2.5.20 rc

veg · Oct 15, 2020 · e60cc17 · e60cc17
1 parent 4390996
commit e60cc17
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Showing 5 changed files with 9 additions and 10 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -579,7 +579,7 @@ add_test (NAME SLAC COMMAND HYPHYMP tests/hbltests/libv3/SLAC.wbf)
 add_test (NAME SLAC-PARTITIONED COMMAND HYPHYMP tests/hbltests/libv3/SLAC-partitioned.wbf)
 add_test (NAME FEL COMMAND HYPHYMP tests/hbltests/libv3/FEL.wbf)
 add_test (MEME HYPHYMP tests/hbltests/libv3/MEME.wbf)
-add_test (MEME-PARTITIONED HYPHYMP tests/hbltests/libv3/MEME.wbf)
+add_test (MEME-PARTITIONED HYPHYMP tests/hbltests/libv3/MEME-partitioned.wbf)
 add_test (BUSTED HYPHYMP tests/hbltests/libv3/BUSTED.wbf)
 add_test (BUSTED-SRV HYPHYMP tests/hbltests/libv3/BUSTED-SRV.wbf)
 add_test (RELAX HYPHYMP tests/hbltests/libv3/RELAX.wbf)

diff --git a/res/TemplateBatchFiles/SelectionAnalyses/FEL.bf b/res/TemplateBatchFiles/SelectionAnalyses/FEL.bf
@@ -339,7 +339,7 @@ lfunction fel.handle_a_site (lf, filter_data, partition_index, pattern_info, mod
     ^"fel.alpha_scaler" = (^"fel.alpha_scaler" + 3*^"fel.beta_scaler_test")/4;
     parameters.SetConstraint ("fel.beta_scaler_test","fel.alpha_scaler", "");
 
-    //Optimize (results, ^lf, {"OPTIMIZATION_METHOD" : "nedler-mead", OPTIMIZATION_PRECISION: 1e-5});
+    //Optimize (results, ^lf, {"OPTIMIZATION_METHOD" : "nedler-mead"});
     Optimize (results, ^lf);
 
     Null = estimators.ExtractMLEs (lf, model_mapping);

diff --git a/res/TemplateBatchFiles/SelectionAnalyses/MEME.bf b/res/TemplateBatchFiles/SelectionAnalyses/MEME.bf
@@ -605,7 +605,7 @@ lfunction meme.handle_a_site (lf_fel, lf_bsrel, filter_data, partition_index, pa
         LFCompute (^lf_bsrel,LF_DONE_COMPUTE);
 
         ^"meme.site_beta_plus" := ^"meme.site_alpha";
-        Optimize (results, ^lf_bsrel);
+        Optimize (results, ^lf_bsrel, {"OPTIMIZATION_METHOD" : "nedler-mead"});
         //io.SpoolLF (lf_bsrel, "/tmp/meme.debug", "MEME-null");
 
         Null = estimators.ExtractMLEs (lf_bsrel, model_mapping);

diff --git a/res/TemplateBatchFiles/SelectionAnalyses/contrast-fel.bf b/res/TemplateBatchFiles/SelectionAnalyses/contrast-fel.bf
@@ -748,7 +748,7 @@ lfunction fel.handle_a_site (lf, filter_data, partition_index, pattern_info, mod
         );
     }
 
-    Optimize (results, ^lf);
+    Optimize (results, ^lf, {"OPTIMIZATION_METHOD" : "nedler-mead"});
     Null = estimators.ExtractMLEs (lf, model_mapping);
     Null [utility.getGlobalValue("terms.fit.log_likelihood")] = results[1][0];
 
@@ -761,7 +761,7 @@ lfunction fel.handle_a_site (lf, filter_data, partition_index, pattern_info, mod
 
                 estimators.RestoreLFStateFromSnapshot (lf_id, snapshot);
                 parameters.SetConstraint ((^"fel.scaler_parameter_names")[v1n],(^"fel.scaler_parameter_names")[v2n], "");
-                Optimize (results, ^lf);
+                Optimize (results, ^lf, {"OPTIMIZATION_METHOD" : "nedler-mead"});
                 pairwise[v1n + "|" + v2n] = estimators.ExtractMLEs (lf, model_mapping);
                 (pairwise[v1n + "|" + v2n])[utility.getGlobalValue("terms.fit.log_likelihood")] = results[1][0];
            }

diff --git a/tests/hbltests/libv3/MEME-partitioned.wbf b/tests/hbltests/libv3/MEME-partitioned.wbf
@@ -20,7 +20,7 @@ fscanf ("data/CD2.nex.MEME.json","Raw",json);
 
 
 assert (check_value (
-    ((meme.json["fits"])["Unconstrained model"])["Log Likelihood"], -3466.56, 0.001), "Incorrect log-likelihood for the Global MG94xREV model");
+    ((meme.json["fits"])["Global MG94xREV"])["Log Likelihood"], -3466.57, 0.001), "Incorrect log-likelihood for the Global MG94xREV model");
 
 
 p_values   = (((meme.json["MLE"])["content"])["0"])[-1][6];
@@ -60,10 +60,9 @@ function confirm_site (site, p, dict, kind) {
     return FALSE;
 }
 
-utility.ForEachPair (p_values,"_index_", "_p_",
-                 "  
-                   confirm_site (_index_[0], _p_, test.expected_positives, 1))
-                ");
+for (_index_,_p_; in; p_values) {
+    confirm_site (_index_, _p_, test.expected_positives, 1);
+}
 
 assert (check_value (
     test.lrt_sum, 20.33, 0.05), "More than 5% difference in cumulative LRT for positively selected sites");