Merge branch 'sglpendWarn' of github.com:JacquesCarette/Drasil into mnmzDcDsc

Author: balacij

.github/workflows/Build.yaml

@@ -129,7 +129,7 @@ jobs:
 
       - name: "Extract HTML copies of Jupyter Notebooks"
         run: |
-          sudo apt-get install -y --fix-missing jupyter
+          pip install jupyterlab
           make jupyter_html
         if: ${{ steps.changes.outputs.md == 'true' || fromJSON(env.is_deployment) }}
 

code/drasil-docLang/lib/Drasil/DocLang.hs

@@ -10,14 +10,14 @@ module Drasil.DocLang (
   PDSub(..), ProblemDescription(..), SSDSec(..), SSDSub(..), SCSSub(..),
   SolChSpec(..),
   -- Drasil.DocumentLanguage.Core
-  AppndxSec(..), AuxConstntSec(..), DerivationDisplay(..), Emphasis(..),
+  AppndxSec(..), AuxConstntSec(..), DerivationDisplay(..), DocDesc, Emphasis(..),
   OffShelfSolnsSec(..), GSDSec(..), GSDSub(UsrChars, SystCons, SysCntxt),
   IntroSec(..), IntroSub(..), LFunc(..), Literature(Doc', Lit,Manual),
   RefSec(..), RefTab(..), StkhldrSec(..), StkhldrSub(Client, Cstmr),
   TConvention(..), TraceabilitySec(TraceabilityProg), TSIntro(..), TUIntro(..),
   -- *** Functions
   -- Drasil.DocumentLanguage
-  mkDoc, fillTraceSI, fillcdbSRS, findAllRefs,
+  mkDoc, fillcdbSRS, findAllRefs,
   -- ** Notebook
   -- | For generating Jupyter notebook lesson plans.
 
@@ -55,9 +55,9 @@ module Drasil.DocLang (
   unitTableRef, tunit, tunit', tunitNone,
   -- ** Requirements
   -- Drasil.Sections.Requirements
-  inReq, mkInputPropsTable, mkQRTuple, mkQRTupleRef, 
+  inReq, mkInputPropsTable, mkQRTuple, mkQRTupleRef,
   mkValsSourceTable, reqInputsRef, mkMaintainableNFR, mkPortableNFR,
-  mkCorrectNFR, mkVerifiableNFR, mkUnderstandableNFR, mkReusableNFR, 
+  mkCorrectNFR, mkVerifiableNFR, mkUnderstandableNFR, mkReusableNFR,
   mkSecurityNFR,
   -- ** Specific System Description
   -- Drasil.Sections.SpecificSystemDescription
@@ -68,22 +68,22 @@ module Drasil.DocLang (
   -- * References
   -- Drasil.SRS.References
   secRefs
-) where 
+) where
 
 import Drasil.DocDecl (SRSDecl, DocSection(..), ReqrmntSec(..), ReqsSub(..),
   PDSub(..), ProblemDescription(..), SSDSec(..), SSDSub(..), SCSSub(..),
   SolChSpec(..))
-import Drasil.DocumentLanguage (mkDoc, fillTraceSI, fillcdbSRS, findAllRefs)
+import Drasil.DocumentLanguage (mkDoc, fillcdbSRS, findAllRefs)
 import Drasil.DocumentLanguage.Core (AppndxSec(..), AuxConstntSec(..),
-  DerivationDisplay(..), Emphasis(..), OffShelfSolnsSec(..), GSDSec(..),
+  DerivationDisplay(..), DocDesc, Emphasis(..), OffShelfSolnsSec(..), GSDSec(..),
   GSDSub(UsrChars, SystCons, SysCntxt), IntroSec(..), IntroSub(..), LFunc(..),
   Literature(Doc', Lit,Manual), RefSec(..), RefTab(..), StkhldrSec(..),
   StkhldrSub(Client, Cstmr), TConvention(..), TraceabilitySec(TraceabilityProg),
   TSIntro(..), TUIntro(..))
-import Drasil.DocumentLanguage.Notebook.Core (Intro(..), LearnObj(..), Review(..), 
+import Drasil.DocumentLanguage.Notebook.Core (Intro(..), LearnObj(..), Review(..),
   CaseProb(..), Example(..), Smmry(..), Apndx(..))
 import Drasil.DocumentLanguage.Notebook.DocumentLanguage (mkNb)
-import Drasil.DocumentLanguage.Notebook.LsnDecl (LsnDecl, LsnChapter(Intro, LearnObj, Review, 
+import Drasil.DocumentLanguage.Notebook.LsnDecl (LsnDecl, LsnChapter(Intro, LearnObj, Review,
   CaseProb, Example, Smmry, BibSec, Apndx))
 import Drasil.DocumentLanguage.Definitions (Field(..), Fields, InclUnits(IncludeUnits),
   Verbosity(..), ddefn)

code/drasil-docLang/lib/Drasil/DocumentLanguage.hs

@@ -5,7 +5,7 @@
 -- Over time, we'll want to have a cleaner separation, but doing that
 -- all at once would break too much for too long.  So we start here
 -- instead.
-module Drasil.DocumentLanguage where
+module Drasil.DocumentLanguage (mkDoc, fillcdbSRS, findAllRefs) where
 
 import Control.Lens ((^.), set)
 import Data.Function (on)
@@ -16,7 +16,7 @@ import qualified Data.Map as Map (elems, assocs, keys)
 import Utils.Drasil (invert)
 
 import Drasil.DocDecl (SRSDecl, mkDocDesc)
-import qualified Drasil.DocDecl as DD (DocSection(TraceabilitySec))
+import qualified Drasil.DocDecl as DD
 import Drasil.DocumentLanguage.Core (AppndxSec(..), AuxConstntSec(..),
   DerivationDisplay(..), DocDesc, DocSection(..), OffShelfSolnsSec(..), GSDSec(..),
   GSDSub(..), IntroSec(..), IntroSub(..), LCsSec(..), LFunc(..),
@@ -40,7 +40,7 @@ import Drasil.System
 import Drasil.GetChunks (ccss, ccss', citeDB)
 
 import Drasil.Sections.TableOfAbbAndAcronyms (tableAbbAccGen)
-import Drasil.Sections.TableOfContents (toToC, findToC)
+import Drasil.Sections.TableOfContents (toToC)
 import Drasil.Sections.TableOfSymbols (table, tsIntro)
 import Drasil.Sections.TableOfUnits (tOfUnitSIName, tuIntro, defaultTUI)
 import qualified Drasil.DocLang.SRS as SRS (appendix,
@@ -73,12 +73,10 @@ import qualified Data.Drasil.Concepts.Documentation as Doc (likelyChg, section_,
 -- * Main Function
 
 -- | Creates a document from a document description, a title combinator function, and system information.
-mkDoc :: SRSDecl -> (IdeaDict -> IdeaDict -> Sentence) -> System -> Document
-mkDoc dd comb si@SI {_sys = sys, _authors = docauthors} =
-  Document (whatsTheBigIdea si `comb` nw sys) (foldlList Comma List $ map (S . name) docauthors) (findToC l) $
-  mkSections si l
-  where
-    l = mkDocDesc si dd
+mkDoc :: SRSDecl -> (IdeaDict -> IdeaDict -> Sentence) -> (System, DocDesc) -> Document
+mkDoc srs comb (si@SI {_sys = sys, _authors = docauthors}, dd) =
+  Document (whatsTheBigIdea si `comb` nw sys) (foldlList Comma List $ map (S . name) docauthors)
+    (findToC srs) $ mkSections si dd
 
 -- * Functions to Fill 'ChunkDB'
 
@@ -91,12 +89,17 @@ mkDoc dd comb si@SI {_sys = sys, _authors = docauthors} =
 -- | Assuming a given 'ChunkDB' with no traces and minimal/no references, fill
 -- in for rest of system information. Currently fills in references,
 -- traceability matrix information and 'IdeaDict's.
-fillcdbSRS :: SRSDecl -> System -> System
-fillcdbSRS srsDec si = fillLC srsDec $ fillReferences srsDec $ fillTraceSI srsDec si
+fillcdbSRS :: SRSDecl -> System -> (System , DocDesc)
+fillcdbSRS srsDec si =
+  (fillLC dd $ fillReferences sections $ fillTraceSI dd si , dd)
+  where
+    dd :: DocDesc
+    dd = mkDocDesc si srsDec
+    sections :: [Section]
+    sections = mkSections si dd
 
--- | Input the to-be-created 'LabelledContent's into the 'ChunkDB' (to be
--- created by the final SRS artifact renderer).
-fillLC :: SRSDecl -> System -> System
+-- | Fill in the 'Section's and 'LabelledContent' maps of the 'ChunkDB' from the 'SRSDecl'.
+fillLC :: DocDesc -> System -> System
 fillLC sd si@SI{ _sys = sn }
   | containsTraceSec sd = si2
   | otherwise = si
@@ -111,20 +114,18 @@ fillLC sd si@SI{ _sys = sn }
     chkdb2 = chkdb { labelledcontentTable = idMap $ nub $ existingLC ++ createdLCs }
     si2 = set systemdb chkdb2 si
 
-    containsTraceSec :: SRSDecl -> Bool
-    containsTraceSec ((DD.TraceabilitySec _):_) = True
+    containsTraceSec :: DocDesc -> Bool
+    containsTraceSec ((TraceabilitySec _):_) = True
     containsTraceSec (_:ss)                = containsTraceSec ss
     containsTraceSec []                    = False
 
 -- | Takes in existing information from the Chunk database to construct a database of references.
-fillReferences :: SRSDecl -> System -> System
-fillReferences dd si@SI{_sys = sys} = si2
+fillReferences :: [Section] -> System -> System
+fillReferences allSections si@SI{_sys = sys} = si2
   where
     -- get old chunk database + ref database
     chkdb = si ^. systemdb
     cites = citeDB si
-    -- convert SRSDecl into a list of sections (to easily get at all the references used in the SRS)
-    allSections = mkSections si $ mkDocDesc si dd
     -- get refs from SRSDecl. Should include all section labels and labelled content.
     refsFromSRS = concatMap findAllRefs allSections
     -- get refs from the stuff already inside the chunk database
@@ -147,10 +148,6 @@ fillReferences dd si@SI{_sys = sys} = si2
     -- set new chunk database into system information
     si2 = set systemdb chkdb2 si
 
--- | Helper that gets references from definitions and models.
-dRefToRef :: HasDecRef a => a -> [Reference]
-dRefToRef r = map ref $ r ^. getDecRefs
-
 -- | Recursively find all references in a section (meant for getting at 'LabelledContent').
 findAllRefs :: Section -> [Reference]
 findAllRefs (Section _ cs r) = r: concatMap findRefSecCons cs
@@ -161,10 +158,8 @@ findAllRefs (Section _ cs r) = r: concatMap findRefSecCons cs
     findRefSecCons _ = []
 
 -- | Helper for filling in the traceability matrix and graph information into the system.
-fillTraceSI :: SRSDecl -> System -> System
-fillTraceSI dd si = fillTraceMaps l $ fillReqs l si
-  where
-    l = mkDocDesc si dd
+fillTraceSI :: DocDesc -> System -> System
+fillTraceSI dd si = fillTraceMaps dd $ fillReqs dd si
 
 -- | Fills in the traceabiliy matrix and graphs section of the system information using the document description.
 fillTraceMaps :: DocDesc -> System -> System
@@ -439,3 +434,12 @@ mkBib bib = SRS.reference [UlC $ ulcc (Bib bib)] []
 -- | Helper for making the Appendix section.
 mkAppndxSec :: AppndxSec -> Section
 mkAppndxSec (AppndxProg cs) = SRS.appendix cs []
+
+-- ** Find Table of Contents
+
+-- Find more concise way to do this
+-- | Finds whether the Table of Contents is in a SRSDecl.
+findToC :: SRSDecl -> ShowTableOfContents
+findToC [] = NoToC
+findToC (DD.TableOfContents:_) = ToC
+findToC (_:dds) = findToC dds

code/drasil-docLang/lib/Drasil/Sections/Requirements.hs

@@ -28,7 +28,6 @@ import Data.Drasil.Concepts.Math (unit_)
 
 import qualified Drasil.DocLang.SRS as SRS
 import Drasil.DocumentLanguage.Units (toSentence)
-import Data.List (nub)
 
 import Control.Lens ((^.))
 import Data.Bifunctor (bimap)
@@ -42,7 +41,7 @@ reqF = SRS.require [reqIntro]
 -- For listing input requirements.
 fullReqs :: (Quantity i, MayHaveUnit i) => [i] -> Sentence -> [ConceptInstance] -> [ConceptInstance]
 fullReqs [] _ _ = []
-fullReqs i d r = nub $ inReq (inReqDesc (mkInputPropsTable i) d) : r-- ++ [outReq (outReqDesc outTable)]
+fullReqs i d r = inReq (inReqDesc (mkInputPropsTable i) d) : r -- ++ [outReq (outReqDesc outTable)]
 
 -- | Prepends given LabelledContent to an input-value table.
 fullTables :: (Quantity i, MayHaveUnit i) => [i] -> [LabelledContent] -> [LabelledContent]

code/drasil-docLang/lib/Drasil/Sections/TableOfContents.hs

@@ -1,6 +1,6 @@
 {-# Language TupleSections #-}
 -- | Standard code to make a table of contents.
-module Drasil.Sections.TableOfContents (toToC, findToC) where
+module Drasil.Sections.TableOfContents (toToC) where
 
 import qualified Data.Drasil.Concepts.Documentation as Doc
 import qualified Drasil.DocLang.SRS as SRS
@@ -188,9 +188,3 @@ mktAppndxSec (AppndxProg _) = Flat $ namedRef SRS.appendixLabel $ titleize  Doc.
 mktOffShelfSolnSec :: OffShelfSolnsSec -> ItemType
 mktOffShelfSolnSec (OffShelfSolnsProg _) = Flat $ namedRef SRS.offShelfSolnsLabel $ titleize' Doc.offShelfSolution
 
--- Find more concise way to do this
--- | Finds whether the Table of Contents is in a SRSDecl.
-findToC :: [DocSection] -> ShowTableOfContents
-findToC [] = NoToC
-findToC (TableOfContents:_) = ToC
-findToC (_:dds) = findToC dds

code/drasil-example/dblpend/lib/Drasil/DblPend/Body.hs

@@ -8,6 +8,7 @@ import Language.Drasil hiding (organization, section)
 import qualified Language.Drasil.Development as D
 import Theory.Drasil (TheoryModel, output)
 import Drasil.SRSDocument
+import Drasil.DocLang (DocDesc)
 import Drasil.Generator (cdb)
 import qualified Drasil.DocLang.SRS as SRS
 import Drasil.System (SystemKind(Specification), mkSystem, systemdb)
@@ -47,11 +48,15 @@ import Data.Drasil.ExternalLibraries.ODELibraries (scipyODESymbols,
   osloSymbols, apacheODESymbols, odeintSymbols, odeInfoChunks)
 import Drasil.DblPend.ODEs (dblPenODEInfo)
 
-srs :: Document
-srs = mkDoc mkSRS (S.forGen titleize phrase) fullSI
+sd  :: (System , DocDesc)
+sd = fillcdbSRS mkSRS si
 
+-- sigh, this is used by others
 fullSI :: System
-fullSI = fillcdbSRS mkSRS si
+fullSI = fst sd
+
+srs :: Document
+srs = mkDoc mkSRS (S.forGen titleize phrase) sd
 
 printSetting :: PrintingInformation
 printSetting = piSys (fullSI ^. systemdb) Equational defaultConfiguration

code/drasil-example/gamephysics/lib/Drasil/GamePhysics/Body.hs

@@ -5,6 +5,7 @@ import Control.Lens ((^.))
 import Language.Drasil hiding (organization, section)
 import Drasil.Metadata (dataDefn, inModel)
 import Drasil.SRSDocument
+import Drasil.DocLang (DocDesc)
 import Drasil.Generator (cdb)
 import qualified Drasil.DocLang.SRS as SRS
 import Language.Drasil.Chunk.Concept.NamedCombinators
@@ -47,11 +48,15 @@ import Drasil.GamePhysics.Unitals (symbolsAll, outputConstraints,
   inputSymbols, outputSymbols, inputConstraints)
 import Drasil.GamePhysics.GenDefs (generalDefns)
 
-srs :: Document
-srs = mkDoc mkSRS (S.forGen titleize short) fullSI
+sd  :: (System , DocDesc)
+sd = fillcdbSRS mkSRS si
 
+-- sigh, this is used by others
 fullSI :: System
-fullSI = fillcdbSRS mkSRS si
+fullSI = fst sd
+
+srs :: Document
+srs = mkDoc mkSRS (S.forGen titleize short) sd
 
 printSetting :: PrintingInformation
 printSetting = piSys (fullSI ^. systemdb) Equational defaultConfiguration

code/drasil-example/glassbr/lib/Drasil/GlassBR/Body.hs

@@ -8,8 +8,8 @@ import qualified Language.Drasil.Development as D
 
 import Drasil.Metadata as M (dataDefn, inModel, thModel)
 import Drasil.SRSDocument
+import Drasil.DocLang (DocDesc, auxSpecSent, termDefnF')
 import Drasil.Generator (cdb)
-import Drasil.DocLang (auxSpecSent, termDefnF')
 import qualified Drasil.DocLang.SRS as SRS (reference, assumpt, inModel)
 import Language.Drasil.Chunk.Concept.NamedCombinators
 import qualified Language.Drasil.Sentence.Combinators as S
@@ -51,11 +51,15 @@ import Drasil.GlassBR.Unitals (blast, blastTy, bomb, explosion, constants,
   glassTypes, glBreakage, lateralLoad, load, loadTypes, pbTol, probBr, stressDistFac, probBreak,
   sD, termsWithAccDefn, termsWithDefsOnly, concepts, dataConstraints)
 
-srs :: Document
-srs = mkDoc mkSRS (S.forGen titleize phrase) fullSI
+sd  :: (System , DocDesc)
+sd = fillcdbSRS mkSRS si
 
+-- sigh, this is used by others
 fullSI :: System
-fullSI = fillcdbSRS mkSRS si
+fullSI = fst sd
+
+srs :: Document
+srs = mkDoc mkSRS (S.forGen titleize phrase) sd
 
 printSetting :: PrintingInformation
 printSetting = piSys (fullSI ^. systemdb) Equational defaultConfiguration

code/drasil-example/hghc/lib/Drasil/HGHC/Body.hs

@@ -4,6 +4,7 @@ import Control.Lens ((^.))
 
 import Language.Drasil hiding (Manual) -- Citation name conflict. FIXME: Move to different namespace
 import Drasil.SRSDocument
+import Drasil.DocLang (DocDesc)
 import Drasil.Generator (cdb)
 import qualified Language.Drasil.Sentence.Combinators as S
 import Drasil.System (mkSystem, SystemKind(Specification), systemdb)
@@ -15,11 +16,15 @@ import Drasil.HGHC.MetaConcepts (progName)
 import Data.Drasil.People (spencerSmith)
 import Data.Drasil.Concepts.Thermodynamics as CT (heatTrans)
 
-srs :: Document
-srs = mkDoc mkSRS S.forT fullSI
+sd  :: (System , DocDesc)
+sd = fillcdbSRS mkSRS si
 
+-- sigh, this is used by others
 fullSI :: System
-fullSI = fillcdbSRS mkSRS si
+fullSI = fst sd
+
+srs :: Document
+srs = mkDoc mkSRS S.forT sd
 
 printSetting :: PrintingInformation
 printSetting = piSys (fullSI ^. systemdb) Equational defaultConfiguration

code/drasil-example/pdcontroller/lib/Drasil/PDController/Body.hs

@@ -5,6 +5,7 @@ import Control.Lens ((^.))
 import Language.Drasil
 import Drasil.Metadata (dataDefn)
 import Drasil.SRSDocument
+import Drasil.DocLang (DocDesc)
 import Drasil.Generator (cdb)
 import qualified Drasil.DocLang.SRS as SRS (inModel)
 import qualified Language.Drasil.Sentence.Combinators as S
@@ -43,11 +44,15 @@ import Drasil.PDController.ODEs (pidODEInfo)
 naveen :: Person
 naveen = person "Naveen Ganesh" "Muralidharan"
 
-srs :: Document
-srs = mkDoc mkSRS (S.forGen titleize phrase) fullSI
+sd  :: (System , DocDesc)
+sd = fillcdbSRS mkSRS si
 
+-- sigh, this is used by others
 fullSI :: System
-fullSI = fillcdbSRS mkSRS si
+fullSI = fst sd
+
+srs :: Document
+srs = mkDoc mkSRS (S.forGen titleize phrase) sd
 
 printSetting :: PrintingInformation
 printSetting = piSys (fullSI ^. systemdb) Equational defaultConfiguration