force float casting in plantgen extension

conda/meta.yaml

@@ -45,7 +45,7 @@ test:
     - test/data/**
   commands:
     - cd test
-    - pytest -v --ignore=test_povray.py --ignore=test_dataflow.py --ignore=test_plantgen.py
+    - pytest -v --ignore=test_povray.py --ignore=test_dataflow.py
 
 about:
   home: {{ home }}

src/openalea/adel/AdelR.py

@@ -406,7 +406,7 @@ def _devCsv(axeTfn, dimTfn, phenTfn, earTfn=None, ssi2senTfn=None):
 def devCsv(axeTfn, dimTfn, phenTfn, earTfn=None, ssi2senTfn=None):
     """Import development parameters for adel from csv files and/or pandas dataframes"""
     return RdflistAsdicts(
-        _devCsv(axeTfn, dimTfn, phenTfn, earTfn=None, ssi2senTfn=None)
+        _devCsv(axeTfn, dimTfn, phenTfn, earTfn=earTfn, ssi2senTfn=ssi2senTfn)
     )
 
 

src/openalea/adel/plantgen/plantgen_core.py

@@ -365,10 +365,15 @@ def organs_dimensions(
             force=False,
         )
     )
-    dimT_tmp = _create_dimT_tmp(axeT_tmp, force=False)
 
+    dimT_tmp = _create_dimT_tmp(axeT_)
+
+    # 3. merge dimT_tmp and dimT_user
+    dimT_tmp_merged = _merge_dimT_tmp_and_dimT_user(
+        dynT_, dimT_user, dimT_user_completeness, dimT_tmp
+    )
     # 2. create dimT
-    dimT_ = _create_dimT(axeT_, dimT_tmp, dynT_, decimal_elongated_internode_number)
+    dimT_ = _create_dimT(axeT_, dimT_tmp_merged, dynT_, decimal_elongated_internode_number)
 
     return dimT_
 
@@ -830,12 +835,21 @@ def _gen_id_dim_list(id_cohort_series, N_phytomer_series, id_ear_series):
     """Generate the *id_dim* column."""
     is_ear = pd.Series(0, index=id_ear_series.index)
     is_ear[id_ear_series.dropna().index] = 1
-    zfilled_array = np.core.defchararray.zfill(np.char.mod("%d", N_phytomer_series), 2)
+
+    zfilled_array = np.char.zfill(
+        np.char.mod("%d", N_phytomer_series), 2
+    )
+
     id_cohort_str_array = np.char.mod("%d", id_cohort_series)
-    id_dim_array = np.core.defchararray.add(id_cohort_str_array, zfilled_array)
-    id_dim_array = np.core.defchararray.add(
+
+    id_dim_array = np.char.add(
+        id_cohort_str_array, zfilled_array
+    )
+
+    id_dim_array = np.char.add(
         id_dim_array, np.char.mod("%d", is_ear)
     ).astype(int)
+
     return id_dim_array.tolist()
 
 
@@ -2769,7 +2783,7 @@ def __call__(self, axeT_, dynT_, decimal_elongated_internode_number, force=True)
             for (id_cohort, N_phytomer_potential, id_phen), axeT_group in axeT_.groupby(
                 ["id_cohort", "N_phytomer_potential", "id_phen"]
             ):
-                phenT_tmp_group = phenT_tmp_grouped.get_group(id_phen)
+                phenT_tmp_group = phenT_tmp_grouped.get_group(id_phen).copy()
                 dynT_group = dynT_grouped.get_group((id_cohort, N_phytomer_potential))
                 dynT_row = dynT_group.loc[
                     dynT_group[
@@ -2867,9 +2881,7 @@ def __call__(self, axeT_, dynT_, decimal_elongated_internode_number, force=True)
                         # )  # TODO: useful ?
 
                 # compute TT_col_phytomer
-                self.phenT_tmp.loc[
-                    phenT_tmp_group.index, "TT_col_phytomer"
-                ] = phenT_tmp_group.loc[:, "TT_col_phytomer"].values[:] = (
+                phenT_tmp_group["TT_col_phytomer"] = (
                     phenT_tmp_group["index_phytomer"].apply(
                         _calculate_TT_col_phytomer,
                         args=(
@@ -2890,11 +2902,8 @@ def __call__(self, axeT_, dynT_, decimal_elongated_internode_number, force=True)
 
                 # compute TT_em_phytomer
                 first_leaf_indexes = phenT_tmp_group.index[0:2]
-                self.phenT_tmp.loc[
-                    first_leaf_indexes, "TT_em_phytomer"
-                ] = phenT_tmp_group.loc[first_leaf_indexes, "TT_em_phytomer"].values[
-                    :
-                ] = phenT_tmp_group.loc[
+                phenT_tmp_group.loc[first_leaf_indexes, "TT_em_phytomer"] = \
+                    phenT_tmp_group.loc[
                     first_leaf_indexes, ["index_phytomer", "TT_col_phytomer"]
                 ].apply(
                     _calculate_TT_em_phytomer,
@@ -2920,11 +2929,9 @@ def __call__(self, axeT_, dynT_, decimal_elongated_internode_number, force=True)
                         phenT_tmp_group.index - phenT_tmp_group.index[0:2]
                     )
                 if len(other_leaves_indexes) != 0:
-                    self.phenT_tmp.loc[
+                    phenT_tmp_group.loc[
                         other_leaves_indexes, "TT_em_phytomer"
                     ] = phenT_tmp_group.loc[
-                        other_leaves_indexes, "TT_em_phytomer"
-                    ].values[:] = phenT_tmp_group.loc[
                         other_leaves_indexes, ["index_phytomer", "TT_col_phytomer"]
                     ].apply(
                         _calculate_TT_em_phytomer,
@@ -2962,9 +2969,7 @@ def __call__(self, axeT_, dynT_, decimal_elongated_internode_number, force=True)
                     a_cohort_before_start_MS_elongation_2,
                 )
 
-                self.phenT_tmp.loc[
-                    phenT_tmp_group.index, "TT_sen_phytomer"
-                ] = phenT_tmp_group.loc[:, "TT_sen_phytomer"].values[:] = (
+                phenT_tmp_group["TT_sen_phytomer"] = (
                     phenT_tmp_group["index_phytomer"].apply(
                         _calculate_TT_sen_phytomer,
                         args=(
@@ -2984,14 +2989,18 @@ def __call__(self, axeT_, dynT_, decimal_elongated_internode_number, force=True)
                 )
 
                 # compute TT_del_phytomer
-                self.phenT_tmp.loc[
-                    phenT_tmp_group.index, "TT_del_phytomer"
-                ] = phenT_tmp_group.loc[:, "TT_del_phytomer"].values[:] = (
+                phenT_tmp_group["TT_del_phytomer"] = (
                     _calculate_TT_del_phytomer(
                         a_cohort_before_start_MS_elongation_1,
                         phenT_tmp_group["TT_sen_phytomer"],
                     )
                 )
+
+                # update phenT
+                self.phenT_tmp.loc[
+                    phenT_tmp_group.index,
+                    phenT_tmp_group.columns
+                ] = phenT_tmp_group
         return self.phenT_tmp
 
 

src/openalea/adel/plantgen/plantgen_interface.py

@@ -172,7 +172,7 @@ def gen_adel_input_data(
         )
     )
 
-    if sum(MS_leaves_number_probabilities.values()) != 1.0:
+    if not np.isclose(sum(MS_leaves_number_probabilities.values()), 1.0):
         raise tools.InputError(
             "the sum of the probabilities defined in MS_leaves_number_probabilities is not equal to 1.0"
         )

src/openalea/adel/plantgen_extensions.py

@@ -638,7 +638,7 @@ def fit_a(self, HS_since_flag, GL):
         return a, rmse
 
     def hs_t1(self, nff=None):
-        return self.hsfit.HSflag(nff) - self.n_elongated_internode
+        return float(self.hsfit.HSflag(nff)) - self.n_elongated_internode
 
     def dn_nff(self, nff=None):
         return 0.5 * (self.hs_t2(nff) - self.hs_t2())
@@ -647,7 +647,7 @@ def n1(self, nff=None):
         return self.GL_bolting + self.dn_nff(nff)
 
     def hs_t2(self, nff=None):
-        return self.hsfit.HSflag(nff)
+        return float(self.hsfit.HSflag(nff))
 
     def n2(self, nff=None):
         return self.GL_flag + self.dn_nff(nff)
@@ -1116,7 +1116,7 @@ def _dfc(x, y):
             for c in cardnff.loc[int(nff)].index:
                 d[int(c)] = cardinalities(
                     cohort_nff_modalities[int(nff)][int(c)],
-                    int(cardnff.loc[int(nff), c]),
+                    int(cardnff.loc[int(nff), c].values),
                 )
             cohort_nff_cardinalities[int(nff)] = d
         cohort_nff = {