New main + old plumelib version

run.sh

@@ -127,9 +127,9 @@ fi
 
 (
   cd ./src/scripts/merge_tools/merging
-  export JAVA_HOME=$GRAALVM_HOME
+  export JAVA_HOME=$JAVA17_HOME
   export PATH="$JAVA_HOME/bin:$PATH"
-  ./gradlew -q nativeCompile
+  ./gradlew shadowJar
 )
 
 echo "Machine ID: $machine_id"

test/small-goal-files/merges_analyzed/benedikt-schesch/git-hires-merge-example.csv

@@ -1,3 +1,3 @@
-idx,branch_name,merge,left,right,notes,num_diff_files,union_diff_files,num_intersecting_files,num_diff_lines,num_diff_hunks,imports_involved,non_java_involved,diff contains java file,left_tree_fingerprint,left parent test result,right_tree_fingerprint,right parent test result,parents pass,test merge,sampled for testing
-1,refs/heads/main,4ae40d33c3b959e3a15e458eb9b0676251e36a41,48199306f02a82abdeff0c01fab1ce112126d727,488122ce6c91e157d1f49b88b79feaa083fdee5b,,2,2,2,4,1,False,True,True,2252a9465319d00b974abd931cc98e1f435b4fe232b4dd61a828ad40139ec20c,Tests_passed,3782e47be673266f23cba016dc13973231429bb34e4c08a314c5b2f6c37d238f,Tests_passed,True,True,True
-2,refs/remotes/origin/import_1,0209c47c118fcaf978f6ebc5bad8a334b541de0b,b4331092d8c5d1b03e6a9807ab135ed263b52663,8204af9984280ccc7f7793f903fc0807b626bf9c,,2,2,2,5,2,True,True,True,f48eaaf883e49f3e3a1f3e1ddff64beb42c9d9bacec7d273f748baa63093bd9b,Tests_passed,052542ef8f16db238683e23556af730ee0d7c65c3ac0554d01e7ee800ca9b7c6,Tests_passed,True,True,True
+idx,branch_name,merge,left,right,notes,diff contains java file,imports_involved,left parent test result,left_tree_fingerprint,non_java_involved,num_diff_files,num_diff_hunks,num_diff_lines,num_intersecting_files,parents pass,right parent test result,right_tree_fingerprint,test merge,union_diff_files,sampled for testing
+1,refs/heads/main,4ae40d33c3b959e3a15e458eb9b0676251e36a41,48199306f02a82abdeff0c01fab1ce112126d727,488122ce6c91e157d1f49b88b79feaa083fdee5b,,True,False,Tests_passed,2252a9465319d00b974abd931cc98e1f435b4fe232b4dd61a828ad40139ec20c,True,2,1,4,2,True,Tests_passed,3782e47be673266f23cba016dc13973231429bb34e4c08a314c5b2f6c37d238f,True,2,True
+2,refs/remotes/origin/import_1,0209c47c118fcaf978f6ebc5bad8a334b541de0b,b4331092d8c5d1b03e6a9807ab135ed263b52663,8204af9984280ccc7f7793f903fc0807b626bf9c,,True,True,Tests_passed,f48eaaf883e49f3e3a1f3e1ddff64beb42c9d9bacec7d273f748baa63093bd9b,True,2,2,5,2,True,Tests_passed,052542ef8f16db238683e23556af730ee0d7c65c3ac0554d01e7ee800ca9b7c6,True,2,True

test/small-goal-files/merges_analyzed/mangstadt/ez-vcard.csv

@@ -1,14 +1,14 @@
-idx,branch_name,merge,left,right,notes,num_diff_files,union_diff_files,num_intersecting_files,num_diff_lines,num_diff_hunks,imports_involved,non_java_involved,diff contains java file,test merge,left_tree_fingerprint,left parent test result,right_tree_fingerprint,right parent test result,parents pass,sampled for testing
-1,refs/heads/master,8f26d88838bfe671cef10e6a832c0c6a57b42fcd,814aae2b1a8ba6e42074d282b2ff9d1af632aef3,f308a61574b9182d151aa9d0cf5fbe5818a48fb8,,5,5,1,299,30,True,True,False,False,,,,,,False
-2,refs/heads/master,0637f5fc19cf6ad79cd2c58981facc3678d5bbff,b8b0b0c8e1dff237975942022a42c6c25b9d9741,3c10bf587f097be3e2a77b0d2d556e6f9efd97b1,,7,7,1,43,12,True,True,False,False,,,,,,False
-3,refs/heads/master,633e9c677f26c1cae476d9ce43331cc30bd8f9e8,af63ebf1a441d0165bab7f6250caf0e2793b9829,22631a4817aa29b231919cb5d8c05d935386b763,a parent is the base,2,2,0,2,1,False,True,False,False,,,,,,False
-4,refs/heads/master,a927decebd50d02bff3f8c56ade565b98d0ecd4c,2380144cf35bc2c211874ac53db2d846fccffb97,6621980643544df2261bd874717839dd24b28324,,7,7,1,38,8,True,True,False,False,,,,,,False
-5,refs/heads/master,d6a31c5fece9a634b7829df08bd0afa0ef06b69a,4639361f062ee6455b88e31996743e300240e71e,4e959f00b9e3a80ea99486834b0ab164be663fdc,a parent is the base,2,2,0,2,1,False,True,False,False,,,,,,False
-6,refs/heads/master,8b26b8c56130e60347f8f20c17c3eca14b601cc1,e454bdf3e3b7d02bb95ff8a58952e70cb97dd0f9,522254f7ceb5e390cbb0904d698cb6294e081ce2,a parent is the base,4,4,0,18,3,True,True,False,False,,,,,,False
-7,refs/heads/master,63ab6b841a7aa31372315a902b98fc5b2cc3b661,ea6026ee62cc184db68d841d50d58474fcdf4862,ab2032ca9769d452d4906f51cf56ca7d983a27c4,,342,342,10,16131,2526,True,True,True,True,aa82b49dd87edb07fbe37b7c2d6801fce8db7c437d1afe8a7b2723c81806286e,Tests_passed,66055b6c4498a64239ae0e49781e086ed06ec3e58be7d9651c23c53f8c6bab6a,Tests_passed,True,True
-8,refs/heads/master,5e11fc8e2c1f5763ff6e6b37d3e750e369af7c94,b42390b2d6279bf7c23580f0f4ac517cba448cd5,dee07e7edfb332efd5d5207660248f71e96a1a0e,,51,51,1,104,50,True,True,False,False,,,,,,False
-9,refs/heads/master,bce54f56a1da7332cabdec21b26e82cd899ce82b,16b6d6cd734326e55af96146ac89594c8ed1b233,ce422afbecd67144c1e8caceaa151f80d4f8a0cc,,35,35,1,1940,161,True,True,False,False,,,,,,False
-10,refs/heads/master,f238de6e66d3e5d03715aa88dccc660d0ab89318,03bd6bf2c9873b23344b31ca7c39524ad9ee5756,c824e9fabecc54d431d4c860b95a2ad13794556c,a parent is the base,3,3,0,38,2,False,True,False,False,,,,,,False
-11,refs/heads/master,a2a632bba203ee71191e71e11058726f2f030b00,345934e15e82c9cbffb5b297aab51ad105b9ad82,541f59d09b5232b68cda87ee2abba7c62d33ee32,,4,4,1,77,4,True,True,False,False,,,,,,False
-12,refs/remotes/origin/pull/49,72e37df9ec88656844758c7303e8e1f9234295c3,24476c206b8df9f5458e2ec57fa16d3ebe23f898,64164540fa269cd1ed14f04236a88b8a3ac22dcb,,122,122,1,9540,291,True,True,False,False,,,,,,False
-13,refs/remotes/origin/pull/49,073c34351663673f4b53142bacf75033706e067f,64847e218c67593c77b0ebdefc93b5e7b4c82406,e80bea970d0b1a4ee340641f01b30b09f816eaa2,,116,116,1,10364,669,True,True,False,False,,,,,,False
+idx,branch_name,merge,left,right,notes,diff contains java file,imports_involved,non_java_involved,num_diff_files,num_diff_hunks,num_diff_lines,num_intersecting_files,test merge,union_diff_files,left parent test result,left_tree_fingerprint,parents pass,right parent test result,right_tree_fingerprint,sampled for testing
+1,refs/heads/master,8f26d88838bfe671cef10e6a832c0c6a57b42fcd,814aae2b1a8ba6e42074d282b2ff9d1af632aef3,f308a61574b9182d151aa9d0cf5fbe5818a48fb8,,False,True,True,5,30,299,1,False,5,,,,,,False
+2,refs/heads/master,0637f5fc19cf6ad79cd2c58981facc3678d5bbff,b8b0b0c8e1dff237975942022a42c6c25b9d9741,3c10bf587f097be3e2a77b0d2d556e6f9efd97b1,,False,True,True,7,12,43,1,False,7,,,,,,False
+3,refs/heads/master,633e9c677f26c1cae476d9ce43331cc30bd8f9e8,af63ebf1a441d0165bab7f6250caf0e2793b9829,22631a4817aa29b231919cb5d8c05d935386b763,a parent is the base,False,False,True,2,1,2,0,False,2,,,,,,False
+4,refs/heads/master,a927decebd50d02bff3f8c56ade565b98d0ecd4c,2380144cf35bc2c211874ac53db2d846fccffb97,6621980643544df2261bd874717839dd24b28324,,False,True,True,7,8,38,1,False,7,,,,,,False
+5,refs/heads/master,d6a31c5fece9a634b7829df08bd0afa0ef06b69a,4639361f062ee6455b88e31996743e300240e71e,4e959f00b9e3a80ea99486834b0ab164be663fdc,a parent is the base,False,False,True,2,1,2,0,False,2,,,,,,False
+6,refs/heads/master,8b26b8c56130e60347f8f20c17c3eca14b601cc1,e454bdf3e3b7d02bb95ff8a58952e70cb97dd0f9,522254f7ceb5e390cbb0904d698cb6294e081ce2,a parent is the base,False,True,True,4,3,18,0,False,4,,,,,,False
+7,refs/heads/master,63ab6b841a7aa31372315a902b98fc5b2cc3b661,ea6026ee62cc184db68d841d50d58474fcdf4862,ab2032ca9769d452d4906f51cf56ca7d983a27c4,,True,True,True,342,2526,16131,10,True,342,Tests_passed,aa82b49dd87edb07fbe37b7c2d6801fce8db7c437d1afe8a7b2723c81806286e,True,Tests_passed,66055b6c4498a64239ae0e49781e086ed06ec3e58be7d9651c23c53f8c6bab6a,True
+8,refs/heads/master,5e11fc8e2c1f5763ff6e6b37d3e750e369af7c94,b42390b2d6279bf7c23580f0f4ac517cba448cd5,dee07e7edfb332efd5d5207660248f71e96a1a0e,,False,True,True,51,50,104,1,False,51,,,,,,False
+9,refs/heads/master,bce54f56a1da7332cabdec21b26e82cd899ce82b,16b6d6cd734326e55af96146ac89594c8ed1b233,ce422afbecd67144c1e8caceaa151f80d4f8a0cc,,False,True,True,35,161,1940,1,False,35,,,,,,False
+10,refs/heads/master,f238de6e66d3e5d03715aa88dccc660d0ab89318,03bd6bf2c9873b23344b31ca7c39524ad9ee5756,c824e9fabecc54d431d4c860b95a2ad13794556c,a parent is the base,False,False,True,3,2,38,0,False,3,,,,,,False
+11,refs/heads/master,a2a632bba203ee71191e71e11058726f2f030b00,345934e15e82c9cbffb5b297aab51ad105b9ad82,541f59d09b5232b68cda87ee2abba7c62d33ee32,,False,True,True,4,4,77,1,False,4,,,,,,False
+12,refs/remotes/origin/pull/49,72e37df9ec88656844758c7303e8e1f9234295c3,24476c206b8df9f5458e2ec57fa16d3ebe23f898,64164540fa269cd1ed14f04236a88b8a3ac22dcb,,False,True,True,122,291,9540,1,False,122,,,,,,False
+13,refs/remotes/origin/pull/49,073c34351663673f4b53142bacf75033706e067f,64847e218c67593c77b0ebdefc93b5e7b4c82406,e80bea970d0b1a4ee340641f01b30b09f816eaa2,,False,True,True,116,669,10364,1,False,116,,,,,,False

test/small-goal-files/merges_analyzed/pedrovgs/algorithms.csv

@@ -1,21 +1,21 @@
-idx,branch_name,merge,left,right,notes,num_diff_files,union_diff_files,num_intersecting_files,num_diff_lines,num_diff_hunks,imports_involved,non_java_involved,diff contains java file,test merge,left_tree_fingerprint,left parent test result,right_tree_fingerprint,right parent test result,parents pass,sampled for testing
-1,refs/heads/master,44ce61beeb8bb5c5c1289db02f1da53f6bff6d8a,e121b3943958ba1558d8828db6f13c632e99f298,58129e828567fac52e821ca147feeab87a95d780,a parent is the base,3,3,0,44,17,False,True,False,False,,,,,,False
-2,refs/heads/master,e866ae7916d6b763f7d32f72f54edd735b5ea6bc,ae5dac889d19edd6c773e60420f00d4e7177f31f,4342b16e18da9082b32d5b8e9b5b6e3378461ce4,,5,5,1,116,9,False,True,False,False,,,,,,False
-3,refs/heads/master,ae5dac889d19edd6c773e60420f00d4e7177f31f,38ec459e6f163991c6f88210720dcda4fecc64e8,eb3260404e596031bc9ee037b29bd1fcbb87f625,a parent is the base,2,2,0,35,6,False,True,False,False,,,,,,False
-4,refs/heads/master,38ec459e6f163991c6f88210720dcda4fecc64e8,60d87e9a120e330eb34c9d558d0f00e52b5ce438,aa882141f26ef82107658c214ec18a799403bb57,a parent is the base,3,3,0,91,6,False,True,False,False,,,,,,False
-5,refs/heads/master,d7e0b1c03fa7cacf40b32dcfde30871e8947445a,2c4e69eb243a81ba05d24456b3cad7e8a696f630,8a1a1a7fb53732edaf17ef9876545c4bca568e05,,2,3,3,219,20,False,True,True,True,718024edbe6334028acc916e40446b4ae7cb30be97792ae8e2253bdc1112c5a4,Tests_passed,199e1e65500c8ab0fd66d837663440faf9f32711932bdf2136778923a7b0d4d3,Tests_passed,True,True
-6,refs/heads/master,60d87e9a120e330eb34c9d558d0f00e52b5ce438,bceffabe0d850ea9c67c93a9fb578d2ca8600022,9aa3611952f1715d8f5cf6404a3dad0e95bf175f,a parent is the base,2,2,0,2,1,False,True,False,False,,,,,,False
-7,refs/heads/master,bceffabe0d850ea9c67c93a9fb578d2ca8600022,247b66cb2c7792336c5d1c2c1502a55d5222c823,67360ca7159643f3a9fc20f30e164b36a4e4f859,,5,5,0,215,19,False,True,False,False,,,,,,False
-8,refs/heads/master,247b66cb2c7792336c5d1c2c1502a55d5222c823,c7c288a43e324748f1f25ee72f9639d808c70b7e,7f89b8c5fbe85848e96a0cdaffb83664588c8474,a parent is the base,3,3,0,12,6,False,True,False,False,,,,,,False
-9,refs/heads/master,c7c288a43e324748f1f25ee72f9639d808c70b7e,ffa4a6ccd332fad6dc1c5a269b3854a5a2bfff91,296f6b09446b63e8b036e4840879c2d890ae925d,a parent is the base,2,2,0,6,1,False,True,False,False,,,,,,False
-10,refs/heads/master,216529baa98d8646b192b1c6897b01d3181f2ac6,ffa4a6ccd332fad6dc1c5a269b3854a5a2bfff91,deaa316e2165940e50e4e00e83e18d27417fb642,a parent is the base,2,2,0,15,2,False,True,False,False,,,,,,False
-11,refs/heads/master,ffa4a6ccd332fad6dc1c5a269b3854a5a2bfff91,128ccf0f25f401f2218c03166a6f4ebc5ce21385,03d7c1872d5b17434fd460f7b8a0b8c9c90849f7,a parent is the base,3,3,0,18,5,False,True,False,False,,,,,,False
-12,refs/heads/master,128ccf0f25f401f2218c03166a6f4ebc5ce21385,1f8f61c50d4e36ab8677b271a58648e90a2f1b28,22ee3ce03f74349ed3b0f36bfdf1dc119e2be70b,a parent is the base,2,2,0,11,3,False,True,False,False,,,,,,False
-13,refs/heads/master,c8604d6f6d23a0cd5d3f9fac472dbf467fe11b8e,7ebdadbc657a68da22826ce3cc402e3635e80d4c,fd87cbc2cdbe813564f0a2c7e8070964220cdcc6,a parent is the base,2,2,0,7,1,False,True,False,False,,,,,,False
-14,refs/remotes/origin/pull/27,fdd92255570bf37534ba36f632773923d60e32d2,8edac208c376e88626e88a720c9166fef9588853,1a71e9f95183a089b2b72a0cb42337681594e699,,2,4,3,2,1,False,True,False,False,,,,,,False
-15,refs/remotes/origin/pull/37,6b917cc6a33eb87fec2dcdafc845177f470ca374,8ef7da30196fba8e55947acf6168d8cd4a82f2b8,68f656ff10751259284d083e8fdf8e82f7ada15f,,4,4,2,57,13,True,True,True,False,7aa5e2f53ad1560daf3a96bd8e663a929817c73938d959fa60d355658fa2e2be,Tests_failed,755c5c56e067df81d5c17ef49dc1f4e7678609ab296b9a8ab2dece46fe0e4fde,Tests_failed,False,False
-16,refs/remotes/origin/pull/37,8ef7da30196fba8e55947acf6168d8cd4a82f2b8,37e80741a853a6626a77aed38caa07f4e44d85b2,8b2e3b06185e4a111ae987db7fa01901974036cd,,6,6,1,199,12,True,True,False,False,,,,,,False
-17,refs/remotes/origin/pull/37,680f2603dc41bb7c5843b0fa342e829210611d9d,1477ce25eaad76986f50aa5b740e2c023ff31de2,879fb60972e4e83fdb7b5337db66c8afbfb95ffc,,3,3,2,60,12,False,True,True,False,bdf6e72ad28bbb283d5760e9a231b0df40640519b3e3cfd5e3f0ccda8c93fc8d,Tests_passed,1a54a2f1e9d5a185842f1ebcbb59a35d16b5d948671ad2f6eb75fc88bf0831d3,Tests_failed,False,False
-18,refs/remotes/origin/pull/37,d1279d1b59ecba7f01de8b2c1995562f92b2e255,b636ef254a97ae830baa6d783121de7890818785,9497e2f66d7af3feedd3106faa6e8b0aa6118b41,,4,4,1,159,6,True,True,False,False,,,,,,False
-19,refs/remotes/origin/pull/37,104eb9ed88cde145576ea1df50460915af488e74,6baa2ed219e18f9763bb2f2de74c5fb800d15899,99a155f67dfe68de440feb560a7e4c4ee5ae355c,,3,4,4,78,10,True,True,True,True,216098fad46bb19977b73bb3104f281c803911449ff6eb9c13d600efb375ae84,Tests_passed,d80bbdd6216a68130e2bbf0e70dde5edb5e9e02e397fe38c702bc69e74fddebf,Tests_passed,True,True
-20,refs/remotes/origin/pull/73,9c8740d0e38ba93f08bfb462d16cab448a0197f1,7ebdadbc657a68da22826ce3cc402e3635e80d4c,4e2214112de23d1319ce77736547fa8900384e7c,a parent is the base,32,32,0,896,99,True,True,False,False,,,,,,False
+idx,branch_name,merge,left,right,notes,diff contains java file,imports_involved,non_java_involved,num_diff_files,num_diff_hunks,num_diff_lines,num_intersecting_files,test merge,union_diff_files,left parent test result,left_tree_fingerprint,parents pass,right parent test result,right_tree_fingerprint,sampled for testing
+1,refs/heads/master,44ce61beeb8bb5c5c1289db02f1da53f6bff6d8a,e121b3943958ba1558d8828db6f13c632e99f298,58129e828567fac52e821ca147feeab87a95d780,a parent is the base,False,False,True,3,17,44,0,False,3,,,,,,False
+2,refs/heads/master,e866ae7916d6b763f7d32f72f54edd735b5ea6bc,ae5dac889d19edd6c773e60420f00d4e7177f31f,4342b16e18da9082b32d5b8e9b5b6e3378461ce4,,False,False,True,5,9,116,1,False,5,,,,,,False
+3,refs/heads/master,ae5dac889d19edd6c773e60420f00d4e7177f31f,38ec459e6f163991c6f88210720dcda4fecc64e8,eb3260404e596031bc9ee037b29bd1fcbb87f625,a parent is the base,False,False,True,2,6,35,0,False,2,,,,,,False
+4,refs/heads/master,38ec459e6f163991c6f88210720dcda4fecc64e8,60d87e9a120e330eb34c9d558d0f00e52b5ce438,aa882141f26ef82107658c214ec18a799403bb57,a parent is the base,False,False,True,3,6,91,0,False,3,,,,,,False
+5,refs/heads/master,d7e0b1c03fa7cacf40b32dcfde30871e8947445a,2c4e69eb243a81ba05d24456b3cad7e8a696f630,8a1a1a7fb53732edaf17ef9876545c4bca568e05,,True,False,True,2,20,219,3,True,3,Tests_passed,718024edbe6334028acc916e40446b4ae7cb30be97792ae8e2253bdc1112c5a4,True,Tests_passed,199e1e65500c8ab0fd66d837663440faf9f32711932bdf2136778923a7b0d4d3,True
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