Fix missing ci missing api doc

doc/source/api_reference/hdf5_handler.rst

@@ -1,5 +1,23 @@
 .. _api_reference.hdf5_handler:
 
-============
+==============
 Hdf5 handler
-============
+==============
+
+.. currentmodule:: smash.tools.hdf5_handler
+
+Some functions to manipulate hdf5 files
+***************************************
+.. autosummary::
+   :toctree: smash/
+
+   open_hdf5
+   add_hdf5_sub_group
+   _dump_object_to_hdf5_from_list_attribute
+   _dump_object_to_hdf5_from_dict_attribute
+   _dump_object_to_hdf5_from_str_attribute
+   _dump_object_to_hdf5_from_iteratable
+   _dump_dict_to_hdf5
+   save_dict_to_hdf5
+   save_object_to_hdf5
+   read_hdf5_as_dict

doc/source/api_reference/hdf5_io.rst

@@ -1,5 +1,21 @@
 .. _api_reference.hdf5_io:
 
-=======
-Hdf5 io
-=======
+==============
+Smash Hdf5 I/O
+==============
+
+.. currentmodule:: smash.io.hdf5_io
+
+Functions to handle input/output hdf5 of smash model
+****************************************************
+.. autosummary::
+   :toctree: smash/
+
+   save_smash_model_to_hdf5
+   load_hdf5_file
+   generate_smash_object_structure
+   read_hdf5_to_model_object
+   _generate_light_smash_object_structure
+   _generate_medium_smash_object_structure
+   _generate_full_smash_object_structure
+   _parse_hdf5_to_derived_type

doc/source/api_reference/object_handler.rst

@@ -3,3 +3,13 @@
 ==============
 Object handler
 ==============
+
+.. currentmodule:: smash.tools.object_handler
+
+Some functions to manipulate python objects
+*******************************************
+.. autosummary::
+   :toctree: smash/
+
+   generate_object_structure
+   read_object_as_dict

doc/source/release/0.5.1-notes.rst

@@ -0,0 +1,47 @@
+.. _release.0.5.1-notes:
+
+.. currentmodule:: smash
+
+=========================
+smash 0.5.1 Release Notes
+=========================
+
+The smash 0.5.1 fix bugs and clarify the documentation.
+
+------------
+Contributors
+------------
+
+This release was made possible thanks to the contributions of:
+
+- Maxime Jay-Allemand
+- Ngo Nghi Truyen Huynh
+- François Colleoni
+
+------------
+Deprecations
+------------
+
+------------
+Improvements
+------------
+
+Missing documentation API for functions hdf5_handler, hdf5_io and object_handler
+********************************************************************************
+
+The documentation API was missing for the new functions for reading and writting hdf5 files added in release 0.5.0. This has been corrected. `#46 <https://github.com/DassHydro-dev/smash/issues/46`
+
+------------
+New Features
+------------
+
+-----
+Fixes
+-----
+
+Missing interception parameters ci in constant parameters
+*********************************************************
+
+Ci was missing in the parameter constant list and can't be saved and post processed or retrieved at all. This is fixed now. `#46 <https://github.com/DassHydro-dev/smash/issues/45`
+
+

doc/source/release/index.rst

@@ -7,6 +7,7 @@ Release notes
 .. toctree::
     :maxdepth: 3
 
+    0.5.1 <0.5.1-notes>
     0.5.0 <0.5.0-notes>
     0.4.2 <0.4.2-notes>
     0.4.1 <0.4.1-notes>

smash/core/_constant.py

@@ -14,8 +14,8 @@
 
 STRUCTURE_PARAMETERS = {
     "gr-a": ["cp", "cft", "exc", "lr"],
-    "gr-b": ["cp", "cft", "exc", "lr"],
-    "gr-c": ["cp", "cft", "cst", "exc", "lr"],
+    "gr-b": ["ci", "cp", "cft", "exc", "lr"],
+    "gr-c": ["ci", "cp", "cft", "cst", "exc", "lr"],
     "gr-d": ["cp", "cft", "lr"],
     "vic-a": ["b", "cusl1", "cusl2", "clsl", "ks", "ds", "dsm", "ws", "lr"],
 }

smash/core/simulation/_standardize.py

@@ -7,6 +7,7 @@
     WGAUGE_ALIAS,
     STRUCTURE_PARAMETERS,
     STRUCTURE_STATES,
+    STRUCTURE_ADJUST_CI,
     JOBS_FUN,
     JREG_FUN,
     AUTO_WJREG,
@@ -120,7 +121,9 @@ def _standardize_control_vector(
 ) -> np.ndarray:
     if control_vector is None:
         control_vector = np.array(STRUCTURE_PARAMETERS[setup.structure])
-
+        if STRUCTURE_ADJUST_CI[setup.structure]:
+            if "ci" in control_vector:
+                control_vector.remove("ci")
     else:
         if isinstance(control_vector, str):
             control_vector = np.array(control_vector, ndmin=1)

smash/tests/core/test_constant.py

@@ -21,10 +21,10 @@ def test_structure_parameters():
     assert STRUCTURE_PARAMETERS["gr-a"] == ["cp", "cft", "exc", "lr"]
 
     # % Check parameters gr-b
-    assert STRUCTURE_PARAMETERS["gr-b"] == ["cp", "cft", "exc", "lr"]
+    assert STRUCTURE_PARAMETERS["gr-b"] == ["ci", "cp", "cft", "exc", "lr"]
 
     # % Check parameters gr-c
-    assert STRUCTURE_PARAMETERS["gr-c"] == ["cp", "cft", "cst", "exc", "lr"]
+    assert STRUCTURE_PARAMETERS["gr-c"] == ["ci", "cp", "cft", "cst", "exc", "lr"]
 
     # % Check parameters gr-d
     assert STRUCTURE_PARAMETERS["gr-d"] == ["cp", "cft", "lr"]