Merge pull request #47 from LaurentRDC/specifying-executable

Overhauled executable handling

.github/workflows/ci.yml

@@ -176,6 +176,17 @@ jobs:
           exit 1
         fi
         pandoc-plot clean tests/issue30.md
+
+        # The idea here is to install some random package (npstreams) to
+        # check whether the plots will be rendered in the appropriate
+        # environment
+        python -m venv ./issue46
+        ./issue46/bin/python -m pip install npstreams matplotlib
+        pandoc --filter pandoc-plot -i tests/issue46.md -t native
+        if [ $(ls "plots" | wc -l) != 2 ]; then
+          exit 1
+        fi
+        pandoc-plot clean tests/issue46.md
     
     - name: Build documentation
       run: source tools/mkmanual.sh

CHANGELOG.md

@@ -2,6 +2,10 @@
 
 pandoc-plot uses [Semantic Versioning](http://semver.org/spec/v2.0.0.html)
 
+## Release 1.5.2
+
+* Overhauled the way executables are handled. This fixes an issue where executables specified in documents (rather than configuration) were ignored (#46).
+
 ## Release 1.5.1
 
 * Figures with no captions (and no link to the source script), will now be shown as an image, without figure numbering (#37).

cabal.project

@@ -1,2 +1 @@
-packages: pandoc-plot.cabal
-allow-newer: all
+packages: pandoc-plot.cabal

executable/Main.hs

@@ -9,7 +9,6 @@ module Main where
 
 import Control.Monad (join, msum, void, when)
 import Data.List (intersperse, (\\))
-import Data.Maybe (fromJust)
 import Data.Text (unpack)
 import qualified Data.Text.IO as TIO
 import Data.Version (parseVersion, showVersion)
@@ -58,15 +57,15 @@ import Text.Pandoc.Filter.Plot
     plotFilter,
   )
 import Text.Pandoc.Filter.Plot.Internal
-  ( Executable (..),
-    cleanOutputDirs,
+  ( cleanOutputDirs,
     cls,
     configurationPathMeta,
     executable,
     readDoc,
     runPlotM,
     supportedSaveFormats,
-    toolkits,
+    toolkits, 
+    pathToExe
   )
 import Text.Pandoc.JSON (toJSONFilter)
 import Text.ParserCombinators.ReadP (readP_to_S)
@@ -286,8 +285,8 @@ showAvailableToolkits mfp = do
     toolkitInfo avail conf tk = do
       putStrLn $ "Toolkit: " <> show tk
       when avail $ do
-        Executable dir exe <- fmap fromJust $ runPlotM Nothing conf $ executable tk
-        putStrLn $ "    Executable: " <> (dir </> unpack exe)
+        exe <- runPlotM Nothing conf $ executable tk
+        putStrLn $ "    Executable: " <> (pathToExe exe)
       putStrLn $ "    Code block trigger: " <> (unpack . cls $ tk)
       putStrLn $ "    Supported save formats: " <> (mconcat . intersperse ", " . fmap show $ supportedSaveFormats tk)
       putStrLn mempty

pandoc-plot.cabal

@@ -1,6 +1,6 @@
 cabal-version:  2.2
 name:           pandoc-plot
-version:        1.5.1
+version:        1.5.2
 synopsis:       A Pandoc filter to include figures generated from code blocks using your plotting toolkit of choice.
 description:    A Pandoc filter to include figures generated from code blocks. 
                 Keep the document and code in the same location. Output is 
@@ -14,7 +14,11 @@ maintainer:     Laurent P. René de Cotret
 license:        GPL-2.0-or-later
 license-file:   LICENSE
 build-type:     Simple
-tested-with:    GHC == 8.10.4, GHC == 9.0.1
+tested-with:    GHC == 8.10.4, 
+                GHC == 9.0.1, 
+                GHC == 9.0.1, 
+                GHC == 9.2.1, 
+                GHC == 9.2.2
 extra-source-files:
     CHANGELOG.md
     LICENSE
@@ -94,7 +98,7 @@ library
         , directory          >= 1.2.7 && < 2
         , filepath           >= 1.4   && < 2
         , hashable           >= 1     && < 2
-        , pandoc             >= 2.10  && < 3
+        , pandoc             >= 2.11  && < 3
         , pandoc-types       >= 1.22  && < 1.23
         , lifted-async       >= 0.10  && < 1
         , lifted-base        >= 0.2   && < 1
@@ -144,7 +148,6 @@ test-suite tests
                    , containers
                    , directory
                    , filepath
-                   , hspec
                    , hspec-expectations
                    , pandoc-types         >= 1.20 && <= 2
                    , pandoc-plot

src/Text/Pandoc/Filter/Plot/Monad.hs

@@ -74,7 +74,6 @@ import Control.Monad.State.Strict
     evalStateT,
   )
 import Data.ByteString.Lazy (toStrict)
-import Data.Functor ((<&>))
 import Data.Hashable (hash)
 import Data.Map.Strict (Map)
 import qualified Data.Map.Strict as M
@@ -84,7 +83,6 @@ import Data.Text.Encoding (decodeUtf8With)
 import Data.Text.Encoding.Error (lenientDecode)
 import System.Directory
   ( doesFileExist,
-    findExecutable,
     getCurrentDirectory,
     getModificationTime,
   )
@@ -141,7 +139,6 @@ runPlotM fmt conf v = do
   cwd <- getCurrentDirectory
   st <-
     PlotState <$> newMVar mempty
-      <*> newMVar mempty
   let verbosity = logVerbosity conf
       sink = logSink conf
   withLogger verbosity sink $
@@ -224,27 +221,23 @@ throwStrictError msg = do
   logger <- askLogger
   liftIO $ terminateLogging logger >> exitFailure
 
--- Plot state is used for caching.
--- One part consists of a map of filepaths to hashes
+-- Plot state is used for caching a map of filepaths to hashes
 -- This allows multiple plots to depend on the same file/directory, and the file hashes
 -- will only be calculated once. This is OK because pandoc-plot will not run for long.
 -- We note that because figures are rendered possibly in parallel, access to
 -- the state must be synchronized; otherwise, each thread might compute its own
 -- hashes.
--- The other part is comprised of a map of toolkits to renderers (possibly missing)
--- This means that checking if renderers are available will only be done once.
 type FileHash = Word
 
 data PlotState
   = PlotState
       (MVar (Map FilePath FileHash))
-      (MVar (Map Toolkit (Maybe Renderer)))
 
 -- | Get a filehash. If the file hash has been computed before,
 -- it is reused. Otherwise, the filehash is calculated and stored.
 fileHash :: FilePath -> PlotM FileHash
 fileHash path = do
-  PlotState varHashes varExes <- get
+  PlotState varHashes <- get
   hashes <- liftIO $ takeMVar varHashes
   (fh, hashes') <- case M.lookup path hashes of
     Nothing -> do
@@ -256,7 +249,7 @@ fileHash path = do
       debug $ mconcat ["Hash of dependency ", pack path, " already calculated."]
       return (h, hashes)
   liftIO $ putMVar varHashes hashes'
-  put $ PlotState varHashes varExes
+  put $ PlotState varHashes
   return fh
   where
     -- As a proxy for the state of a file dependency, we use the modification time
@@ -269,12 +262,8 @@ fileHash path = do
         else err (mconcat ["Dependency ", pack fp, " does not exist."]) >> return 0
 
 -- | Find an executable.
-executable :: Toolkit -> PlotM (Maybe Executable)
-executable tk =
-  exeSelector tk
-    >>= \name ->
-      liftIO $
-        findExecutable name <&> fmap exeFromPath
+executable :: Toolkit -> PlotM Executable
+executable tk = exeSelector tk >>= return . exeFromPath
   where
     exeSelector Matplotlib = asksConfig matplotlibExe
     exeSelector PlotlyPython = asksConfig plotlyPythonExe

src/Text/Pandoc/Filter/Plot/Monad/Types.hs

@@ -14,6 +14,7 @@
 module Text.Pandoc.Filter.Plot.Monad.Types
   ( Toolkit (..),
     Renderer (..),
+    AvailabilityCheck(..),
     Script,
     CheckResult (..),
     InclusionKey (..),
@@ -26,6 +27,7 @@ module Text.Pandoc.Filter.Plot.Monad.Types
     inclusionKeys,
     Executable (..),
     exeFromPath,
+    pathToExe,
     -- Utilities
     isWindows,
   )
@@ -37,7 +39,7 @@ import Data.String (IsString (..))
 import Data.Text (Text, pack, unpack)
 import Data.Yaml (FromJSON(..), ToJSON (toJSON), withText)
 import GHC.Generics (Generic)
-import System.FilePath (splitFileName)
+import System.FilePath (splitFileName, (</>), isAbsolute)
 import System.Info (os)
 import Text.Pandoc.Definition (Attr)
 
@@ -94,13 +96,20 @@ cls Plotsjl = "plotsjl"
 cls PlantUML = "plantuml"
 cls SageMath = "sageplot"
 
--- | Executable program and directory where it can be found.
-data Executable = Executable FilePath Text
+-- | Executable program, and sometimes the directory where it can be found.
+data Executable 
+  = AbsExe FilePath Text
+  | RelExe Text
 
 exeFromPath :: FilePath -> Executable
-exeFromPath fp =
-  let (dir, name) = splitFileName fp
-   in Executable dir (pack name)
+exeFromPath fp
+  | isAbsolute fp = let (dir, name) = splitFileName fp
+                     in AbsExe dir (pack name)
+  | otherwise     = RelExe (pack fp) 
+
+pathToExe :: Executable -> FilePath
+pathToExe (AbsExe dir name) = dir </> unpack name 
+pathToExe (RelExe name)            = unpack name
 
 -- | Source context for plotting scripts
 type Script = Text
@@ -170,6 +179,8 @@ inclusionKeys = enumFromTo (minBound :: InclusionKey) maxBound
 data FigureSpec = FigureSpec
   { -- | Renderer to use for this figure.
     renderer_ :: !Renderer,
+    -- | Executable to use in rendering this figure.
+    fsExecutable :: Executable,
     -- | Figure caption.
     caption :: !Text,
     -- | Append link to source code in caption.
@@ -263,15 +274,21 @@ data OutputSpec = OutputSpec
     oScriptPath :: FilePath,
     -- | Figure output path
     oFigurePath :: FilePath,
+    -- | Executable to use during rendering
+    oExecutable :: Executable,
     -- | Current working directory
     oCWD :: FilePath
   }
 
+data AvailabilityCheck
+  = CommandSuccess (Executable -> Text)
+  | ExecutableExists
+
 data Renderer = Renderer
   { rendererToolkit :: Toolkit,
-    rendererExe :: Executable,
     rendererCapture :: FigureSpec -> FilePath -> Script,
     rendererCommand :: OutputSpec -> Text,
+    rendererAvailability :: AvailabilityCheck,
     rendererSupportedSaveFormats :: [SaveFormat],
     rendererChecks :: [Script -> CheckResult],
     rendererLanguage :: Text,

src/Text/Pandoc/Filter/Plot/Parse.hs

@@ -70,11 +70,7 @@ parseFigureSpec block@(CodeBlock (id', classes, attrs) _) = do
     Nothing -> return NotAFigure
     Just tk -> do
       r <- renderer tk
-      case r of
-        Nothing -> do
-          err $ mconcat ["Renderer for ", tshow tk, " needed but is not installed"]
-          return $ MissingToolkit tk
-        Just r' -> figureSpec r'
+      figureSpec r
   where
     attrs' = Map.fromList attrs
     preamblePath = unpack <$> Map.lookup (tshow PreambleK) attrs'
@@ -108,8 +104,11 @@ parseFigureSpec block@(CodeBlock (id', classes, attrs) _) = do
 
           -- Decide between reading from file or using document content
           content <- parseContent block
+
+          defaultExe <- executable rendererToolkit
 
           let caption = Map.findWithDefault mempty (tshow CaptionK) attrs'
+              fsExecutable = maybe defaultExe (exeFromPath . unpack) $ Map.lookup (tshow ExecutableK) attrs'
               withSource = maybe defWithSource readBool (Map.lookup (tshow WithSourceK) attrs')
               script = mconcat $ intersperse "\n" [header, includeScript, content]
               directory = makeValid $ unpack $ Map.findWithDefault (pack $ defaultDirectory conf) (tshow DirectoryK) attrs'