Vector integration in the DblPend example

.github/ISSUE_TEMPLATE/tmpltMeetIssue.md

@@ -1,22 +1,26 @@
 ---
 name: Drasil Meeting
 about: Create an agenda for Drasil team meetings and to track details.
-title: 'Drasil Team Meeting - Tuesday, Date, 1:30 pm, ITB/225'
+title: 'Drasil Team Meeting - Tuesday, Date, 1:30 pm, ITB/112'
 labels: 'meeting'
 assignees: 
  - balacij
  - JacquesCarette
  - smiths
  - sarrasoussia
- - jackwyand
+ - B-rando1
+ - Xinlu-Y
+ - JoeZZG
+
 
 ---
 
 **Agenda**
 
 1. Blockers for @sarrasoussia
-
-2. Blockers for @jackwyand
+2. Blockers for @B-rando1 
+3. Blockers for @Xinlu-Y 
+4. Blockers for @JoeZZG 
 
 Regrets:
 

.github/workflows/Build.yaml

@@ -29,7 +29,7 @@ jobs:
     name: "Build & Deploy"
     runs-on: ubuntu-22.04
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
 
       - name: "Update apt package list"
         run: |
@@ -65,7 +65,7 @@ jobs:
           stack-version: 'latest'
 
       - name: "Cache dependencies"
-        uses: actions/cache@v4.2.4
+        uses: actions/cache@v4.3.0
         with:
           path: |
             ~/.stack
@@ -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) }}
 
@@ -144,7 +144,7 @@ jobs:
 
       - name: "Deploy 🚀"
         if: ${{ fromJSON(env.is_deployment) }}
-        uses: JamesIves/github-pages-deploy-action@v4.7.3
+        uses: JamesIves/github-pages-deploy-action@v4.7.4
         with:
           git-config-name: ${{ secrets.BOT_NAME }}
           git-config-email: ${{ secrets.BOT_EMAIL }}

.github/workflows/Lint.yaml

@@ -16,7 +16,7 @@ jobs:
     name: "Linter"
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
 
       # Prepare more specific paths filters
       - uses: dorny/paths-filter@v3.0.2
@@ -34,7 +34,7 @@ jobs:
         if: ${{ steps.filter.outputs.hs == 'true' }}
         uses: haskell-actions/hlint-setup@v2
         with: # DO NOT MODIFY THE BELOW LINE MANUALLY -- code/scripts/update_default_stackage.sh is in charge of this!
-          version: '3.6.1' # HLINT VERSION TIED TO CURRENT TARGET (LTS-22.31)
+          version: '3.6.1' # HLINT VERSION TIED TO CURRENT TARGET (LTS-22.44)
 
       - name: 'Run HLint'
         if: ${{ steps.filter.outputs.hs == 'true' }}
@@ -44,6 +44,10 @@ jobs:
           path: code/
           fail-on: status
 
+      - name: 'Check lines have no trailing whitespace, all files have trailing newlines, and no file contains exessive newlines'
+        if: ${{ steps.filter.outputs.hs == 'true' }}
+        run: scripts/check_whitespace.sh
+
       # If a sh script was edited, then run shellcheck
       - name: "Run ShellCheck"
         if: ${{ steps.filter.outputs.sh == 'true' }}

.github/workflows/Wiki.yaml

@@ -14,7 +14,7 @@ jobs:
     runs-on: ubuntu-latest
     if: github.event_name == 'pull_request'
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
 
@@ -49,7 +49,7 @@ jobs:
     runs-on: ubuntu-latest
     if: github.event_name == 'push' && github.ref == 'refs/heads/main'
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with: # Fetch enough history to resolve HEAD^ -- https://github.com/actions/checkout?tab=readme-ov-file#checkout-head
           fetch-depth: 2
 

code/Makefile

@@ -212,7 +212,7 @@ debug: setup_debug_vars test ##@Examples Run test target with better debugging t
 # Debugging individual examples
 $(DEBUG_EXAMPLES): %$(DEBUG_E_SUFFIX): setup_debug_vars %$(TEST_E_SUFFIX)
 
-pr_ready: all stan hlint ##@General Check if your current work is ready to for a PR via `all` and `hlint` and stan.
+pr_ready: all stan hlint check_whitespace ##@General Check if your current work is ready to for a PR via `all` and `hlint` and stan.
 	@echo "Your build/ and stable/ match, and your code currently passes HLint tests."
 	@echo "Feel free to create a PR for your code if you feel it's ready."
 
@@ -475,6 +475,9 @@ hlint: check_stack ##@Linters Run HLint through the drasil packages. Uses a loca
 hot_hlint: ##@Linters Run HLint through the drasil packages. Uses the latest HLint version, downloading the binary each time.
 	curl --max-time 60 -sSL https://raw.github.com/ndmitchell/hlint/master/misc/run.sh | sh -s .
 
+check_whitespace: ##@Linters Check whitespace rules in all Haskell code (i.e., no per-line trailing whitespace and always trailing newline)
+	scripts/check_whitespace.sh
+
 shellcheck: ##@Linters Run ShellCheck static analyzer on all shell script files.
 	find . -type f -name '*.sh' -exec shellcheck {} +
 
@@ -627,4 +630,4 @@ help_packages: ##@Help Lists all packages.
 		echo "  $$package"; \
 	done
 
-.PHONY: help setup_debug_vars clean clean_artifacts cleanArtifacts gool code deps hlint hot_hlint analysis tex doc debug test graphs graphmod check_stack nographs graphs website deploy_code_path deploy deploy_lite all install examples tracegraphs doxygen shellcheck mdbook_build jupyter_html $(GOOLTEST) $(ALL_EXPANDED_TARGETS)
+.PHONY: help setup_debug_vars clean clean_artifacts cleanArtifacts gool code deps hlint hot_hlint check_whitespace analysis tex doc debug test graphs graphmod check_stack nographs graphs website deploy_code_path deploy deploy_lite all install examples tracegraphs doxygen shellcheck mdbook_build jupyter_html $(GOOLTEST) $(ALL_EXPANDED_TARGETS)

code/drasil-build/lib/Build/Drasil.hs

@@ -6,7 +6,7 @@ module Build.Drasil (
     RuleTransformer(makeRule)
   -- ** Types and Functions
   -- AST
-  ,  Annotation, Command, mkCheckedCommand, mkCommand, Dependencies, Rule, 
+  ,  Annotation, Command, mkCheckedCommand, mkCommand, Dependencies, Rule,
   mkFile, mkRule
     -- MakeString
   , MakeString, (+:+), makeS, mkFreeVar, mkImplicitVar, mkWindowsVar, mkOSVar
@@ -15,9 +15,9 @@ module Build.Drasil (
   )
   where
 
-import Build.Drasil.Make.AST (Annotation, Command, Dependencies, mkCheckedCommand, 
+import Build.Drasil.Make.AST (Annotation, Command, Dependencies, mkCheckedCommand,
   mkCommand, mkFile, mkRule, Rule)
 import Build.Drasil.Make.Import (RuleTransformer(makeRule))
-import Build.Drasil.Make.MakeString ((+:+), makeS, MakeString, mkFreeVar, 
+import Build.Drasil.Make.MakeString ((+:+), makeS, MakeString, mkFreeVar,
   mkImplicitVar, mkWindowsVar, mkOSVar)
 import Build.Drasil.Make.Print (genMake)

code/drasil-build/lib/Build/Drasil/Make/Print.hs

@@ -7,8 +7,8 @@ import Text.PrettyPrint (Doc, empty, text, (<>), (<+>), ($+$), ($$), hsep, vcat)
 import qualified Data.Text as T
 import Text.Wrap
 
-import Build.Drasil.Make.AST (Annotation, Command(C), 
-  CommandOpts(IgnoreReturnCode), Dependencies, Makefile(M), Rule(R), Target, 
+import Build.Drasil.Make.AST (Annotation, Command(C),
+  CommandOpts(IgnoreReturnCode), Dependencies, Makefile(M), Rule(R), Target,
   Type(Abstract))
 import Build.Drasil.Make.Helpers (addCommonFeatures, tab)
 import Build.Drasil.Make.Import (RuleTransformer, toMake)

code/drasil-build/stack.yaml

@@ -17,7 +17,7 @@
 #
 # resolver: ./custom-snapshot.yaml
 # resolver: https://example.com/snapshots/2018-01-01.yaml
-resolver: lts-22.31
+resolver: lts-22.44
 
 # User packages to be built.
 # Various formats can be used as shown in the example below.

code/drasil-code/lib/Data/Drasil/ExternalLibraries/ODELibraries.hs

@@ -7,11 +7,17 @@ module Data.Drasil.ExternalLibraries.ODELibraries (
   -- * Apache Commons (Java)
   apacheODEPckg, apacheODESymbols,
   -- * Odeint (C++)
-  odeintPckg, odeintSymbols, diffCodeChunk
+  odeintPckg, odeintSymbols, diffCodeChunk, odeInfoChunks
 ) where
+import Control.Lens ((^.), _1, _2, over)
+
+import Drasil.Database (HasUID(..), (+++))
 import Language.Drasil hiding (dim)
+import Language.Drasil (HasSymbol(symbol), MayHaveUnit(getUnit),
+  HasSpace(typ), Space (Actor, Natural, Real, Void, Boolean, String, Array, Vect, ClifS), implVar, implVar',
+  compoundPhrase, nounPhrase, nounPhraseSP, label, sub, Idea(getA), NamedIdea(term), Stage(..),
+  Definition (defn), (+:+), Sentence (S), DefinedQuantityDict, dqdWr, implVarAU')
 import Language.Drasil.Space (ClifKind(..))
-
 import Language.Drasil.Display (Symbol(Label, Concat))
 
 import Language.Drasil.Code (Lang(..), ExternalLibrary, Step, Argument,
@@ -39,8 +45,6 @@ import Language.Drasil.Code (Lang(..), ExternalLibrary, Step, Argument,
 
 import qualified Drasil.Code.CodeExpr.Development as CE
 
-import Control.Lens ((^.), _1, _2, over)
-
 -- SciPy Library (Python)
 
 -- | [SciPy](https://www.scipy.org/) ODE library package.
@@ -114,13 +118,12 @@ mthdArg = narg $ implVar "method_scipy" (nounPhrase
 atolArg = narg $ implVar "atol_scipy" (nounPhrase
   "absolute tolerance for ODE solution" "absolute tolerances for ODE solution")
   "the absolute tolerance for the ODE solution"
-  Real (label "atol") 
+  Real (label "atol")
 rtolArg = narg $ implVar "rtol_scipy" (nounPhrase
   "relative tolerance for ODE solution" "relative tolerances for ODE solution")
   "the relative tolerance for the ODE solution"
   Real (label "rtol")
 
-
 r, xAxis, ut, transpose :: CodeVarChunk
 r = quantvar $ implVar "r_scipy" (nounPhrase "ODE object" "ODE objects")
   "the ODE object"
@@ -137,7 +140,6 @@ transpose = quantvar $ implVar "transpose_numpy"
   "the Numpy Array Transpose"
   (Array Real) (label "u_t.T") -- (ccObjVar ut transpose) does not seem to work.
 
-
 f, odefunc, setIntegrator, setInitVal, successful,
   integrateStep, arange, odeintFunc :: CodeFuncChunk
 f = quantfunc $ implVar "f_scipy" (nounPhrase "function representing ODE system"
@@ -245,9 +247,9 @@ rTol = quantvar $ implVar "rTol_oslo" (nounPhrase
   "relative tolerance for ODE solution" "relative tolerances for ODE solution")
   "the relative tolerance for the ODE solution"
   Real (label "RelativeTolerance")
-sol = quantvar $ implVar "sol_oslo" (nounPhrase 
-  "container for ODE information" "containers for ODE information") 
-  "the container for ODE information" solT(label "sol") 
+sol = quantvar $ implVar "sol_oslo" (nounPhrase
+  "container for ODE information" "containers for ODE information")
+  "the container for ODE information" solT(label "sol")
 points = quantvar $ implVar "points_oslo" (nounPhrase
   "container holding ODE solution" "containers holding ODE solution")
   "the container holding the ODE solution"
@@ -425,7 +427,7 @@ adamsC, dp54C, stepHandlerCtor, addStepHandler, initMethod, handleStep,
   getInterpState, integrate, getDimension, computeDerivatives :: CodeFuncChunk
 adamsC = quantfunc $ implVar "adams_ctor_apache" (nounPhrase
   "constructor for an Adams-Bashforth integrator"
-  "constructors for an Adams-Bashforth integrator") 
+  "constructors for an Adams-Bashforth integrator")
   "the constructors for an Adams-Bashforth integrator"
   (Actor adams) (Label adams)
 dp54C = quantfunc $ implVar "dp54_ctor_apache" (nounPhrase
@@ -639,8 +641,8 @@ odeMethodUnavailable = "Chosen ODE solving method is not available" ++
 -- | Change in @X@ chunk constructor (where @X@ is a given argument).
 diffCodeChunk :: CodeVarChunk -> CodeVarChunk
 diffCodeChunk c = quantvar $ implVarAU' (show $ c +++ "d" )
-  (compoundPhrase (nounPhraseSP "change in") (c ^. term)) 
-  (S "the change in" +:+ (c ^. defn)) (getA c) 
+  (compoundPhrase (nounPhraseSP "change in") (c ^. term))
+  (S "the change in" +:+ (c ^. defn)) (getA c)
   (c ^. typ) (Concat [label "d", symbol c Implementation]) (getUnit c)
 
 -- FIXME: This is surely a hack, but I can't think of a better way right now.
@@ -682,4 +684,15 @@ modifiedODESyst sufx info = map replaceDepVar (odeSyst info)
     replaceDepVar (CE.CCCBinaryOp b e1 e2)   = CE.CCCBinaryOp b
       (replaceDepVar e1) (replaceDepVar e2)
     replaceDepVar (CE.Operator ao dd e)      = CE.Operator ao dd $ replaceDepVar e
-    replaceDepVar e = e
+    replaceDepVar e = e
+
+-- | Collect all chunks related to a specific ODE
+odeInfoChunks :: ODEInfo -> [DefinedQuantityDict]
+odeInfoChunks info =
+  let dv = depVar info
+  in map dqdWr [ dv
+               , listToArray dv
+               , arrayVecDepVar info
+               , diffCodeChunk dv
+               , listToArray $ diffCodeChunk dv
+               ]

code/drasil-code/lib/Language/Drasil/Choices.hs

@@ -10,18 +10,18 @@ module Language.Drasil.Choices (
   Logging(..), AuxFile(..), getSampleData, hasSampleInput, defaultChoices,
   choicesSent, showChs, InternalConcept(..)) where
 
+import Control.Lens ((^.))
+import Data.Map (Map)
+import qualified Data.Map as Map
+
+import Drasil.Database (UID, HasUID (..))
+import Drasil.GOOL (CodeType)
 import Language.Drasil hiding (None, Var)
 import Language.Drasil.Code.Code (spaceToCodeType)
 import Language.Drasil.Code.Lang (Lang(..))
 import Language.Drasil.Data.ODEInfo (ODEInfo)
 import Language.Drasil.Data.ODELibPckg (ODELibPckg)
 import Language.Drasil.Mod (Name)
-import Data.Map (Map)
-import qualified Data.Map as Map
-
-import Drasil.GOOL (CodeType)
-
-import Control.Lens ((^.))
 
 -- | The instruction indicates how the generated program should be written down.
 -- Full details of Choices documentation https://github.com/JacquesCarette/Drasil/wiki/The-Code-Generator
@@ -361,13 +361,13 @@ chsFieldSent :: (Sentence, Sentence) -> Sentence
 chsFieldSent (rec, chc) = rec +:+ S "selected as" +:+. chc
 
 -- | Data type of internal concepts
-data InternalConcept = 
+data InternalConcept =
     InputConstraintsFn
   | InputConstraintsMod
-  | WriteOutput 
+  | WriteOutput
   | DerivedValuesFn
   | DerivedValuesMod
-  | GetInput 
+  | GetInput
   | InputParameters
   | InputFormat
   | OutputFormat

code/drasil-code/lib/Language/Drasil/Chunk/CodeBase.hs

@@ -1,6 +1,6 @@
 module Language.Drasil.Chunk.CodeBase where
 
-import Database.Drasil (ChunkDB, findOrErr)
+import Drasil.Database (ChunkDB, findOrErr, UID)
 import Drasil.Code.CodeExpr.Development
 import Language.Drasil
 

code/drasil-code/lib/Language/Drasil/Chunk/CodeDefinition.hs

@@ -3,13 +3,14 @@ module Language.Drasil.Chunk.CodeDefinition (
   CodeDefinition, DefinitionType(..), qtoc, qtov, odeDef, auxExprs, defType,
 ) where
 
+import Control.Lens ((^.), makeLenses, view)
+
 import Drasil.Code.CodeExpr.Development (expr, CanGenCode(..))
+import Drasil.Database (HasUID (..))
 import Language.Drasil
 import Language.Drasil.Chunk.Code (quantvar, quantfunc)
 import Language.Drasil.Data.ODEInfo (ODEInfo(..), ODEOptions(..))
 
-import Control.Lens ((^.), makeLenses, view)
-
 -- | The definition may be specialized to use ODEs.
 data DefinitionType = Definition | ODE
 

code/drasil-code/lib/Language/Drasil/Chunk/ConstraintMap.hs

@@ -3,11 +3,11 @@ module Language.Drasil.Chunk.ConstraintMap (ConstraintCEMap, ConstraintCE,
 ) where
 
 import Control.Lens ((^.))
+import qualified Data.Map as Map
 
+import Drasil.Database (UID, HasUID(..))
 import Drasil.Code.CodeExpr.Development (CodeExpr, constraint)
-import Language.Drasil (Constraint, HasUID(..), UID, Constrained(..),
-  isPhysC, isSfwrC)
-import qualified Data.Map as Map
+import Language.Drasil (Constraint, Constrained(..), isPhysC, isSfwrC)
 
 -- | Type synonym for 'Constraint CodeExpr'
 type ConstraintCE = Constraint CodeExpr

code/drasil-code/lib/Language/Drasil/Chunk/NamedArgument.hs

@@ -4,14 +4,16 @@ module Language.Drasil.Chunk.NamedArgument (
   -- * Chunk Type
   NamedArgument(..),
   -- * Constructor
-  narg) where
+  narg
+) where
 
-import Language.Drasil (HasSpace(..), HasSymbol(..), HasUID(..),
+import Control.Lens ((^.), makeLenses, view)
+
+import Drasil.Database (HasUID(..))
+import Language.Drasil (HasSpace(..), HasSymbol(..),
   Idea(..), MayHaveUnit(..), NamedIdea(..), Quantity, IsArgumentName,
   DefinedQuantityDict, Concept, dqdWr, Definition (defn), ConceptDomain (cdom))
 
-import Control.Lens ((^.), makeLenses, view)
-
 -- | Any quantity can be a named argument (wrapper for 'DefinedQuantityDict'),
 -- but with more of a focus on generating code arguments.
 newtype NamedArgument = NA {_qtd :: DefinedQuantityDict}