python-microscopy · David-Baddeley · Sep 3, 2026 · Aug 26, 2026 · Aug 27, 2026 · Aug 27, 2026
diff --git a/.github/workflows/make_installers.yaml b/.github/workflows/make_installers.yaml
@@ -30,7 +30,7 @@ jobs:
         id: version
         shell: pwsh
         run: |
-          $v = & "bundle\venv\Scripts\python.exe" `
+          $v = & "bundle\python\python.exe" `
             -c "import importlib.metadata; print(importlib.metadata.version('python-microscopy'))"
           "version=$v" | Out-File -FilePath $env:GITHUB_OUTPUT -Append
 

diff --git a/installers/install-python-microscopy.bat b/installers/install-python-microscopy.bat
@@ -23,27 +23,28 @@ if not errorlevel 1 (
     if errorlevel 1 exit /b 1
 )
 
-:: ---- Managed Python + virtual environment ----
-echo Installing Python !TARGET_PYTHON!...
-"!UV!" python install !TARGET_PYTHON!
-if errorlevel 1 (echo ERROR: uv python install failed & exit /b 1)
+:: ---- Standalone Python installation via py-app-standalone ----
+echo Creating standalone Python installation...
+"!UV!" tool run py-app-standalone --python-version !TARGET_PYTHON! --target "!DEST!" --force !PACKAGE_NAME!
+if errorlevel 1 (echo ERROR: py-app-standalone failed & exit /b 1)
 
-echo Creating virtual environment...
-"!UV!" venv --python !TARGET_PYTHON! "!DEST!\venv"
-if errorlevel 1 (echo ERROR: venv creation failed & exit /b 1)
-
-:: ---- Install PYME from pip ----
-echo Installing !PACKAGE_NAME!...
-"!UV!" pip install --python "!DEST!\venv\Scripts\python.exe" !PACKAGE_NAME!
-if errorlevel 1 (echo ERROR: package installation failed & exit /b 1)
+:: ---- Normalize cpython-* to a stable directory name ----
+:: pushd+ren avoids the CMD quirk where a quoted glob isn't expanded in for /d.
+pushd "!DEST!"
+for /d %%d in (cpython-*) do ren "%%d" python
+popd
+if not exist "!DEST!\python\" (echo ERROR: standalone Python directory not found & exit /b 1)
+:: Remove the bare-venv temp directory that py-app-standalone leaves behind.
+if exist "!DEST!\bare-venv\" rd /s /q "!DEST!\bare-venv"
 
 :: ---- Entry point .cmd wrappers ----
 for %%e in (%ENTRY_POINTS%) do call :mk_wrapper "%%e"
 
-:: ---- Activated-console helper ----
+:: ---- Console helper (adds python dir to PATH for the session) ----
 (
     echo @echo off
-    echo start cmd.exe /k "%%~dp0venv\Scripts\activate.bat"
+    echo set "PATH=%%~dp0python;%%~dp0python\Scripts;%%PATH%%"
+    echo cmd.exe /k
 ) > "!DEST!\pyme-console.cmd"
 
 echo.
@@ -72,11 +73,10 @@ exit /b 0
 
 :: ----------------------------------------------------------------
 :mk_wrapper
-:: Writes a thin .cmd shim that forwards all arguments to the venv entry point exe.
-:: Uses %~dp0 so wrappers work even if the install folder is moved.
+:: Uses %~dp0 so wrappers stay valid if the install folder is moved.
 set "_EP=%~1"
 (
     echo @echo off
-    echo "%%~dp0venv\Scripts\!_EP!.exe" %%*
+    echo "%%~dp0python\Scripts\!_EP!.exe" %%*
 ) > "!DEST!\!_EP!.cmd"
 exit /b 0
diff --git a/installers/install-python-microscopy.sh b/installers/install-python-microscopy.sh
@@ -43,26 +43,27 @@ if ! command -v uv &>/dev/null; then
     fi
 fi
 
-# --- Managed Python ---
-uv python install "$TARGET_PYTHON"
+# --- Standalone Python installation via py-app-standalone ---
+echo "==> Creating standalone Python installation..."
+uv tool run py-app-standalone --python-version "$TARGET_PYTHON" --target "$DEST" --force "$PACKAGE_NAME"
 
-# --- Virtual environment ---
-uv venv --python "$TARGET_PYTHON" "$DEST/venv"
-
-# --- Install PYME from pip ---
-echo "==> Installing $PACKAGE_NAME..."
-uv pip install --python "$DEST/venv/bin/python" "$PACKAGE_NAME"
+# --- Normalize cpython-* to a stable directory name ---
+PYTHON_DIRS=( "$DEST"/cpython-* )
+[[ -d "${PYTHON_DIRS[0]}" ]] || { echo "ERROR: standalone Python directory not found" >&2; exit 1; }
+mv "${PYTHON_DIRS[0]}" "$DEST/python"
+# Remove the bare-venv temp directory that py-app-standalone leaves behind.
+rm -rf "$DEST/bare-venv"
 
 # --- Top-level entry point symlinks ---
 for ep in "${ENTRY_POINTS[@]}"; do
-    ln -sf "$DEST/venv/bin/$ep" "$DEST/$ep"
+    ln -sf "$DEST/python/bin/$ep" "$DEST/$ep"
 done
 
-# --- Activated-shell helper ---
+# --- Shell helper (adds python/bin to PATH) ---
 cat > "$DEST/pyme-shell" <<'SHELL_SCRIPT'
 #!/usr/bin/env bash
 PYME_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
-source "$PYME_DIR/venv/bin/activate"
+export PATH="$PYME_DIR/python/bin:$PATH"
 exec "${SHELL:-bash}"
 SHELL_SCRIPT
 chmod +x "$DEST/pyme-shell"

diff --git a/installers/windows/pyme_setup.iss b/installers/windows/pyme_setup.iss
@@ -13,17 +13,17 @@
 
 #define AppName      "PYME"
 #define AppPublisher "Baddeley Lab, University of Auckland"
-; Icons ship with the package inside the venv tree.
+; Icons ship with the package inside the standalone Python tree.
 ; pymeLogo.png has no .ico equivalent — pmanal.ico is used in its place.
-#define IconsDir     "{app}\venv\Lib\site-packages\PYME\resources\icons"
+#define IconsDir     "{app}\python\Lib\site-packages\PYME\resources\icons"
 
 [Setup]
 ; AppId uniquely identifies this application for upgrades and uninstall — do not change.
 AppId={{8F3A2E1D-6B4C-4D9F-A7E2-3C1B5F8A2D6E}
 AppName={#AppName}
 AppVersion={#AppVersion}
 AppPublisher={#AppPublisher}
-DefaultDirName={autopf}\{#AppName}
+DefaultDirName={%USERPROFILE}\PYME
 DefaultGroupName={#AppName}
 ; Per-user install by default; elevation dialog allows all-users install.
 PrivilegesRequired=lowest
@@ -39,9 +39,9 @@ CloseApplications=no
 Source: "{#AppSourceDir}\*"; DestDir: "{app}"; Flags: recursesubdirs createallsubdirs
 
 [Icons]
-Name: "{group}\PYMEAcquire";      Filename: "{app}\PYMEAcquire.cmd";      IconFilename: "{#IconsDir}\pmacquire.ico"
-Name: "{group}\PYMEImage";        Filename: "{app}\PYMEImage.cmd";        IconFilename: "{#IconsDir}\pmanal.ico"
-Name: "{group}\PYMEVis";          Filename: "{app}\PYMEVis.cmd";          IconFilename: "{#IconsDir}\pmvis.ico"
-Name: "{group}\PYMEClusterOfOne"; Filename: "{app}\PYMEClusterOfOne.cmd"; IconFilename: "{#IconsDir}\pmanal.ico"
-Name: "{group}\PYME Console";     Filename: "{app}\pyme-console.cmd";     IconFilename: "{#IconsDir}\pmanal.ico"
+Name: "{group}\PYMEAcquire";      Filename: "{app}\python\Scripts\PYMEAcquire.exe";      WorkingDir: "{app}"; IconFilename: "{#IconsDir}\pmacquire.ico"
+Name: "{group}\PYMEImage";        Filename: "{app}\python\Scripts\PYMEImage.exe";        WorkingDir: "{app}"; IconFilename: "{#IconsDir}\pmanal.ico"
+Name: "{group}\PYMEVis";          Filename: "{app}\python\Scripts\PYMEVis.exe";          WorkingDir: "{app}"; IconFilename: "{#IconsDir}\pmvis.ico"
+Name: "{group}\PYMEClusterOfOne"; Filename: "{app}\python\Scripts\PYMEClusterOfOne.exe"; WorkingDir: "{app}"; IconFilename: "{#IconsDir}\pmanal.ico"
+Name: "{group}\PYME Console";     Filename: "{sys}\cmd.exe"; Parameters: "/k set ""PATH={app}\python;{app}\python\Scripts;%PATH%"""; WorkingDir: "{%USERPROFILE}"; IconFilename: "{#IconsDir}\pmanal.ico"
 Name: "{group}\Uninstall PYME";   Filename: "{uninstallexe}"