setup_windows.bat

@echo off
setlocal EnableExtensions EnableDelayedExpansion
title MOSNA GUI — Installation Windows

rem =============================================================
rem  MOSNA GUI — Windows installer
rem  Double-click to run, or:  setup_windows.bat [--no-shortcut]
rem  Requirements: conda / miniconda (auto-installed if missing)
rem =============================================================

rem ── Configuration ────────────────────────────────────────────
set "ENV_NAME=mosna-GUI"
set "PYTHON_VERSION=3.10"

rem Resolve project root (folder containing this .bat)
set "PROJECT_DIR=%~dp0"
if "%PROJECT_DIR:~-1%"=="\" set "PROJECT_DIR=%PROJECT_DIR:~0,-1%"

set "GUI_SCRIPT=%PROJECT_DIR%\GUI_MOSNA.py"
set "MOSNA_PACKAGE=%PROJECT_DIR%\mosna-package"
set "ICON_FILE=%PROJECT_DIR%\assets\logo.ico"
set "LAUNCHER_BAT=%PROJECT_DIR%\MosnaGUI.bat"
set "DESKTOP_SHORTCUT=%USERPROFILE%\Desktop\MOSNA GUI.lnk"

set "MINICONDA_DIR=%USERPROFILE%\miniconda3"
set "MINICONDA_INSTALLER=%TEMP%\Miniconda3-latest-Windows-x86_64.exe"
set "MINICONDA_URL=https://repo.anaconda.com/miniconda/Miniconda3-latest-Windows-x86_64.exe"

set "CONDA_BAT="
set "CREATE_SHORTCUT=1"

rem ── Parse optional arguments ─────────────────────────────────
for %%A in (%*) do (
    if /I "%%A"=="--no-shortcut" set "CREATE_SHORTCUT=0"
)

rem ── Banner ───────────────────────────────────────────────────
echo.
echo ============================================================
echo          MOSNA GUI ^— Windows Installation
echo ============================================================
echo.
echo  Project : %PROJECT_DIR%
echo.

rem ── Sanity checks ────────────────────────────────────────────
echo [0/5] Sanity checks...

if not exist "%GUI_SCRIPT%" (
    echo [ERROR] GUI_MOSNA.py not found.
    echo         Run this script from the project root directory.
    goto :fail
)

if not exist "%MOSNA_PACKAGE%" (
    echo [ERROR] mosna-package directory not found:
    echo         %MOSNA_PACKAGE%
    goto :fail
)

cd /d "%PROJECT_DIR%"

rem ── Locate conda ────────────────────────────────────────────
call :find_conda
if errorlevel 1 (
    echo [INFO] Conda not found — downloading Miniconda automatically...
    call :install_miniconda
    if errorlevel 1 goto :fail
    call :find_conda
    if errorlevel 1 (
        echo [ERROR] Conda still not found after Miniconda installation.
        goto :fail
    )
)
echo [OK]   Conda: %CONDA_BAT%
echo.

rem ── Step 1: Environment ──────────────────────────────────────
echo [1/5] Conda environment "%ENV_NAME%"...
call :ensure_env
if errorlevel 1 goto :fail

rem ── Step 2: Conda packages ───────────────────────────────────
echo.
echo [2/5] Installing conda-forge packages...
call "%CONDA_BAT%" install -n "%ENV_NAME%" -y -c conda-forge ^
    "python=%PYTHON_VERSION%" ^
    pyside6 ^
    pyyaml ^
    pandas ^
    pyarrow ^
    "scipy=1.13" ^
    scikit-learn ^
    networkx ^
    matplotlib ^
    seaborn ^
    scanpy ^
    tqdm ^
    lifelines ^
    ipykernel ^
    ipywidgets ^
    markdown
if errorlevel 1 (
    echo [ERROR] conda install failed.
    goto :fail
)
echo [OK]   Conda packages installed.

rem ── Step 3: mosna-package ────────────────────────────────────
echo.
echo [3/5] Installing mosna-package...
call "%CONDA_BAT%" run -n "%ENV_NAME%" python -m pip install "%MOSNA_PACKAGE%" --quiet
if errorlevel 1 (
    echo [ERROR] mosna-package installation failed.
    goto :fail
)
echo [OK]   mosna-package installed.

rem ── Step 4: Verify imports ───────────────────────────────────
echo.
echo [4/5] Verifying key imports...
call "%CONDA_BAT%" run -n "%ENV_NAME%" python -c ^
    "import PySide6, yaml, pandas, mosna; print('[OK]   All imports successful.')"
if errorlevel 1 (
    echo [ERROR] Import verification failed. Check the output above.
    goto :fail
)

rem ── Step 5: Launcher + shortcut ──────────────────────────────
echo.
echo [5/5] Creating launcher and desktop shortcut...

rem Generate MosnaGUI.bat launcher
(
    echo @echo off
    echo rem Auto-generated by setup_windows.bat
    echo set "CONDA_BAT=%CONDA_BAT%"
    echo call "%%CONDA_BAT%%" activate "%ENV_NAME%"
    echo cd /d "%PROJECT_DIR%"
    echo python "%GUI_SCRIPT%"
) > "%LAUNCHER_BAT%"
echo [OK]   Launcher: %LAUNCHER_BAT%

if "%CREATE_SHORTCUT%"=="1" (
    call :create_shortcut
    if errorlevel 1 (
        echo [WARN]  Could not create desktop shortcut ^(non-fatal^).
    ) else (
        echo [OK]   Shortcut: %DESKTOP_SHORTCUT%
    )
) else (
    echo [INFO]  Desktop shortcut skipped ^(--no-shortcut^).
)

rem ── Done ─────────────────────────────────────────────────────
echo.
echo ============================================================
echo  Installation complete!
echo ============================================================
echo.
echo  To launch: double-click  MosnaGUI.bat  in the project folder
echo             or the shortcut on your Desktop.
echo.
pause
goto :eof


rem =============================================================
rem  Subroutines
rem =============================================================

:find_conda
set "CONDA_BAT="
if exist "%MINICONDA_DIR%\condabin\conda.bat" (
    set "CONDA_BAT=%MINICONDA_DIR%\condabin\conda.bat"
    exit /b 0
)
if exist "%USERPROFILE%\anaconda3\condabin\conda.bat" (
    set "CONDA_BAT=%USERPROFILE%\anaconda3\condabin\conda.bat"
    exit /b 0
)
if exist "%USERPROFILE%\Miniconda3\condabin\conda.bat" (
    set "CONDA_BAT=%USERPROFILE%\Miniconda3\condabin\conda.bat"
    exit /b 0
)
rem Search PATH
for /f "delims=" %%I in ('where conda.bat 2^>nul') do (
    set "CONDA_BAT=%%I"
    exit /b 0
)
exit /b 1


:install_miniconda
echo.
echo ── Miniconda auto-install ──────────────────────────────────
echo.
echo [INFO] Downloading installer from:
echo        %MINICONDA_URL%
echo.
powershell -NoProfile -ExecutionPolicy Bypass -Command ^
    "try { Invoke-WebRequest -Uri '%MINICONDA_URL%' -OutFile '%MINICONDA_INSTALLER%' -UseBasicParsing } catch { Write-Error $_; exit 1 }"
if errorlevel 1 (
    echo [ERROR] Download failed. Check your internet connection.
    exit /b 1
)
if not exist "%MINICONDA_INSTALLER%" (
    echo [ERROR] Installer file missing after download.
    exit /b 1
)
echo [INFO] Installing Miniconda silently to:
echo        %MINICONDA_DIR%
start /wait "" "%MINICONDA_INSTALLER%" /InstallationType=JustMe /RegisterPython=0 /S /D=%MINICONDA_DIR%
if errorlevel 1 (
    echo [ERROR] Miniconda installer returned an error.
    exit /b 1
)
if not exist "%MINICONDA_DIR%\condabin\conda.bat" (
    echo [ERROR] Miniconda installed but conda.bat not found.
    exit /b 1
)
echo [OK]   Miniconda installed at %MINICONDA_DIR%
exit /b 0


:ensure_env
call "%CONDA_BAT%" env list > "%TEMP%\mosna_envs.txt" 2>nul
if errorlevel 1 (
    echo [ERROR] Cannot list conda environments.
    exit /b 1
)
findstr /C:"%ENV_NAME%" "%TEMP%\mosna_envs.txt" >nul 2>nul
if not errorlevel 1 (
    echo [OK]   Environment "%ENV_NAME%" already exists — reusing.
    del /f /q "%TEMP%\mosna_envs.txt" >nul 2>nul
    exit /b 0
)
echo [INFO] Creating environment "%ENV_NAME%" ...
call "%CONDA_BAT%" create -n "%ENV_NAME%" python=%PYTHON_VERSION% -y
if errorlevel 1 (
    echo [ERROR] conda env create failed.
    del /f /q "%TEMP%\mosna_envs.txt" >nul 2>nul
    exit /b 1
)
del /f /q "%TEMP%\mosna_envs.txt" >nul 2>nul
exit /b 0


:create_shortcut
set "ICON_ARG=%GUI_SCRIPT%"
if exist "%ICON_FILE%" set "ICON_ARG=%ICON_FILE%"

powershell -NoProfile -ExecutionPolicy Bypass -Command ^
    "$s = (New-Object -Com WScript.Shell).CreateShortcut('%DESKTOP_SHORTCUT%'); ^
    $s.TargetPath = '%LAUNCHER_BAT%'; ^
    $s.WorkingDirectory = '%PROJECT_DIR%'; ^
    $s.IconLocation = '%ICON_ARG%'; ^
    $s.Description = 'Launch MOSNA GUI'; ^
    $s.Save()"
exit /b %ERRORLEVEL%


:fail
echo.
echo ============================================================
echo  Installation FAILED — see errors above.
echo ============================================================
echo.
pause
exit /b 1