Improve parsing of --defaults.

- Add FromYAML instances to Opt and to all subsidiary types.
- Remove the use of HsYAML-aeson, which doesn't give good
  position information on errors.
- Rename some fields in Opt to better match cli options or
  reflect what the ycontain [API change]:

  + optMetadataFile -> optMetadataFiles
  + optPDFEngineArgs -> optPDFEngineOpts
  + optWrapText -> optWrap
- Add IpynbOutput enumerated type to Text.Pandoc.App.Opts.
  Use this instead fo a string for optIpynbOutput.
- Add FromYAML instance for Filter in Text.Pandoc.Filters.

With these changes parsing of defaults files should be
complete and should give decent error messages.

Now (unlike before) we get an error if an unknown field
is used.

8 files changed, 390 insertions, 45 deletions

diff --git a/src/Text/Pandoc/App.hs b/src/Text/Pandoc/App.hs
index f3d342ebf..0f379419c 100644
--- a/src/Text/Pandoc/App.hs
+++ b/src/Text/Pandoc/App.hs
@@ -46,7 +46,8 @@ import System.IO (nativeNewline, stdout)
 import qualified System.IO as IO (Newline (..))
 import Text.Pandoc
 import Text.Pandoc.App.FormatHeuristics (formatFromFilePaths)
-import Text.Pandoc.App.Opt (Opt (..), LineEnding (..), defaultOpts)
+import Text.Pandoc.App.Opt (Opt (..), LineEnding (..), defaultOpts,
+                            IpynbOutput (..) )
 import Text.Pandoc.App.CommandLineOptions (parseOptions, options)
 import Text.Pandoc.App.OutputSettings (OutputSettings (..), optToOutputSettings)
 import Text.Pandoc.BCP47 (Lang (..), parseBCP47)
@@ -227,7 +228,7 @@ convertWithOpts opts = do
           }
 
     metadataFromFile <-
-      case optMetadataFile opts of
+      case optMetadataFiles opts of
         []    -> return mempty
         paths -> mapM readFileLazy paths >>= mapM (yamlToMeta readerOpts)
                    >>= return . (foldr1 (<>))
@@ -250,17 +251,16 @@ convertWithOpts opts = do
                          then (eastAsianLineBreakFilter :)
                          else id) .
                      (case optIpynbOutput opts of
-                       "all"    -> id
-                       "none"   -> (filterIpynbOutput Nothing :)
-                       "best"   -> (filterIpynbOutput (Just $
+                       IpynbOutputAll  -> id
+                       IpynbOutputNone -> (filterIpynbOutput Nothing :)
+                       IpynbOutputBest -> (filterIpynbOutput (Just $
                                      if htmlFormat format
                                         then Format "html"
                                         else
                                           case format of
                                             "latex"  -> Format "latex"
                                             "beamer" -> Format "latex"
-                                            _        -> Format format) :)
-                       _  -> id)  -- should not happen
+                                            _        -> Format format) :))
                      $ []
 
     let sourceToDoc :: [FilePath] -> PandocIO Pandoc
@@ -297,7 +297,7 @@ convertWithOpts opts = do
       ByteStringWriter f -> f writerOptions doc >>= writeFnBinary outputFile
       TextWriter f -> case outputPdfProgram outputSettings of
         Just pdfProg -> do
-                res <- makePDF pdfProg (optPdfEngineArgs opts) f
+                res <- makePDF pdfProg (optPdfEngineOpts opts) f
                         writerOptions doc
                 case res of
                      Right pdf -> writeFnBinary outputFile pdf
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
diff --git a/src/Text/Pandoc/Filter.hs b/src/Text/Pandoc/Filter.hs
index a32c26fbd..5670d028e 100644
--- a/src/Text/Pandoc/Filter.hs
+++ b/src/Text/Pandoc/Filter.hs
@@ -2,6 +2,7 @@
 {-# LANGUAGE DeriveGeneric     #-}
 {-# LANGUAGE NoImplicitPrelude #-}
 {-# LANGUAGE TemplateHaskell   #-}
+{-# LANGUAGE OverloadedStrings #-}
 {- |
    Module      : Text.Pandoc.Filter
    Copyright   : Copyright (C) 2006-2019 John MacFarlane
@@ -28,12 +29,32 @@ import Text.Pandoc.Options (ReaderOptions)
 import qualified Text.Pandoc.Filter.JSON as JSONFilter
 import qualified Text.Pandoc.Filter.Lua as LuaFilter
 import qualified Text.Pandoc.Filter.Path as Path
+import Data.YAML
+import qualified Data.Text as T
+import System.FilePath (takeExtension)
+import Control.Applicative ((<|>))
 
 -- | Type of filter and path to filter file.
 data Filter = LuaFilter FilePath
             | JSONFilter FilePath
             deriving (Show, Generic)
 
+instance FromYAML Filter where
+ parseYAML node =
+  (withMap "Filter" $ \m -> do
+    ty <- m .: "type"
+    fp <- m .: "path"
+    case ty of
+      "lua"  -> return $ LuaFilter $ T.unpack fp
+      "json" -> return $ JSONFilter $ T.unpack fp
+      _      -> fail $ "Unknown filter type " ++ show (ty :: T.Text)) node
+  <|>
+  (withStr "Filter" $ \t -> do
+    let fp = T.unpack t
+    case takeExtension fp of
+      ".lua"  -> return $ LuaFilter fp
+      _       -> return $ JSONFilter fp) node
+
 -- | Modify the given document using a filter.
 applyFilters :: ReaderOptions
              -> [Filter]
diff --git a/src/Text/Pandoc/Logging.hs b/src/Text/Pandoc/Logging.hs
index fad236dd3..74b8e1bb2 100644
--- a/src/Text/Pandoc/Logging.hs
+++ b/src/Text/Pandoc/Logging.hs
@@ -25,6 +25,7 @@ module Text.Pandoc.Logging (
 
 import Prelude
 import Control.Monad (mzero)
+import Data.YAML (withStr, FromYAML(..))
 import Data.Aeson
 import Data.Aeson.Encode.Pretty (Config (..), defConfig, encodePretty',
                                  keyOrder)
@@ -52,6 +53,14 @@ instance FromJSON Verbosity where
          _         -> mzero
   parseJSON _      =  mzero
 
+instance FromYAML Verbosity where
+  parseYAML = withStr "Verbosity" $ \t ->
+    case t of
+         "ERROR"   -> return ERROR
+         "WARNING" -> return WARNING
+         "INFO"    -> return INFO
+         _         -> mzero
+
 data LogMessage =
     SkippedContent String SourcePos
   | IgnoredElement String
diff --git a/src/Text/Pandoc/Options.hs b/src/Text/Pandoc/Options.hs
index 5dc94b2ad..5ff4504df 100644
--- a/src/Text/Pandoc/Options.hs
+++ b/src/Text/Pandoc/Options.hs
@@ -3,6 +3,7 @@
 {-# LANGUAGE DeriveGeneric      #-}
 {-# LANGUAGE NoImplicitPrelude  #-}
 {-# LANGUAGE TemplateHaskell    #-}
+{-# LANGUAGE OverloadedStrings  #-}
 {- |
    Module      : Text.Pandoc.Options
    Copyright   : Copyright (C) 2012-2019 John MacFarlane
@@ -29,12 +30,15 @@ module Text.Pandoc.Options ( module Text.Pandoc.Extensions
                            , ReferenceLocation (..)
                            , def
                            , isEnabled
+                           , defaultMathJaxURL
+                           , defaultKaTeXURL
                            ) where
 import Prelude
+import Control.Applicative ((<|>))
 import Data.Char (toLower)
 import Data.Data (Data)
 import Data.Default
-import Data.Text (Text)
+import Data.Text (Text, unpack)
 import Text.DocTemplates (Context(..))
 import qualified Data.Set as Set
 import Data.Typeable (Typeable)
@@ -46,6 +50,7 @@ import Text.Pandoc.Shared (camelCaseToHyphenated)
 import Text.DocTemplates (Template)
 import Data.Aeson.TH (deriveJSON, defaultOptions, Options(..),
                       SumEncoding(..))
+import Data.YAML
 
 class HasSyntaxExtensions a where
   getExtensions :: a -> Extensions
@@ -101,17 +106,58 @@ data HTMLMathMethod = PlainMath
                     | KaTeX String                -- url of KaTeX files
                     deriving (Show, Read, Eq, Data, Typeable, Generic)
 
+instance FromYAML HTMLMathMethod where
+   parseYAML node =
+     (withMap "HTMLMathMethod" $ \m -> do
+        method <- m .: "method"
+        mburl <- m .:? "url"
+        case unpack method of
+          "plain" -> return PlainMath
+          "webtex" -> return $ WebTeX $ maybe "" unpack mburl
+          "gladtex" -> return GladTeX
+          "mathml" -> return MathML
+          "mathjax" -> return $ MathJax $
+                         maybe defaultMathJaxURL unpack mburl
+          "katex" -> return $ KaTeX $
+                         maybe defaultKaTeXURL unpack mburl
+          _ -> fail $ "Unknown HTML math method " ++ show method) node
+       <|> (withStr "HTMLMathMethod" $ \method ->
+             case unpack method of
+               "plain" -> return PlainMath
+               "webtex" -> return $ WebTeX ""
+               "gladtex" -> return GladTeX
+               "mathml" -> return MathML
+               "mathjax" -> return $ MathJax defaultMathJaxURL
+               "katex" -> return $ KaTeX defaultKaTeXURL
+               _  -> fail $ "Unknown HTML math method " ++ show method) node
+
 data CiteMethod = Citeproc                        -- use citeproc to render them
                   | Natbib                        -- output natbib cite commands
                   | Biblatex                      -- output biblatex cite commands
                 deriving (Show, Read, Eq, Data, Typeable, Generic)
 
+instance FromYAML CiteMethod where
+  parseYAML = withStr "Citeproc" $ \t ->
+    case t of
+      "citeproc" -> return Citeproc
+      "natbib"   -> return Natbib
+      "biblatex" -> return Biblatex
+      _          -> fail $ "Unknown citation method " ++ show t
+
 -- | Methods for obfuscating email addresses in HTML.
 data ObfuscationMethod = NoObfuscation
                        | ReferenceObfuscation
                        | JavascriptObfuscation
                        deriving (Show, Read, Eq, Data, Typeable, Generic)
 
+instance FromYAML ObfuscationMethod where
+  parseYAML = withStr "Citeproc" $ \t ->
+    case t of
+      "none"       -> return NoObfuscation
+      "references" -> return ReferenceObfuscation
+      "javascript" -> return JavascriptObfuscation
+      _            -> fail $ "Unknown obfuscation method " ++ show t
+
 -- | Varieties of HTML slide shows.
 data HTMLSlideVariant = S5Slides
                       | SlidySlides
@@ -127,12 +173,29 @@ data TrackChanges = AcceptChanges
                   | AllChanges
                   deriving (Show, Read, Eq, Data, Typeable, Generic)
 
+instance FromYAML TrackChanges where
+  parseYAML = withStr "TrackChanges" $ \t ->
+    case t of
+      "accept"     -> return AcceptChanges
+      "reject"     -> return RejectChanges
+      "all"        -> return AllChanges
+      _            -> fail $ "Unknown track changes method " ++ show t
+
 -- | Options for wrapping text in the output.
 data WrapOption = WrapAuto        -- ^ Automatically wrap to width
                 | WrapNone        -- ^ No non-semantic newlines
                 | WrapPreserve    -- ^ Preserve wrapping of input source
                 deriving (Show, Read, Eq, Data, Typeable, Generic)
 
+instance FromYAML WrapOption where
+  parseYAML = withStr "WrapOption" $ \t ->
+    case t of
+      "auto"     -> return WrapAuto
+      "none"     -> return WrapNone
+      "preserve" -> return WrapPreserve
+      _          -> fail $ "Unknown wrap method " ++ show t
+
+
 -- | Options defining the type of top-level headers.
 data TopLevelDivision = TopLevelPart      -- ^ Top-level headers become parts
                       | TopLevelChapter   -- ^ Top-level headers become chapters
@@ -141,12 +204,31 @@ data TopLevelDivision = TopLevelPart      -- ^ Top-level headers become parts
                                           --   heuristics
                       deriving (Show, Read, Eq, Data, Typeable, Generic)
 
+instance FromYAML TopLevelDivision where
+  parseYAML = withStr "TopLevelDivision" $ \t ->
+    case t of
+      "part"     -> return TopLevelPart
+      "chapter"  -> return TopLevelChapter
+      "section"  -> return TopLevelSection
+      "default"  -> return TopLevelDefault
+      _          -> fail $ "Unknown top level division " ++ show t
+
+
 -- | Locations for footnotes and references in markdown output
 data ReferenceLocation = EndOfBlock    -- ^ End of block
                        | EndOfSection  -- ^ prior to next section header (or end of document)
                        | EndOfDocument -- ^ at end of document
                        deriving (Show, Read, Eq, Data, Typeable, Generic)
 
+instance FromYAML ReferenceLocation where
+  parseYAML = withStr "ReferenceLocation" $ \t ->
+    case t of
+      "block"    -> return EndOfBlock
+      "section"  -> return EndOfSection
+      "document" -> return EndOfDocument
+      _          -> fail $ "Unknown reference location " ++ show t
+
+
 -- | Options for writers
 data WriterOptions = WriterOptions
   { writerTemplate          :: Maybe Template -- ^ Template to use
@@ -227,16 +309,25 @@ instance HasSyntaxExtensions WriterOptions where
 isEnabled :: HasSyntaxExtensions a => Extension -> a -> Bool
 isEnabled ext opts = ext `extensionEnabled` getExtensions opts
 
+defaultMathJaxURL :: String
+defaultMathJaxURL = "https://cdn.jsdelivr.net/npm/mathjax@3/es5/"
+
+defaultKaTeXURL :: String
+defaultKaTeXURL = "https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.9.0/"
+
 $(deriveJSON defaultOptions ''ReaderOptions)
+
 $(deriveJSON defaultOptions{
    constructorTagModifier = map toLower,
    sumEncoding = TaggedObject{
                     tagFieldName = "method",
                     contentsFieldName = "url" }
                            } ''HTMLMathMethod)
+
 $(deriveJSON defaultOptions{ constructorTagModifier =
                                camelCaseToHyphenated
                            } ''CiteMethod)
+
 $(deriveJSON defaultOptions{ constructorTagModifier =
                             \t -> case t of
                                     "NoObfuscation"         -> "none"
@@ -244,16 +335,21 @@ $(deriveJSON defaultOptions{ constructorTagModifier =
                                     "JavascriptObfuscation" -> "javascript"
                                     _                       -> "none"
                            } ''ObfuscationMethod)
+
 $(deriveJSON defaultOptions ''HTMLSlideVariant)
+
 $(deriveJSON defaultOptions{ constructorTagModifier =
                                camelCaseToHyphenated
                            } ''TrackChanges)
+
 $(deriveJSON defaultOptions{ constructorTagModifier =
                                camelCaseToHyphenated
                            } ''WrapOption)
+
 $(deriveJSON defaultOptions{ constructorTagModifier =
                                camelCaseToHyphenated . drop 8
                            } ''TopLevelDivision)
+
 $(deriveJSON defaultOptions{ constructorTagModifier =
                                camelCaseToHyphenated
                            } ''ReferenceLocation)
diff --git a/src/Text/Pandoc/Writers/Math.hs b/src/Text/Pandoc/Writers/Math.hs
index a84f74f00..3905a3abc 100644
--- a/src/Text/Pandoc/Writers/Math.hs
+++ b/src/Text/Pandoc/Writers/Math.hs
@@ -12,6 +12,7 @@ import Text.Pandoc.Class
 import Text.Pandoc.Definition
 import Text.Pandoc.Logging
 import Text.TeXMath (DisplayType (..), Exp, readTeX, writePandoc)
+import Text.Pandoc.Options (defaultMathJaxURL, defaultKaTeXURL)
 
 -- | Converts a raw TeX math formula to a list of 'Pandoc' inlines.
 -- Defaults to raw formula between @$@ or @$$@ characters if entire formula
@@ -51,8 +52,3 @@ convertMath writer mt str =
                    DisplayMath -> DisplayBlock
                    InlineMath  -> DisplayInline
 
-defaultMathJaxURL :: String
-defaultMathJaxURL = "https://cdn.jsdelivr.net/npm/mathjax@3/es5/"
-
-defaultKaTeXURL :: String
-defaultKaTeXURL = "https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.9.0/"