From 714ab7db0b1b7d5864f3ca037cfb4cbf5b9ff42a Mon Sep 17 00:00:00 2001
From: Rich FitzJohn <r.fitzjohn@imperial.ac.uk>
Date: Fri, 18 Aug 2023 16:38:02 +0100
Subject: [PATCH 1/6] Use new js

---
 scripts/update_js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/update_js b/scripts/update_js
index a449dc58..05557b0b 100755
--- a/scripts/update_js
+++ b/scripts/update_js
@@ -1,7 +1,7 @@
 #!/usr/bin/env bash
 set -exu
 
-ODIN_JS_BRANCH=main
+ODIN_JS_BRANCH=mrc-4455
 DUST_JS_BRANCH=main
 
 HERE=$(dirname $0)

From 10d2bc78942d5833c0679bdd21fc0eeb46098365 Mon Sep 17 00:00:00 2001
From: Rich FitzJohn <r.fitzjohn@imperial.ac.uk>
Date: Fri, 18 Aug 2023 16:38:26 +0100
Subject: [PATCH 2/6] bump version

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 4a3f0a41..efec8be7 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: odin
 Title: ODE Generation and Integration
-Version: 1.5.6
+Version: 1.5.7
 Authors@R: c(person("Rich", "FitzJohn", role = c("aut", "cre"),
                     email = "rich.fitzjohn@gmail.com"),
              person("Thibaut", "Jombart", role = "ctb"),

From 366523e6506973094852b76e009dff21049c450b Mon Sep 17 00:00:00 2001
From: Rich FitzJohn <r.fitzjohn@imperial.ac.uk>
Date: Wed, 30 Aug 2023 12:15:22 +0100
Subject: [PATCH 3/6] Update odin js code

---
 inst/js/odin.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/inst/js/odin.js b/inst/js/odin.js
index 8683a5b8..ba751842 100644
--- a/inst/js/odin.js
+++ b/inst/js/odin.js
@@ -1 +1 @@
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From 99e49e47829f7bcc6c9de2dbced696a943dcf58e Mon Sep 17 00:00:00 2001
From: EmmaLRussell <EmmaRussellKilburn@gmail.com>
Date: Wed, 30 Aug 2023 15:51:50 +0100
Subject: [PATCH 4/6] update dust js

---
 inst/js/dust.js   | 2 +-
 inst/js/odin.js   | 2 +-
 scripts/update_js | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/inst/js/dust.js b/inst/js/dust.js
index 055b0fbf..e2de79fa 100644
--- a/inst/js/dust.js
+++ b/inst/js/dust.js
@@ -1,2 +1,2 @@
 /*! For license information please see dust.js.LICENSE.txt */
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diff --git a/inst/js/odin.js b/inst/js/odin.js
index ba751842..31315d37 100644
--- a/inst/js/odin.js
+++ b/inst/js/odin.js
@@ -1 +1 @@
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a=1;a<=t;++a)this._simplex[a]=this._shrink(this._simplex[a],e.location);this._sort()}}else this._update(i);return!1},t.prototype.run=function(t){if(!this._converged)for(var e=0;e<t&&!this.step();++e);return this.result()},t.prototype.result=function(){var t=this._simplex[0];return{converged:this._converged,data:t.data,evaluations:this._id,iterations:this._iterations,location:t.location,value:t.value}},t.prototype.simplex=function(){return this._simplex.map((function(t){return{location:t.location,value:t.value}}))},t.prototype._point=function(t){var e=i.checkResult(this._target(t));return{data:e.data,id:this._id++,location:t,value:e.value}},t.prototype._sort=function(){this._simplex.sort((function(t,e){return t.value-e.value}))},t.prototype._centroid=function(){for(var t=this._n,e=new Array(t),r=0;r<t;++r){e[r]=0;for(var n=0;n<t;++n)e[r]+=this._simplex[n].location[r];e[r]/=t}return e},t.prototype._update=function(t){this._simplex[this._n]=t,this._sort()},t.prototype._reflect=function(t,e){return this._point(o(this.rho,e,t.location))},t.prototype._expand=function(t,e){return this._point(o(this.chi,e,t.location))},t.prototype._contractInside=function(t,e){return this._point(o(this.psi,e,t.location))},t.prototype._contractOutside=function(t,e){return this._point(o(-this.psi*this.rho,e,t.location))},t.prototype._shrink=function(t,e){return this._point(o(-this.sigma,e,t.location))},t.prototype._isConverged=function(){for(var t=this._control.tolerance,e=this._simplex[0],r=this._simplex[this._n],n=r.value-e.value<t||1-e.value/r.value<t,i=0,o=0;o<this._n;++o)i=Math.max(i,Math.abs(e.location[o]-r.location[o]));return i<t&&n},t}();e.Simplex=s},3:(t,e)=>{Object.defineProperty(e,"__esModule",{value:!0}),e.checkResult=void 0,e.checkResult=function(t){return"number"==typeof t?{data:null,value:t}:t}},886:function(t,e){var r=this&&this.__spreadArray||function(t,e,r){if(r||2===arguments.length)for(var n,i=0,o=e.length;i<o;i++)!n&&i in e||(n||(n=Array.prototype.slice.call(e,0,i)),n[i]=e[i]);return t.concat(n||Array.prototype.slice.call(e))};function n(t,e){return new Error("Invalid control parameter: '".concat(t,"' ").concat(e))}function i(t,e){return void 0===t?e:t}Object.defineProperty(e,"__esModule",{value:!0}),e.dopriControl=void 0,e.dopriControl=function(t){void 0===t&&(t={});var e=1e-6,o=1e4,s=1e-6,a=1/0,u=1e-8,l=!1,c=0,h=[],f={atol:i(t.atol,e),maxSteps:i(t.maxSteps,o),rtol:i(t.rtol,s),stepSizeMax:i(t.stepSizeMax,a),stepSizeMin:i(t.stepSizeMin,u),stepSizeMinAllow:i(t.stepSizeMinAllow,l),stiffCheck:i(t.stiffCheck,c),tcrit:i(t.tcrit,h)};if(f.tcrit.length>0&&(f.tcrit=r([],f.tcrit,!0).sort()),f.maxSteps<1)throw n("maxSteps","must be at least 1");if(f.atol<=0)throw n("atol","must be strictly positive");if(f.rtol<=0)throw n("rtol","must be strictly positive");return f}},742:function(t,e,r){var n,i=this&&this.__extends||(n=function(t,e){return n=Object.setPrototypeOf||{__proto__:[]}instanceof Array&&function(t,e){t.__proto__=e}||function(t,e){for(var r in e)Object.prototype.hasOwnProperty.call(e,r)&&(t[r]=e[r])},n(t,e)},function(t,e){if("function"!=typeof e&&null!==e)throw new TypeError("Class extends value "+String(e)+" is not a constructor or null");function r(){this.constructor=t}n(t,e),t.prototype=null===e?Object.create(e):(r.prototype=e.prototype,new r)});Object.defineProperty(e,"__esModule",{value:!0}),e.DDE=e.integrateDDE=void 0;var o=r(223),s=r(660);e.integrateDDE=function(t,e,r,n,i,o){void 0===i&&(i={}),void 0===o&&(o=null);var s=new a(t,e.length,i,o);return s.initialise(r,e),s.run(n)};var a=function(t){function e(e,r,n,i){void 0===n&&(n={}),void 0===i&&(i=null);var o=this,s=function(t){return o._interpolate(t)},a=null===i?null:function(t,e){return i(t,e,s)};return(o=t.call(this,(function(t,r,n){return e(t,r,n,s)}),r,n,a)||this)._y0=new Array(r),o}return 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e>t._t})),0===this._tcrit.length?1/0:this._tcrit[0])},t.prototype._step=function(){for(var t=this._t,e=this._h,r=!1,n=!1,i=Math.max(this._lastError,1e-4),o=this._stepper.stepControl,s=this._control,a=this._nextTcrit();!r;){if(this._nSteps>s.maxSteps)throw f("too many steps",t);if(e<s.stepSizeMin){if(!s.stepSizeMinAllow)throw f("step too small",t);e=s.stepSizeMin}if(e<=Math.abs(t)*h)throw f("step size vanished",t);t+e>a&&(e=a-t),this._stepper.step(t,e),this._nSteps++;var u=this._stepper.error(s.atol,s.rtol),l=Math.pow(u,o.constant),p=1/o.factorMin,d=1/o.factorMax;if(u<=1){if(r=!0,this._nStepsAccepted++,this._isStiff(e))throw f("problem became stiff",t);this._stepper.stepComplete(t,e);var v=l/Math.pow(i,o.beta),_=e/(v=c.constrain(v/o.factorSafe,d,p));this._t+=e,this._h=n?Math.min(_,e):Math.min(_,s.stepSizeMax),this._lastError=u}else n=!0,this._nStepsAccepted>=1&&this._nStepsRejected++,e/=Math.min(p,l/o.factorSafe)}return 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diff --git a/scripts/update_js b/scripts/update_js
index 05557b0b..61e9c679 100755
--- a/scripts/update_js
+++ b/scripts/update_js
@@ -2,7 +2,7 @@
 set -exu
 
 ODIN_JS_BRANCH=mrc-4455
-DUST_JS_BRANCH=main
+DUST_JS_BRANCH=update-odin-js
 
 HERE=$(dirname $0)
 PACKAGE_ROOT=$(realpath $HERE/..)

From 52cea3153502dd5708f9dce486f06bcda2f2dad5 Mon Sep 17 00:00:00 2001
From: EmmaLRussell <EmmaRussellKilburn@gmail.com>
Date: Wed, 30 Aug 2023 17:05:42 +0100
Subject: [PATCH 5/6] bump version

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index efec8be7..53966b58 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: odin
 Title: ODE Generation and Integration
-Version: 1.5.7
+Version: 1.5.8
 Authors@R: c(person("Rich", "FitzJohn", role = c("aut", "cre"),
                     email = "rich.fitzjohn@gmail.com"),
              person("Thibaut", "Jombart", role = "ctb"),

From 590ea82c898bd91ad7cd7394be0a87d698f10dff Mon Sep 17 00:00:00 2001
From: EmmaLRussell <EmmaRussellKilburn@gmail.com>
Date: Fri, 1 Sep 2023 10:23:29 +0100
Subject: [PATCH 6/6] reset odin-js and dust-js branches to main

---
 scripts/update_js | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/scripts/update_js b/scripts/update_js
index 61e9c679..a449dc58 100755
--- a/scripts/update_js
+++ b/scripts/update_js
@@ -1,8 +1,8 @@
 #!/usr/bin/env bash
 set -exu
 
-ODIN_JS_BRANCH=mrc-4455
-DUST_JS_BRANCH=update-odin-js
+ODIN_JS_BRANCH=main
+DUST_JS_BRANCH=main
 
 HERE=$(dirname $0)
 PACKAGE_ROOT=$(realpath $HERE/..)