Merge pull request #45 from LaurentRDC/SageMath-support

Support for sage

Author: LaurentRDC

CHANGELOG.md

@@ -2,8 +2,9 @@
 
 pandoc-plot uses [Semantic Versioning](http://semver.org/spec/v2.0.0.html)
 
-## Release 1.4.2
+## Release 1.5.0
 
+* Added support for [Sage](https://www.sagemath.org/) (#44)
 * Fixed an issue where the parsing of default save format from configuration was overly restrictive (#42).
 
 ## Release 1.4.1

README.md

@@ -69,7 +69,8 @@ The resulting `output.html` looks like this:
   - `graphviz`: graphs using [Graphviz](http://graphviz.org/);
   - `bokeh`: plots using the [Bokeh](https://bokeh.org/) visualization library;
   - `plotsjl`: plots using the [Julia `Plots.jl`](https://docs.juliaplots.org/latest/) package;
-  - `plantuml`: diagrams using the [PlantUML](https://plantuml.com/) software suite.
+  - `plantuml`: diagrams using the [PlantUML](https://plantuml.com/) software suite;
+  - `sageplot`: plots using the [Sage](https://www.sagemath.org/) software system.
 
 To know which toolkits are useable on *your machine* (and which ones are
 not available), you can check with the `toolkits` command:

example-config.yml

@@ -136,4 +136,9 @@ plantuml:
   # use the following configuration instead:
   # plantuml:
   #   executable: plantuml
-  #   command_line_arguments:
+  #   command_line_arguments:
+
+sageplot:
+  # preamble: sageplot.sage
+  executable: sage
+  command_line_arguments:

pandoc-plot.cabal

@@ -1,6 +1,6 @@
 cabal-version:  2.2
 name:           pandoc-plot
-version:        1.4.1
+version:        1.5.0
 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 
@@ -73,6 +73,7 @@ library
         Text.Pandoc.Filter.Plot.Renderers.Bokeh
         Text.Pandoc.Filter.Plot.Renderers.Plotsjl
         Text.Pandoc.Filter.Plot.Renderers.PlantUML
+        Text.Pandoc.Filter.Plot.Renderers.SageMath
         Text.Pandoc.Filter.Plot.Monad
         Text.Pandoc.Filter.Plot.Monad.Logging
         Text.Pandoc.Filter.Plot.Monad.Types

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

@@ -63,6 +63,7 @@ defaultConfiguration =
       bokehPreamble = mempty,
       plotsjlPreamble = mempty,
       plantumlPreamble = mempty,
+      sagemathPreamble = mempty,
       -- Executables
       matplotlibExe = python,
       matlabExe = "matlab",
@@ -76,6 +77,7 @@ defaultConfiguration =
       bokehExe = python,
       plotsjlExe = "julia",
       plantumlExe = "java",
+      sagemathExe = "sage",
       -- Command line arguments
       matplotlibCmdArgs = mempty,
       matlabCmdArgs = mempty,
@@ -89,6 +91,7 @@ defaultConfiguration =
       bokehCmdArgs = mempty,
       plotsjlCmdArgs = mempty,
       plantumlCmdArgs = "-jar plantuml.jar",
+      sagemathCmdArgs = mempty,
       -- Extras
       matplotlibTightBBox = False,
       matplotlibTransparent = False
@@ -147,7 +150,8 @@ data ConfigPrecursor = ConfigPrecursor
     _graphvizPrec :: !GraphvizPrecursor,
     _bokehPrec :: !BokehPrecursor,
     _plotsjlPrec :: !PlotsjlPrecursor,
-    _plantumlPrec :: !PlantUMLPrecursor
+    _plantumlPrec :: !PlantUMLPrecursor,
+    _sagemathPrec :: !SageMathPrecursor
   }
 
 defaultConfigPrecursor :: ConfigPrecursor
@@ -173,7 +177,8 @@ defaultConfigPrecursor =
       _graphvizPrec = GraphvizPrecursor Nothing (graphvizExe defaultConfiguration) (graphvizCmdArgs defaultConfiguration),
       _bokehPrec = BokehPrecursor Nothing (bokehExe defaultConfiguration) (bokehCmdArgs defaultConfiguration),
       _plotsjlPrec = PlotsjlPrecursor Nothing (plotsjlExe defaultConfiguration) (plotsjlCmdArgs defaultConfiguration),
-      _plantumlPrec = PlantUMLPrecursor Nothing (plantumlExe defaultConfiguration) (plantumlCmdArgs defaultConfiguration)
+      _plantumlPrec = PlantUMLPrecursor Nothing (plantumlExe defaultConfiguration) (plantumlCmdArgs defaultConfiguration),
+      _sagemathPrec = SageMathPrecursor Nothing (sagemathExe defaultConfiguration) (sagemathCmdArgs defaultConfiguration)
     }
 
 data LoggingPrecursor = LoggingPrecursor
@@ -212,6 +217,8 @@ data PlotsjlPrecursor = PlotsjlPrecursor {_plotsjlPreamble :: !(Maybe FilePath),
 
 data PlantUMLPrecursor = PlantUMLPrecursor {_plantumlPreamble :: !(Maybe FilePath), _plantumlExe :: !FilePath, _plantumlCmdArgs :: !Text}
 
+data SageMathPrecursor = SageMathPrecursor {_sagemathPreamble :: !(Maybe FilePath), _sagemathExe :: !FilePath, _sagemathCmdArgs :: !Text}
+
 instance FromJSON LoggingPrecursor where
   parseJSON (Object v) =
     LoggingPrecursor <$> v .:? "verbosity" .!= logVerbosity defaultConfiguration
@@ -275,6 +282,10 @@ instance FromJSON PlantUMLPrecursor where
   parseJSON (Object v) = PlantUMLPrecursor <$> v .:? asKey PreambleK <*> v .:? asKey ExecutableK .!= plantumlExe defaultConfiguration <*> v .:? asKey CommandLineArgsK .!= plantumlCmdArgs defaultConfiguration
   parseJSON _ = fail $ mconcat ["Could not parse ", show PlantUML, " configuration."]
 
+instance FromJSON SageMathPrecursor where
+  parseJSON (Object v) = SageMathPrecursor <$> v .:? asKey PreambleK <*> v .:? asKey ExecutableK .!= sagemathExe defaultConfiguration <*> v .:? asKey CommandLineArgsK .!= sagemathCmdArgs defaultConfiguration
+  parseJSON _ = fail $ mconcat ["Could not parse ", show SageMath, " configuration."]
+
 toolkitAsKey :: Toolkit -> Key 
 toolkitAsKey = fromString . unpack . cls
 
@@ -303,6 +314,7 @@ instance FromJSON ConfigPrecursor where
     _bokehPrec <- v .:? toolkitAsKey Bokeh .!= _bokehPrec defaultConfigPrecursor
     _plotsjlPrec <- v .:? toolkitAsKey Plotsjl .!= _plotsjlPrec defaultConfigPrecursor
     _plantumlPrec <- v .:? toolkitAsKey PlantUML .!= _plantumlPrec defaultConfigPrecursor
+    _sagemathPrec <- v .:? toolkitAsKey SageMath .!= _sagemathPrec defaultConfigPrecursor
 
     return $ ConfigPrecursor {..}
   parseJSON _ = fail "Could not parse configuration."
@@ -336,6 +348,7 @@ renderConfig ConfigPrecursor {..} = do
       bokehExe = _bokehExe _bokehPrec
       plotsjlExe = _plotsjlExe _plotsjlPrec
       plantumlExe = _plantumlExe _plantumlPrec
+      sagemathExe = _sagemathExe _sagemathPrec
 
       matplotlibCmdArgs = _matplotlibCmdArgs _matplotlibPrec
       matlabCmdArgs = _matlabCmdArgs _matlabPrec
@@ -349,6 +362,7 @@ renderConfig ConfigPrecursor {..} = do
       bokehCmdArgs = _bokehCmdArgs _bokehPrec
       plotsjlCmdArgs = _plotsjlCmdArgs _plotsjlPrec
       plantumlCmdArgs = _plantumlCmdArgs _plantumlPrec
+      sagemathCmdArgs = _sagemathCmdArgs _sagemathPrec
 
   matplotlibPreamble <- readPreamble (_matplotlibPreamble _matplotlibPrec)
   matlabPreamble <- readPreamble (_matlabPreamble _matlabPrec)
@@ -362,6 +376,7 @@ renderConfig ConfigPrecursor {..} = do
   bokehPreamble <- readPreamble (_bokehPreamble _bokehPrec)
   plotsjlPreamble <- readPreamble (_plotsjlPreamble _plotsjlPrec)
   plantumlPreamble <- readPreamble (_plantumlPreamble _plantumlPrec)
+  sagemathPreamble <- readPreamble (_sagemathPreamble _sagemathPrec)
 
   return Configuration {..}
   where

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

@@ -288,6 +288,7 @@ executable tk =
     exeSelector Bokeh = asksConfig bokehExe
     exeSelector Plotsjl = asksConfig plotsjlExe
     exeSelector PlantUML = asksConfig plantumlExe
+    exeSelector SageMath = asksConfig sagemathExe
 
 -- | The @Configuration@ type holds the default values to use
 -- when running pandoc-plot. These values can be overridden in code blocks.
@@ -354,6 +355,8 @@ data Configuration = Configuration
     plotsjlPreamble :: !Script,
     -- | The default preamble script for the PlantUML toolkit.
     plantumlPreamble :: !Script,
+    -- | The default preamble script for the SageMath toolkit.
+    sagemathPreamble :: !Script,
     -- | The executable to use to generate figures using the matplotlib toolkit.
     matplotlibExe :: !FilePath,
     -- | The executable to use to generate figures using the MATLAB toolkit.
@@ -378,6 +381,8 @@ data Configuration = Configuration
     plotsjlExe :: !FilePath,
     -- | The executable to use to generate figures using the PlantUML toolkit.
     plantumlExe :: !FilePath,
+    -- | The executable to use to generate figures using SageMath.
+    sagemathExe :: !FilePath,
     -- | Command-line arguments to pass to the Python interpreter for the Matplotlib toolkit
     matplotlibCmdArgs :: !Text,
     -- | Command-line arguments to pass to the interpreter for the MATLAB toolkit.
@@ -402,6 +407,8 @@ data Configuration = Configuration
     plotsjlCmdArgs :: !Text,
     -- | Command-line arguments to pass to the interpreter for the plantUML toolkit.
     plantumlCmdArgs :: !Text,
+    -- | Command-line arguments to pass to the interpreter for the SageMath toolkit.
+    sagemathCmdArgs :: !Text,
     -- | Whether or not to make Matplotlib figures tight by default.
     matplotlibTightBBox :: !Bool,
     -- | Whether or not to make Matplotlib figures transparent by default.

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

@@ -59,6 +59,7 @@ data Toolkit
   | Bokeh
   | Plotsjl
   | PlantUML
+  | SageMath
   deriving (Bounded, Eq, Enum, Generic, Ord)
 
 -- | This instance should only be used to display toolkit names
@@ -75,6 +76,7 @@ instance Show Toolkit where
   show Bokeh = "Python/Bokeh"
   show Plotsjl = "Julia/Plots.jl"
   show PlantUML = "PlantUML"
+  show SageMath = "SageMath"
 
 -- | Class name which will trigger the filter
 cls :: Toolkit -> Text
@@ -90,6 +92,7 @@ cls Graphviz = "graphviz"
 cls Bokeh = "bokeh"
 cls Plotsjl = "plotsjl"
 cls PlantUML = "plantuml"
+cls SageMath = "sageplot"
 
 -- | Executable program and directory where it can be found.
 data Executable = Executable FilePath Text

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

@@ -42,17 +42,31 @@ import Text.Pandoc.Filter.Plot.Monad.Logging
   ( Logger (lVerbosity),
   )
 import Text.Pandoc.Filter.Plot.Renderers.Bokeh
+    ( bokeh, bokehSupportedSaveFormats )
 import Text.Pandoc.Filter.Plot.Renderers.GGPlot2
+    ( ggplot2, ggplot2SupportedSaveFormats )
 import Text.Pandoc.Filter.Plot.Renderers.GNUPlot
+    ( gnuplot, gnuplotSupportedSaveFormats )
 import Text.Pandoc.Filter.Plot.Renderers.Graphviz
+    ( graphviz, graphvizSupportedSaveFormats )
 import Text.Pandoc.Filter.Plot.Renderers.Mathematica
+    ( mathematica, mathematicaSupportedSaveFormats )
 import Text.Pandoc.Filter.Plot.Renderers.Matlab
+    ( matlab, matlabSupportedSaveFormats )
 import Text.Pandoc.Filter.Plot.Renderers.Matplotlib
+    ( matplotlib, matplotlibSupportedSaveFormats )
 import Text.Pandoc.Filter.Plot.Renderers.Octave
+    ( octave, octaveSupportedSaveFormats )
 import Text.Pandoc.Filter.Plot.Renderers.PlantUML
+    ( plantuml, plantumlSupportedSaveFormats )
 import Text.Pandoc.Filter.Plot.Renderers.PlotlyPython
+    ( plotlyPython, plotlyPythonSupportedSaveFormats )
 import Text.Pandoc.Filter.Plot.Renderers.PlotlyR
+    ( plotlyR, plotlyRSupportedSaveFormats )
 import Text.Pandoc.Filter.Plot.Renderers.Plotsjl
+    ( plotsjl, plotsjlSupportedSaveFormats )
+import Text.Pandoc.Filter.Plot.Renderers.SageMath
+    ( sagemath, sagemathSupportedSaveFormats )
 
 -- | Get the renderer associated with a toolkit.
 -- If the renderer has not been used before,
@@ -87,6 +101,7 @@ renderer tk = do
     sel Bokeh = bokeh
     sel Plotsjl = plotsjl
     sel PlantUML = plantuml
+    sel SageMath = sagemath
 
 -- | Save formats supported by this renderer.
 supportedSaveFormats :: Toolkit -> [SaveFormat]
@@ -102,6 +117,7 @@ supportedSaveFormats Graphviz = graphvizSupportedSaveFormats
 supportedSaveFormats Bokeh = bokehSupportedSaveFormats
 supportedSaveFormats Plotsjl = plotsjlSupportedSaveFormats
 supportedSaveFormats PlantUML = plantumlSupportedSaveFormats
+supportedSaveFormats SageMath = sagemathSupportedSaveFormats
 
 -- | The function that maps from configuration to the preamble.
 preambleSelector :: Toolkit -> (Configuration -> Script)
@@ -117,6 +133,7 @@ preambleSelector Graphviz = graphvizPreamble
 preambleSelector Bokeh = bokehPreamble
 preambleSelector Plotsjl = plotsjlPreamble
 preambleSelector PlantUML = plantumlPreamble
+preambleSelector SageMath = sagemathPreamble
 
 -- | Parse code block headers for extra attributes that are specific
 -- to this renderer. By default, no extra attributes are parsed.

src/Text/Pandoc/Filter/Plot/Renderers/SageMath.hs

@@ -0,0 +1,88 @@
+{-# LANGUAGE OverloadedStrings #-}
+{-# LANGUAGE QuasiQuotes #-}
+{-# LANGUAGE RecordWildCards #-}
+{-# LANGUAGE NoImplicitPrelude #-}
+
+-- |
+-- Module      : $header$
+-- Copyright   : (c) Laurent P René de Cotret, 2019 - present
+-- License     : GNU GPL, version 2 or above
+-- Maintainer  : laurent.decotret@outlook.com
+-- Stability   : internal
+-- Portability : portable
+--
+-- Rendering SageMath figures
+module Text.Pandoc.Filter.Plot.Renderers.SageMath
+  ( sagemath,
+    sagemathSupportedSaveFormats,
+  )
+where
+
+import Text.Pandoc.Filter.Plot.Renderers.Prelude
+
+sagemath :: PlotM (Maybe Renderer)
+sagemath = do
+  avail <- sagemathAvailable
+  if not avail
+    then return Nothing
+    else do
+      cmdargs <- asksConfig sagemathCmdArgs
+      mexe <- executable SageMath
+      return $
+        mexe >>= \exe@(Executable _ exename) ->
+          return
+            Renderer
+              { rendererToolkit = SageMath,
+                rendererExe = exe,
+                rendererCapture = sagemathCapture,
+                rendererCommand = sagemathCommand cmdargs exename,
+                rendererSupportedSaveFormats = sagemathSupportedSaveFormats,
+                rendererChecks = mempty,
+                rendererLanguage = "sagemath",
+                rendererComment = mappend "# ",
+                rendererScriptExtension = ".sage"
+              }
+
+-- See here:
+-- https://doc.sagemath.org/html/en/reference/plotting/sage/plot/graphics.html#sage.plot.graphics.Graphics.save
+sagemathSupportedSaveFormats :: [SaveFormat]
+sagemathSupportedSaveFormats = [EPS, PDF, PNG, SVG]
+
+sagemathCommand :: Text -> Text -> OutputSpec -> Text
+sagemathCommand cmdargs exe OutputSpec {..} = [st|#{exe} #{cmdargs} "#{oScriptPath}"|]
+
+sagemathAvailable :: PlotM Bool
+sagemathAvailable = do
+  mexe <- executable SageMath
+  case mexe of
+    Nothing -> return False
+    Just (Executable dir exe) -> do
+      withPrependedPath dir $ asks envCWD >>= flip commandSuccess [st|#{exe} -v|]
+
+
+sagemathCapture :: FigureSpec -> FilePath -> Script
+sagemathCapture = appendCapture sagemathCaptureFragment
+
+
+-- This capture fragment is a bit ugly because sage does not have the
+-- equivalent of matplotlib's `plt.gca()` to get a pointer to the most
+-- recent graphical object. We must search for it
+sagemathCaptureFragment :: FigureSpec -> FilePath -> Script
+sagemathCaptureFragment FigureSpec {..} fname =
+  [st|
+import sage.plot.graphics as go
+import sage.plot.plot3d.base as go3d
+import builtins
+# Try to concatenate 3D graphics objects first; if this doesn't work, then 
+# concatenate all 2D graphic objects.
+__all_graphics = builtins.sum( (obj for obj in globals().values() if isinstance(obj, go3d.Graphics3d)))
+if not __all_graphics:
+    __all_graphics = builtins.sum( (obj for obj in globals().values() if isinstance(obj, go.Graphics)))
+if not __all_graphics:
+    raise RuntimeError(''.join([
+        "No plotting objects detected. ",
+        "Make sure that all of your plotting objects are named, e.g. `G = plot(...)` rather than just `plot(...)`. ",
+        "This is a limitation specific to the interaction between sage and pandoc-plot."
+    ]))
+__all_graphics.save_image(r"#{fname}", dpi=#{dpi})
+|]

tests/Common.hs

@@ -118,6 +118,7 @@ testFileInclusion tk =
     include Bokeh = "tests/includes/bokeh.py"
     include Plotsjl = "tests/includes/plotsjl.jl"
     include PlantUML = "tests/includes/plantuml.txt"
+    include SageMath = "tests/includes/sagemath.sage"
 
 -------------------------------------------------------------------------------
 -- Test that the files are saved in the appropriate format
@@ -378,6 +379,7 @@ trivialContent Bokeh =
     ]
 trivialContent Plotsjl = "using Plots; x = 1:10; y = rand(10); plot(x, y);"
 trivialContent PlantUML = "@startuml\nAlice -> Bob: test\n@enduml"
+trivialContent SageMath = "G = plot(sin, 1, 10)"
 
 addCaption :: String -> Block -> Block
 addCaption caption (CodeBlock (id', cls, attrs) script) =