From 595f0548fb67e4727f033981579255ca6bdafb60 Mon Sep 17 00:00:00 2001 From: Palma-Bifani Date: Sat, 3 Aug 2024 18:19:56 +0200 Subject: [PATCH] PPB: rtd updates --- ForMoSA/__init__.py | 2 +- docs/_build/doctrees/environment.pickle | Bin 290476 -> 291362 bytes docs/_build/doctrees/index.doctree | Bin 6177 -> 7790 bytes docs/_build/html/_sources/index.rst.txt | 25 +++++++++++++++++++----- docs/_build/html/index.html | 21 +++++++++++++------- docs/_build/html/searchindex.js | 2 +- docs/index.rst | 25 +++++++++++++++++++----- setup.py | 19 +++++++++++++++--- 8 files changed, 72 insertions(+), 22 deletions(-) diff --git a/ForMoSA/__init__.py b/ForMoSA/__init__.py index fd9425a..519596c 100644 --- a/ForMoSA/__init__.py +++ b/ForMoSA/__init__.py @@ -1,5 +1,5 @@ import os -__version__ = "2.0.0" +__version__ = "1.1.0" __all__ = ['adapt', 'nested_sampling','plotting'] \ No newline at end of file diff --git a/docs/_build/doctrees/environment.pickle b/docs/_build/doctrees/environment.pickle index 5ba5bae32c0588d74e4c205d1950545390d26fee..b84eaddeb18cac2810f4c38c7f020f62a0309b3c 100644 GIT binary patch delta 38463 zcmd5_d0$&UdDjr$Qi`C+^m>ulO z*Z53fX3DqZdR(j3?sP)s*p+W^;fSnDNIirf$bnQrI86>G$>9t+kO~Mtk^?DO_=y}y zS;ARz_?jI0gu#K}3yA#t=3#Nfq%eG>_?jVVsXc2WJ>zEVel9zLVy%rVShnkl7qM&9 zC3r$f4iYdbn~h6Hr{bp3Ln6ll)Qz5D_=1vLG!j>q=HXqV`{HNIO7Miz!MLL&89z6= z9sZBS&z7`DZxqT{`kTg9BO3tC!*7t{5x+TRSlC9P z9NWegV>Gr9pD1g`ca`O$D@YxpoJ$*9iXF~I{B&74V5~^ls1f8w4@iLjIjTRlm;VPX z$5Y1*M^|F|I7?!leH%nmbbS2$Nks(C9qzO^ zt!57(j`5F(b7yD9Q^O&5-1D9K8c4odk7sDW#d%N=92+m=wi9JCdUCN;Z~ z97@Q6v>nzi2+xd9!j(WdA^N74AP}7iR5wI!fyzhf&a9Y}?{XWR_68^fzdIpn_;N_) zj$P!kTFuUSs|7kF?9pw<%W-^VdQ?~2#zmE5$9J6o1T=Jt6y0WCY;H5#8qB_MIw3W# z9oIjFwc7K$Gy>6*O&ElYc-x#T{8MF0K5fPdP?o8Th@m#57}=2UX~$`)@Ef%Me0n^gs6Ip)7&E2eqr}=I#gMNYiJ7AmVD}?7!v6zYM3zA#}%Q% z*9D~L_-=tjnvSoFUB?NN^m?Z6>Qft93{H#%fpBea@={h zyDCPg+Me4B&iH+!yC&q;kc8uEGV#-&M(0XHqTDY2qn~fkRoP6}a;rGdJ*B1vT@NW( zZT8Z%A<`&S=sSSe&5A}*Uw~MAOryoLq`t-E99E#xV@!CrCUu@lkHTl(N=HIkjftpL zn6GVqM*SQ*%0t~#{@ThL=~Z52yV+s0YcyBRp}8^LrBiC|rprJvM8itUK_RR>pmZHfNQO=@XZAo`K=s*d15XDx?vH`mVpo2s4$q5;~6X zwd&>|+zZLTKe?X;53*o83wBaZK~870upgTI;azJ70vE@ zi25C9R_ZPSaXbPj-W}0u0w2s7<`GKqJF~_Z?hD6BbuCdVprq<3p&hTTo6YL>hu(+= zBC0(`)=HV2-qzGZJv#^|T^iTAGwr>smhd#wHJ$DFZ-c+lo2&7AIh|zYR6=<^2xTi= z0^v#4!k%WqKUwfE7Cc9r-JwfTs`VY*S2YUoi$x(-O>SRrvIC5}n`8M3CsK!(RMngU zW}tMQ;-3>8N_aiba5_?ui6|q*2%ejglzmM92UzeL3l6g24NA(I*}h0YfTb981;1Dn zQbo#7RFyva0pCs?uMWI}W!y} zBV>6YawtTAikS;}<;4|#gVlA;SfhDs?f}*+RzZaVZZus)L#TChFXGk>{_~tvyk>S1 z-g5c*7tm>utmzAR&@i|sj4D~r6L|oXVs+~kE}%#~`OMWit6@H;i@tdwicJ@{okVFJ zYKM6_)S@>u39}(1YrRe`mEb$)WKwpXm_Jp^&QcyEJ$7t7019@57Oymc(IT+|1F&pI zy`&}DYF}ctG@CX4_}x&W9*L>$>UEW}$jofxQHRuVC*i#d$7+eWoeN0EY_{+KD23@I zF%yF%24`K7&HAwef$-p;hP~XvyQ3^NC%%79619|p_B?!SVYGNf3`(qI?w%lbX)p7j z>lw{%9sqyb$Zo6OQN2Tfq2~j$p)5c!1(w2y2T+lG^sV4t_1YUqsIfO%7PsftwVGkQ z)1>wXq9Ow@*@IzFH<(FvIZ8=5x1mhy5QGB~x0eK}P&fnz3i0bZ1VxP*%#aEL(+*RP zl2*At8^)~`wIRi~jGVq`QGG*eWBuX=r!;d?m{L9uzMd)N@c<}gl)Jec3gM&aLc39U zYatnb8cf!P`i5rB_%jFU5$yOgn@1hq@#n$EVsT<~9?o78qaBB4aRKU#Ll^S^gn*!+ z$Dv70naq4v1;U5_ap+oZ;nn7Ix~ZE#-N6H?XE9gt0Gtbi%oI`?A%6{?knP;Us|jJ2 zGD2%55AeY1k#a8&KnO?)MK>1LLPq9#2Mo-bp6r7jiJA%hs(;gYmq#Pso-DqlLd(rt zTtGTK*y}t1A>bzH9_$L6v?34}6~Kt%pN43F;PZ>r1~bq;K}$#k52T*4gz*4`fRIoa zOaEmKi_Joupn6k7gR9Nt)J{Lg`y}f!;=O7X{gh(K?phg-X1qqTzC90jewBiom&R(j zD&+#yF`iL807{{H>7NB{JR921W24PtpL_&NM+3L;YU3%qo)NR&k)$Q&3La=ZBU-=% za4rz@s56fdgM%k#Be(EsVvb%%h{@@`G_alrSdW&qJOKV^32-*ATpAEg!$g^_FtWL9 zfEfDK@Vg@5T@dKdxqIUK=^T3NG_khLVsFcx=CU=Ahf^KuC4m?DS_i&sP6l1_d1`ru zc1_^<-f|%?UO!7Ae*HCpeJchsS>Tt6b0BT`RLi0MFxnWUyZf><_D{WJe>IZ zbX@y&M0Yp9$^)*~pILYSlmg0b^I{6|3-)J8a9eFg{gf%w>MwUSG@G?O+8?1lK9@J^ z0-N7#%?Zf#a`@*7j((a)IgeXgBi!gn*===QhRHNw?Tu@yA7ARJ_P7yxM+_ zUN=Qc$n!jqdRFr+55T!V$n;gY%q{yqctTEc3$G?5X7xo{LcZaF)Fb2=4?qYAnHuB> z166RRiU-_={qam_I)f)776hiCr61FT2O-8=yPXbEr*=wlwq z=0pKv=vRZyBYT2i%sRleFP2Y_D z*`AT^s~poiF}!BWrpe!F8u>>|$WK`CDGQFU;B%M@jPUcW#0gEC@{2_wRnJI&O|u6y zKUPnVd;L^Y>}2wOf9`K8;q7qs`e#P0+FkK03aDiy&cs95%4Za0Wy`;*@K5Qm_yy_G z2ZTa`7b2NL_|%DdUaGpo7Rn_9sFOR6ehZWt z8CX|3N7*li(q?ehEm_QuxP?bAidG;@hm4H5&D>h)@*@W0%GYCX^r<*}^p-TOt=z-| zD|->Lt=z~1pcGARlx`jfl^4+jIhlGG<3EFKXibB6HG172q}AxXP**qGd ziE8H3%kd<-(cEBnwQ3&-{8Jz#Rd>yBm9oek*_}Mch_Z=YZB#@K3=RZsC=EnDlCfOvd*-aC)8BNgjX@kP!+yiC+v~d#tya;nN)s z?YDtOz}lU^xkD{|^~^s<1%MH-D@M&^-@+I?{0B z%QmvwKjH%M4pOqxKj2Y1NFf_k@0O5LyL~c{ydBet|MrOVWK(iHhjBuMybqk807+O| zOaus}3(zw|(%7?gFn;Ktp+3IPO}no4dR$kg1ttCG0{GAHNr!0B-^jt4*~QaNN~tt~Jz zBrbyX(Z2Y*WG6PLK#*iKa|zPm75K@g^)RJ>(kO4S2o#wJdk=VAMer z?9LMtTa3B*p?^rv;hqg%<7ar(L))9I@tJF5#1|17Cg!#nle&8o-}6B0Y5pV+fW9q! zLm_%{BSJNDEqx_ZygCC#bZBmYjz|c4AS(cffE_;SN>A8RPAU`GotU9qSUMi{U><-F z5EF`L*v}IWA(SGvwipw&^vn&Op38VNLh0H0+;6pmSsfRM4llJl0OtrV8I%`1^7%OC zfv*mpjO)17Aopp^&q&9e`%)&?UfT7huRNS|@?h(AYAbmFLcmeb?s)NT>FW;<2hYq7 zZsBES7Vay@#VAr-+BQqHXanUID1q%S_n9vLtv~8oAXV z)AHo}80Fyye2&-DBH;f9ymQR z*6{%NBO|~y8RY_x@NbxYvL#fuiVz@%el`5A>v%uP+7X&1aj1ejW)W;f*=TZ_G}GBV z{#r?$pt-xK6h>Ype~E_{I$^4OeWcb>U*H1KnJ_)a1E3T{UK?ku1W2rp#=&k228f|w zjVA-TOD5f}{!xh`w^4SdHmGWB@m~$8{H`0%+G@bd_Jm~jhtreP4qFuL zuLBkp!-6;##Iqm~Pu?-g$8IkvfTQ%<{NhkJ)vfY=H2W{J)JVS@mN})(44+-hHQ|)E zrOj`~bE)E*$424}Z|AUE<-;H=>+Q;VqX%dWLa`U3ln0`tOP7Gr{a)fI3KifYpmG7% z=fkU1d0CT-a;LK`f$`n%NG)jrl%>39<+lZ3qP_v|c2nQwJhCf9SE%oIJP=Ct370`m z#^TSUw}BUW^+vZ+&UNDP@AYSf*vYNF2i_Z`ZG9_wWY<^Ul{^r?tol->!I%DO+iP4_ zr-f__lwT4u{L^m?%H-G78%J^W2KN z|HD|V;-2M^T3>PhLP`I)q&!ROG2C^WB1%p^H7+iv^4!W;9(mv(G1i$+b3YQTiY2$LC=ki&- zscez36JZ-{O78*X&eZIuzS@K1r}n>y#5P!6jpoI$xhzd64DJWz<&(pCa4@^0T1+b% z&8^NRPqo1v*#PhC!xu|E?&v9Yn-dCvZb9enNkd?!y8`(N9?}8vxogSOP!8P`>;q z0{cqvq4O6#KE9fWf9$V+}WidUj4{AUdbRjIC?Ru7uB|5 zd0_KvtxB2-yk^kBdg5MS$kjO6+wlOZf%|?mv?N?0+w@i=f$WqD!B`Rupx>XVPM{B; zS0~d+b#(+CNUM$5{L!=y?MC+?l$j#ItoJ_n_>GAsCWEM^`*yh#Y1dxwwAZ(p7r89f zM!Mic0B?lkqoMqb!V=Y)MRnE;XO(hNQW`lUVr-6LqDY9509ncW1q$1WuJ{RWG3SspRF^bCgTa8x018%pRXc8+5b97uqz9mFE^9GdUP8J621}%%FN@1czb(1KJ?W@5}S97rg`ibW*1kG z$lb?jWc}A7Is1+Uo4(mX&WgUJXa~N%jhwZfc$kS(D}LB%NWqmSuSaG0g_F-B0k1nX z8`;aL3rO>q3z_t(R*`iHe}eEo+uI8Hx(H5_-JCNXtqTuGZZ zwxK@c*Hkgn35444{xci!^CuIr?Z*RX3!e1TN;p3K(|S10I7|M&bhb+T#(?th{>S=? zwsaI5C1u^Rc>!uiTQYgTHB>We~d&GktGl<7?Z^hBhm1rLr}Y60*#7c=4G;)L;Bl6v|OXC$Z>HqR{ZZEHyEBAw5~l zibm6=lr(ApOZod~G+7y)!=evIqY`Cw9*ZuIK^4mAd=|Ya291!UqS(WTR42r}F=&!9 zbsW8u=k!eB)5qY7Qo$PHWGU)yCZIhP!CUVEi6w~3?E&_&8LcZk=fd0C=q?h@ZkL(`OL{wx-yqZ!JW zd&Sl1XsR;i0rB;8bg43CyLfLVuni9lMk%BJD&CZVE?36AA)u9443F>#yp!<*VPy zSEcS&nKufuNqN1!qnx)`b9GvBhca`8<}&FG1GpsP`dcv}uCMy2AO95fh>5s&Afax_*f$VDZnOq`#KhNE(EO)eU37#Ai!o{PqG zoFUaAho*|v9wCAh6iEw!Gg1;g&}&KLtY6o)6mmwKP9YWkLE;P&K^e|u5d%pCapi<; z7BPrK5T{PaV-fi&eJ<$3wzVJ1VhTtSs`240VkC*6dMaWOqe%q4SyhrE-a80YjaUqb zva?FgR(l*Ig8bdM$Q{{eWs4%hw3J-~^H9xD)FL)lp==1&R-uwSQfYToqs6qOzQyG9 zP$Asm?PiC~&Q4t7u}GA$>r@pw{a{WfRG_-5CJn9exD)7h8TBx$wK>T48Su85m~;x| zqfW8>6v~Yt%@RK13_EY97Jws5&LX7^pQY382xE6`J%tV~FQ(H4;r8yn3wi*1RN zOxy#dFtw!P)}!fpQo>|;OR_e*vwl&V-PFh~xx|g&1nru&)UeeE)%(h2$buktnIR{Y z7TQ;}a|z_xHEEe)RVt);-fb8J!4bD12ZE^ehT$<(A(N|TgFad}7}5vQ^EuTP&_=v> z$AAml>`N?!$))QJ10d%H7TmwykW)g7Ozr`fs1x zkk0-ccNti6 z^tj`!CfIJMsh)oM%OjLM`n_TFqAZ#wwmKU`iBo6X-l zlNJ!G_;?se_rScc0g&#+d0}}Fd;!TJNSYruD4(F$yo74bKsFb2>zb^@V%=#t`}VXj zsF1jHepm){H|yqyW#-dMkpU zH4_(v?V7m2I6ThKFI8-|7zdJYtrXsCG3Jx={TAb35}vRaCzEiTU@Yw0FBNq8d`&Hp zKTCYZhz5iSaP3CHSU}P|E*OWA@Dsr}oP>$Z#v&3txMMaO57Ak%6rm`4-rGuF%vhXe_=@QSn(Yy$2l)!6GMdxRWPrycYv zRj&FCVcPwy^a#>XLIq6eC?lQz?_O597~5hzkEP5a zRUHt{aPDX}7IXp7C-#Yl!6MR$o>F6oYe7+|-crT)T8xohKtz#|>}onyKw0++;2n{mYd1D+6(qyPW_ delta 37745 zcmd5_d0-Sp)=y0)_mKM{0g{j)0TKuaIk-YN1wtS!A}fd?#{knzW|+az~YW; zpa$C&QQ1S+6%kh?9;<%1y50x)iLST;e(SmGfgmcE->a&g>7Gu{WGWMt{Lz)Jr2H8Jn#xXKZu5$x`RAo6IJ= z$!K#qBU{W?yWM12;c|x6H`TY;T~33^Vzbwq&GmMZ)#7r-S&TNjv8m2h-`rw`iumdg zL$bfog@iaG0C{Aq&F&ITlG8|X33mQ9-aR61+Lt6Z%4BIWwz2H5NJhL8p5>n*`H9|L zV!XoL0w?K6TR?Q3LJ2g!#g*?A@a{1S@s!c2cyw77{^jVrs4}Uf5Qi5Jj`RreMA5buKe+K6+!5yud8--uA^)K8mUGtafjMFt_z{_b(3U%tF9j%}jvVUA zp%MS3>J4V?)o`xe*&=4`-i)vjvYs0?t~OF?6h-)}Gue&JlHKR}yiSMYRoZC{reeNi zk}nK}T3XV|7Ycop2*th%DE}j{VPXlBMJH6$_I#A__}K}#^M3shYAaKrE)&Mh@SnB> z8>ErV_SC(J*7Z&KJSdk&*PUiz0m13!=m*9wCi&Dfm%x9xEZ=Z#uuGq&1BwcxblvzScpA(b?ZVW@(4CP^k8Ewys%$n}86 z>TaR9KGmVO+K@QQ(qw8h+Oq2{P1*MP1~V+cVEW4P%wKQ7b^Yo{;)JAJSeg)!LI5e0 zK%~LSYV&H3f|1qcr5@|51>;YMlA)3HkZ(=wb32Qz!T*?&!j$5?e(z;Q&h>Wy#|#`5Qj8BoqIoHl2ar(ugkl+i+ z7NCP}0glt=J{`K?cReWY4Lpm&o-gkVZ>fh(kv-HUjKLRc#)QR&hlJGQy;Y`Iwv>xx zOS!o??)Z!jIb1}$d$Bj8g;8tmA=uDm<7|<`y=e|G-T5ivMCw@Tl2!~}(EwnI#uc=f@=Fx2^9W-xHV6q7Q?*~|&5H0YlmB}x zd7mZ6S@HosxzishMwKl5Vo^vhQW|J;pAN(K3XoR@R0ME+r(rIQEoV=vfv~i9z-=q1 zTnh2Y1tl!h)CNu2@3DFE-acrgA}rq@8Lnh8>Q}2e6c}1dUp8L_2&TYNSnTywzkE2+auWFEpV`*q z7ne#a9y5;;P$QalO{scjH}zKR@~pF*Lj3$Q`~158%sOu25sZ>L*+DtE#UfjWVcA%< zb!_E<)3T1uJOIie$=0!vLio@|xF6@Gi+wVGG}fCN>l#<7=8wNYKYE#Xm#y=@@!&Xw5uAp$uJIl7p+7VsNt% zuby!PE-(#>R`3Ay0YyPOwjHZ-m}A@JpNl}KxSf0OvST~8mXab~ACHo{n~unXtmWBU zJOGyhFAp^jWxTu;JTK344_@YF-bN2E(RiOFL2WV5@?dK*bC3t1515%2ep1?N=h+9g6ThO~0Z$&+Tk2Yf2vuvgS}ULE zV8bH~Rt^u;@W_j<2*~6Evd72miE3k-%>|~hBDkCfKwFEaQHTJ813|9{qOXHC&4QBUlALda5YEE(OW7Uz&eZ7^o?86?Q5P|qGaA7~uO>VKs_Hk_OWVN$;g9lE_C|>0OP!36sWWGcpekx~Gah-J2B{Vu{XB7eveDkbK z#;%r}?Y~N&zSz;Y%Gm0jlH|zD1s=I-5p$LYpbv=Yi^xm@+@hRQH+AZax<-f1Zf#ag z^+o;|TOg<&3Q>+pwx2>C%BXK*MB%T_M0B51hI655%=JTg0F)#8xy;9WeKzxDOZ|}% z7#EAV2QQn?$PLrfzHAW>oR-O4!2{3-Wc04gI1JDPI1icjAd!rN_>k6KP{oI3>&12mY(fC)J#;XZ=hzC-Oki9$rmjWTL zZ7yK`>fgZ=a)NvCG9hIUD+yEIG-N zQ!M!gA3Eso;pVGUn&uaaLV7*id?jrj;2s&8dmcmV)zeM@;EZ8E*1x>6)zsu21YO4| zmO?!7w|OjXV1}kF2E4X6@_>E`HV?!a3gJ^G-aA#VeNSJ9J`MEUBXui4RI0tu-OxuG zYBNLM$xr12;+@D}^}O>g9(jQ-7UJ)2$!AlUEcDyCKs@^(S>z%Q0F1&N#O?mW2UkEy zlE3&y3FY;}2c}F+6J*B~sE~!{pcf3nPW$7nGa(_B!PyZ$ux$j3wfz&|l_6KZJ*4zi zZ6B((nIi$ojLJ$-icDcMZ?a(q=3sxR@FU(2swoS6-cRxU=sB*$nQUEgo<}YUEf5}n zhK#xIxuwFEdq)rE;&ZrAZ6jxR;N&%hY$K<50F*x3RyV+91NP#|p34+;a1UPgRxiI6jbm>wRTFX@52TjIYUcq^4(sP4WXVn` zeDh%NgzVuSyiCZ`3#0L@yEE}!7d($P$&0P~c!0HNxrYbfQlO<}*I;HR?*&iGKe-1l z)3Wf7L-191rmF4a2oIzdA#d^k^Z_AWdzM}-v!Dyks3v2h)zPBdvB{8 zi|oq60VCk4m(C`W?jEHkC6o(9V>Sul0Zu<2}+3Vr6D- z;sVhylPx>|eZWl6X7bRzd2F74vIhDFj~T1V1j)u|&_3aF#^s@#>ZgJo|0> zGE5(@o(Tg$<*La)pcF!tUyG!p&3y(dd~S&Ym4lZUfKX@F6)TO|+O(HA9R4cq?+}QRD2;;PR zJ?t?DdI^yOt0#IB5bXq0bsu0Bm&7D}OvI1w9X*l0_e7Tc3_hf7GY2yEWYJIM5j~7W zHn85^fJxPURUm%nLFr+qHB8FfLKd!qhSGfiE~yanWb@J5mIN^TM11?cGPR&rb3tMa zL0h;GB%eW)r`sE5R#7CMUP20J&gh#r%-}B{%4Z9OKfz^{fwMrhUqQ_8xntEj;bdKJ`0|qk9mZF++mSKeDUA}H8cO_fzoR+bAk)u(qJY-Ot9!var55| z%xco&gZ5>~01?bop84!VH8%-dkXqctav=oIO&`oK!xQYrmuuo z3)|ekJCxVqm0ZwT%#7zkxFnd##1B3n$JkjNJUbR{0jSxjQrpWaE=Vm_R&pT(&q`m+ zG8y9hD3q?AW$p}~p`AR!P|Px!&z4VJZnAf`n%j5)HRqZgTnNGQ6RbZIH?-(eaM3ei z_^X$bnCZM6JTWhDOTpW8jxCDD556*1Z9dO&!D^Y$Gh7HiKRw%D8^%caE_hPD;U2p; zDKEb^NlnPtT##CXe9492hmZgRG|Fg?Fbo!kEXc|t3ISsDBFN*}=yvo?t?V9eP~G@J_4tA+L@Hh1bKhDaQPK^# z+fF~0`cvI)hcBQYimG zis2V{Ag-kl0Y)LKf(%2h$CKY0%4D#!S2E~&Ym{0Bw*@bQ9Xt?TMs=A-j@y|W`}$Ks znUhCm&r*EqJKK)`b0m?8@Tp#jaL(J^MEC^H_^Db-cT8k8dXxv^rxoGADcwZa{!TIz z;fY>}@V$3NtF`cbp7Cpo@F)+&PbeQ z@Id(0KY30Mn8O^8BV`j(PY{c!4GEb_Q<9yrjYkiZ5IK0mhxx@i`f>B>F#2WlYD7P4 z4hi}8SoHw<+x_Y|`k-EQ5?w)5hvTCk&gf8oV;g{t^sCI|-sr<{ru+=^7yyIyH2wIV z!x_Ka1Rol%vs>$0jSUWyxrr{Y3E(ZzmVAD_lYYHhJ|my;md_gDtWrKD7b9onlhB>? zs`4563bcGiu20U!gyQ!gD3lCGowucJruA?UfndVKB^BS;W0`LsfJZzA6D>7R9b6Y-?amXPF*&lbi>Loa0# zDEsSw!ch3rfZ&`%ztgm%5vAZazD&c%7e?YM|2x}2%O3|fB=s8+c5MS$j=BzTOs*lI6W(hK-=K#8J1iTNi&Z}A`vp%qR=gn zL`EY^B3a7A5AhvNonWKZvq`)q8s(u);{Iqf3!M=!Mx#_XONl|_B1%B_g!>Z3D`U{` zgiSEWd}{K-9#A7;v$!n=jp(Py-j^u87=wzHSq~?Q+hS3Ym}x*+%KQUT{$c|fF6Gm2 z7Cs621~f~Vbx^8$)_^7}^PiRSJNlz2{OO_`9QS!dtiZZMv7VPIJkSq~Q#O1_%8!Ue z1<8u~uaZ&y4n`^78HYxTZL!FpZ1x6icDXX^O$q6{SX80RKSJ{>$@d$)dh}1ok3+MS zRo{~!pp)6s`|4x8+8mQAER08!lnp;f6nDp?Un;Xcl&bbmKvl~8Po(_o6X6>02HYf< zQcVA$!xj%FqG8hOapS!@@P*WRa3ZQyqMnpdizMZsVn6M{o2jh+tyFzjl6U9MO8Hw= z`4^=8Pm|CTgMy_HadJFL7ORudbY*rZ%ifoarYf_;S$0winybu?@_@j{UAM;fQ_91@ z%05a#nNkz_8kz*LUn;6l=A?-8Q&Djy>l>|;4$33wl0!na+Fcu5&V1Z*HW^o)ix3}6 zMRCfend};$q@p2`=xF;vw7obe4UJRQ&SACN($GX@cAj`J4b4&J3}qDy)6rOE_HdTH zIUN-$vkO`Fo9U=TnO)=o$rESyM=8p(5>^H#SFFq~W7&uLqw&h@u`IhF0}Yn4>0|qq z;^GW6S(!6Myf?!`C#^GG{4N8{O=Gg9IWs{v&hTcVeWkTYd?*8zf|qskMk`c{mVv0m z^SoL=_VPjEzd!7dUb2cpHwii^pG+;XRvUMju~ zO%oa$m%A;CW-lX%waTWABxe@fxeAN*s=1s1)F^A3#G)*;K$&9}Z^=UQlsQ)Mvn-EF z&?~kQi6_B##@j$zE(IZE~26(=GPacKAxYI(3p<92{bvZ9Jkpe{Dqv|?>-|}64>RS>=ANyz+LtjIV0;|;c@s6ik~DI zbozdZWgH|KWJxJJ!!n*D8Dw!O{DWn@m>e=8gnc>qC6@ClsX`_G8p}9DGN_ymvy8V$ z28|9LNfxt)pqT|z0a0Ezle5h(8_6L5b~ZR8n#^<&?-D*s?!rS*&1EP-JW-7Xp@duK zpyENK&(6puQ~ip%=6bt}j=>p5zgiC`UA1#i`d*YLn$7|*dE%C{Xb2<^oJH9n*w-L) z1ko<|odo-Cri+fp8Ao42Uk5+4wb+(hTbo(7L$uC8!@H`^p?lY)=B2={#ZbL?i^~}y zt%6-bo_L{Emp*`&-CF$sl=bua&<&|E+NR5nrZrx#{$z_wTxQn|fG)K`b}7lOF`$}K z1WltG8tNKbn#c!opdBe0i)!jyDlSwlsKHja8A>(uIKH#UHXA^RQl>9=zOgA`}|2a zH?-5XyW4dH>4$B)A!PZ`^=Z5A7pWkC37xteNUrIGT6yC7PTg=w?qiuRcj_|7Q*?9n z20)MVyhB)ewKA1Y^^MiHdlj-543lf;Y@^qnyiJ#yPDdmoxGR;3)@{1T#H-Hh21o^& zWLod)Jg-Y@xcmm9HZj$Mpq~ci?^9g@Ey=AO4JAqLUwB&^Y{u4W>&dqyqzYx#4NxHs zCtOG$%bKjH2_rfYqj>oXt6LL;YVt@?KQ|ox!8jC(lj=eT$C3-ym{HAkQYVFMSW@8Q z^*4xH>O#o??yCzO6i!CQuEsX#&csHm#cr}V9L;qQurh(k8C^oTh?a$B455`Hq*n$& zE@`X2cDYyuRa0o0N&w}eby?^DRKCTzEVRqHOuxXOJCGutFzW|GdTTRH#H?oh5RyHk zS)WVNRn7XzB;DJrA3@Ti&HDVP17u_iP|aHLM6*6KiaiA*KxvUhpHFHnw&;hGbhAZ2 z(m-pE)79Lh18dx{T0el4yl>GLkknw+mymR_Reu>tO;&dOPOE+xIe)?m{rY=~_%5Uw z#M3zwlt1Gd3BJqh5-P-m7Jc?WjdHRFgmP#o&V|0F(<*VbkPA{?0r9~a>w?Jy0B*$( z4X34<72$%1BODDQ{~s|`h;;w} diff --git a/docs/_build/doctrees/index.doctree b/docs/_build/doctrees/index.doctree index 31ae7b7d35b3b90a1f6bef8bb1f634bedd22b01b..18a4ee09b9b034c60f8f733991772412cc67284c 100644 GIT binary patch delta 2839 zcmb_e&2Jk;6t8KW%C4!M23$%%SWrLWfY)wJ6A_}SR#Ao2Dp-6}YNe_>_D(aqacpaM zHdT?(!U2&;DE@OM%o0;Ex z@ArGpx9blUv+rj=?Hv0udo$A+s7)f_`bx{cblN|3dNEM3LAQ-j|%=GZ(jJJ(cIb#A_X2|iwFF$=X&ho05k>uQK| zngNv`3=*JsBZy0+vIGEgUe3Zdu!Vaa9Qc8Nd*!hpUfKc1>pYWFW0D}@{1Fm*()ITA z&?*kRvCiHEV0SDd@Xr0$+yxFfLB5AN-VKv7L6NnLY2ZpJIsZRYD2n|cqs*aefj2n_ zc~Hf)in>)+-2jopz_X)ZoC4$3G)ut#9N3=+I}e`x!m$79pizg{T0n3T;-X4fw1&dQLcsHUA(>+0!-rsXdfmQ9tl_%Yo8NigYR z{Uv2!VH@}0tAePao$vM?U1@fZj#qCf4K=AM>KeF*kwuBE+5>d8gKHh;Tt$&{wNX2( z35Dgny%L$AL)qvC~7U{z2&Y z+`q>A`cS~*9llhN^rKv+RJRFL=#<3(`Al>=v!ismVZKr#&9hWi!(2+733qFJH$4T-&lmtnnK2-)%vhM| zRQs*cvuq0LF9U};KZXWj5tu9UPC`^lnYQ6^!+$sT$yTfM&J&qGwl)tu+&yo82cXSw zS@|E4zsP-Z&$QXjfGw}FrOB3W*zz@7zF^Cyf4e+|!m}IX(FVD{9-i6=PppUD8=>dA pLk_`Tjp%_kJaC8HBfm$tv%wnO{;Ig0#cyu1<#SlJek#9}`5QK^$(sNG delta 1277 zcmb7^&ubG=5XTeqb8Vw;u(7d;NwL)}81X2vs9+I95W#auHpw%y>t-9WyCw?KdJqge z@UX8ZPagaON(zO7_y>qkMFbVpvx4{sc<8*{Y_j$j?O`ALX6DU&--mhgXa3ct$Z}*Q zHMtt;2=>c~7xuM8rkK2?*OeME^0Hpfn{rhn27_3Mfk=0AJ!4PV6DC0l-q@?j!V+x2 zIS9ddkYMiiv{eOxj#Vv9BW77s43pVx&OH!;C{HV4fWSRv#UxFin;tK=$^BxbL3Bm0 zlWxUT@o;$jlcOp?$6Evy>y2_3;}?7xz>N@SRM9m>Cp%ptjeF_Y=psMyBBw7(G|Uq+ z8Zyi}qcL0yd`}>YFmm`!mzV{!@Ez~|&E6C;4`>tv>Wei7D^zfPo3f%a_)TNDGat1G zX5%^N7_Ow-(v+HFvYzAa$ZefHcg~q|yFpCm6UXa(89+UY^*&?0yj_@xNBHg|-z{z8 z-}@2#JIMZn2g`%mTtrg4z*NVBfq=vFt9N8%`mxi5;Jj2GxG<#DlXgYSUXb9|L7=H3 z*5uq8dvH_FV8FrA!9SlUKd>28cFe8iFpG1;(Sc!qYzemq4I;N|u)PD-tC(XOw4rGP zZD@M GFSrHo`_WYZ diff --git a/docs/_build/html/_sources/index.rst.txt b/docs/_build/html/_sources/index.rst.txt index 01814bf..cf02986 100644 --- a/docs/_build/html/_sources/index.rst.txt +++ b/docs/_build/html/_sources/index.rst.txt @@ -29,9 +29,24 @@ We encourage the community to exploit its capabilities! api.rst -Indices and tables -================== -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` +Attribution: +++++++++++++ + +Please cite `Petrus et al (2023) `_. + + + +Version Track: +++++++++++++++ + +``1.0.13`` +First version distributed, presented at `Cloud Academy 3. `_. + +``1.0.5`` +First operational release. + + +Acknowledgments: +++++++++++++++++ +Our sincere thanks to `Code/Astro `_. diff --git a/docs/_build/html/index.html b/docs/_build/html/index.html index 282960e..c8b6c4c 100644 --- a/docs/_build/html/index.html +++ b/docs/_build/html/index.html @@ -105,14 +105,21 @@

Forward Modeling Tool for Spectral Analysis +

Attribution:

+

Please cite Petrus et al (2023).

+ +
+

Version Track:

+

1.0.13 +First version distributed, presented at Cloud Academy 3..

+

1.0.5 +First operational release.

+
+
+

Acknowledgments:

+

Our sincere thanks to Code/Astro.

-
-

Indices and tables

-
diff --git a/docs/_build/html/searchindex.js b/docs/_build/html/searchindex.js index 5ea3f39..b671bb5 100644 --- a/docs/_build/html/searchindex.js +++ b/docs/_build/html/searchindex.js @@ -1 +1 @@ -Search.setIndex({"alltitles": {"A. Installation though PyPI": [[5, "a-installation-though-pypi"]], "Adapt Grid:": [[0, "module-ForMoSA.adapt.adapt_grid"]], "Adapt Observations and Models:": [[0, "module-ForMoSA.adapt.adapt_obs_mod"]], "Adapt the data": [[0, null]], "B. Installation though GitHub": [[5, "b-installation-though-github"]], "Contents:": [[4, null]], "Create a conda environment": [[5, "create-a-conda-environment"]], "DEMO": [[2, null]], "DEMO classic:": [[3, null]], "Extraction Functions:": [[0, "module-ForMoSA.adapt.extraction_functions"]], "For PyMultiNest users": [[5, "for-pymultinest-users"]], "ForMoSA API": [[1, null]], "Forward Modeling Tool for Spectral Analysis": [[4, null]], "Global functions:": [[6, "module-ForMoSA.main_utilities"]], "Indices and tables": [[4, "indices-and-tables"]], "Installation": [[5, null]], "Issues?": [[5, "issues"]], "Likelihood Functions:": [[7, "module-ForMoSA.nested_sampling.nested_logL_functions"]], "Main Utilities": [[6, null]], "Modify Spectra:": [[7, "module-ForMoSA.nested_sampling.nested_modif_spec"]], "Nested Main:": [[7, "module-ForMoSA.nested_sampling.nested_sampling"]], "Nested Sampling": [[7, null]], "Plotting Class": [[8, null]], "Prior Functions:": [[7, "module-ForMoSA.nested_sampling.nested_prior_function"]], "The plotting module of ForMoSA:": [[8, "module-ForMoSA.plotting.plotting_class"]]}, "docnames": ["adapt", "api", "demo", "demo_classic", "index", "installation", "main_utilities", "nested_sampling", "plotting"], "envversion": {"sphinx": 62, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.viewcode": 1}, "filenames": ["adapt.rst", "api.rst", "demo.rst", "demo_classic.rst", "index.rst", "installation.rst", "main_utilities.rst", "nested_sampling.rst", "plotting.rst"], "indexentries": {}, "objects": {"": [[6, 0, 0, "-", "ForMoSA"]], "ForMoSA": [[6, 0, 0, "-", "main_utilities"]], "ForMoSA.adapt": [[0, 0, 0, "-", "adapt_grid"], [0, 0, 0, "-", "adapt_obs_mod"], [0, 0, 0, "-", "extraction_functions"]], "ForMoSA.adapt.adapt_grid": [[0, 1, 1, "", "adapt_grid"]], "ForMoSA.adapt.adapt_obs_mod": [[0, 1, 1, "", "launch_adapt"]], "ForMoSA.adapt.extraction_functions": [[0, 1, 1, "", "adapt_model"], [0, 1, 1, "", "adapt_observation_range"], [0, 1, 1, "", "continuum_estimate"], [0, 1, 1, "", "convolve_and_sample"], [0, 1, 1, "", "decoupe"], [0, 1, 1, "", "extract_model"], [0, 1, 1, "", "extract_observation"], [0, 1, 1, "", "find_nearest"], [0, 1, 1, "", "resolution_decreasing"]], "ForMoSA.main_utilities": [[6, 2, 1, "", "GlobFile"], [6, 1, 1, "", "diag_mat"], [6, 1, 1, "", "yesno"]], "ForMoSA.nested_sampling": [[7, 0, 0, "-", "nested_logL_functions"], [7, 0, 0, "-", "nested_modif_spec"], [7, 0, 0, "-", "nested_prior_function"], [7, 0, 0, "-", "nested_sampling"]], "ForMoSA.nested_sampling.nested_logL_functions": [[7, 1, 1, "", "logL_CCF_Brogi"], [7, 1, 1, "", "logL_CCF_Zucker"], [7, 1, 1, "", "logL_CCF_custom"], [7, 1, 1, "", "logL_chi2_classic"], [7, 1, 1, "", "logL_chi2_covariance"], [7, 1, 1, "", "logL_chi2_extended"], [7, 1, 1, "", "logL_chi2_extended_covariance"], [7, 1, 1, "", "logL_full_covariance"]], "ForMoSA.nested_sampling.nested_modif_spec": [[7, 1, 1, "", "bb_cpd_fct"], [7, 1, 1, "", "calc_ck"], [7, 1, 1, "", "doppler_fct"], [7, 1, 1, "", "lsq_fct"], [7, 1, 1, "", "modif_spec"], [7, 1, 1, "", "reddening_fct"], [7, 1, 1, "", "vsini_fct_accurate"], [7, 1, 1, "", "vsini_fct_fast_rot_broad"], [7, 1, 1, "", "vsini_fct_rot_broad"]], "ForMoSA.nested_sampling.nested_prior_function": [[7, 1, 1, "", "gaussian_prior"], [7, 1, 1, "", "uniform_prior"]], "ForMoSA.nested_sampling.nested_sampling": [[7, 1, 1, "", "import_obsmod"], [7, 1, 1, "", "launch_nested_sampling"], [7, 1, 1, "", "loglike"], [7, 1, 1, "", "prior_transform"]], "ForMoSA.plotting": [[8, 0, 0, "-", "plotting_class"]], "ForMoSA.plotting.plotting_class": [[8, 2, 1, "", "ComplexRadar"], [8, 2, 1, "", "PlottingForMoSA"], [8, 1, 1, "", "bin_data"]], "ForMoSA.plotting.plotting_class.ComplexRadar": [[8, 3, 1, "", "fill"], [8, 3, 1, "", "fill_between"], [8, 3, 1, "", "plot"], [8, 3, 1, "", "scale_data"]], "ForMoSA.plotting.plotting_class.PlottingForMoSA": [[8, 3, 1, "", "get_FULL_spectra"], [8, 3, 1, "", "plot_Clouds"], [8, 3, 1, "", "plot_HiRes_comp_model"], [8, 3, 1, "", "plot_PT"], [8, 3, 1, "", "plot_ccf"], [8, 3, 1, "", "plot_chains"], [8, 3, 1, "", "plot_corner"], [8, 3, 1, "", "plot_fit"], [8, 3, 1, "", "plot_fit_HiRes"], [8, 3, 1, "", "plot_radar"]]}, "objnames": {"0": ["py", "module", "Python module"], "1": ["py", "function", "Python function"], "2": ["py", "class", "Python class"], "3": ["py", "method", "Python method"]}, "objtypes": {"0": "py:module", "1": "py:function", "2": "py:class", "3": "py:method"}, "terms": {"": [7, 8], "0": [0, 5, 6, 7, 8], "1": [0, 5, 7, 8], "10": [5, 7, 8], "100": [7, 8], "1000": 8, "11": 5, "13": 5, "15": 8, "16": 8, "1994": 7, "2": [0, 7, 8], "2003": 7, "2008": 7, "2019": 7, "202019": 8, "2023": [5, 7], "2023rnaa": 7, "20cup": 8, "20visualis": 8, "20women": 8, "20world": 8, "23": 7, "287": 7, "3": [5, 8], "300": 8, "4": 5, "42154606": 6, "5": 8, "50": 7, "523": 7, "534": 7, "6": 8, "65415996": [], "675": 7, "68": 8, "7": [7, 8], "84": 8, "91c": 7, "95": 8, "997": 8, "A": [4, 7], "For": 4, "IN": 0, "If": [0, 5, 6, 7, 8], "In": [], "It": [0, 7, 8], "OF": 0, "The": [0, 5, 7], "Then": [0, 5, 7], "There": [2, 5], "To": 5, "a1": [], "a2": [], "a3": [], "a4": [], "ab": 7, "about": 5, "abov": 7, "abstract": 7, "accord": 7, "acf": 8, "activ": 5, "actual": 5, "adapt": [1, 4, 7, 8], "adapt_grid": 0, "adapt_model": 0, "adapt_obs_mod": 0, "adapt_observation_rang": 0, "add": [6, 7, 8], "adpat": 8, "adsab": 7, "al": 7, "align": 6, "all": [5, 6, 7, 8], "allan": [0, 7, 8], "allong": 6, "almost": 5, "alpha": 7, "also": 0, "an": [0, 4, 5, 6], "anaconda3": 5, "analyt": 7, "ani": 5, "annulu": 7, "anoth": 8, "answer": 6, "api": 4, "appl": [], "appli": [7, 8], "applic": 7, "approach": 4, "ar": [0, 2, 5, 7, 8], "arbitrari": 8, "architectur": 5, "arg": 8, "argument": 8, "arm64": 5, "arrai": [0, 6, 7, 8], "arrang": 0, "arraymatrix": 6, "associ": 8, "assumpt": 7, "astropi": 5, "asw": 6, "asymmetr": 8, "atmo": 0, "atmospher": [4, 7], "author": [0, 6, 7, 8], "auto": 8, "automat": 5, "av_pick": 7, "ax": 8, "ax1": 8, "axi": 8, "axr": 8, "axr2": 8, "azimuth": 7, "b": 4, "b1": [], "b2": [], "b3": [], "b4": [], "back": 0, "bar": 8, "base": 7, "bb_cpd_fct": 7, "bb_r_pick": 7, "bb_rad": 7, "bb_t_pick": 7, "bb_temp": 7, "befor": 7, "below": [5, 7], "best": 8, "bifani": [0, 6, 7, 8], "big": 6, "bin": [7, 8], "bin_data": 8, "bin_siz": 8, "blob": 8, "block": 6, "boolean": [0, 8], "both": 7, "bottleneck": 5, "boundari": 7, "branch": 5, "brew": 5, "broaden": [7, 8], "brogi": 7, "build": 5, "burn_in": 8, "c": [5, 7], "calc_ck": 7, "calcul": [0, 7], "calibr": 7, "call": 7, "can": [5, 7], "capabl": 4, "carvalho": 7, "ccf": [7, 8], "ccf_method": 7, "cd": 5, "chain": 8, "chang": 7, "channel": 0, "check": [7, 8], "chi2": 7, "chip": 5, "choic": 7, "choos": 8, "chosen": 7, "circum": 7, "circumplanetari": 7, "ck": [7, 8], "class": [0, 1, 4, 6, 7], "classic": [2, 4, 7], "clone": 5, "closest": 0, "cloud": 8, "cloud_opacity_f": 8, "cloud_opacity_mg2sio4": 8, "cloud_particle_radius_f": 8, "cloud_particle_radius_mg2sio4": 8, "cloud_prop": 8, "cloud_vmr_f": 8, "cloud_vmr_mg2sio4": 8, "cmake": 5, "co": 7, "coeffici": 7, "color": 8, "color_out": 8, "com": [5, 6, 8], "command": [], "commun": 4, "companion": 7, "compar": [0, 8], "complexradar": 8, "comput": 7, "concaten": 6, "conda": 4, "conda_subdir": 5, "config": [5, 6, 7, 8], "config_file_path": [6, 8], "configobj": 5, "consist": 7, "constant": 7, "construct": 6, "cont": 0, "contain": [0, 7, 8], "continuum": 0, "continuum_estim": 0, "continuum_unfilt": 7, "contour": 8, "contribut": 7, "converg": 8, "convolv": 0, "convolve_and_sampl": 0, "copi": 5, "corner": [5, 8], "correctli": 8, "correl": [7, 8], "corrobor": 5, "count": 7, "cov_1": 0, "cov_n": 0, "covari": [0, 7], "cp": [5, 7], "cpd": 7, "creat": [4, 8], "cross": 8, "ctt": 7, "cummin": 8, "current": [0, 7, 8], "curv": 8, "cush": 7, "custom": [0, 7, 8], "d": 7, "d_pick": 7, "damian": 8, "damiancummin": 8, "darken": 7, "dask": 5, "data": [1, 4, 7, 8], "data_bin": 8, "data_resolut": 8, "deal": 7, "decid": 6, "decoup": 0, "decreas": 0, "default": [0, 7, 8], "defin": [0, 7], "delta_flx": 7, "demo": 4, "deni": [0, 7, 8], "densiti": 8, "depend": [5, 7], "design": 4, "desir": [0, 5, 8], "detail": 5, "deviat": [0, 7], "diag": 6, "diag_mat": 6, "diagon": 6, "dif": 7, "differ": [0, 6, 7, 8], "differenti": 7, "dilut": 7, "directli": [], "directori": 5, "disc": 7, "disk": 7, "displai": 8, "distanc": 7, "distribut": 8, "do": 5, "doc": [], "document": 4, "doe": 8, "don": [], "doppler": 7, "doppler_fct": 7, "dopplershift": 7, "dtype": 6, "due": 7, "dure": 6, "each": [0, 6, 7, 8], "eddy_diffusion_coeffici": 8, "edu": 7, "effect": 7, "empi": 6, "empti": [5, 6], "encourag": 4, "env": 5, "env_formosa": 5, "environ": 4, "eq": 7, "err": 7, "err_1": 0, "err_n": 0, "err_ob": 7, "err_obs_photo": 7, "err_obs_spectro": 7, "err_phot": 0, "error": [0, 5, 7, 8], "estim": [0, 7], "et": 7, "evalu": [0, 7], "event": 8, "everi": 7, "exoatmospher": 5, "exoplanetari": 4, "exorem": 8, "exploit": 4, "explor": [0, 7], "express": 7, "extend": 7, "extens": 7, "extim": 7, "extinct": [5, 7], "extra": [5, 7], "extract": [6, 8], "extract_model": 0, "extract_observ": 0, "extraction_funct": 0, "factor": [7, 8], "fals": 8, "few": 5, "fig": 8, "fig1": 8, "figsiz": 8, "figur": 8, "file": [0, 5, 6, 7, 8], "fill": 8, "fill_between": 8, "filter": 0, "filter_phot_1": 0, "filter_phot_2": 0, "filter_phot_n": 0, "final": [5, 6, 7], "final_logl": 7, "find_nearest": 0, "first": [5, 7], "fit": 8, "float": [0, 7, 8], "float64": 6, "flux": [0, 7, 8], "flx": 0, "flx_1": 0, "flx_final": 8, "flx_mod": 7, "flx_mod_extract": [], "flx_mod_nativ": 0, "flx_mod_photo": 7, "flx_mod_spectro": 7, "flx_n": 0, "flx_ob": [0, 7], "flx_obs_fin": 0, "flx_obs_photo": 7, "flx_obs_spectro": 7, "flx_phot": 0, "flx_post_doppl": 7, "fm07": 7, "folder": 5, "follow": 5, "footbal": 8, "for_plot": 7, "forg": 5, "format": 0, "formosa": [0, 2, 4, 5, 6, 7], "formula": 7, "fortran": 5, "fourth": [], "free": 7, "from": [0, 5, 6, 7, 8], "full": 8, "function": 8, "fwhm": 0, "gaussian": [0, 7], "gaussian_prior": 7, "gcc": 5, "gener": [5, 6, 7], "get": 5, "get_full_spectra": 8, "git": 5, "github": [4, 8], "given": 8, "global": 8, "global_param": [0, 7], "globfil": 6, "go": [], "gp": 7, "grid": [7, 8], "grid_us": 8, "gridlin": 8, "guid": [], "ha": 5, "harvard": 7, "here": [0, 5], "high": 8, "highest": 0, "hiris": 7, "histogram": 8, "hour": 0, "how": 6, "howev": [], "html": [], "http": [5, 6, 7, 8], "i": [0, 5, 6, 7, 8], "identif": 7, "identifi": 0, "idx": 0, "implement": 7, "import": [6, 7], "import_obsmod": 7, "importlib": 5, "includ": [0, 8], "index": [0, 4, 7], "indic": 0, "indob": [0, 7], "inform": [0, 7], "inherit": 8, "ini": [7, 8], "initi": 8, "input": [6, 7], "inst": 0, "instal": 4, "installmost": [], "instru_1": [], "instru_n": [], "instru_range_1": 0, "instru_range_n": 0, "instruct": 5, "instrument": [0, 7], "int": [0, 7, 8], "int_method": 8, "integr": 7, "interact": 6, "interpol": [7, 8], "interpret": 5, "interstellar": 7, "inv_cov": 7, "invers": [5, 6, 7], "io": [], "ipynb": 8, "ishigoya": 6, "issu": 4, "iterativli": 6, "its": [0, 4], "jason": 0, "johannesbuchn": 5, "john": 7, "justob": 0, "k": 7, "keyword": 8, "km": [7, 8], "krull": 7, "kw": 8, "label": 8, "largest": 7, "last": 5, "latest": 5, "latitud": 7, "launch": 7, "launch_adapt": 0, "launch_nested_sampl": 7, "law": 7, "ld_pick": 7, "learn": 5, "length": 8, "level": 8, "levels_sig": 8, "lib": 5, "lim_param_grid": 7, "limd": 7, "limit": 8, "line": [5, 7], "linear": [7, 8], "list": [0, 6, 7, 8], "list_down": 8, "list_up": 8, "log": 8, "logarithm": 7, "logi": 8, "logl": 7, "logl_ccf_brogi": 7, "logl_ccf_custom": 7, "logl_ccf_zuck": 7, "logl_chi2_class": 7, "logl_chi2_covari": 7, "logl_chi2_extend": 7, "logl_chi2_extended_covari": 7, "logl_full_covari": 7, "loglik": 7, "loglikelihood": 7, "logx": 8, "loop": [0, 6, 7], "lower": 8, "lowest": 0, "lsf": 0, "lsq_fct": 7, "m": 0, "m1": 5, "maco": 5, "mag": 7, "mai": 7, "main": [1, 4, 5, 8], "main_fil": 7, "main_util": 6, "make": [0, 5, 6], "manag": [0, 5], "manual": 7, "map": 7, "master": 8, "mat1": 6, "mat2": 6, "matplotlib": [5, 8], "matric": 6, "matrix": [6, 7], "matthieu": [0, 7, 8], "max": 8, "maximum": 8, "me": 7, "mean": 8, "merg": 0, "metadata": 5, "method": [7, 8], "min": 8, "miniconda": [], "minumum": 8, "minut": 0, "mod": 0, "mod_photo": 0, "mod_spectro": 0, "mode": 6, "model": [7, 8], "model_flux": 0, "model_nam": 8, "model_resolut": 8, "model_spectra": 8, "model_wavelength": 8, "model_wv": 0, "modif": 7, "modif_spec": 7, "modul": [4, 7], "more": 5, "move": 5, "mpi": 5, "mpi4pi": 5, "multinest": 5, "multipl": 8, "n": [0, 5, 6, 7], "n_ordinate_level": 8, "n_point": 8, "name": [0, 8], "nathan": 8, "need": [5, 7], "nest": [1, 4], "nested_logl_funct": 7, "nested_modif_spec": 7, "nested_prior_funct": 7, "nested_sampl": 7, "nestl": [5, 7], "netcdf4": 5, "new": 7, "next": 5, "nice": 7, "nois": 7, "none": [0, 7, 8], "norm": 8, "normal": [7, 8], "normalys": 7, "note": 7, "nr": 7, "ntheta": 7, "num_sigma": 0, "number": [0, 7, 8], "numpi": [5, 6], "ob": 0, "object": [0, 7, 8], "obs_nam": 0, "obs_opt": 0, "obs_or_mod": 0, "obs_photo": 0, "obs_photo_in": 0, "obs_spectro": 0, "obs_spectro_in": 0, "observ": 7, "omeg": 7, "onc": 5, "one": 0, "onto": 5, "open": [4, 5], "opt": 5, "option": [0, 6, 8], "order": 8, "origin": 8, "osx": 5, "other": 5, "our": 5, "output": 7, "output_model": 0, "overflow": 6, "p": 7, "packag": [4, 5], "page": 4, "palma": [0, 6, 7, 8], "paralel": 5, "parallel": [], "paramet": [0, 6, 7, 8], "path": 8, "path_cloud_profil": 8, "path_temp_profil": 8, "paulina": [0, 6, 7, 8], "pc": 7, "per": 0, "perform": 7, "petru": [0, 6, 7, 8], "photometr": [0, 7], "photometri": [0, 7, 8], "pick": 7, "pip": 5, "planet": 7, "planetari": [7, 8], "platform": [], "pleas": 5, "plot": [1, 4, 7], "plot_ccf": 8, "plot_chain": 8, "plot_cloud": 8, "plot_corn": 8, "plot_fit": 8, "plot_fit_hir": 8, "plot_hires_comp_model": 8, "plot_pt": 8, "plot_radar": 8, "plotting_class": 8, "plottingformosa": 8, "point": [0, 8], "possibl": 5, "posterior": 8, "pressur": 8, "prior_fct_arg": 7, "prior_transform": 7, "problem": 5, "proce": [], "process": 5, "profil": 8, "project": 7, "propos": 7, "py": 5, "pyasl": 7, "pyastronomi": 5, "pymultinest": [4, 7], "pypi": 4, "python": [4, 5, 6], "pyyaml": 5, "quantil": 8, "question": 6, "quickli": 7, "r": 7, "r_pick": 7, "radar": 8, "radial": [7, 8], "radiu": 7, "randomli": 7, "rang": [0, 8], "ravet": [0, 7, 8], "re": [0, 7], "re_interp": 8, "recommend": 5, "reddening_fct": 7, "reinterpol": 8, "releas": [], "rem": 6, "remov": 8, "repeat": 6, "replac": 0, "report": 8, "repositori": 5, "reproduc": 7, "requir": 5, "res_mod_nativ": 0, "res_mod_ob": 0, "res_mod_obs_merg": 0, "res_ob": 0, "resampl": 0, "residu": [7, 8], "reso_1": 0, "reso_n": 0, "resolut": [0, 8], "resolution_decreas": 0, "result": 6, "return": [0, 6, 7, 8], "right": 8, "rjup": 7, "rotat": 7, "rotation": 7, "routin": 7, "run": [5, 6], "rv_cor": 8, "rv_grid": 8, "rv_pick": 7, "rv_step": 8, "same": [7, 8], "sampl": [0, 1, 4], "scale": [7, 8], "scale_data": 8, "scipi": 5, "search": 4, "second": [0, 5], "sequenc": [], "set": [5, 7], "setup": 5, "sever": 2, "sh": [], "shape": 6, "shift": [7, 8], "side": [7, 8], "sigma": [0, 8], "sigmas_wv": 0, "similar": 7, "simon": [0, 6, 7, 8], "simul": 0, "sin": 7, "size": 8, "small": 6, "smith": 7, "solar": 7, "solv": 5, "sourc": [0, 4, 6, 7, 8], "speci": 8, "specif": 8, "specifi": 0, "spectr": 5, "spectra": [0, 8], "spectral": [0, 7], "spectroscop": 7, "spectroscopi": [7, 8], "spectrum": [0, 7, 8], "stack": 6, "stackoverflow": 6, "standard": [0, 5, 7], "star": [0, 7], "star_1": 0, "star_flx_ob": 7, "star_n": 0, "statsbomb": 8, "stellar": [7, 8], "step": [5, 8], "str": [0, 6, 7, 8], "string": 0, "strongli": 5, "sub": [0, 6, 8], "subdir": 5, "substellar": 7, "succesfulli": 7, "sure": 5, "symmetr": 8, "synthet": [0, 7], "system": 5, "system_ob": 7, "systemat": 7, "sythet": 7, "t": [], "take": 0, "task": [], "temperatur": [7, 8], "termin": [5, 6], "terminal": 6, "text": 6, "th": 7, "than": 5, "them": [0, 6], "theta": [7, 8], "theta_index": 7, "thi": [0, 4, 5, 7], "third": [], "though": 4, "thourgh": [], "throgh": [], "through": 5, "time": 7, "too": 0, "tran": 8, "tran_1": 0, "tran_n": 0, "transm_ob": 7, "transmis": 8, "transmiss": [0, 7], "tupl": 8, "two": [5, 6, 7], "type": [0, 6, 7, 8], "ui": 7, "um": 0, "uncert": 8, "uncorrel": 7, "under": [5, 7], "unifi": 7, "uniform": 7, "uniform_prior": 7, "unit": [0, 7], "up": 7, "upper": 8, "us": [0, 2, 4, 5, 6, 7, 8], "useful": 6, "user": 4, "util": [1, 4], "v": [5, 7], "vacuum": 0, "valu": [0, 7, 8], "variabl": [0, 6, 7, 8], "veloc": [7, 8], "version": [5, 7], "visualis": 8, "vmr_ch4": 8, "vmr_co": 8, "vmr_co2": 8, "vmr_feh": 8, "vmr_h2": 8, "vmr_h2o": 8, "vmr_hcn": 8, "vmr_k": 8, "vmr_na": 8, "vmr_nh3": 8, "vmr_ph3": 8, "vmr_tio": 8, "vmr_vo": 8, "vol": 7, "vsini_fct_accur": 7, "vsini_fct_fast_rot_broad": 7, "vsini_fct_rot_broad": 7, "vsini_pick": 7, "w": 0, "wai": 2, "wang": 0, "want": [0, 5], "warn": [], "wav": 0, "wav_1": 0, "wav_fin": 8, "wav_for_adapt": [0, 8], "wav_mod_nativ": 0, "wav_n": 0, "wav_ob": 0, "wav_obs_photo": [0, 7], "wav_obs_spectro": [0, 7], "wav_phot": 0, "wave": 8, "wave_bin": 8, "wave_obs_merg": 7, "wave_reso_tab": 0, "wavelength": [0, 7, 8], "we": [4, 5, 7], "welcom": 4, "were": 5, "when": [6, 7], "where": [7, 8], "which": [0, 5], "window_normalis": 8, "without": [], "work": [], "write": 5, "wtt": 7, "wull": 6, "wv_channel": 0, "xarrai": 5, "y": 6, "ye": [0, 7, 8], "yesno": 6, "you": [0, 5], "your": 5, "your_path": 5, "zimniak": 8, "zucker": 7, "\u00b2": 7}, "titles": ["Adapt the data", "ForMoSA API", "DEMO", "DEMO classic:", "Forward Modeling Tool for Spectral Analysis", "Installation", "Main Utilities", "Nested Sampling", "Plotting Class"], "titleterms": {"": [], "A": 5, "For": 5, "The": 8, "adapt": 0, "analysi": 4, "api": 1, "b": 5, "class": 8, "classic": 3, "clone": [], "conda": 5, "content": 4, "creat": 5, "data": 0, "demo": [2, 3], "document": [], "environ": 5, "extract": 0, "formosa": [1, 8], "forward": 4, "function": [0, 6, 7], "git": [], "github": 5, "global": 6, "grid": 0, "indic": 4, "instal": 5, "issu": 5, "likelihood": 7, "main": [6, 7], "model": [0, 4], "modifi": 7, "modul": 8, "nest": 7, "observ": 0, "pip": [], "plot": 8, "prior": 7, "pymultinest": 5, "pypi": 5, "sampl": 7, "spectra": 7, "spectral": 4, "tabl": 4, "though": 5, "tool": 4, "user": 5, "util": 6, "welcom": []}}) \ No newline at end of file +Search.setIndex({"alltitles": {"A. Installation though PyPI": [[5, "a-installation-though-pypi"]], "Acknowledgments:": [[4, "acknowledgments"]], "Adapt Grid:": [[0, "module-ForMoSA.adapt.adapt_grid"]], "Adapt Observations and Models:": [[0, "module-ForMoSA.adapt.adapt_obs_mod"]], "Adapt the data": [[0, null]], "Attribution:": [[4, "attribution"]], "B. Installation though GitHub": [[5, "b-installation-though-github"]], "Contents:": [[4, null]], "Create a conda environment": [[5, "create-a-conda-environment"]], "DEMO": [[2, null]], "DEMO classic:": [[3, null]], "Extraction Functions:": [[0, "module-ForMoSA.adapt.extraction_functions"]], "For PyMultiNest users": [[5, "for-pymultinest-users"]], "ForMoSA API": [[1, null]], "Forward Modeling Tool for Spectral Analysis": [[4, null]], "Global functions:": [[6, "module-ForMoSA.main_utilities"]], "Installation": [[5, null]], "Issues?": [[5, "issues"]], "Likelihood Functions:": [[7, "module-ForMoSA.nested_sampling.nested_logL_functions"]], "Main Utilities": [[6, null]], "Modify Spectra:": [[7, "module-ForMoSA.nested_sampling.nested_modif_spec"]], "Nested Main:": [[7, "module-ForMoSA.nested_sampling.nested_sampling"]], "Nested Sampling": [[7, null]], "Plotting Class": [[8, null]], "Prior Functions:": [[7, "module-ForMoSA.nested_sampling.nested_prior_function"]], "The plotting module of ForMoSA:": [[8, "module-ForMoSA.plotting.plotting_class"]], "Version Track:": [[4, "version-track"]]}, "docnames": ["adapt", "api", "demo", "demo_classic", "index", "installation", "main_utilities", "nested_sampling", "plotting"], "envversion": {"sphinx": 62, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.viewcode": 1}, "filenames": ["adapt.rst", "api.rst", "demo.rst", "demo_classic.rst", "index.rst", "installation.rst", "main_utilities.rst", "nested_sampling.rst", "plotting.rst"], "indexentries": {}, "objects": {"": [[6, 0, 0, "-", "ForMoSA"]], "ForMoSA": [[6, 0, 0, "-", "main_utilities"]], "ForMoSA.adapt": [[0, 0, 0, "-", "adapt_grid"], [0, 0, 0, "-", "adapt_obs_mod"], [0, 0, 0, "-", "extraction_functions"]], "ForMoSA.adapt.adapt_grid": [[0, 1, 1, "", "adapt_grid"]], "ForMoSA.adapt.adapt_obs_mod": [[0, 1, 1, "", "launch_adapt"]], "ForMoSA.adapt.extraction_functions": [[0, 1, 1, "", "adapt_model"], [0, 1, 1, "", "adapt_observation_range"], [0, 1, 1, "", "continuum_estimate"], [0, 1, 1, "", "convolve_and_sample"], [0, 1, 1, "", "decoupe"], [0, 1, 1, "", "extract_model"], [0, 1, 1, "", "extract_observation"], [0, 1, 1, "", "find_nearest"], [0, 1, 1, "", "resolution_decreasing"]], "ForMoSA.main_utilities": [[6, 2, 1, "", "GlobFile"], [6, 1, 1, "", "diag_mat"], [6, 1, 1, "", "yesno"]], "ForMoSA.nested_sampling": [[7, 0, 0, "-", "nested_logL_functions"], [7, 0, 0, "-", "nested_modif_spec"], [7, 0, 0, "-", "nested_prior_function"], [7, 0, 0, "-", "nested_sampling"]], "ForMoSA.nested_sampling.nested_logL_functions": [[7, 1, 1, "", "logL_CCF_Brogi"], [7, 1, 1, "", "logL_CCF_Zucker"], [7, 1, 1, "", "logL_CCF_custom"], [7, 1, 1, "", "logL_chi2_classic"], [7, 1, 1, "", "logL_chi2_covariance"], [7, 1, 1, "", "logL_chi2_extended"], [7, 1, 1, "", "logL_chi2_extended_covariance"], [7, 1, 1, "", "logL_full_covariance"]], "ForMoSA.nested_sampling.nested_modif_spec": [[7, 1, 1, "", "bb_cpd_fct"], [7, 1, 1, "", "calc_ck"], [7, 1, 1, "", "doppler_fct"], [7, 1, 1, "", "lsq_fct"], [7, 1, 1, "", "modif_spec"], [7, 1, 1, "", "reddening_fct"], [7, 1, 1, "", "vsini_fct_accurate"], [7, 1, 1, "", "vsini_fct_fast_rot_broad"], [7, 1, 1, "", "vsini_fct_rot_broad"]], "ForMoSA.nested_sampling.nested_prior_function": [[7, 1, 1, "", "gaussian_prior"], [7, 1, 1, "", "uniform_prior"]], "ForMoSA.nested_sampling.nested_sampling": [[7, 1, 1, "", "import_obsmod"], [7, 1, 1, "", "launch_nested_sampling"], [7, 1, 1, "", "loglike"], [7, 1, 1, "", "prior_transform"]], "ForMoSA.plotting": [[8, 0, 0, "-", "plotting_class"]], "ForMoSA.plotting.plotting_class": [[8, 2, 1, "", "ComplexRadar"], [8, 2, 1, "", "PlottingForMoSA"], [8, 1, 1, "", "bin_data"]], "ForMoSA.plotting.plotting_class.ComplexRadar": [[8, 3, 1, "", "fill"], [8, 3, 1, "", "fill_between"], [8, 3, 1, "", "plot"], [8, 3, 1, "", "scale_data"]], "ForMoSA.plotting.plotting_class.PlottingForMoSA": [[8, 3, 1, "", "get_FULL_spectra"], [8, 3, 1, "", "plot_Clouds"], [8, 3, 1, "", "plot_HiRes_comp_model"], [8, 3, 1, "", "plot_PT"], [8, 3, 1, "", "plot_ccf"], [8, 3, 1, "", "plot_chains"], [8, 3, 1, "", "plot_corner"], [8, 3, 1, "", "plot_fit"], [8, 3, 1, "", "plot_fit_HiRes"], [8, 3, 1, "", "plot_radar"]]}, "objnames": {"0": ["py", "module", "Python module"], "1": ["py", "function", "Python function"], "2": ["py", "class", "Python class"], "3": ["py", "method", "Python method"]}, "objtypes": {"0": "py:module", "1": "py:function", "2": "py:class", "3": "py:method"}, "terms": {"": [7, 8], "0": [0, 4, 5, 6, 7, 8], "1": [0, 4, 5, 7, 8], "10": [5, 7, 8], "100": [7, 8], "1000": 8, "11": 5, "13": [4, 5], "15": 8, "16": 8, "1994": 7, "2": [0, 7, 8], "2003": 7, "2008": 7, "2019": 7, "2020": [], "202019": 8, "2023": [4, 5, 7], "2023rnaa": 7, "20cup": 8, "20visualis": 8, "20women": 8, "20world": 8, "23": 7, "287": 7, "3": [4, 5, 8], "300": 8, "4": 5, "42154606": 6, "5": [4, 8], "50": 7, "523": 7, "534": 7, "6": 8, "65415996": [], "675": 7, "68": 8, "7": [7, 8], "84": 8, "91c": 7, "95": 8, "997": 8, "A": [4, 7], "By": [], "For": 4, "IN": 0, "If": [0, 5, 6, 7, 8], "In": [], "It": [0, 7, 8], "OF": 0, "The": [0, 5, 7], "Then": [0, 5, 7], "There": [2, 5], "To": 5, "a1": [], "a2": [], "a3": [], "a4": [], "ab": 7, "about": 5, "abov": 7, "abstract": 7, "academi": 4, "accord": 7, "acf": 8, "activ": 5, "actual": 5, "adapt": [1, 4, 7, 8], "adapt_grid": 0, "adapt_model": 0, "adapt_obs_mod": 0, "adapt_observation_rang": 0, "add": [6, 7, 8], "adpat": 8, "adsab": 7, "al": [4, 7], "align": 6, "all": [5, 6, 7, 8], "allan": [0, 7, 8], "allong": 6, "almost": 5, "alpha": 7, "also": 0, "an": [0, 4, 5, 6], "anaconda3": 5, "analyt": 7, "ani": 5, "annulu": 7, "anoth": 8, "answer": 6, "api": 4, "appl": [], "appli": [7, 8], "applic": 7, "approach": 4, "ar": [0, 2, 5, 7, 8], "arbitrari": 8, "architectur": 5, "arg": 8, "argument": 8, "arm64": 5, "arrai": [0, 6, 7, 8], "arrang": 0, "arraymatrix": 6, "associ": 8, "assumpt": 7, "astro": 4, "astropi": 5, "asw": 6, "asymmetr": 8, "atmo": 0, "atmospher": [4, 7], "attend": [], "author": [0, 6, 7, 8], "auto": 8, "automat": 5, "av_pick": 7, "ax": 8, "ax1": 8, "axi": 8, "axr": 8, "axr2": 8, "azimuth": 7, "b": 4, "b1": [], "b2": [], "b3": [], "b4": [], "back": 0, "bar": 8, "base": 7, "bb_cpd_fct": 7, "bb_r_pick": 7, "bb_rad": 7, "bb_t_pick": 7, "bb_temp": 7, "becam": [], "befor": 7, "being": [], "below": [5, 7], "best": 8, "bifani": [0, 6, 7, 8], "big": 6, "bin": [7, 8], "bin_data": 8, "bin_siz": 8, "blob": 8, "block": 6, "boolean": [0, 8], "both": 7, "bottleneck": 5, "boundari": 7, "branch": 5, "brew": 5, "broaden": [7, 8], "brogi": 7, "build": 5, "burn_in": 8, "c": [5, 7], "calc_ck": 7, "calcul": [0, 7], "calibr": 7, "call": 7, "can": [5, 7], "capabl": 4, "carvalho": 7, "ccf": [7, 8], "ccf_method": 7, "cd": 5, "chain": 8, "chang": 7, "channel": 0, "check": [7, 8], "chi2": 7, "chip": 5, "choic": 7, "choos": 8, "chosen": 7, "circum": 7, "circumplanetari": 7, "cite": 4, "ck": [7, 8], "class": [0, 1, 4, 6, 7], "classic": [2, 4, 7], "clone": 5, "closest": 0, "cloud": [4, 8], "cloud_opacity_f": 8, "cloud_opacity_mg2sio4": 8, "cloud_particle_radius_f": 8, "cloud_particle_radius_mg2sio4": 8, "cloud_prop": 8, "cloud_vmr_f": 8, "cloud_vmr_mg2sio4": 8, "cmake": 5, "co": 7, "code": 4, "coeffici": 7, "color": 8, "color_out": 8, "com": [5, 6, 8], "command": [], "commun": 4, "companion": 7, "compar": [0, 8], "complexradar": 8, "comput": 7, "concaten": 6, "conda": 4, "conda_subdir": 5, "config": [5, 6, 7, 8], "config_file_path": [6, 8], "configobj": 5, "consist": 7, "constant": 7, "construct": 6, "cont": 0, "contain": [0, 7, 8], "continuum": 0, "continuum_estim": 0, "continuum_unfilt": 7, "contour": 8, "contribut": 7, "converg": 8, "convolv": 0, "convolve_and_sampl": 0, "copi": 5, "corner": [5, 8], "correctli": 8, "correl": [7, 8], "corrobor": 5, "count": 7, "cov_1": 0, "cov_n": 0, "covari": [0, 7], "cp": [5, 7], "cpd": 7, "creat": [4, 8], "cross": 8, "ctt": 7, "cummin": 8, "current": [0, 7, 8], "curv": 8, "cush": 7, "custom": [0, 7, 8], "d": 7, "d_pick": 7, "damian": 8, "damiancummin": 8, "darken": 7, "dask": 5, "data": [1, 4, 7, 8], "data_bin": 8, "data_resolut": 8, "deal": 7, "decid": 6, "decoup": 0, "decreas": 0, "default": [0, 7, 8], "defin": [0, 7], "delta_flx": 7, "demo": 4, "deni": [0, 7, 8], "densiti": 8, "depend": [5, 7], "design": 4, "desir": [0, 5, 8], "detail": 5, "deviat": [0, 7], "diag": 6, "diag_mat": 6, "diagon": 6, "dif": 7, "differ": [0, 6, 7, 8], "differenti": 7, "dilut": 7, "directli": [], "directori": 5, "disc": 7, "disk": 7, "displai": 8, "distanc": 7, "distribut": [4, 8], "do": 5, "doc": [], "document": 4, "doe": 8, "don": [], "doppler": 7, "doppler_fct": 7, "dopplershift": 7, "dream": [], "dtype": 6, "due": 7, "dure": 6, "each": [0, 6, 7, 8], "eddy_diffusion_coeffici": 8, "edu": 7, "effect": 7, "empi": 6, "empti": [5, 6], "encourag": 4, "env": 5, "env_formosa": 5, "environ": 4, "eq": 7, "err": 7, "err_1": 0, "err_n": 0, "err_ob": 7, "err_obs_photo": 7, "err_obs_spectro": 7, "err_phot": 0, "error": [0, 5, 7, 8], "estim": [0, 7], "et": [4, 7], "evalu": [0, 7], "event": 8, "everi": 7, "exoatmospher": 5, "exoplanetari": 4, "exorem": 8, "exploit": 4, "explor": [0, 7], "express": 7, "extend": 7, "extens": 7, "extim": 7, "extinct": [5, 7], "extra": [5, 7], "extract": [6, 8], "extract_model": 0, "extract_observ": 0, "extraction_funct": 0, "factor": [7, 8], "fals": 8, "few": 5, "fig": 8, "fig1": 8, "figsiz": 8, "figur": 8, "file": [0, 5, 6, 7, 8], "fill": 8, "fill_between": 8, "filter": 0, "filter_phot_1": 0, "filter_phot_2": 0, "filter_phot_n": 0, "final": [5, 6, 7], "final_logl": 7, "find_nearest": 0, "first": [4, 5, 7], "fit": 8, "float": [0, 7, 8], "float64": 6, "flux": [0, 7, 8], "flx": 0, "flx_1": 0, "flx_final": 8, "flx_mod": 7, "flx_mod_extract": [], "flx_mod_nativ": 0, "flx_mod_photo": 7, "flx_mod_spectro": 7, "flx_n": 0, "flx_ob": [0, 7], "flx_obs_fin": 0, "flx_obs_photo": 7, "flx_obs_spectro": 7, "flx_phot": 0, "flx_post_doppl": 7, "fm07": 7, "folder": 5, "follow": 5, "footbal": 8, "for_plot": 7, "forg": 5, "format": 0, "formosa": [0, 2, 4, 5, 6, 7], "formula": 7, "fortran": 5, "fourth": [], "free": 7, "from": [0, 5, 6, 7, 8], "full": 8, "function": 8, "fwhm": 0, "gaussian": [0, 7], "gaussian_prior": 7, "gcc": 5, "gener": [5, 6, 7], "get": 5, "get_full_spectra": 8, "git": 5, "github": [4, 8], "given": 8, "global": 8, "global_param": [0, 7], "globfil": 6, "go": [], "gp": 7, "grid": [7, 8], "grid_us": 8, "gridlin": 8, "guid": [], "ha": 5, "harvard": 7, "here": [0, 5], "high": 8, "highest": 0, "hiris": 7, "histogram": 8, "hour": 0, "how": 6, "howev": [], "html": [], "http": [5, 6, 7, 8], "i": [0, 5, 6, 7, 8], "identif": 7, "identifi": 0, "idx": 0, "implement": 7, "import": [6, 7], "import_obsmod": 7, "importlib": 5, "includ": [0, 8], "index": [0, 7], "indic": 0, "indob": [0, 7], "inform": [0, 7], "inherit": 8, "ini": [7, 8], "initi": 8, "input": [6, 7], "inst": 0, "instal": 4, "installmost": [], "instru_1": [], "instru_n": [], "instru_range_1": 0, "instru_range_n": 0, "instruct": 5, "instrument": [0, 7], "int": [0, 7, 8], "int_method": 8, "integr": 7, "interact": 6, "interpol": [7, 8], "interpret": 5, "interstellar": 7, "inv_cov": 7, "invers": [5, 6, 7], "io": [], "ipynb": 8, "ishigoya": 6, "issu": 4, "iterativli": 6, "its": [0, 4], "jason": 0, "johannesbuchn": 5, "john": 7, "justob": 0, "k": 7, "keyword": 8, "km": [7, 8], "krull": 7, "kw": 8, "label": 8, "largest": 7, "last": 5, "latest": 5, "latitud": 7, "launch": 7, "launch_adapt": 0, "launch_nested_sampl": 7, "law": 7, "ld_pick": 7, "learn": 5, "length": 8, "level": 8, "levels_sig": 8, "lib": 5, "lim_param_grid": 7, "limd": 7, "limit": 8, "line": [5, 7], "linear": [7, 8], "list": [0, 6, 7, 8], "list_down": 8, "list_up": 8, "log": 8, "logarithm": 7, "logi": 8, "logl": 7, "logl_ccf_brogi": 7, "logl_ccf_custom": 7, "logl_ccf_zuck": 7, "logl_chi2_class": 7, "logl_chi2_covari": 7, "logl_chi2_extend": 7, "logl_chi2_extended_covari": 7, "logl_full_covari": 7, "loglik": 7, "loglikelihood": 7, "logx": 8, "loop": [0, 6, 7], "lower": 8, "lowest": 0, "lsf": 0, "lsq_fct": 7, "m": 0, "m1": 5, "maco": 5, "mag": 7, "mai": 7, "main": [1, 4, 5, 8], "main_fil": 7, "main_util": 6, "make": [0, 5, 6], "manag": [0, 5], "manual": 7, "map": 7, "master": 8, "mat1": 6, "mat2": 6, "matplotlib": [5, 8], "matric": 6, "matrix": [6, 7], "matthieu": [0, 7, 8], "max": 8, "maximum": 8, "me": 7, "mean": 8, "merg": 0, "metadata": 5, "method": [7, 8], "min": 8, "miniconda": [], "minumum": 8, "minut": 0, "mod": 0, "mod_photo": 0, "mod_spectro": 0, "mode": 6, "model": [7, 8], "model_flux": 0, "model_nam": 8, "model_resolut": 8, "model_spectra": 8, "model_wavelength": 8, "model_wv": 0, "modif": 7, "modif_spec": 7, "modul": 7, "more": 5, "move": 5, "mpi": 5, "mpi4pi": 5, "multinest": 5, "multipl": 8, "n": [0, 5, 6, 7], "n_ordinate_level": 8, "n_point": 8, "name": [0, 8], "nathan": 8, "need": [5, 7], "nest": [1, 4], "nested_logl_funct": 7, "nested_modif_spec": 7, "nested_prior_funct": 7, "nested_sampl": 7, "nestl": [5, 7], "netcdf4": 5, "new": 7, "next": 5, "nice": 7, "nois": 7, "none": [0, 7, 8], "norm": 8, "normal": [7, 8], "normalys": 7, "note": 7, "nr": 7, "ntheta": 7, "num_sigma": 0, "number": [0, 7, 8], "numpi": [5, 6], "ob": 0, "object": [0, 7, 8], "obs_nam": 0, "obs_opt": 0, "obs_or_mod": 0, "obs_photo": 0, "obs_photo_in": 0, "obs_spectro": 0, "obs_spectro_in": 0, "observ": 7, "omeg": 7, "onc": 5, "one": 0, "onto": 5, "open": [4, 5], "oper": 4, "opt": 5, "option": [0, 6, 8], "order": 8, "origin": 8, "osx": 5, "other": 5, "our": [4, 5], "output": 7, "output_model": 0, "overflow": 6, "p": 7, "packag": [4, 5], "page": [], "palma": [0, 6, 7, 8], "paralel": 5, "parallel": [], "paramet": [0, 6, 7, 8], "path": 8, "path_cloud_profil": 8, "path_temp_profil": 8, "paulina": [0, 6, 7, 8], "pc": 7, "per": 0, "perform": 7, "petru": [0, 4, 6, 7, 8], "photometr": [0, 7], "photometri": [0, 7, 8], "pick": 7, "pip": 5, "planet": 7, "planetari": [7, 8], "platform": [], "pleas": [4, 5], "plot": [1, 4, 7], "plot_ccf": 8, "plot_chain": 8, "plot_cloud": 8, "plot_corn": 8, "plot_fit": 8, "plot_fit_hir": 8, "plot_hires_comp_model": 8, "plot_pt": 8, "plot_radar": 8, "plotting_class": 8, "plottingformosa": 8, "point": [0, 8], "possibl": 5, "posterior": 8, "present": 4, "pressur": 8, "prior_fct_arg": 7, "prior_transform": 7, "problem": 5, "proce": [], "process": 5, "profil": 8, "project": 7, "propos": 7, "py": 5, "pyasl": 7, "pyastronomi": 5, "pymultinest": [4, 7], "pypi": 4, "python": [4, 5, 6], "pyyaml": 5, "quantil": 8, "question": 6, "quickli": 7, "r": 7, "r_pick": 7, "radar": 8, "radial": [7, 8], "radiu": 7, "randomli": 7, "rang": [0, 8], "ravet": [0, 7, 8], "re": [0, 7], "re_interp": 8, "realiti": [], "recommend": 5, "reddening_fct": 7, "reinterpol": 8, "releas": 4, "rem": 6, "remov": 8, "repeat": 6, "replac": 0, "report": 8, "repositori": 5, "reproduc": 7, "requir": 5, "res_mod_nativ": 0, "res_mod_ob": 0, "res_mod_obs_merg": 0, "res_ob": 0, "resampl": 0, "residu": [7, 8], "reso_1": 0, "reso_n": 0, "resolut": [0, 8], "resolution_decreas": 0, "result": 6, "return": [0, 6, 7, 8], "right": 8, "rjup": 7, "rotat": 7, "rotation": 7, "routin": 7, "run": [5, 6], "rv_cor": 8, "rv_grid": 8, "rv_pick": 7, "rv_step": 8, "same": [7, 8], "sampl": [0, 1, 4], "scale": [7, 8], "scale_data": 8, "scipi": 5, "search": [], "second": [0, 5], "sequenc": [], "set": [5, 7], "setup": 5, "sever": 2, "sh": [], "shape": 6, "shift": [7, 8], "side": [7, 8], "sigma": [0, 8], "sigmas_wv": 0, "similar": 7, "simon": [0, 6, 7, 8], "simul": 0, "sin": 7, "sincer": 4, "size": 8, "small": 6, "smith": 7, "solar": 7, "solv": 5, "sourc": [0, 4, 6, 7, 8], "speci": 8, "specif": 8, "specifi": 0, "spectr": 5, "spectra": [0, 8], "spectral": [0, 7], "spectroscop": 7, "spectroscopi": [7, 8], "spectrum": [0, 7, 8], "stack": 6, "stackoverflow": 6, "standard": [0, 5, 7], "star": [0, 7], "star_1": 0, "star_flx_ob": 7, "star_n": 0, "statsbomb": 8, "stellar": [7, 8], "step": [5, 8], "str": [0, 6, 7, 8], "string": 0, "strongli": 5, "sub": [0, 6, 8], "subdir": 5, "substellar": 7, "succesfulli": 7, "sure": 5, "symmetr": 8, "synthet": [0, 7], "system": 5, "system_ob": 7, "systemat": 7, "sythet": 7, "t": [], "ta": [], "take": 0, "task": [], "temperatur": [7, 8], "termin": [5, 6], "terminal": 6, "text": 6, "th": 7, "than": 5, "thank": 4, "them": [0, 6], "theta": [7, 8], "theta_index": 7, "thi": [0, 4, 5, 7], "third": [], "though": 4, "thourgh": [], "three": [], "throgh": [], "through": 5, "time": 7, "too": 0, "tran": 8, "tran_1": 0, "tran_n": 0, "transm_ob": 7, "transmis": 8, "transmiss": [0, 7], "tupl": 8, "two": [5, 6, 7], "type": [0, 6, 7, 8], "ui": 7, "um": 0, "uncert": 8, "uncorrel": 7, "under": [5, 7], "unifi": 7, "uniform": 7, "uniform_prior": 7, "unit": [0, 7], "up": 7, "upper": 8, "us": [0, 2, 4, 5, 6, 7, 8], "useful": 6, "user": 4, "util": [1, 4], "v": [5, 7], "vacuum": 0, "valu": [0, 7, 8], "variabl": [0, 6, 7, 8], "veloc": [7, 8], "version": [5, 7], "visualis": 8, "vmr_ch4": 8, "vmr_co": 8, "vmr_co2": 8, "vmr_feh": 8, "vmr_h2": 8, "vmr_h2o": 8, "vmr_hcn": 8, "vmr_k": 8, "vmr_na": 8, "vmr_nh3": 8, "vmr_ph3": 8, "vmr_tio": 8, "vmr_vo": 8, "vol": 7, "vsini_fct_accur": 7, "vsini_fct_fast_rot_broad": 7, "vsini_fct_rot_broad": 7, "vsini_pick": 7, "w": 0, "wai": 2, "wang": 0, "want": [0, 5], "warn": [], "wav": 0, "wav_1": 0, "wav_fin": 8, "wav_for_adapt": [0, 8], "wav_mod_nativ": 0, "wav_n": 0, "wav_ob": 0, "wav_obs_photo": [0, 7], "wav_obs_spectro": [0, 7], "wav_phot": 0, "wave": 8, "wave_bin": 8, "wave_obs_merg": 7, "wave_reso_tab": 0, "wavelength": [0, 7, 8], "we": [4, 5, 7], "welcom": 4, "were": 5, "when": [6, 7], "where": [7, 8], "which": [0, 5], "window_normalis": 8, "without": [], "work": [], "workshop": [], "write": 5, "wtt": 7, "wull": 6, "wv_channel": 0, "xarrai": 5, "y": 6, "ye": [0, 7, 8], "year": [], "yesno": 6, "you": [0, 5], "your": 5, "your_path": 5, "zimniak": 8, "zucker": 7, "\u00b2": 7}, "titles": ["Adapt the data", "ForMoSA API", "DEMO", "DEMO classic:", "Forward Modeling Tool for Spectral Analysis", "Installation", "Main Utilities", "Nested Sampling", "Plotting Class"], "titleterms": {"": [], "A": 5, "For": 5, "The": 8, "acknowledg": 4, "adapt": 0, "analysi": 4, "api": 1, "attribut": 4, "b": 5, "class": 8, "classic": 3, "clone": [], "conda": 5, "content": 4, "creat": 5, "data": 0, "demo": [2, 3], "document": [], "environ": 5, "extract": 0, "formosa": [1, 8], "forward": 4, "function": [0, 6, 7], "git": [], "github": 5, "global": 6, "grid": 0, "indic": [], "instal": 5, "issu": 5, "likelihood": 7, "main": [6, 7], "model": [0, 4], "modifi": 7, "modul": 8, "nest": 7, "observ": 0, "pip": [], "plot": 8, "prior": 7, "pymultinest": 5, "pypi": 5, "sampl": 7, "spectra": 7, "spectral": 4, "tabl": [], "though": 5, "tool": 4, "track": 4, "user": 5, "util": 6, "version": 4, "welcom": []}}) \ No newline at end of file diff --git a/docs/index.rst b/docs/index.rst index 01814bf..cf02986 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -29,9 +29,24 @@ We encourage the community to exploit its capabilities! api.rst -Indices and tables -================== -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` +Attribution: +++++++++++++ + +Please cite `Petrus et al (2023) `_. + + + +Version Track: +++++++++++++++ + +``1.0.13`` +First version distributed, presented at `Cloud Academy 3. `_. + +``1.0.5`` +First operational release. + + +Acknowledgments: +++++++++++++++++ +Our sincere thanks to `Code/Astro `_. diff --git a/setup.py b/setup.py index 3450d80..a1688bb 100644 --- a/setup.py +++ b/setup.py @@ -1,8 +1,21 @@ -from setuptools import setup +from setuptools import setup, find_packages, Extension +import numpy, sys +import re + with open("README.md", "r") as fh: long_description = fh.read() + +# auto-updating version code stolen from RadVel +def get_property(prop, project): + result = re.search( + r'{}\s*=\s*[\'"]([^\'"]*)[\'"]'.format(prop), + open(project + "/__init__.py").read(), + ) + return result.group(1) + + def get_requires(): reqs = [] for line in open('requirements.txt', 'r').readlines(): @@ -10,12 +23,12 @@ def get_requires(): return reqs setup(name='ForMoSA', - version='2.0.0', + version=get_property("__version__", "exoSpin"), description='ForMoSA: Forward Modeling Tool for Spectral Analysis', url='https://github.com/exoAtmospheres/ForMoSA', author='P. Palma-Bifani, S. Petrus, M. Ravet, A. Denis, M. Bonnefoy, G. Chauvin', author_email='paulina.palma-bifani@oca.eu', - license='BSD 2-Clause License', + license='BSD 3-Clause License', packages=['ForMoSA', 'ForMoSA.adapt', 'ForMoSA.nested_sampling', 'ForMoSA.plotting'], install_requires=get_requires(), include_package_data = True,