Candidate (#50)
* Squashed commit of the following: commit 496f723378feac04e2299687d7b39e6173437e0d Author: Alex Zarebski <aezarebski@gmail.com> Date: Sat Aug 6 17:03:33 2022 +0100 bump minor because new feature commit 2dd6ed3927c1cb6a550f0f19e11debdc7647899d Author: Alex Zarebski <aezarebski@gmail.com> Date: Sat Aug 6 16:55:34 2022 +0100 lint commit 367540e22fe23a514d1d9ccc76d5af15598f2f34 Author: Alex Zarebski <aezarebski@gmail.com> Date: Sat Aug 6 16:51:14 2022 +0100 fix bug where history size wasn't updating properly commit ceb7b11690b03a21292520760846ba9cb1589935 Author: Alex Zarebski <aezarebski@gmail.com> Date: Fri Aug 5 14:19:09 2022 +0100 add run configuration from intellij commit 2fcadb3999474a68c8042ad158d34285580b349e Author: Alex Zarebski <aezarebski@gmail.com> Date: Fri Aug 5 14:15:49 2022 +0100 add file that helps intellij work out what is happening commit 52c0f8bbc7ce0dae6a24dfa6616462af699c19f6 Author: Alex Zarebski <aezarebski@gmail.com> Date: Fri Aug 5 13:47:34 2022 +0100 implement use of history parameters commit dec4d39bdf6781e83b4944e0ec5fb5068b470eb7 Author: Alex Zarebski <aezarebski@gmail.com> Date: Fri Aug 5 13:45:32 2022 +0100 split the numerical functions out into a separate class commit 423610f5fb555c20483b66a5b00daaf5eea42cfc Author: Alex Zarebski <aezarebski@gmail.com> Date: Fri Aug 5 13:41:55 2022 +0100 change class name to be more informative commit 569acb2b4859bd177e7bf88a3eae0bf1befcb130 Author: Alex Zarebski <aezarebski@gmail.com> Date: Tue Aug 2 18:06:08 2022 +0100 upgrade the interval terminator class commit 2b480a81f4c66f902fcdf36c41d6aae555398e5f Author: Alex Zarebski <aezarebski@gmail.com> Date: Tue Aug 2 17:31:54 2022 +0100 apply code suggestions for clarity * include check that parameter dimensions make sense * Squashed commit of the following: commit b943a704e944bf950a26f7b8ea2dc65cf83552d9 Author: Alex Zarebski <aezarebski@gmail.com> Date: Wed Aug 10 13:09:42 2022 +0100 add an example showing the history check stuff commit a4732fab3a62aca155e2fc8263b11f2263a0fe85 Author: Alex Zarebski <aezarebski@gmail.com> Date: Wed Aug 10 12:55:12 2022 +0100 extend beauti template to support history checks * include a sanity check that the distribution actually makes sense * Squashed commit of the following: commit 504daa184ecdfd65f13e0bd36bce1fd5a8bef1ca Author: Alex Zarebski <aezarebski@gmail.com> Date: Mon Aug 22 14:10:20 2022 +0100 finish r0 implementation commit 12827b8c83c6a4320b44be22ed80bb3f900993f6 Author: Alex Zarebski <aezarebski@gmail.com> Date: Mon Aug 22 12:07:57 2022 +0100 fix a broken validation check commit 07438ceea4307a53139114b0f76f77f51d33cce2 Author: Alex Zarebski <aezarebski@gmail.com> Date: Mon Aug 22 12:05:11 2022 +0100 add a convenience function commit 33cda40479fa97492f1aef0bb33ee489c644a0ed Author: Alex Zarebski <aezarebski@gmail.com> Date: Mon Aug 22 12:04:48 2022 +0100 remove a bunch of dead code commit e83cb670f2e77d2c79652ac419d8592a4e141526 Author: Alex Zarebski <aezarebski@gmail.com> Date: Mon Aug 22 11:36:13 2022 +0100 implement single pass parameter update commit 50d8344155b29050e0928246389eee2fb992d6ee Author: Alex Zarebski <aezarebski@gmail.com> Date: Sat Aug 20 17:29:30 2022 +0100 use a set to compute the param change times properly commit 92d0ad659fd2dc804519c2d869839405fd2f16b4 Author: Alex Zarebski <aezarebski@gmail.com> Date: Sat Aug 20 16:52:07 2022 +0100 set up for working out the param change times based on unique times commit a939bd97223f5448adb6e5ab93389fda601bdacc Author: Alex Zarebski <aezarebski@gmail.com> Date: Sat Aug 20 15:32:35 2022 +0100 include inputs for alternative parameterisation commit dbf13fdcca39a171ab0c33935e5dd81c0aef80b6 Author: Alex Zarebski <aezarebski@gmail.com> Date: Sat Aug 20 14:45:25 2022 +0100 organise parameters in a clearer way commit ed2c265d34679eb53d3df60c0bb7955bcbfd56a2 Author: Alex Zarebski <aezarebski@gmail.com> Date: Fri Aug 19 16:24:15 2022 +0100 deprecate the logger as it is no longer needed * bug fix for edge case where omega not provided * Squashed commit of the following: commit 41e0dfd0072321b447c25a95999d2429f2c307d8 Author: Alex Zarebski <aezarebski@gmail.com> Date: Wed Aug 24 16:13:44 2022 +0100 further tweaks to the templates commit 6249209f2f83b0336dcfa36b1bdf7eb6fd71ea61 Author: Alex Zarebski <aezarebski@gmail.com> Date: Wed Aug 24 15:53:10 2022 +0100 tweak template commit fbc4f8412525a90f44c18967cb4c041c53c2e1b3 Author: Alex Zarebski <aezarebski@gmail.com> Date: Wed Aug 24 15:27:16 2022 +0100 draft template file commit 29768e3c9cbdbdfbc3dbd6ad0ba0a0d77db43db6 Author: Alex Zarebski <aezarebski@gmail.com> Date: Wed Aug 24 15:03:07 2022 +0100 docs commit 1b6afc664d852d7206d92dd07dd590f807cd48fb Author: Alex Zarebski <aezarebski@gmail.com> Date: Wed Aug 24 15:02:34 2022 +0100 fix silly omission commit 33fab005eb0f8b61a1a64d93b3cfc38af750b28c Author: Alex Zarebski <aezarebski@gmail.com> Date: Wed Aug 24 13:44:00 2022 +0100 implement the time series r0 commit 58d4c02f35ed9242288fc7f6262399d7c0e96859 Author: Alex Zarebski <aezarebski@gmail.com> Date: Wed Aug 24 12:36:25 2022 +0100 document and refactor some existing code * fix bug where if only some parameters change initialisation fails * use the migrate script * bring the templates up to date * remove timtamlogger as was deprecated * rename the templates directory * update version file based on package health checker feedback * update buildscript to work with 2.7 * apply migration script to examples * adjust version xml to use latest versions * use a more sensible version number * copy over fix on prior
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- build.xml 13 additions, 13 deletionsbuild.xml
- examples/ex1.xml 14 additions, 16 deletionsexamples/ex1.xml
- examples/ex2.xml 14 additions, 16 deletionsexamples/ex2.xml
- examples/ex3.xml 20 additions, 22 deletionsexamples/ex3.xml
- examples/ex4.xml 14 additions, 14 deletionsexamples/ex4.xml
- fxtemplates/timtam-time-series-r0.xml 5 additions, 20 deletionsfxtemplates/timtam-time-series-r0.xml
- fxtemplates/timtam.xml 4 additions, 18 deletionsfxtemplates/timtam.xml
- src/timtam/HiddenLineageDist.java 1 addition, 1 deletionsrc/timtam/HiddenLineageDist.java
- src/timtam/Numerics.java 1 addition, 1 deletionsrc/timtam/Numerics.java
- src/timtam/TimTam.java 7 additions, 7 deletionssrc/timtam/TimTam.java
- src/timtam/TimTamLogger.java 0 additions, 59 deletionssrc/timtam/TimTamLogger.java
- test/timtam/TestTimTam.java 4 additions, 4 deletionstest/timtam/TestTimTam.java
- version.xml 8 additions, 3 deletionsversion.xml
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