[med-svn] [Git][med-team/hyphy][master] 4 commits: routine-update: New upstream version
Nilesh Patra
gitlab at salsa.debian.org
Wed Nov 18 20:14:16 GMT 2020
Nilesh Patra pushed to branch master at Debian Med / hyphy
Commits:
cb557a21 by Nilesh Patra at 2020-11-18T20:06:36+00:00
routine-update: New upstream version
- - - - -
e5b51d8b by Nilesh Patra at 2020-11-18T20:06:37+00:00
New upstream version 2.5.23+dfsg
- - - - -
6b5647e2 by Nilesh Patra at 2020-11-18T20:06:48+00:00
Update upstream source from tag 'upstream/2.5.23+dfsg'
Update to upstream version '2.5.23+dfsg'
with Debian dir 663e8a5e5fa591dd68e426eff00d81ba38caca26
- - - - -
93ac5b94 by Nilesh Patra at 2020-11-18T20:07:16+00:00
routine-update: Ready to upload to unstable
- - - - -
12 changed files:
- .github/workflows/coverage.yml
- debian/changelog
- res/TemplateBatchFiles/SelectionAnalyses/BUSTED.bf
- res/TemplateBatchFiles/SelectionAnalyses/PRIME.bf
- res/TemplateBatchFiles/SelectionAnalyses/RELAX.bf
- res/TemplateBatchFiles/SelectionAnalyses/SLAC.bf
- res/TemplateBatchFiles/SelectionAnalyses/contrast-fel.bf
- src/core/batchlanhelpers.cpp
- src/core/global_things.cpp
- src/core/likefunc.cpp
- src/core/trie.cpp
- src/mains/unix.cpp
Changes:
=====================================
.github/workflows/coverage.yml
=====================================
@@ -21,7 +21,7 @@ jobs:
- name: Get HyPhy code
uses: actions/checkout at v2
- name: Install and activate miniconda
- uses: goanpeca/setup-miniconda at v1
+ uses: conda-incubator/setup-miniconda at v2
with:
activate-environment: 'hyphy-test-env'
environment-file: '.coveralls.env.yml'
=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+hyphy (2.5.23+dfsg-1) unstable; urgency=medium
+
+ * Team upload.
+ * New upstream version
+
+ -- Nilesh Patra <npatra974 at gmail.com> Wed, 18 Nov 2020 20:07:16 +0000
+
hyphy (2.5.22+dfsg-1) unstable; urgency=medium
* Team upload.
=====================================
res/TemplateBatchFiles/SelectionAnalyses/BUSTED.bf
=====================================
@@ -166,6 +166,8 @@ busted.json[busted.json.background] = busted.has_background;
selection.io.startTimer (busted.json [terms.json.timers], "Preliminary model fitting", 1);
+namespace_tag = "busted";
+
namespace busted {
doGTR ("busted");
}
=====================================
res/TemplateBatchFiles/SelectionAnalyses/PRIME.bf
=====================================
@@ -159,6 +159,7 @@ prime.pairwise_counts = genetic_code.ComputePairwiseDifferencesAndExpectedSites(
selection.io.startTimer (prime.json [terms.json.timers], "Model fitting",1);
if (Type (debug.checkpoint) != "String") {
+ namespace_tag = "prime";
namespace prime {
doGTR ("prime");
}
=====================================
res/TemplateBatchFiles/SelectionAnalyses/RELAX.bf
=====================================
@@ -263,6 +263,8 @@ if (relax.do_srv) {
selection.io.startTimer (relax.json [terms.json.timers], "Preliminary model fitting", 1);
+namespace_tag = "relax";
+
namespace relax {
doGTR ("relax");
}
=====================================
res/TemplateBatchFiles/SelectionAnalyses/SLAC.bf
=====================================
@@ -145,6 +145,8 @@ utility.ForEachPair (slac.selected_branches, "_partition_", "_selection_",
selection.io.startTimer (slac.json [terms.json.timers], "Model fitting",1 );
+namespace_tag = "slac";
+
namespace slac {
doGTR ("slac");
}
=====================================
res/TemplateBatchFiles/SelectionAnalyses/contrast-fel.bf
=====================================
@@ -268,6 +268,8 @@ fel.table_output_options = {terms.table_options.header : TRUE, terms.table_optio
selection.io.startTimer (fel.json [terms.json.timers], "Model fitting",1);
+namespace_tag = "fel";
+
namespace fel {
doGTR ("fel");
}
@@ -394,12 +396,26 @@ fel.site_patterns = alignments.Extract_site_patterns ((fel.filter_specification[
// alpha = alpha_scaler * branch_length
// beta = beta_scaler_test * branch_length or beta_nuisance_test * branch_length
-utility.ForEach (fel.case_respecting_node_names, "_node_",
- '_node_class_ = (fel.selected_branches[fel.partition_index])[_node_];
- _beta_scaler = fel.scaler_parameter_names[_node_class_];
- fel.apply_proportional_site_constraint ("fel.site_tree", _node_, fel.alpha, fel.beta, fel.alpha.scaler, _beta_scaler, (( fel.final_partitioned_mg_results[terms.branch_length])[fel.partition_index])[_node_]);
- ');
+fel.lengths_by_class = {};
+for (_node_; in; fel.case_respecting_node_names) {
+ _node_class_ = (fel.selected_branches[fel.partition_index])[_node_];
+ _beta_scaler = fel.scaler_parameter_names[_node_class_];
+ fel.lengths_by_class[_node_class_] += fel.apply_proportional_site_constraint ("fel.site_tree", _node_, fel.alpha, fel.beta, fel.alpha.scaler, _beta_scaler, (( fel.final_partitioned_mg_results[terms.branch_length])[fel.partition_index])[_node_]);
+}
+
+fel.ignorable = {};
+for (fel.t; in; fel.branches.testable) {
+ if ( fel.lengths_by_class[fel.t] == 0) {
+ fprintf(stdout, "\n-------\n", io.FormatLongStringToWidth(
+ ">[WARNING] The cumulative branch length in the _" + fel.t + "_ class is 0.
+ Rates along these branches are not identifiable; testing will not be formally conducted (all p-values set to 1).", 72),
+ "\n-------\n");
+ fel.ignorable [fel.scaler_parameter_names[fel.t]] = 1;
+ } else {
+ fel.ignorable [fel.scaler_parameter_names[fel.t]] = 0;
+ }
+}
// create the likelihood function for this site
@@ -422,7 +438,7 @@ fel.queue = mpi.CreateQueue ({"LikelihoodFunctions": {{"fel.site_likelihood"}},
"Models" : {{"fel.site.mg_rev"}},
"Headers" : {{"libv3/all-terms.bf","libv3/tasks/ancestral.bf", "libv3/convenience/math.bf"}},
"Functions" : {{"fel.apply_proportional_site_constraint"}},
- "Variables" : {{"terms.fel.test_keys","fel.permutations", "fel.alpha","fel.beta","fel.alpha.scaler","terms.fel.permutation","fel.final_partitioned_mg_results","fel.srv","fel.site_tested_classes","fel.scaler_parameter_names","fel.branches.testable","fel.branches.has_background","fel.alpha.scaler","terms.fel.pairwise","fel.branch_class_counter","fel.report.test_count", "fel.p_value","fel.site.permutations"}}
+ "Variables" : {{"terms.fel.test_keys","fel.permutations","fel.ignorable","fel.alpha","fel.beta","fel.alpha.scaler","terms.fel.permutation","fel.final_partitioned_mg_results","fel.srv","fel.site_tested_classes","fel.scaler_parameter_names","fel.branches.testable","fel.branches.has_background","fel.alpha.scaler","terms.fel.pairwise","fel.branch_class_counter","fel.report.test_count", "fel.p_value","fel.site.permutations"}}
});
@@ -642,6 +658,8 @@ function fel.apply_proportional_site_constraint (tree_name, node_name, alpha_par
`node_name`.`alpha_parameter` := (`alpha_factor`) * fel.branch_length__;
`node_name`.`beta_parameter` := (`beta_factor`) * fel.branch_length__;
");
+
+ return fel.branch_length;
}
//----------------------------------------------------------------------------------------
@@ -685,17 +703,27 @@ lfunction fel.handle_a_site (lf, filter_data, partition_index, pattern_info, mod
for (vi, vv; in; v) {
values[pnames[vi]] = +vv;
}
+ if (^"fel.srv"){
+ values[^"fel.alpha.scaler"] = Random (0.75, 1.25);
+ }
start.grid + values;
}
-
+ /*
+ GetString (p, ^lf, -1);
+ console.log (p);
+ console.log (values);
+ assert (0);
+ */
+
Optimize (results, ^lf, {
"OPTIMIZATION_METHOD" : "nedler-mead",
"OPTIMIZATION_PRECISION" : 1e-5,
"OPTIMIZATION_START_GRID" : start.grid
}
);
-
+
+
/**
infer and report ancestral substitutions
*/
@@ -712,8 +740,6 @@ lfunction fel.handle_a_site (lf, filter_data, partition_index, pattern_info, mod
');
}
-
-
snapshot = estimators.TakeLFStateSnapshot (lf);
alternative = estimators.ExtractMLEs (lf, model_mapping);
alternative [utility.getGlobalValue("terms.fit.log_likelihood")] = results[1][0];
@@ -738,20 +764,17 @@ lfunction fel.handle_a_site (lf, filter_data, partition_index, pattern_info, mod
ref_parameter = (^"fel.scaler_parameter_names")[(^"fel.branches.testable")["VALUEINDEXORDER"][0]];
^ref_parameter = sum /denominator;
+
if (testable == 1) {
parameters.SetConstraint ((^"fel.scaler_parameter_names")[^"terms.tree_attributes.background"],ref_parameter, "");
} else {
- utility.ForEach (^"fel.branches.testable", "_gname_",
- '
- //console.log ("REF " + `&ref_parameter`);
+ for (_gname_; in; ^"fel.branches.testable") {
_pname_ = (^"fel.scaler_parameter_names")[_gname_];
- if (_pname_ != `&ref_parameter`) {
- //console.log (_pname_ + "=>" + `&ref_parameter`);
- parameters.SetConstraint (_pname_,`&ref_parameter`, "");
+ if (_pname_ != ref_parameter && (^"fel.ignorable")[_pname_] == 0) {
+ parameters.SetConstraint (_pname_,ref_parameter, "");
}
- '
- );
+ }
}
Optimize (results, ^lf, {"OPTIMIZATION_METHOD" : "nedler-mead"});
@@ -764,12 +787,17 @@ lfunction fel.handle_a_site (lf, filter_data, partition_index, pattern_info, mod
for (v2 = v + 1; v2 < testable; v2+=1) {
v1n = (^"fel.branches.testable")[v];
v2n = (^"fel.branches.testable")[v2];
-
estimators.RestoreLFStateFromSnapshot (lf_id, snapshot);
- parameters.SetConstraint ((^"fel.scaler_parameter_names")[v1n],(^"fel.scaler_parameter_names")[v2n], "");
- 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];
+
+ if ((^"fel.ignorable")[(^"fel.scaler_parameter_names")[v1n]] || (^"fel.ignorable")[(^"fel.scaler_parameter_names")[v2n]]) {
+ //console.log (v1n + "|" + v2n + " is ignorable");
+ (pairwise[v1n + "|" + v2n]) = alternative;
+ } else {
+ parameters.SetConstraint ((^"fel.scaler_parameter_names")[v1n],(^"fel.scaler_parameter_names")[v2n], "");
+ 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];
+ }
}
}
} else {
=====================================
src/core/batchlanhelpers.cpp
=====================================
@@ -68,14 +68,18 @@ _String const _HYGenerateANameSpace () {
//____________________________________________________________________________________
void _HYClearANameSpace (const _String& nm) {
+ /*BufferToConsole("Deleting key: ");
+ BufferToConsole(nm.get_str());
+ NLToConsole();
+ ObjectToConsole(&_HY_HBL_Namespaces);
+ NLToConsole();*/
_HY_HBL_Namespaces.Delete(nm);
}
//____________________________________________________________________________________
-void ReadModelList(void)
-{
+void ReadModelList(void) {
if (templateModelList.empty() == false) return;
_String modelListFile (GetStandardDirectory (HY_HBL_DIRECTORY_TEMPLATE_MODELS) & "models.lst"),
=====================================
src/core/global_things.cpp
=====================================
@@ -121,7 +121,7 @@ namespace hy_global {
kErrorStringDatasetRefIndexError ("Dataset index reference out of range"),
kErrorStringMatrixExportError ("Export matrix called with a non-polynomial matrix argument"),
kErrorStringNullOperand ("Attempting to operate on an undefined value; this is probably the result of an earlier 'soft' error condition"),
- kHyPhyVersion = _String ("2.5.22"),
+ kHyPhyVersion = _String ("2.5.23"),
kNoneToken = "None",
kNullToken = "null",
=====================================
src/core/likefunc.cpp
=====================================
@@ -256,8 +256,14 @@ void BenchmarkThreads (_LikelihoodFunction* lf) {
lf->SetThreadCount (1);
#endif
TimeDifference timer;
- lf->SetIthIndependent (alterIndex,lf->GetIthIndependent(alterIndex));
- lf->Compute ();
+#ifdef __HYPHYMPI__
+ if (hy_mpi_node_rank == 0)
+#endif
+
+ {
+ lf->SetIthIndependent (alterIndex,lf->GetIthIndependent(alterIndex));
+ lf->Compute ();
+ }
@@ -276,6 +282,7 @@ hyFloat tdiff = timer.TimeSinceStart();
lf->SetThreadCount (k);
TimeDifference timer;
lf->SetIthIndependent (alterIndex,lf->GetIthIndependent(alterIndex));
+
lf->Compute ();
tdiff = timer.TimeSinceStart();
if (tdiff < minDiff) {
@@ -4063,15 +4070,8 @@ _Matrix* _LikelihoodFunction::Optimize (_AssociativeList const * options)
SetupLFCaches ();
SetupCategoryCaches ();
computationalResults.Clear();
- _variables_changed_during_last_compute = new _SimpleList ();
- variables_changed_during_last_compute = new _AVLList (_variables_changed_during_last_compute);
- for (unsigned long i=0UL; i<indexInd.lLength; i++) {
- if (GetIthIndependentVar(i)->varFlags & HY_VARIABLE_CHANGED) {
- variables_changed_during_last_compute->InsertNumber (GetIthIndependentVar(i)->get_index());
- }
- }
-
+
#ifdef __HYPHYMPI__
if (hy_mpi_node_rank == 0) {
@@ -4101,13 +4101,13 @@ _Matrix* _LikelihoodFunction::Optimize (_AssociativeList const * options)
#endif
+ _variables_changed_during_last_compute = new _SimpleList ();
+ variables_changed_during_last_compute = new _AVLList (_variables_changed_during_last_compute);
+
#ifdef __HYPHYMPI__
if (hy_mpi_node_rank == 0) {
#endif
-
BenchmarkThreads (this);
-
-
#ifdef __HYPHYMPI__
}
#endif
@@ -4133,7 +4133,7 @@ _Matrix* _LikelihoodFunction::Optimize (_AssociativeList const * options)
if (keepStartingPoint) {
indexInd.Each ([this, &untag] (long v, unsigned long i) -> void {
_Variable *iv = GetIthIndependentVar (i);
- if (iv->HasBeenInitialized()) {
+ if (!iv->IsGlobal() && iv->HasBeenInitialized()) {
if (!iv->IsModified()) {
iv->MarkModified();
untag << i;
@@ -4178,6 +4178,13 @@ _Matrix* _LikelihoodFunction::Optimize (_AssociativeList const * options)
}
}
}
+
+ for (unsigned long i=0UL; i<indexInd.lLength; i++) {
+ if (GetIthIndependentVar(i)->varFlags & HY_VARIABLE_CHANGED) {
+ variables_changed_during_last_compute->InsertNumber (GetIthIndependentVar(i)->get_index());
+ }
+ }
+
#if !defined __UNIX__ || defined __HEADLESS__
SetStatusBarValue (5,maxSoFar,(likeFuncEvalCallCount-evalsIn)/timer.TimeSinceStart());
=====================================
src/core/trie.cpp
=====================================
@@ -344,10 +344,11 @@ bool _Trie::Delete (const _String& key){
emptySlots << history.list_data[k];
payload.list_data[history.list_data[k]] = 0L;
parents.list_data[history.list_data[k]] = -1L;
- _SimpleList * parentList = ((_SimpleList**)list_data)[history.list_data[k-1]];
+ _SimpleList * parentList = ((_SimpleList**)list_data)[k ? history.list_data[k-1] : 0];
unsigned long parentNode = parentList->FindStepping (history.list_data[k],2, 1) - 1;
parentList->Delete (parentNode);
parentList->Delete (parentNode);
+
DeleteObject (current_list);
((_SimpleList**)list_data)[history.list_data[k]] = nil;
inserted_values--;
@@ -450,7 +451,9 @@ BaseRef _Trie::toStr(unsigned long) {
}
} else {
_String * this_string = RetrieveStringFromPath(traversal_history, &alph);
- (*serialized) << '"' << this_string << "\":" << _String (GetValue (traversal_history.list_data[traversal_history.lLength-2]));
+ (*serialized) << '"';
+ (*serialized).AppendNewInstance(this_string);
+ (*serialized) << "\":" << _String (GetValue (traversal_history.list_data[traversal_history.lLength-2]));
if (doComma) {
(*serialized) << ',';
} else {
=====================================
src/mains/unix.cpp
=====================================
@@ -694,51 +694,6 @@ void SetStatusLineUser (_String const s) {
#ifndef __UNITTEST__
int main (int argc, char* argv[]) {
- /*long N = 1000L;
- long repeats = 20L;
- long density = 0.25 * RAND_MAX;
-
- auto start = std::chrono::high_resolution_clock::now();
-
- srand(time(0));
-
- _Matrix::switchThreshold = atoi (argv[1]);
-
- printf ("%ld\n", _Matrix::switchThreshold);
-
- for (long i = 0; i < N; i++) {
- _Matrix test (61,61,false,true);
- test.ForEachCellNumeric([density] (hyFloat& e, long i, long r, long c) -> void {
- if (r != c && rand() < density) {
- e = genrand_real1 ();
- } else {
- e = 0.0;
- }
- });
- for (long r = 0; r < 61; r++) {
- double s = 0.;
- for (long c = 0; c < 61; c++) {
- s += test (r, c);
- }
- test.theData[r*61+r] = -s;
- }
-
- test.AmISparse();
- //ObjectToConsole(&test);
-
- //printf ("%d\n", test.is_dense());
- for (long j = 0; j < repeats; j++) {
- DeleteObject (test.Exponentiate());
- //return 0;
- }
- }
-
- auto end = std::chrono::high_resolution_clock::now();
- std::chrono::duration<double> elapsed = end - start;
- printf ("%15.12g s\n", elapsed.count());
-
- return 0;*/
-
#ifdef _COMPARATIVE_LF_DEBUG_DUMP
FILE * comparative_lf_debug_matrix_content_file = doFileOpen (_COMPARATIVE_LF_DEBUG_DUMP, "w");
View it on GitLab: https://salsa.debian.org/med-team/hyphy/-/compare/2f1b4ebae84f25fe800d3e0f134358c42d70884e...93ac5b946e31deb92501e95fb4d9ee737d6b4f44
--
View it on GitLab: https://salsa.debian.org/med-team/hyphy/-/compare/2f1b4ebae84f25fe800d3e0f134358c42d70884e...93ac5b946e31deb92501e95fb4d9ee737d6b4f44
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