     if os.path.exists(tmpdir):
-        print("clean the slate, tmpdir", tmpdir)
         shutil.rmtree(tmpdir)
 
     if include_files:
-        print("include files true")
-        # TODO: Switch this to tempfile.mkdtmp? This will scope perms to the userID
-        # QUESTION what is the user id? The system user? How does that work in Connect?
         shutil.copytree(os.path.dirname(path), tmpdir)
     else:
-        print("include files false")
-        # This should probably use the temp file syntax
         os.makedirs(tmpdir, exist_ok=True)
         shutil.copy(path, path_dest)
 
@@ -259,8 +240,6 @@ def maybe_copy_files(path: Path | str, include_files: bool) -> tuple[str, str]:
 def get_hash(path: Path | str, include_files: bool) -> str:
     if include_files:
         dir = os.path.dirname(path)
-        # This is recursively listing everything in the dir and making that part of the hash even though we're not pulling it over
-        # Ex. we make a hash, we copy over one file, then we jsut don't keep going
         files = glob.iglob(os.path.join(dir, "**"), recursive=True)
         key = "\n".join([get_file_key(x) for x in files])
     else:

From e6b8260add9a2a25bf047996ed8cba7037910266 Mon Sep 17 00:00:00 2001
From: Liz Nelson <liz.nelson@posit.co>
Date: Mon, 25 Aug 2025 12:27:34 -0400
Subject: [PATCH 03/20] cleanup

---
 shiny/ui/_include_helpers.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/shiny/ui/_include_helpers.py b/shiny/ui/_include_helpers.py
index 0a9be9075..33840b94b 100644
--- a/shiny/ui/_include_helpers.py
+++ b/shiny/ui/_include_helpers.py
@@ -215,9 +215,10 @@ def create_include_dependency(
 def maybe_copy_files(path: Path | str, include_files: bool) -> tuple[str, str]:
     hash = get_hash(path, include_files)
 
+    # To avoid unnecessary work when the same file is included multiple times,
+    # use a directory scoped by a hash of the file.
     tmpdir = os.path.join(tempfile.gettempdir(), "shiny_include_files", hash)
     path_dest = os.path.join(tmpdir, os.path.basename(path))
-    print("tmpdir, path_dest: ", tmpdir, path_dest)
 
     # Since the hash/tmpdir should represent all the files in the path's directory,
     # we can simply return here

From f4c53fdcf62c36545a891c7684a3164a51f81235 Mon Sep 17 00:00:00 2001
From: Liz Nelson <liz.nelson@posit.co>
Date: Tue, 26 Aug 2025 13:15:10 -0400
Subject: [PATCH 04/20] With prints

---
 shiny/ui/_include_helpers.py                  | 32 ++++++++++++++++---
 .../shiny/bugs/2061-css-js-inclusion/app.py   |  4 ++-
 2 files changed, 31 insertions(+), 5 deletions(-)

diff --git a/shiny/ui/_include_helpers.py b/shiny/ui/_include_helpers.py
index 33840b94b..f5427d5f5 100644
--- a/shiny/ui/_include_helpers.py
+++ b/shiny/ui/_include_helpers.py
@@ -214,37 +214,61 @@ def create_include_dependency(
 
 def maybe_copy_files(path: Path | str, include_files: bool) -> tuple[str, str]:
     hash = get_hash(path, include_files)
+    print("path: ", path, "Hash: ", hash)
 
     # To avoid unnecessary work when the same file is included multiple times,
     # use a directory scoped by a hash of the file.
     tmpdir = os.path.join(tempfile.gettempdir(), "shiny_include_files", hash)
     path_dest = os.path.join(tmpdir, os.path.basename(path))
+    print("path_dest:", path_dest)
 
     # Since the hash/tmpdir should represent all the files in the path's directory,
-    # we can simply return here
+    # we can check if it exists to determine if we have a cache hit
     if os.path.exists(path_dest):
+        print("Already exists", path_dest)
         return path_dest, hash
 
+    permissions = (
+        0o755  # Store permissions var set to -rwxr-xr-x (owner rwx, others rx)
+    )
+
     # Otherwise, make sure we have a clean slate
     if os.path.exists(tmpdir):
+        print("folder exists, not contents:", os.stat(tmpdir))
         shutil.rmtree(tmpdir)
 
+    # Looks like this is copying twice? puts stuff in diff folders?
     if include_files:
         shutil.copytree(os.path.dirname(path), tmpdir)
-    else:
-        os.makedirs(tmpdir, exist_ok=True)
-        shutil.copy(path, path_dest)
+        print("new folder, perms: ", oct(os.stat(tmpdir).st_mode))
+        for root, dirs, files in os.walk(tmpdir):
+            # set perms on sub-directories
+            for dir in dirs:
+                os.chmod(os.path.join(root, dir), permissions)
+                print("Dir: ", dir)
+                print("dir perms: ", oct(os.stat(os.path.join(root, dir)).st_mode))
+
+            # set perms on files
+            for file in files:
+                print("File: ", file)
+                os.chmod(os.path.join(root, file), permissions)
+                print("file perms: ", oct(os.stat(os.path.join(root, file)).st_mode))
 
+        shutil.copy(path, path_dest)
+    print("PATH_DEST: ", path_dest)
     return path_dest, hash
 
 
 def get_hash(path: Path | str, include_files: bool) -> str:
     if include_files:
+        print("get_hash, include_files is true")
         dir = os.path.dirname(path)
         files = glob.iglob(os.path.join(dir, "**"), recursive=True)
         key = "\n".join([get_file_key(x) for x in files])
+        print("KEY: ", key)
     else:
         key = get_file_key(path)
+        print("not include key: ", key)
 
     return hash_deterministic(key)
 
diff --git a/tests/playwright/shiny/bugs/2061-css-js-inclusion/app.py b/tests/playwright/shiny/bugs/2061-css-js-inclusion/app.py
index 438af56dd..b994a7057 100644
--- a/tests/playwright/shiny/bugs/2061-css-js-inclusion/app.py
+++ b/tests/playwright/shiny/bugs/2061-css-js-inclusion/app.py
@@ -2,7 +2,9 @@
 
 # Define the UI
 app_ui = ui.page_fluid(
-    ui.include_css("./www/style.css"),  # Reference the external CSS file
+    ui.include_css(
+        "./www/style.css", method="link_files"
+    ),  # Reference the external CSS file
     ui.include_js("./www/customjs.js"),
     ui.h1("Simple Shiny App with External CSS"),
     ui.div(

From 2764cbe5dc90824fb5cdf23ae123ba9c8bc59d4d Mon Sep 17 00:00:00 2001
From: Liz Nelson <liz.nelson@posit.co>
Date: Tue, 26 Aug 2025 13:31:51 -0400
Subject: [PATCH 05/20] Add multifile example, notes

---
 shiny/ui/_include_helpers.py                  |  1 +
 .../{ => app-lite}/app.py                     |  0
 .../{ => app-lite}/www/customjs.js            |  0
 .../{ => app-lite}/www/style.css              |  0
 .../2061-css-js-inclusion/app-multi/app.py    | 22 +++++++++++++++++++
 .../app-multi/css/more.css                    |  3 +++
 .../app-multi/css/style.css                   | 19 ++++++++++++++++
 .../app-multi/js/customjs.js                  |  4 ++++
 .../app-multi/js/more.js                      |  3 +++
 9 files changed, 52 insertions(+)
 rename tests/playwright/shiny/bugs/2061-css-js-inclusion/{ => app-lite}/app.py (100%)
 rename tests/playwright/shiny/bugs/2061-css-js-inclusion/{ => app-lite}/www/customjs.js (100%)
 rename tests/playwright/shiny/bugs/2061-css-js-inclusion/{ => app-lite}/www/style.css (100%)
 create mode 100644 tests/playwright/shiny/bugs/2061-css-js-inclusion/app-multi/app.py
 create mode 100644 tests/playwright/shiny/bugs/2061-css-js-inclusion/app-multi/css/more.css
 create mode 100644 tests/playwright/shiny/bugs/2061-css-js-inclusion/app-multi/css/style.css
 create mode 100644 tests/playwright/shiny/bugs/2061-css-js-inclusion/app-multi/js/customjs.js
 create mode 100644 tests/playwright/shiny/bugs/2061-css-js-inclusion/app-multi/js/more.js

diff --git a/shiny/ui/_include_helpers.py b/shiny/ui/_include_helpers.py
index f5427d5f5..7b135e887 100644
--- a/shiny/ui/_include_helpers.py
+++ b/shiny/ui/_include_helpers.py
@@ -19,6 +19,7 @@
 # as the app, the app's source will be included. Should we just not copy .py/.r files?
 
 
+# TODO: This does throw js errors if you're loading in other stuff depending on your config
 @add_example()
 def include_js(
     path: Path | str,
diff --git a/tests/playwright/shiny/bugs/2061-css-js-inclusion/app.py b/tests/playwright/shiny/bugs/2061-css-js-inclusion/app-lite/app.py
similarity index 100%
rename from tests/playwright/shiny/bugs/2061-css-js-inclusion/app.py
rename to tests/playwright/shiny/bugs/2061-css-js-inclusion/app-lite/app.py
diff --git a/tests/playwright/shiny/bugs/2061-css-js-inclusion/www/customjs.js b/tests/playwright/shiny/bugs/2061-css-js-inclusion/app-lite/www/customjs.js
similarity index 100%
rename from tests/playwright/shiny/bugs/2061-css-js-inclusion/www/customjs.js
rename to tests/playwright/shiny/bugs/2061-css-js-inclusion/app-lite/www/customjs.js
diff --git a/tests/playwright/shiny/bugs/2061-css-js-inclusion/www/style.css b/tests/playwright/shiny/bugs/2061-css-js-inclusion/app-lite/www/style.css
similarity index 100%
rename from tests/playwright/shiny/bugs/2061-css-js-inclusion/www/style.css
rename to tests/playwright/shiny/bugs/2061-css-js-inclusion/app-lite/www/style.css
diff --git a/tests/playwright/shiny/bugs/2061-css-js-inclusion/app-multi/app.py b/tests/playwright/shiny/bugs/2061-css-js-inclusion/app-multi/app.py
new file mode 100644
index 000000000..7a37f8dab
--- /dev/null
+++ b/tests/playwright/shiny/bugs/2061-css-js-inclusion/app-multi/app.py
@@ -0,0 +1,22 @@
+from shiny import App, ui
+
+# Define the UI
+app_ui = ui.page_fluid(
+    ui.include_css("./css/style.css", method="link_files"),
+    ui.include_js("./js/customjs.js", method="link_files"),
+    ui.h1("Simple Shiny App with External CSS"),
+    ui.div(
+        ui.p("This is a simple Shiny app that demonstrates ui.include_css()"),
+        ui.p("The styling comes from an external CSS file!"),
+        class_="content",
+    ),
+)
+
+
+# Define the server
+def server(input, output, session):
+    pass
+
+
+# Create and run the app
+app = App(app_ui, server)
diff --git a/tests/playwright/shiny/bugs/2061-css-js-inclusion/app-multi/css/more.css b/tests/playwright/shiny/bugs/2061-css-js-inclusion/app-multi/css/more.css
new file mode 100644
index 000000000..67039459e
--- /dev/null
+++ b/tests/playwright/shiny/bugs/2061-css-js-inclusion/app-multi/css/more.css
@@ -0,0 +1,3 @@
+body {
+  background-color: #506577;
+}
\ No newline at end of file
diff --git a/tests/playwright/shiny/bugs/2061-css-js-inclusion/app-multi/css/style.css b/tests/playwright/shiny/bugs/2061-css-js-inclusion/app-multi/css/style.css
new file mode 100644
index 000000000..60303125d
--- /dev/null
+++ b/tests/playwright/shiny/bugs/2061-css-js-inclusion/app-multi/css/style.css
@@ -0,0 +1,19 @@
+@import url("more.css");
+
+body {
+  font-family: Arial, sans-serif;
+}
+
+h1 {
+  color: #4682b4;
+  border-bottom: 2px solid #4682b4;
+  padding-bottom: 10px;
+}
+
+.content {
+  margin: 20px;
+  padding: 15px;
+  background-color: white;
+  border-radius: 5px;
+  box-shadow: 0 0 10px rgba(0, 0, 0, 0.1);
+}
diff --git a/tests/playwright/shiny/bugs/2061-css-js-inclusion/app-multi/js/customjs.js b/tests/playwright/shiny/bugs/2061-css-js-inclusion/app-multi/js/customjs.js
new file mode 100644
index 000000000..bdf776034
--- /dev/null
+++ b/tests/playwright/shiny/bugs/2061-css-js-inclusion/app-multi/js/customjs.js
@@ -0,0 +1,4 @@
+const heyo = require('./more.js');
+
+
+console.log(heyo())
\ No newline at end of file
diff --git a/tests/playwright/shiny/bugs/2061-css-js-inclusion/app-multi/js/more.js b/tests/playwright/shiny/bugs/2061-css-js-inclusion/app-multi/js/more.js
new file mode 100644
index 000000000..6dade946a
--- /dev/null
+++ b/tests/playwright/shiny/bugs/2061-css-js-inclusion/app-multi/js/more.js
@@ -0,0 +1,3 @@
+export function heyo() {
+    console.log(heyo)
+}
\ No newline at end of file

From 03839f05d8e7cf5d97ed9aff6c5751b423fb33a4 Mon Sep 17 00:00:00 2001
From: Liz Nelson <liz.nelson@posit.co>
Date: Tue, 26 Aug 2025 14:00:40 -0400
Subject: [PATCH 06/20] Fixing types

---
 tests/playwright/shiny/bugs/2061-css-js-inclusion/app.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/playwright/shiny/bugs/2061-css-js-inclusion/app.py b/tests/playwright/shiny/bugs/2061-css-js-inclusion/app.py
index 438af56dd..41696c8ca 100644
--- a/tests/playwright/shiny/bugs/2061-css-js-inclusion/app.py
+++ b/tests/playwright/shiny/bugs/2061-css-js-inclusion/app.py
@@ -1,4 +1,4 @@
-from shiny import App, ui
+from shiny import App, Inputs, Outputs, Session, ui
 
 # Define the UI
 app_ui = ui.page_fluid(
@@ -14,7 +14,7 @@
 
 
 # Define the server
-def server(input, output, session):
+def server(input: Inputs, output: Outputs, session: Session):
     pass
 
 

From c1a11a1cd7b0678b6c8ee63781ec3ff54d2694f8 Mon Sep 17 00:00:00 2001
From: Liz Nelson <liz.nelson@posit.co>
Date: Wed, 27 Aug 2025 12:27:52 -0400
Subject: [PATCH 07/20] Updating tests

---
 tests/playwright/shiny/bugs/2061-css-js-inclusion/app.py | 4 ++--
 .../shiny/bugs/2061-css-js-inclusion/css/more.css        | 3 +++
 .../bugs/2061-css-js-inclusion/{www => css}/style.css    | 4 ++--
 .../shiny/bugs/2061-css-js-inclusion/js/customjs.js      | 4 ++++
 .../bugs/2061-css-js-inclusion/test_css-js-inclusion.py  | 9 +++++++++
 .../shiny/bugs/2061-css-js-inclusion/www/customjs.js     | 1 -
 6 files changed, 20 insertions(+), 5 deletions(-)
 create mode 100644 tests/playwright/shiny/bugs/2061-css-js-inclusion/css/more.css
 rename tests/playwright/shiny/bugs/2061-css-js-inclusion/{www => css}/style.css (84%)
 create mode 100644 tests/playwright/shiny/bugs/2061-css-js-inclusion/js/customjs.js
 create mode 100644 tests/playwright/shiny/bugs/2061-css-js-inclusion/test_css-js-inclusion.py
 delete mode 100644 tests/playwright/shiny/bugs/2061-css-js-inclusion/www/customjs.js

diff --git a/tests/playwright/shiny/bugs/2061-css-js-inclusion/app.py b/tests/playwright/shiny/bugs/2061-css-js-inclusion/app.py
index 41696c8ca..847bcc6eb 100644
--- a/tests/playwright/shiny/bugs/2061-css-js-inclusion/app.py
+++ b/tests/playwright/shiny/bugs/2061-css-js-inclusion/app.py
@@ -2,8 +2,8 @@
 
 # Define the UI
 app_ui = ui.page_fluid(
-    ui.include_css("./www/style.css"),  # Reference the external CSS file
-    ui.include_js("./www/customjs.js"),
+    ui.include_css("./css/style.css", method="link_files"),
+    ui.include_js("./js/customjs.js", method="link_files"),
     ui.h1("Simple Shiny App with External CSS"),
     ui.div(
         ui.p("This is a simple Shiny app that demonstrates ui.include_css()"),
diff --git a/tests/playwright/shiny/bugs/2061-css-js-inclusion/css/more.css b/tests/playwright/shiny/bugs/2061-css-js-inclusion/css/more.css
new file mode 100644
index 000000000..3eda1891b
--- /dev/null
+++ b/tests/playwright/shiny/bugs/2061-css-js-inclusion/css/more.css
@@ -0,0 +1,3 @@
+body {
+  background-color: #c8e1f7;
+}
\ No newline at end of file
diff --git a/tests/playwright/shiny/bugs/2061-css-js-inclusion/www/style.css b/tests/playwright/shiny/bugs/2061-css-js-inclusion/css/style.css
similarity index 84%
rename from tests/playwright/shiny/bugs/2061-css-js-inclusion/www/style.css
rename to tests/playwright/shiny/bugs/2061-css-js-inclusion/css/style.css
index e86131d86..810040c7a 100644
--- a/tests/playwright/shiny/bugs/2061-css-js-inclusion/www/style.css
+++ b/tests/playwright/shiny/bugs/2061-css-js-inclusion/css/style.css
@@ -1,11 +1,11 @@
+@import url("more.css");
 
 body {
-  background-color: #f0f8ff;
   font-family: Arial, sans-serif;
 }
 
 h1 {
-  color: #4682b4;
+  color: black;
   border-bottom: 2px solid #4682b4;
   padding-bottom: 10px;
 }
diff --git a/tests/playwright/shiny/bugs/2061-css-js-inclusion/js/customjs.js b/tests/playwright/shiny/bugs/2061-css-js-inclusion/js/customjs.js
new file mode 100644
index 000000000..70925a499
--- /dev/null
+++ b/tests/playwright/shiny/bugs/2061-css-js-inclusion/js/customjs.js
@@ -0,0 +1,4 @@
+const newParagraph = document.createElement('p');
+newParagraph.textContent = 'Heyo!';
+const bodyElement = document.body;
+bodyElement.appendChild(newParagraph);
diff --git a/tests/playwright/shiny/bugs/2061-css-js-inclusion/test_css-js-inclusion.py b/tests/playwright/shiny/bugs/2061-css-js-inclusion/test_css-js-inclusion.py
new file mode 100644
index 000000000..b144f78f6
--- /dev/null
+++ b/tests/playwright/shiny/bugs/2061-css-js-inclusion/test_css-js-inclusion.py
@@ -0,0 +1,9 @@
+from playwright.sync_api import Page, expect
+
+from shiny.run import ShinyAppProc
+
+
+def test_inclusion(page: Page, local_app: ShinyAppProc) -> None:
+    page.goto(local_app.url)
+
+    expect(page.locator("body > p")).to_have_text("Heyo!")
diff --git a/tests/playwright/shiny/bugs/2061-css-js-inclusion/www/customjs.js b/tests/playwright/shiny/bugs/2061-css-js-inclusion/www/customjs.js
deleted file mode 100644
index dbb1b36fa..000000000
--- a/tests/playwright/shiny/bugs/2061-css-js-inclusion/www/customjs.js
+++ /dev/null
@@ -1 +0,0 @@
-console.log("heyo")
\ No newline at end of file

From ff8581eae0efcf4f9ce522187512f2d02f7a51b6 Mon Sep 17 00:00:00 2001
From: Liz Nelson <liz.nelson@posit.co>
Date: Wed, 27 Aug 2025 12:49:29 -0400
Subject: [PATCH 08/20] Debugging

---
 tests/playwright/shiny/bugs/2061-css-js-inclusion/app.py | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/tests/playwright/shiny/bugs/2061-css-js-inclusion/app.py b/tests/playwright/shiny/bugs/2061-css-js-inclusion/app.py
index 847bcc6eb..aa823bfd0 100644
--- a/tests/playwright/shiny/bugs/2061-css-js-inclusion/app.py
+++ b/tests/playwright/shiny/bugs/2061-css-js-inclusion/app.py
@@ -1,9 +1,13 @@
 from shiny import App, Inputs, Outputs, Session, ui
+from pathlib import Path
+
+js_file = Path(__file__).parent / "js" / "customjs.js"
+css_file = Path(__file__).parent / "css" / "style.css"
 
 # Define the UI
 app_ui = ui.page_fluid(
-    ui.include_css("./css/style.css", method="link_files"),
-    ui.include_js("./js/customjs.js", method="link_files"),
+    ui.include_css(css_file, method="link_files"),
+    ui.include_js(js_file, method="link_files"),
     ui.h1("Simple Shiny App with External CSS"),
     ui.div(
         ui.p("This is a simple Shiny app that demonstrates ui.include_css()"),

From c888903703f34a9d71e936b363df6a284b4663c2 Mon Sep 17 00:00:00 2001
From: Liz Nelson <liz.nelson@posit.co>
Date: Wed, 27 Aug 2025 12:56:52 -0400
Subject: [PATCH 09/20] fixes

---
 tests/playwright/shiny/bugs/2061-css-js-inclusion/app.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/tests/playwright/shiny/bugs/2061-css-js-inclusion/app.py b/tests/playwright/shiny/bugs/2061-css-js-inclusion/app.py
index aa823bfd0..c8e979769 100644
--- a/tests/playwright/shiny/bugs/2061-css-js-inclusion/app.py
+++ b/tests/playwright/shiny/bugs/2061-css-js-inclusion/app.py
@@ -1,6 +1,7 @@
-from shiny import App, Inputs, Outputs, Session, ui
 from pathlib import Path
 
+from shiny import App, Inputs, Outputs, Session, ui
+
 js_file = Path(__file__).parent / "js" / "customjs.js"
 css_file = Path(__file__).parent / "css" / "style.css"
 

From e99f7959230a0e77b5e18423096c1dee6a5e90fb Mon Sep 17 00:00:00 2001
From: Liz Nelson <liz.nelson@posit.co>
Date: Wed, 27 Aug 2025 13:07:08 -0400
Subject: [PATCH 10/20] Deleting old test

---
 .../2061-css-js-inclusion/app-lite/app.py     | 24 -------------------
 .../app-lite/www/customjs.js                  |  1 -
 .../app-lite/www/style.css                    | 19 ---------------
 .../2061-css-js-inclusion/app-multi/app.py    | 22 -----------------
 .../app-multi/css/more.css                    |  3 ---
 .../app-multi/css/style.css                   | 19 ---------------
 .../app-multi/js/customjs.js                  |  4 ----
 .../app-multi/js/more.js                      |  3 ---
 8 files changed, 95 deletions(-)
 delete mode 100644 tests/playwright/shiny/bugs/2061-css-js-inclusion/app-lite/app.py
 delete mode 100644 tests/playwright/shiny/bugs/2061-css-js-inclusion/app-lite/www/customjs.js
 delete mode 100644 tests/playwright/shiny/bugs/2061-css-js-inclusion/app-lite/www/style.css
 delete mode 100644 tests/playwright/shiny/bugs/2061-css-js-inclusion/app-multi/app.py
 delete mode 100644 tests/playwright/shiny/bugs/2061-css-js-inclusion/app-multi/css/more.css
 delete mode 100644 tests/playwright/shiny/bugs/2061-css-js-inclusion/app-multi/css/style.css
 delete mode 100644 tests/playwright/shiny/bugs/2061-css-js-inclusion/app-multi/js/customjs.js
 delete mode 100644 tests/playwright/shiny/bugs/2061-css-js-inclusion/app-multi/js/more.js

diff --git a/tests/playwright/shiny/bugs/2061-css-js-inclusion/app-lite/app.py b/tests/playwright/shiny/bugs/2061-css-js-inclusion/app-lite/app.py
deleted file mode 100644
index b994a7057..000000000
--- a/tests/playwright/shiny/bugs/2061-css-js-inclusion/app-lite/app.py
+++ /dev/null
@@ -1,24 +0,0 @@
-from shiny import App, ui
-
-# Define the UI
-app_ui = ui.page_fluid(
-    ui.include_css(
-        "./www/style.css", method="link_files"
-    ),  # Reference the external CSS file
-    ui.include_js("./www/customjs.js"),
-    ui.h1("Simple Shiny App with External CSS"),
-    ui.div(
-        ui.p("This is a simple Shiny app that demonstrates ui.include_css()"),
-        ui.p("The styling comes from an external CSS file!"),
-        class_="content",
-    ),
-)
-
-
-# Define the server
-def server(input, output, session):
-    pass
-
-
-# Create and run the app
-app = App(app_ui, server)
diff --git a/tests/playwright/shiny/bugs/2061-css-js-inclusion/app-lite/www/customjs.js b/tests/playwright/shiny/bugs/2061-css-js-inclusion/app-lite/www/customjs.js
deleted file mode 100644
index dbb1b36fa..000000000
--- a/tests/playwright/shiny/bugs/2061-css-js-inclusion/app-lite/www/customjs.js
+++ /dev/null
@@ -1 +0,0 @@
-console.log("heyo")
\ No newline at end of file
diff --git a/tests/playwright/shiny/bugs/2061-css-js-inclusion/app-lite/www/style.css b/tests/playwright/shiny/bugs/2061-css-js-inclusion/app-lite/www/style.css
deleted file mode 100644
index e86131d86..000000000
--- a/tests/playwright/shiny/bugs/2061-css-js-inclusion/app-lite/www/style.css
+++ /dev/null
@@ -1,19 +0,0 @@
-
-body {
-  background-color: #f0f8ff;
-  font-family: Arial, sans-serif;
-}
-
-h1 {
-  color: #4682b4;
-  border-bottom: 2px solid #4682b4;
-  padding-bottom: 10px;
-}
-
-.content {
-  margin: 20px;
-  padding: 15px;
-  background-color: white;
-  border-radius: 5px;
-  box-shadow: 0 0 10px rgba(0, 0, 0, 0.1);
-}
diff --git a/tests/playwright/shiny/bugs/2061-css-js-inclusion/app-multi/app.py b/tests/playwright/shiny/bugs/2061-css-js-inclusion/app-multi/app.py
deleted file mode 100644
index 7a37f8dab..000000000
--- a/tests/playwright/shiny/bugs/2061-css-js-inclusion/app-multi/app.py
+++ /dev/null
@@ -1,22 +0,0 @@
-from shiny import App, ui
-
-# Define the UI
-app_ui = ui.page_fluid(
-    ui.include_css("./css/style.css", method="link_files"),
-    ui.include_js("./js/customjs.js", method="link_files"),
-    ui.h1("Simple Shiny App with External CSS"),
-    ui.div(
-        ui.p("This is a simple Shiny app that demonstrates ui.include_css()"),
-        ui.p("The styling comes from an external CSS file!"),
-        class_="content",
-    ),
-)
-
-
-# Define the server
-def server(input, output, session):
-    pass
-
-
-# Create and run the app
-app = App(app_ui, server)
diff --git a/tests/playwright/shiny/bugs/2061-css-js-inclusion/app-multi/css/more.css b/tests/playwright/shiny/bugs/2061-css-js-inclusion/app-multi/css/more.css
deleted file mode 100644
index 67039459e..000000000
--- a/tests/playwright/shiny/bugs/2061-css-js-inclusion/app-multi/css/more.css
+++ /dev/null
@@ -1,3 +0,0 @@
-body {
-  background-color: #506577;
-}
\ No newline at end of file
diff --git a/tests/playwright/shiny/bugs/2061-css-js-inclusion/app-multi/css/style.css b/tests/playwright/shiny/bugs/2061-css-js-inclusion/app-multi/css/style.css
deleted file mode 100644
index 60303125d..000000000
--- a/tests/playwright/shiny/bugs/2061-css-js-inclusion/app-multi/css/style.css
+++ /dev/null
@@ -1,19 +0,0 @@
-@import url("more.css");
-
-body {
-  font-family: Arial, sans-serif;
-}
-
-h1 {
-  color: #4682b4;
-  border-bottom: 2px solid #4682b4;
-  padding-bottom: 10px;
-}
-
-.content {
-  margin: 20px;
-  padding: 15px;
-  background-color: white;
-  border-radius: 5px;
-  box-shadow: 0 0 10px rgba(0, 0, 0, 0.1);
-}
diff --git a/tests/playwright/shiny/bugs/2061-css-js-inclusion/app-multi/js/customjs.js b/tests/playwright/shiny/bugs/2061-css-js-inclusion/app-multi/js/customjs.js
deleted file mode 100644
index bdf776034..000000000
--- a/tests/playwright/shiny/bugs/2061-css-js-inclusion/app-multi/js/customjs.js
+++ /dev/null
@@ -1,4 +0,0 @@
-const heyo = require('./more.js');
-
-
-console.log(heyo())
\ No newline at end of file
diff --git a/tests/playwright/shiny/bugs/2061-css-js-inclusion/app-multi/js/more.js b/tests/playwright/shiny/bugs/2061-css-js-inclusion/app-multi/js/more.js
deleted file mode 100644
index 6dade946a..000000000
--- a/tests/playwright/shiny/bugs/2061-css-js-inclusion/app-multi/js/more.js
+++ /dev/null
@@ -1,3 +0,0 @@
-export function heyo() {
-    console.log(heyo)
-}
\ No newline at end of file

From 14012c8815eb81bca28fe39115aaff8565621e3c Mon Sep 17 00:00:00 2001
From: Liz Nelson <liz.nelson@posit.co>
Date: Thu, 28 Aug 2025 09:57:12 -0400
Subject: [PATCH 11/20] Added comments, minor changes

---
 shiny/ui/_include_helpers.py                  | 43 ++++++++-----------
 .../{ => include_files_case}/app.py           |  0
 .../css/evenmorecss}/more.css                 |  0
 .../include_files_case/css/style.css          | 19 ++++++++
 .../{ => include_files_case}/js/customjs.js   |  0
 .../test_css-js-inclusion.py                  |  0
 .../not_include_files_case/app.py             | 27 ++++++++++++
 .../not_include_files_case/customjs.js        |  4 ++
 .../{css => not_include_files_case}/style.css |  3 +-
 .../test_css-js-inclusion.py                  |  9 ++++
 10 files changed, 79 insertions(+), 26 deletions(-)
 rename tests/playwright/shiny/bugs/2061-css-js-inclusion/{ => include_files_case}/app.py (100%)
 rename tests/playwright/shiny/bugs/2061-css-js-inclusion/{css => include_files_case/css/evenmorecss}/more.css (100%)
 create mode 100644 tests/playwright/shiny/bugs/2061-css-js-inclusion/include_files_case/css/style.css
 rename tests/playwright/shiny/bugs/2061-css-js-inclusion/{ => include_files_case}/js/customjs.js (100%)
 rename tests/playwright/shiny/bugs/2061-css-js-inclusion/{ => include_files_case}/test_css-js-inclusion.py (100%)
 create mode 100644 tests/playwright/shiny/bugs/2061-css-js-inclusion/not_include_files_case/app.py
 create mode 100644 tests/playwright/shiny/bugs/2061-css-js-inclusion/not_include_files_case/customjs.js
 rename tests/playwright/shiny/bugs/2061-css-js-inclusion/{css => not_include_files_case}/style.css (90%)
 create mode 100644 tests/playwright/shiny/bugs/2061-css-js-inclusion/not_include_files_case/test_css-js-inclusion.py

diff --git a/shiny/ui/_include_helpers.py b/shiny/ui/_include_helpers.py
index 7b135e887..28a3d4c4e 100644
--- a/shiny/ui/_include_helpers.py
+++ b/shiny/ui/_include_helpers.py
@@ -226,50 +226,45 @@ def maybe_copy_files(path: Path | str, include_files: bool) -> tuple[str, str]:
     # Since the hash/tmpdir should represent all the files in the path's directory,
     # we can check if it exists to determine if we have a cache hit
     if os.path.exists(path_dest):
-        print("Already exists", path_dest)
+        print("Path already exists:", path_dest)
         return path_dest, hash
 
-    permissions = (
-        0o755  # Store permissions var set to -rwxr-xr-x (owner rwx, others rx)
-    )
-
     # Otherwise, make sure we have a clean slate
     if os.path.exists(tmpdir):
-        print("folder exists, not contents:", os.stat(tmpdir))
+        print("Folder already exists, but not files, removing.")
         shutil.rmtree(tmpdir)
 
-    # Looks like this is copying twice? puts stuff in diff folders?
+    # This recursively changes permissions to 755 (owner rwx, other rx) for all files
+    # under `tmp/unique_hash` so that the app can be run by other collaborators
+    # on a multi-tenant system. See #2061
     if include_files:
         shutil.copytree(os.path.dirname(path), tmpdir)
-        print("new folder, perms: ", oct(os.stat(tmpdir).st_mode))
-        for root, dirs, files in os.walk(tmpdir):
-            # set perms on sub-directories
-            for dir in dirs:
-                os.chmod(os.path.join(root, dir), permissions)
-                print("Dir: ", dir)
-                print("dir perms: ", oct(os.stat(os.path.join(root, dir)).st_mode))
-
+        for dirpath, dirs, filenames in os.walk(tmpdir):
             # set perms on files
-            for file in files:
-                print("File: ", file)
-                os.chmod(os.path.join(root, file), permissions)
-                print("file perms: ", oct(os.stat(os.path.join(root, file)).st_mode))
-
+            for file in filenames:
+                os.chmod(os.path.join(dirpath, file), 0o755)
+                print(
+                    "File: ",
+                    file,
+                    "File perms: ",
+                    oct(os.stat(os.path.join(dirpath, file)).st_mode),
+                )
+    else:
+        os.mkdir(tmpdir, mode=0o755)
         shutil.copy(path, path_dest)
-    print("PATH_DEST: ", path_dest)
+        os.chmod(path_dest, 0o755)
+        print("File: ", path_dest, "perms", oct(os.stat(path_dest).st_mode))
+
     return path_dest, hash
 
 
 def get_hash(path: Path | str, include_files: bool) -> str:
     if include_files:
-        print("get_hash, include_files is true")
         dir = os.path.dirname(path)
         files = glob.iglob(os.path.join(dir, "**"), recursive=True)
         key = "\n".join([get_file_key(x) for x in files])
-        print("KEY: ", key)
     else:
         key = get_file_key(path)
-        print("not include key: ", key)
 
     return hash_deterministic(key)
 
diff --git a/tests/playwright/shiny/bugs/2061-css-js-inclusion/app.py b/tests/playwright/shiny/bugs/2061-css-js-inclusion/include_files_case/app.py
similarity index 100%
rename from tests/playwright/shiny/bugs/2061-css-js-inclusion/app.py
rename to tests/playwright/shiny/bugs/2061-css-js-inclusion/include_files_case/app.py
diff --git a/tests/playwright/shiny/bugs/2061-css-js-inclusion/css/more.css b/tests/playwright/shiny/bugs/2061-css-js-inclusion/include_files_case/css/evenmorecss/more.css
similarity index 100%
rename from tests/playwright/shiny/bugs/2061-css-js-inclusion/css/more.css
rename to tests/playwright/shiny/bugs/2061-css-js-inclusion/include_files_case/css/evenmorecss/more.css
diff --git a/tests/playwright/shiny/bugs/2061-css-js-inclusion/include_files_case/css/style.css b/tests/playwright/shiny/bugs/2061-css-js-inclusion/include_files_case/css/style.css
new file mode 100644
index 000000000..5d9a8e294
--- /dev/null
+++ b/tests/playwright/shiny/bugs/2061-css-js-inclusion/include_files_case/css/style.css
@@ -0,0 +1,19 @@
+@import url("./evenmorecss/more.css");
+
+body {
+  font-family: Arial, sans-serif;
+}
+
+h1 {
+  color: black;
+  border-bottom: 2px solid #4682b4;
+  padding-bottom: 10px;
+}
+
+.content {
+  margin: 20px;
+  padding: 15px;
+  background-color: white;
+  border-radius: 5px;
+  box-shadow: 0 0 10px rgba(0, 0, 0, 0.1);
+}
diff --git a/tests/playwright/shiny/bugs/2061-css-js-inclusion/js/customjs.js b/tests/playwright/shiny/bugs/2061-css-js-inclusion/include_files_case/js/customjs.js
similarity index 100%
rename from tests/playwright/shiny/bugs/2061-css-js-inclusion/js/customjs.js
rename to tests/playwright/shiny/bugs/2061-css-js-inclusion/include_files_case/js/customjs.js
diff --git a/tests/playwright/shiny/bugs/2061-css-js-inclusion/test_css-js-inclusion.py b/tests/playwright/shiny/bugs/2061-css-js-inclusion/include_files_case/test_css-js-inclusion.py
similarity index 100%
rename from tests/playwright/shiny/bugs/2061-css-js-inclusion/test_css-js-inclusion.py
rename to tests/playwright/shiny/bugs/2061-css-js-inclusion/include_files_case/test_css-js-inclusion.py
diff --git a/tests/playwright/shiny/bugs/2061-css-js-inclusion/not_include_files_case/app.py b/tests/playwright/shiny/bugs/2061-css-js-inclusion/not_include_files_case/app.py
new file mode 100644
index 000000000..bfccf95fb
--- /dev/null
+++ b/tests/playwright/shiny/bugs/2061-css-js-inclusion/not_include_files_case/app.py
@@ -0,0 +1,27 @@
+from pathlib import Path
+
+from shiny import App, Inputs, Outputs, Session, ui
+
+js_file = Path(__file__).parent / "customjs.js"
+css_file = Path(__file__).parent / "style.css"
+
+# Define the UI
+app_ui = ui.page_fluid(
+    ui.include_css(css_file, method="link"),
+    ui.include_js(js_file, method="inline"),
+    ui.h1("Simple Shiny App with External CSS"),
+    ui.div(
+        ui.p("This is a simple Shiny app that demonstrates ui.include_css()"),
+        ui.p("The styling comes from an external CSS file!"),
+        class_="content",
+    ),
+)
+
+
+# Define the server
+def server(input: Inputs, output: Outputs, session: Session):
+    pass
+
+
+# Create and run the app
+app = App(app_ui, server)
diff --git a/tests/playwright/shiny/bugs/2061-css-js-inclusion/not_include_files_case/customjs.js b/tests/playwright/shiny/bugs/2061-css-js-inclusion/not_include_files_case/customjs.js
new file mode 100644
index 000000000..70925a499
--- /dev/null
+++ b/tests/playwright/shiny/bugs/2061-css-js-inclusion/not_include_files_case/customjs.js
@@ -0,0 +1,4 @@
+const newParagraph = document.createElement('p');
+newParagraph.textContent = 'Heyo!';
+const bodyElement = document.body;
+bodyElement.appendChild(newParagraph);
diff --git a/tests/playwright/shiny/bugs/2061-css-js-inclusion/css/style.css b/tests/playwright/shiny/bugs/2061-css-js-inclusion/not_include_files_case/style.css
similarity index 90%
rename from tests/playwright/shiny/bugs/2061-css-js-inclusion/css/style.css
rename to tests/playwright/shiny/bugs/2061-css-js-inclusion/not_include_files_case/style.css
index 810040c7a..078238b67 100644
--- a/tests/playwright/shiny/bugs/2061-css-js-inclusion/css/style.css
+++ b/tests/playwright/shiny/bugs/2061-css-js-inclusion/not_include_files_case/style.css
@@ -1,6 +1,5 @@
-@import url("more.css");
-
 body {
+  background-color: #70bfef;
   font-family: Arial, sans-serif;
 }
 
diff --git a/tests/playwright/shiny/bugs/2061-css-js-inclusion/not_include_files_case/test_css-js-inclusion.py b/tests/playwright/shiny/bugs/2061-css-js-inclusion/not_include_files_case/test_css-js-inclusion.py
new file mode 100644
index 000000000..b144f78f6
--- /dev/null
+++ b/tests/playwright/shiny/bugs/2061-css-js-inclusion/not_include_files_case/test_css-js-inclusion.py
@@ -0,0 +1,9 @@
+from playwright.sync_api import Page, expect
+
+from shiny.run import ShinyAppProc
+
+
+def test_inclusion(page: Page, local_app: ShinyAppProc) -> None:
+    page.goto(local_app.url)
+
+    expect(page.locator("body > p")).to_have_text("Heyo!")

From 7ffeab5cce0c8c9b7d30023eff3c1a347cfcc934 Mon Sep 17 00:00:00 2001
From: Liz Nelson <liz.nelson@posit.co>
Date: Thu, 28 Aug 2025 11:45:18 -0400
Subject: [PATCH 12/20] Relinking vs inline

---
 .../bugs/2061-css-js-inclusion/not_include_files_case/app.py    | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/playwright/shiny/bugs/2061-css-js-inclusion/not_include_files_case/app.py b/tests/playwright/shiny/bugs/2061-css-js-inclusion/not_include_files_case/app.py
index bfccf95fb..4072ca609 100644
--- a/tests/playwright/shiny/bugs/2061-css-js-inclusion/not_include_files_case/app.py
+++ b/tests/playwright/shiny/bugs/2061-css-js-inclusion/not_include_files_case/app.py
@@ -8,7 +8,7 @@
 # Define the UI
 app_ui = ui.page_fluid(
     ui.include_css(css_file, method="link"),
-    ui.include_js(js_file, method="inline"),
+    ui.include_js(js_file, method="link"),
     ui.h1("Simple Shiny App with External CSS"),
     ui.div(
         ui.p("This is a simple Shiny app that demonstrates ui.include_css()"),

From 63a3c40a09e49ff29da831b8f0e8b8285763bc50 Mon Sep 17 00:00:00 2001
From: E Nelson <elizabethwnelson5@gmail.com>
Date: Thu, 28 Aug 2025 16:43:25 -0400
Subject: [PATCH 13/20] Update shiny/ui/_include_helpers.py

Co-authored-by: Carson Sievert <cpsievert1@gmail.com>
---
 shiny/ui/_include_helpers.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/shiny/ui/_include_helpers.py b/shiny/ui/_include_helpers.py
index 28a3d4c4e..49b2c8a14 100644
--- a/shiny/ui/_include_helpers.py
+++ b/shiny/ui/_include_helpers.py
@@ -19,7 +19,6 @@
 # as the app, the app's source will be included. Should we just not copy .py/.r files?
 
 
-# TODO: This does throw js errors if you're loading in other stuff depending on your config
 @add_example()
 def include_js(
     path: Path | str,

From 6609d20e82f5a88d2dd801974f01af63b4fc4ba9 Mon Sep 17 00:00:00 2001
From: Liz Nelson <liz.nelson@posit.co>
Date: Thu, 28 Aug 2025 16:48:00 -0400
Subject: [PATCH 14/20] Updating prints

---
 shiny/ui/_include_helpers.py | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/shiny/ui/_include_helpers.py b/shiny/ui/_include_helpers.py
index 49b2c8a14..5ac87189d 100644
--- a/shiny/ui/_include_helpers.py
+++ b/shiny/ui/_include_helpers.py
@@ -249,7 +249,13 @@ def maybe_copy_files(path: Path | str, include_files: bool) -> tuple[str, str]:
                     oct(os.stat(os.path.join(dirpath, file)).st_mode),
                 )
     else:
-        os.mkdir(tmpdir, mode=0o755)
+        os.makedirs(tmpdir, mode=0o755, exist_ok=True)
+        print(
+            "Copying files from: ",
+            path,
+            " with perms: ",
+            oct(os.stat(path).st_mode),
+        )
         shutil.copy(path, path_dest)
         os.chmod(path_dest, 0o755)
         print("File: ", path_dest, "perms", oct(os.stat(path_dest).st_mode))

From b477812db581590468ff079bc49780fb0e899452 Mon Sep 17 00:00:00 2001
From: Liz Nelson <liz.nelson@posit.co>
Date: Fri, 29 Aug 2025 16:57:28 -0400
Subject: [PATCH 15/20] Updating 'shiny_include_files to have 777 perms

---
 shiny/ui/_include_helpers.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/shiny/ui/_include_helpers.py b/shiny/ui/_include_helpers.py
index 5ac87189d..0da403f68 100644
--- a/shiny/ui/_include_helpers.py
+++ b/shiny/ui/_include_helpers.py
@@ -218,9 +218,14 @@ def maybe_copy_files(path: Path | str, include_files: bool) -> tuple[str, str]:
 
     # To avoid unnecessary work when the same file is included multiple times,
     # use a directory scoped by a hash of the file.
-    tmpdir = os.path.join(tempfile.gettempdir(), "shiny_include_files", hash)
+    tmp_folder = os.path.join(
+        os.path.basename(path), tempfile.gettempdir(), "shiny_include_files"
+    )
+    tmpdir = os.path.join(tmp_folder, hash)
     path_dest = os.path.join(tmpdir, os.path.basename(path))
     print("path_dest:", path_dest)
+    print(tmp_folder)
+    os.chmod(tmp_folder, 0o755)
 
     # Since the hash/tmpdir should represent all the files in the path's directory,
     # we can check if it exists to determine if we have a cache hit

From 30fc4f78f72b4e5772a5231814cdb586c5aa2b57 Mon Sep 17 00:00:00 2001
From: Liz Nelson <liz.nelson@posit.co>
Date: Tue, 2 Sep 2025 16:44:59 -0400
Subject: [PATCH 16/20] Testing only new dir change

---
 shiny/ui/_include_helpers.py | 42 ++++++++++++------------------------
 1 file changed, 14 insertions(+), 28 deletions(-)

diff --git a/shiny/ui/_include_helpers.py b/shiny/ui/_include_helpers.py
index 0da403f68..f63b2b122 100644
--- a/shiny/ui/_include_helpers.py
+++ b/shiny/ui/_include_helpers.py
@@ -216,17 +216,12 @@ def maybe_copy_files(path: Path | str, include_files: bool) -> tuple[str, str]:
     hash = get_hash(path, include_files)
     print("path: ", path, "Hash: ", hash)
 
-    # To avoid unnecessary work when the same file is included multiple times,
-    # use a directory scoped by a hash of the file.
-    tmp_folder = os.path.join(
-        os.path.basename(path), tempfile.gettempdir(), "shiny_include_files"
-    )
-    tmpdir = os.path.join(tmp_folder, hash)
+    tmpdir = os.path.join(tempfile.gettempdir(), f"shiny_include_files_{hash}")
     path_dest = os.path.join(tmpdir, os.path.basename(path))
-    print("path_dest:", path_dest)
-    print(tmp_folder)
-    os.chmod(tmp_folder, 0o755)
+    print("tmpdir: ", tmpdir, "path_dest: ", path_dest)
 
+    # To avoid unnecessary work when the same file is included multiple times,
+    # use a directory scoped by a hash of the file.
     # Since the hash/tmpdir should represent all the files in the path's directory,
     # we can check if it exists to determine if we have a cache hit
     if os.path.exists(path_dest):
@@ -234,27 +229,21 @@ def maybe_copy_files(path: Path | str, include_files: bool) -> tuple[str, str]:
         return path_dest, hash
 
     # Otherwise, make sure we have a clean slate
-    if os.path.exists(tmpdir):
+    if os.path.exists(path_dest):
         print("Folder already exists, but not files, removing.")
-        shutil.rmtree(tmpdir)
+        shutil.rmtree(path_dest)
 
-    # This recursively changes permissions to 755 (owner rwx, other rx) for all files
-    # under `tmp/unique_hash` so that the app can be run by other collaborators
-    # on a multi-tenant system. See #2061
     if include_files:
+        print(
+            "Copying all included files from: ",
+            path,
+            " with perms: ",
+            oct(os.stat(path).st_mode),
+        )
         shutil.copytree(os.path.dirname(path), tmpdir)
-        for dirpath, dirs, filenames in os.walk(tmpdir):
-            # set perms on files
-            for file in filenames:
-                os.chmod(os.path.join(dirpath, file), 0o755)
-                print(
-                    "File: ",
-                    file,
-                    "File perms: ",
-                    oct(os.stat(os.path.join(dirpath, file)).st_mode),
-                )
+
     else:
-        os.makedirs(tmpdir, mode=0o755, exist_ok=True)
+        os.makedirs(path_dest, mode=0o755, exist_ok=True)
         print(
             "Copying files from: ",
             path,
@@ -262,9 +251,6 @@ def maybe_copy_files(path: Path | str, include_files: bool) -> tuple[str, str]:
             oct(os.stat(path).st_mode),
         )
         shutil.copy(path, path_dest)
-        os.chmod(path_dest, 0o755)
-        print("File: ", path_dest, "perms", oct(os.stat(path_dest).st_mode))
-
     return path_dest, hash
 
 

From 87afb30d110fb836490d7242c33e6f918f92e49c Mon Sep 17 00:00:00 2001
From: Liz Nelson <liz.nelson@posit.co>
Date: Wed, 3 Sep 2025 15:23:55 -0400
Subject: [PATCH 17/20] Updating to deal with 404

---
 shiny/ui/_include_helpers.py                              | 8 +++++---
 .../include_files_case/css/style.css                      | 2 ++
 .../include_files_case/js/customjs.js                     | 4 ++--
 .../not_include_files_case/customjs.js                    | 3 +--
 4 files changed, 10 insertions(+), 7 deletions(-)

diff --git a/shiny/ui/_include_helpers.py b/shiny/ui/_include_helpers.py
index f63b2b122..57d9ca180 100644
--- a/shiny/ui/_include_helpers.py
+++ b/shiny/ui/_include_helpers.py
@@ -197,6 +197,7 @@ def check_path(path: Path | str) -> Path:
 def create_include_dependency(
     name: str, path: str, include_files: bool
 ) -> tuple[HTMLDependency, str]:
+    print("create include: ", name, os.path.dirname(path))
     dep = HTMLDependency(
         name,
         DEFAULT_VERSION,
@@ -216,7 +217,7 @@ def maybe_copy_files(path: Path | str, include_files: bool) -> tuple[str, str]:
     hash = get_hash(path, include_files)
     print("path: ", path, "Hash: ", hash)
 
-    tmpdir = os.path.join(tempfile.gettempdir(), f"shiny_include_files_{hash}")
+    tmpdir = os.path.join(tempfile.gettempdir(), f"shiny_include_{hash}")
     path_dest = os.path.join(tmpdir, os.path.basename(path))
     print("tmpdir: ", tmpdir, "path_dest: ", path_dest)
 
@@ -229,7 +230,7 @@ def maybe_copy_files(path: Path | str, include_files: bool) -> tuple[str, str]:
         return path_dest, hash
 
     # Otherwise, make sure we have a clean slate
-    if os.path.exists(path_dest):
+    if os.path.exists(tmpdir):
         print("Folder already exists, but not files, removing.")
         shutil.rmtree(path_dest)
 
@@ -243,7 +244,7 @@ def maybe_copy_files(path: Path | str, include_files: bool) -> tuple[str, str]:
         shutil.copytree(os.path.dirname(path), tmpdir)
 
     else:
-        os.makedirs(path_dest, mode=0o755, exist_ok=True)
+        os.makedirs(tmpdir, exist_ok=True)
         print(
             "Copying files from: ",
             path,
@@ -251,6 +252,7 @@ def maybe_copy_files(path: Path | str, include_files: bool) -> tuple[str, str]:
             oct(os.stat(path).st_mode),
         )
         shutil.copy(path, path_dest)
+
     return path_dest, hash
 
 
diff --git a/tests/playwright/shiny/bugs/2061-css-js-inclusion/include_files_case/css/style.css b/tests/playwright/shiny/bugs/2061-css-js-inclusion/include_files_case/css/style.css
index 5d9a8e294..99c3ee888 100644
--- a/tests/playwright/shiny/bugs/2061-css-js-inclusion/include_files_case/css/style.css
+++ b/tests/playwright/shiny/bugs/2061-css-js-inclusion/include_files_case/css/style.css
@@ -17,3 +17,5 @@ h1 {
   border-radius: 5px;
   box-shadow: 0 0 10px rgba(0, 0, 0, 0.1);
 }
+
+
diff --git a/tests/playwright/shiny/bugs/2061-css-js-inclusion/include_files_case/js/customjs.js b/tests/playwright/shiny/bugs/2061-css-js-inclusion/include_files_case/js/customjs.js
index 70925a499..4dc8fcc69 100644
--- a/tests/playwright/shiny/bugs/2061-css-js-inclusion/include_files_case/js/customjs.js
+++ b/tests/playwright/shiny/bugs/2061-css-js-inclusion/include_files_case/js/customjs.js
@@ -1,4 +1,4 @@
 const newParagraph = document.createElement('p');
 newParagraph.textContent = 'Heyo!';
-const bodyElement = document.body;
-bodyElement.appendChild(newParagraph);
+document.body.appendChild(newParagraph);
+
diff --git a/tests/playwright/shiny/bugs/2061-css-js-inclusion/not_include_files_case/customjs.js b/tests/playwright/shiny/bugs/2061-css-js-inclusion/not_include_files_case/customjs.js
index 70925a499..c7e8ae251 100644
--- a/tests/playwright/shiny/bugs/2061-css-js-inclusion/not_include_files_case/customjs.js
+++ b/tests/playwright/shiny/bugs/2061-css-js-inclusion/not_include_files_case/customjs.js
@@ -1,4 +1,3 @@
 const newParagraph = document.createElement('p');
 newParagraph.textContent = 'Heyo!';
-const bodyElement = document.body;
-bodyElement.appendChild(newParagraph);
+document.body.appendChild(newParagraph);

From 8ae64602b56d3aeabcfc413f6542ef39d75ad425 Mon Sep 17 00:00:00 2001
From: Liz Nelson <liz.nelson@posit.co>
Date: Wed, 3 Sep 2025 15:25:13 -0400
Subject: [PATCH 18/20] Updating one missing piece

---
 shiny/ui/_include_helpers.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/shiny/ui/_include_helpers.py b/shiny/ui/_include_helpers.py
index 57d9ca180..ddaf1ac2c 100644
--- a/shiny/ui/_include_helpers.py
+++ b/shiny/ui/_include_helpers.py
@@ -232,7 +232,7 @@ def maybe_copy_files(path: Path | str, include_files: bool) -> tuple[str, str]:
     # Otherwise, make sure we have a clean slate
     if os.path.exists(tmpdir):
         print("Folder already exists, but not files, removing.")
-        shutil.rmtree(path_dest)
+        shutil.rmtree(tmpdir)
 
     if include_files:
         print(

From 64f978e5861f1fb41ba102551aed09af449b641c Mon Sep 17 00:00:00 2001
From: Liz Nelson <liz.nelson@posit.co>
Date: Wed, 3 Sep 2025 16:22:32 -0400
Subject: [PATCH 19/20] Adding del

---
 shiny/_app.py                | 13 +++++++++++++
 shiny/ui/_include_helpers.py |  1 -
 2 files changed, 13 insertions(+), 1 deletion(-)

diff --git a/shiny/_app.py b/shiny/_app.py
index 0de886a69..a569883f0 100644
--- a/shiny/_app.py
+++ b/shiny/_app.py
@@ -2,6 +2,7 @@
 
 import copy
 import os
+import shutil
 import secrets
 from contextlib import AsyncExitStack, asynccontextmanager
 from inspect import signature
@@ -214,6 +215,18 @@ def __init__(
                 cast("Tag | TagList", ui), lib_prefix=self.lib_prefix
             )
 
+    def __del__(self):
+        user_dependencies = [
+            v.source["subdir"]
+            for k, v in self._registered_dependencies.items()
+            if k.startswith("include-")
+        ]
+
+        for item in user_dependencies:
+            if os.path.exists(item):
+                print("Removing dependency: ", item)
+                shutil.rmtree(item)
+
     def init_starlette_app(self) -> starlette.applications.Starlette:
         routes: list[starlette.routing.BaseRoute] = [
             starlette.routing.WebSocketRoute("/websocket/", self._on_connect_cb),
diff --git a/shiny/ui/_include_helpers.py b/shiny/ui/_include_helpers.py
index ddaf1ac2c..3c7fa923e 100644
--- a/shiny/ui/_include_helpers.py
+++ b/shiny/ui/_include_helpers.py
@@ -197,7 +197,6 @@ def check_path(path: Path | str) -> Path:
 def create_include_dependency(
     name: str, path: str, include_files: bool
 ) -> tuple[HTMLDependency, str]:
-    print("create include: ", name, os.path.dirname(path))
     dep = HTMLDependency(
         name,
         DEFAULT_VERSION,

From c3e3e22aadb8d07e3018451e3c0c5cca642665f4 Mon Sep 17 00:00:00 2001
From: Liz Nelson <liz.nelson@posit.co>
Date: Wed, 3 Sep 2025 17:03:00 -0400
Subject: [PATCH 20/20] adding check to make sure it's in the temp dir

---
 shiny/_app.py | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/shiny/_app.py b/shiny/_app.py
index a569883f0..835e93a10 100644
--- a/shiny/_app.py
+++ b/shiny/_app.py
@@ -3,6 +3,7 @@
 import copy
 import os
 import shutil
+import tempfile
 import secrets
 from contextlib import AsyncExitStack, asynccontextmanager
 from inspect import signature
@@ -216,6 +217,8 @@ def __init__(
             )
 
     def __del__(self):
+        current_temp_dir = os.path.realpath(tempfile.gettempdir())
+
         user_dependencies = [
             v.source["subdir"]
             for k, v in self._registered_dependencies.items()
@@ -223,7 +226,12 @@ def __del__(self):
         ]
 
         for item in user_dependencies:
-            if os.path.exists(item):
+            # Only remove the item if it exists and it is in the current temp directory
+            if (
+                os.path.exists(item)
+                and os.path.commonprefix([os.path.realpath(item), current_temp_dir])
+                == current_temp_dir
+            ):
                 print("Removing dependency: ", item)
                 shutil.rmtree(item)