Merging 1-release-2025 into main

Author: jbdurand

src/openalea/sequence_analysis/data_transform.py

@@ -57,7 +57,7 @@
     markovian_sequence_type, output_map, histogram_type,
     mode_type, func_map, estimator_map, model_type, seq_map,
     renewal_nb_event_map, sub_func_map, nb_segment_map,
-    output_type, index_parameter_type_map
+    output_type, index_parameter_type_map, run_map
 )
 
 
@@ -186,9 +186,9 @@ def RemoveRun(obj, *args, **kargs):
         error.CheckType([variable, value, position], [int, int, str])
 
     if position in ['End', 'e']:
-        position = 'e'
+        position = run_map['End']
     elif position == ['b', 'Begin']:
-        position = 'b'
+        position = run_map['Begin']
     else:
         raise TypeError("position must be 'End' or 'e' or 'Begin' or 'b'")
 

src/openalea/sequence_analysis/enums_seq.py

@@ -255,6 +255,12 @@
                   }
 end_aligned_map = begin_aligned_map
 
+
+run_map = {
+               "Begin" : RunPosition.BEGIN,
+               "End" : RunPosition.END
+            }
+
 from openalea.sequence_analysis._sequence_analysis import (
     _Sequences, _MarkovianSequences, _VariableOrderMarkovData, 
     _SemiMarkovData, _NonHomogeneousMarkovData, _VariableOrderMarkov,

src/openalea/sequence_analysis/estimate.py

@@ -303,7 +303,7 @@ def _estimate_semi_markov(obj, *args, **kargs):
     Type = 'v'
     #error.CheckType([args[0]], [str])
 
-    Type = error.CheckDictKeys(args[0], stochastic_stochastic_process_type)
+    Type = error.CheckDictKeys(args[0], stochastic_process_type)
 
     NbIteration = kargs.get("NbIteration", I_DEFAULT)
     Counting = kargs.get("Counting", True)
@@ -489,7 +489,7 @@ def _estimate_variable_order_markov(obj, *args, **kargs):
     #args0 is a string
     if len(args)>0 and isinstance(args[0], str):
         Type = 'v'
-        Type = error.CheckDictKeys(args[0], stochastic_stochastic_process_type)
+        Type = error.CheckDictKeys(args[0].upper(), stochastic_process_type)
 
         # check validity of the input arguments following AML's code
         if Algorithm != LOCAL_BIC and not kargs.get("Threshold"):

src/openalea/sequence_analysis/top_parameters.py

@@ -377,6 +377,12 @@ const int TOP_SIZE = 2000000;          // taille memoire maximum (en int) d'un e
      .value("POSTERIOR_PROBABILITY", POSTERIOR_PROBABILITY)
      .export_values();
 
+   enum_<sequence_analysis::wrap_util::UniqueInt<2, 113> >("RunPosition")
+     .value("BEGIN", BEGIN_RUN)
+     .value("END", END_RUN)
+     .export_values();
+
+
    /*
    const double MIN_NB_EVENT = 0.4;       // nombre d'evenements moyen minimum
   const double MIN_INTER_EVENT = 1.;     // temps moyen minimum entre 2 evenements