From 79607a80270f781d16841956db409d125692fda2 Mon Sep 17 00:00:00 2001 From: VisruthSK <67435125+VisruthSK@users.noreply.github.com> Date: Wed, 3 Dec 2025 11:48:37 -0800 Subject: [PATCH 01/12] Added action and pkgdown config --- .github/workflows/pkgdown.yml | 54 +++++++++++++++++++++++++++ README.md | 2 +- rstan/rstan/_pkgdown.yml | 50 +++++++++++++++++++++++++ rstan/rstan/man/figures/logo.svg | 1 + rstan/rstan/man/figures/stanlogo.png | Bin 11746 -> 0 bytes rstan/rstan/man/rstan.Rd | 2 +- rstan/rstan/man/sbc.Rd | 2 +- rstan/rstan/man/stan.Rd | 2 +- 8 files changed, 109 insertions(+), 4 deletions(-) create mode 100644 .github/workflows/pkgdown.yml create mode 100644 rstan/rstan/_pkgdown.yml create mode 100644 rstan/rstan/man/figures/logo.svg delete mode 100644 rstan/rstan/man/figures/stanlogo.png diff --git a/.github/workflows/pkgdown.yml b/.github/workflows/pkgdown.yml new file mode 100644 index 000000000..bf3e55724 --- /dev/null +++ b/.github/workflows/pkgdown.yml @@ -0,0 +1,54 @@ +# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples +# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help +on: + pull_request: + # build dev site on merged pushes + push: + branches: [main, master] + # build full site on releases + release: + types: [published] + workflow_dispatch: + +name: pkgdown.yaml + +jobs: + pkgdown: + runs-on: ubuntu-latest + # Only restrict concurrency for non-PR jobs + concurrency: + group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }} + cancel-in-progress: true + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + NOT_CRAN: true + permissions: + contents: write + steps: + - uses: actions/checkout@v6 + + - uses: r-lib/actions/setup-pandoc@v2 + + - uses: r-lib/actions/setup-r@v2 + with: + use-public-rspm: true + + - uses: r-lib/actions/setup-r-dependencies@v2 + with: + extra-packages: any::pkgdown, local::., stan-dev/pkgdown-config + + - name: Build site + run: | + pkgdown::build_site_github_pages( + lazy = FALSE, # change to TRUE if runner times out. + run_dont_run = TRUE, + new_process = TRUE + ) + shell: Rscript {0} + + - name: Deploy to GitHub pages 🚀 + uses: JamesIves/github-pages-deploy-action@v4 + with: + clean: false + branch: gh-pages + folder: docs diff --git a/README.md b/README.md index 4ec3b8a05..7f1344161 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ -# RStan +# RStan [![CRAN\_Status\_Badge](https://www.r-pkg.org/badges/version/rstan?color=blue)](https://cran.r-project.org/package=rstan) diff --git a/rstan/rstan/_pkgdown.yml b/rstan/rstan/_pkgdown.yml new file mode 100644 index 000000000..12f522d11 --- /dev/null +++ b/rstan/rstan/_pkgdown.yml @@ -0,0 +1,50 @@ +url: https://mc-stan.org/rstan + +destination: "../.." + +development: + mode: auto + +template: + package: pkgdownconfig + +navbar: + title: "rstan" + + structure: + left: [home, vignettes, functions, news, pkgs, stan] + right: [search, bluesky, forum, github, lightswitch] + + components: + pkgs: + text: Other Packages + menu: + - text: bayesplot + href: https://mc-stan.org/bayesplot + - text: cmdstanr + href: https://mc-stan.org/cmdstanr + - text: loo + href: https://mc-stan.org/loo + - text: posterior + href: https://mc-stan.org/posterior + - text: projpred + href: https://mc-stan.org/projpred + - text: rstanarm + href: https://mc-stan.org/rstanarm + - text: rstantools + href: https://mc-stan.org/rstantools + - text: shinystan + href: https://mc-stan.org/shinystan + +articles: + - title: "Using the RStan package" + desc: > + These vignettes provide an introduction to fitting a model in + RStan, extracting the important contents from fitted model objects, + including external C++ code in a Stan program, and performing simulation + based calibration. + contents: + - rstan + - stanfit_objects + - external + - SBC diff --git a/rstan/rstan/man/figures/logo.svg b/rstan/rstan/man/figures/logo.svg new file mode 100644 index 000000000..496f04025 --- /dev/null +++ b/rstan/rstan/man/figures/logo.svg @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/rstan/rstan/man/figures/stanlogo.png b/rstan/rstan/man/figures/stanlogo.png deleted file mode 100644 index 3fa976a2846493c4aeb79a0825deba70276a5bc0..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 11746 zcmX9^1ys}D7l)0IR*^2H8-&rNbc<5bAl=GGcmS92^`n4Rz%gI5@aEx1T!%z%Ori<-P-7c)p4n z26uoz=pDOv!2d*E>L$Lx{E6ESt|E745bz_NpUO)=eNP9!KpP)>oWQ_9L1zzFUt1e5 zdqGbh$INY6dK{dGI2y`N4T7?^=7Q7B4Pn=NJEes(L?3Hn?xOf%Zv~#Ji)`|K7UnfR zlmO+ku5*(wMWZ%I*HN94+g*~pC>Xz>D7pC)QcymB?T*&{JKuCb?EFMTd7~D;&aS*Y zMzxw{<_sIx4gQ2F42>pe6t}GZVD}ts!p{1_>!}lw%ACEpqOeL>Wl}2^_t_<>gaYNl zDO^@cM)E9zEK;{6sdzURxm_8|D@^lnH`P#Z0Xgr0I8}!AGmJ%F5C4$2-K7z38ZJ$Y zczahMZH8ou1H*gm8Zi$@Fug~;+4M|4ngaz28w;eRV@Yv{)oLJU!BcA~^ze-EUc`lMMG#U5jE$+R1c zG0a(dXGPr@wkCrT&_0iyW;H+vJj{sbpgd*VK2}NWWX5eLG%u;tx-NytX&xJ1gLj>0 z!{%9SgKqD#bEbnXNwyL8X;{f5xgjtXLmlU5Zt>Fq z!4s?P#p)5->(O4PzFLXXj(2Gu^R_^(Fe9lKFBE5iP>arGuelIeO9FfLR{Zr~;KzWXkqRZdhzT(EZ_Y6H2zgEy6*j6p63Lh1K*mbB z8D~}~I~7QsNN+)yb#MCg@xs$-xTY^CDfGJn=#nplI|JDPN2kF&qs0Y*6A2n1mL6na z?qCQ}T+$!>k_f{o-io*X0jPW)nT=bP-`fH0fa9=|tne53?f6jDo?&<;M&=10a2T9j zS8J;U6J>h4$6jQ+p_pg9{R8^W@vI`93K*mAdbqlD9|0!BT;p0ExkveW3CWVOD%|IH z8G|luuX|UpY?G9P=K)+ttkg3zeP{Cf8Pj6J}ock$FJqLI+2m8zA2I z;_dXz5tOc>koknPDDmLrhPz_At6HKWovEm`Q<*Twdl}*WXcljdU>&C=s+2DFRT^V3&DCZL~z~1(=)OxL*IY;+c zaCdGsK}$0G3+=QoBu!X%WLE}BjufxLT|FOUO?nCD|CX}MqR5~C7?PW+gC;=94MXwo zY;n<;3YBd4lWex?w_RwTva>4Z%RA;|ZaXrub|bt5s>u`UcQMD~dxdlv7)eYAOd!lL zv7a0K#>N^FoUpyN&B$Z{ur`l-$;cfN&zkKi1?C90a9W~~!zL1}O^(EA?>@%N{F9V$ zj{gOHwz{O0xvNh1XVioWsyR5tkdV6E`ZcbQ6G~N7J>CWW#+caLm~ttAIUG z6}wQ6PD^>tfjXf}3vgQN@LU|v{cM%ia!_N^1AC_>4q%7?Y2gf7z|lQmQfyu8tPHRs zS8kT)85lRZ6>2h?D-8RwC^R0nksRyC6@NM=UXBHn-Nn?N7ur|%R|OM@E<}Na{Zn>%cl*Z8J!aE} zT9#~a+QMWfcOg^`7iJLvA^Pc{(j8&eBbUCB@9vfh6M=V1r$R7kX#70*&M}iJyN-Y{ za1-Q7FSB(m{75y1pp1<-5i>C@l^8)ZacN)Z;D|IN+c{vqg^kQ!udZmeA&=zlE8-2^($K;PS~oP_ z6)~p@L?3iSi(78W#Hp9>$;sW^U| z9{7};b!5F&dx(v)AKwGaDRDJmU!#Ja%7c5JFew*UK-z#ay5Y_eZH|sfq;_6Y7^g~{ z0ZTlf+Cv?&#G`3uUiQIlI}cg6%1YS)HL76-pO3NeAvVZo#eTU$3GX=v>hJ--2hX}E z9U%6jLA%_$eZ$?xw`6&IbfDD$d{Wu(+bj;@Bg9nZ-hCE1tW-aHMo5;~`}y#~sM z+~W$1x!c#Qsy(ETKrHHxEfH2RRVrf}SRTyn_<~I>UMtUo4;?cpDrX_p5V^`x8AW^s z>8zC;^?+^FFzqHdx8>}z?=mkuQno9Bs3BOu4eEPGwH0_-_osv4x3U!!=^R^r{1d&nmZV=pr;=^^>O6knRF8sRf!Hh zhcip){t(4pzH2Gu-o!0?1$HiSC|c~It`eX4-z^DHON_Xs;ReZ=%m`G1w;$O`dN~|; zClSf6zwtL##24nwY^wv3Cx;e|)06}kWXM|h@HE?t2q@ffH=jU0{T^fI(ngV)YKzd{ zfK(Dj40pS_o~?$cBHjS97cj)Mv@5-H)3u8T*ZK9;M1KS678NSJZR~QkinvuJ>F&cC zD*;d5Oq48g&kP!KcTM8kSO~MnpK0uvw9XK2OSJgB zrNJSu?@ynqEIj(2+l!a%Jqj==Ni#X(SVbxwN%UzIRgCTXvEn$q#6P0fnccAecIV*; zVSkaNjU{ZF^@V#YO>kmWbFOsq0bb0V!nHS%@;kV8^3eaU^ ziSW!byNK*bzeAM7n!<0x%SmQQf|tl9A;z7|J&i^w03YQz{OL0yBhsKCkos+XxZ_3QG1jfvOFxIo{M|QbQ-!sL~hr`{4 zU)!Bz*#`3UfV&;atF4f9Z@HcH!7^x;+b3zreB?y~Zalb(ej~P9A2FSo5nqpf78cVR zVTT_|4qlODk-Q@?+`F3n%|X+*e=WH7?3ix0D!6n=LXlwt`n^4lzX^(z0Iy6c42%)1ui0eU>}p2$|FUt?eA9>^aZNHU?f_fWNq5C~WDx`0s-QZF74zK6{0 zB@+4M3rxqG0#}~=2^W3g-}&Kgz;XX}Nz(sLK^U)oee%SQr2!eet@q;C6Vkh)iZDr!=H4oCe?fO1pVOn7^P7S?yGoYBq!b#@u8ZOjB zrI=5r)jNb2Q}gX|XMF#C32hrBbD!O#$cxn$j>*&C3d30v`=lQB6Wx#ppP;yj`mKtn zR*W*KCf)@vJQ_)rO+kAp15qWy8-GSJr)~;eyX6ffH#lq; z^uzFr0yBZFzm#0A|vj134?KqKi5H zmLWtJ+K({z?+MYBnXf|FS~j6|d7t$)hzN@zy`SB1MJGTgRH950N;0C(;`?M)9gTcF z!Scw#$*7G3@p}E<+#$oJyz&I5r2X0FD?C#MXeNcA1I#nhqSD|nL@kb=(TQ$#^|z@X zj4_q{hFtrb=R~36#w*QL@IB*Yq58`xd+Y$21cGUle=r8`% zcSj4YxQzx%RQxn-YA8>j(+Kt`-~Y5p>to>?Z5M*IrqWFkL+SM$g!_0JZ$IS zY`y<$F2gkAGi;gc+@Bu7Ka9RwDh&dx)8cOPVYzH|6ll+1OHRag|c7ad~7 zEdmQh>Ajvf=ze`UW$y1${Z&A&fP^=AHI+o$Fj&)Zh6lOFODjE+6-8WUq)^!?tT5j; z8mBQ1b#)Iss&v%}A(4htWBK@pj3+CTu;D(iN`st{3~G?^x8YkQiyLATT(4H21rA8o z3{A2qq?HR+G^}~MPzSME{q2KB$pMm6T;a*Kw=zJKHiewFl`eS)OvKraGlb69ovpW5 zdR2;$Q3uId{e2Hi<_kU+qDlX<|7lRT<%TdSQJ#lVBoF_y5KZ9gi-V^1rlFPcr^TOE zybLj4p;0}_iP&~TgVqJZSBTh17K#I1zjXGknkw*ma^3tWH&?(w^x*9e-WqmoBaGC|~jJjQW5Xt!uO%+jUa1h?qdoEl&%0X`mYQ+TBd@_KW26NrLlDT=@Yjm^J3Ed)9=m z(6qdmEBG^Dqv!16BL6t`UISfNx$wcpv4(-Xe4LF_dFv$2TOPhBwqi->RZwxqd<4w3B~W zy^cBow}bGsadEI%!L;OZcZIq`q1D1&T{V}2`sb$kz~gdrYe%^JkKAk=;yyOBlVirB zY(T=3Idfu5vs@%8L!ZKm`*27q`VCE{{`4$A%^wmFJO8wbAh)ivp0EgC$>~DIriEun zP-|f;dyVH;WVFY(41ise9Md$J$&Ly&8U%1=PIZ5)3bvNNJVy}MiOD9H?`v0S2IloM z_bn#Imn0KpT0R+)WNC~cUP<}2pHh7`_(n#*Ziw86)3K!@jz5)!Y$U-hn;d zP64fh6d^+>VdCRkt;snZHW_nNcPX;#0Hdbn+&dk=C%^14ipWQ*<&Gx*F0KmGBo27t z96y?*7>w8}SiEQwVPQx{Qhp_Zj&^{~0HK3Ywp?=G=Aq zVmgDS**lg(wK6xB6k*a+^PO^7H-!#~0+4ISFQZeWER2 z4t~@XfMgNXUiN`Pfizl&WwLd;Yys+}&wU2;NmMfmN3u#7z3fVR z=XnRUd2vsuek#wk$>vml_I6w?fwz2=pmFE^n9XO#J$HQKJq7i!yhKq?5YX#&MN!iQT>hQ_|#kp_QUm6Zh(U# z=cn=W48@iq_$K}3Y6^GQvoRdDP5Cbu>2xMU1PB@R1OYqyY$hr*bk4Yak31N6YXj0U@@+<%P`VzB6 z!x}riv$*CBld|W(t#Kl0ItTBGmg??dpksx#B{z^+80EmJK?6Ccb}+wAx! z0*|~yzbfYjm?A~tkW70L*Oz*{KCe6_F49Q+))0=I0>6w=W#tJg!8(&OKzVSgxzYxR zJ@4D*7!3r4O;$3b7~m^Kuij@u*4@-Lh@C>VRd6SZ&8-8P&{hXj)HFXUMy)<;o8(m2 za2l_av`4w5I!IyfD$Bg&P!V zxPNO`oOEIGiPisbt(pGW+up{qsKPJXysmP*0|7`Kv7QJ(*P1Fut9-H<<@*Nh5#5~G z`NXqE{9ieZ?b~y7{%9gsO0rkH)e`YjWD8#;uAC7+Tjc|yqW_nmn3srZ>+nd!tjbqm zxG%9XQDfD2Hck5K965$mZQuJE=JXo}=}vS{&nH2n1YIScJR^3(-ylI-g%yAF)2WS~ z>Pr@tp#7EHcgL@?L8!ixkl4OCX~B5UrSj|e{S1uCA@@T3$>L{FmTzMQ%|2>R*9zx+msNOH9_*1wphryv&9YWDZN$jD)MY-#vJtm}!Yc(@O9X4_ z+5$<4brU+a&vKY*nq>Mepnkwi{_QSy(|H$^{&?t|?mRABX^z2}_4Qt~d!!MwRh0js z1@c8Eir!&ttx3Jh-I)xC*PAgj+8xkghmg`aQ`@N@f$s(jM?Q_$sN5WU^x{fAu>yw~ z;Y-^{|0uKJMb}>Ew$`rPc_`93iq>UTd{6p2c^3YF3%^WyvURIm%Cfpr4PL{K+_St= zpnJ{N2}f%T3;^kE-*`-*toY-#R0#dinfxmy{_*$kxtA-(zw__S@0y+2v!@Vih%pfVRA`@1_;CJ(c?O? zY%lT!T_^LC91}Ei?$?NzL=7#%SP3R|X5jQTY`bYddhA2;)M<&=OJ9`oeL>zGK%u?{ zrM)*ZlJC2;R0672dw)*4s){u_d;qrg@^xC82bQe0mosEOP%U^wjCwxddfptQ1w!6tv6Lh~Q0V`bQbNlyM4&Gw0-!b=- zUH~KBjnX_2#MoPFb}hYw{2qHsk!qG*zOU>DGugd*Z%>GD)3mS7wU!W~tNMA%i{;X29J=%Ig|~D~(l}qQ^#RJ#ZH(l^@dFl*|_=1V_q(57jPj4Icij`8kduw70UXc_$v|7eL zVEi(t8u?uyYi@jY!FBUnqh}T*?Os)r25$~wz#aG2KF_mvY2JzqC!ZHc@8JZLtV(_{ zSpGimaeM+D_DmCdvn6)?Pbp~*>1KjnK%j~#g!m6V z?L!j^uA79tcw@sEuM#z-E)jPWn|YDl2Kn)jl}RW@MsoSIT@X;$R9UwQa5)!w8H2os z)(_N9?FDee##d~w7FRV7IIZnNOq6SFCxFPrNf@nd_aiJxjOK_=2Ah=gCxP^)z86mv zCQ+QBAN>-nY#Y{@UYNm1b+Q4Wd~c^go^H`c$vKnKExqUSK`a)AuP}#NM*?E?WL)_r zk7L^&H-??)N{C?akfpH{)Z&R#cc6j=uYkA?1Ari)ulVbO zU6nbxLB$fXZVeWwCLvn?BPh^q1Zo?j>g=rB-Yq9oT5<%h+eM78{s9t}kfMEs>c!*A z%dlc23tnG#Qf)bbqJD)BO{A$Q-w!i0JBXY(^bdQ4+&d?N=2C~#Z+zK<{th}(arz+m zLLv5|1?lOuRLA)u9e6b3Th5eNg9=O#d2kjS<|@8;^#%(HexUw+Jlvfyv3td$A@h;c z`yl9z6=yBjI8p-Fda0elJixWbCNnJu=%T9`hXzLQKq`H%LhS`*Uv!3 zxP&p{*Gk#dN4STl8LI2{AQHDFQ@I_Q42-VzYqC7$+QoaAg>bDTwVp8!Af-39c4({S z$Ug^KO36JJKb9=yb^_^mbrKV2$+N)b^3zgrV$yU}4*76b+>!-ltpi02AG(0(b*_4G zGqog8JxPy|9s65B&{icm1nS7`mC*jjojTlIo`J^KPb4?Qe+}-ZaEF@b69YB7=S~h2 zPHFLn-}}C5`xOxFy3bachYZ%*4e(+d(Pv^F38ZIurM1zf6MgQHjePZ9*AjB#7rART^u zWZGU@l*swSF2W3^5k_A;w-KL~s(-*aW{l_nGpng}YlN18V!bAK*{t$^{$-_H zh9#U2{{EYTBNzs)O8}4q`nOnss-sL-!GYoKlwQ0A-0S@DiMx9kXG}5b`3hxDUEK2A z6O4><%!R7ljrurLhZ2Y_53HqX+y{hMM}iD76u`8UN|7=~pg7$F^ZeXn0vQ=aGiQbt z{CK&ZkwZCsy3&iMfOB1#GjY!uhh#Qd=G|Wjpm!TICy* zparholl^bRVuIv-!4kRo^J{6O_oht$DsYDgPo<{ckB|<5TcX70^@d`{#76J{f5t1) zse+kMU9a>DQ)E?W$h?q9r_it%opS{t9rw?|_AYG$ADkWqaL>hH(o<}- z__aB`(5G>A%Gpugg=pRMR6n_IPoB#!%JeI%0RHJc+A&;7uBWez86)G|_R@t-2Y6gt z;kAF7Cebt!u>Z`>a>!H!KpL9E195Xft3mO}{tLj3b1)T34RF@&oEvS@auMP+@us+o zdjrT#e!<2CX!-Mc5$ry;j>bxY!q63v#;ih91P;(bD~uLhXZH>9N~ni>F$@}q4CV!um_YcCFC(3ouG7*`@mYkk<>+SMJ{d25*x&xdBE71z&$yoq(}%Ii_9Xsp z<3R4MICnTHY2IFkYOgmn>}DZeT-jFdGXoS>q@M96nK3QAWq96x56){gmy!qXQf>8O zE5csM!)4|yo>gr^`7|`|qpB#2=5~Ju-o$D2wRIL3V@MqT#n}K$+C-l}eEh zNM@rlebj(P++G%!VIt8grf9wx)N-N2CMGF^^j@D3xe#lHG=7s~bP4I2S4P<5drXH3 zc-(UYx}Bv!?g!pIK|L>|empbr!rH@Wsa>`0sgl+$+ZV6{hI7u5I~%Z@u9Rf};X!i& zPj0t+iq%2$pv)K;f}1oEOQ_-Q3Gsb0#B+qyEb%&wER3zxm@cqly1uWcvNGhQryNkS zjcOUccEG6nVLZ9c{GFEc>907+gl=^o1Cq#7_+0701N4oRfMQF|L4n|z+QnUh4?YSV z?+c!egD)VqjjH@Auoq?yAQDvi9yz|d_@L{E%NV0skd%O6t*LNq$4xq zL!g>80l-1VeRHA#gbAA$|8DcLQbKbIP|M7n@0U3I`eX6p$-9d#A<9N_6wD4nHy!jI zD@&HlD0b>Xpy|ULQt*K^2rsbKKwm7ZfavZmQUlj|qo^bJf@g_YWkvzf+D6$3!Ueh$ zV4$MSZbir#zrB~5c!cw2Y3ZYjP$94c!-TS3w$qQ**lz7~$2Z-Pde#MagG^YGEd7-d z@6tj0aJRzIUiZ8vrQiLLhgW7W>c2&^zvQsav=(Wf9$bnb_gbKBO*=E)*F=HF-Ge#4 z5HptT*54|qd-iHsqEZ0ZLk6t&w@QZ@pE0~jOLL2QNw?>ud*eUJ?V-gil^{Jzs0ees zOQ59qE9U^BY!_id`f0fwX7ZX+gK!O(oXGt$eCY1{f0rs49RtOxPr1yB^
sxfxU zy!4r0z9x-hwbD6uARCb_1~5D5z;{MG13aiM*6Fi$OlRN%KWKXc$rA{GkG$@J^LyD~ z?rqUY6(~vMUTM41lh{wUDv|Rxb8R@uwg)kzsg_x1=OmcCUj=t8v(!Zan^S-r4(T;( zorr240$`^0$R{Kzw`=mf^rwyHGEYds7aY}O?w4_ZNoX9aZ&O?jd`rO)N^;=>qIMuFgFJIih23B zSY~SLax5g|;Y+2BU-jtO$>!k1JN z31qF04W~FIe@+625YicZ>?)q*RZl#e1+`XLJj4Ix=1k7ld!1zP^aEsE3H=;s)tr*Q zDA#_V{Nm#Qt@Mxi+_=k=Sme7H*wS>9a2{C8R_`f!&a3i=DwpRZ9tY2|oa!B|Bxh zASJ0v7wHJreSwC+*f6f>EO4jsRe2B+nA<&T}5S z^AMi;e&nq&bGEnGHk~wUQVtb*56E$knF{EnU5=pqK$?Q1_C-L0)j0%DQkE}@2*@^p zhV4eU1m-yYy?WR+gCy{l_E~s};1L}?_zQ%rd#50}ix?$#{5CX~5<@Ol<{d@Ge+>8F z(BR5k0JJ$%|9ZS{oe8{aB_j8e*c~dj9faZo@KVm;4g&H)9~;GPHAJKe=jol@ohOZe zNCX_%w*NXR95NM9l|TsJYkNK1K3l&y1$JUhT`XD>xCz>H=sP@wqLwMTp%@T={xU^# zprKT&di4JxzckPZu*%#0Ynd_md2q2HT9~FUX(CZT*OhB13Lv0UODnm4zw6(sU+*N%axRwp4NjKzRxJLfbW0F;wzffi%5c>B~XCM|JQ5&*kU z)(GwT&obR(-SUw0qW0J+B=*gMj8p&!0uywgcf$BxXSFn3AckEccOGu37MjEWNS|*h zSW7^Kaigy=U3qZ-X=6ABD)Auxk%&pojv_O}4;FAhxkiaer>R!paX9-Kgj#JK_BD><9Q4(iZ}fQ$kIL0Fs)68DOZ5&^}+sV_i|Mg+Yhc`toa zDjqWAGTS*p1L&jY|Cr4mDx8zVL43Qqn3u?fI?5xEF=o)UjT7lT<;zSLsaXdHj!6`_ zbzoo(!%DvBFayA!<-^_0p%pqMkQo2~JB9j6 z8f4>n?i^5Jw}X9({*88p<%d^79oD^E!xeBRz!Ct4au~qP-A!>&W#^F2h259C4`2_9 z#2cAW_aqRl%m6<3EAv4XF7H5`X3;(gE%$G>Z~>@;i?EQftN?JpcL9jI z;nIz6w_HHLRZW6F8`J|iRE?W60)iK;-GCdPYdqaD>9GOu*f<(0y2@3G))D^$DgVN^ diff --git a/rstan/rstan/man/rstan.Rd b/rstan/rstan/man/rstan.Rd index 9e5ffbf53..2501108ee 100644 --- a/rstan/rstan/man/rstan.Rd +++ b/rstan/rstan/man/rstan.Rd @@ -6,7 +6,7 @@ \title{RStan --- the \R interface to Stan} \description{ \if{html}{ - \figure{stanlogo.png}{options: width="50" alt="mc-stan.org"} + \figure{logo.svg}{options: width="50" alt="mc-stan.org"} \emph{Stan Development Team} } diff --git a/rstan/rstan/man/sbc.Rd b/rstan/rstan/man/sbc.Rd index aecaad55d..4cddacfb7 100644 --- a/rstan/rstan/man/sbc.Rd +++ b/rstan/rstan/man/sbc.Rd @@ -4,7 +4,7 @@ \alias{plot.sbc} \title{Simulation Based Calibration (sbc)} \description{ -\if{html}{\figure{stanlogo.png}{options: width="25" alt="https://mc-stan.org/about/logo/"}} +\if{html}{\figure{logo.svg}{options: width="25" alt="https://mc-stan.org/about/logo/"}} Check whether a model is well-calibrated with respect to the prior distribution and hence possibly amenable to obtaining a posterior distribution conditional on observed data. diff --git a/rstan/rstan/man/stan.Rd b/rstan/rstan/man/stan.Rd index b30ba009e..dd1e72656 100644 --- a/rstan/rstan/man/stan.Rd +++ b/rstan/rstan/man/stan.Rd @@ -2,7 +2,7 @@ \alias{stan} \title{Fit a model with Stan} \description{ -\if{html}{\figure{stanlogo.png}{options: width="25" alt="https://mc-stan.org/about/logo/"}} +\if{html}{\figure{logo.svg}{options: width="25" alt="https://mc-stan.org/about/logo/"}} Fit a model defined in the Stan modeling language and return the fitted result as an instance of \code{stanfit}. } From 7ad28fae7f01ee1808ab697deeaf477c6b8b1012 Mon Sep 17 00:00:00 2001 From: VisruthSK <67435125+VisruthSK@users.noreply.github.com> Date: Wed, 3 Dec 2025 11:49:40 -0800 Subject: [PATCH 02/12] Don't autobuild on PRs --- .github/workflows/pkgdown.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/pkgdown.yml b/.github/workflows/pkgdown.yml index bf3e55724..17231da0f 100644 --- a/.github/workflows/pkgdown.yml +++ b/.github/workflows/pkgdown.yml @@ -1,7 +1,6 @@ # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help on: - pull_request: # build dev site on merged pushes push: branches: [main, master] From c3787be776aa2b8166794e4ad1d92cbf2fa831d4 Mon Sep 17 00:00:00 2001 From: VisruthSK <67435125+VisruthSK@users.noreply.github.com> Date: Wed, 3 Dec 2025 13:36:40 -0800 Subject: [PATCH 03/12] Specified working directory in pkgdown GHA --- .github/workflows/pkgdown.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/pkgdown.yml b/.github/workflows/pkgdown.yml index 17231da0f..b92ef9039 100644 --- a/.github/workflows/pkgdown.yml +++ b/.github/workflows/pkgdown.yml @@ -35,6 +35,7 @@ jobs: - uses: r-lib/actions/setup-r-dependencies@v2 with: extra-packages: any::pkgdown, local::., stan-dev/pkgdown-config + working-directory: ./rstan/rstan - name: Build site run: | @@ -44,10 +45,11 @@ jobs: new_process = TRUE ) shell: Rscript {0} + working-directory: ./rstan/rstan - name: Deploy to GitHub pages 🚀 uses: JamesIves/github-pages-deploy-action@v4 with: clean: false branch: gh-pages - folder: docs + folder: rstan/rstan/docs From 2ceb423e79bf694bfff2227b39126dcf34ae637f Mon Sep 17 00:00:00 2001 From: VisruthSK <67435125+VisruthSK@users.noreply.github.com> Date: Wed, 3 Dec 2025 13:41:04 -0800 Subject: [PATCH 04/12] Fixed action --- .github/workflows/pkgdown.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pkgdown.yml b/.github/workflows/pkgdown.yml index b92ef9039..9f4931977 100644 --- a/.github/workflows/pkgdown.yml +++ b/.github/workflows/pkgdown.yml @@ -35,7 +35,7 @@ jobs: - uses: r-lib/actions/setup-r-dependencies@v2 with: extra-packages: any::pkgdown, local::., stan-dev/pkgdown-config - working-directory: ./rstan/rstan + working-directory: ./rstan/rstan - name: Build site run: | From 4597a5a8b679979c818e1f6ed36f1e42175b17cd Mon Sep 17 00:00:00 2001 From: VisruthSK <67435125+VisruthSK@users.noreply.github.com> Date: Wed, 3 Dec 2025 13:48:12 -0800 Subject: [PATCH 05/12] Trying to get action to run --- .github/workflows/pkgdown.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/pkgdown.yml b/.github/workflows/pkgdown.yml index 9f4931977..aa82be4da 100644 --- a/.github/workflows/pkgdown.yml +++ b/.github/workflows/pkgdown.yml @@ -1,6 +1,7 @@ # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help on: + pull_request: # build dev site on merged pushes push: branches: [main, master] From 8c1b0366fdd933d6c16a43d5ff400cac6ff448a1 Mon Sep 17 00:00:00 2001 From: VisruthSK <67435125+VisruthSK@users.noreply.github.com> Date: Wed, 3 Dec 2025 14:26:45 -0800 Subject: [PATCH 06/12] Added Stan r-universe repo to GHA --- .github/workflows/pkgdown.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/pkgdown.yml b/.github/workflows/pkgdown.yml index aa82be4da..73f0ba08e 100644 --- a/.github/workflows/pkgdown.yml +++ b/.github/workflows/pkgdown.yml @@ -32,6 +32,7 @@ jobs: - uses: r-lib/actions/setup-r@v2 with: use-public-rspm: true + extra-repositories: 'https://stan-dev.r-universe.dev' - uses: r-lib/actions/setup-r-dependencies@v2 with: From a173d1ba967602d7c5320f7259dbdf35ded5bb91 Mon Sep 17 00:00:00 2001 From: VisruthSK <67435125+VisruthSK@users.noreply.github.com> Date: Wed, 3 Dec 2025 16:33:20 -0800 Subject: [PATCH 07/12] Fixed article name and branch --- .github/workflows/pkgdown.yml | 2 +- rstan/rstan/_pkgdown.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/pkgdown.yml b/.github/workflows/pkgdown.yml index 73f0ba08e..2ac5fe80a 100644 --- a/.github/workflows/pkgdown.yml +++ b/.github/workflows/pkgdown.yml @@ -4,7 +4,7 @@ on: pull_request: # build dev site on merged pushes push: - branches: [main, master] + branches: [develop] # build full site on releases release: types: [published] diff --git a/rstan/rstan/_pkgdown.yml b/rstan/rstan/_pkgdown.yml index 12f522d11..c353ef722 100644 --- a/rstan/rstan/_pkgdown.yml +++ b/rstan/rstan/_pkgdown.yml @@ -45,6 +45,6 @@ articles: based calibration. contents: - rstan - - stanfit_objects + - stanfit-objects - external - SBC From bf5be6d486c3b710ea24a252b07f79c2b5fef28a Mon Sep 17 00:00:00 2001 From: VisruthSK <67435125+VisruthSK@users.noreply.github.com> Date: Wed, 3 Dec 2025 18:23:45 -0800 Subject: [PATCH 08/12] Copy README to R package dir in GHA. Added to gitignore too. --- .github/workflows/pkgdown.yml | 3 +++ rstan/.gitignore | 2 ++ 2 files changed, 5 insertions(+) diff --git a/.github/workflows/pkgdown.yml b/.github/workflows/pkgdown.yml index 2ac5fe80a..550270576 100644 --- a/.github/workflows/pkgdown.yml +++ b/.github/workflows/pkgdown.yml @@ -39,6 +39,9 @@ jobs: extra-packages: any::pkgdown, local::., stan-dev/pkgdown-config working-directory: ./rstan/rstan + - name: Copy root README into package dir + run: cp ./README.md ./rstan/rstan/README.md + - name: Build site run: | pkgdown::build_site_github_pages( diff --git a/rstan/.gitignore b/rstan/.gitignore index 844e32077..32bf230e4 100644 --- a/rstan/.gitignore +++ b/rstan/.gitignore @@ -20,3 +20,5 @@ tests/cpp/* R_Makevars rstan.Rcheck/ + +/rstan/README.md From ac7bafe52b3f2b77d892c6507ddc7617b12af682 Mon Sep 17 00:00:00 2001 From: jgabry Date: Thu, 4 Dec 2025 17:49:28 -0700 Subject: [PATCH 09/12] fix old syntax in stan.Rd --- rstan/rstan/man/stan.Rd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/rstan/rstan/man/stan.Rd b/rstan/rstan/man/stan.Rd index dd1e72656..f8b542974 100644 --- a/rstan/rstan/man/stan.Rd +++ b/rstan/rstan/man/stan.Rd @@ -459,7 +459,7 @@ excode <- ' parameters { real mu; real sigma; - vector[2] z[3]; + array[3] vector[2] z; real alpha; } model { From f017795dc32fa3669b074a57c54a48c94a284e9d Mon Sep 17 00:00:00 2001 From: Visruth <67435125+VisruthSK@users.noreply.github.com> Date: Thu, 4 Dec 2025 17:36:12 -0800 Subject: [PATCH 10/12] Clean gh-pages branch on builds --- .github/workflows/pkgdown.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pkgdown.yml b/.github/workflows/pkgdown.yml index 550270576..12a961903 100644 --- a/.github/workflows/pkgdown.yml +++ b/.github/workflows/pkgdown.yml @@ -55,6 +55,6 @@ jobs: - name: Deploy to GitHub pages 🚀 uses: JamesIves/github-pages-deploy-action@v4 with: - clean: false + clean: true branch: gh-pages folder: rstan/rstan/docs From 352122bdff83d31637a24815bf9625bc98002b4c Mon Sep 17 00:00:00 2001 From: VisruthSK <67435125+VisruthSK@users.noreply.github.com> Date: Fri, 5 Dec 2025 15:52:24 -0800 Subject: [PATCH 11/12] Revert "Clean gh-pages branch on builds" This reverts commit f017795dc32fa3669b074a57c54a48c94a284e9d. --- .github/workflows/pkgdown.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pkgdown.yml b/.github/workflows/pkgdown.yml index 12a961903..550270576 100644 --- a/.github/workflows/pkgdown.yml +++ b/.github/workflows/pkgdown.yml @@ -55,6 +55,6 @@ jobs: - name: Deploy to GitHub pages 🚀 uses: JamesIves/github-pages-deploy-action@v4 with: - clean: true + clean: false branch: gh-pages folder: rstan/rstan/docs From e8867436f5f56dc5bb8567b69209e57d7fdff46b Mon Sep 17 00:00:00 2001 From: Visruth <67435125+VisruthSK@users.noreply.github.com> Date: Tue, 9 Dec 2025 08:02:07 -0800 Subject: [PATCH 12/12] Don't build on PRs --- .github/workflows/pkgdown.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/pkgdown.yml b/.github/workflows/pkgdown.yml index 550270576..63df44654 100644 --- a/.github/workflows/pkgdown.yml +++ b/.github/workflows/pkgdown.yml @@ -1,7 +1,6 @@ # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help on: - pull_request: # build dev site on merged pushes push: branches: [develop]