From 631f7756288f283cface8050a7cb95885029842a Mon Sep 17 00:00:00 2001
From: Josh Jeppson <joshua.jeppson@usu.edu>
Date: Tue, 27 Sep 2022 14:52:17 -0600
Subject: [PATCH 1/5] gitignore and remove pycache

---
 .gitignore                                    |  21 ++++++++++++++++++
 scripts/__pycache__/depgraph.cpython-310.pyc  | Bin 6321 -> 0 bytes
 scripts/__pycache__/depgraph.cpython-39.pyc   | Bin 6296 -> 0 bytes
 .../__pycache__/prefix_parser.cpython-310.pyc | Bin 1829 -> 0 bytes
 .../__pycache__/prefix_parser.cpython-39.pyc  | Bin 1801 -> 0 bytes
 .../__pycache__/reactions_v5.cpython-310.pyc  | Bin 23276 -> 0 bytes
 .../__pycache__/reactions_v5.cpython-39.pyc   | Bin 22221 -> 0 bytes
 7 files changed, 21 insertions(+)
 create mode 100644 .gitignore
 delete mode 100644 scripts/__pycache__/depgraph.cpython-310.pyc
 delete mode 100644 scripts/__pycache__/depgraph.cpython-39.pyc
 delete mode 100644 scripts/__pycache__/prefix_parser.cpython-310.pyc
 delete mode 100644 scripts/__pycache__/prefix_parser.cpython-39.pyc
 delete mode 100644 scripts/__pycache__/reactions_v5.cpython-310.pyc
 delete mode 100644 scripts/__pycache__/reactions_v5.cpython-39.pyc

diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..9e63f40
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,21 @@
+# Files created by OS
+.DS_Store
+desktop.ini
+.directory
+
+# Things visual studio code creates
+.vscode
+
+# Some editors create a yourfile.name~ file as a backup file
+.py~
+.ivy~
+.sm~
+.prism~
+.csl~
+.xml~
+.bak
+
+# Python distribution files
+.Python
+__pycache__/
+.pyc
diff --git a/scripts/__pycache__/depgraph.cpython-310.pyc b/scripts/__pycache__/depgraph.cpython-310.pyc
deleted file mode 100644
index a3f146fefa1ab7dd5296a57f454d1b1b4bdf0f23..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 6321
zcmb7IO^h5z74GW4>FN2|*&pwZlR!I(Ars<tVn;|2+lkp-$E%pJ*&PEODU8Nbz1~^R
z_Uu;o#PO&{7_IME2yQ`I;|sZP<HP~w5V#?3NX-R7E|DTGks@I!f$zQUnO!?UQF_!h
zRj;aEy?*uTd+$}RRB|;uzg>R1{i~{`{fioh9|Mio@P?Zxq}I@+ka|}%1pn&|9sfqx
z*ftxc&|cT1DXqJjwD$CdC2g6zt2OMrCMRTGx_3n*$Mu3NqVD*4S-PpKQ@$h1(%I96
zCiQiGtChh^?wa3fN1a~a^{#LE?I`rZsHc2S`cbRX4ZYU&UO)0wHYi+lKZJl<ttt}x
z`{#eWTC2CIefSxF%6CEaHGG1`;_DF7kcKqz5Amgqe@o`1gMVA*{oIBwU0JwmHXK=8
z*Q%w&8Ohcro}-8AI^HF`;cF;j5o=8?)=`QZ8cLl@gG-Z3OVSuy(wLkyP&!P>OARZT
zH6_63!~f#BP<0bCXl?t6salbr<oVNEK@=v=j_S!iRFveUzvBloyc{Hjw7S&m2T|hs
zZ~N^&X){dBsN<_7*AM-!ABIWA4_eo|zO46Fc#K~)5)*wJ%EHphM)9tuD)@VN`s8MB
z+dtWD1+o`x`5PNi>vp%NPO8?8sI%>>lVMwRcB1ekmcF4{JDZC;w-cw?>;#>t*(`%a
zID^6#kN;dTm>j8eaWuY7x*R=JC;gIcKPF*fZA;r1vA8c_Hqh0(qE^*a4n2w8+94&N
zIYCWlq$vJ~w3wuhLQ6_s6-s;pgpX;FiWtm{ML9I!|4O5#F-y^RVL^xLN76bkp3Ao8
z@wHvBzLM_R*J;i?iox{Zg|pr^?ZW8Eqe5-Au-~8}#n2*6ENgE%Lpz2Y-85858bfQ>
ziY;|15|JK@J^V1@^e_io%q@^zqMX-;PHa$3nmC5f#|~zj;maA#0&SIPnp$O>G-6XN
z!BWjF4O~&~32D!3XEd3E-QxJuKJ3m?$(C%e4Lh|u8}Wriv=R}1NCvG;6je(R^dy#Q
z1vmV}==y;wQD>1l^XcXl1OFD=Pp8!llLED(mb&4?)=7oUo@$2u>xsS7QhpFMraHj}
zS)1QHI0!-}qLbLt??$b)$M>Pq-t^lyn>Y*`{ceEs@H7_Z!n9rC2vg{HOi{t_Io;Mx
zeTHopv`^gPU}3ypk8??E<wt!LwCQU{583Z{_x^$gX?07R(}u8Psn2N<we>xbQH+dY
zj45VDF~<}uqgZ2#ol)#DC6`fhM3Kxra-uxeax=?V7{W@VlZ|s@eF1Xu=zK;i5REA=
zNw>R<*+u1JRw0!ZXjQBw!W}r?32zMm<qZlcgcC%01J}(A8ucUS*zI?eFTE6V2$#IU
zjJuLT(IZsbtpl&TK^c6PQ*`q#2i`;B4RRjAPUtprSJziAt*ozCOAK0x5k`uUivb}$
zl?5nV5eBh+sjpFuj~*Q=wnVnRs*xI=Q0iIgAgnor8M$T?yqnDnAcu5lT`@KO&7$@q
z41~;PP#GIXHl<e06BrVNH=BvuY;FUzyHqbWo4fs1H|<eVwBj5UN2&NG72l%b1QiGJ
zaE*XWkzvv2g>-Tp%`u#kV>-svv)t3B!!~*d&IzO#L1I*5eT!`(PVGXV4GRPk01+bi
zBWdjEKc5(yv9WKaXq(r5gp+RKw`Zhh{v|CuehWBEziW7j2k@p0Y_hg2po^(qiR_qg
z$BK<TAjR$p#s;hQP~;gM6ajDw3%S(sjQ1undw_FBRo=R!w4*vfbVd0aowxn4YA4P{
z2jIc3ai<k+W{3}?N-S!JiP%st5dQ<^vEELD_CvhkEQ+!y8%5y?UH3k9O;?oZ<bS4U
zOubDuGJ0rNNZYJJ2M79wHq7I7@fIR{{GJ#Vag>V;x@U)_*o;d6SphX%Nb7)DPyoQ?
zILCdY?&spNG#G$W8iDdDrfK2Jfb?>l-`C?ZIlS0KO{baMDvap6JVqKsMcq*wks+<f
zB$?)Le1(R#jduP}JBKzy1NGw@Cg3!%LIw@>VTIcxC-TN{GA_gwd=F$*zm8q1V`C=)
z8P;2xdMBQMG~8y{9Q6*?bg~f$r_vd01aFNwY3jX4IOV|Uz0Yxa?-5S!VNSb2Jh80Z
z6L0<j@;Uc}nuv@&m?CBr=(}QD{R8zP47wCgZrQRN+gtXYEwsRWoKDoyyfK#v=nxSq
z=oOf7TAPf`tTqLWrnG5jF0IYP1**|%F*F02j<aOXj(D;hN7B(G>+bu|{#0zSGoOy9
zpvP&_;XSci<rX+m8@4brwy&$hBXK@HlI{oA=<se$Zowh2{ml<&VJYaxYF0eEps^%=
zIwzjFX<|;+8qQ#)8s2kbjwJOjGLEnj=6LiF$K06Xy>w1N%Xp64%=H#?o!oNbnK?+(
zbXXG)pv_sxmB#*JI5+;P=Y|zXO_nve1zUg=f5n-}td3iAus@=|pVEhOSmE8Y9?x-4
zHY4kywNv`vX~p4OJO?@G+|G|zed^Gv>5ly;p2sfm$|QNV8y_4{M-=c`81s4I5Fe6W
zS1-g1;A8R^Wqi^WP(erk^YH?I-5j)o+8NB*bq?n6DnxNG_5!pvAJ52zc%DuXT1UCH
zK&{xuh^w$|LWoJ4hdSZI4A)7YMQBG4TU5(dmw@KUW|6ty1n5sPQj~C3NFKO^cpg$s
z#gjlQXD?4Sy<cWpF1GIzoWIX-{zQ!tJjHU3^PU7w4oZlQwmWSEaGvMo2PKZg>Kw&U
z6Jgv*#Bh;9x|bi6mna|`=XHa8)I$P@lrP{aVupU(ADlYzm7j)LUtL*iILyBj+!z!t
zsNS}h29AT-OPw(CdK(_P$Ff4Y*`>as$kJOyREZeWTaOUi9HM96!DJf0Okt*%QcsK~
z(fBdnaqL6Nm|YFLXwwgU4-r5RVGSQz$`6irg0T*~O~}?$w->#oYfG0_yycbp%2Iu0
zdC~piNGh+MVzrM}Kfe+AYG6~S73K%UOk$>1C(;;*qan&$;4#U$rU3_MGZe9=Vbnnc
zbr3R9#F4ny`<<?QoiaWSSE@%FNV?hx!QqV4Je4!ge0!vX#GxpiWBOc_#q$-F<?_w!
zd(|_vGzH|8;X*3xS_5e<6r6rTBOmy_B+Z5mqy}mA2hr_@6ZE&4td0|lZ=h(DXuv2Y
zLrBo(kf32JUaq05%|=f7yQC$K{1UO#C~tRyEGA{TN8FB4@mM55Hws<6;Rh&8(?kI1
zh$7+%${S4Knq^TGMdS~ZNmK;>jS47Jh%!tuk4WQiUH`-_*~m61jGPxU__q<49Q=v~
z<<CXDx^5Z{coc<+waVZ(gA()Zn4gwSYE>}Lxl=T0yr~zlei;;uCGK~MIyiv`$%)`K
ztC3WY@y--vDC=cmqrWKT!2>esPZ}8a3q@c2NKQ-{Fy(U`7X1mSG$0Z89Yfr93~|>n
zv=CGv2tqXZXUbIf#eHpGzpo)D&8eetjw8-v05fDe05y{wVw~Hz?o)1CK&Gni+Y!N!
zpjiZFyT>2nayH|#3@*r!KF1|L%p;1mBZtBt=5X;b4nN5__}~Bs`h^_KM>ury0N6*q
z<xa-qXThaZ{viSti7XqzA%dR>EyUN(yhiyH0>uJ?pyHlBEXn+^92KQ=Fk+9Q=x2r#
zl0uyca^328(jJy~AIQR(^84KfaasK_F72068h_aXw9AjQt$jN#abI*eeh(Z(?|(ZS
zy<@K`u}~jC2MA#~B%F+jkP17)0l-tk3AjYa0~dypLkKgi%iK*1PT7Qmuw}a1M_lKy
zb@!ua0(S)#9189d;);YL!R-V&6oFZ1MuAbfF4mvmJ;>zXz^H_9y0lf16<+n*a8@N6
z1Lu!yC7lNir9srpa5|pG*i@!<)F<zWa2<1|x29+oG(Lryuf-@;i)Cnn3%fsZXt9N?
zcB;lek!XYJ%G%oHHE*>B1ite6+W9LNk9kYyYqiUDZ*ArLvUg#1ZN2VYTCJ@Np8t}e
z>nlr_Ys=}_FJoK3xVn}OO)pXy-7h>8=MwSa;MCc#{3vqD?4t+MwUs5L&F9yy(HAV$
zS1;Gr*@X{Yb+6Wlbn*Q6;Bl_3UB0riR=;-4yVmO~4|iJETh}|?PITMr;3l>o^|o6P
zdHC*aZ{VxmF}FIcPGK2N#bmb=_=$zQxwE6bLsS#le+0@7Sfq&^CAf(Jj8CkMZm$)k
zZpk1?**9@2%t<i;PnyE>Wf8fj>P%wO#ZT8)uTk$AD$Y`Ij*3@MBxWbri4v1VG06`l
z##^m!!wQMguoR__d}V<9DDp#%N_eXiwKwa%(Y;0LOI{_8<dYhOen2BP>Gt%C(#xc{
z-MZ=H%7Pu^w19W`CFYs%2lOlI<R1vzi@@oFI{d<zUJ*KDua0pJM!A?bi}5r^M;*RI
zN5=YZ-FWh!=4q2K9e%|_Z&9B&QXfJy9p-4>aV#2>@-gqAAAOKTS8JpqTuy8w&T2LX
zlZ%TdaXaC67e`mSRZ++NGj2a*uZ<fE6Z^f1YnIz#qxAN6SM9VH+uaW0Bn9A4FC;i~
zW;emy)gpBqxJ|C{HLP<cy$Cr64QU}6C!D7V_lbnuc|)IYbJ|b!r(N5*S=P<Z{s&D#
BsU83T

diff --git a/scripts/__pycache__/depgraph.cpython-39.pyc b/scripts/__pycache__/depgraph.cpython-39.pyc
deleted file mode 100644
index 3300b8a91d928b4106558e9df3ea4a12a0a94803..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 6296
zcmb7I&5t8T74PaVx7#1%@i_CbETIz;6o<|1CPENk30Y=llM#z|@fyflLB{Lq+3~EW
zJyYEdS*tA$6Gah1WQ0J9P!!ExA|gfn1&9OUfDqz<5JD}K3l}0q9COG8e(!bL>m5KS
zJ>%+Eud3dA_3HKesBWp`YIwYrhkHM(YuewbGyfRqJd0oWJv35lYf?ykAlic8dRxca
z7#RCz+Z5V!nlz>LiYBciy=_Tb=3dd-wp@^T>AoV`Ia!efSp?+xd0D!xs~3GomZfu~
z3r*_Rwff@tNw?{Ddr^NFc*C1}elH5WFd8b~lYZ3g4??edb2y4Tl}!rQ-S;7w)~Jib
z{>G&jwi~S;_2-}27QO_muR(N;#nvI5Aq{Eb4Y8$-w<UAZ!Q1w8GXJKKt}MJ_wjEi7
zaHYhV%GM*A(}!RkzYYAtXVJtW);e0OqZPL_v^uv2w<foiq&c>vIXP*dbr_SE8aSB^
zB|zu>f8n`YcM~({?)!<Ux{;scdF$OE3KQo*4dn<bO7hY_@B<lM4U$3%ZVX33l(_!O
zes4tD3==cz`zpzeLVw_gVN&sf?#+QOTf;4$<JXPE#Mq9qz*^a8-qBPAuaD~IcZd7_
z`9U|3!{EH?-irGBzB(WFRR16f&x7GD)jil<Ke&@PolZaKN1aX?3&R>3P1yhOH(s17
za(z0#M;e?y1d~=-qa;GC?P(_>7Iy^<1sZxsH0rv_VI;A;2efr`7pUt@)x)Bv%_0pH
zx>7P%sO}R$gv?NkYco;iCVV_;)Dq}H00%Ecd!7oD%MR$YEG}4GOV938bD}KGi;|7^
z=rpEJ9su=OFK+>mVq%eQHns0oCUy*ax@{;|8WZc#jV<-lNJM%pj_`*Wa*~5h=GMqQ
z(XMI}CpHL@CO*Yh>|nJS?q)a(xO0rt)H$|IBR18muvl|X168y~LfWg^MNQ^lzxezQ
ze|~r_u-TdowqvK!Vne>1h;Aan_sOW0iKcETayyBoy1^|!F$R91N;Fuc!F+m@#lZhQ
zTT{O~2$KT!qOQ8-!`?}OouTT4qnn9+&{cjAwX6MLhiuR9-1``WOhiAir9X(e&C{n)
z>FxTx+Z}umJEK8>Z{lGv56_~}Y*V<xf!&&-A}ac0x~-d{hQ6bZ*Jh`5dOi6d<wqkG
z^k}Ekhb(z^YJWtBw7I9PXcJhp)K|2K`udT`Fh+(kW*9TWm@|x(VXPU(&M@{2lgltU
z!bqkbIZ+<G+{_}Ln!q}wlg)EueGPK)?0kkR5RNe}Nq6`fRu|Rpv8s?t3vX3yB*Gm#
z-V<IE4$2!BQWs7x${V|GX2^gaz`)_CuYBpHK8O60H?Fx`sVlk<Yr8G@D{ou|-Obdy
zc~=APBjJs69yy@UZRfsqee25B_3QN#JFUbBBgLMJT|@dk7NBrN-iU2W(ebKJQbQjT
zTOnIs-AIj2C`D#)+E#L%4rq5emoXNuqS0U=)!E-NpbKOkVqBS-N4BI<&y!mu7vAY4
zZl|*kr#&FJ*y$XOx`T8?Rf+8~HAG)MN(~~iranszdBM4cT$&=oqV0wBEjfl$a!j<3
zFuq5h+4Lc2PR@z_#uz}X@3BS1sZ|K{VSo7kb=8azjihm;zkYUN#>R=6dfo59@0$2K
zGExuxq!vDZK@<FU11(X2k2wo}WbIk-D5iQLvSac!R%{%RcX)w)g4Os)<k>5zHAs@W
zgIpSPX6KTaLpXKzrF?8j=|J^^=$i6(`Y-!o-A<gHKAZ-J#e;6NoB4ehRANy-OvH|Q
zoao<E9P8{!;J%GtNO(<@jj|{TSNCw7u23}E>XBtkpECeR$E>;{KI2>3B#)nqUm?P_
zkHn;i54gxKc04J?W?X_x6;QyBQWy>u7`WSVoZ~T4^R>7v4R*IFj$E*0oEGlFftTa_
zi5{0J;KeQ=omO(MFvTC9r8&|dEMQ0dAu^;DnIzK+K3bunZ=;`|>*vsChd|@l!vaDC
zIAjjtmy-(jry=9b$zoiHE7%WYJr?TO*rgs0brG(@dPxKBwRiy%F^1)H2nWtiHp`az
zbQK%H2Qzw_`rtllxt9oYikAA|K1%L9rNh6)3!B=p@!begI>);DOk^Cv6tSW}yNhi|
z@;mg3Fz8aexM$09Z134ew$OswX*^-4D`#{TpiAVYz*k_zDYO`y8B~R4Q`{0Xm_oI<
zKoD_@Nk1G|A;<BQCd=_aI-8_D7Kg_;hiYtb5MPR`(B=|p@>oB7k$a#;eON_pW@*2e
zJP_yO2eOmVRl?`CxQBqimUv;Z44c6?_*wDtn#Qucovw*%I89w;y-5w6-VT~GdL;F$
z89mqv)BD^Uz1)o6hv}MvmQkGbndXO}`zrW5acu>1bR3+Lp&HQUGGR#vQcPB6dumK7
zkeTdjaSzsjxovzqQ|qJN3ha>Z$0>fY5-g`syu$cw{$%CYIBYZL6#pxNCoAy^q@b^N
zb;k4QIi7T0hWapG#R)K9lAAOil<(pAWQ@Z<g38*A%D3mJkmM$0T>}-9cau>`d+-c8
z#&_d2-q{K?1Lz|0n5|$Q=3x!`GS!cvuhqCF*Wy+Bg3vp|y*28=#!dAuteSkpBCP{V
z9-_uDX|f2-nBi{;%6R`CZh5g&Wa@u~yI*8qQNmY3(jXYbtB|Q0FT!6rM|ra56KDXq
zTx{P3SF%}l=AUS=|4uzQXLsZ;$0cM&`~4o$HqZ0&;}YjzEzaGji{$M*GPg*f(94g@
z8<d94D!Oq#8lv<=u@^9iY+=;%$4@=+v7fft+TLom9j4z8ZjB3<)o|ZS)5Y=fm3|m`
z!yOO9Gg%?s^2SI}KIv^Emqh02U5}8}%;B?rFq-CXQgZ2~*e9loX#R}uEbAd<EN=&1
zwCjhyhu9xP;Ne3{`SGLuV5S3a7qSi2opo>H#>SN`Z*!})wb9zzTzCI_4wY9_(Tqz|
z?w58VUyW@_vcmkhm`Tjo`a+uha2`ap3gRV&)-=`N3WjpkG=aL8JKal`C__)&o1^|f
zK1Wp_Co1(bZ4_QTB;E+cX@$x)XTCR8LgG+v&Y65J%Ch*1%BuKIwqNxSvG#}qYFkK!
zQ){E3g@V&PwDW=QOVVuEMnRB*-;D0GonW-jX!U6#@d%oBi6%_5F(d>%P6*nzVs>p^
z?Y48uKO`-2&X<UTc6q-aWZ5X=A0%p2qn*wpo(67!U-&09nrWg^Fok0jkxigp5T@x0
zWEOf6bpt90;7o(wWmFMmB#LJ+uL{T%XAKwC1*ML*Sk-I%rd%ZZ14XKz(Siav5LLX3
zcvqQLIfE*qYSLVA)FA_~prEr1SZni|im2(;3?lATy$ar-U=W9*xk@v2$2hAi+TVRu
zFxd*_nVbl{hvFFy5ce7r+-gj4r!ldRMrcwT>Br*rx2P695qGr{{jP?pGp9Zu=Qz9E
zg!@8W12<+;@QZUN)?KPzmr;xACw4>*N6;#AUx!ytQHe7uKLi!jLjOUfI>{qrwIhd8
z9;Wb<QxtxkQQ%bRe^4;*qwweZDIk=;o6-P;ROb*q+QS5?iL}=!DMY#xp@)1rx2jR~
zgaomGw5NEaPfF66l%t}|-J5Yld2@4uOEM%k3mmA0lG2@&gQsO-4)-#+T?rnE%i#Ru
zxO7rV$7r7j9woSFUQd0R8CxfITw*Q!V?KKis!w7({LOs!j`OR;0(9SlW|7KrYPc8`
zAtg?W6M&181q4ONhcJeg6Nm>>SlYKOqzn%tOxTh+1}?*#zCxCNMhg<@5CRMC5aNnN
zK*6m91r~vIv(zZ%3<(zaWHL!OF*<|9y0ll373MoY&??a!Bp86xb<kLvL_IcHikC1q
zmFf+^i^qES2G%U?RcRH@po*1m#AsE*GW-QpI1Ex)i!D^O)dstZL>t$)n$4?CZ@U3M
zeC@gBrEAYW<ZWDPG_JP1=GLW6@A7u@dds`A-PjsG{(q)k-`cp^*i7gCKeDaox0~tI
zv|1t;fB7TvOe+x=#!r3aV?T;QGe_$2Qe$faW%H%x4cfs*Yx`>BItTLcSKV(l2=)A>
zuOaSSYhJy!)ok5($h$EdDG#?<H@i3cgMM_!>*FSN6b<*g5yknz9dGQb;X`hHNnHRN
zF304cANYxdy19R#zCc(L)qe!c0Z6399Tm8V0Z*S;JA+|2N`sR@l5&LNQkaWka!6?j
z&lg1$r0TWArc0lJub!dNFH!SlYA#aqMKp=o4-TTlWKm3tMv3uKchI&%!n7?#B_v-N
z0H$cvu7uz3N4?$FaC&c%MwG7*MGsB8FbZhqF5RB~w-Pfc?ssqdxU%5zxP+`Id=2X~
zL<0WP%N!-h-xoz~4zA3@@Z}YXDEO<vlbd20{@UiBjc8I8=WLUr2E2Jic<}mVV>OE-
zSYtTk&n*W$)AbJKQj9TmbrrJEg~UEGtWIaVxW0ZKHxm9}eR{E57cKgC6I^=8VGkD-
zCXRU*w<~wTcIoB)fja1|_Xd3=Ns2B}`M!ZmXO0@oK%Jw3d$l)1RDdVW#q|E;8CuFW
W#HLBREE?snJIn45w8z}rj{a|o*s7rb

diff --git a/scripts/__pycache__/prefix_parser.cpython-310.pyc b/scripts/__pycache__/prefix_parser.cpython-310.pyc
deleted file mode 100644
index 7b951b18326da440e1411acd8610012cd80cb318..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 1829
zcma)6OK;;g5GE-~mTmcwTowhkMY>xQHBi{-Vo?-99|4+XQ4}zOCVdGg1jVEsC9<TD
zw6ihfB7pb0=y9*ft@~&C19<IePrc{T4yneQZ7(Ik;fyr%ab`Hfywz$T7{Bd47|9w!
ze;DEJ@IlytC4UFP5W^`7s~v~f$|NLD5F^ZahM2P=p~EP1pP`U)mwBf|aE`7#R%8A(
z32WSEb=FvsUt3|F*RL9^d5tmp0dOgzXyss(`5z(q@i}}o^Cwumwu^plhfUr*2^a#z
zZve3cIPm2fEY3dT<fP34)|wF3W}W9G?C>t@t^k8~dFP*<8qV+xAK2B~cm*+`;mFXt
z!vSFjmV5w&BNJyx7-j^ba+t&EnAjL;2oWBjUQK)Zf{&A@BMb(&!|(*wm$2l0AQM!g
zsG`{N#8QVLz`(;E)&4vdSv=)Zw+fLT#Yah+s075O5^*Mh&oimLd7RF;e2F!cJRQG8
zq7LXcpA3%kDIcV9#`5fhkH;#$NOLg|@kAw4E(UTWl0wNrVSSB?SV%7V#fA2xD9I8P
zMNj}pnj819nGL+?RDtzxHMA$Vnu+W`k(!*@NFM{EAkq`aHN*ERo~(ddOU@e-H4<ci
z3^i`_T<u6Dgn<*(5Z4gT5aXQ<wIZf&buEfOJ&IZ&NR#cyc+p<_Y<~@Vo{7-pHHvg2
zil#Z6rG^ip=xi3J)gRF`@NGjnhM1h*A?7q;4lw>m<ByMgvgz4xZ)C%08l@^5Pz4ID
z&=PX7Bqh3nD!Rr{&(D`mNyH=Ol+GN9N2LRQ=rv~UTSmtNu4Xy^8ZT){!6I0?rOWE4
zju@2qgj_kLYkKGGA!{rNYg(M|CTQtdtYB@|S=Lyqtj)0)mNjcXEIqKUS?ezVi-H6v
zLT9us$}fQ8{|}FvYmd%Lf9+2Sh%QLrIUsf{;tSS=9g7zhb)$-NNtIW^?Jw(KQ3H#*
z^{7!ofA%(qhr(RyqVat!lK3d)a{C5<@XB=64ep6*|4^g7MR54KIY6f#`qBQkU+sPU
zW3=!NRIK>+BG_NI)5W%S4|5f#i`LzbTRq=irFLZjO=k;GdvQ_ljJ>Ww?T*ttR<<&G
z4UKc{RoxW&8RraKm71nW#x+hgo`<gOTa8snp=qVY#lK2QH*FhM6}thk$sHgbp}0)~
z{0{bE2AEt@*eNumkGnw0Wnks%e<gQu`&O5T_W;Bc{WMOpC|Ydv`va(Yp7w7agS|x?
zTpRHyO{D6pr%K~<anD%MX?)5xRa~mW9@d+)ESYm5<21_nxd}}!-rW~Trjl&3mCsZ$
zQ(NO)Y%zW`n`{XlOL(Jt8`@{Qn25MI)+Cp@A!kSMq>Z?gHqF*U(KQDK=D=NEJTc1f
z&Q3JVA?w0CzS=z(iGpkj@F?NJyo+#jl`eP}gV8Y`oko=#;%#eTHSVO@HnM#z{7<Xa
n|J)Rhd>;t(FeI%_{J?)05SaM>U%u0TRFcb0$0v|(LjU|5<9oI)

diff --git a/scripts/__pycache__/prefix_parser.cpython-39.pyc b/scripts/__pycache__/prefix_parser.cpython-39.pyc
deleted file mode 100644
index a9777f0eb6e7897d085643c9c8556f39fcd6bbd6..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 1801
zcma)6&2HpG5bkcbe`dz>lPDsvT0&Sj>_}(^B!p0e&`N~ta)}}~;>Xg;a;AGGPCT~L
z?V0Ra9x2l76~O~=$Q)PVIXLhLedV;TkOQK+&CX`wf-Qfpva7zXs;=s&-EJbd-rK%6
zk}g7jYUTFjf${(z`3C?)3@0e4-#EZVCjohg7-80P#H=L=EJm6A90ioy%sD6GcaE+d
z<}z<Z0+)NN!J13*^PQl<8`n+NT49X72VROOT3Q&Ty-$!#K1SHwKLT=hA3eDnw0P^x
zX9yTeU~B^qd|83VMajuohxx2MA*{o?Karrzd#twvX5Qo7f8JC}T4wk$>TkS+e9+-Y
z<L%1=<pDhM9sox=$AB=*2xMe&%B)|p$&Ut*9q_oyITCyvKOJFkcy(!+!1EP6@-Dyx
zRVb_x8<`li7y=G_*r&>yM<R`;T&i|1vXkf}PU0d4wN;2Hl^|!SRL(p~W?a6&ib|f0
zUm(!{_M5@*G@J5a5~VClha#F3@sx|99EmtD<S;i8hIu3;7lZtn^1?7q<01@U%aPQ3
zjId+wvRkJ!cxBPY$`QPniS$1i>ROo$KLw$H49}px3~$#mS%S3ItT!~OHOQPCD%|Yb
z%94c;nodv+wgyLoj?bi6gYH%3h9Q`TVH*^wtBi2jSx0St9rhiaqpoKds%98YGd4@K
z?1$mSEK2G>q6N;PqoJ!o*YXzV)r4L^$0K!Q9`PLW<&9csJ8fcW@fqxWftF|il~|Ap
zT|@7z@ILwlKe@B8Dk8?rs;oH@<H~}6bcLDyj<#|@a*gDz@Pbwpy8i8jUD>R0Ziz<~
zJ|ovwW$Sslc*L3u!diysw+UJ}hRa|3?JQi@uG~2mSCwo0uPO(;UE_TPTog1|5vHMI
zSpEVQ?|($});c0pdFyx-FxsF&<iOZ9j9aV+Z!ES9>qedDf)-8%yT53FhYKDJ6VX<s
zXL9rKSm;eHo8Ltuj!qIT_iph0mwK9Ra9`B#j}$s6{o~g|0XB`m3y;42`rw-%!qRzM
zL<Qd~{iF35J=;_EaaKf0*}na8x9^$FRJP1v*h~W|C(3i4ve!MR>~WGsh3U+GQ{hZG
z^*jY$$~l8jrJ_lka)lFx=YehJRpBC_FsxGH{9i4lT4oUIj@^LV<mUj0IGB<i_VEt(
z;O<}wNO2QTfAx)4|I=CzEWnD055ZSA`!tHvFf2C)gCTS~PX@1!frGLGA&q#L#IhI^
zPYZ=F#kTgM)99QlT5wq$!<=u<(s<5=jFK?rmpUa`zJDa*w20HmZZ<3OS+P6L#4h6}
zv&pXDk%Tj;zo9(F^NEP^Q$;eVnsRmmN7#r<Y07IN6g|D5uNU0s`9p0C=jue!45}^k
zVXN#*5f@NJ0TIPq=yMR3uFC}Hpg%h0qw}y1L%eG|jK!_;ngKS4g!e@~@?Ywvkvjmo
Zs2=I~-UlA>iI49S4~pBfHsS4&zX2((uK@r6

diff --git a/scripts/__pycache__/reactions_v5.cpython-310.pyc b/scripts/__pycache__/reactions_v5.cpython-310.pyc
deleted file mode 100644
index b9e14bfad38f48faf06762f8b20ac1c6ac8a617e..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 23276
zcmeHv4SXDDdFRgT>}qzjl2#v<WLs9oc5F+wB3rg&CywPLI1b5O>IB<-bbCf!Yew=a
zt6lB8D}PL8xfDb1uE3#i6lkdryBy?b@1V^c*IrwWyGwKJQMk4c3QP%<5(;kl2uUEs
zkfi_Td1q#4rIjsT_@%#Jf0ceS`+hvn^FCki*E2J3sjbb3;V*k^<K!KmjK#iAndn~}
zncHwx-j16Uvy?(CD}R-&!g)2T@^3sF=U*+W@oyrV;NN66`RbUZTJg8UtoS)K+k%{C
zC6G%Xrz4lNT99i&E`^+KrI1S@XCP--t;n?^*J@>~cB|tpN;YjNM`OdCm%vf%@Fd-%
ze+n|U;i~Mw&5jY5;7|c~DmaUSD=nL}64@3jnbob9Y|7HJhLr++15{hRmV4)_`BJgs
zbdHX0pDkH-VN~R%tNB@5IIUH?Qk^)pb2NYIY_`SE)Jv;pszGK~6l7Pult9|6A~$JI
z6!MkoDCIkaotvaK!=l5(X-}V+DCTDEi3!h`m;fL11xlwUCd%`<f?t!&7pL+C+iRQ3
zi%RwGQ)hpM`1Lv)vWG#%>)@heVE>3+nJ-km_KH1ODq0~<S7V-#vKd(x!Addf_keRR
z9dJ##kHkbf)Xlfcd$*q~&Dz@wxuR7n&e&5^)!f-aNo)_)xV<td@^jV7_JBfV;?#|!
zb7zGL5-BoW4{mx)Q#B>}uPY3(#Nvc@8?I*vt!{BkeM<~hkHe~(ryuckJgEUF_@gvo
zAH-D|#cev~#wO%l;k3&4xT~OCb5-0EZXEZd6+0UHh;n$i#Y?dmxni~A>x7br=Vv{A
zPQYxFC~pl?esR7e^3}6ms+zaO!P0!O>KXPKdvcx~58P@MyD%mCz>w&t+iJRn3Kkv6
zl7Hlj`Rc?(FLD*COe*z%LvcC-kw*i_!ynNEb!b6yiv-=)(ydOJQ$${L;<gIcGX$&0
z(h8R>t9y|F7&vb^I%iMj?aCyz6Z}y+Q1dec$m)!-I?+9k#zYqihgC0eDp#1dJ&oLZ
zI4;(pRG4&IPq#Xo%ptK(mCRvMfy5cV@w&ibpb@by-ykZkqsn!3quf<xOCRMfb1WyO
z?dq}u3Z^OrV!pl9Y`%E=ESWiwiN(2|8g3%fCMw^6o3kp~;7Wwr2rMScLQ(FjLbXeA
z0$*8?Sf0)<j}gmj^M?r5NhOePGl{T;ZcXIdO64qHUt`-Vk&u)#Oaxd$%H4TvGKrty
z?+_B*xDMi~d>C_prPPv^T5Fk()pRRfOS#G&vEx?Fa8s7HH-@}16RWl2uGG?iX~WfC
zRjYBg^_+5!U|VV(ZrcUT(k?1WtZZ^!I#Smj){TOGhUuqkoo?q$0#p<CtKv>K!);~C
z`&|8kR!vg5o58*1T%4%7t*%b|^v70X_;J&boZ_}ca=P0d$)(DWqSobV;$7fZKc`q)
zU#!;c>fpM!*5mff7#6kvklXF{Oc+)Y_f|I{9;&8M7o+-fDr9;9W$&w|F$IGc$iK=}
zXWCfuUU$_6&Fy8$&jacaK<QLVcu1$*Rg?lwAFh5}t8uNVwpTl5G8U-6^BuLd?%E5T
z7h@N?F2-sD?tu7=J7BeftH*&4J%Ud6xfpaXaG~d746U}-*17%A(kge|Ifbye^)E)L
zKw5RC*Nv}^LFV}V+JYi5ILi`HNYw`2)u7Pl4xUpO`}yLaI{>J(Y#XU=wBFXFb)$Bj
zk9(cOT~Nw>(YBe+j*!k?&}m<W&Kl;SPUn`_$E=u!|8sFAR!oh>7L>|sPD2Cq|Ffin
zRp8#N8SJP1NcY3{0zd6=jr&z_KJWH{Zoj)a@EEt_oJvxH(>LOJgPQ=<yTDfm@#Xfh
zP7T=Hm|1O+*R7%U0r_UYu+6!>HGu1l_6zbIQ2HPs-{bZNt<_A|sIBKRqPzzfpzE3p
z`y_Nu^cDQBKc}!|9<w@Y8vy^YMRnjne9r1>T1V|Z3GTXCvunvem_pj^<C3(yA(YLH
zaG;9&-3?Y3cu_@WQF{rLwJ)Lh6ySRperOTA2KdcQ;X4`rwngv?;14u~U&Zj&BKR2K
zU)KoluD5y__5{kMq=D>Dp`^b-8&AQ`s;HuTHI=gsWzVmVZ3OWSK&(M;N};c;#jk;0
zubk7MQMG)Ad+LBSa89jlbT?jDXRULS?~hr7e80|ZLE7Z>dQNZP`^NKa<Zq#-KW<%L
zyS~^LYVs4-CgeMimzsLa+KhY)@=_C@wzkx+=hlXp_AuYK@_n0oJ=z>`*W-Qzw>H|)
zawoS;oNlL7DD{V;p3CE2d?7C0%dPBiQ}2(R=RN}XO*B>p-aI2m5EZae{xRlaC%3ul
ze1iLxT7HH{easa8xL-iO+{9!0Ci;cV;^J0rYqz@zoZon!$Ms^0%l1UeTxy>wG1f0L
z#9nUoCW!?eH&<166VE;-TH4GlZKhwwnP;4v-OXrepTt>+mnXRNmZqg6On*O1HO}b+
z5#8Q;zLn*Sm$$+vo?$w-g?hfdLC+s+qGwIKmT_KH*K;5vMrYE^<6M7`>S0^*usgW@
zL+4xkmLF!z(7apM^64g8ewry=o0c_kl(FuNwEt>pTdC`YR`)H@xF&WpzSQ_#;7})9
z&}<FA(nx}0h9RW(n?ksogI1ssO}vKT?`G+>azE_%1g?j<^q)~Fr~Wymz+=jd^lZ%W
zv}&QbJq}6^L*B!({fzGoTG{5(!_DyhRZoEbs}cNrL;Sa{82|So`1ghQA6hZK7r}o`
zi2vA%@h?a4kA(Q&;L@X4l|LcYFeJuIc;zu4KT%F_>1$Vjzb}ISx)6U8m$H2W`z<KP
z&ot>hN%0AWZM`r!9kX8lkV2e1q*!A}p{F4AhOq2s!&Ej*{al#(7f4Br<6+qw!_-8W
z`gx=<vV-zCQWE1pSe6UnPK2q+5Y7tA>@YPIrl!Nx$uN~i%9v^8_GXZlE#Dv37m$)X
z)M?L#wO7L~Ho-2f7<;Y>_R2XgzbtIg1bgM2SDIk2Tx-=P*jJOg?kjaW&4Z4#=V&x_
zkyqUdiSi-#>{HZ>ICYv+w8~ARC(tZ@#x>CI&ief(S^krtw;W#`=_}eovhr*=<|W0m
zjO%cpeIUgBGMBpC2CYpy{WfaAT#Z)Vgx@vz{g?i{o-DtxOlvKbZDDIIVjI(yBgBJ#
zYc1t&F8zh*2!S5{(FoVU7_EyZ8TQT0?>X{z>n)T%pCs&HUf{X1MO<Q7IZM8kp){6A
zTWG1c42ylK59>1QFEZVK#rJ<LWh)+pWSjg|3*dPzv9&&*VtrxEq-gCzvl!Q|#-5cd
z@^4V11U2CFmloyU=4-E|{O*O8@>^Zv>yyjz!CIs>K#O>SVczbVpgBUTJYM5TIp4vh
z|CZMT?>wI-d5dxcekaRLd@WE4E$)d(7OcmLb;<nom@cF=5j|QDfty%eGO7Jy8}s$9
zMRmMd3@qbrf&{vdE3CH>AK(FNw4grJuD?=a?dm~GOSBuSuO6&_$L)rz2`kX9UOu>>
zmv=+nr=elJa<;+px;VR>#@X^)mRNqs-NLI#)S$%_<sz0JW@^&%eobikdcMxvL*VVr
z%-0_*#|K)$K9=<+XZW9j<+-hQhaU0Ez9r=9=xmdoml6fWc@Oua2AeW(DY1d;rI)-n
z(%Z=6-p3xNm*r>^fw6uiTs;PTEbzqLOFS_p?&CIS6pDHub8{u{YuG8I#0*pURpu#G
z-U|yzzTO||<JZE}c}mgPhAYEs$7U;!lz1wLOwlh^lPPhYTlx2dA9%N~sgH5Z2Y8gZ
zAV<OC?M?dP-X<D&Jc7Hp7i!ejHR$2HOzR?HEu_l7>!w`V@27-Z2mZQWevY9&NI6dZ
z2TGAfSQ~@VR~lB*hS<W89|~~fo;k=_a;IV-=0?8p;T6!kmmwbxC@e#7Cqw;5AL_b`
zh;>xW3+t_qSifQYruCl?NgJ5PKD4&g-FjgI*QTxi%#nbN7p}MB)lD;-FRHa|)h!o>
ztd9bE7(Mr6?l#<i3%RY~ER(i=+m92B@UDL=$LIFcZXm6sV(twTrK1Slf>HUk;zmTc
z5MQ(Y3v_FU-$L%cS|5L_ijw~ZKcSKl9#2NN=6AT}cNz8*h&TLqYH7hJzk5l<%cy*+
zA>uV+{oefv(EBp5exIdUYiazOw*J5!;W#5j6Suvr7)7gSX^2s@ijIaDMXTs*h*7kP
z!B;3o(dy6lD~VCGBKAkV*DOZST0XRBK3W>1XhkHL@ULz6+$z4wSl1GxXcd3NIE^ui
z*79$2X=98cD3#;u)nXK_Wp@FxGM#IQQKZGgjI&&fA}uy^{qix2*7EaBM!TgkinO?c
zDP5bE)8a#n_5T~ANQ+-&{GVQoA}v116lIJeU7lG;m$yUr&vWUu#3<6@(~Q#?qez#3
zhfA*>qezQyNAQCfMY{Zj72>xc?oWO%+Ye$C>GE?c#vh5`2Qi8^JQpCUSLeS?+!MhM
zViaxVy<B?r7)6`EifN2dw3T1a_*ainw28Mfq{M%nzk_KjpXSoVF^Y$ptfM-_5X1gs
zh*5kZ+^PPLhp<l#W@k&v_DR&r_{;x9YH?iRYJ22=ifa7hk7~4)-^+br<x!0e-m}V;
zXJb^OqcXw!B#PvA`1{Mos76Qm)!f?3qZ%FMli@mdacl31wDumR+Zfg8D8GqIR}$6e
z6mosLlBh;T9AmnX-MEaKV-ML;`DVl3w!>d<{KG^wI?69Cbd;Y0Uzy5Q=D7(U;odeQ
z?qZmiySMEqUu?3rSQ^#H2pRE-=<#JnH8SE;EWs-i)yR}Tx{xV<0M~KW@RJRe&-ih&
zCK`VQq8gd<Pr%oAz*lEw%T+DkDdZaTr(k(*YniA9B8vS@=Ho6Q=kDd=8lB=ROf?d-
zko^r_mLX4LDZjvb;X4uc^WRUwJ1g`wpWZX*6pvE;3eSop>?3|$ty4V0l>e8T!4C6(
z%e4ekBlt(Lmm^GC7yV%aM22_io#OLc_gFCNVo%(Ow_tb{Ug#_@aIK8Hbox&;BQiwd
zE{mgY6nF8XZ~k-AE`QZ0<1S%@O+E*1h&L>%Yj{%E<?jo)e}KbhA{y+f2-e_jO*Pmh
z-WY07J|ph(BSDS2lUgI_<+Ro%=9XxU-W`%!>ne{m(ONw!)DR0I+vD1dYYXwdpdRmT
z>R&H}J|QDRUE(*mm8FrPE+J!pOCv);6f%g7QDn%ELeek1tV?{2sY+ZK84BZ#(qkJe
zRj=ddnY)F@571{?KW17N$+s4|%8&Vxp&s$;@XzkbB-j2Q_B?u;`dU~m@NoD&N4dJi
zzR-&{)kb|!>K1bSZ}4;cz~?u!w-bi68$I_A>Nc^rcZ;9rx<8^e1C1Z=t8K4q!5szX
z-O~2%_8EHL;%(AH5fejA`7T^(KNkMS%)7SGQ~8y^j_iNgMUs$ayTu2ZN+Kfw|F@|m
zAGm@fp8_>{)2iE_FRm`r9}~5vGCcyB%2$-&QAp4u5G|E9z$g^F{m?Ds8vxBDAdKZ~
z(SxTrQUXd5)YT;D5gZk7B0*2N8xnl>iV}Q^CCD|ApvQk3p}7RPD@gG6Py)H1ySfCw
zw2TdU%GHIQ@-A-cPxz_Jr~O@FSNWY>dbnxnwZv0<#Gf*yE5}oN%5pyWu-`|PkI(jq
z=a}BZ+zVjArt#FCvV7WbrFiPLMe)==7b8e*2i{y9b9Y#uftRlmTir3d*ZCQ43uQOO
zYCD3u$^cT-7gpiD5J0&*nD^G&PI$yFcMN088*01VT|9g4LR|Czfz#dRl)jktr+qP`
zcX9g9D2?%JjGoT*fdhVz@<#VYv`cZ^k>H&rF8Oo7-f&?QQP<D*;EhPapjN95F<^%L
z99q~G)N{$>LHjJt&Z;@H-M!Iz#QOX@RP?N!3#-cez~x`~9PGgpqAq@BrDMF_18(?T
zCP1Bse0y=-#PQ=D9Fe`5(_@_82MykWYd>IUhDo_QFZ58{9P^BFd=#<eV1^!8SXKEm
zjM56?%%F(AvP%5O-G^TJ1?CYc@QgPfNiRW(^+ie%eZ1?rlivP>ruEveyB{_fraJKW
zy-3`;S8QJtx2BT4Y?r<6Ug&dIpigknD+Zy3FUeLdkKU176x#+iAUL*N^`q2&Yk$f3
zQ^-Av2>F-&+)dolO(Yj;p0K_`QSwlluX2ibZ>-yc_XG#5B){8=XLJcXpCvl+*nZ-N
zV)B2*^uO=!cW*fr1K)1~S6}1jGJg%f*+K6lku8h;?k%9cU$z5XwZfh^gO?7>GGCRm
z%t9}o;G#@E-5}ZF5h=FB*8@(;5)msr87bczDgQ>K{3clrAHef5-<vj~b+Yi^MBq9W
zS@@fgx;<_O>3~YCxQpC=$XfnGrtvLVD!ma_e-s+HBxSe$_I#YAN6FuzWDK(UCBWpT
zE0C9e!QD8n1MsL@LoUhZZw-CEuT1YX--hdUT(4??desGOnytCeSKjLP0(#^5H=8_B
z>8l(nzR$Pbw_&|Lal##EJAX%d1@+h3xO+RlF+5;}r6gw&&t%x{-(}1<xd#~Yd)8Cr
zPmFoMz0JoAO9?aN_YJiUSkc#Z?Vx422hrXgMAv$hsJM49?Jr?G8o=8HALrcfySI`J
zxV7(FPY110DSYu&ROh!E)>5m`$D4gRPfMy%I+EjNGy-cAKCba4&yM;k-)eYvlvwB&
z_rlK4ur8sAwK4y_^k=KP-P<v)%D2>iP`xpd`yuNu3jG|QZwsM+1n3|a`0gn5m$sgl
z8niBl@<=Lpmlm}@_G^CvYOEVjlr=AeH8)0U7W&H@=<64{hF?5<S$W{HQWNz3+9kfd
zguhGl>5r!vPRE?Er}Ae;Pvr!C9aG6_NAEjy&{KpLbJiU?a^&74>&=6=A3l8VG4sfw
z+wU;%y!*(}W9B_~A3o#^HmN>(=-|DF?~wJ)(2w19_YuF^Ja*DH=~JV8u3+*9Iu%pc
zb0tx=Ei)(VeV3JSPub-uW6oU$e}OZVM@^MK2{H2(GgrXpBGy?mH+eE|pF&l>7}Qp(
zxvD*4&K2xj#Ws->RkL);7M`-xQ+9jG4rkXPAxdJzESAiQ{ItlN%oV`^sF^v*k69?4
zwuM<ei3-OSCFd9J6QvUcd)7RiubxD6QzbE*qmQdhyI8daSQwf-X;0p7&gSk%v-83>
z&z9zenJZR^5YlF;SU4L(=Rl)sPowIDT|I5vMRN?Wmbshn)srAenvhK5+rG-MbE{#H
z-lj?gFqbb*n{$G{`ogzS=E>YC8<aq%SRy5YJuq*xQ2YtlKGP8N4b5d`pQoI5uHT4n
z>84G5bZCx^?llY(f29*M_GHzZpR=GrVUC;5SGk<(s%PiG%lvFuK->#BP?bu}8xEK!
zPW{~2j^klHBhVLU6L7Dvw2l>2`KUKF!-Vms?d5Q}(#PIa#}2{e_m9x>q!>E04@?e2
z8P$1FtPGu%SqNx`;3VW(bKkgm#@uF(g~iUEFc~I%%9ef2ly8VqPB1|yDV6WU4}c%_
zfa%2dQ)0jAbTfc&mFW_?3MvjPW+UhVL#OunmK!BuLogqoJe}~@g%u?62^)?AM+>@<
zv!<b%KysCejV^S`ysVhc*ey%y@f~8dG+8Q)=B<KF3al%S(4AC>;jHs{v5Pr$C2N8^
z413xGhLLi*1Cv!I0tn%BN33?DR4NRU5Z8q?sR=e)Rm|62#Tje>ARzh+3!T&ue{P1)
zDxGvxZBA+=tmuh4OxScLBtjJPQ)X6vxkjWCCTuw7w3?e`zoW7(4e*4slwB%yx*7oO
z0tPQ<sG%%Gp30%Np~~rP$c7n5Girw6^!kd=7s(B(7#qgT2cYpDU*l|uiRt;AuqH&r
zMSS;YtX>~dCx(3YXjFe)mJrtI8#Yo+>Ggy#5qgeBx<uzlf&Y}F8a1cSFalq;3sEW3
z`J$CSmACK_vniZ46Ew7#`+{+7G#F`^ObYb^!&~$EwG)%{O=a^+Q&wI9ecgl{loquu
zhp`kaY@~8iG_=yxM+Qha9YKrZ=8jvaKm!mA)6mwqxtr@UzPU)E`Kk?5wKwQaIEF9$
zI25r~rZJi|c3Svs2nZbuCn-g8ZfGDDdK;Oxkpfl0O~SUoITc0!@L_vhGU4?3nds0;
z;7(T~D)Sa#GIQyuCKh!PqCgG#S|?co6D*Nh!VcD%YRdG+XloeDpm#!y{s|}Ly8!&N
zt)Y5RFXTS#OC(vu=wLdF+t}5tjX<bzbLUcw8?TJ9%M5h_38I-BqnSO?%wE&!uj_F~
zqgZhaBF@pE_XPt!k0C~iC;FWy@>L^MpWP`REDDZOMc6^*EMYQ&;j~Aq#Dvok>3X!<
zaM~IG{LU>uYF`Z6xukbxRglzZPI5HvKt1fT0eaBoI)a&Nhd<hM`29@Ir|4!HWHp@)
z4O)R=@ku?8Lp;RD4r!wIrY3WR0{XZ=){Zs~pGo2*6?C6EFTv!^3l`y|BdiWPEfQ%0
z(;=j31f9673_At`kh4u-4o3r$30gIb2DAGR>Jk`*F}}occUo$`ym6|DkKoooo)<VM
z?5A;yPm?gADOz}9_TXW8ZM|kHmoH4v@fBfZhd<hfTD%#J`qKq#+}FQf6ioU4qF^*1
zT?HhF)6`{U$Vox~Br!FH(}~a2153z{5hz3Y!>;6hDWEjGv#U<CE>06@(zVa^kQ2vj
z?+jd#dmTFAIonCm@<k>!62#d`8ss^lX^V2Er#TRUti_2Av`50a-(PZtIEK@|xGq%t
z$l@BQFC#z8#2Q@0a0dP2<=ppmM!r%i&<u*-3FZVM1suuU(IRDx1P(i5Qez`wzZt1_
zlB|KP$V9a?F*!Hqboxz<hfUzL6W;rclZQFRiTQlN8mEcL8NkRYs^pZ_k}2kkJh#%e
zk|EX6?M@Qy+19wT%FJW#t&ETDz#oAkX&!J^O<^{!oa8;E+>jFHvCGPVORcnTrc*1j
zNvX3-bR0-F6{_7C=B=bznw*>$v<I~21+gONoRZnRgAyW!qV@R<4li(SIY#HS&>jst
zw0Ugzz%=hcqx;(_QJQT+!WrdVGs%GE<zz`%;XV&L;$SyzpUKT)?+fc-K=)TO=x7Z?
zm($)jfjHWtS!xGnwy2YfY-?mVx<m(WU`*VG`Bob?u~TUoHeGXQXb8g#FWb~%EZxvA
zhK9tYI047u>{!GZmo8JT^T>R$$R?xlg0`y88ncq0orho1j+$%(fy`-9nxDhiZI-4$
zPg-vp1n~FltxiIkHNln~R=lqHVjlbaO0F<bv`=H4vMbKo(6~!Y;%Hz4+pT?AARBDQ
z^(mA%*I9XsEhGa1w2Srw4{)`rZCqCNdrJNiouYDyjuW}8q&%hSv~1nFl?jfRr*nu<
zz!&BU`AO<2w68yjGTxt8Pm0p%qFI_pSc1ed4940Gfy0=BVcZQfvoZ*a_h|koN3@wS
z+uDaY+c-Qwdjcy;kit1S#R@za2MwV{H86+Bg`!`Al_ey-i(?3U=1#<oh(i)I!UMt;
zC@Nta;saAOqJq5x_Y`x>Wn~M7R&q(d{=``#F^fs@6ao?iEnOUj+~O&RFVWdEo^tmk
zib7nX12-<wNgkKz@D^v(Fm8wKu-&I{!cu|A8*;KCc=kT$W@`6DetMc5s5wU1MHZp%
zBh<<)rs!+O-PMFka!cP*MT|32J5gS5YR>CYJn9GmBFyYd*@V><pbj)sC~s}y4bJMi
zV=UI}U~_Im)D02T<y3s#GAa&;4DS(io{FHufV>3UcG~vh1-s}ab8~Zc(egAp#fVP_
zlIIlBuq)_LqWS?wUINiCoN}ZG(MwM&0hf<+5_EbCpD05UzU?I{Rh$mxY32ER6&ZBP
zsuxF@mz1$bFAhq4V2?Z%$Ru>lK9jGC7D^^g<7_3IAv9CU7rn$}0iD7#D)T2W>me{#
z@e=n@)1G!Z2f|4?(s(WOOB}{4XDeRIZ0<}26N0CfDqa#LReM(GATH>1DnTcv37T#^
z4N=9Do;GRc3tn2T95GbP%~wU5VA=?#HPY3+#8jbF5?&k);Fd2AAIcg61L$c)A8gAr
z0;N~Ryrc~HX4CQ)hdo*L87~2R2!x}hz%52)PbqoIWLBO*MPmm<<^!eT*nVf*m>y_X
zj@h$wL`oh=C39SfA&GN*M3tZMlrz~RlNs}rv)Oj^*?Xss_y=fJkhf1CgU#=rx`&v_
zCYTTotwOlMQ!3e3o+RxG9SoLDK`pZwSqqh{?oWGAupFZi#LgGzs-8xM&uRqeDW|+R
z44rM0AV+1)H=B}KFqqZn=k67EU|7z!U>R~J&OgiQHXVwFBei_Ccly7({9i<p9dQ?|
zk?pFlTrlCz&cf_;+Lmo)Tls{v3F@vDPniPaq({<?r<BoDv5KL;0!`z7l)MtO=jLE;
zFTqov7$y2-&4ZF|wwv_=qwsVr=XWo`4Tur}xA9<1=fKe^Zk+Weh1uL3M5g5j)p`j|
zW>d#X)m(x6$xjk3FTthRHvXX!Lh-W%%UOde<j9vzQ4cFl!>TY9Cz;VjXEmWqLOI7U
z?vh}Y4e)wCkPU~j>2aNp8l%J6GD?~+lp>`o>Vv&XJO5`Cz^hbd_|WaB)l?nj24Jbq
zP_!;B4mxVPnr7G}YI>A(yazNgiuzK9+e#~4N;;VVEvoNA`QX=eliDQe{fhRW_Chj=
zoZ5qn+MsexNmB}RQ5s%JK<j?F!KGAkrIZ0|iADD$IFc<Sx#hH)R8>`bQ8lz5s%h<6
zwOxB!&1g@loyPZ!Rdg^}aA^u4740Q8uDzgY+E3Jk_G7+UwC7b_`;nS5o-^7cZPKa+
z`e{W~+h6R0Y{X$#JOk+it@bLtkd50WibO4GT-G1N(t)gmf1;8>``jwG-2Q^r(uEqP
zre;V2RpvJ+Ci1Y%gN6!xm2^b9hHi*jG)LO2*R4F~^W@Wn7Z8;V;7)&uFI9h04K7WG
zest&uS5m*Mw&>5RDg8Os(0>?St@;mCy3+cyYMcIy+O9vX;Zi&F@2eU8DZV=O@2Oq-
zcQssUxBeZqNB=fotMtE9d-cE7aH)OzCADAw7GJCNZ>nqbztM21YxQra1NxJEt<%4*
z4(flc;Zm>Dzowe{U-7kG|Ejt{|B8l7-KamIUax<duTA=2s+)CB!=-M~zoZW7U*v08
z|AM+z{|gP5x=sJQI-)<W-k^U@9o0XpZg2l{XnUst-S_%F*5zA3SItEw)QhAQNOu`v
z^eSt7YxXKTVC|$z{<A|d)b`NIL&_SqvIe?3FbGb2uvc9U6TK+#2X2l0iF$ZHd_wxo
zfKL&A7nhzB_#Szg0r;M<^$kJm=x<Cp$)3iP4N&E>c+dmF64D2G8RRgzf48G`NX?$z
z&U_Fr=t1$p9~)`%PD4${U%`F}o&Hn5Y~C;1pV`n6^ln)8MK!Kt^h56sdN_Kw7W8mk
z|B*_U-_tef?LiO!hw9~i4_7y~KY_lmc}2YwKK#n|PT895oir~ec~ovkPaw~vOZG+W
z!Df9I^C#f|T1PLWeoOE^j><Ct_wM?Utg^i;_i&o`<V=CS*+4UxxzT47?M3ZD^=YFE
zb1VLr!uJ4kF+8mqBqaR?+`c@>-gp;Dnz*JBDM@mXl*Wq~{V>jfA839A9Cs-L&?SxE
z7`s+s&Zbcqet~rkW>@~lY_7K?Rnn7`K?4T;(`eSiR+APXo3KUVM3YuL<b^%#V{(+F
zQqaeEA83PDSKvo`u#0DSS{IRqnGZ@~?SQtBs*j{Spxlm@dqIa*Ze7R?D1*57qYPg1
z9U5VieN;|d(mkyXV%`~4v>#}?cpKJ=!|I*KhTFs>lA=Jj8QeVGvgf8nZtkR*qHLSL
zt(nUSJhB!i364TlawAFSv5Jj!<I_-yYGipzp$PvF-2L)o<O2$dDiq++W2CX*zg=xl
Kw;SyV`u}^H^cC>{

diff --git a/scripts/__pycache__/reactions_v5.cpython-39.pyc b/scripts/__pycache__/reactions_v5.cpython-39.pyc
deleted file mode 100644
index ce16b960aa701cf7a7efeaaa3edd7d6e7383e58d..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 22221
zcmeHv3wRvYb>7atusc{R9>j|z2o6CK1Sk*$ACf4Fq)3rcBv+wa5>1qiWORucfJ-fQ
zv3CZ1jAm0ubX-?<;;rkpX&kDQ>$-NDrmpL%?#pr2G)>dgbzL`2r>WgKsvEYct2(Ny
zFpk{+oO@?>7Fdvw{P@0pUx9BP_ug~PJ+FK2J$H9+v8zju;V*k?Z2rtI$6~)jh3H=b
zg_F4K58!6TOsyO%$fs7&xEwFU`I#sr_?avu`I#!D_?a%Ge<)_g&BS|RX5xCh(1B9Y
zOrexQDT7kl>_Djlr7TJrGmBCdB^@Q*>_n*(rB1WQ%$wcs(F!?JJ0F|uy#<b9XXoi2
z{nJo5iOZhB&59A1;7|j1ad4IZSII)!OcgrJbRlDQ6tZTfpqp9H*Fm+@?|5?ADOD@B
z+dDnIf2nF(<!Mn|bV^H>a628#cIGZ0oGx9yR_IWLX03D82?~dzAcvZ@1d?||ao(CM
zmuzR6%DuuW&QqUZ)!E6MpP8Gh6ql^IIbWZf10O48de6<x)mDmS)sik%7D{Ey?^-Ac
z+j;!*wI3#a{oa=1Sy1u2xoQ^dpR??hvg7A%Yra}BL!7?WG9eXuWL*R+%d9^E&i!1#
zHI+UY6M3kcZ@2gDzgS(e_Lqwlvs&37C~v<#FG|afy+6RS=Putny?jl?ftV$O_2HI@
zC$-jpZeL?%LOMxE{kS!)Y{uUcgQXL&WYW)^Q+l0G0x0;Scfvl6%bvz<G3LeQ<Xz+U
zINuYVhWexz$35jGa8H}D^RZ8AXD2)SEDKSrIJVLQy`EiJ@-xc<rkY26XYi(~OI1;F
zuK8J~WQo(&m5Sr*)>UhMg`ExDCT**{AO^vZ7^2%S-9n{`ZWPHUN|ll`H%DMLHO91b
z<lpTLM4k>H&wer~Xb=mMTcqf=g>FsC{6^$O4{igvY|>9g<MP|me8>4^YrbUJ^VD<j
zNAIEHsVi1+j1`PQdOjw4Q8^j+Q<sb770XYOlTRkZX4HypbQ`5xlX2#mgfVd0Y-8xc
z?NOaKRUo#uA~q!+LBn>!RuWVBZAqLv&%<f9C>AZ}ZHdj&`PrpX<<t_nM<6*1ZGf+K
zlJ6$oL&*oCOl(Aa5`7nuP~ubhZHb?kf(PFBwiMuJcu*k@`dupUur}>L6Jy{`?4(;8
zAJ|J`gqj#?<!2+h*Z~5QL`3O=%8$;@r|}5>9>L4c;5v=VetH@cqE=6v@p{K%te!Cw
z^{l6zi9Pdcb=}LF$@^m{>z88nPTaM64lrG~@=n}Ic%9d^>jayxcY9qolV<WIO^ek|
za$7FamJi#W2K^qUKV0widM~9wHT7&<I9?C;)l+l4%*~{erh2aj_m1lcqUv>e8RBO+
zwi#j0%SB3>*A*#cynLjTt@V4^dY_kUXkr{3XRd2zawt~c<YmD3RK4HpzoeVQ!5iKt
zuYXQA)3|qfDe;DrLtBj6ug4+P8(s=D4m&wa@!$tK81Ukkx<I9;KIjeHOnQUFXG5!<
zV8}8cGXz1{c+YwR^ai{kT*J6F<J#ino$gCLCi-Y-9~`T1^|s#ZeJOUc@1<CM#2Z16
zpYTS^&S%joUIrCt71TCek3l0NH~U|Tq5t9fHg6a@8}PPW*9cSb@wq51$R58m=p{DC
zpn=4*$wpjk32H#2zdq`128|(a^t#6Q@mjoc3>?J8Ud2IN903PiZ8+$!Z&%pcL+q2$
z-kFXF>AV|s^6Svq!dx`zyzfV2W-N*S>j^DZ={pc>#O=?_Kz{oFG19{T_&-_K*>i{S
zJ_BzIJh$7^p}V;Ff;R-Z!`|k=hrI6VaV6&$8u8jIuvtRf2fn(AFK-BR2J1R}K)<xv
zBtP6j{WlV|LBOyFaDQ6>Hys@*<V&Db0OW~Ek2f6jS2sMpzJqF+_C?@;vS%=~fZnMG
z4bL6dHCQJhe%|b@k5!JXY5@o0WwQ@0W2;)IR{`EOv0k^5hoCpqctc#1^TtBSUTf+7
zHE+!910P8-y^3ZEbzf<vS@{&8`x*M_RnW;c(9Z+9m!V%+1+BG#o(1#(Lw|7<bPUks
z{}JiD9p)gz5{FVomb#KhdALOjufe)W@fzwkQ$1Twj{jziBM6Lna|^~%7Gq>9o;t?9
zc0CDACTnl-NF6apuE*;;y`49=ncKYdM`GqE-?w`mcsKZc2fvT;edmoX@-n62ln~~w
z`mV~f(qT$GZ|+8URB0(CK4gxgoL72CiJRu0`Y!Hmf@x3keJ|hd@phrlDQ^ev`?$C1
zmY#dLXX11}y#-P?v}YcTdMwAkL?b1>!Trp5*^k6-@Yn#xZi<<K4_}h8Bi=}hvkZHH
z`8deE9=egDUMgSb=#Lpg#sA;LXxz=QeK$Q}v9x$EV;}Z*gY$cDaD1=yaov5<I*)p1
zN{sb1L)_1O9+6n!aNLP|yLlEmfu6>>r*V2R&TEYGfH#hwj<)plV6?80uKg-QPBHak
zEYWd(KM~RFLpM4}MnFH^NY$jiPKH`OwMxtHYNO>2G0Xit+|+U)BcgJ=(IGy??Wd_7
zwj~cc!yG(vql5eIsLirnX#Q<#`5SAr+#!CCDZMo<cZgRQ>(NO6KO`+Hb=}gdvqs|?
zvCQ~V<Bx&E4B3KaZFp6ZB&Zk+A@$!D!lRiwuzN-vVfe>c`b_Oeqoei;E~&?NP%XFr
zF?s`!SuZlOG1JrPg=Y9fBO|`VkWa8|KP<hWk*Uerv+eNJ>PO;dh4fL0|D?jt)@1EQ
z@Xtm1e`km<Yd3=bp$PsT5AkK~M)1EB!9N$`%i8mIm0wr#BWA)YXBED#<o^>Jz(2?R
zOZ*=R@ntRBH?SXK)R)_g9$kEhDf}pNAfwMy{QhHnFYx`x`TjJIooD#{U3{P8`=4Ah
zwu@YUf$#H-W%9el_XWN$^8F&;OYo>pXy6i4dY0?T5xk{!p(+um>bg+N5vcWhtZfKN
zM4;C1(T+f^&%G0YYR8w1mr{2tk*GO+<Nf3t4ZS9<cbQ6T$1D6s>$hQ8n`Wx3o(|1k
zQ@)X_Js)_)GY2F7kZk1akA>qpCqBlwE^G9;5LecE+y|}a##A45U~Wb)KY`~KJpYu8
zZ;f2->+AH^W%q@>b+wFwcdOpI)F}8#>MfwsNIdg&gzF#<b&02#-{+a%>#WuH(EE)v
zVF$5~=YzcX9K*_);HMZW$r2?SUG}RCiyVw$yTq#u`(CE|r}_RqH7matJndF9GvIl?
zoNdk-m_zkTS(=|IQgiD;<Y#1&KZ6!6Xo0p~SXF+%(q6vS-{`7+3z=5lzO)`6tVNpV
z^5WwR^8wEQ%_&;R@H$4y`O{qcGweejypbb$E7Ctc$g&e(4SGY5PemjP)*QdxluWHT
zx<#J*i|En(v*0GyluT;BvW4M3w5pBQLxE+y-7LWu8IpY)JYXFXw1?VNs}a_2Cg^F6
zc4N&M()@GWZ#ZL`fp)uVqS0NOZRBfTgoeBAue4acTYQCiS<mu&)>wYR+ruj*w4lc<
zl_Hj(WNOm#swK31vmEf&Q_F+5*T7egZLY@$dO?N;z4eHj4D&s(Jk$Ab=n;RO-h#3B
z4COdM78s1Y9`R+y`3pRbT5QU^^@?e3mtOK0BcqKx?q`X9<-@BX%)b<_kAe{v_~FGh
ze%LEsV0?-}QQu=;?&NzdYvEoML4J<MKyU4-Mo&#j_K{E<KOer`pf}PBt{z?;wbM<X
z`1N29hMrh2^@&}~>x+aR_%`dQPdvsgf0<*<O&J3#6suQjpt42-eQFMuxU0utlKR@P
z9{NOq`FM%28htg){~l$sy+W@0Kg#vJ@J+JcU!fAeeT?2hPdO$%rDd(yC*EYpzZ&4k
ztS~5<axLChlTaVOE4@uBWBO|Wg|_rI)ns1v2?aI!60&$_`%T0Ar1=ZxUpIdddqpFQ
z$g}Euy}dVgaBI%|8=UKo-P~y=oL!f8zZ9?E<BZ?jWBwALCopdRrgsnSpF(LeoMUq4
z-%^?I6z8>*v;+0Qa(y3bWgqQ9@%~f4J=W;2UBu1}c8<(XL%03n9Vq>6^D{pcN6p`X
zpHR&dN0TXTd6`@OF2nX9qy8-Q1S&mic5?ddpJ>_1nKJ+0vnkN~D6sxMOSRQZ@-t`t
z18<6V(rCYI?{}4j_lq}LvhV?sY01I|#BfU%J|M<_U|IM8c0$QlH<E=9sA%@~vhYEX
z<DTAHemEe$##nD93m+7h8Rza<_+ae`hLrL5Zdv$1?Q4wz>=%>1-dYwuD163RFAE<M
z_i_9BS@>YhZxij-X5m9ZFr~Mq<slVc-)<H@B)-MHe($pIA+-*bS@=-xbB&?eV-0A5
z`*|x__^_J0TC?!snp_j#J&PR{Kg)f#X5qs%S-TPZ--_S|S@>{G*4`a|vlx!x2U+;$
znylRj{!<bBAPe8D<iC3szFEoNnuTvx^4~oR-z=o0ty%bHCI9Ly{F`l7QCpM-e(+iN
zKje(yAKjP?W>NEVyaM^<yJV*SKSvLCE7s4^OQh4r7Ujnq&(TL}<KarGHAf$@X?IWV
zosFo7)|#V_)Z{vH<2m|B?S*xFdpXkE%RI)Uj|VyWNKMvmBu5_+-)0IM$<ar}1%{2}
zmU5>P8PPWTeJz>VHt{}&T`yA$*3aLc9DQ5uvyE-Fp95c`w#<jy@DXNeqgdC`-1^;S
zY9qC8x0x%~=IEp1)2sFPUFPVcYBlwP$<eph1{<TbH*h)7@OJz87RzrJ&)?DV-`^a4
zd+pPW?X?esFT>8P$46*+L!9|uS)S>vlcP7{_^ftqmTrivjI~~tzC*1i*JSDNvL5m@
zNV&tl$eHd3u#2U>S%7aF&}XjndGHQ#l6GUTyDwo!)h^KvG0HuE-s?fe^p9m;%hU+|
z733y_Nn_%lv_SN5)@i6!<*x*@6LP#>e1AdX$ZDvy67M23jGB}&B12>!Vf9`T?IWnY
zB=yPG4)s}v+(!uai{$5aE&21RwwBLUcBs7=xj(z3b~B>EG5bZ<;Je#ua11sGG$=pS
z8&kP>tL~)M2zouOjfoL%i)xL&^&z!3R+Fu*T5IldwCrt=?Qzk3w1;?aB=HT8wf?nJ
zd?xe>xzn*z?GCQp>DVa_GIwitI)d>U?Df!2huTx4C%kN@@FKW!rz6}wlQTq%rJ8NL
z8|3W?_FR~j9FcOTV`uG*+UXd>YA)H>Wy{#|PucV6^RHio)dKs#?|Ii|7k0M-FWOz_
zcTnCH?q}1dv4PKzv$qq5v|F@oH+%a|<$=FSeFhrGc;4UCf;Y|dc^2{ZU!qUQ-!DBB
zD~+ACFEw`6-a${bxBJhS`($I>{$^lF_Q01{$wIo_C2qHsMec+C8h?tsT9(`E%Cbwm
z2x|1L7<wa#?<Uo5VG!IJsdm*~Z0xQXknF`f%J2$g*o~Y@*#VI#_{@5@_$YJGP6onQ
z&mOz63Xw9<+s0&gwXF=hYZoBHtGF)QQHFmG8OAZIt(9S1EUYU7VXP;^xF9W%9q4T%
zGK}N<QGi=xhw<8YW4!hWT$0YObLQ|b)J|m|(>@!mYmBK3=&kG$?om6Wcitu3Q<M9s
zA6FwqenQ=D*Kv<puiSZ;aF5#axYI7--c`GVLmuK(eFon+JK)WjzX1(TAm$yw_ws&&
zM;+>p#OgDRJ@{6`3|nAAj8VHc!(4aP55gA?c?S?%K2<;L9pc&Z5ccW*C1$z9*R`RT
z`Guhv-VgEnzoK`<uLJa1(-8XRZ@%5@-HRS+UlKc#G7@mj7XdqUb02mQ|8+mUy+#<+
ztJAWl$&g<{5BCJ^T=Q>&{#lNL&h|^w-o56R&42sTag3^ijfvVcxcp7U!F~9=qmMs<
z=|Q}{58Uv#PXP5g<hvi&5#A5o&pV6{@cRtEABFB7#B~fXG{a=QgE#wW9~kpY9G~-z
zgz;#kF=-bN;qIy3^gt1#WK#TscN9_O-!YGP1JC$ug7gy9n7>7DL?7SEJ3!ylgQk1x
zlio4dfb-qPBy#-bKI~p(;jR0yRC7Pu<$mve=<{HpPv+oT(89l$y_!CKmu=NvEwBN>
zd$o?*bydCn2jK6;cXme1SFq#z+p2VgdpbgLq2)iCU!h&!P@1pu8}Z)Sb|1diHDdlJ
z{uUxWaZ2ISMxv959V32dkNH0{w<o=0-h-E8=$F3r^)=4&e+PcEpT0#xwyex}4}$tJ
z*$;Fz2zx#NUb->Md{z2ZV{h$Os7~(IlkD(_EL-B$fK#$W#0vi<Qh$G>{_BzYBeEVo
zfNV{9)1&B}Ec{<1aNVmc{JW91`@C+_0o9lZ52a(|FAp<~Te4PqBdmTB8u)KgcJsgA
zNRafX`90LkKvq=)O#ZY0^70eh9mjP79`#VjCHeeAq0iq_`(3o2#B~bS!!1w`-%KvD
zH5*g4ycz}aJF2s5J|md2A8qVIOp^BdAF$t)c(-?)E&UDY7c^q)$Gubh-Odp+tR+b+
zM-=A&WX#WcCm8cJ^M8>?G3E*Hq{0kq2{YvQm+IZHqtbW%w5fZi(cc-OYraBMyfaMu
z^N2_z__X{pDD4w7-a}*s?(LiA?+3k6ExhqzYE!+2t<3K+MdkM;%_tSgZ#xQswV}_?
z<2t<NvygrE3oW08q#D!WDcJdS)+F?>HO8NR<jnu=9P&;fuFCHff6F->Dg7VTUKIKb
zK%Weu{{YZIDe&E=puL=VTk6mJ!%!Yc1>b%|>$g?wAAuTc1{7t>n_<i0XbU{zP5L#&
z<af^A)}Fhq)dl^c=@#F<gTGt*Q1mt3?OqnvLh0)C<)WZpO4x<u`FB2Y+Si01bGJQm
z?%b2-b{MBmojv>Hta0v<Q)i4vA3t|~)_CIavyZr=ZJN(Na{9@$XJmUj^x4NAKc||F
z*^8DzKSU`N%Le~g!#0GqTosOG8bx6py{#ShwL`vkz<o^TUt=tk(Bkmd`Hhlo6wCOk
zzj@6l&R;B9m(f(J1g*AHbgU_3xoj0}%RosuM)k5KeC?pG9rm>u_s}CkRK=80sT#KY
znTau9tbhSfGm4TQqg=gW3B$RF2G<f*_b1;esu#-El5wTvTts&ZRk2j0pWYZ&#jylf
zn3%t4%|B}_6`w`7E5b6aRab;jtk^^d??$y!z7|3kLBp{Y(R9Ibu2@#ZH~?7FILvqF
zB1n=ZB$N2Hmp$n|r0b-&g=!hhl`4zIvf$qY;de5|#o}cPlt89ZB_)DAFmJI?`~#t*
zhA!y$54W|WzIMgkwG+RtS~T!8G~>YZ{km@8uX^E<HSZWJ%O*4^jN^v;Rj#Kt=h`xO
zSy>7zh<gDCa;VnWcfz=E`Nt2;JQKDv0{uQ|4(=7!HnD;xg?gkNCXBaet%u8v3j0tK
zI|P@%h=Z2r#l+R4U~&@5a8^Xcp13B95YPz0Nyux)(c{Kd;~wKcSnb{yzJ@P~vT40#
z%KM^}Q%ulJOXa(X6W}L)!f+GE=;fH<ZejpsmBlKC3K~wVW+NB^6PJ%F%T1H8A(+A^
zPbd6sVFO8g!Gfc}(Sl**ZfR*IkfLo{7($ng+nV7XcyLWSex>GA=d0!El3BJ$flcKR
zx|<C#+--^%t5U>JGUs@}u%|tz>sfbGU^06yfDrDch}AAstK~@&VtYuFx?r<8Vx{RS
z?q~}D0nuMr>1HSRr$YGAotulQ&CO1Q4gFDv3A^qIi4euof>DsaIwDdj12#P1b{gYy
z+)>@07I?y0%P!TreJy}i8Nth)XsHX47m8?YX>tc!iebS`>UCXr2bJPW6><XyvEjJ!
z95mjqG|q;YTU;p$b52BDM7c+6^Nx@@F{Iq1RsBs_LRfcbQqQ)f*B`<}=($PKB?d<p
z{Ab;`UU!FdJ@93#9F-zhs+gtAB@;huHH5omjzWuZG>Bu<L8M_aS+om;xAyH@=jQ2`
zbL|@q*?0%^ZF4dxt?FBbu`DdCXNwCIT50Md17zLqpvU9J%!5>s1P~0<(${h0Ft_z6
zbCE<Vjs;WYTXZK}T?v02ir6aO5zSf$EqpcvgpP%qmLj?PT8M?-My740KuvIyurF{<
zRnb5E)VV2{aEDYO8d?e5?Q2D4-U3W!E*I6rszE{&s3WCyk|i*~8mT4hXp^b7Oz({L
zhFAu@6JqpFxLM@_@XxN6=2fGR$FPz}vWVzlxU2g()UJ;}sN=@LwHWu_8RL)<>I4!*
z3-?9~_eBf$8}4vZk29@eB@jg1^TFr~0zStOJ<AjQ!3!lv&o*awDhG>#XQ&|@pmLTl
z7(sXQ(IzqHc1MODtv1}Q763K4<xiehgZ8c&U4=MECTUJ`lRSX>*<}OtV90d`GuMoY
zHr;BR$@vt+ED2c+cdSJ#Ff4v>&2flBj2w^#MsIe$ST19Xt5`eT8a~s+Nj4ZhO<sb@
zn-?s?%|%$9bUP%{9Hv7^(+WCwTbp!s1|Vmf!yJwdBonl1m=0$53ACjUg%Mv8xVs&7
zC2xXS5>vRfkmm&sDu*d<@%aJ<G(`(f%pM$;w>DcAily=#9cU0XcB^O~YViSds-_Fp
zxYEC>3Z{IuD3~rqR{<&FG<#c{aMKU~ub3Lc=|nO0+#2!+2$UgJ*p=L`1(b$&4>f5v
z#c2agx>j6IxCzYm?#Lav&p;<UXS-QizR1@k3F7W04f34OwnsVB(;Nsvw&M5xlp|r?
zua;aPj_wYxZVS~uwYo*>OD`=ku@)E6-BDG&p8NiYUb3rYnnCfLV@@Daz>&<3Rw-jD
zaM&q>I-3f|%~W%c6m+B_b53<`etFsLRb3npyTJJuockRo4|DYkE2Xk|oF*oB1d&xZ
z<dja;5Gxg)TPdw%$oTYrH;w)*^SC=;lrZ<&#}CZlk3jKioNxygFdN$!Ifs-9DPi8$
zPTcCGw3&_+D5RyzZqZp0g>0yGcak$nqdGsoA}9qkR|Ih)=-`T_l8YLmg{mE;o;|Uc
z``|1c+(9WC60{X$d*GQ<&}e$QAgW7kNVwCSG?NHeUCvj98K!wih=XL>x>{U9>I>r_
zo~y+S##u|`a`Ub8hnrkANzGtli~6`IbVj1lE&6>sLgGD`Zj+M+5|xfg!!sr(CJ<eC
z)fS(`$_>L}VnW<X5O4y%jy0Tq>o%2o&#hD{Y%vNKl&QK~47;?n0=J@snoI+Mj73ph
zSw`qKstceejkgE__<Q{!Hzlo_VnfbOYJT5JrGz}+E|%vi))mAl%XYVh#$9U@HwiwF
zZXLw}S!YA;$fCyGZk9|ok=ziVELv?mz||Z}zpWkfwbCs*UgH)W9&uaC-l8KWe9dt?
z_U_%wRHuw9MQl^RBbLjhc^WR1++Rc;C+W^bQN2<zsw>!=AmMbKu?|D*aAQH&ABVA7
zC4|L^nhJG9o4K>hqnNn$vnxv%u&e|r9IsNb;l?<B1}$+N6Ny|csv0aWA?{<mk-$f>
zM4X8@Bxxf&V9x?oRpcTHn6@NrBoI7Yj6JutJ&3R5n5zB4H6pQunej4qB?wwNI?TDp
z*UsLelSzE-@mu4hJvuGn79GWKi%#=!r*-`l42Ybc_7v6%L_SfJ9l^hkx(`sl7fOqZ
z<VNi=!hy01^(dj*OPHtMI_{x1T#|DtOH~kTq;{gb9%;|(T09yK0V2$-q-?|L22e-Z
zDU|bDc!RsS=@_duJKCPx5Opkqx}J)+ucP9C$mG3(&g&5rQ~ea&cG2<^Wvk++i_6Pa
z#q^VO&<!6UBagD#M9_4)O!JHzKZPx@ic`o0TbO>b3S2(%N6^6=d?X0X`j(%v9ULFz
zCu=Ju2L%jE$4{WnPs<HRKLJXD&To;&#L$5;e$u*HazqEcrmo=l9gvwXV>tM_y>bDQ
z9`@yIKlM)P)K6Y1f@E3-nnDLXK@ojiv;B^x;#C_Hf*-Hiei}87wInjs7ad$A=m;%A
z(~Y0Rrs73EId7H9eoihN5hRvZ9FZfKE`sTd4Dv#1p<JyBKY<Q#D^(^RDd++L^a?f~
zEYsHmb=wF0wA}A4<m3}40h!iSKLvaUgmZ_$EuyloRef!~AP*>_r~#4rw4nsD??M;T
z18sZOT3RMj^0XpZ;zk4`F7f$As^Du^3uz{Ez}K!7@))g8E}T=RE7>SpS7u@D#}}R;
zW(p}LgcFUhTj6VVp_3;`%chf}3R$RS2{E;77cy$vgMwv<#vXR5vh4UtGI=3MkiK@=
zPr$^5E(vm8Zuu6nvIqtXnU&=y#Tf+TLI+kMkK#bALdK#~vT)v#V*8+a9#T(iB)fu+
zb1C#S7cQ7^mzH4m0*+#`%t9w0nKefP)%LXoFiv_T-S}D!T~!<eeH)s_{XF?2XfH3r
z+<uCuK0!y)ur*IBx|>)pFbYq{a(?$y+<_<&a2JPRIv9+O_2QzM4wj0`5Sf-A)LKaK
zYau&Zb&6&3C-q9S{1n#~y7)mgj3SE!%SD|UWXvmMX>3&%VO5xlUzyQW$LwG*LOHXD
zxH$PHX1`9uicagIE0NJMd=3?z-PNPz_)4NKr|H_DmgoPTcru<wO$K#zY84<+rW3z(
zEzd1_UoycI<2`YrK{RvPU?QjWgF=5isOd{LTMx!FphW%anvo!S89)+MS(gSSsv{a{
zbpaMNvQ|f(glzXrgQ|qonYN^w)<)vFcsd?`Gf7u2{(AVtyFNhjH7}An{+(oSrQ&~>
zq^l$T2f?Lx>8u6fvIo)(YdO%(rTbW_{zM;Y`v4(z*B>9`c3t(4jj6Z}EaH^#d(gY;
zFA@Kvd`D7KbmBy37<6QLEN-AY7zZ{iLpp%2iBj`jX_4zU@~$iqz)OxEPRDQSxDMx&
z-%R2;@;0A6z$N_rLE<<AUZpkqScZ&dw3GvVjKFIK@xKMFB=?|p82W*RwHe5oSGBq}
z5#IuBkRBz}kvrh9#y~63H`!xYVe0S=qSTilD6*^MQrb>OOMlqs7(?dKYd#&NiL#al
zet^kkk{OmKugybNcz8U|wxW@gXRiCSDab_rswaMc{>gsz|Gs}tz_;}7(RlLBB*x9i
z+kEx_m+<rBWYIf%DO*^Mk?)_EHlxBI{Dfi=`E4E-e3UO8{)hOw#)IKq_;14NfR~pZ
z?~jvzO7AA9V6;&bUeCu>EafOh@F6u|6Hipr1OFv|4m_V?djQ#ww<e_IPL4sU{qCR;
zQ&SrrfoaK=4oM&_jc|^bQ{b*o8{x6o7ats;5t_p|#tezsB8NNvF~9Y6WMBo-hUA$>
zFa1;8>1T^b3z3bWBSe3qsUvbz1RyPtv>Y|~N%KM=J>Dp4U_^o%&w|7qxL_^`GLLvj
z{K}}&k4T7_6|pXdf9fxf-l)G}?F6`_GI54GsEle`H1Ry<{mJ;Fvy)xoU3e7>bTe`D
zGp4n?D2mG$MUjeKYN5JZ6!;8MTp&2we2_^2FV*S5K|v?&G1bU|gVIWM=H)SY_~{Ay
V282y%J838UkLPoFJ)ffg{|ipM`yBuP


From 2bbdab5cc421b9f9a1629870eb65de5f2583de55 Mon Sep 17 00:00:00 2001
From: Josh Jeppson <joshua.jeppson@usu.edu>
Date: Tue, 27 Sep 2022 14:53:27 -0600
Subject: [PATCH 2/5] Moved results into a 'textfiles' folder

---
 scripts/{ => textfiles}/2reaction_100runs_out.txt | 0
 scripts/{ => textfiles}/6reaction_output.txt      | 0
 scripts/{ => textfiles}/checkoutput.txt           | 0
 scripts/{ => textfiles}/lazy_paths.txt            | 0
 scripts/{ => textfiles}/nolines.txt               | 0
 scripts/{ => textfiles}/prefix_result.txt         | 0
 scripts/{ => textfiles}/prefix_test.txt           | 0
 scripts/{ => textfiles}/prefix_time.txt           | 0
 scripts/{ => textfiles}/quick_result.txt          | 0
 scripts/{ => textfiles}/quick_result_time.txt     | 0
 scripts/{ => textfiles}/reaction_list.txt         | 0
 scripts/{ => textfiles}/subtract_test.txt         | 0
 scripts/{ => textfiles}/test.txt                  | 0
 scripts/{ => textfiles}/test_print_all_lines.txt  | 0
 scripts/{ => textfiles}/test_v2.txt               | 0
 scripts/{ => textfiles}/testprint.txt             | 0
 scripts/{ => textfiles}/trace_list.txt            | 0
 17 files changed, 0 insertions(+), 0 deletions(-)
 rename scripts/{ => textfiles}/2reaction_100runs_out.txt (100%)
 rename scripts/{ => textfiles}/6reaction_output.txt (100%)
 rename scripts/{ => textfiles}/checkoutput.txt (100%)
 rename scripts/{ => textfiles}/lazy_paths.txt (100%)
 rename scripts/{ => textfiles}/nolines.txt (100%)
 rename scripts/{ => textfiles}/prefix_result.txt (100%)
 rename scripts/{ => textfiles}/prefix_test.txt (100%)
 rename scripts/{ => textfiles}/prefix_time.txt (100%)
 rename scripts/{ => textfiles}/quick_result.txt (100%)
 rename scripts/{ => textfiles}/quick_result_time.txt (100%)
 rename scripts/{ => textfiles}/reaction_list.txt (100%)
 rename scripts/{ => textfiles}/subtract_test.txt (100%)
 rename scripts/{ => textfiles}/test.txt (100%)
 rename scripts/{ => textfiles}/test_print_all_lines.txt (100%)
 rename scripts/{ => textfiles}/test_v2.txt (100%)
 rename scripts/{ => textfiles}/testprint.txt (100%)
 rename scripts/{ => textfiles}/trace_list.txt (100%)

diff --git a/scripts/2reaction_100runs_out.txt b/scripts/textfiles/2reaction_100runs_out.txt
similarity index 100%
rename from scripts/2reaction_100runs_out.txt
rename to scripts/textfiles/2reaction_100runs_out.txt
diff --git a/scripts/6reaction_output.txt b/scripts/textfiles/6reaction_output.txt
similarity index 100%
rename from scripts/6reaction_output.txt
rename to scripts/textfiles/6reaction_output.txt
diff --git a/scripts/checkoutput.txt b/scripts/textfiles/checkoutput.txt
similarity index 100%
rename from scripts/checkoutput.txt
rename to scripts/textfiles/checkoutput.txt
diff --git a/scripts/lazy_paths.txt b/scripts/textfiles/lazy_paths.txt
similarity index 100%
rename from scripts/lazy_paths.txt
rename to scripts/textfiles/lazy_paths.txt
diff --git a/scripts/nolines.txt b/scripts/textfiles/nolines.txt
similarity index 100%
rename from scripts/nolines.txt
rename to scripts/textfiles/nolines.txt
diff --git a/scripts/prefix_result.txt b/scripts/textfiles/prefix_result.txt
similarity index 100%
rename from scripts/prefix_result.txt
rename to scripts/textfiles/prefix_result.txt
diff --git a/scripts/prefix_test.txt b/scripts/textfiles/prefix_test.txt
similarity index 100%
rename from scripts/prefix_test.txt
rename to scripts/textfiles/prefix_test.txt
diff --git a/scripts/prefix_time.txt b/scripts/textfiles/prefix_time.txt
similarity index 100%
rename from scripts/prefix_time.txt
rename to scripts/textfiles/prefix_time.txt
diff --git a/scripts/quick_result.txt b/scripts/textfiles/quick_result.txt
similarity index 100%
rename from scripts/quick_result.txt
rename to scripts/textfiles/quick_result.txt
diff --git a/scripts/quick_result_time.txt b/scripts/textfiles/quick_result_time.txt
similarity index 100%
rename from scripts/quick_result_time.txt
rename to scripts/textfiles/quick_result_time.txt
diff --git a/scripts/reaction_list.txt b/scripts/textfiles/reaction_list.txt
similarity index 100%
rename from scripts/reaction_list.txt
rename to scripts/textfiles/reaction_list.txt
diff --git a/scripts/subtract_test.txt b/scripts/textfiles/subtract_test.txt
similarity index 100%
rename from scripts/subtract_test.txt
rename to scripts/textfiles/subtract_test.txt
diff --git a/scripts/test.txt b/scripts/textfiles/test.txt
similarity index 100%
rename from scripts/test.txt
rename to scripts/textfiles/test.txt
diff --git a/scripts/test_print_all_lines.txt b/scripts/textfiles/test_print_all_lines.txt
similarity index 100%
rename from scripts/test_print_all_lines.txt
rename to scripts/textfiles/test_print_all_lines.txt
diff --git a/scripts/test_v2.txt b/scripts/textfiles/test_v2.txt
similarity index 100%
rename from scripts/test_v2.txt
rename to scripts/textfiles/test_v2.txt
diff --git a/scripts/testprint.txt b/scripts/textfiles/testprint.txt
similarity index 100%
rename from scripts/testprint.txt
rename to scripts/textfiles/testprint.txt
diff --git a/scripts/trace_list.txt b/scripts/textfiles/trace_list.txt
similarity index 100%
rename from scripts/trace_list.txt
rename to scripts/textfiles/trace_list.txt

From 327cc762392396b5276865ab47f999431318acee Mon Sep 17 00:00:00 2001
From: Josh Jeppson <joshua.jeppson@usu.edu>
Date: Tue, 27 Sep 2022 14:55:48 -0600
Subject: [PATCH 3/5] Moved models to 'models' folder

---
 {scripts => models}/model.csl | 0
 {scripts => models}/model.sm  | 0
 2 files changed, 0 insertions(+), 0 deletions(-)
 rename {scripts => models}/model.csl (100%)
 rename {scripts => models}/model.sm (100%)

diff --git a/scripts/model.csl b/models/model.csl
similarity index 100%
rename from scripts/model.csl
rename to models/model.csl
diff --git a/scripts/model.sm b/models/model.sm
similarity index 100%
rename from scripts/model.sm
rename to models/model.sm

From a0f42c50a7cfd2c78aceb9c6f1422a59b11e048c Mon Sep 17 00:00:00 2001
From: Josh Jeppson <joshua.jeppson@usu.edu>
Date: Tue, 27 Sep 2022 15:15:41 -0600
Subject: [PATCH 4/5] changes to main.py print statements

---
 scripts/admin.sh     | 49 +++++++++++++++++++++++++++++++-------------
 scripts/admin150k.sh | 14 -------------
 scripts/admin250k.sh | 14 -------------
 scripts/admin500k.sh | 14 -------------
 scripts/main.py      | 39 ++++++++++++++++-------------------
 5 files changed, 53 insertions(+), 77 deletions(-)
 delete mode 100755 scripts/admin150k.sh
 delete mode 100755 scripts/admin250k.sh
 delete mode 100755 scripts/admin500k.sh

diff --git a/scripts/admin.sh b/scripts/admin.sh
index 6db42fc..0eb3cf8 100755
--- a/scripts/admin.sh
+++ b/scripts/admin.sh
@@ -1,14 +1,35 @@
-cp ../models/SingleSpecies/2reaction.ragtimer ../model.ragtimer
-cp ../models/SingleSpecies/model.sm ../model.sm
-cp ../models/SingleSpecies/model.csl ../model.csl
-/usr/bin/time -o ../results/ragtimer/2reaction_50000time.txt python3 main.py 50000 loose &> ../results/ragtimer/2reaction_50000.txt
-
-cp ../models/KuwaharaEnzyme/6reaction.ragtimer ../model.ragtimer
-cp ../models/KuwaharaEnzyme/model.sm ../model.sm
-cp ../models/KuwaharaEnzyme/model.csl ../model.csl
-/usr/bin/time -o ../results/ragtimer/6reaction_50000time.txt python3 main.py 50000 loose &> ../results/ragtimer/6reaction_50000.txt
-
-cp ../models/DonovanYeastPolarization/8reaction_input_adding.txt ../model.ragtimer
-cp ../models/DonovanYeastPolarization/model.sm ../model.sm
-cp ../models/DonovanYeastPolarization/model.csl ../model.csl
-/usr/bin/time -o ../results/ragtimer/8reaction_50000time.txt python3 main.py 50000 &> ../results/ragtimer/8reaction_50000.txt
+#!/bin/sh
+
+# Rather than having four shell scripts with basically the same thing in them, you could just pass
+# in the model size via a parameter
+
+set -e
+
+ragrun() {
+	export MODEL_SIZE=$1
+	echo "Running Ragtimer for model size ${MODEL_SIZE}.."
+
+	echo -n "Testing on the Single-species models..."
+	cp ../models/SingleSpecies/2reaction.ragtimer ../model.ragtimer
+	cp ../models/SingleSpecies/model.sm ../model.sm
+	cp ../models/SingleSpecies/model.csl ../model.csl
+	/usr/bin/time -o "../results/ragtimer/2reaction_${MODEL_SIZE}time.txt" python3 main.py $MODEL_SIZE loose &> "../results/ragtimer/2reaction_${MODEL_SIZE}.txt"
+	echo "done."
+
+	echo -n "Testing on the Kuwahara Enzyme models..."
+	cp ../models/KuwaharaEnzyme/6reaction.ragtimer ../model.ragtimer
+	cp ../models/KuwaharaEnzyme/model.sm ../model.sm
+	cp ../models/KuwaharaEnzyme/model.csl ../model.csl
+	/usr/bin/time -o "../results/ragtimer/6reaction_${MODEL_SIZE}time.txt" python3 main.py ${MODEL_SIZE} loose &> "../results/ragtimer/6reaction_${MODEL_SIZE}.txt"
+	echo "done."
+
+	echo -n "Testing on Donovan Yeast Polarization models..."
+	cp ../models/DonovanYeastPolarization/8reaction_input_adding.txt ../model.ragtimer
+	cp ../models/DonovanYeastPolarization/model.sm ../model.sm
+	cp ../models/DonovanYeastPolarization/model.csl ../model.csl
+	/usr/bin/time -o "../results/ragtimer/8reaction_${MODEL_SIZE}time.txt" python3 main.py ${MODEL_SIZE} &> "../results/ragtimer/8reaction_${MODEL_SIZE}.txt"
+	echo "done."
+
+}
+
+ragrun $1
diff --git a/scripts/admin150k.sh b/scripts/admin150k.sh
deleted file mode 100755
index fa848ea..0000000
--- a/scripts/admin150k.sh
+++ /dev/null
@@ -1,14 +0,0 @@
-cp ../models/SingleSpecies/2reaction.ragtimer ../model.ragtimer
-cp ../models/SingleSpecies/model.sm ../model.sm
-cp ../models/SingleSpecies/model.csl ../model.csl
-/usr/bin/time -o ../results/ragtimer/2reaction_150000time.txt python3 main.py 150000 loose &> ../results/ragtimer/2reaction_150000.txt
-
-cp ../models/KuwaharaEnzyme/6reaction.ragtimer ../model.ragtimer
-cp ../models/KuwaharaEnzyme/model.sm ../model.sm
-cp ../models/KuwaharaEnzyme/model.csl ../model.csl
-/usr/bin/time -o ../results/ragtimer/6reaction_150000time.txt python3 main.py 150000 loose &> ../results/ragtimer/6reaction_150000.txt
-
-cp ../models/DonovanYeastPolarization/8reaction_input_adding.txt ../model.ragtimer
-cp ../models/DonovanYeastPolarization/model.sm ../model.sm
-cp ../models/DonovanYeastPolarization/model.csl ../model.csl
-/usr/bin/time -o ../results/ragtimer/8reaction_150000time.txt python3 main.py 150000 &> ../results/ragtimer/8reaction_150000.txt
diff --git a/scripts/admin250k.sh b/scripts/admin250k.sh
deleted file mode 100755
index 2b6fda9..0000000
--- a/scripts/admin250k.sh
+++ /dev/null
@@ -1,14 +0,0 @@
-cp ../models/SingleSpecies/2reaction.ragtimer ../model.ragtimer
-cp ../models/SingleSpecies/model.sm ../model.sm
-cp ../models/SingleSpecies/model.csl ../model.csl
-/usr/bin/time -o ../results/ragtimer/2reaction_250000time.txt python3 main.py 250000 loose &> ../results/ragtimer/2reaction_250000.txt
-
-cp ../models/KuwaharaEnzyme/6reaction.ragtimer ../model.ragtimer
-cp ../models/KuwaharaEnzyme/model.sm ../model.sm
-cp ../models/KuwaharaEnzyme/model.csl ../model.csl
-/usr/bin/time -o ../results/ragtimer/6reaction_250000time.txt python3 main.py 250000 loose &> ../results/ragtimer/6reaction_250000.txt
-
-cp ../models/DonovanYeastPolarization/8reaction_input_adding.txt ../model.ragtimer
-cp ../models/DonovanYeastPolarization/model.sm ../model.sm
-cp ../models/DonovanYeastPolarization/model.csl ../model.csl
-/usr/bin/time -o ../results/ragtimer/8reaction_250000time.txt python3 main.py 250000 &> ../results/ragtimer/8reaction_250000.txt
diff --git a/scripts/admin500k.sh b/scripts/admin500k.sh
deleted file mode 100755
index c8be07c..0000000
--- a/scripts/admin500k.sh
+++ /dev/null
@@ -1,14 +0,0 @@
-cp ../models/SingleSpecies/2reaction.ragtimer ../model.ragtimer
-cp ../models/SingleSpecies/model.sm ../model.sm
-cp ../models/SingleSpecies/model.csl ../model.csl
-/usr/bin/time -o ../results/ragtimer/2reaction_500000time.txt python3 main.py 500000 loose &> ../results/ragtimer/2reaction_500000.txt
-
-cp ../models/KuwaharaEnzyme/6reaction.ragtimer ../model.ragtimer
-cp ../models/KuwaharaEnzyme/model.sm ../model.sm
-cp ../models/KuwaharaEnzyme/model.csl ../model.csl
-/usr/bin/time -o ../results/ragtimer/6reaction_500000time.txt python3 main.py 500000 loose &> ../results/ragtimer/6reaction_500000.txt
-
-cp ../models/DonovanYeastPolarization/8reaction_input_adding.txt ../model.ragtimer
-cp ../models/DonovanYeastPolarization/model.sm ../model.sm
-cp ../models/DonovanYeastPolarization/model.csl ../model.csl
-/usr/bin/time -o ../results/ragtimer/8reaction_500000time.txt python3 main.py 500000 &> ../results/ragtimer/8reaction_500000.txt
diff --git a/scripts/main.py b/scripts/main.py
index 5bf7f22..6441e3d 100644
--- a/scripts/main.py
+++ b/scripts/main.py
@@ -11,12 +11,12 @@
 
     PRINTING = False
 
-    print()
-    print(80*"=")
-    print("Expect to see a message claiming an error: assertion failure.")
-    print("This message indicates correct functionality.")
-    print(80*"=")
-    print()
+    print(f"""
+{80*"="}
+Expect to see a message claiming an error: assertion failure.
+This message indicates correct functionality.
+{80*"="}
+""")
 
     i = sys.argv[1]
     each = False
@@ -29,7 +29,7 @@
         loose = True
 
     reactions1 = depgraph.makeDepGraph(reactions_v5.Options.infile, printing=PRINTING)
-    
+
     # with open("trace_list.txt", "w") as t:
     #     t.write("")
 
@@ -39,9 +39,9 @@
         # print(r)
         if (r.tier == 0):
             depgraph.printPrefixes("trace_list.txt", "", r, paths)
-            
+
                 # NEED TO HANDLE CASE WHERE THEY MAKE EQUIV. TRACES???
-            
+
             # extraEnabled = 0
             # for dr in range(len(r.dependCount)):
             #     if r.dependCount[dr] > 0:
@@ -58,7 +58,7 @@
 
     # print(paths)
     # quit()
-    
+
     o = subprocess.check_output(["make", "test"],universal_newlines=True)
     prefix = prefix_parser.parsePrefix(o)
 
@@ -82,7 +82,7 @@
                         if s2 not in enabledReacts:
                             enabledReacts.append(s2)
                         # print("enabledReacts",enabledReacts)
-                # invalid trace at line 1 at 0 with transition r6 
+                # invalid trace at line 1 at 0 with transition r6
                 pathnumber = int(lines[line].split(" trace at line ")[1].split(" ")[0]) - 1
                 # print(pathnumber)
                 rempath = paths[pathnumber]
@@ -107,7 +107,7 @@
 
         o = subprocess.check_output(["make", "test"],universal_newlines=True)
         prefix = prefix_parser.parsePrefix(o)
-                            
+
 
                 # reactionname = line.split("with transition ")[1].strip()
                 # for r in reactions1:
@@ -124,7 +124,7 @@
         #     prefix = prefix_parser.parsePrefix(o)
         # input("===")
 
-                    
+
         # print(prefix)
 
     j = len(prefix.values)
@@ -150,11 +150,8 @@
             if "Total" in line:
                 prob += float(line.split(": ")[1])
 
-    print()
-    print(80*"=")
-    print("Total Sum of Unique Path Probabilities:", prob)
-    print(80*"=")
-    print()
-    print()
-    print()
-    print()
+    print(f"""
+{80*"="}
+Total Sum of Unique Path Probabilities: {prob}
+{80*"="}
+    """)

From 3ea0e251816c18ccd3c0ff09f8c340519fe40eaa Mon Sep 17 00:00:00 2001
From: Josh Jeppson <joshua.jeppson@usu.edu>
Date: Tue, 27 Sep 2022 15:22:06 -0600
Subject: [PATCH 5/5] A change or two to main.py

---
 scripts/main.py | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/scripts/main.py b/scripts/main.py
index 6441e3d..590bde5 100644
--- a/scripts/main.py
+++ b/scripts/main.py
@@ -38,7 +38,7 @@
     for r in reactions1:
         # print(r)
         if (r.tier == 0):
-            depgraph.printPrefixes("trace_list.txt", "", r, paths)
+            depgraph.printPrefixes("textfiles/trace_list.txt", "", r, paths)
 
                 # NEED TO HANDLE CASE WHERE THEY MAKE EQUIV. TRACES???
 
@@ -52,7 +52,7 @@
             # # print(paths)
             # # input("newpaths")
 
-    with open("trace_list.txt", "w") as trace_list:
+    with open("textfiles/trace_list.txt", "w") as trace_list:
         for path in paths:
             trace_list.write("_PREFIX_\t" + path + "\n")
 
@@ -100,7 +100,7 @@
                 break
         # print("new1", paths)
 
-        with open("trace_list.txt", "w") as trace_list:
+        with open("textfiles/trace_list.txt", "w") as trace_list:
             for path in paths:
                 # print("PREFIX PATH: ", paths)
                 trace_list.write("_PREFIX_\t" + path + "\n")
@@ -138,9 +138,9 @@
     prob = float(0.0)
 
     for a in range(len(paths)):
-        print(50*"-")
-        print(paths[a])
-        print(50*"-")
+        print(f"""{50*"-"}
+{paths[a]}
+{50*"-"}""")
         reactions_v5.randTest(iters, reactions1, prefix, a, loose=loose, printing=PRINTING)
 
         # os.system("make test")