CD-EXCALIBUR-FMS0033-1.10-D3.4_DevelopmentPlan
==============================================

.. meta::
   :description: technical note

   :keywords: ExCALIBUR,Development,Plan,D3.4,Abstract,The,report,describes,work,for,ExCALIBUR,project,NEPTUNE,at,Mile-,stone,M3.4.,This,report,surveys,the,textbook,and,standards,literature,re-,garding,the,documents,that,should,be,produced,as,part,of,a,major,software,development.,The,focus,is,on,documents,that,should,be,produced,before,development,starts,,and,on,living,documents,that,may,require,amendment,as,the,development,proceeds.,The,documents,serve,to,define,a,software,development,process,that,is,provisional,in,that,it,awaits,confirmation,from,grantee,reports.,The,key,infrastructure,for,the,next,step,of,NEPTUNE,is,expected,to,be,web-based,,and,an,investigation,into,the,suitability,of,the,PANDOC,and,the,LATEX2HTML,tools,for,generating,web-based,material,is,reported,,with,the,latter,to,be,preferred.,2,UKAEA,REFERENCE,AND,APPROVAL,SHEET,Client,Reference:,UKAEA,Reference:,CD/EXCALIBUR-FMS/0033,Issue:,Date:,1.10,25,October,2021,Project,Name:,ExCALIBUR,Fusion,Modelling,System,Prepared,By:,Name,and,Department,Ed,Threlfall,Wayne,Arter,Joseph,Parker,Will,Saunders,Signature,N/A,N/A,N/A,N/A,Date,25,October,2021,25,October,2021,25,October,2021,25,October,2021,BD,Reviewed,By:,Rob,Akers,25,October,2021,Advanced,Dept.,Manager,Computing,Approved,By:,Rob,Akers,25,October,2021,Advanced,Dept.,Manager,Computing,1,1,Introduction,Drawing,on,the,lessons,learnt,from,earlier,NEPTUNE,work,,especially,ref,[1],,not,only,will,the,software,will,be,opensource,,but,in,the,interests,of,encouraging,as,wide,a,possible,range,of,de-,velopers,,NEPTUNE,will,be,treated,as,a,community,project,with,maximal,transparency,regarded,decision-making,,resource,allocation,etc.,Successful,examples,of,such,projects,set,out,princi-,ples,that,community,members,are,expected,to,adhere,to,,and,guidelines,for,them,to,follow.,This,amounts,to,significantly,more,detail,both,concerning,the,management,of,the,development,and,the,production,of,the,software,,than,appears,in,the,NEPTUNE,Science,Plan,and,Charter,[2,,3],and,the,subsequent,initial,reports,[4,,5].,The,present,report,looks,in,detail,at,a,number,of,sources,recommending,what,documents,are,required,for,the,successful,conduct,of,a,software,development,project.,Following,from,the,re-,port,[4],,the,first,of,these,is,the,book,chapter,by,Spencer,Smith,[6],,as,specifically,directed,to,scientific,software.,The,conclusion,of,the,report,[1,,§,3],draws,attention,to,Sommerville,[7],who,has,relevant,material,dispersed,throughout,the,book,and,Hewitt,[8],,although,these,are,aimed,at,a,wider,,more,commercially-oriented,range,of,developments.,Focussing,on,science,,specifically,space,applications,there,is,the,European,Space,Agency,(ESA),standards,document,[9],which,in,a,“lite”,form,has,proved,successful,in,two,UKAEA,developments,this,century,,viz.,FISPACT,[10],and,SMARDDA,[11].,None,of,these,sources,is,entirely,suitable,for,NEPTUNE.,The,proposed,“faking”,of,documents,by,Smith,seems,unsatisfactory.,Hurried,writing,is,suggested,by,the,inconsistency,between,his,state-,ments,that,no-one,likes,documenting,software,and,his,recommendations,that,more,documents,be,produced,,a,suggestion,supported,by,the,fact,that,the,proposed,division,of,material,between,vari-,ous,documents,seems,unsatisfactory,in,some,places,,eg.,where,the,functional,and,nonfunctional,requirements,are,combined,together,in,one,section,of,a,document,entitled,the,“Software,Require-,ments,Specification”.,As,a,text-book,,Sommerville,offers,a,multitude,of,possibilities,,but,few,are,relevant,to,open-source,scientific,software;,therefore,Hewitt,scores,by,being,more,focussed,and,by,an,emphasis,on,awareness,of,the,surrounding,business,environment.,The,ESA,approach,does,not,meet,NEPTUNE,needs,in,that,it,assumes,a,single,expert,customer,for,the,project,,and,any-,way,the,full,standard,,intended,for,flight-critical,software,,is,arguably,too,onerous,,where,the,“lite”,version,is,more,appropriate,for,a,contractor,with,a,single,worker.,In,addition,to,the,points,in,the,preceding,paragraph,,none,of,the,sources,fully,addresses,the,Ideally,,material,should,be,issue,that,scientist,developers,do,not,like,producing,documentation.,written,up,only,once,to,be,presented,to,developers,and,users,of,whatever,level,of,competence,as,appropriate.,This,is,probably,best,addressed,by,producing,documentation,as,web,pages,,as,indeed,indicated,by,both,Spencer,Smith,and,Hewitt.,The,main,Section,2,provides,a,concordance,of,the,documents,from,the,texts,[12,,6,,7],in,Sec-,tion,2.1,,then,gives,more,details,as,to,what,information,should,be,provided,in,each,in,Section,2.2.,It,is,followed,by,discussion,of,how,best,to,format,the,documentation,as,a,website,in,Section,2.3.,2,Figure,1:,Documents,according,to,ECSS-E-ST-40C,[9],,which,is,based,on,a,customer-supplier,re-,lationship.,The,two-,and,three-letter,acronyms,indicate,document,titles,as,explained,in,Section,2.2.,2,Task,Work,2.1,Concordance,The,ECSS-E-ST-40C,document,or,ESA,standard,for,short,is,shown,schematically,in,Figure,1.,As,the,report’s,first,author,has,developed,software,using,a,‘lite’,version,of,this,standard,[13],,it,is,taken,as,the,reference,point.,The,documents,and,sections,of,documents,from,the,other,texts,[8,,6,,7],are,are,thus,grouped,according,to,the,ESA,documents,,as,shown,in,Figure,2.,The,other,major,reference,consulted,for,design,of,scientific,software,,namely,Rouson,et,al,[14],,mainly,promotes,use,of,software,patterns,,albeit,illustrated,by,UML,diagrams,as,advocated,by,refs,[8,,7].,The,ESA,standard,[9],is,central,because,of,personal,experience,that,it,works,,at,least,in,the,“lite”,version,,seemingly,for,the,reasons,that,it,encourages,conversation,between,the,supplier/paymaster,and,the,developer.,These,interactions,lead,to,documentation,that,sets,out,an,agreed,scope,for,the,software,before,each,stage,of,development,,thus,avoiding,the,project,‘creep’,and,on-the-fly,re-,design,that,may,fatally,slow,code,production.,The,Design,Justification,File,(DJF,,see,Section,2.2.5),3,Figure,2:,Concordance,of,documents,needed,during,software,development,,grouped,according,to,ECSS-E-ST-40C,[9],-,or,labelled,‘(N)’,,texts,as,follows:,Hewitt,“Semantic,Software,Design”,[8],,(Spencer),Smith,“A,Rational,Document,Driven,Design,Process,for,Scientific,Software”,[6],,and,Sommerville,“Software,Engineering”,[7].,4,Figure,3:,The,Design,Thinking,process,,Figure,4-1,from,Hewitt,[8].,Progression,is,from,left,to,right:,forming,insights,and,generating,ideas,are,both,part,of,the,problem,and,the,opportunity.,produced,in,the,process,is,unique,to,the,ESA,documents.,Not,only,does,it,prevent,untimely,cus-,tomer,‘what-if’s,by,setting,out,and,analysing,options,to,a,specified,time-table,,but,constitutes,a,useful,fall-back,should,the,agreed,options,turn,out,to,be,unworkable,when,external,circumstances,change,unexpectedly.,Hewitt,[8],has,a,good,deal,of,discussion,of,philosophy,which,is,interesting,,amidst,what,personal,experience,indicates,should,be,a,very,successful,methodology,for,producing,software,in,a,com-,mercial,environment,,an,approach,which,is,set,out,both,succinctly,and,comprehensively.,His,“Design,thinking”,method,should,be,equally,useful,for,encouraging,scientific,as,well,as,commer-,cial,creativity.,This,is,illustrated,in,Figure,3,,although,more,than,one,excursion,to,the,tip,of,the,“Λ”,might,be,expected,in,a,research,context.,It,has,to,be,accompanied,by,a,careful,recording,of,both,the,good,and,the,bad,ideas,which,emerge.,Hewitt,[8],is,also,very,strong,on,identifying,and,managing,stakeholders,beyond,the,immediate,ambit,of,the,software,project.,He,is,understandably,less,succinct,here,,letting,it,emerge,that,the,average,manager,is,to,be,treated,as,someone,with,a,short,attention,span,,principally,focussed,on,advancing,his/her,own,career,(which,might,include,promoting,a,rival,project),,is,technically,ignorant,and,likely,to,demand,a,PowerPoint,justifying,any,aspect,of,the,project,at,a,moment’s,notice.,However,,in,any,context,,collaborators,will,appreciate,short,,to-the-point,communications,which,are,clearly,presented,and,well,argued.,Hewitt,notably,also,insists,on,having,two,reasons,for,every,design,decision,,and,producing,documentation,from,which,it,is,easy,to,generate,presentations,of,5-15,slides.,For,commercial,reasons,,there,is,also,de-,tailed,consideration,as,to,how,to,manage,data,and,exploit,Machine,Learning,(ML),tools,,and,how,to,ensure,reliability,of,both,the,software,and,the,hardware,that,it,uses,,all,of,which,are,germane,to,the,Exascale.,Spencer,Smith,[6],naturally,highlights,what,documents,are,needed,in,the,development,of,scientific,software.,Smith,provides,reminders,of,the,need,to,include,details,such,as,choice,of,physical,units,,and,to,plan,validation,and,verification,(V,&,V),of,results.,Last,in,the,list,of,sources,,Sommerville,[7],is,comprehensive,and,can,be,used,as,the,authority,on,software,terminology,in,what,is,still,a,rapidly,expanding,subject,that,can,give,rise,to,overlapping,and,even,conflicting,definitions.,5,2.2,Detailed,Information,In,this,section,,the,documents,labelled,“N”,are,introductions,upon,the,ESA,standard,for,use,in,a,community,project.,Citations,in,the,present,section,to,Hewitt,refer,specifically,to,ref,[12,,§,5],,to,Smith,imply,ref,[6,,§,2.2],and,to,Sommerville,imply,ref,[7,,§,4],unless,stated,otherwise.,2.2.1,Program,Name,PN,(N),Choice,of,name,for,the,software,is,recognised,as,important,,but,this,section,should,mainly,aim,to,give,the,reader,enough,information,about,the,purpose,of,the,software,that,he/she,can,decide,whether,they,want,to,look,further.,Hewitt,also,requires,the,equivalent,of,the,approval,box,for,a,report,,giving,names,of,authors,,collaborators,and,reviewers.,At,this,point,,Hewitt,further,intro-,duces,the,RFC2119,subset,of,the,Internet,Engineering,Task,Force,(IETF),keyword,[15],for,use,throughout,the,document.,This,usage,implies,specific,meanings,for,“MUST”,,“MUST,NOT”,,“RE-,QUIRED”,,“SHALL”,,“SHALL,NOT”,,“SHOULD”,,“SHOULD,NOT”,,“RECOMMENDED”,,“MAY”,,and,“OPTIONAL”,when,the,words,are,capitalised.,(It,will,not,be,adopted,herein.),Think,preface,to,a,textbook,,plus,document,approval,box.,2.2.2,Business,Design,BD,(N),This,section,should,aim,to,make,it,clear,to,the,reader,why,it,woud,be,good,to,allocate,funding,for,the,software,development.,From,Hewitt’s,list:,•,Capabilities,-,what,new,benefits,arise,•,Strategic,fit,-,to,UKAEA,mission,•,Business,drivers,-,why,are,we,doing,this?,•,Assumptions,-,regarding,available,funding,•,Constraints,-,laws,and,regulations,,mention,software,licensing,•,Risks,-,if,resources,not,available,•,Impacts,-,new,processes,,training,needed,•,Stakeholders,-,who,will,win,or,lose,by,good,or,bad,outcome,Think,introductory,chapter,of,a,textbook.,2.2.3,Requirements,Baseline,RB,The,ESA,standard,RB,expresses,the,customer’s,requirements,,including,interface.,Sommerville,devotes,an,entire,chapter,to,requirements,engineering,,in,contrast,to,Hewitt,who,instead,recom-,mends,‘observation’,of,those,working,with,the,software,intended,for,replacement,,and,the,produc-,tion,of,use,cases,to,a,detailed,template,,as,follows:,6,•,Overview,•,Actors,•,Relationship,to,other,use,cases,•,Flow,including,input,to,output,•,Special,requirements,The,collection,of,the,above,use,cases,then,defines,the,so-called,functional,requirements,,other,In,the,scientific,case,,Spencer,Smith,requires,requirements,are,referred,to,as,non-functional.,specification,of,the,experiment,and,the,assumptions,to,be,used,in,modelling,it.,It,is,clear,since,(design),engineers,talk,of,workflows,,that,Hewitt’s,approach,has,much,to,be,recommended,for,a,mixed,engineering/scientific,application.,This,describes,the,use,cases,for,the,software.,2.2.4,Technical,Specification,TS,The,ESA,standard,TS,is,the,supplier’s,response,to,the,RB,,so,provides,probably,the,least,useful,ESA,document,description,for,a,community,process.,Material,ought,nonetheless,to,be,presented,which,encompasses,the,content,of,the,ESA,ICD,or,Interface,Control,Document.,Other,material,that,would,also,not,be,included,elsewhere,concerns,the,higher,level,aspects,of,Hewitt’s,Applica-,tion,Design,and,Smith’s,Software,Requirements,Specification,[6,,§,2.2.3].,Hewitt,would,include,prescription,of,software,standards,such,as,C++17,,and,guidelines/conventions,such,as,indicated,for,Object,Fortran,in,ref,[16].,Smith,would,specify,what,the,software,needs,to,compute,to,compare,with,experiment.,The,need,for,the,code,to,have,good,in-line,documentation,capable,of,formatting,by,say,DOXYGEN,[17],will,be,described,here.,This,outlines,inputs,and,outputs,of,the,software,,plus,set,outs,principles,for,code-writing.,2.2.5,Design,Justification,File,DJF,The,ESA,standard,DJF,is,generated,and,reviewed,at,all,stages,of,the,development,and,review,It,contains,the,documents,that,describe,the,trade-offs,,design,choice,justifications,,processes.,verification,plan,,validation,plan,,validation,testing,specification,,test,procedures,,test,results,,eval-,uations,and,any,other,documentation,called,for,to,justify,the,design,of,the,supplier’s,product.,This,describes,why,the,equations,,methods,and,algorithms,were,chosen,,and,the,testing,regime.,2.2.6,Design,Definition,File,DDF,The,ESA,standard,DDF,is,a,supplier-generated,file,that,documents,the,result,of,the,design,engi-,neering,processes.,The,DDF,is,the,primary,input,to,the,CDR,review,process,and,it,contains,all,the,documents,called,for,by,the,design,engineering,requirements.,This,describes,the,equations,,methods,and,algorithms,to,be,used,in,software.,7,2.2.7,Management,File,MGT,The,ESA,standard,MGT,is,a,supplier,generated,file,that,describes,the,management,features,of,the,software,project,(for,instance,,organisational,breakdown,and,responsibilities,,work,activities,breakdown,,selected,life,cycle,,deliveries,,milestones,and,risks).,It,also,describes,governance,-,eg.,PRINCE2,[18].,This,collates,the,project,plans,of,all,participants.,2.2.8,Maintenance,File,MF,The,MF,is,a,maintainer,generated,file,that,describes,the,planning,and,status,of,the,maintenance,,migration,and,retirement,activities.,This,is,basically,unnecessary,given,one,of,the,common,repository-based,projects.,2.2.9,Operational,Documentation,OP,In,the,ESA,standard,OP,,the,user’s,experience,of,the,software,feeds,back,into,the,instructions,as,to,how,to,use,the,software.,This,includes,the,user,manual,,the,developer,manual,and,describes,output,of,test,cases.,2.2.10,Reference,Material,REF,(N),In,a,web-based,system,,this,material,can,be,presented,stand-alone,to,avoid,duplication,throughout,many,different,documents.,It,should,provide,an,ontology,for,the,project,,by,which,it,is,meant,a,glossary,of,terminology,used,,meanings,of,acronyms,and,an,index,of,mathematical,notation.,2.2.11,Index,IND,(N),The,construction,of,an,index,is,recommended,by,Sommerville,,and,although,an,alphabetic,index,is,made,redundant,by,web,search,engines,,it,might,be,helpful,to,have,an,index,of,diagrams,and,figures.,2.3,Production,of,.html,It,has,become,recently,very,popular,to,construct,web-based,code,documentation,using,‘Read,the,Docs’,[19],,which,is,open-source,software,that,indeed,produces,a,very,attractive,website,,see,eg.,the,plasmapy,[20],website.,The,problem,is,the,need,to,use,reStructuredText,or,Markdown,formats,to,input,to,‘Read,the,Docs’.,For,many,people,,both,formats,represent,yet,more,markup,languages,to,learn,,and,although,many,know,Markdown,,it,has,many,slightly,incompatible,variants.,Similar,criticism,applies,to,the,use,of,DOXYGEN,for,producing,documentation,other,than,in-line,at,a,relatively,low,level.,8,MS,WordT,M,is,widely,used,by,engineers,to,produce,manuscripts,for,publication,and,has,a,built-in,capability,to,write,.html,,but,is,proprietary,software,and,although,widely,available,has,the,disad-,vantage,that,even,the,modern,(and,html-friendly),.docx,format,uses,an,extended,character,repre-,sentation,which,is,unnecessary,for,technical,work,,and,potentially,hazardous,in,that,non-printing,and/or,non-standard,characters,may,be,inadvertently,cut,and,pasted,eg.,into,software,documen-,tation,,which,expects,only,the,restricted,ASCII,set.,For,the,preceding,reason,,like,most,papers,in,mathematics,and,physics,,the,bulk,of,the,documentation,for,the,ExCALIBUR,project,NEPTUNE,has,been,drafted,using,LATEX.,There,are,at,least,two,open,source,tools,for,producing,.html,from,LATEXsource,,namely,PANDOC,and,LATEX2HTML.,The,PANDOC,project,[21],has,in,the,last,few,years,(Version,2.5,from,2018,,or,later),developed,to,the,point,where,it,can,turn,relatively,complex,LATEX,documents,into,.html,for,display,using,web,browsers,,see,Section,2.3.1,below.,PANDOC,also,tightly,defines,(see,Annex,A,,Section,A),a,variant,of,Markdown,that,it,would,be,good,to,employ,as,a,standard,,since,PANDOC,can,then,use,files,conforming,to,this,standard,to,produce,output,in,many,different,formats.,Unfortunately,,the,PANDOC,development,seems,to,have,stalled,in,respect,of,LATEX,to,.html,conversion,,whereas,LATEX2HTML,has,had,all,the,necessary,features,for,many,years.,LATEX2HTML,[22],is,packaged,and,freely,available,for,both,linux,and,MacOS.,The,main,ob-,jection,is,that,the,default,style,of,web-page,now,looks,very,dated.,However,the,investigations,in,Section,2.3.2,indicate,that,this,is,a,purely,cosmetic,objection,,and,should,a,‘smarter’,appear-,ance,be,thought,desirable,,easily,met,by,employing,experienced,web,developers,such,as,those,who,produced,the,excalibur.ac.uk,website.,Moreover,,it,is,outweighed,by,the,ease,with,which,webpages,may,be,produced,from,the,existing,NEPTUNE,report,base.,2.3.1,PANDOC,As,with,many,open,source,projects,,a,certain,amount,of,experimentation,is,needed,to,locate,suitable,options,for,PANDOC,,especially,as,it,is,under,active,development,at,the,time,of,writing.,The,following,bash,shell,script,produces,readable,.html,from,a,report,including,all,the,\input,files,with,Version,2.5,,current,on,Ubuntu,as,of,March,2021:,pandoc,$1.tex,--metadata,pagetitle=$1,--toc,\,--number-sections,\,--bibliography,../bib/exc.bib,\,--bibliography,../bib/reac.bib,\,-s,--mathml,--default-image-extension=png,-o,$1.html,The,--verbose,option,is,useful,as,otherwise,only,terse,error,messages,appear.,PANDOC,is,strict,in,its,interpretation,of,LATEX,,so,that,eg.,\mathbf,and,\texttt,need,to,be,used,instead,of,\bf,and,\tt,,and,extended,character,sets,may,cause,PANDOC,to,fail.,\rotatebox,and,\protect,are,not,recognised,and,should,be,stripped,from,the,.tex,file,using,sed,before,processing.,For,the,power,shell,with,PANDOC,Version,2.12,dated,2021,,the,following,produces,readable,.html,from,the,report:,pandoc,rp3.tex,--metadata,pagetitle=rp3,--toc,‘,--number-sections,‘,9,--bibliography,../bib/exc.bib,‘,--bibliography,../bib/reac.bib,‘,--bibliography,../bib/waynes.bib,‘,--bibliography,../bib/new.bib,‘,--bibliography,../bib/active.bib,‘,--bibliography,../bib/mc.bib,‘,-s,--citeproc,--mathml,--default-image-extension=png,-o,rp3.html,However,the,--mathjax,option,needs,to,replace,--mathml,for,mathematics,to,display,correctly,in,the,Microsoft,Edge,browser.,Unfortunately,there,are,still,significant,issues,regarding,the,.html,produced,,eg.,equations,are,not,numbered,,and,it,is,not,easy,to,see,how,this,and,related,omissions,can,be,remedied,without,modi-,fication,of,the,Haskell,code,underlying,PANDOC.,Nonetheless,,the,tool,has,demonstrated,an,ability,to,format,equations,and,produce,bibliographies,that,suggests,that,it,could,become,a,powerful,tool,in,the,production,of,documentation,to,underpin,the,NEPTUNE,software,development.,Consid-,eration,should,be,given,to,making,resource,available,to,ensure,PANDOC,provides,all,necessary,In,the,interim,,however,the,preceding,deficiencies,indicate,facilities,in,an,easy-to-use,wrapper.,that,LATEX2HTML,is,to,be,preferred.,2.3.2,LATEX2HTML,The,package,is,simple,to,use,,in,that,the,following,script,will,produce,readable,webpages,in,a,separate,Linux,directory,,provided,that,rp1.pdf,has,already,been,produced,correctly,in,the,original,directory.,(The,proviso,ensures,that,.aux,and,.bbl,files,have,been,produced,for,the,document.),latex2html,-t,"ExCALIBUR,project,NEPTUNE",-mkdir,-dir,web,-prefix,rp1,rp1,The,key,options,are,-dir,to,set,the,name,of,the,directory,in,which,to,produce,.html,and,supporting,graphics,and,other,files,,and,-prefix,to,distinguish,these,files,from,others,produced,for,different,documents.,Option,-mkdir,saves,a,separate,mkdir,command,,and,option,-t,plays,a,minor,role,describing,the,linkage,of,the,top,level,.html,file,contents,to,lower,levels.,Another,useful,option,is,-split,,which,specifies,the,level,of,LATEX,subdivision,at,which,separate,files,are,produced,,thus,-split,+1,causes,each,full,section,to,occupy,a,separate,.html,file.,(The,default,is,to,divide,the,document,among,many,small,files,corresponding,to,each,subdivision,of,the,text,,down,at,least,to,paragraph.),There,is,a,working,facility,to,link,to,other,local,files,as,described,by,Swan,[23].,The,vintage,of,the,software,is,very,noticeable.,It,was,originally,developed,in,the,1990s,(see,ref,[24]),by,N.,Drakos,,who,no,longer,seems,to,be,active.,There,are,several,attempts,at,docu-,mentation,available,from,around,the,turn,of,the,century,on,the,web,[24,,23,,25],,none,of,which,appears,to,be,entirely,reliable.,Recently,,other,authors,have,taken,the,package,forward,,but,their,documentation,seems,incomplete,[22].,Another,point,also,noticed,is,that,with,the,above,script,,LATEX2HTML,produces,a,file,index.html,identical,to,rp1.html.,The,main,restrictions,discovered,in,an,exploratory,investigation,like,that,conducted,for,PANDOC,,are,that,•,in,figures,,although,according,to,Swan,[23],,\rotatebox,should,work,,it,does,not.,10,•,only,a,restricted,set,of,packages,,mostly,those,current,at,the,turn,of,the,century,,is,recog-,nised,,see,list,in,Annex,B,(Section,B).,•,for,TEXusers,,there,are,problems,with,the,use,of,\def.,The,output,in,file,WARNINGS,typically,notes,an,absence,of,recognition,of,the,helvet,and,fancyhdr,packages.,This,does,not,cause,problems,,apparently,since,neither,package,invokes,special,com-,mands,,and,although,for,other,unrecognised,packages,of,course,error,messages,might,be,ex-,pecte.d,.from,missing,specials,,the,software,commonly,produces,useful,.html,output.,None,of,the,restrictions,above,is,expected,to,be,very,serious,,since,figures,may,be,easily,rotated,,and,LATEX,has,generally,been,very,stable,since,the,turn,of,the,century.,11,Acknowledgement,The,support,of,the,UK,Meteorological,Office,and,Strategic,Priorities,Fund,is,acknowledged.,References,[1],W.,Arter,,E.,Threlfall,,J.,Parker,,and,S.,Pamela.,Report,on,user,frameworks,for,tokamak,multiphysics.,Technical,Report,CD/EXCALIBUR-FMS/0022-M3.1.2,,UKAEA,,2020.,[2],W.,Arter,,L.,Anton,,D.,Samaddar,,and,R.,Akers.,ExCALIBUR,Fusion,Mod-,Technical,Report,CD/EXCALIBUR-FMS/0001,,UKAEA,,elling,System,Science,Plan.,2019.,https://www.metoffice.gov.uk/binaries/content/assets/metofficegovuk/pdf/,research/spf/ukaea-excalibur-fms-scienceplan.pdf.,[3],W.,Arter.,EXCALIBUR,NEPTUNE,Charter.,Technical,Report,CD/EXCALIBUR-FMS/0020,,UKAEA,,2020.,[4],L.,Anton.,NEPTUNE:,Report,on,system,requirements.,Technical,Report,CD/EXCALIBUR-,FMS/0014-1.00-M3.1.1,,UKAEA,,2020.,[5],L.,Anton.,NEPTUNE:,Background,information,and,user,requirements,for,design,patterns.,Technical,Report,CD/EXCALIBUR-FMS/0015-1.00-M3.3.1,,UKAEA,,2020.,[6],W.S.,Smith.,A,Rational,Document,Driven,Design,Process,for,Scientific,Software.,In,J.C.,Carver,,N.P.,Chue,Hong,,and,G.K.,Thiruvathukal,,editors,,Software,Engineering,for,Science,,pages,27–52.,Chapman,and,Hall/CRC,,2017.,[7],I.,Sommerville.,Software,Engineering,,Tenth,Edition.,Pearson,Education,Limited,,Harlow,,2016.,[8],E.,Hewitt.,Semantic,Software,Design:,A,New,Theory,and,Practical,Guide,for,Modern,Archi-,tects.,O’Reilly,Media,,2019.,[9],J.,Drabbe.,ECSS-E-ST-40C,-,Software,(6,March,2009).,Technical,report,,ESA,,2009.,https:,//ecss.nl/standard/ecss-e-st-40c-software-general-requirements/.,[10],J.-Ch.,Sublet,,J.W.,Eastwood,,J.G.,Morgan,,M.R.,Gilbert,,M.,Fleming,,and,W.,Arter.,FISPACT-,II:,An,Advanced,Simulation,System,for,Activation,,Transmutation,and,Material,Modelling.,Nuclear,Data,Sheets,,139:77–137,,2017.,http://dx.doi.org/10.1016/j.nds.2017.01.,002,,website:,https://fispact.ukaea.uk/.,[11],W.,Arter,,E.,Surrey,,and,D.B.,King.,The,SMARDDA,Approach,to,Ray-Tracing,and,Particle,Tracking.,IEEE,Transactions,on,Plasma,Science,,43(9):3323–3331,,2015.,http://dx.doi.,org/10.1109/TPS.2015.2458897.,[12],E.,Hewitt.,Semantic,Software,Design:,A,New,Theory,and,Practical,Guide,for,Modern,Archi-,tects.,O’Reilly,Media,,2019.,12,[13],W.,Arter.,A,Rough,Guilde,to,Software,Development,,July,31,,2007.,Unpublished,note.,[14],D.,Rouson,,J.,Xia,,and,X.,Xu.,Scientific,software,design:,the,object-oriented,way.,Cambridge,University,Press,,2011.,[15],Keywords,for,documentation.,https://www.ietf.org/rfc/rfc2119.txt,,2021.,Accessed:,March,2021.,[16],W.,Arter,,J.,Parker,,and,E.,Threlfall.,Module,Guide.,Technical,Report,CD/EXCALIBUR-,FMS/0032-D3.3,,UKAEA,,2021.,[17],D.,van,Heesch.,doxygen,Manual,for,version,1.9.1.,Technical,report,,www.doxygen.org,,2021.,[18],Axelos,Staff,et,al.,Managing,Successful,Projects,with,PRINCE2,,6th,Edition.,ALEXOS,,2017.,[19],Create,,host,,and,browse,documentation.,https://readthedocs.org,,2021.,Accessed:,March,2021.,[20],Open,source,Python,ecosystem,for,plasma,research,and,education.,https://www.,plasmapy.org,,2020.,Accessed:,August,2020.,[21],a,universal,document,converter.,https://pandoc.org,,2021.,Accessed:,March,2021.,[22],A,utility,that,converts,LaTeX,documents,to,web,pages,in,HTML.,https://www.latex2html.,org,,on,github,as,https://www.github.com/latex2html/latex2html/,,2021.,Accessed:,October,2021.,[23],H.W.,Swan.,The,LaTeX2HTML,translator:,An,Overview.,https://www.ntg.nl/cgi-bin/22.,pdf,,1996.,Accessed:,October,2021.,[24],N.,Drakos,and,R.,Moore.,The,LaTeX2HTML,Translator.,https://mirrors.up.pt/pub/CTAN/,obsolete/support/latex2html/manual.pdf,,1999.,Accessed:,October,2021.,[25],A.,Bridle.,LaTeX2HTML,Authors’,Guide.,Technical,Report,Online,,NRAO,,2001.,Accessed:,October,2021.,A,Annex,A:,Recommended,Markdown,Dialect,The,following,is,an,edited,version,of,the,Pandoc,Cheatsheet,by,David,Sanson,,dated,31,January,2011.,He,remarks,that,it,is,incomplete,and,possibly,incorrect,,and,is,intended,only,for,quick,reference,purposes.,Backslash,Escapes,Except,inside,a,code,block,or,inline,code,,any,punctuation,or,space,character,preceded,by,a,backslash,will,be,treated,literally,,even,if,it,would,normally,indicate,formatting.,Title,Block,%,title,13,%,author(s),(separated,by,semicolons),%,date,Inline,TeX,and,HTML,*,TeX,commands,are,passed,through,to,Markdown,,LaTeX,and,ConTeXt,output;,otherwise,they,are,deleted.,*,HTML,is,passed,through,untouched,but,*,Markdown,inside,HTML,blocks,is,parsed,as,markdown.,Paragraphs,and,line,breaks,*,A,paragraph,is,one,or,more,lines,of,text,separated,by,a,blank,line.,*,A,line,that,ends,with,two,spaces,,or,a,line,that,ends,with,an,escaped,new-line,(a,backslash,followed,by,a,carriage,return),indicates,a,manual,line,break.,Italics,,bold,,superscript,,subscript,,strikeout,*Italics*,and,**bold**,are,indicated,with,asterisks.,To,~~strikeout~~,text,use,double,tildas.,Superscripts,use,carats,,like,so:,2^nd^.,Subscripts,use,single,tildas,,like,so:,H~2~O.,Spaces,inside,subscripts,and,superscripts,must,be,escaped,,e.g.,,H~this\,is\,a\,long\,subscript~.,Inline,TeX,math,and,Inline,Code,Inline,TeX,math,goes,inside,dollar,signs:,$2,+,2$.,Inline,code,goes,between,backticks:,‘echo,’hello’‘.,Links,and,images,<http://example.com>,<foo@bar.com>,[inline,link](http://example.com,"Title"),![inline,image](/path/to/image,,"alt,text"),[reference,link][id],[implicit,reference,link][],![reference,image][id2],[id]:,http://example.com,"Title",[implicit,reference,link]:,http://example.com,[id2]:,/path/to/image,"alt,text",Footnotes,Inline,notes,are,like,this.^[Note,that,inline,notes,cannot,contain,multiple,paragraphs.],Reference,notes,are,like,this.[^id],14,[^id]:,Reference,notes,can,contain,multiple,paragraphs.,Subsequent,paragraphs,must,be,indented.,Citations,Blah,blah,[see,@doe99,,pp.,33-35;,also,@smith04,,ch.,1].,Blah,blah,[@doe99,,pp.,33-35,,38-39,and,*passim*].,Blah,blah,[@smith04;,@doe99].,Smith,says,blah,[-@smith04].,@smith04,says,blah.,@smith04,[p.,33],says,blah.,Headers,Header,1,========,Header,2,--------,#,Header,1,#,##,Header,2,##,Closing,#s,are,optional.,Blank,line,required,before,and,after,each,header.,Lists,Ordered,lists,1.,example,2.,example,A),example,B),example,Unordered,lists,Items,may,be,marked,by,’*’,,’+’,,or,’-’.,+,example,-,example,*,example,Lists,may,be,nested,in,the,usual,way:,+,example,+,example,+,example,Definition,lists,Term,1,~,Definition,1,15,Term,2,~,Definition,2a,~,Definition,2b,Term,1,:,Definition,1,Term,2,:,Definition,2,Second,paragraph,of,definition,2.,Blockquotes,>,blockquote,>>,nested,blockquote,Blank,lines,required,before,and,after,blockquotes.,Left,Tables,Right,Center,Default,------,------,---------,-------,12,123,1,12,12,123,123,1,1,12,123,1,Table:,Demonstration,of,simple,table,syntax.,(For,more,complex,tables,,see,the,pandoc,documentation.),Code,Blocks,Begin,with,three,or,more,tildes;,end,with,at,least,as,many,tildes:,~~~~~~~,{code,here},~~~~~~~,Optionally,,you,can,specify,the,language,of,the,code,block:,~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~,{.haskell,.numberLines},qsort,[],=,[],qsort,(x:xs),=,qsort,(filter,(<,x),xs),++,[x],++,qsort,(filter,(>=,x),xs),~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~,Horizontal,Rules,3,or,more,dashes,or,asterisks,on,a,line,(space,between,okay),---,*,*,*,-,-,-,-,16,B,Annex,B:,Styles,recognised,by,LATEX2HTML,The,packages,supported,may,according,to,Swan’s,description,[23],,be,deduced,from,the,names,of,the,.perl,files,in,directory,$LATEX2HTMLDIR/styles,,where,the,variable,is,set,on,installation,to,a,directory,name,eg.,$LATEX2HTMLDIR=/usr/share.,Users,requiring,other,packages,are,invited,to,write,the,necessary,.perl,scripts,after,studying,those,provided.,Note,that,the,majority,of,packages,supported,were,extant,around,the,turn,of,the,century.,For,descriptions,of,the,packages,that,remain,available,,see,https://ctan.org/pkg.,The,following,packages,are,supported,and,may,be,useful,for,scientific,work,in,English.,abnt,alltt,amsart,amsbook,amsfonts,amsmath,amssymb,amstex,article,book,changebar,colordvi,color,enumerate,epsbox,epsfig,eurosym,floatfig,floatflt,fontenc,frames,getimagesize,graphics,graphicx,harvard,heqn,hthtml,htmllist,html,hyperref,inputenc,justify,17,latexsym,letter,longtable,lyx,makeidx,multicol,natbib,psfrag,report,seminar,SIunits,slides,supertabular,texdefs,texnames,textcomp,verbatimfiles,verbatim,webtex,wrapfig,xspace,18

:pdfembed:`src:_static/CD-EXCALIBUR-FMS0033-1.10-D3.4_DevelopmentPlan.pdf, height:1600, width:1100, align:middle`