3 files changed, 254 insertions, 31 deletions
diff --git a/src/Text/Pandoc/App/CommandLineOptions.hs b/src/Text/Pandoc/App/CommandLineOptions.hs
index d22ca3f86..9d2ec695f 100644
--- a/src/Text/Pandoc/App/CommandLineOptions.hs
+++ b/src/Text/Pandoc/App/CommandLineOptions.hs
@@ -42,7 +42,7 @@ import System.FilePath
 import System.IO (stdout)
 import Text.Pandoc
 import Text.Pandoc.Builder (setMeta)
-import Text.Pandoc.App.Opt (Opt (..), LineEnding (..))
+import Text.Pandoc.App.Opt (Opt (..), LineEnding (..), IpynbOutput (..))
 import Text.Pandoc.Filter (Filter (..))
 import Text.Pandoc.Highlighting (highlightingStyles)
 import Text.Pandoc.Writers.Math (defaultMathJaxURL, defaultKaTeXURL)
@@ -64,7 +64,6 @@ import qualified Data.Text as T
 import Data.Text (Text)
 import Text.DocTemplates (ToContext(toVal), Context(..))
 import qualified Text.Pandoc.UTF8 as UTF8
-import qualified Data.YAML.Aeson as YA
 import qualified Data.YAML as Y
 
 parseOptions :: [OptDescr (Opt -> IO Opt)] -> Opt -> IO Opt
@@ -156,8 +155,8 @@ options =
 
     , Option "" ["metadata-file"]
                  (ReqArg
-                  (\arg opt -> return opt{ optMetadataFile =
-                    normalizePath arg : optMetadataFile opt })
+                  (\arg opt -> return opt{ optMetadataFiles =
+                    normalizePath arg : optMetadataFiles opt })
                   "FILE")
                  ""
 
@@ -175,15 +174,14 @@ options =
                                 Just dd -> [fp, dd </> "defaults" </> fp]
                     fp' <- fromMaybe fp <$> findFile fps
                     inp <- readFileLazy fp'
-                    let defaults = YA.encode1 opt
-                    case YA.decode1 (defaults <> inp) of
+                    case Y.decode1 inp of
                         Right (newopts :: Opt) -> return newopts
                         Left (errpos, errmsg)  -> throwError $
                            PandocParseError $
-                           "Error parsing " ++ fp' ++
-                           " (line " ++ show (Y.posLine errpos) ++
-                           " column " ++ show (Y.posColumn errpos) ++
-                           ")\n" ++ errmsg
+                           "Error parsing " ++ fp' ++ " line " ++
+                            show (Y.posLine errpos) ++ " column " ++
+                            show (Y.posColumn errpos) ++ ":\n" ++ errmsg
+
                   )
                   "FILE")
                 ""
@@ -219,9 +217,9 @@ options =
                  (ReqArg
                   (\arg opt ->
                     case arg of
-                      "auto" -> return opt{ optWrapText = WrapAuto }
-                      "none" -> return opt{ optWrapText = WrapNone }
-                      "preserve" -> return opt{ optWrapText = WrapPreserve }
+                      "auto" -> return opt{ optWrap = WrapAuto }
+                      "none" -> return opt{ optWrap = WrapNone }
+                      "preserve" -> return opt{ optWrap = WrapPreserve }
                       _      -> E.throwIO $ PandocOptionError
                                  "--wrap must be auto, none, or preserve")
                  "auto|none|preserve")
@@ -409,8 +407,8 @@ options =
     , Option "" ["pdf-engine-opt"]
                  (ReqArg
                   (\arg opt -> do
-                      let oldArgs = optPdfEngineArgs opt
-                      return opt { optPdfEngineArgs = oldArgs ++ [arg]})
+                      let oldArgs = optPdfEngineOpts opt
+                      return opt { optPdfEngineOpts = oldArgs ++ [arg]})
                   "STRING")
                  "" -- "Flags to pass to the PDF-engine, all instances of this option are accumulated and used"
 
@@ -655,10 +653,12 @@ options =
     , Option "" ["ipynb-output"]
                  (ReqArg
                   (\arg opt ->
-                    if arg `notElem` ["all","none","best"]
-                       then E.throwIO $ PandocOptionError $
-                             "ipynb-output must be all, none, or best"
-                       else return opt { optIpynbOutput = arg })
+                    case arg of
+                      "all" -> return opt{ optIpynbOutput = IpynbOutputAll }
+                      "best" -> return opt{ optIpynbOutput = IpynbOutputBest }
+                      "none" -> return opt{ optIpynbOutput = IpynbOutputNone }
+                      _ -> E.throwIO $ PandocOptionError $
+                             "ipynb-output must be all, none, or best")
                  "all|none|best")
                  "" -- "Starting number for sections, subsections, etc."
 
diff --git a/src/Text/Pandoc/App/Opt.hs b/src/Text/Pandoc/App/Opt.hs
index c491d8ae2..d14365e85 100644
--- a/src/Text/Pandoc/App/Opt.hs
+++ b/src/Text/Pandoc/App/Opt.hs
@@ -1,3 +1,4 @@
+{-# LANGUAGE ScopedTypeVariables #-}
 {-# LANGUAGE OverloadedStrings   #-}
 {-# LANGUAGE NoImplicitPrelude   #-}
 {-# LANGUAGE CPP                 #-}
@@ -17,6 +18,7 @@ Options for pandoc when used as an app.
 module Text.Pandoc.App.Opt (
             Opt(..)
           , LineEnding (..)
+          , IpynbOutput (..)
           , defaultOpts
           ) where
 import Prelude
@@ -31,15 +33,43 @@ import Text.Pandoc.Options (TopLevelDivision (TopLevelDefault),
                             ObfuscationMethod (NoObfuscation),
                             CiteMethod (Citeproc))
 import Text.Pandoc.Shared (camelCaseToHyphenated)
-import Text.DocTemplates (Context(..))
-import Data.Text (Text)
+import Text.DocTemplates (Context(..), Val(..))
+import Data.Text (Text, unpack)
+import qualified Data.Text as T
+import qualified Data.Map as M
+import Text.Pandoc.Definition (Meta(..), MetaValue(..))
 import Data.Aeson (defaultOptions, Options(..))
 import Data.Aeson.TH (deriveJSON)
-import Text.Pandoc.Definition (Meta)
+import Control.Monad (foldM)
+import Control.Applicative ((<|>))
+import Data.YAML
 
 -- | The type of line-endings to be used when writing plain-text.
 data LineEnding = LF | CRLF | Native deriving (Show, Generic)
 
+instance FromYAML LineEnding where
+  parseYAML = withStr "LineEnding" $ \t ->
+    case T.toLower t of
+      "lf"     -> return LF
+      "crlf"   -> return CRLF
+      "native" -> return Native
+      _        -> fail $ "Unknown line ending type " ++ show t
+
+-- | How to handle output blocks in ipynb.
+data IpynbOutput =
+    IpynbOutputAll
+  | IpynbOutputNone
+  | IpynbOutputBest
+  deriving (Show, Generic)
+
+instance FromYAML IpynbOutput where
+  parseYAML = withStr "LineEnding" $ \t ->
+    case t of
+      "none"  -> return IpynbOutputNone
+      "all"   -> return IpynbOutputAll
+      "best"  -> return IpynbOutputBest
+      _       -> fail $ "Unknown ipynb output type " ++ show t
+
 -- | Data structure for command line options.
 data Opt = Opt
     { optTabStop               :: Int     -- ^ Number of spaces per tab
@@ -52,7 +82,7 @@ data Opt = Opt
     , optTemplate              :: Maybe FilePath  -- ^ Custom template
     , optVariables             :: Context Text    -- ^ Template variables to set
     , optMetadata              :: Meta -- ^ Metadata fields to set
-    , optMetadataFile          :: [FilePath]  -- ^ Name of YAML metadata file
+    , optMetadataFiles         :: [FilePath]  -- ^ Name of YAML metadata files
     , optOutputFile            :: Maybe FilePath  -- ^ Name of output file
     , optInputFiles            :: [FilePath] -- ^ Names of input files
     , optNumberSections        :: Bool    -- ^ Number sections in LaTeX
@@ -82,7 +112,7 @@ data Opt = Opt
     , optReferenceLinks        :: Bool    -- ^ Use reference links in writing markdown, rst
     , optReferenceLocation     :: ReferenceLocation -- ^ location for footnotes and link references in markdown output
     , optDpi                   :: Int     -- ^ Dpi
-    , optWrapText              :: WrapOption  -- ^ Options for wrapping text
+    , optWrap                  :: WrapOption  -- ^ Options for wrapping text
     , optColumns               :: Int     -- ^ Line length in characters
     , optFilters               :: [Filter] -- ^ Filters to apply
     , optEmailObfuscation      :: ObfuscationMethod
@@ -93,7 +123,7 @@ data Opt = Opt
     , optCiteMethod            :: CiteMethod -- ^ Method to output cites
     , optListings              :: Bool       -- ^ Use listings package for code blocks
     , optPdfEngine             :: Maybe String -- ^ Program to use for latex/html -> pdf
-    , optPdfEngineArgs         :: [String]   -- ^ Flags to pass to the engine
+    , optPdfEngineOpts         :: [String]   -- ^ Flags to pass to the engine
     , optSlideLevel            :: Maybe Int  -- ^ Header level that creates slides
     , optSetextHeaders         :: Bool       -- ^ Use atx headers for markdown level 1-2
     , optAscii                 :: Bool       -- ^ Prefer ascii output
@@ -103,7 +133,7 @@ data Opt = Opt
     , optFileScope             :: Bool         -- ^ Parse input files before combining
     , optTitlePrefix           :: Maybe String     -- ^ Prefix for title
     , optCss                   :: [FilePath]       -- ^ CSS files to link to
-    , optIpynbOutput           :: String           -- ^ Maybe f to use best data; Nothing to omit
+    , optIpynbOutput           :: IpynbOutput      -- ^ How to treat ipynb output blocks
     , optIncludeBeforeBody     :: [FilePath]       -- ^ Files to include before
     , optIncludeAfterBody      :: [FilePath]       -- ^ Files to include after body
     , optIncludeInHeader       :: [FilePath]       -- ^ Files to include in header
@@ -113,6 +143,186 @@ data Opt = Opt
     , optStripComments         :: Bool       -- ^ Skip HTML comments
     } deriving (Generic, Show)
 
+instance FromYAML Opt where
+  parseYAML (Mapping _ _ m) =
+    foldM doOpt defaultOpts (M.toList m)
+  parseYAML n = failAtNode n "Expected a mapping"
+
+doOpt :: Opt -> (Node Pos, Node Pos) -> Parser Opt
+doOpt opt (k',v) = do
+  k <- case k' of
+         Scalar _ (SStr t) -> return t
+         Scalar _ _ -> failAtNode k' "Non-string key"
+         _ -> failAtNode k' "Non-scalar key"
+  case k of
+    "tab-stop" ->
+      parseYAML v >>= \x -> return opt{ optTabStop = x }
+    "preserve-tabs" ->
+      parseYAML v >>= \x -> return opt { optPreserveTabs = x }
+    "standalone" ->
+      parseYAML v >>= \x -> return opt { optStandalone = x }
+    "table-of-contents" ->
+      parseYAML v >>= \x -> return opt { optTableOfContents = x }
+    "toc" ->
+      parseYAML v >>= \x -> return opt { optTableOfContents = x }
+    "from" ->
+      parseYAML v >>= \x -> return opt { optFrom = unpack <$> x }
+    "reader" ->
+      parseYAML v >>= \x -> return opt { optFrom = unpack <$> x }
+    "to" ->
+      parseYAML v >>= \x -> return opt { optTo = unpack <$> x }
+    "writer" ->
+      parseYAML v >>= \x -> return opt { optTo = unpack <$> x }
+    "shift-heading-level-by" ->
+      parseYAML v >>= \x -> return opt { optShiftHeadingLevelBy = x }
+    "template" ->
+      parseYAML v >>= \x -> return opt { optTemplate = unpack <$> x }
+    "variables" ->
+      parseYAML v >>= \x -> return opt { optVariables = x }
+    "metadata" ->
+      parseYAML v >>= \x -> return opt { optMetadata = contextToMeta x }
+    "metadata-files" ->
+      (parseYAML v >>= \x -> return opt { optMetadataFiles = map unpack x })
+    "metadata-file" -> -- allow either a list or a single value
+      (parseYAML v >>= \x -> return opt { optMetadataFiles = map unpack x })
+      <|>
+      (parseYAML v >>= \x -> return opt { optMetadataFiles = [unpack x] })
+    "output-file" ->
+      parseYAML v >>= \x -> return opt { optOutputFile = Just $ unpack x }
+    "input-files" ->
+      parseYAML v >>= \x -> return opt { optInputFiles = map unpack x }
+    "number-sections" ->
+      parseYAML v >>= \x -> return opt { optNumberSections = x }
+    "number-offset" ->
+      parseYAML v >>= \x -> return opt { optNumberOffset = x }
+    "section-divs" ->
+      parseYAML v >>= \x -> return opt { optSectionDivs = x }
+    "incremental" ->
+      parseYAML v >>= \x -> return opt { optIncremental = x }
+    "self-contained" ->
+      parseYAML v >>= \x -> return opt { optSelfContained = x }
+    "html-q-tags" ->
+      parseYAML v >>= \x -> return opt { optHtmlQTags = x }
+    "highlight-style" ->
+      parseYAML v >>= \x -> return opt { optHighlightStyle = unpack <$> x }
+    "syntax-definition" ->
+      (parseYAML v >>= \x -> return opt { optSyntaxDefinitions = map unpack x })
+      <|>
+      (parseYAML v >>= \x -> return opt { optSyntaxDefinitions = [unpack x] })
+    "syntax-definitions" ->
+      parseYAML v >>= \x -> return opt { optSyntaxDefinitions = map unpack x }
+    "top-level-division" ->
+      parseYAML v >>= \x -> return opt { optTopLevelDivision = x }
+    "html-math-method" ->
+      parseYAML v >>= \x -> return opt { optHTMLMathMethod = x }
+    "abbreviations" ->
+      parseYAML v >>= \x -> return opt { optAbbreviations = unpack <$> x }
+    "reference-doc" ->
+      parseYAML v >>= \x -> return opt { optReferenceDoc = unpack <$> x }
+    "epub-subdirectory" ->
+      parseYAML v >>= \x -> return opt { optEpubSubdirectory = unpack x }
+    "epub-metadata" ->
+      parseYAML v >>= \x -> return opt { optEpubMetadata = unpack <$> x }
+    "epub-fonts" ->
+      parseYAML v >>= \x -> return opt { optEpubFonts = map unpack x }
+    "epub-chapter-level" ->
+      parseYAML v >>= \x -> return opt { optEpubChapterLevel = x }
+    "epub-cover-image" ->
+      parseYAML v >>= \x -> return opt { optEpubCoverImage = unpack <$> x }
+    "toc-depth" ->
+      parseYAML v >>= \x -> return opt { optTOCDepth = x }
+    "dump-args" ->
+      parseYAML v >>= \x -> return opt { optDumpArgs = x }
+    "ignore-args" ->
+      parseYAML v >>= \x -> return opt { optIgnoreArgs = x }
+    "verbosity" ->
+      parseYAML v >>= \x -> return opt { optVerbosity = x }
+    "trace" ->
+      parseYAML v >>= \x -> return opt { optTrace = x }
+    "log-file" ->
+      parseYAML v >>= \x -> return opt { optLogFile = unpack <$> x }
+    "fail-if-warnings" ->
+      parseYAML v >>= \x -> return opt { optFailIfWarnings = x }
+    "reference-links" ->
+      parseYAML v >>= \x -> return opt { optReferenceLinks = x }
+    "reference-location" ->
+      parseYAML v >>= \x -> return opt { optReferenceLocation = x }
+    "dpi" ->
+      parseYAML v >>= \x -> return opt { optDpi = x }
+    "wrap" ->
+      parseYAML v >>= \x -> return opt { optWrap = x }
+    "columns" ->
+      parseYAML v >>= \x -> return opt { optColumns = x }
+    "filters" ->
+      parseYAML v >>= \x -> return opt { optFilters = x }
+    "email-obfuscation" ->
+      parseYAML v >>= \x -> return opt { optEmailObfuscation = x }
+    "identifier-prefix" ->
+      parseYAML v >>= \x -> return opt { optIdentifierPrefix = unpack x }
+    "strip-empty-paragraphs" ->
+      parseYAML v >>= \x -> return opt { optStripEmptyParagraphs = x }
+    "indented-code-classes" ->
+      parseYAML v >>= \x -> return opt { optIndentedCodeClasses = map unpack x }
+    "data-dir" ->
+      parseYAML v >>= \x -> return opt { optDataDir = unpack <$> x }
+    "cite-method" ->
+      parseYAML v >>= \x -> return opt { optCiteMethod = x }
+    "listings" ->
+      parseYAML v >>= \x -> return opt { optListings = x }
+    "pdf-engine" ->
+      parseYAML v >>= \x -> return opt { optPdfEngine = unpack <$> x }
+    "pdf-engine-opts" ->
+      parseYAML v >>= \x -> return opt { optPdfEngineOpts = map unpack x }
+    "pdf-engine-opt" ->
+      (parseYAML v >>= \x -> return opt { optPdfEngineOpts = map unpack x })
+      <|>
+      (parseYAML v >>= \x -> return opt { optPdfEngineOpts = [unpack x] })
+    "slide-level" ->
+      parseYAML v >>= \x -> return opt { optSlideLevel = x }
+    "setext-headers" ->
+      parseYAML v >>= \x -> return opt { optSetextHeaders = x }
+    "ascii" ->
+      parseYAML v >>= \x -> return opt { optAscii = x }
+    "default-image-extension" ->
+      parseYAML v >>= \x -> return opt { optDefaultImageExtension = unpack x }
+    "extract-media" ->
+      parseYAML v >>= \x -> return opt { optExtractMedia = unpack <$> x }
+    "track-changes" ->
+      parseYAML v >>= \x -> return opt { optTrackChanges = x }
+    "file-scope" ->
+      parseYAML v >>= \x -> return opt { optFileScope = x }
+    "title-prefix" ->
+      parseYAML v >>= \x -> return opt { optTitlePrefix = unpack <$> x }
+    "css" ->
+      (parseYAML v >>= \x -> return opt { optCss = map unpack x })
+      <|>
+      (parseYAML v >>= \x -> return opt { optCss = [unpack x] })
+    "ipynb-output" ->
+      parseYAML v >>= \x -> return opt { optIpynbOutput = x }
+    "include-before-body" ->
+      (parseYAML v >>= \x -> return opt { optIncludeBeforeBody = map unpack x })
+      <|>
+      (parseYAML v >>= \x -> return opt { optIncludeBeforeBody = [unpack x] })
+    "include-after-body" ->
+      (parseYAML v >>= \x -> return opt { optIncludeAfterBody = map unpack x })
+      <|>
+      (parseYAML v >>= \x -> return opt { optIncludeAfterBody = [unpack x] })
+    "include-in-header" ->
+      (parseYAML v >>= \x -> return opt { optIncludeInHeader = map unpack x })
+      <|>
+      (parseYAML v >>= \x -> return opt { optIncludeInHeader = [unpack x] })
+    "resource-path" ->
+      parseYAML v >>= \x -> return opt { optResourcePath = map unpack x }
+    "request-headers" ->
+      parseYAML v >>= \x -> return opt { optRequestHeaders =
+                              map (\(key,val) ->
+                                     (unpack key, unpack val)) x }
+    "eol" ->
+      parseYAML v >>= \x -> return opt { optEol = x }
+    "strip-comments" ->
+      parseYAML v >>= \x -> return opt { optStripComments = x }
+    _ -> failAtNode k' $ "Unknown option " ++ show k
+
 -- | Defaults for command-line options.
 defaultOpts :: Opt
 defaultOpts = Opt
@@ -126,7 +336,7 @@ defaultOpts = Opt
     , optTemplate              = Nothing
     , optVariables             = mempty
     , optMetadata              = mempty
-    , optMetadataFile          = []
+    , optMetadataFiles         = []
     , optOutputFile            = Nothing
     , optInputFiles            = []
     , optNumberSections        = False
@@ -156,7 +366,7 @@ defaultOpts = Opt
     , optReferenceLinks        = False
     , optReferenceLocation     = EndOfDocument
     , optDpi                   = 96
-    , optWrapText              = WrapAuto
+    , optWrap                  = WrapAuto
     , optColumns               = 72
     , optFilters               = []
     , optEmailObfuscation      = NoObfuscation
@@ -167,7 +377,7 @@ defaultOpts = Opt
     , optCiteMethod            = Citeproc
     , optListings              = False
     , optPdfEngine             = Nothing
-    , optPdfEngineArgs         = []
+    , optPdfEngineOpts         = []
     , optSlideLevel            = Nothing
     , optSetextHeaders         = True
     , optAscii                 = False
@@ -177,7 +387,7 @@ defaultOpts = Opt
     , optFileScope             = False
     , optTitlePrefix           = Nothing
     , optCss                   = []
-    , optIpynbOutput           = "best"
+    , optIpynbOutput           = IpynbOutputBest
     , optIncludeBeforeBody     = []
     , optIncludeAfterBody      = []
     , optIncludeInHeader       = []
@@ -187,9 +397,22 @@ defaultOpts = Opt
     , optStripComments         = False
     }
 
+contextToMeta :: Context Text -> Meta
+contextToMeta (Context m) =
+  Meta . M.mapKeys unpack . M.map valToMetaVal $ m
+
+valToMetaVal :: Val Text -> MetaValue
+valToMetaVal (MapVal (Context m)) =
+  MetaMap . M.mapKeys unpack . M.map valToMetaVal $ m
+valToMetaVal (ListVal xs) = MetaList $ map valToMetaVal xs
+valToMetaVal (SimpleVal t) = MetaString (unpack t)
+valToMetaVal NullVal = MetaString ""
+
 -- see https://github.com/jgm/pandoc/pull/4083
 -- using generic deriving caused long compilation times
 $(deriveJSON
+   defaultOptions{ fieldLabelModifier = drop 11 . map toLower } ''IpynbOutput)
+$(deriveJSON
    defaultOptions{ fieldLabelModifier = map toLower } ''LineEnding)
 $(deriveJSON
    defaultOptions{ fieldLabelModifier =
diff --git a/src/Text/Pandoc/App/OutputSettings.hs b/src/Text/Pandoc/App/OutputSettings.hs
index bdfb4cde2..3edeea1a1 100644
--- a/src/Text/Pandoc/App/OutputSettings.hs
+++ b/src/Text/Pandoc/App/OutputSettings.hs
@@ -211,7 +211,7 @@ optToOutputSettings opts = do
         , writerReferenceLinks   = optReferenceLinks opts
         , writerReferenceLocation = optReferenceLocation opts
         , writerDpi              = optDpi opts
-        , writerWrapText         = optWrapText opts
+        , writerWrapText         = optWrap opts
         , writerColumns          = optColumns opts
         , writerEmailObfuscation = optEmailObfuscation opts
         , writerIdentifierPrefix = optIdentifierPrefix opts