mednotes-opencode 0.1.0

package/.opencode/mednotes/scripts/reset_windows_python_uv.ps1

@@ -0,0 +1,625 @@
+#Requires -Version 5.1
+<#
+.SYNOPSIS
+Reset the Medical Notes Workbench Python environment on Windows and rebuild it with uv.
+
+.DESCRIPTION
+By default this script resets only the Medical Notes Workbench environment.
+Pass -RemoveGlobalPython -YesReallyRemoveGlobalPython to uninstall global
+Python Software Foundation installs and the Python Launcher, clean Python PATH
+entries, then rebuild everything with uv-managed Python.
+Pass -FullReset for the one-command workflow: ensure standalone uv, remove
+global Python/launcher, clean WindowsApps aliases from PATH, sync, and check.
+#>
+
+[CmdletBinding(SupportsShouldProcess = $true)]
+param(
+    [string] $ExtensionRoot,
+    [string] $StateDir = (Join-Path $HOME ".gemini\medical-notes-workbench"),
+    [string] $PythonVersion = "3.12",
+    [switch] $FullReset,
+    [switch] $RemoveGlobalPython,
+    [switch] $YesReallyRemoveGlobalPython,
+    [switch] $RemoveWindowsAppsFromPath,
+    [switch] $Dev,
+    [switch] $Pdf,
+    [switch] $SkipChecks
+)
+
+$ErrorActionPreference = "Stop"
+
+function Resolve-WorkbenchExtensionRoot {
+    if ($ExtensionRoot) {
+        return (Resolve-Path $ExtensionRoot).Path
+    }
+    if ($PSScriptRoot) {
+        $candidate = Resolve-Path (Join-Path $PSScriptRoot "..") -ErrorAction SilentlyContinue
+        if ($candidate -and (Test-Path (Join-Path $candidate.Path "pyproject.toml"))) {
+            return $candidate.Path
+        }
+    }
+    $default = Join-Path $HOME ".gemini\extensions\medical-notes-workbench"
+    if (Test-Path (Join-Path $default "pyproject.toml")) {
+        return $default
+    }
+    throw "Nao encontrei a extensao medical-notes-workbench. Passe -ExtensionRoot com a raiz instalada."
+}
+
+$ResolvedExtensionRoot = Resolve-WorkbenchExtensionRoot
+
+if ($FullReset) {
+    $RemoveGlobalPython = $true
+    $YesReallyRemoveGlobalPython = $true
+}
+
+function Write-Step {
+    param([string] $Message)
+    Write-Host ""
+    Write-Host "==> $Message" -ForegroundColor Cyan
+}
+
+function Invoke-Checked {
+    param(
+        [string] $FilePath,
+        [string[]] $Arguments
+    )
+    & $FilePath @Arguments
+    if ($LASTEXITCODE -ne 0) {
+        throw "Command failed ($LASTEXITCODE): $FilePath $($Arguments -join ' ')"
+    }
+}
+
+function Get-PythonUninstallEntries {
+    $roots = @(
+        "HKCU:\Software\Microsoft\Windows\CurrentVersion\Uninstall\*",
+        "HKLM:\Software\Microsoft\Windows\CurrentVersion\Uninstall\*",
+        "HKLM:\Software\WOW6432Node\Microsoft\Windows\CurrentVersion\Uninstall\*"
+    )
+
+    foreach ($root in $roots) {
+        Get-ItemProperty -Path $root -ErrorAction SilentlyContinue |
+            Where-Object {
+                $name = [string] $_.DisplayName
+                $publisher = [string] $_.Publisher
+                $name -and (
+                    $publisher -match "Python Software Foundation" -or
+                    $name -match "^Python( \d| Launcher|$)"
+                )
+            } |
+            ForEach-Object {
+                [pscustomobject] @{
+                    DisplayName = [string] $_.DisplayName
+                    Publisher = [string] $_.Publisher
+                    QuietUninstallString = [string] $_.QuietUninstallString
+                    UninstallString = [string] $_.UninstallString
+                    RegistryPath = [string] $_.PSPath
+                }
+            }
+    }
+}
+
+function Get-PythonInstallRoots {
+    $roots = @(
+        "HKCU:\Software\Python\PythonCore\*\InstallPath",
+        "HKLM:\Software\Python\PythonCore\*\InstallPath",
+        "HKLM:\Software\WOW6432Node\Python\PythonCore\*\InstallPath"
+    )
+
+    foreach ($root in $roots) {
+        Get-ItemProperty -Path $root -ErrorAction SilentlyContinue |
+            ForEach-Object {
+                if ($_.ExecutablePath) {
+                    Split-Path -Parent ([string] $_.ExecutablePath)
+                }
+                elseif ($_.PSChildName) {
+                    [string] $_.PSChildName
+                }
+                elseif ($_.InstallPath) {
+                    [string] $_.InstallPath
+                }
+            }
+    }
+}
+
+function Get-CommandPaths {
+    param([string[]] $Names)
+
+    foreach ($name in $Names) {
+        $output = & cmd.exe /d /c "where.exe $name 2>nul"
+        if ($LASTEXITCODE -eq 0) {
+            $output | Where-Object { $_ }
+        }
+        elseif ($LASTEXITCODE -eq 1) {
+            continue
+        }
+        else {
+            Write-Warning "where.exe retornou codigo $LASTEXITCODE para $name"
+        }
+    }
+}
+
+function ConvertTo-QuietUninstallCommand {
+    param([object] $Entry)
+
+    $cmdLine = if ($Entry.QuietUninstallString) {
+        $Entry.QuietUninstallString
+    }
+    else {
+        $Entry.UninstallString
+    }
+
+    if (-not $cmdLine) {
+        return $null
+    }
+
+    if ($cmdLine -match "\{[0-9A-Fa-f-]{36}\}") {
+        return "msiexec.exe /x $($Matches[0]) /qn /norestart"
+    }
+
+    if (-not $Entry.QuietUninstallString -and $cmdLine -notmatch "(?i)(/quiet|/qn|/passive)") {
+        $cmdLine = "$cmdLine /quiet"
+    }
+
+    return $cmdLine
+}
+
+function Invoke-GlobalPythonRemoval {
+    param([string[]] $KnownRoots)
+
+    $entries = @(Get-PythonUninstallEntries | Sort-Object RegistryPath -Unique)
+    Write-Step "Inventario de Python global"
+
+    $commandPaths = @(Get-CommandPaths @("python", "python3", "py") | Sort-Object -Unique)
+    if ($commandPaths.Count -gt 0) {
+        Write-Host "Comandos encontrados no PATH:"
+        $commandPaths | ForEach-Object { Write-Host "  $_" }
+    }
+    else {
+        Write-Host "Nenhum python/python3/py encontrado no PATH."
+    }
+
+    if ($entries.Count -gt 0) {
+        Write-Host "Instalacoes registradas para remocao:"
+        $entries | ForEach-Object { Write-Host "  $($_.DisplayName) [$($_.Publisher)]" }
+    }
+    else {
+        Write-Host "Nenhuma instalacao PSF/Python Launcher registrada para remocao."
+    }
+
+    if (-not $YesReallyRemoveGlobalPython) {
+        throw "Remocao global bloqueada. Rode novamente com -RemoveGlobalPython -YesReallyRemoveGlobalPython para confirmar."
+    }
+
+    foreach ($entry in $entries) {
+        $cmdLine = ConvertTo-QuietUninstallCommand $entry
+        if (-not $cmdLine) {
+            Write-Warning "Sem comando de uninstall para $($entry.DisplayName). Pulei."
+            continue
+        }
+        if ($PSCmdlet.ShouldProcess($entry.DisplayName, "Uninstall global Python")) {
+            Write-Step "Removendo $($entry.DisplayName)"
+            $process = Start-Process -FilePath "cmd.exe" -ArgumentList @("/d", "/s", "/c", $cmdLine) -Wait -PassThru
+            if ($process.ExitCode -ne 0) {
+                Write-Warning "Uninstall retornou codigo $($process.ExitCode): $($entry.DisplayName)"
+            }
+        }
+    }
+
+    Remove-PythonEnvironmentVariables
+    Disable-PythonWindowsAppAliases
+    Remove-PythonPathEntries -KnownRoots $KnownRoots
+    Remove-ResidualPythonDirectories -KnownRoots $KnownRoots
+}
+
+function Disable-PythonWindowsAppAliases {
+    $windowsApps = Join-Path $env:LOCALAPPDATA "Microsoft\WindowsApps"
+    if (-not (Test-Path $windowsApps)) {
+        return
+    }
+
+    foreach ($name in @("python.exe", "python3.exe")) {
+        $aliasPath = Join-Path $windowsApps $name
+        if (Test-Path $aliasPath) {
+            try {
+                if ($PSCmdlet.ShouldProcess($aliasPath, "Remove Windows Python app execution alias")) {
+                    Remove-Item -LiteralPath $aliasPath -Force -ErrorAction Stop
+                    Write-Host "Alias WindowsApps removido: $aliasPath"
+                }
+            }
+            catch {
+                Write-Warning "Nao consegui remover alias $aliasPath. Desative em Settings > Apps > Advanced app settings > App execution aliases."
+            }
+        }
+    }
+}
+
+function Remove-PythonEnvironmentVariables {
+    foreach ($target in @("User", "Machine")) {
+        foreach ($name in @("PYTHONHOME", "PYTHONPATH", "PYLAUNCHER_ALLOW_INSTALL", "PYLAUNCHER_NO_SEARCH_PATH")) {
+            try {
+                if ([Environment]::GetEnvironmentVariable($name, $target)) {
+                    if ($PSCmdlet.ShouldProcess("$target $name", "Remove Python environment variable")) {
+                        [Environment]::SetEnvironmentVariable($name, $null, $target)
+                    }
+                }
+            }
+            catch {
+                Write-Warning "Nao consegui limpar $target ${name}: $($_.Exception.Message)"
+            }
+        }
+    }
+}
+
+function Test-PythonPathEntry {
+    param(
+        [string] $Entry,
+        [string[]] $KnownRoots
+    )
+
+    if (-not $Entry) {
+        return $false
+    }
+
+    $expanded = [Environment]::ExpandEnvironmentVariables($Entry).Trim('"').TrimEnd("\")
+    if (-not $expanded) {
+        return $false
+    }
+
+    if ($RemoveWindowsAppsFromPath -and $expanded -like "*\Microsoft\WindowsApps") {
+        return $true
+    }
+
+    foreach ($root in $KnownRoots) {
+        if ($root) {
+            $normalizedRoot = [Environment]::ExpandEnvironmentVariables($root).Trim('"').TrimEnd("\")
+            if ($normalizedRoot -and $expanded.StartsWith($normalizedRoot, [StringComparison]::OrdinalIgnoreCase)) {
+                return $true
+            }
+        }
+    }
+
+    return ($expanded -match "(?i)\\Programs\\Python\\Python\d+" -or
+            $expanded -match "(?i)\\Python\d+(\\Scripts)?$" -or
+            $expanded -match "(?i)\\PythonCore\\" -or
+            $expanded -match "(?i)\\Python\\Launcher$")
+}
+
+function Remove-PythonPathEntries {
+    param([string[]] $KnownRoots)
+
+    foreach ($target in @("User", "Machine")) {
+        try {
+            $pathValue = [Environment]::GetEnvironmentVariable("Path", $target)
+            if (-not $pathValue) {
+                continue
+            }
+            $entries = @($pathValue -split ";" | Where-Object { $_ -ne "" })
+            $kept = @()
+            $removed = @()
+            foreach ($entry in $entries) {
+                if (Test-PythonPathEntry -Entry $entry -KnownRoots $KnownRoots) {
+                    $removed += $entry
+                }
+                else {
+                    $kept += $entry
+                }
+            }
+            if ($removed.Count -gt 0) {
+                if ($PSCmdlet.ShouldProcess("$target PATH", "Remove Python PATH entries")) {
+                    [Environment]::SetEnvironmentVariable("Path", ($kept -join ";"), $target)
+                }
+                Write-Host "PATH ${target}: removido"
+                $removed | ForEach-Object { Write-Host "  $_" }
+            }
+        }
+        catch {
+            Write-Warning "Nao consegui editar PATH ${target}: $($_.Exception.Message)"
+        }
+    }
+}
+
+function Remove-ResidualPythonDirectories {
+    param([string[]] $KnownRoots)
+
+    $candidates = @()
+    $candidates += $KnownRoots
+    if ($env:LOCALAPPDATA) {
+        $candidates += Get-ChildItem -Path (Join-Path $env:LOCALAPPDATA "Programs\Python") -Directory -ErrorAction SilentlyContinue |
+            Select-Object -ExpandProperty FullName
+    }
+    if ($env:ProgramFiles) {
+        $candidates += Get-ChildItem -Path $env:ProgramFiles -Directory -Filter "Python*" -ErrorAction SilentlyContinue |
+            Select-Object -ExpandProperty FullName
+    }
+    if (${env:ProgramFiles(x86)}) {
+        $candidates += Get-ChildItem -Path ${env:ProgramFiles(x86)} -Directory -Filter "Python*" -ErrorAction SilentlyContinue |
+            Select-Object -ExpandProperty FullName
+    }
+
+    $safeCandidates = $candidates |
+        Where-Object { $_ -and (Test-Path $_) } |
+        Sort-Object -Unique |
+        Where-Object {
+            $_ -match "(?i)\\Programs\\Python\\Python\d+" -or
+            $_ -match "(?i)\\Python\d+$" -or
+            $_ -match "(?i)\\Python\\Launcher$"
+        }
+
+    foreach ($dir in $safeCandidates) {
+        if ($PSCmdlet.ShouldProcess($dir, "Remove residual Python directory")) {
+            Write-Step "Removendo diretorio residual: $dir"
+            Remove-Item -LiteralPath $dir -Recurse -Force -ErrorAction SilentlyContinue
+        }
+    }
+}
+
+function Add-UvCandidatePaths {
+    $paths = @(
+        (Join-Path $HOME ".local\bin"),
+        (Join-Path $env:USERPROFILE ".local\bin"),
+        (Join-Path $env:LOCALAPPDATA "Programs\uv")
+    )
+
+    foreach ($path in $paths) {
+        if ($path -and (Test-Path $path) -and (($env:Path -split ";") -notcontains $path)) {
+            $env:Path = "$path;$env:Path"
+        }
+    }
+
+    $wingetRoot = Join-Path $env:LOCALAPPDATA "Microsoft\WinGet\Packages"
+    if (Test-Path $wingetRoot) {
+        Get-ChildItem -Path $wingetRoot -Recurse -Filter "uv.exe" -ErrorAction SilentlyContinue |
+            Select-Object -ExpandProperty DirectoryName -Unique |
+            ForEach-Object {
+                if (($env:Path -split ";") -notcontains $_) {
+                    $env:Path = "$_;$env:Path"
+                }
+            }
+    }
+}
+
+function Find-UvExecutable {
+    Add-UvCandidatePaths
+    $command = Get-Command uv -ErrorAction SilentlyContinue
+    if ($command) {
+        return $command.Source
+    }
+    return $null
+}
+
+function Invoke-UvInstallerUrl {
+    param([string] $Url)
+
+    Write-Step "Tentando instalador uv: $Url"
+    try {
+        $command = "[Net.ServicePointManager]::SecurityProtocol=[Net.SecurityProtocolType]::Tls12; irm '$Url' | iex"
+        powershell -NoProfile -ExecutionPolicy Bypass -Command $command
+        if ($LASTEXITCODE -eq 0) {
+            return $true
+        }
+        Write-Warning "Instalador uv retornou codigo $LASTEXITCODE."
+    }
+    catch {
+        Write-Warning "Instalador uv falhou: $($_.Exception.Message)"
+    }
+    return $false
+}
+
+function Install-UvWithWinget {
+    $winget = Get-Command winget -ErrorAction SilentlyContinue
+    if (-not $winget) {
+        return $false
+    }
+
+    Write-Step "Tentando instalar uv via winget"
+    try {
+        & $winget.Source install --id astral-sh.uv -e --accept-package-agreements --accept-source-agreements --silent
+        if ($LASTEXITCODE -eq 0) {
+            return $true
+        }
+        Write-Warning "winget retornou codigo $LASTEXITCODE."
+    }
+    catch {
+        Write-Warning "winget falhou: $($_.Exception.Message)"
+    }
+    return $false
+}
+
+function Install-UvFromReleaseZip {
+    Write-Step "Tentando instalar uv pelo zip do GitHub Releases"
+    try {
+        [Net.ServicePointManager]::SecurityProtocol = [Net.SecurityProtocolType]::Tls12
+        $arch = if ($env:PROCESSOR_ARCHITECTURE -eq "ARM64") {
+            "aarch64"
+        }
+        elseif ([Environment]::Is64BitOperatingSystem) {
+            "x86_64"
+        }
+        else {
+            "i686"
+        }
+        $release = Invoke-RestMethod -Uri "https://api.github.com/repos/astral-sh/uv/releases/latest" -UseBasicParsing
+        $assetName = "uv-$arch-pc-windows-msvc.zip"
+        $asset = $release.assets | Where-Object { $_.name -eq $assetName } | Select-Object -First 1
+        if (-not $asset) {
+            throw "Asset nao encontrado: $assetName"
+        }
+
+        $binDir = Join-Path $env:USERPROFILE ".local\bin"
+        $tmpDir = Join-Path $env:TEMP ("uv-release-" + [guid]::NewGuid().ToString("N"))
+        $zipPath = Join-Path $env:TEMP $assetName
+        New-Item -ItemType Directory -Force $binDir | Out-Null
+        New-Item -ItemType Directory -Force $tmpDir | Out-Null
+        Invoke-WebRequest -Uri $asset.browser_download_url -OutFile $zipPath -UseBasicParsing
+        Expand-Archive -LiteralPath $zipPath -DestinationPath $tmpDir -Force
+
+        foreach ($exeName in @("uv.exe", "uvx.exe")) {
+            $exe = Get-ChildItem -Path $tmpDir -Recurse -Filter $exeName -ErrorAction SilentlyContinue | Select-Object -First 1
+            if ($exe) {
+                $destination = Join-Path $binDir $exeName
+                try {
+                    Copy-Item -LiteralPath $exe.FullName -Destination $destination -Force
+                }
+                catch {
+                    if (Test-Path $destination) {
+                        Write-Warning "$exeName ja existe e esta em uso; mantendo executavel existente."
+                    }
+                    else {
+                        throw
+                    }
+                }
+            }
+        }
+        Remove-Item -LiteralPath $tmpDir -Recurse -Force -ErrorAction SilentlyContinue
+        Remove-Item -LiteralPath $zipPath -Force -ErrorAction SilentlyContinue
+
+        if (($env:Path -split ";") -notcontains $binDir) {
+            $env:Path = "$binDir;$env:Path"
+        }
+        $userPath = [Environment]::GetEnvironmentVariable("Path", "User")
+        if (($userPath -split ";") -notcontains $binDir) {
+            [Environment]::SetEnvironmentVariable("Path", "$binDir;$userPath", "User")
+        }
+        return $true
+    }
+    catch {
+        Write-Warning "Download direto do uv falhou: $($_.Exception.Message)"
+    }
+    return $false
+}
+
+function Install-UvStandalone {
+    Write-Step "Instalando/atualizando uv"
+    $installed = $false
+    foreach ($url in @(
+        "https://astral.sh/uv/install.ps1",
+        "https://releases.astral.sh/github/uv/releases/download/0.11.8/uv-installer.ps1"
+    )) {
+        if (Invoke-UvInstallerUrl $url) {
+            $installed = $true
+            break
+        }
+    }
+    if (-not $installed) {
+        $installed = Install-UvWithWinget
+    }
+    if (-not $installed) {
+        $installed = Install-UvFromReleaseZip
+    }
+    if (-not $installed) {
+        throw "Falha ao instalar uv por instalador oficial, winget e zip direto."
+    }
+}
+
+function Resolve-Uv {
+    param([switch] $ForceInstall)
+
+    $uv = Find-UvExecutable
+    if ($uv -and $uv -notmatch "(?i)\\Python\d+\\Scripts\\") {
+        return $uv
+    }
+    if ($ForceInstall) {
+        Write-Step "Garantindo uv standalone antes do reset global"
+    }
+
+    Install-UvStandalone
+
+    $uv = Find-UvExecutable
+    if ($uv) {
+        return $uv
+    }
+
+    throw "uv foi instalado, mas nao entrou no PATH desta sessao. Abra um novo PowerShell e rode novamente."
+}
+
+if (-not (Test-Path (Join-Path $ResolvedExtensionRoot "pyproject.toml"))) {
+    throw "ExtensionRoot invalido: nao encontrei pyproject.toml em $ResolvedExtensionRoot"
+}
+
+$knownPythonRoots = @(Get-PythonInstallRoots | Where-Object { $_ } | Sort-Object -Unique)
+
+Write-Step "Preparando diretorio persistente"
+New-Item -ItemType Directory -Force $StateDir | Out-Null
+
+$configPath = Join-Path $StateDir "config.toml"
+if (-not (Test-Path $configPath)) {
+    $configExample = Join-Path $ResolvedExtensionRoot "config.example.toml"
+    if (Test-Path $configExample) {
+        Copy-Item $configExample $configPath
+        Write-Host "config.toml criado em $configPath"
+    }
+}
+
+$envPath = Join-Path $StateDir ".env"
+if (-not (Test-Path $envPath)) {
+    $envExample = Join-Path $ResolvedExtensionRoot ".env.example"
+    if (Test-Path $envExample) {
+        Copy-Item $envExample $envPath
+        Write-Host ".env criado em $envPath"
+    }
+}
+
+$uv = Resolve-Uv -ForceInstall:$FullReset
+Write-Step "Usando uv: $uv"
+Invoke-Checked $uv @("--version")
+
+if ($RemoveGlobalPython) {
+    Invoke-GlobalPythonRemoval -KnownRoots $knownPythonRoots
+    $env:Path = [Environment]::GetEnvironmentVariable("Path", "Machine") + ";" + [Environment]::GetEnvironmentVariable("Path", "User")
+}
+
+Write-Step "Instalando Python gerenciado pelo uv ($PythonVersion)"
+Invoke-Checked $uv @("python", "install", $PythonVersion)
+
+$persistentVenv = Join-Path $StateDir ".venv"
+$bundleVenv = Join-Path $ResolvedExtensionRoot ".venv"
+foreach ($venv in @($persistentVenv, $bundleVenv)) {
+    if (Test-Path $venv) {
+        if ($PSCmdlet.ShouldProcess($venv, "Remove project virtual environment")) {
+            Write-Step "Removendo ambiente antigo: $venv"
+            Remove-Item -LiteralPath $venv -Recurse -Force
+        }
+    }
+}
+
+$env:UV_PROJECT_ENVIRONMENT = $persistentVenv
+$syncArgs = @("sync", "--project", $ResolvedExtensionRoot, "--python", $PythonVersion)
+if ($Dev) {
+    $syncArgs += @("--extra", "dev")
+}
+if ($Pdf) {
+    $syncArgs += @("--extra", "pdf")
+}
+
+Write-Step "Sincronizando dependencias com uv"
+Push-Location $ResolvedExtensionRoot
+try {
+    # Equivalent command: uv sync --project "$ResolvedExtensionRoot"
+    Invoke-Checked $uv $syncArgs
+
+    if (-not $SkipChecks) {
+        Write-Step "Rodando checks basicos"
+        Invoke-Checked $uv @("run", "python", "-m", "enricher", "--help")
+        Invoke-Checked $uv @("run", "python", "scripts\mednotes\wiki\cli.py", "validate", "--config", $configPath)
+        Invoke-Checked $uv @("run", "python", "scripts\mednotes\wiki\cli.py", "run-linker", "--help")
+    }
+}
+finally {
+    Pop-Location
+}
+
+Write-Host ""
+Write-Host "Pronto. Ambiente Python do workbench reconstruido com uv." -ForegroundColor Green
+Write-Host "ExtensionRoot: $ResolvedExtensionRoot"
+Write-Host "StateDir:      $StateDir"
+Write-Host "Venv uv:       $persistentVenv"
+Write-Host ""
+Write-Host "Para comandos manuais nesta sessao:"
+Write-Host ('$env:UV_PROJECT_ENVIRONMENT = "{0}"' -f $persistentVenv)
+Write-Host 'uv run python scripts\mednotes\wiki\cli.py fix-wiki --dry-run --json'
+if ($RemoveGlobalPython) {
+    Write-Host ""
+    Write-Host "Se 'where python' ainda apontar para Microsoft\\WindowsApps, desative o alias"
+    Write-Host "python.exe/python3.exe em Settings > Apps > Advanced app settings > App execution aliases,"
+    Write-Host "ou rode novamente com -RemoveWindowsAppsFromPath para remover WindowsApps do PATH."
+}